title: hnRNP A2/B1 ASO 3

data_processing:
Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
http://exon.ucsc.edu/documentation/mjay_library/mjay.pgf

source_name: spinal cord

growth_protocol: eight-week old female C57Bl/6j mice were grown under normal coniditons

treatment_protocol: Sterotactic injections of ASO complementary to Hnrnpa2b1 were performed in eight-week old female C57Bl/b mice to deplete Hnrnpa2b1. ASOs were delivered specifically to the later ventricle (12.5 mg)  injection (300 mg). Mice were regularly monitored for 28 days until sacrificed.

tag: age

value: spinal cord

value: ASO Hnrnpa2/b1


title: 14272.Yeo.9.sh_(HTA-2_0)

status: Public on Oct 20 2016

type: RNA

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

hyb_protocol: Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.

scan_protocol: Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files.

data_processing:
Cel files were analyzed using Expression Console (build 1.4.1.46, Affymetrix), with RMA normalization and DABG probe-level detection. Only probesets with detection p-value ≤ 0.05 in more than half of the microarray samples were considered for downstream analysis. All probes corresponding to cassette exons profiled on the microarray (comprising exclusion junction, upstream and downstream inclusion junction, and inclusion exonic probes) were identified and normalized against the average signal on a per-gene basis to remove gene expression changes. Student’s t-test was performed on residuals for inclusion probes and exclusion probes separately to identify robust splicing changes, which were quantified by SepScore ( defined as the normalized change in exclusion minus the normalized change in inclusion).
HTA-2_0.r1.pgf
HTA-2_0.r1.Psrs.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: iPSC-MNs

label_protocol: WT Terminal Labeling Kit, Affymetrix

growth_protocol: iPSC-MNs were differentiated from MSP and control individuals

extract_protocol: RNA was extracted by standard Trizol extraction.

treatment_protocol: iPSC-MNs were treated with ASO against hnRNP A2/B1 or nontarget ASO for 28 days

tag: genotype

value: WT

tag: treatment

value: hnRNP A2/B1 ASO 2

tag: disease

tag: tissue type

value: iPSC-MN


title: hnRNP A2/B1 ASO 1

organism: Mus musculus

tag: strain


title: saline control 1

value: saline


title: saline control 2


title: 14277.Yeo.14.sh_(HTA-2_0)

value: hnRNP A2/B1 D290V

value: nontarget ASO

value: MSP


title: 7d osteogen

type: genomic

city: Saarbruecken

first: Valentina

last: Galata

state: Saarland

address: Campus, E2.1

department: Chair for Clinical Bioinformatics

country: Germany

institute: Saarland University

hyb_protocol:
according to Oligo aCGH Hybridization (Kit #5188-5220) and aCGH/ChIP-on-chip WashBuffer (Kit #5188-5226
) with Stabilization and Drying Solution (#5188-5979)

scan_protocol: G2565 Microarray Scanner Version C

data_processing:
Feature Extraction Software Version: 10.7.3.1
File: bc_norm_prCGH.tsv  Raw files were read in using read.maimages from R-package limma (3.26.5) and  modified version of readPositionalInfo from R-package snapCGH (1.40.0)  (changes: process chr. IDs X, Y, and M; add column Position and set values to start values).  Background correction was performed using backgroundCorrect from limma (method='minimum').  Normalization within ararys was done using normalizeWithinArrays from limma (method="printtiploess", bc.method="none").  Between array normalization was performed using normalizeBetweenArrays from limma (method="quantile").  Normalized data was processed using processCGH from snapCGH  (method.of.averaging=mean, ID="ProbeUID", minChromThreshold=1, maxChromThreshold=22).  File: ave25kb_seg_merged.tsv  Window averaging was performed on each chromosome using a window width of 25Kb as follows:  The chromosome was divided into intervals of given width based on  minimal start and maximal end position of the corresponding probes;  the values of the probes within each interval were assigned to the interval mean.  Position of an interval was defined as it start position.  Segmentation was run using runDNAcopy from snapCGH (alpha=0.01, smooth.region=10)  and states were merged using mergeStates from snapCGH (MergeType=2,  minDiff=0.25).

molecule: genomic DNA

label_protocol: according to Agilent SureTagDNA Labeling Kit #5190-4240

growth_protocol: hMSC from Lonza were cultured in mesenchymal stem cell medium as described in manufactureres instruction

extract_protocol: genomic DNA was isolated using NaCl/chloroform extraction

treatment_protocol: hMSC were cultured until they become near confluent. Adipogenic differentiation was induced by 3 cycles of induction and maintenance. Each cycle consists of feeding with adipogenic induction medium for 3 days followed by culture in adipogenic maintenance medium for 1-3 days. Osteogenesis induction (osetoegenic differentiation) was induced by osteogenesis medium for 7 days. Culture and media were according to Lonza instructions for use of PoieticsTM human mesenchymal stem cells.

tag: cell type

value: human mesechymal stem cells

tag: test

value: 7d osteogenesis

source_name: PB

tag: reference

value: control human DNA

value: peripheral blood lymphocytes


title: hnRNP A2/B1 ASO 2


title: treated with non-targetting ASO_3

data_processing:
Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
http://exon.ucsc.edu/documentation/mjay_library/hjay.pgf

source_name: primary fibroblasts

growth_protocol: human primary fibroblasts were grown under normal conditions

treatment_protocol: Cells were lipofected with ASO against HNRNPA2B1 or non targeting control ASOs. After 48 hours, cells were harvested and depletion was validated by qPCR and western blot.

value: ASO non-targetting

tag: tissue type type

value: skin


title: 14268.Yeo.5.sh_(HTA-2_0)

value: hnRNP A2/B1 ASO 1


title: 3d osteogen

value: 3d osteogenesis


title: treated with non-targetting ASO_1


title: 2 cycles adipogen

value: 2 cycles differentiated towards adipocytes


title: treated with non-targetting ASO_2


title: VCP Q155H patient 1

treatment_protocol: no treatment

value: VCP Q155H


title: VCP Q155H patient 2


title: second unaffected control 1

value: WT


title: treated with ASO agaisnt HNRNPA2B1_2

value: ASO targeting hnRNP A2/B1


title: saline control 3

value: spinal cord


title: first unaffected control 3


title: VCP Q155H patient 3


title: treated with ASO agaisnt HNRNPA2B1_3


title: first unaffected control 1


title: Osteogenic adipocyte like cells, biological rep.3

status: Public on Oct 19 2016

city: Hangzhou

first: Chenxia

last: Hu

state: Zhejiang

address: School of Medicine; First Affiliated Hospital; Zhejiang University

country: China

institute: Zhejiang University

description: Gene expression data from osteogenic adipocyte like cells

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

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

data_processing: The data were analyzed with Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized byRMA algorithm, Affy packages in R.

source_name: Placenta

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

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

value: Adipocyte like cells after osteogenic differentiaiton for 7 days


title: MSC-like cells, biological rep.2

department: First Affiliated Hospital; Zhejiang University

description: Gene expression data from MSC-like cells

value: MSC-like cells in general medium for 21 days


title: 14266.Yeo.3.sh_(HTA-2_0)

value: nontarget ASO

value: iPSC-MN


title: second hnRNP A2/B1 D290V patient 1

value: hnRNP A2/B1 D290V

value: MSP


title: second unaffected control 3


title: Osteogenic adipocyte like cells, biological rep.1


title: Osteogenic adipocyte like cells, biological rep.2


title: MSC-like cells, biological rep.1


title: Adipogenic PDMSCs, biological rep.3

description: Gene expression data from Adipogenic PDMSCs

value: PDMSCs after adipogenic differentiation for 14 days


title: second hnRNP A2/B1 D290V patient 3


title: Adipogenic PDMSCs, biological rep.2


title: 14267.Yeo.4.sh_(HTA-2_0)


title: Human PDMSCs, biological rep.3

description: Gene expression data from human PDMSCs

value: Human PDMSCs isolated from one individual


title: Human PDMSCs, biological rep.2

description: Gene expression data from human PDMSCs


title: first hnRNP A2/B1 D290V patient 3


title: 14275.Yeo.12.sh_(HTA-2_0)


title: second hnRNP A2/B1 D290V patient 2


title: first hnRNP A2/B1 D290V patient 2


title: 3 cycles adipogen

value: human mesechymal stem cells

value: 3 cycles differentiated towards adipocytes

value: control human DNA

value: peripheral blood lymphocytes


title: MSC-like cells, biological rep.3


title: second unaffected control 2

value: skin


title: 14279.Yeo.16.sh_(HTA-2_0)

value: hnRNP A2/B1 ASO 1


title: first hnRNP A2/B1 D290V patient 1


title: Human PDMSCs, biological rep.1

description: Gene expression data from human PDMSCs


title: Adipogenic PDMSCs, biological rep.1


title: Primary Alveolar Type 2 Cells Replicate 2

city: Salisbury

first: James

middle: Ross

last: Cooper

state: Wiltshire

address: PHE Porton, Manor Farm Road

department: ECACC

country: United Kingdom

institute: Public Health England

description:
Gene expression - Primary Cell Culture
RH_253949414708_S01_GE1_107_Sep09_1_1

hyb_protocol: For each sample, 600ng of Cy3 labelled cRNA was prepared for hybridisation using fragmentation mix and 2XHI RPM Hybridisation Buffer, according to the manufacturer’s instructions. 40 µl of hybridisation mix was then loaded onto eight-position Agilent Microarray Gaskets, inverted onto SurePrint G3 Whole Human Genome Gene Expression 8x60K v2 Microarray slides, each in a hand-tightened hybridisation chamber, then incubated in an Agilent Microarray rotating oven at 65oC for 17 hours. A record was made of the position of each sample on each slide

scan_protocol: After incubation, the microarrays were disassembled and washed in Agilent bespoke Wash Buffers, according to the manufacturer’s instructions. Slides were then loaded into an Agilent G2565CA Microarray Scanner and scanned at a Resolution of 3µm (3 microns).

data_processing: Scanned images were analysed using Genespring version 13 (Agilent Technologies, Santa Clara, USA). Data was quality controlled by excluding any compromised entities and only entities where all replicates were either detected or not detected.  Samples were normalised by shift to the 75th percentile and the baseline transformation on the median of all samples and statistical and comparative analysis at the probe and gene level using parametric statistical analyses including analysis of variance (one way ANOVA) with Benjamini and Hochberg False Discovery Rate (BH FDR) correction.

label: Cyanine 3

source_name: Cultured Primary Alveolar Type 2 Cells Donor HL338

label_protocol: Total RNA samples isolated/extracted from  the  cultures at all time points and conditions were labelled using Agilent’s One-Color Quick Amp Labelling Kit and samples were processed according to corresponding One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling) and Hybridisation protocol (where samples are transformed from total RNA to cDNA and then to labelled cRNA). One-Color spike mix was added to each total RNA sample prior to cDNA synthesis. In short, sample and reagent volumes (including spike mix) were prepared for cDNA synthesis according to the manufacturer’s protocols for samples containing up to 600ng and 200ng of total RNA respectively. Cy3-labelled cRNA was amplified from the cDNA template, purified using the Qiagen RNeasy Mini Kit and quantified using a Nanodrop Spectrophotometer, prior to use. Some samples required additional labelling, purification and quantification steps as the initial labelled cRNA final concentrations were too low for use.

