title: 92-1400 map2

city: Beijing

first: Xiao

last: Zheng

address: Liuzi five hao

institute: China CDC

description: Mutation mapping 92-1400

hyb_protocol: Labeled genomic DNA was hybridized to arrays in the NimbleGen Hybridization Buffer for 16 hours at 42 ℃ using a MAUI hybridization system (BioMicro Systems, Inc. Salt Lake City, Utah). Labeled genomic DNA (5ug) from the reference strain Streptococcus suis 89/1591 and from each test strain were co-hybridized to each array. Arrays were washed with NimbleGen wash buffer, and then were spun dry in a microarray high-speed centrifuge (TeleChem International, Inc., Sunnyvale, CA) and stored until scanned.(http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 CGS data extraction.

organism: Streptococcus suis

label_protocol: Genomic DNA was labeled with a Random prime reaction. DNA (1 ug) was mixed with 1 O.D. of 5’-fluorescence dye labeled random nonamer (Cy3 for test strains and Cy5 for reference strain) (TriLink Biotechnologies) in 62.5 mM Tris-HCl, 6.25 mM MgCl2 and 0.0875% ß-mercaptoethanol, denatured at 98°C for 5 min, chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each in TE) for 2 h at 37°C. Reactions were terminated with 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water. A fifty-fold amplification was typically achieved.(http://www.nimblegen.com/products/lit/lit.html)

growth_protocol: Cells were cultured in Todd-Hewitt broth (THB)(Difco Laboratories, Detroit, MI) medium

extract_protocol: Genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit (Qiagen)

treatment_protocol: test strain

tag: serotype

tag: sequence type

tag: site isolated

value: Canada

tag: origin

value: diseased pig

tag: pathogenicity

value: virulent

source_name: Reference 89/1591 DNA

treatment_protocol: Reference


title: Pedicel_AZ_Central_X3177_Hybrid2_17DAP_replicate 2

status: Public on May 20 2014

type: RNA

city: Beaucouzé

first: Jean-Marc

last: Celton

address: 42 rue Georges Morel

country: France

institute: INRA-IRHS

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

molecule: total RNA

organism: Malus domestica

source_name: Wild type X3177 central pedicel abscission zone

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol:
orchard conditions
Trees were grown in orchard at the INRA experimental station ' la Rétuzière', Champigné, France

extract_protocol:
Macherey-Nagel NucleoSpin RNA Plant
RNA was purified using NucleoSpin RNA Plant extraction kit (Macherey-Nagel) according to the manufacturer specifications

treatment_protocol: Trees were trained according to horticultural practices. No thinning reagent was applied

tag: tissus

value: Abscission zone

tag: genetic background

value: Hybrid X3177

tag: genotype

value: Wild-type

tag: phenotype

value: no abscission

tag: treatment

tag: age

value: 17 days after flower pollination


title: Pedicel_AZ_Central_X3177_Hybrid1_21DAP_replicate 2

value: 21 days after flower pollination


title: Heart fibroblast 2

city: Melbourne

first: Milena

middle: B

last: Furtado

state: VIC

address: Wellington Road, Building 75, Level 1

country: Australia

institute: Monash University-Australian Regenerative Medicine Institute

hyb_protocol: 600ng of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60oC for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion 25ul of 2x Agilent gene expression hybridisation buffer was added and 40ul of sample hybridised for 17 hours at 65oC in a rotating Agilent hybridisation oven. After hybridisation, microarrays were washed 1 minute at room temperature with GE wash buffer 1(Agilent) and 1 minute with 37oC GE wash buffer 2(Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent C, DNA microarray scanner using one color scan settings for 8x60k array slides; scan area 61x21.6mm, scan resolution 3um, dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analysed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid: (028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities. Agilent.SingleColor.28005 microarray, Software GeneSpring 12.6; Threshold: 1.0, Logbase: 2; Normalization: Quantile; Baseline Transformation: None; Filtered on Expression (20.0-100.0); Filtered on Flags (Detected, Not Detected); T test unpaired , P<=:0.05, FC>=2.0 Benjamini-Hochberg