growth_protocol: Authentic A549 cells (European Collection of Cell Cultures (ECACC), Salisbury, UK), catalogue number 86012804, were cultured in Ham’s F12 Nutrient Medium (Ham’s F12) (from Sigma Aldrich, Dorset, United Kingdom) supplemented with 2mM L-Glutamine and 10% v/v Foetal Bovine Serum (FBS) (Hyclone SH30071.03 (Hyclone Laboratories, Utah, USA)).  Proliferative cultures were incubated at 37°C in a humidified 5% CO2 incubator and subculture carried out by washing the cell monolayers twice with calcium and magnesium-free phosphate buffered saline (PBS) (Severn Biotech (Kidderminster, UK, catalogue number 20-74) followed by addition of 1x Trypsin/EDTA solution (Sigma Aldrich) and incubation at 37°C until the cells detached. Trypsin was inactivated by the addition of growth medium before seeding into fresh flasks at densities of 1.5-2x104 cells/cm2.  Primary ATII cells were isolated by protease digestion and selective adherence according to published protocols[16] and the commonly adopted strategy of using macroscopically normal tissue from three ex-smokers undergoing lung resection. Written consent from the donors of the primary lung tissue was given under the governance of the National Health Service (NHS) England Southampton and South West Hampshire ‘A’ Research Ethics Committee. Local Research Ethics Committee (LREC) Reference Number 08/H0502/32.  The purified ATII cells were re-suspended in DCCM-1 medium (Biological Industries, Israel) supplemented with 1% penicillin, 1%streptomycin and 1% L-glutamine and 10% NCS before plating on collagen I (PureCol 5005-b, Advanced BioMatrix Inc, Carlsbad, USA) coated 24 well plates at 60% confluence.  The presence of ATII cells was confirmed by staining for alkaline phosphatase.

extract_protocol: A549 Cells were harvested using trypsin/EDTA, counted and washed with PBS by centrifugation at 500g for 5 minutes and snap frozen in pellets of 1.5 x 106 cells before storage at -80°C prior to RNA extraction.  RNA was extracted using the Promega Maxwell® Low Elution Volume (LEV) Simply RNA Cell kit according to the manufacturer’s instructions. In brief 16 samples were processed at a time. Pellets were thawed rapidly and as briefly as possible in a 37°C water-bath, transferred to wet ice where 200µl of homogenisation solution was added to each sample and vortexed to mix before the addition of 200 µl of lysis solution and another vortex mix prior to loading into the Maxwell® cassettes.  DNAse was added to remove contaminating genomic DNA.  RNA was eluted into 50µl of nuclease free water and supplemented with RNAse inhibitor (“Superase In™”, Ambion, Life Technologies, Paisley, UK) before being quantified by spectrophotometry (Nanodrop, Labtech International, Uckfield East Sussex UK) and analyzed by electrophoresis in a 1.4% agarose (Sigma Aldrich) gel and visualised using Ethidium Bromide and UV illumination to ensure there were intact 18S and 28S bands.  Extracted RNA was stored at -80°C before RNA microarray analysis prior to which repeat assessment of RNA integrity was carried out using a bio-analyzer (BioAnalyzer 2100, Agilent Technologies, Santa Clara, USA).  Replicate RNA samples were isolated from wells of the Primary Alveolar Type 2 Cells  from 24 well plates using Trizol according to the manufacturer’s instructions (Life Technologies, Paisley, UK).

treatment_protocol: This study comapred untreated samples of the cells

tag: gender

value: Female

tag: age at tissue sampling

value: 69 Years

value: Culture Primary tissue


title: Day 25 A549 Cells Replicate 2

description:
Gene expression after 25 days in culture
RH_253949414713_S01_GE1_107_Sep09_2_2

source_name: Day 25 A549 Cells

growth_protocol: Authentic A549 cells (European Collection of Cell Cultures (ECACC), Salisbury, UK), catalogue number 86012804, were cultured in Ham’s F12 Nutrient Medium (Ham’s F12) (from Sigma Aldrich, Dorset, United Kingdom) supplemented with 2mM L-Glutamine and 10% v/v Foetal Bovine Serum (FBS) (Hyclone SH30071.03 (Hyclone Laboratories, Utah, USA)).  Proliferative cultures were incubated at 37°C in a humidified 5% CO2 incubator and subculture carried out by washing the cell monolayers twice with calcium and magnesium-free phosphate buffered saline (PBS) (Severn Biotech (Kidderminster, UK, catalogue number 20-74) followed by addition of 1x Trypsin/EDTA solution (Sigma Aldrich) and incubation at 37°C until the cells detached. Trypsin was inactivated by the addition of growth medium before seeding into fresh flasks at densities of 1.5-2x104 cells/cm2.   For the long term 25 day cultures A549 cells were seeded into replicate T25 flasks and medium changed every 2-4 days.  Phase contrast images were captured of the monolayers throughout the time course. Cell numbers, viability and size were assessed by Trypan Blue staining and by DAPI dye exclusion using the Nucleocounter™ 3000 viability assay (Chemometec, Allerod, Denmark).

extract_protocol: A549 Cells were harvested using trypsin/EDTA, counted and washed with PBS by centrifugation at 500g for 5 minutes and snap frozen in pellets of 1.5 x 106 cells before storage at -80°C prior to RNA extraction.  RNA was extracted using the Promega Maxwell® Low Elution Volume (LEV) Simply RNA Cell kit according to the manufacturer’s instructions. In brief 16 samples were processed at a time. Pellets were thawed rapidly and as briefly as possible in a 37°C water-bath, transferred to wet ice where 200µl of homogenisation solution was added to each sample and vortexed to mix before the addition of 200 µl of lysis solution and another vortex mix prior to loading into the Maxwell® cassettes.  DNAse was added to remove contaminating genomic DNA.  RNA was eluted into 50µl of nuclease free water and supplemented with RNAse inhibitor (“Superase In™”, Ambion, Life Technologies, Paisley, UK) before being quantified by spectrophotometry (Nanodrop, Labtech International, Uckfield East Sussex UK) and analyzed by electrophoresis in a 1.4% agarose (Sigma Aldrich) gel and visualised using Ethidium Bromide and UV illumination to ensure there were intact 18S and 28S bands.  Extracted RNA was stored at -80°C before RNA microarray analysis prior to which repeat assessment of RNA integrity was carried out using a bio-analyzer (BioAnalyzer 2100, Agilent Technologies, Santa Clara, USA).

treatment_protocol: A549 cells were sampled at time points 0 (log phase growth), days 7, 11, 18 and 25.

tag: source gender

value: Male

value: 58 years

tag: cell line

value: Continous cancer derived cell line

tag: time point

value: after 25 days in culture


title: Log Phase A549 Cells Replicate 1 [re-analysis]

description:
Gene expression; log phase culture
RH_253949414713_S01_GE1_107_Sep09_1_1

source_name: Log Phase A549 Cells

value: log phase culture


title: Log Phase A549 Cells Replicate 3 [re-analysis]

description:
Gene expression; log phase culture
RH_253949414714_S01_GE1_107_Sep09_1_1


title: Day 18 A549 Cells Replicate 1

description:
Gene expression after 18 days in culture
RH_253949411093_S01_GE1_107_Sep09_2_1

source_name: Day 18 A549 Cells

value: after 18 days in culture


title: Day 25 A549 Cells Replicate 1

description:
Gene expression after 25 days in culture
RH_253949411093_S01_GE1_107_Sep09_2_3


title: Day 11 A549 Cells Replicate 2

description:
Gene expression after 11 days in culture
RH_253949414713_S01_GE1_107_Sep09_1_3

source_name: Day 11 A549 Cells

value: after 11 days in culture


title: Day 11 A549 Cells Replicate 1

description:
Gene expression after 11 days in culture
RH_253949411093_S01_GE1_107_Sep09_1_4


title: Primary Alveolar Type 2 Cells Replicate 1

description:
Gene expression - Primary Cell Culture
RH_253949414715_S01_GE1_107_Sep09_1_1


title: HR_AMY_Adult_rep3

city: Blacksburg

first: Sarah

middle: Megan

last: Clinton

state: Virginia

address: 1981 Kraft Dr., Integrated Life Sciences Building 0913

department: School of Neuroscience

institute: Virginia Polytechnic Institute and State University

hyb_protocol: Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation)

data_processing:
canned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 12.0) for further analysis.
Genes that at least 40 out of 80 samples for hippocampal or for amygdalar samples have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for data analysis.

organism: Rattus norvegicus

source_name: Amygdala, Dissected whole

label_protocol: Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit. ds-cDNA labeling with NimbleGen one-color DNA labeling kit.

extract_protocol: Male rats (n=5 per phenotype) were sacrificed by rapid decapitation to harvest brain tissue for genome-wide expression profiling. Brains were removed, flash frozen in isopentane cooled to -30°C on dry ice, and then stored at -80°C until further use. Brains were sectioned on a cryostat at -10 to -12°C, and alternating sections of 20 and 300 µm were collected. The 20 µm sections were stained with cresyl violet to identify target anatomical regions in the 300 µm sections. Portions of the hippocampus and amygdala were then dissected and homogenized. RNA was isolated (NucleoSpin RNA II), quantified using a Nanodrop ND-1000 (Wilmington, DE), and stored at -80°C.

value: Sprague-Dawley

tag: Sex

value: male

tag: selectively bred line (biological parents)

value: HR

tag: brain region

value: Amygdala

tag: caregiver dame

value: Mother HR

tag: postnatal age


title: HR_AMY_Adult_rep4


title: 14265.Yeo.2.sh_(HTA-2_0)

tag: genotype

value: WT

tag: treatment

value: nontarget ASO

tag: disease

value: iPSC-MN


title: Log Phase A549 Cells Replicate 2 [re-analysis]

description:
Gene expression; log phase culture
RH_253949411094_S01_GE1_107_Sep09_1_1

tag: cell type


title: Day 18 A549 Cells Replicate 2

description:
Gene expression after 18 days in culture
RH_253949411094_S01_GE1_107_Sep09_2_1


title: Day 11 A549 Cells Replicate 3

description:
Gene expression after 11 days in culture
RH_253949414714_S01_GE1_107_Sep09_1_3


title: Log Phase A549 Cells Replicate 2


title: Day 7 A549 Cells Replicate 2

description:
Gene expression after 7 days in culture
RH_253949411094_S01_GE1_107_Sep09_1_2

source_name: Day 7 A549 Cells

value: after 7 days in culture


title: HR_AMY_Adult_rep5

tag: strain


title: Log Phase A549 Cells Replicate 3


title: Day 7 A549 Cells Replicate 1

description:
Gene expression after 7 days in culture
RH_253949411093_S01_GE1_107_Sep09_1_2


title: LR-HR_AMY_Adult_rep4

value: LR

value: Foster HR


title: Day 7 A549 Cells Replicate 3

description:
Gene expression after 7 days in culture
RH_253949414713_S01_GE1_107_Sep09_1_2

value: Male

value: 58 years


title: Log Phase A549 Cells Replicate 1

value: Continous cancer derived cell line


title: HR_AMY_Adult_rep2


title: HR_AMY_Adult_rep1


title: LR-HR_AMY_Adult_rep5


title: first unaffected control 2

tag: tissue type

value: skin


title: Day 25 A549 Cells Replicate 3

description:
Gene expression after 25 days in culture
RH_253949414714_S01_GE1_107_Sep09_2_2

value: after 25 days in culture


title: LR-LR_AMY_Adult_rep4

value: Foster LR


title: LR-HR_AMY_Adult_rep2

value: Sprague-Dawley


title: LR-HR_AMY_Adult_rep1

value: male


title: LR-LR_AMY_Adult_rep5


title: LR-LR_AMY_Adult_rep3


title: LR-LR_AMY_Adult_rep2


title: LR_AMY_Adult_rep4

value: Mother LR


title: LR_AMY_Adult_rep2

value: Amygdala


title: LR_AMY_Adult_rep5


title: LR_AMY_Adult_rep3


title: HR_AMY_P21_rep2

value: HR

value: Mother HR


title: HR_AMY_P21_rep3


title: hMSC

value: human mesechymal stem cells

tag: test

value: undifferentiated

tag: reference

value: control human DNA

value: peripheral blood lymphocytes


title: 14264.Yeo.1.sh_(HTA-2_0)

value: WT

value: nontarget ASO

value: iPSC-MN


title: LR-HR_AMY_Adult_rep3

value: LR

value: Foster HR


title: LR-LR_AMY_Adult_rep1


title: LR_AMY_Adult_rep1


title: HR_AMY_P21_rep4


title: HR_AMY_P21_rep5


title: HR_AMY_P21_rep1


title: LR-HR_AMY_P21_rep5


title: LR-HR_AMY_P21_rep4


title: LR-HR_AMY_P21_rep3


title: LR-HR_AMY_P21_rep2


title: LR-LR_AMY_P21_rep5


title: LR-LR_AMY_P21_rep4


title: After HSCT_80B

city: Krakow

first: Miroslaw

last: Bik-Multanowski

address: ul. Wielicka 265

department: Dept. of Medical Genetics

country: Poland

institute: Jagiellonian University

hyb_protocol: cDNA was hybridized as described in the GeneChipWhole Transcript Sense Target Labeling Assay Manual (default amount of cDNA was used for each sample)

scan_protocol: Affymetrix scanner

data_processing: RMA background correction; Quantile normalization; Probeset summarization - mean; Log probes using base - 2

source_name: Blood mononuclears

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip Whole Transcript Sense Target Labeling Assay)

growth_protocol: not applicable

extract_protocol: Ribo Pure Blood Kit (Ambion)

treatment_protocol: not applicable

tag: individual id

value: After HSCT

value: Blood mononuclears


title: LR-HR_AMY_P21_rep1

value: Sprague-Dawley


title: LR-LR_AMY_P21_rep3

value: male

value: Foster LR


title: After HSCT_74B


title: LR-LR_AMY_P21_rep2

value: Amygdala


title: LR-LR_AMY_P21_rep1


title: After HSCT_103B


title: After HSCT_79B


title: LR_AMY_P21_rep4

value: Mother LR


title: LR_AMY_P21_rep3


title: LR_AMY_P21_rep1


title: After HSCT_85B


title: After HSCT_67B


title: LR_AMY_P21_rep2


title: After HSCT_51B


title: LR_AMY_P21_rep5


title: After HSCT_56B


title: After HSCT_72B


title: After HSCT_38B


title: HR_AMY_P14_rep3

value: HR

value: Mother HR


title: After HSCT_73B


title: After HSCT_42B


title: HR_AMY_P14_rep4


title: After HSCT_57B


title: After HSCT_41B


title: After HSCT_33B


title: After HSCT_53B


title: After HSCT_76B


title: HR_AMY_P14_rep5


title: HR_AMY_P14_rep1


title: HR_AMY_P14_rep2


title: Day 18 A549 Cells Replicate 3

description:
Gene expression after 18 days in culture
RH_253949414713_S01_GE1_107_Sep09_2_1

tag: source gender

value: Male

tag: age at tissue sampling

value: 58 years

value: Continous cancer derived cell line

value: after 18 days in culture


title: After HSCT_29B


title: After HSCT_24B


title: LSCC-adjacent Normal-1215174N

city: Shanghai

first: cheng

last: zule

address: NO.865 Changning Street

institute: Shanghai Institute of Microsystem And Information Technology,Chinese Academy of Sciences

description: lncRNA and mRNA expression profile in adjacent normal tissues

hyb_protocol: 1.5 ug of cyanine 3-labeled, linearly amplified cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2xgGEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Hybridization Chamber gasket slides (Agilent p/n G2534-60003) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: paired adjacent normal lung tissues

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions,

extract_protocol: RNA was puriﬁed from total RNA after removal of rRNA using mRNA-ONLYTM Eukaryotic mRNA Isolation Kit (Epicentre, Madison, WI, USA).

treatment_protocol: Paired LSCC and adjacent normal lung tissues from each subject were snap-frozen in liquid nitrogen immediately after resection and stored at -80 °C until later use.

tag: gender

tag: age

tag: tnm stage

tag: tissue

value: paired adjacent normal lung tissues


title: LSCC-Tumor-1215174T

description: lncRNA and mRNA expression profile in tumor tissues

source_name: early stage lung squamous cell carcinoma tissues

value: Ib


title: LR-HR_AMY_P14_rep5

tag: Sex

tag: selectively bred line (biological parents)

value: LR

tag: brain region

tag: caregiver dame


title: LR-HR_AMY_P14_rep4

value: Foster HR

tag: postnatal age


title: LSCC-adjacent Normal-9515N


title: LSCC-Tumor-11500T

value: Ia

value: early stage lung squamous cell carcinoma tissues


title: LR-LR_AMY_P14_rep5

value: Sprague-Dawley


title: After HSCT_11B

tag: treatment

value: After HSCT

tag: cell type

value: Blood mononuclears


title: LSCC-adjacent Normal-11500N

value: male


title: LR-HR_AMY_P14_rep1

tag: strain

value: Amygdala


title: After HSCT_20B


title: LR-HR_AMY_P14_rep2


title: After HSCT_27B


title: After HSCT_10B


title: OIL_lac_3

city: New York

first: Kalpana

last: Gopalakrishnan

state: NY

address: 1428 Madison Avenue, Atran Building 03-02

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from rat mammary tissues at postnatal day 146 following treatment with olive oil (control) from postnatal day 1 to postnatal day 145

hyb_protocol: Following fragmentation, 5.2 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0 St arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000.

data_processing: The data was preprocessed in Expression Console software (Affymetrix) using RMA-sketch workflow and default settings. Transcriptome results from MPB and TCS treatment during three short term windows – perinatal, prepubertal and pubertal windows – were pre-processed independently to generate two separate datasets (MPB and control - table 1, TCS and control - table 2).  Transcriptome data from chronically exposed TCS animals and corresponding controls were pre-processed separately from short term data (Chronic TCS and control - table 3).  Batch effects were removed using the ComBat package in R (Leek J. T. et al, 2012) for datasets in table 1 and table 2 (no batch covariate in table 3). Data submitted here have not been corrected for batch effects. Batch information is provided in the sample datasheet.

source_name: Rats treated with olive oil (control) from postnatal day 1 to 145

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays, Affymetrix 2015).

growth_protocol: The breeder animals (F0) were weighed weekly to determine treatment dose, starting from gestation for the perinatal group and during lactation for prepubertal, pubertal, and adult groups and the dose to be administered was calculated on the basis of the weekly weight.  For the perinatal group, all the F1 pups were housed with their dams until sacrifice (postnatal (PND) 21).  F1 pups from all the other groups were housed with their dams (F0) until weaning (PND 28) then separated from the dam, identified by ear punch, weighed individually every week and dosed by gavage following the protocol, based on the weekly mean body weight of each group.  Animals were randomized into different treatment groups in order to have minimal differences in body weight among them, with a standard deviation of no more than 10% from the average.

extract_protocol: The 5th left and right caudal mammary glands were used for transciptome profiling.  Mammary tissues were pulverized in liquid nitrogen and total RNA was extracted using the Maxwell 16 LEV simplyRNA Blood kit (Promega, WI) or the Direct-zol RNA MiniPrep kit (Zymo Research, CA).  Total RNA concentration was determined using Nanodrop (Thermo Scientific, MA), and RNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies, CA); only samples with RNA Integrity Number ≥ 7 were used for microarrays.

treatment_protocol: Perinatal animals: five animals were treated in utero daily through oral gavage of their pregnant dams (F0) from gestation day (GD) 1 to GD 20; another five animals were treated daily from post natal day (PND)1 to PND 20 through milk of lactating dams (F0) exposed by oral gavage.  One female pup per litter was randomly selected and sacrificed at PND 21.  Prepubertal animals: treated daily from PND 21 through breast milk, then by oral gavage from PND 28 to PND 41, and sacrificed at PND 42.  Pubertal animals: treated daily by oral gavage from PND 42 to PND 62, and sacrificed at PND 63.  Chronic treatment group: animals were treated daily from PND 1 through milk of dams (F0) exposed from parturition.  After weaning, the female offspring (F1) were treated through oral gavage 3 times a week.  Animals were mated (outbred) at PND 97 and treatments were continued through pregnancy, delivery of pups (F2) and lactation.  At the end of lactation at lactating day 28 (PND 146), F1 animals were sacrificed.

value: Female

value: Caudal mammary tissue

tag: exposure/treatment condition

value: Olive oil

tag: window of exposure

value: Chronic

tag: age at sacrifice

value: Rats sacrificed at postnatal day 146

tag: batch

value: One

tag: rna extraction kit

value: Promega


title: OIL_lac_1


title: After HSCT_2B

tag: individual id


title: After HSCT_1C


title: After HSCT_9B


title: Before HSCT_133A

value: Before HSCT


title: Before HSCT_132A


title: LR-HR_AMY_P14_rep3

value: LR


title: LR-LR_AMY_P14_rep4

value: Foster LR


title: LR-LR_AMY_P14_rep2


title: LR-LR_AMY_P14_rep3


title: OIL_lac_2


title: Before HSCT_110A


title: TCS_lac_242

description: Gene expression data from rat mammary tissues at postnatal day 146 following treatment with triclosan from postnatal day 1 to postnatal day 145

source_name: Rats treated with triclosan from postnatal day 1 to 145

value: Triclosan


title: LR_AMY_P14_rep5

value: Mother LR


title: OIL_pub_423

description: Gene expression data from rat mammary tissues at postnatal day 63 following treatment with olive oil (control) from postnatal day 42 to postnatal day 62

source_name: Rats treated with olive oil (control) from postnatal day 42 to 62

value: Sprague-Dawley

value: Pubertal

value: Rats sacrificed at postnatal day 63

value: Two


title: LR-LR_AMY_P14_rep1

value: male

value: Amygdala


title: LR_AMY_P14_rep4


title: LR_AMY_P14_rep3


title: Before HSCT_103A

value: Blood mononuclears


title: LR_AMY_P14_rep1


title: TCS_lac_241

value: Female

value: Caudal mammary tissue


title: LR_AMY_P14_rep2


title: Before HSCT_121A


title: Before HSCT_102A


title: LSCC-Tumor-9515T

tag: gender

tag: age

value: IIa

value: early stage lung squamous cell carcinoma tissues


title: HR_AMY_P07_rep5

value: HR

value: Mother HR


title: OIL_pub_421

tag: tissue

value: Olive oil

value: One

value: Promega


title: TCS_lac_244

tag: Sex

value: Triclosan

value: Chronic

value: Rats sacrificed at postnatal day 146


title: OIL_pub_422

value: Sprague-Dawley

value: Pubertal

value: Rats sacrificed at postnatal day 63


title: OIL_pub_420


title: Before HSCT_93A

value: Before HSCT


title: Before HSCT_94A

value: Blood mononuclears


title: HR_AMY_P07_rep4

value: male

tag: selectively bred line (biological parents)