organism: Mus musculus

source_name: heart fibroblast

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.1ug total RNA using the One-Color Low input Quick Amp labelling Kit (Agilent) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using the mirVana kit (Invitrogen) folowed by DNAseI digestion following the manufacturer's recommendations. RNA was quantified  and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 8-10week old mouse hearts were finely chopped with surgical scissors and whole tails were skinned and cut into 2-3mm pieces. Both tissues were subjected to enzymatic digestion [0.05% trypsin/EDTA (Gibco) or 0.5mg/mL collagenase type II (Worthington)] at 37oC under agitation for 40 minutes, washed in HBSS and plated on 10cm dishes in DMEM high glucose supplemented with 10% FBS, 1x pen/strep and sodium pyruvate for 5 days at 37 ºC in a humidified incubator with 5% CO2

tag: gender

value: male

tag: strain

value: 8 weeks adult

tag: tissue

value: heart

tag: cell type

value: fibroblast


title: Tail fibroblast 2

source_name: tail fibroblast

value: tail


title: 92-4172 map2

type: genomic

country: China

description: Mutation mapping 92-4172

molecule: genomic DNA

value: diseased calf


title: Pedicel_AZ_Lateral1_X3177_Hybrid1_21DAP_replicate1

source_name: Wild type X3177 lateral1 pedicel abscission zone

value: abscission


title: 89-5259 map2

description: Mutation mapping 89-5259


title: Heart fibroblast 3


title: 92-1191 map2

description: Mutation mapping 92-1191


title: 8236.PMEC.WT.3

city: Houston

first: Elizabeth

last: Villegas

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine

description: Gene expression for primary mammary epithelial cells at 8 weeks of age

hyb_protocol: Samples were hybridized to Agilent Sure Print 3 Mouse GE 8x60K Microarrays by the Baylor College of Medicine Genomic and RNA Profiling Core

scan_protocol: Following hybridization samples were scanned  with ScanArray 5000 Laser

data_processing: Data was quantile normalized, significantly regulated genes were identified by comparing Plk2 +/+ with Plk2-/- using t-test and fold change

source_name: Mouse primary mammary epithelial cells isolated from mammary glands of 8 week old mice

label_protocol: RNA was amplified and labeled with Cy-3 using Agilent Quick Amp Labeling Kit Protocol Version 6.5

growth_protocol: Female mice were allowed to reach 8 weeks of age

extract_protocol: RNA was extracted using Trizol reagent according to manufacturer's protocol

treatment_protocol: At 8 weeks of age mammary glands were isolated and dissociated to produce primary mammary epithelial cells

value: wild type

value: female

value: 8 weeks

value: primary mammary epithelial cells


title: 8239.PMEC.WT.2


title: Pedicel_AZ_Central_X3177_Hybrid1_21DAP_replicate 1

value: Abscission zone


title: 8221.PMEC.NULL.3


title: 8223.PMEC.NULL.1


title: 8222.PMEC.NULL.2


title: 88-5299A map2

description: Mutation mapping 88-5299A

value: Canada

value: diseased pig

value: virulent


title: 8327.PMEC.WT.1


title: Pedicel_AZ_Lateral1_X3177_Hybrid2_17DAP_replicate1

value: Hybrid X3177

value: Wild-type

value: 17 days after flower pollination


title: LS_NS_dox

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description: Cells transduced with non-silencing control (NS) in presence of doxycycline (dox: 1 µg mL-1; Sigma Aldrich)

hyb_protocol: Hybridization mixture was prepared according to Affymetrix protocol. Samples were hybridized to Affymetrix Human Genome 133 PM Strip arrays at 45ºC for 16h

scan_protocol: Arrays scanning and CEL files generation was performed using an Affymetrix GeneAtlas scanner.