value: Amygdala


title: Before HSCT_92A


title: HR_AMY_P07_rep3

tag: brain region


title: HR_AMY_P07_rep2

tag: caregiver dame


title: Before HSCT_128A


title: LR-HR_AMY_P07_rep3

value: LR

value: Foster HR

tag: postnatal age


title: OIL_pub_419

value: Female

value: Caudal mammary tissue


title: OIL_peri_409

description: Gene expression data from rat mammary tissues at postnatal day 21 following treatment with olive oil (control) from postnatal day 1 to postnatal day 20

source_name: Rats treated with olive oil (control) from postnatal day 1 to 20

value: Olive oil

value: Perinatal

value: Rats sacrificed at postnatal day 21

value: Two


title: LR-HR_AMY_P07_rep4


title: OIL_prep_414

description: Gene expression data from rat mammary tissues at postnatal day 42 following treatment with olive oil (control) from postnatal day 21 to postnatal day 41

source_name: Rats treated with olive oil (control) from postnatal day 21 to 41

value: Prepubertal

value: Rats sacrificed at postnatal day 42

value: Promega


title: LR-HR_AMY_P07_rep5

value: Sprague-Dawley


title: OIL_prep_415


title: LR-HR_AMY_P07_rep2


title: Before HSCT_79A

tag: treatment


title: OIL_prep_412

value: One


title: OIL_peri_410


title: Before HSCT_85A

value: Before HSCT

tag: cell type


title: Before HSCT_86A

value: Blood mononuclears


title: OIL_peri_408

tag: strain


title: Before HSCT_76A


title: HR_AMY_P07_rep1

value: male

value: HR

value: Mother HR


title: After HSCT_18B

value: After HSCT


title: Before HSCT_78A


title: Before HSCT_80A


title: OIL_prep_413

value: Female

tag: exposure/treatment condition


title: Before HSCT_75A


title: Before HSCT_82A


title: OIL_peri_406

value: Caudal mammary tissue

tag: window of exposure


title: Before HSCT_72A


title: OIL_peri_402

description: Gene expression data from rat mammary tissues at postnatal day 21 following treatment with olive oil (control) from gestation day 1 to gestation day 20

source_name: Rats treated with olive oil (control) from gestation day 1 to 20

value: Olive oil

tag: age at sacrifice


title: LR-LR_AMY_P07_rep1

value: LR

value: Amygdala

value: Foster LR


title: LR_AMY_P07_rep5

value: Mother LR


title: OIL_peri_404

value: Perinatal

value: Rats sacrificed at postnatal day 21

tag: batch

value: Two


title: OIL_peri_407

value: Sprague-Dawley

value: One

tag: rna extraction kit

value: Promega


title: OIL_prep_411

value: Prepubertal

value: Rats sacrificed at postnatal day 42


title: LR-LR_AMY_P07_rep2

value: male


title: LR-HR_AMY_P07_rep1

value: Foster HR


title: LR-LR_AMY_P07_rep5


title: OIL_peri_403

value: Female


title: Before HSCT_66A

tag: individual id

value: Before HSCT

value: Blood mononuclears


title: LR-LR_AMY_P07_rep3

value: LR


title: Before HSCT_56A


title: Before HSCT_67A


title: Before HSCT_57A


title: Before HSCT_59A


title: Mutant 3

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

description: Gene expression data from 4 weeks of age

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 12.6 (Agilent technologies, CA).

source_name: uteri of mutant  at 4 weeks of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Collect intact 4 weeks-old mice

extract_protocol: RNA was extracted from the uterine tissues using the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA).

tag: gender

value: uterus

tag: genotype/variation

value: Pgr cre/+ Ctnnb1f(ex3)/+


title: Mutant 2

tag: tissue


title: OIL_peri_401

tag: Sex

value: Caudal mammary tissue

value: Olive oil


title: Before HSCT_53A


title: LR_AMY_P07_rep4

tag: selectively bred line (biological parents)

value: Amygdala

value: Mother LR


title: TCS_pub_221

description: Gene expression data from rat mammary tissues at postnatal day 63 following treatment with triclosan from postnatal day 42 to postnatal day 62

source_name: Rats treated with triclosan from postnatal day 42 to 62

value: Sprague-Dawley

value: Triclosan

value: Pubertal

value: Rats sacrificed at postnatal day 63


title: Mutant 1


title: Before HSCT_74A


title: Control 3

source_name: uteri of control at 4 weeks of age

value: wild type


title: LR_AMY_P07_rep2

value: male

tag: brain region


title: LR_AMY_P07_rep1

tag: caregiver dame


title: TCS_pub_219

value: One

value: Promega


title: TCS_pub_220

value: Female


title: Control 1


title: TCS_prep_212

description: Gene expression data from rat mammary tissues at postnatal day 42 following treatment with triclosan from postnatal day 21 to postnatal day 41

source_name: Rats treated with triclosan from postnatal day 21 to 41

value: Prepubertal

value: Rats sacrificed at postnatal day 42


title: HR_HPC_Adult_rep5

source_name: Hippocampus, Dissected whole

value: HR

value: Hippocampus

value: Mother HR

tag: postnatal age


title: miRNA from colorectal cancer colon CRC 12_R45

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

description: Non

hyb_protocol: The samples were hybridized for 16 hours in a GeneChip Hybridization Oven 645 for at 45C on GeneChip miRNA 3.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner

data_processing: RMA-DABG

source_name: colorectal cancer colon

label_protocol: Biotin-labeled using the Flashtag Biotin HSR RNA Labeling Kit  from 8 microg total RNA

growth_protocol: miRNA of different biopsy samples (healthy, tubular and tubulo-villosus adenoma and CRC samples) were compared

extract_protocol: Total RNA including miRNA was isolated using the High Pure miRNA Isolation Kit

treatment_protocol: There was no treatment of miRNA

tag: disease state

value: Colorectal cancer


title: Before HSCT_51A

tag: treatment

value: Before HSCT

tag: cell type

value: Blood mononuclears


title: Before HSCT_48A


title: Before HSCT_42A


title: LR_AMY_P07_rep3

source_name: Amygdala, Dissected whole

tag: strain

value: Sprague-Dawley

value: LR

value: Amygdala

value: Mother LR


title: miRNA from colorectal cancer colon CRC 11_4927

description: Non


title: miRNA from colorectal cancer colon CRC 4989

description: Non


title: miRNA from colorectal cancer colon CRC 4988

description: Non


title: TCS_prep_211

value: Caudal mammary tissue

tag: exposure/treatment condition

value: Triclosan

tag: window of exposure


title: miRNA from colorectal cancer colon CRC 60_5020

description: Non


title: TCS_prep_213

tag: age at sacrifice

tag: batch

value: One


title: HR_HPC_Adult_rep4

value: male


title: Before HSCT_41A

tag: individual id


title: HR_HPC_Adult_rep3


title: Control 2

tag: gender

value: Female

value: uterus

value: wild type


title: HR_HPC_Adult_rep2

value: HR


title: TCS_peri_208

description: Gene expression data from rat mammary tissues at postnatal day 21 following treatment with triclosan from postnatal day 1 to postnatal day 20

source_name: Rats treated with triclosan from postnatal day 1 to 20

value: Perinatal

value: Rats sacrificed at postnatal day 21

tag: rna extraction kit

value: Promega


title: HR_HPC_Adult_rep1

value: Hippocampus

value: Mother HR


title: TCS_peri_209

value: Sprague-Dawley

tag: tissue

value: Two


title: LR-HR_HPC_Adult_rep5

tag: Sex

value: LR

value: Foster HR


title: TCS_peri_206

value: Caudal mammary tissue


title: Before HSCT_38A

source_name: Blood mononuclears

value: Before HSCT

value: Blood mononuclears


title: Before HSCT_33A


title: miRNA from colorectal cancer colon CRC 58_4847

description: Non

value: Colorectal cancer


title: LR-HR_HPC_Adult_rep4

value: male

tag: selectively bred line (biological parents)


title: Before HSCT_27A


title: Before HSCT_29A


title: Before HSCT_24A


title: miRNA from colorectal cancer colon CRC 52_R42.

description: Non


title: TCS_peri_207

value: Female

value: Triclosan

value: One


title: miRNA from colorectal cancer colon CRC 50_R61

description: Non


title: miRNA from colorectal cancer colon CRC 49_4973

description: Non


title: TCS_peri_203

description: Gene expression data from rat mammary tissues at postnatal day 21 following treatment with triclosan from gestation day 1 to gestation day 20

source_name: Rats treated with triclosan from gestation day 1 to 20

value: Perinatal


title: miRNA from colorectal cancer colon CRC 51_R32

description: Non


title: LR-HR_HPC_Adult_rep3

tag: brain region


title: TCS_peri_202

value: Rats sacrificed at postnatal day 21


title: LR-LR_HPC_Adult_rep5

tag: caregiver dame

value: Foster LR


title: miRNA from colorectal cancer colon CRC 40_R22

description: Non


title: TCS_peri_204

value: Promega


title: TCS_peri_201


title: Before HSCT_20A


title: LR-LR_HPC_Adult_rep4

value: Hippocampus

tag: postnatal age


title: miRNA from colorectal cancer colon CRC 57_4803CRC

description: Non

tag: disease state


title: MPB_pub_123

description: Gene expression data from rat mammary tissues at postnatal day 63 following treatment with methyl paraben from postnatal day 42 to postnatal day 62

source_name: Rats treated with methyl paraben from postnatal day 42 to 62

value: Sprague-Dawley

value: Methyl paraben

value: Pubertal

value: Rats sacrificed at postnatal day 63


title: LR-HR_HPC_Adult_rep2

value: LR

value: Foster HR


title: TCS_peri_205

value: Caudal mammary tissue

value: Two


title: LR-HR_HPC_Adult_rep1

value: male


title: LR-LR_HPC_Adult_rep3


title: Before HSCT_19A

tag: treatment

value: Before HSCT

value: Blood mononuclears


title: Before HSCT_18A

tag: cell type


title: Before HSCT_11A


title: Before HSCT_9A


title: miRNA from colorectal cancer colon CRC 39_R41

description: Non

value: Colorectal cancer


title: miRNA from colorectal cancer colon CRC 31_4905

description: Non


title: MPB_pub_121

tag: strain

value: Female

value: One


title: miRNA from colorectal cancer colon CRC 32_R33

description: Non


title: Before HSCT_2A


title: MPB_pub_120

tag: exposure/treatment condition


title: OIL_peri_405

value: Olive oil

tag: window of exposure

value: Perinatal

value: Rats sacrificed at postnatal day 21


title: miRNA from colorectal cancer colon CRC 30_R44

description: Non


title: miRNA from colorectal cancer colon CRC 29_4934

description: Non


title: LR-LR_HPC_Adult_rep2

value: Sprague-Dawley

value: Hippocampus

value: Foster LR


title: MPB_prep_115

description: Gene expression data from rat mammary tissues at postnatal day 42 following treatment with methyl paraben from postnatal day 21 to postnatal day 41

source_name: Rats treated with methyl paraben from postnatal day 21 to 41

value: Methyl paraben

value: Prepubertal

tag: age at sacrifice

value: Rats sacrificed at postnatal day 42

value: Promega


title: LR_HPC_Adult_rep3

value: LR

value: Mother LR


title: LR-LR_HPC_Adult_rep1

value: male


title: CD14+_monocytes_PAM3CYS_donor_E

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.2).

source_name: CD14+ monocytes, obtained from donor E, stimulated with Pam3Cys (10 μg/mL) for 24h

label_protocol: One hundred nanogram of total RNA was used for whole transcript cDNA synthesis with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from blood donated by 5 healthy male volunteers. PBMCs were isolated by differential centrifugation over Ficoll-Paque™ PLUS (GE Healthcare Biosciences). CD14+ monocytes were subsequently purified from the freshly isolated PBMCs using MACS microbeads for positive selection, according to the manufacturer's instructions (Miltenyi Biotec, Germany). All donors gave full written informed consent.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: CD14+ monocytes (2x10^6 per well) were cultured in RPMI 1640 (no glucose, Gibco) cell culture medium, supplemented with 10 μg/mL gentamicin (Gibco), 10 mM pyruvate (Gibco), 10 mM HEPES (Sigma), 5.5 mM glucose (Sigma) and 10% human pool serum, and stimulated with either RPMI, 10 μg/mL Pam3Cys (EMC Microcollections, Germany) or 10 ng/mL LPS from Escherichia coli (Sigma) for 24 hrs.

tag: donor id

value: E

tag: donor disease state

value: healthy

tag: donor sex

value: CD14-positive monocytes

value: Pam3Cys (10 ug/mL), dissolved in cell culture medium [RPMI]


title: Before HSCT_73A

tag: individual id

value: Before HSCT

value: Blood mononuclears


title: LR_HPC_Adult_rep5


title: miRNA from colorectal cancer colon CRC 20_4728

description: Non

value: Colorectal cancer


title: MPB_pub_122

value: Sprague-Dawley

value: Female

tag: tissue

value: Caudal mammary tissue

value: Pubertal

value: Rats sacrificed at postnatal day 63

tag: batch

value: Two

tag: rna extraction kit


title: LR_HPC_Adult_rep4

tag: Sex

tag: selectively bred line (biological parents)

tag: brain region

value: Hippocampus


title: MPB_pub_119

value: Methyl paraben

value: One

value: Promega


title: CD14+_monocytes_control_donor_E

source_name: CD14+ monocytes, obtained from donor E, incubated with cell culture medium only (RPMI) for 24h

value: E

value: male

value: Control (cell culture medium [RPMI] only)


title: MPB_prep_114

value: Prepubertal

value: Rats sacrificed at postnatal day 42


title: MPB_prep_113


title: CD14+_monocytes_LPS_donor_E

source_name: CD14+ monocytes, obtained from donor E, stimulated with LPS (10 ng/mL) for 24h

value: healthy

value: CD14-positive monocytes

value: LPS (10 ng/mL) from E. coli, dissolved in cell culture medium [RPMI]


title: CD14+_monocytes_PAM3CYS_donor_D

source_name: CD14+ monocytes, obtained from donor D, stimulated with Pam3Cys (10 μg/mL) for 24h

value: D

value: Pam3Cys (10 ug/mL), dissolved in cell culture medium [RPMI]


title: LR_HPC_Adult_rep2

value: Sprague-Dawley

value: LR

tag: caregiver dame

value: Mother LR

tag: postnatal age


title: Before HSCT_1A

tag: treatment

value: Before HSCT

tag: cell type

value: Blood mononuclears


title: miRNA from colorectal cancer colon CRC 19_4851

description: Non

tag: disease state

value: Colorectal cancer


title: miRNA from tubulo-villosus adenoma colon TUBVILL 8_4472

description: Non

source_name: tubulo-villosus adenoma colon

value: Tubulo-villosus adenoma


title: CD14+_monocytes_LPS_donor_D

source_name: CD14+ monocytes, obtained from donor D, stimulated with LPS (10 ng/mL) for 24h


title: LR_HPC_Adult_rep1

tag: strain

value: Hippocampus


title: MPB_prep_111

value: Female

value: Caudal mammary tissue

tag: exposure/treatment condition

value: Methyl paraben

tag: window of exposure

tag: age at sacrifice

value: One

value: Promega


title: MPB_peri_110

description: Gene expression data from rat mammary tissues at postnatal day 21 following treatment with methyl paraben from postnatal day 1 to postnatal day 20

source_name: Rats treated with methyl paraben from postnatal day 1 to 20

value: Perinatal

value: Rats sacrificed at postnatal day 21

value: Two


title: HR_HPC_P21_rep5

value: male

value: HR

value: Mother HR


title: miRNA from tubulo-villosus adenoma colon TUBVILL 43_4831

description: Non


title: miRNA from tubulo-villosus adenoma colon TUBVILL 44_4931

description: Non


title: HR_HPC_P21_rep3

value: Sprague-Dawley


title: MPB_peri_109


title: CD14+_monocytes_control_donor_D

source_name: CD14+ monocytes, obtained from donor D, incubated with cell culture medium only (RPMI) for 24h

tag: donor id

value: D

tag: donor disease state

value: healthy

tag: donor sex

value: CD14-positive monocytes

value: Control (cell culture medium [RPMI] only)


title: CD14+_monocytes_control_donor_C

source_name: CD14+ monocytes, obtained from donor C, incubated with cell culture medium only (RPMI) for 24h

value: C


title: HR_HPC_P21_rep2

source_name: Hippocampus, Dissected whole

value: Hippocampus


title: miRNA from tubulo-villosus adenoma colon TUBVILL 36_4944

description: Non

value: Tubulo-villosus adenoma


title: HR_HPC_P21_rep4


title: MPB_peri_108

value: Female

tag: tissue

value: Caudal mammary tissue

value: Methyl paraben

tag: batch


title: CD14+_monocytes_LPS_donor_B

source_name: CD14+ monocytes, obtained from donor B, stimulated with LPS (10 ng/mL) for 24h

value: B

value: LPS (10 ng/mL) from E. coli, dissolved in cell culture medium [RPMI]


title: CD14+_monocytes_PAM3CYS_donor_C

source_name: CD14+ monocytes, obtained from donor C, stimulated with Pam3Cys (10 μg/mL) for 24h

value: Pam3Cys (10 ug/mL), dissolved in cell culture medium [RPMI]


title: HR_HPC_P21_rep1

tag: Sex

value: male


title: CD14+_monocytes_PAM3CYS_donor_B

source_name: CD14+ monocytes, obtained from donor B, stimulated with Pam3Cys (10 μg/mL) for 24h


title: MPB_peri_106

value: Perinatal

value: Rats sacrificed at postnatal day 21

value: One

tag: rna extraction kit

value: Promega


title: miRNA from tubulo-villosus adenoma colon TUBVILL 23_4526

description: Non


title: CD14+_monocytes_LPS_donor_C

source_name: CD14+ monocytes, obtained from donor C, stimulated with LPS (10 ng/mL) for 24h

value: healthy


title: LR-HR_HPC_P21_rep5

value: Sprague-Dawley

tag: selectively bred line (biological parents)

value: LR

tag: brain region

value: Foster HR


title: miRNA from tubulo-villosus adenoma colon TUBVILL 35_4617

description: Non


title: MPB_peri_107


title: miRNA from tubulo-villosus adenoma colon TUBVILL 7_4881

description: Non


title: MPB_prep_112

value: Prepubertal

value: Rats sacrificed at postnatal day 42


title: miRNA from tubulo-villosus adenoma colon TUBVILL 16_R9

description: Non

value: Tubulo-villosus adenoma


title: miRNA from tubulo-villosus adenoma colon TUBVILL 15_4788

description: Non


title: CD14+_monocytes_control_donor_B

source_name: CD14+ monocytes, obtained from donor B, incubated with cell culture medium only (RPMI) for 24h

value: CD14-positive monocytes

value: Control (cell culture medium [RPMI] only)


title: LR-HR_HPC_P21_rep4

value: Hippocampus

tag: caregiver dame

tag: postnatal age


title: CD14+_monocytes_PAM3CYS_donor_A

source_name: CD14+ monocytes, obtained from donor A, stimulated with Pam3Cys (10 μg/mL) for 24h

value: A

tag: cell type

tag: treatment


title: LR-HR_HPC_P21_rep3

tag: strain


title: MPB_peri_104

description: Gene expression data from rat mammary tissues at postnatal day 21 following treatment with methyl paraben from gestation day 1 to gestation day 20

source_name: Rats treated with methyl paraben from gestation day 1 to 20

value: Female

value: Caudal mammary tissue

tag: exposure/treatment condition

value: Methyl paraben

value: Two


title: miRNA from tubular adenoma colon TUB 6_4550

description: Non

source_name: tubular adenoma colon

tag: disease state

value: Tubular adenoma


title: CD14+_monocytes_LPS_donor_A

source_name: CD14+ monocytes, obtained from donor A, stimulated with LPS (10 ng/mL) for 24h

value: male

value: LPS (10 ng/mL) from E. coli, dissolved in cell culture medium [RPMI]


title: MPB_peri_103

value: Sprague-Dawley

tag: window of exposure

value: Perinatal

tag: age at sacrifice

value: Rats sacrificed at postnatal day 21

value: One

value: Promega


title: miRNA from tubular adenoma colon TUB 5_4913

description: Non


title: MPB_peri_102


title: CD14+_monocytes_control_donor_A

source_name: CD14+ monocytes, obtained from donor A, incubated with cell culture medium only (RPMI) for 24h

tag: donor id

tag: donor disease state

value: healthy


title: LR-HR_HPC_P21_rep1

value: LR

value: Foster HR


title: MPB_peri_105

tag: tissue


title: MPB_peri_101

tag: batch


title: LR-LR_HPC_P21_rep5

tag: Sex

value: Hippocampus

value: Foster LR


title: miRNA from tubular adenoma colon TUB 41_4536

description: Non


title: LR-LR_HPC_P21_rep4


title: LR-LR_HPC_P21_rep3


title: miRNA from tubular adenoma colon TUB 34_R25

description: Non


title: LR-LR_HPC_P21_rep2


title: miRNA from tubular adenoma colon TUB 42_4522

description: Non


title: miRNA from tubular adenoma colon TUB 33_R21

description: Non


title: LR-LR_HPC_P21_rep1


title: miRNA from tubular adenoma colon TUB 24_4493

description: Non


title: LR-HR_HPC_P21_rep2


title: LR_HPC_P21_rep5

value: Mother LR


title: miRNA from tubular adenoma colon TUB 22_4538

description: Non


title: miRNA from tubular adenoma colon TUB 21_4967

description: Non


title: miRNA from tubular adenoma colon TUB 14_4948

description: Non


title: miRNA from tubular adenoma colon TUB 13_4942

description: Non


title: miRNA from healthy normal colon N 4982

description: Non

source_name: healthy colon

value: Healthy


title: miRNA from healthy normal colon N 4111

description: Non


title: LR_HPC_P21_rep4


title: LR_HPC_P21_rep3


title: LR_HPC_P21_rep2


title: CREB1_5mC_rep2

type: protein

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

description:
Sample name: SAMPLE 11
CREB1 PBM experiment, 5mC, replicate 2

hyb_protocol: The double-stranded arrays were blocked with 4% milk for 1 hour and washed with 0.1% Tween-20 in 1x PBS.  Freshly synthesized protein (25 µL) was mixed with 125 µL of protein binding reaction mixture consisting of 4% milk in 1x PBS, 50 ng of salmon testes DNA and 0.2 µg/µL bovine serum albumin and added to double-stranded array.  The protein binding reactions were carried out in hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS.  The protein bound array was incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20.  Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 micron resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low). The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing:
For all possible 65,536 8-mers, a transformed 8-mer median intensity (Z-score) was calculated from the average signal intensity across array probes containing each 8-mer.  8-mer Z-scores of the modified strand (the reverse complement of the array probe sequence) were used for downstream analyses.  Some of the probes on the array contain multiple 8-mers that are targeted by the proteins which allows for analysis of ~65k 8-mers from ~40K probes.
The processed data file (z-score_8-mers.txt) contains the 8-mer Z-Score of the modified strand.