data_processing: RMA normalization using the normqc function of Bioconductor's MDA package

label: Biotin

organism: Homo sapiens

source_name: LS174T colorectal cancer cells

label_protocol: cDNA library preparation and amplification were performed from 25ng total RNA using WTA2 (Sigma-Aldrich) with 17cycles of amplification. 8µg cDNA were subsequently fragmented by DNaseI and biotinylated by terminal transferase obtained from GeneChip Mapping 250K Nsp Assay Kit (Affymetrix)

growth_protocol: Cells grown in DMEM supplemented with 10% FBS in the presence of doxycycline (dox: 1 µg mL-1; Sigma Aldrich) or vehicle (70% ethanol) for a period of 72h

extract_protocol: Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies)

treatment_protocol: Cells transduced with either short hairpin against GATA6 (shGATA6) or non-silencing control (NS)

tag: cell line

value: colorectal cancer


title: 89-3576-3 map2

description: Mutation mapping 89-3576-3


title: 89-590 map2

description: Mutation mapping 89-590


title: LS_shGATA6_dox_3

description: Cells transduced with short hairpin against GATA6 (shGATA6) in presence of doxycycline (dox: 1 µg mL-1; Sigma Aldrich)


title: LS_NS_ctrl

description: Cells transduced with non-silencing control (NS) in presence of vehicle (70% ethanol)


title: LS_shGATA6_ctrl_3

description: Cells transduced with short hairpin against GATA6 (shGATA6) in presence of vehicle (70% ethanol)


title: 89-2479 map2

description: Mutation mapping 89-2479


title: LS_shGATA6_dox_1


title: Pedicel_AZ_Central_X3177_Hybrid2_17DAP_replicate 1

value: no abscission


title: LS_shGATA6_ctrl_1


title: Pedicel_AZ_Lateral1_X3177_Hybrid1_17DAP_replicate1


title: Pedicel_AZ_Central_X3177_Hybrid1_17DAP_replicate 2


title: LS_shGATA6_dox_2


title: 86-5192 map2

description: Mutation mapping 86-5192

value: Unknown

value: United States


title: LS_shGATA6_ctrl_2


title: (High glucose+Ninjurin siRNA) MCECs (si)

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

country: South Korea

institute: Inha university hospital

description: Pooling : si 1 + si 2 + si 3 = si

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: The mouse penis cavernous primary endothelial cell was maintained in Medium 199 (M199) containing 20% heat-inactivated FBS,1% penicillin/streptomycin, 0.5 mg/ml heparin (Sigma-Aldrich), and 5 ng/ml vascular endothelial growth factor A (R&D Systems Inc.)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: MCECs cells at the density of 2 × 106 cells/well were transfected with siRNAs against nerve injury-induced protein 1, Ninjurin1 (Ninj1, Bioneer; 200 pmol) by using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. And then exposed to the normal-glucose (5 mmol, Sigma-Aldrich) or high-glucose (30 mmol) condition for 48 hours.

value: HG+ninjurin1 siRNA


title: normal glucose MCECs (normal)

description: Pooling : normal 1 + normal 2 + normal 3 = normal

source_name: mouse penis cavernous primary endothelial cell


title: Pedicel_AZ_Lateral1_X3177_Hybrid2_14DAP_replicate2

value: abscission

value: 14 days after flower pollination


title: Pedicel_AZ_Central_X3177_Hybrid1_17DAP_replicate 1


title: High glucose MCECs (HG)

description: Pooling : HG 1 + HG 2 + HG 3 = HG

value: high glucose


title: Pedicel_AZ_Central_X3177_Hybrid2_14DAP_replicate 2


title: Pedicel_AZ_Lateral1_X3177_Hybrid2_14DAP_replicate1


title: Pedicel_AZ_Central_X3177_Hybrid2_14DAP_replicate 1


title: NT77 map2

description: Mutation mapping NT77

value: healthy pig

value: unknown


title: NCTC1046 map2

description: Mutation mapping NCTC1046

value: Netherland


title: 13730 map2

description: Mutation mapping 13730

value: patient

value: Canada


title: 93A map2

description: Mutation mapping 93A

value: diseased pig

value: virulent


title: Pedicel_AZ_Lateral1_X3177_Hybrid1_17DAP_replicate2

value: Abscission zone

value: Hybrid X3177

value: Wild-type


title: 2726 map2

description: Mutation mapping 2726

value: Denmark


title: 4417 map2

description: Mutation mapping 4417


title: SMMC-7721_lncRNA-hPVT1_overexpression rep2

city: shanghai

first: shu-han

last: sun

address: 800 Xiang-Yin Road

institute: Second Military Medical University

description:
lncRNA-hPVT1_rep2
H005-1101004153

hyb_protocol: Using the Phalanx hybridization system.