label: Alexa Fluor 647

molecule: protein

source_name: CREB1, HK design

label_protocol: 180 ng of plasmid containing DNA binding domains of CREB1 or ATF1 or JUND were used to express proteins using PureExpress in-vitro transcription translation kit (NEB) in 25 µL reaction volume as per manufacturer’s instructions.

extract_protocol: DBD sequences along with 15 amino acid residues on either side of the DBD in the native protein were cloned as NcoI-SacI fragments into a T7-driven C-terminal GST expression vector (Sharrocks 1994, Gene:138, 105-108).

treatment_protocol: The single-stranded oligonucleotide microarrays were double-stranded by primer extension as described in Badis et al. Science (2009).   Arrays were double-stranded using either cytosine, 5-methylcytosine (5mC, NEB) or 5-hydroxymethylcytosine (5hmC, Zymo Research). The resulting double-stranded DNA on the array thus contained probes with either cytosine on both strands or modified cytosine (5mC/5hmC) on one strand and cytosine on the second strand. This results in a hemi-methylated or hemi-hydroxymethylated state.

tag: dbd

value: BZIP

tag: protein

tag: double-stranding treatment


title: CREB1_5hmC_rep2

description:
Sample name: SAMPLE 12
CREB1 PBM experiment, 5hmC, replicate 2


title: LR_HPC_P21_rep1

tag: selectively bred line (biological parents)

tag: brain region

tag: caregiver dame


title: dmy rat

city: Izumisano

first: Mitsuru

last: Kuwamura

address: Rinku-Orai

country: Japan

institute: Osaka Prefecture University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Spinal cord of dmy Rat at 6 wks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA using GeneChip One-Cycle Target Labeling and Control Reagents.

growth_protocol: A homozygous dmy (dmy/dmy) and a control rats at 6 weeks were deeply anesthetized and exsanguinated from the abdominal aorta.

treatment_protocol: The cervical spinal cord were removed and processed for total RNA extraction.

value: cervical spinal cord


title: control rat

source_name: Spinal cord of Control Rat at 6 wks


title: miRNA from healthy normal colon N 9_4962

description: Non


title: miRNA from healthy normal colon N 10_4955

description: Non


title: HR_HPC_P14_rep4

value: HR

value: Mother HR

tag: postnatal age


title: miRNA from healthy normal colon N 56_4880

description: Non


title: CREB1_Cytosine_rep2

description:
Sample name: SAMPLE 10
CREB1 PBM experiment, cytosine replicate 2, replicate 2

value: cytosine


title: HR_HPC_P14_rep3

tag: strain

value: Sprague-Dawley

value: male


title: JUND_5hmC

description:
Sample name: SAMPLE 9
JUND PBM experiment, 5hmC

source_name: JUND, HK design

value: JUND


title: miRNA from colorectal cancer colon CRC 59_4887

description: Non

source_name: colorectal cancer colon

value: Colorectal cancer


title: miRNA from healthy normal colon N 55_4981

description: Non


title: HR_HPC_P14_rep1

source_name: Hippocampus, Dissected whole


title: LR-HR_HPC_P14_rep5


title: miRNA from healthy normal colon N 54_4911

description: Non


title: HR_HPC_P14_rep5


title: JUND_5mC

description:
Sample name: SAMPLE 8
JUND PBM experiment, 5mC


title: Before HSCT_10A

source_name: Blood mononuclears

tag: individual id

tag: treatment

value: Before HSCT

tag: cell type

value: Blood mononuclears


title: LR-HR_HPC_P14_rep4

value: LR


title: JUND_Cytosine

description:
Sample name: SAMPLE 7
JUND PBM experiment, cytosine


title: ATF1_5hmC

description:
Sample name: SAMPLE 6
ATF1 PBM experiment, 5hmC

source_name: ATF1, HK design


title: ATF1_Cytosine

description:
Sample name: SAMPLE 4
ATF1 PBM experiment, cytosine


title: CREB1_5hmC

description:
Sample name: SAMPLE 3
CREB1 PBM experiment, 5hmC


title: LR-HR_HPC_P14_rep3

value: Foster HR


title: HR_HPC_P14_rep2

value: Hippocampus


title: CREB1_5mC

description:
Sample name: SAMPLE 2
CREB1 PBM experiment, 5mC


title: miRNA from healthy normal colon N 46_4899

description: Non

tag: disease state


title: CREB1_Cytosine

description:
Sample name: SAMPLE 1
CREB1 PBM experiment, cytosine


title: miRNA from healthy normal colon N 47_4885

description: Non


title: LR-LR_HPC_P14_rep3

value: Foster LR


title: miRNA from healthy normal colon N 38_R38

description: Non


title: miRNA from healthy normal colon N 37_4959

description: Non


title: LR-LR_HPC_P14_rep5


title: JUND_5hmC_rep2

description:
Sample name: SAMPLE 18
JUND PBM experiment, 5hmC, replicate 2


title: LR-HR_HPC_P14_rep1


title: LR-LR_HPC_P14_rep2


title: miRNA from healthy normal colon N 53_R48

description: Non


title: LR-LR_HPC_P14_rep4


title: miRNA from healthy normal colon N 48_R26

description: Non


title: LR-HR_HPC_P14_rep2


title: miRNA from healthy normal colon N 27_4954

description: Non


title: JUND_5mC_rep2

description:
Sample name: SAMPLE 17
JUND PBM experiment, 5mC, replicate 2


title: miRNA from healthy normal colon N 28_4879

description: Non


title: LR_HPC_P14_rep5

value: Mother LR


title: LR-LR_HPC_P14_rep1


title: miRNA from healthy normal colon N 45_4960

description: Non

value: Healthy


title: JUND_Cytosine_rep2

description:
Sample name: SAMPLE 16
JUND PBM experiment, cytosine, replicate 2

value: BZIP


title: miRNA from healthy normal colon N 26_4953

description: Non


title: Bmp2cKO_Wnt3a_BMP2

city: Boston

first: Valerie

middle: S

last: Salazar

state: MA

address: 188 Longwood Avenue REB 513

department: Developmental Biology

institute: Harvard School of Dental Medicine

description:
BMSC Day 7 OB Bmp2FF_Prx1-Cre_Wnt3a_BMP2
Gene expression data on Bmp2 cKO BMSC differentiated 7 days in osteogenic medium plus rmWnt3a (40 ng/ml) plus rhBMP2 (100 ng/ml) (pooled sample from 3 biological replicates)

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse ST 2.1 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

data_processing: Data were analyzed with Expression Console and Transcriptome Analysis Console v3.0 using Affymetrix default analysis settings.

source_name: Bmp2 Flox/Flox; Prx1-Cre cells + BMP2 + Wnt3a

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA according to the standard protocol of Ambion WT Expression Kit.

growth_protocol: Bone marrow from 4-6 month old mice (male and female) was collected and plated in bone marrow stromal cells (BMSC) medium (ascorbic acid free α-MEM (Invitrogen) containing 20% FBS, 40 mM L-glutamine, 100 U/ml penicillin-G, and 100 mg/ml streptomycin). After 3 days, non-adherent cells were removed by vigorous washing with PBS.  After expansion, BMSC were seeded in BMSC medium at 300,000 cells per well in 24-well dishes (Day 0).

extract_protocol: Extraction of total RNA was performed using Trizol and columns from the RNEasy Plus Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Day 1: Confluent cultures of BMSC from Bmp2F/F or Bmp2Prx1Δ/Δ mice were stimulated with Osteogenic Medium (OM: BMSC medium plus 50 μg/ml ascorbic acid and 10 mM β-glycerophosphate).  Cells were differentiated for 7 days with osteogenic medium alone, plus BMP2 (100 ng/ml, Genetics Institute), plus Wnt3a (40 ng/ml, R&D Systems), or both.

tag: genotype

value: Bmp2 flox/flox; Prx1-Cre

tag: age

value: 3 months of age at collection

value: bone marrow stromal cells

tag: culture medium

value: Bmp2 + Wnt3a


title: LR_HPC_P14_rep4

value: Sprague-Dawley


title: miRNA from healthy normal colon N 25_4958

description: Non


title: ATF1_5hmC_rep2

description:
Sample name: SAMPLE 15
ATF1 PBM experiment, 5hmC, replicate 2


title: Bmp2cKO_Wnt3a_3

description:
BMSC_Day7OB_Bmp2FF_PrxCre_Wnt3a_3
Gene expression data on Bmp2 cKO BMSC differentiated 7 days in osteogenic medium plus rmWnt3a (40 ng/ml) Sample 3

source_name: Bmp2 Flox/Flox; Prx1-Cre cells + Wnt3a

tag: tissue


title: ATF1_5mC_rep2

description:
Sample name: SAMPLE 14
ATF1 PBM experiment, 5mC, replicate 2


title: ATF1_Cytosine_rep2

description:
Sample name: SAMPLE 13
ATF1 PBM experiment, cytosine, replicate 2

value: cytosine


title: Bmp2cKO_Wnt3a_1

description:
BMSC_Day7OB_Bmp2FF_PrxCre_Wnt3a_1
Gene expression data on Bmp2 cKO BMSC differentiated 7 days in osteogenic medium plus rmWnt3a (40 ng/ml) Sample 1


title: miRNA from healthy normal colon N 18_4123

description: Non


title: miRNA from healthy normal colon N 17_4964

description: Non


title: ATF1_5mC

description:
Sample name: SAMPLE 5
ATF1 PBM experiment, 5mC


title: WT_Wnt3a_3

description:
BMSC_Day7OB_Bmp2FF_Wnt3a_3
Gene expression data on wildtype BMSC differentiated 7 days in osteogenic medium plus rmWnt3a (40 ng/ml) Sample 3

source_name: Bmp2 Flox/Flox cells + Wnt3a

value: Bmp2 flox/flox


title: LR_HPC_P14_rep2

tag: Sex

value: male


title: LR_HPC_P14_rep1


title: HR_HPC_P07_rep5

value: HR

value: Mother HR


title: WT_Wnt3a_2

description:
BMSC_Day7OB_Bmp2FF_Wnt3a_2
Gene expression data on wildtype BMSC differentiated 7 days in osteogenic medium plus rmWnt3a (40 ng/ml) Sample 2


title: HR_HPC_P07_rep4


title: Bmp2cKO_Wnt3a_2

description:
BMSC_Day7OB_Bmp2FF_PrxCre_Wnt3a_2
Gene expression data on Bmp2 cKO BMSC differentiated 7 days in osteogenic medium plus rmWnt3a (40 ng/ml) Sample 2


title: HR_HPC_P07_rep3


title: US45102915_252800513506_S02_GE1_1100_Jul11_2_4

city: bunkyou-ku

first: Moe

last: Kitazawa

state: Tokyo

address: Yusima 1-5-45

department: Medical Research Institute

institute: Tokyo Medical and Dental University

description: Gene expression of the WT mouse placenta.