scan_protocol: Data extraction using GenePix™  4100 from Molecular Devices.

data_processing: The .GPR raw  intensity   of  each  spot  was  loaded  into  Rosetta  Resolver  System (Rosetta Biosoftware)  to process data analysis.  The error  model  of Rosetta Resolver System could remove  both  systematic  and  random  errors  form  the  data.  Those  probes  with  background signals  were  filtered  out.  Probes  that  passed  the  criteria  were  normalized  by  50%  median scaling  normalization  method.  The  technical  repeat  data  was  tested  by  Pearson  correlation coefficient  calculation  to  check  the  reproducibility  (R  value  >  0.975).  Normalized  spot intensities were  transformed  to gene expression  log 2  ratios  between the control  and treatment groups.  The probes  with log 2  ratio  >=  1 or  log 2  ratio  <=  -1  and  P-value < 0.05  were defined as differential genes for further pathway enrichment analysis.

source_name: SMMC-7721 stably overexpress lncRNA-hPVT1

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: The total RNA was extracted from the SMMC-7721 cells with overexpressed hPVT1 or control using TRIzol reagent (ambion).

value: HCC cell line SMMC-7721

tag: genotype/variation

value: lncRNA-hPVT1 overexpression


title: 8830 map2

description: Mutation mapping 8830

tag: serotype


title: SMMC-7721_lncRNA-hPVT1_overexpression rep1

description:
lncRNA-hPVT1_rep1
H004-1101004152


title: SMMC-7721_control rep3

description:
control_rep3
H003-1101004150

source_name: control SMMC-7721

value: control


title: Pedicel_AZ_Central_X3177_Hybrid1_14DAP_replicate 2

value: no abscission


title: Pedicel_AZ_Lateral1_X3177_Hybrid1_14DAP_replicate1

value: abscission

value: 14 days after flower pollination


title: SMMC-7721_lncRNA-hPVT1_overexpression rep3

description:
lncRNA-hPVT1_rep3
H006-1101004154


title: SMMC-7721_control rep2

description:
control_rep2
H002-1101004149


title: Pedicel_AZ_Central_X3177_Hybrid1_14DAP_replicate 1


title: Pedicel_AZ_Lateral1_X3177_Hybrid1_14DAP_replicate2


title: SMMC-7721_control rep1

description:
control_rep1
H001-1101004148


title: oviduct in contact with Y spermatozoa Y4, biological rep 4

city: Sheffield

first: Carmen

last: Alminana

address: Tree Root Walk

department: Academic Unit of Reproductive and Developmental Medicine, Human Metabolism Department

country: United Kingdom

institute: University of Sheffield

description:
Y4_2
Gene expression data from oviduct in response to Y spermatozoa

hyb_protocol: 12 μg of cRNA molecules were heat fragmented and injected to the Porcine GeneChips in a hybridization solution according to the Affymetrix protocol. Hybridization took place overnight in a rotating hybridization oven at 60rpm, 45°C for 16 hours. The GeneChip arrays were washed using the Affymetrix Fluidics Station.

scan_protocol: After washing, the GeneChip arrays were scanned using Affymetrix GC3000 scanner.

data_processing: The resultant images were analysed using the Microarray Suite software version 5.1 (MAS 5.1 Affymetrix).

label: biotin

organism: Sus scrofa

source_name: oviduct in contact with Y spermatozoa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix,P/N 702232 Rev. 3 ).

extract_protocol: Total RNA was isolated using a standard procedure involving phenol:chloroform extraction followed by ethanol precipitation.

treatment_protocol: In order to investigate if females have the ability to recognise X or Y chromosome bearing spermatozoa and present a different response to different spermatozoa. Samples of semen were sorted for chromosomal sex by ﬂow cytometric-sorting. Using laparoscopic insemination one oviduct was inseminated with X spermatozoa and the contralateral oviduct was inseminated with Y spermatozoa.This allowed us to obtain samples from the oviduct in contact with X sperm and Y sperm in the the contrlateral oviduct from the same sow. Oviduct pig samples were collected 24h after insemination. Scraped cells from the oviduct samples were transferred immediately to Tri Reagent (Sigma, Sigma-Aldrich Co, Madrid, Spain), homogenised, snap-frozen in liquid nitrogen and stored at -80C until further processing.

value: oviduct


title: 10581 map2

description: Mutation mapping 10581

tag: sequence type


title: 22083 map2

description: Mutation mapping 22083

tag: site isolated


title: 12814 map2

description: Mutation mapping 12814

tag: origin


title: oviduct in contact with X spermatozoa X4, biological rep 4

description:
X4
Gene expression data from oviduct in response to X spermatozoa

source_name: oviduct in contact with X spermatozoa


title: oviduct in contact with Y spermatozoa Y3, biological rep 3

description:
Y3_2
Gene expression data from oviduct in response to Y spermatozoa


title: 8074 map2

description: Mutation mapping 8074

tag: pathogenicity


title: 2524 map2

description: Mutation mapping 2524


title: 231_ADI 24hr Arg 24hr

city: Taipei City

first: Cheng-Ying

last: Chu

address: 250 Wu-Hsing Street

department: Center for Translational Medicine

country: Taiwan

institute: Taipei Medical University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina iScan was used to scan the images.

data_processing: Illumina GenomeStudio was used to calculate and create matrix table. Quantile normalization is used to normalize the matrix table.

source_name: MDA-MB-231 cells

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

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) (Cellgro, 10-013-CV) containing fetal bovine serum (10%; Gibco, 26140), penicillin (100 U/ml) and streptomycin (100 ug/ml) (Gibco, 15240) at 37° C and 5% CO2 in a humidified incubator.

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

treatment_protocol: MDA-MB-231 cells were grown untreated (48 hours), or treated with ADI-PEG20 (0.3 μg/ml, 48 hours), or treated with ADI-PEG20 (0.3 μg/m, 24 hours) followed by L-arginine (420 μg/ml, 24 hours).

value: mammary gland/breast; derived from metastatic site:pleural effusion


title: 11538 map2

description: Mutation mapping 11538


title: 231_ADI 48hr

value: ADI-PEG20 (0.3 μg/ml, 48 hours)


title: 4961 map2

description: Mutation mapping 4961


title: 6407 map2

description: Mutation mapping 6407


title: oviduct in contact with X spermatozoa X1, biological rep 1

description:
X1
Gene expression data from oviduct in response to X spermatozoa


title: oviduct in contact with Y spermatozoa Y1, biological rep 1

description:
Y1_2
Gene expression data from oviduct in response to Y spermatozoa


title: 14636 map2

description: Mutation mapping 14636


title: oviduct in contact with X spermatozoa X2, biological rep 2

description:
X2
Gene expression data from oviduct in response to X spermatozoa


title: oviduct in contact with X spermatozoa X3, biological rep 3

description:
X3
Gene expression data from oviduct in response to X spermatozoa


title: siLSD1 rep1

city: Sendai

first: Atsushi

last: Yokoyama

state: Miyagi

address: seiryo-machi 2-1, Aoba-ku, Sendai

country: Japan

institute: Tohoku University Graduate School of Medicine

hyb_protocol: 7.5 mg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control (1.5 pM BioB, five pM BioC, 25 pM BioD and 100 pM cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/ml acetylated BSA and 1x manufacturer-recommended hybridyzation buffer in a 45 ºC rotator for 16 h.