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 Whole Mouse Genome Oligo Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 0280055_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: day 12.5 placenta, WT

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50-100 ng RNA using the Low Input Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from whole embryo using Trizol Reagent (Life Technologies). RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: strain/background

tag: genotype/variation

value: WT

value: placenta

tag: developmental stage

tag: embryo gender

value: female


title: US45102915_252800513506_S02_GE1_1100_Jul11_2_1


title: HR_HPC_P07_rep1

tag: selectively bred line (biological parents)

tag: brain region

value: Hippocampus


title: proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer) G154_G04_C33_PBS

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).

source_name: proximal colon

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The generation and characterization of Ercc1+/∆7 and Ercc1-/+ mice has been previously described [PMID: 9197240]. Ercc1-/∆7 mice were obtained by crossing Ercc1+/∆7 with Ercc1-/+ mice of pure C57Bl6/J and FVB backgrounds to yield Ercc1-/∆7 with an F1 C57Bl6J/FVB hybrid background. Wild-type littermates (C57Bl/6xFVB F1) were used as controls.

extract_protocol: Total RNA was isolated from proximal colon samples using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer’s protocol.

treatment_protocol: Lactobacillus plantarum WCFS1, Lactobacillus casei BL23, and Bifidobacterium breve DSM20213 were grown on MRS medium (Merck, Darmstadt, Germany) until stationary phase, frozen in glycerol, and stored in -80°C until use. Upon use, bacteria were thawed and 10x diluted in NaHCO3/PBS buffer. Around 2*108 CFU in 200 µL were administered to mice by gavage, three times per week. Treatment of mice started at 6 weeks of age until one day before sacrifice at 16 weeks or until death.

value: vehicle (NaHCO3/PBS)

tag: mouse strain

value: Ercc1-/∆7 with F1 C57Bl6J/FVB hybrid background

tag: mouse id


title: US45102915_252800513506_S02_GE1_1100_Jul11_1_4

description: Gene expression of the KO mouse placenta.

source_name: day 12.5 placenta, Peg11/Rtl1 KO

value: Peg11/Rtl1 KO


title: proximal colon of Ercc1-/∆7 mouse treated with Lactobacillus plantarum WCFS1 G154_G05_C50_WCFS1

value: Lactobacillus plantarum WCFS1 (~2*108 CFU in 200 µL in NaHCO3/PBS buffer; 3x week)


title: proximal colon of Ercc1-/∆7 mouse treated with Bifidobacterium breve DSM20213 G154_F06_C39_Breve

value: Bifidobacterium breve DSM20213 (~2*108 CFU in 200 µL in NaHCO3/PBS buffer; 3x week)


title: proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer) G154_H04_C38_PBS


title: LR_HPC_P14_rep3

tag: strain

value: LR

tag: caregiver dame

value: Mother LR

tag: postnatal age


title: WT_Wnt3a_1

description:
BMSC_Day7OB_Bmp2FF_Wnt3a_1
Gene expression data on wildtype BMSC differentiated 7 days in osteogenic medium plus rmWnt3a (40 ng/ml) Sample 1

value: 3 months of age at collection

value: bone marrow stromal cells


title: US45102915_252800513506_S02_GE1_1100_Jul11_2_3


title: US45102915_252800513506_S02_GE1_1100_Jul11_2_2


title: proximal colon of Ercc1-/∆7 mouse treated with Lactobacillus casei BL23 G154_H05_C4_BL23

tag: treatment

value: Lactobacillus casei BL23 (~2*108 CFU in 200 µL in NaHCO3/PBS buffer; 3x week)


title: LR-HR_HPC_P07_rep5

value: Sprague-Dawley

value: male

value: Foster HR


title: WT_OM

description:
BMSC_Day7OB_Bmp2FF_OsteogenicMedium
Gene expression data on wildtype BMSC differentiated 7 days in osteogenic medium (pooled sample comprised of 3 biological replicates)

source_name: Bmp2 Flox/Flox cells + Osteogenic Media

tag: genotype

value: Bmp2 flox/flox

value: control


title: US45102915_252800513506_S02_GE1_1100_Jul11_1_3

value: placenta

value: female


title: proximal colon of Ercc1-/∆7 mouse treated with Lactobacillus plantarum WCFS1 G154_F05_C35_WCFS1


title: HR_HPC_P07_rep2

value: HR

value: Hippocampus

value: Mother HR


title: proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer) G154_F04_C20_PBS

value: vehicle (NaHCO3/PBS)

value: Ercc1-/∆7 with F1 C57Bl6J/FVB hybrid background


title: US45102915_252800513506_S02_GE1_1100_Jul11_1_2

value: Peg11/Rtl1 KO


title: LR-HR_HPC_P07_rep3

value: LR


title: PA1Lysates_phage-40min_rep3

city: ChongQing

first: Xia

last: Zhao

address: Shapingba

institute: Third military medical school

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution at#5185-5979, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions.Hybridization Kit (Cat#5188-5242, Agilent technologies,  Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent  technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings，Scan resolution=5μm, PMT 100%，10%.

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

organism: Pseudomonas aeruginosa PA1

source_name: PA1 lysates after phage infection of 40min

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa  Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed  the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: PA1 with or wihout phage infection was grown in Luria-Bertani (LB) broth medium aerobically.

extract_protocol: Total RNA was isolated using SV Total RNA Isolation System (Promega) according to 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).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Bacterial culture were infected with phage PaP1 at MOI of 10 for 0min, 5min, 15min, 40min.The uninfected samples (0 min) served as reference.

tag: infected with

value: phage PaP1

tag: time after infection

tag: sample type

value: PA1 Lysates


title: LR-HR_HPC_P07_rep2

tag: Sex


title: LR-HR_HPC_P07_rep4


title: US45102915_252800513506_S02_GE1_1100_Jul11_1_1

tag: strain/background

tag: tissue


title: proximal colon of Ercc1-/∆7 mouse treated with Bifidobacterium breve DSM20213 G154_E06_C31_Breve

value: Bifidobacterium breve DSM20213 (~2*108 CFU in 200 µL in NaHCO3/PBS buffer; 3x week)


title: LR-HR_HPC_P07_rep1

value: Sprague-Dawley


title: PA1Lysates_phage-40min_rep2


title: proximal colon of Ercc1-/∆7 mouse treated with Lactobacillus plantarum WCFS1 G154_E05_C28_WCFS1

value: Lactobacillus plantarum WCFS1 (~2*108 CFU in 200 µL in NaHCO3/PBS buffer; 3x week)


title: LR-LR_HPC_P07_rep3

value: male

value: Foster LR


title: US45102915_252800513505_S02_GE1_1100_Jul11_2_3

source_name: day 10.5 placenta, WT

tag: genotype/variation

value: WT

tag: developmental stage


title: PA1Lysates_phage-15min_rep3

source_name: PA1 lysates after phage infection of 15min


title: PA1Lysates_phage-40min_rep1


title: LR-LR_HPC_P07_rep4

tag: selectively bred line (biological parents)


title: US45102915_252800513505_S02_GE1_1100_Jul11_1_4

source_name: day 10.5 placenta, Peg11/Rtl1 KO

value: placenta

tag: embryo gender


title: proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer) G154_E04_C6_PBS

value: female

tag: mouse strain


title: US45102915_252800513505_S02_GE1_1100_Jul11_2_4


title: PA1Lysates_phage-15min_rep2


title: US45102915_252800513505_S02_GE1_1100_Jul11_2_2


title: proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer) G154_D04_C3_PBS

tag: mouse id


title: proximal colon of Ercc1-/∆7 mouse treated with Bifidobacterium breve DSM20213 G154_D06_C17_Breve


title: LR-LR_HPC_P07_rep5

tag: strain

tag: brain region


title: PA1Lysates_phage-15min_rep1


title: US45102915_252800513505_S02_GE1_1100_Jul11_1_3


title: proximal colon of Ercc1-/∆7 mouse treated with Lactobacillus plantarum WCFS1 G154_D05_C11_WCFS1


title: LR-LR_HPC_P07_rep1

tag: caregiver dame

tag: postnatal age


title: proximal colon of Ercc1-/∆7 mouse treated with Lactobacillus casei BL23 G154_C06_C32_BL23

tag: treatment

value: Lactobacillus casei BL23 (~2*108 CFU in 200 µL in NaHCO3/PBS buffer; 3x week)


title: LR_HPC_P07_rep5

value: Hippocampus

value: Mother LR


title: US45102915_252800513505_S02_GE1_1100_Jul11_1_2


title: LR-LR_HPC_P07_rep2


title: US45102915_252800513505_S02_GE1_1100_Jul11_1_1


title: proximal colon of Ercc1-/∆7 mouse treated with Lactobacillus plantarum WCFS1 G154_C05_C9_WCFS1


title: US45102915_252800513505_S02_GE1_1100_Jul11_2_1


title: PA1Lysates_phage-5min_rep1

description: 1_4 (5min-rep1)

source_name: PA1 lysates after phage infection of 5min

tag: infected with


title: PA1Lysates_phage-0min_rep3

description: 1_3 (0min-rep3)

source_name: PA1 lysates without phage infection control

tag: time after infection


title: LR_HPC_P07_rep3


title: LR_HPC_P07_rep4


title: PA1Lysates_phage-5min_rep3

description: 2_2 (5min-rep3)

tag: sample type


title: Data Cow Rep3

city: Quebec

first: David

middle: André

last: Landry

state: Quebec

address: 2440 boul. Hochelaga

department: Animal Science

country: Canada

institute: University Laval

description: Rep 3 of 4

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

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

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

organism: Bos taurus

source_name: Pool#7_Poor Donors_GranulosaCells

label_protocol: For each sample, aRNA was labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (Cy3/Cy5) (Kreatech Diagnostics, Amsterdam, Netherlands). The labeled product was then purified with the Pico-Pure RNA Isolation Kit.

growth_protocol: [Embryo production] In vitro maturation (IVM), in vitro fertilization (IVF), in vitro culture (IVC)

extract_protocol:
Total RNA was extracted from the pools using the AllPrep DNA/RNA micro kit, following the Parallel gDNA and total RNA extraction protocol. Total RNA integrity and concentration were evaluated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) with the RNA PicoLab Chip (Agilent Technologies).
[Amp protocol] To generate enough material for hybridization, the samples were linearly amplified. Antisense RNA (aRNA) was produced using the RiboAmp®HSPlus RNA Amplification kit (Thermo fisher Scientific). After two amplification rounds of 6 hr each, the aRNA output was quantified using the NanoDrop ND-1000 (Nano-Drop Technologies, Wilmington, DE).