scan_protocol: The phycoerythrin-stained arrays were scanned as digital image files that were then analyzed with GeneChip Operating Software(Affymetrix)

data_processing: The expression data were converted to copy numbers of mRNA per cell by the Percellomemethod, quality controlled, and analyzed using Percellome software

source_name: Neuro2a cells treated with siLSD1

label_protocol: cDNAs were labeled with BioArray High Yield RNA transcript labeling kit (Enzo Life Sciences)

extract_protocol: total RNAs were extracted with Rneasy Mini kit(Qiagen)

treatment_protocol: Neuro2a cells were treated with either siControl, siLSD1 or siMyT1 for 48 h (n=3)


title: siMyT1 rep1

source_name: Neuro2a cells treated with siMyT1


title: THP-1 macrophage-derived foam cells_2

city: Guangzhou

first: Yan-Wei

last: Hu

address: No.1838,Dadaobei Road

institute: Nanfang Hospital

description: Gene expression after monocyte transform into foam cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 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 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k 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: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (All Targets Value) were chosen for further data analysis.

source_name: THP-1 cells + 160 nmol/L PMA 72h + 50μg/ml oxLDL 48h

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

growth_protocol: THP-1 cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium containing 10% fetal calf serum  (FCS) and differentiated for 72 h with 100 nM phorbol 12-myristate 13-acetate (PMA).Cells were incubated at 37°C in an atmosphere of 5% CO2

extract_protocol: RNA was prepared using the TRIzol Reagent (Invitrogen life technologies) following the manufacturer's recommendations.

treatment_protocol: Macrophages were transformed into foam cells by incubation in the presence or absence of 50 μg/mL of Ox-LDL in serum-free RPMI 1640 medium containing  0.3% BSA for 48 h.

value: monocyte

value: foam

value: male


title: siControl rep1

source_name: Neuro2a cells treated with siControl

value: siControl


title: THP-1 macrophage-derived foam cells_1


title: 231_untreated

value: untreated (48 hours)


title: siControl rep3


title: siMyT1 rep2


title: oviduct in contact with Y spermatozoa Y2, biological rep 2

description:
Y2_2
Gene expression data from oviduct in response to Y spermatozoa


title: siLSD1 rep2


title: siControl rep2


title: TD10 map2

description: Mutation mapping TD10

value: United Kingdom

value: Diseased pig

value: virulent

source_name: Reference 89/1591 DNA

value: Canada

value: diseased pig


title: siLSD1 rep3


title: siMyT1 rep3


title: THP-1 macrophage-derived foam cells_3


title: RC4716 map2

description: Mutation mapping RC4716


title: 2651 map2

description: Mutation mapping 2651

value: Netherland


title: THP-1 macrophages_2

description: Gene expression after monocyte transform into macrophages

source_name: THP-1 cells + 160 nmol/L PMA 72h + 0 μg/ ml oxLDL 48h

value: macrophage


title: control mouse kidney glomerulus, biological rep3

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Gene expression data from control mouse kidney glomeruli

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCRMA package in the bioconductor project (gcrma version 2.30.0).

source_name: control kidney glomeruli

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix small sample amplification protocol from app. 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed using RNeasy® Mini Kit (Qiagen)

value: kidney glomeruli

value: 13 months

value: wild type


title: GX407 map2

description: Mutation mapping GX407

value: China

value: patient

value: high virulent


title: Dendrin knockout mouse kidney glomerulus, biological rep3

description: Gene expression data from mouse dendrin knockout kidney glomeruli

source_name: Dendrin knockout kidney glomeruli

value: Dendrin KO


title: THP-1 macrophages_3

value: monocyte

value: male


title: Folllicle_thecal_large healthy_rep3

city: Adelaide

first: Nicholas

last: Hatzirodos

state: SA

address: Medical School Nth Frome Rd

department: Obstetrics and Gynaecology

institute: Adelaide University

description: Gene expression data from theca of antral follicles

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

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

data_processing: The data were analysed in Partek Genomics Suite (v6.5) using RMA (Robust Multi Array Algorithm, Irizarry et al 2003) background corrrection with quantile normalization, mean probe set summarization and adjustment for GC content