value: in vitro

tag: breed

value: Holstein

tag: oocyte developmental competence

value: Poor

tag: cell type

value: Granulosa Cells

source_name: Pool#3_Good Donors_GranulosaCells

tag: breed (cattle)

value: Good


title: PA1Lysates_phage-0min_rep2

description: 1_2 (0min-rep2)

value: PA1 Lysates


title: LR_HPC_P07_rep2

source_name: Hippocampus, Dissected whole

tag: Sex

value: LR


title: Data Cow Rep4

description: Rep 4 of 4

source_name: Pool#8_Poor Donors_GranulosaCells

source_name: Pool#4_Good Donors_GranulosaCells


title: proximal colon of Ercc1-/∆7 mouse treated with Lactobacillus casei BL23 G154_B06_C24_BL23

value: Ercc1-/∆7 with F1 C57Bl6J/FVB hybrid background


title: proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer)

value: vehicle (NaHCO3/PBS; 3x week)

tag: array id


title: PA1Lysates_phage-0min_rep1

description: 1_1 (0min-rep1)


title: LR_HPC_P07_rep1

value: Sprague-Dawley

value: male

tag: selectively bred line (biological parents)


title: Data Cow Rep1

description: Rep 1 of 4

source_name: Pool#1_Good Donors_GranulosaCells

source_name: Pool#5_Poor Donors_GranulosaCells


title: PA1Lysates_phage-5min_rep2

description: 2_1 (5min-rep2)

value: phage PaP1


title: proximal colon of Ercc1-/∆7 mouse treated with Lactobacillus plantarum WCFS1

value: Lactobacillus plantarum WCFS1 (~2*108 CFU in 200 µL in NaHCO3/PBS buffer; 3x week)

tag: mouse strain


title: proximal colon of Ercc1-/∆7 mouse treated with Lactobacillus casei BL23

value: female

tag: mouse id


title: Non Egg Allergic Patinent_14_(Media Incubation)

status: Public on Oct 18 2016

first: Roman

last: Kosoy

state: New York

address: 1468 Madison Avenue, 18-88

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
AC14_M

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw microarray data were processed by Lumi package in R, with background adjustment, variance-stabilizing transformation, and quantile normalization within each batch.

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: PBMCs were isolated from whole blood by Ficoll-Paque PLUS, washed, and cultured in AimV with 2.5% autologous plasma. 4 x 106 cells were plated in 1 ml in 24-well culture plates, in the presence or absence of 300 ug of egg white (EW) protein cleaned of endotoxin using Detoxi-Gel columns. Media was removed and cells harvested for RNA isolation using the Qiagen RNeasy mini kit according to manufacturer’s instructions.

tag: patient

tag: batch

tag: gender

value: Female

tag: incubation conditions

value: Media

tag: food allergy status

value: Non Egg Allergic

tag: cytokine measurements availability

value: Yes


title: Data Cow Rep2

description: Rep 2 of 4

source_name: Pool#2_Good Donors_GranulosaCells

value: in vitro

value: Holstein

source_name: Pool#6_Poor Donors_GranulosaCells


title: Baked Egg Reactive Patinent_34_(Media Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BER34_M

value: Male

value: Baked Egg Responsive


title: Non Egg Allergic Patinent_14_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
AC14_EW

value: Purified Egg Whites Protein


title: Non Egg Allergic Patinent_13_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
AC13_EW


title: Baked Egg Tolerant Patinent_20_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET20_EW

value: Baked EggTolerant

value: No


title: Baked Egg Tolerant Patinent_18_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET18_EW


title: Baked Egg Tolerant Patinent_20_(Media Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET20_M


title: Baked Egg Tolerant Patinent_19_(Media Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET19_M


title: Baked Egg Tolerant Patinent_16_(Media Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET16_M


title: Baked Egg Reactive Patinent_34_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BER34_EW


title: Baked Egg Tolerant Patinent_19_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET19_EW


title: Baked Egg Tolerant Patinent_13_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET13_EW


title: Non Egg Allergic Patinent_13_(Media Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
AC13_M


title: Baked Egg Tolerant Patinent_15_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET15_EW


title: Baked Egg Tolerant Patinent_17_(Media Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET17_M


title: Baked Egg Tolerant Patinent_14_(Media Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET14_M


title: Baked Egg Tolerant Patinent_16_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET16_EW


title: Baked Egg Tolerant Patinent_18_(Media Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET18_M


title: Baked Egg Reactive Patinent_31_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER31_EW


title: Baked Egg Tolerant Patinent_12_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET12_EW


title: Baked Egg Tolerant Patinent_15_(Media Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET15_M


title: Baked Egg Reactive Patinent_33_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BER33_EW


title: Baked Egg Tolerant Patinent_14_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET14_EW


title: Baked Egg Tolerant Patinent_12_(Media Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET12_M


title: Baked Egg Tolerant Patinent_17_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET17_EW


title: Baked Egg Reactive Patinent_23_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER23_EW


title: Baked Egg Tolerant Patinent_13_(Media Incubation)

description:
HumanHT-12_V4_0_R1_15002873_B.bgx
BET13_M


title: Baked Egg Reactive Patinent_22_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER22_M


title: Non Egg Allergic Patinent_12_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC12_M


title: Baked Egg Tolerant Patinent_8_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET8_M


title: LR-LR_AMY_P07_rep4

source_name: Amygdala, Dissected whole

tag: strain

value: LR

tag: brain region

value: Amygdala

tag: caregiver dame

value: Foster LR

tag: postnatal age


title: Non Egg Allergic Patinent_10_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC10_M


title: Non Egg Allergic Patinent_9_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC9_M


title: Non Egg Allergic Patinent_4_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC4_M


title: Baked Egg Reactive Patinent_27_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER27_M


title: Baked Egg Tolerant Patinent_9_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET9_EW


title: Baked Egg Tolerant Patinent_11_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET11_EW


title: Non Egg Allergic Patinent_11_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC11_M


title: Baked Egg Reactive Patinent_29_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER29_EW


title: Baked Egg Reactive Patinent_31_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER31_M


title: Non Egg Allergic Patinent_8_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC8_EW


title: Baked Egg Tolerant Patinent_8_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET8_EW


title: Non Egg Allergic Patinent_7_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC7_M


title: Non Egg Allergic Patinent_9_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC9_EW


title: Baked Egg Reactive Patinent_30_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER30_M


title: Baked Egg Tolerant Patinent_9_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET9_M


title: Baked Egg Reactive Patinent_29_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER29_M


title: Baked Egg Reactive Patinent_32_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER32_EW


title: Non Egg Allergic Patinent_11_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC11_EW


title: Non Egg Allergic Patinent_12_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC12_EW


title: Baked Egg Reactive Patinent_32_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER32_M


title: Non Egg Allergic Patinent_8_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC8_M


title: Baked Egg Tolerant Patinent_10_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET10_EW


title: Non Egg Allergic Patinent_6_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC6_EW


title: Baked Egg Reactive Patinent_30_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER30_EW


title: Baked Egg Tolerant Patinent_10_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET10_M


title: Baked Egg Tolerant Patinent_7_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET7_M


title: Non Egg Allergic Patinent_10_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC10_EW


title: Baked Egg Tolerant Patinent_7_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET7_EW


title: Baked Egg Reactive Patinent_27_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER27_EW


title: Baked Egg Reactive Patinent_26_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER26_EW


title: Non Egg Allergic Patinent_3_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC3_EW


title: Baked Egg Tolerant Patinent_6_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET6_EW


title: Non Egg Allergic Patinent_1_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC1_EW


title: Non Egg Allergic Patinent_6_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC6_M


title: JP123_1589_rfa1-t11_IP_Rad50_60min_HU

city: Basel

first: Jérôme

last: Poli

address: 66 Maulbeerstrasse

department: Quantitative Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: test CEL file: JP123_PP1589_60HU_(Sc03b_MR_v04).CEL; control CEL files: LC029_WCEA.CEL, JP012_WCEA.CEL

hyb_protocol: standard Affymetrix protocol

scan_protocol: Tiling arrays were scanned with the GeneChip scanner 3000 7G

data_processing:
Signals from two to four biological replicates were normalized with TAS 1.1.02 (Affymetrix) using quantile normalisation. Analysis results were stored in Log2 scale for signal intensity and in -10Log10 for p-values. Probe signals were analysed using perfect matches only with a bandwidth of 300. P-value intervals were generated using the following parameters: cutoff: 10-5, max gap: 80 and min run: 40. Significant intervals were scored as active origins when signal intensity was above a threshold arbitrarily determined as 50% of the signal range and when BrdU tracks were larger than 1 kb. Replication profiles (signal log ratio) were displayed with IGB 6.1. BrdU peaks overlapping with replication origins referenced in OriDB were scored with Galaxy. BrdU peaks that overlap with repetitive sequences such as transposons and subtelomeric repeats were not used in this study.
Supplementary files: signal bar files generated for each strains contains log2 (IP/Input) for signal intensity.

organism: Saccharomyces cerevisiae

source_name: test: ChIP-Rad50 from rfa1-t1 mutant cells in HU, 60 min

label_protocol: 7 µg of amplified DNA was fragmented and labelled using the GeneChip WT Double-Stranded DNA Terminal Labelling kit (Affymetrix, PN 900812) following manufacturer recommendations.

growth_protocol: G1-synchronised cells were released into S phase in the presence of Hydroxyurea (200mM) and collected after 60 min

extract_protocol: For chromatin immunoprecipitation of Rad50-HA, 1.5x109 cells were lysed for 5 x 2 minutes in lysis buffer (50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) supplemented with Complete EDTA-free protease inhibitor (Roche, 11 873 580 001) and 1mM PMSF ; with silica beads on a multi-bead shocker (MB400U, Yasui Kikai, Osaka) at 4°C 5 cycles of 12 mins (1' breakage, 1' pause, repeated 4 times with 5' pause at each cycle). Total chromatin was sonicated  with a Bioruptor (Diagenode) 20 cycles 30" ON ; 30" OFF to reach an average size of 300-600 bp. For each immunoprecipitation, 80 µl of anti-HA (F7, Santa Cruz, sc7392) was prebound to Dynabeads protein A (Invitrogen 100.01D) and added to the total chromatin extract.

tag: genotype

value: rfa1-t11 mutant

source_name: control: Genomic DNA from S.cerevisiae


title: JP123_1416_WT_IP_Rad50_60min_HU

description: test CEL file: JP123_PP1416_60HU_(Sc03b_MR_v04).CEL; control CEL files: LC029_WCEA.CEL, JP012_WCEA.CEL

source_name: test: ChIP-Rad50 from wild-type cells in HU, 60 min

value: wild-type


title: Non Egg Allergic Patinent_7_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC7_EW


title: Baked Egg Reactive Patinent_22_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER22_EW


title: Baked Egg Reactive Patinent_21_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER21_M