organism: Bos taurus

source_name: Follicle_large healthy_rep3

label_protocol: Biotinylated cRNA was prepared according to the 3' IVT Express labelling kit protocol from 2-5 ug total RNA for the small healthy and large follicles. 250 ng was used for the small atretic follicles(Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Ovarian follicles were obtained from freshly slaughtered non pregnant Bos taurus heifers

extract_protocol: Large follicle RNA was extracted using Trizol and purified with Qiagen Rneasy kit columns. Small healthy follicle RNA was extracted using Qiagen Rneasy mini kit columns and small atretic follicle RNA was extracted with RNAqueous Micro kit columns.

treatment_protocol: Follicles were excised from the ovary, and a piece of wall removed for histological classification. The follicular fluid was released and the granulosa cells scraped from the follicle. The theca interna was then dissected from the follicle wall in cold Hank’s balanced-salt solution with Mg2+ and Ca2+ and stored at -80°C prior to RNA extraction.

value: ovarian follicular theca


title: Folllicle_thecal_large healthy_rep4

source_name: Follicle_large healthy_rep4


title: Dendrin knockout mouse kidney glomerulus, biological rep2


title: control mouse kidney glomerulus, biological rep2


title: THP-1 macrophages_1


title: Dendrin knockout mouse kidney glomerulus, biological rep1


title: Folllicle_thecal_large healthy_rep2

source_name: Follicle_large healthy_rep2


title: siRNA control VS knockdown of Twist1

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

institute: Chang Gung Memorial Hospital at Linkou

description: H1299 siRNA control VS knockdown of Twist1

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: H1299 siRNA control

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

growth_protocol: Cells were cultured under DMEM(10%FBS, 1% penicillin-streptomycine). Atmosphere: air, 95%; carbon dioxide (CO2), 5%. Temperature, 37.0°C

extract_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

treatment_protocol: Extraction was performed using TriZol and routine protocol.

tag: transfection

value: siRNA control

source_name: H1299: knockdown of Twist1

value: knockdown of Twist1


title: Folllicle_thecal_small healthy columnar_rep5

source_name: Follicle_small healthy columnar_rep5


title: Folllicle_thecal_large healthy_rep1

source_name: Follicle_large healthy_rep1


title: 94-3037 map2

description: Mutation mapping 94-3037

value: low virulent

value: virulent


title: Folllicle_thecal_small healthy columnar_rep3

source_name: Follicle_small healthy columnar_rep3


title: 5428 map2

description: Mutation mapping 5428

value: Denmark

value: diseased pig

value: Canada


title: 11611 map2

description: Mutation mapping 11611

value: Germany

value: Unknown


title: 9801 map2

description: Mutation mapping 9801


title: Folllicle_thecal_small healthy columnar_rep2

source_name: Follicle_small healthy columnar_rep2


title: Folllicle_thecal_small healthy columnar_rep1

source_name: Follicle_small healthy columnar_rep1


title: Folllicle_thecal_small healthy rounded_rep4

source_name: Follicle_small healthy rounded_rep4


title: Folllicle_thecal_small healthy rounded_rep1

source_name: Follicle_small healthy rounded_rep1


title: Folllicle_thecal_small healthy rounded_rep5

source_name: Follicle_small healthy rounded_rep5


title: Folllicle_thecal_small healthy rounded_rep2

source_name: Follicle_small healthy rounded_rep2


title: Folllicle_thecal_small healthy columnar_rep4

source_name: Follicle_small healthy columnar_rep4


title: 31533 map2

description: Mutation mapping 31533

value: France

source_name: Reference 89/1591 DNA


title: WT muscle biological replicate 2 technical replicate 1

city: Cambridge

first: Sarah

middle: E

last: Allen

address: Downing Street

department: PDN

institute: University of Cambridge

description: Pool of RNA from tissues from 5 individual embryos. Biological replicate (RNA pool) 2 of 3. Technical replicate 1 of 2.

hyb_protocol: 14 hours at 58C

scan_protocol: Ilumina BeadStation 500

data_processing: Beadarray Subversion of Harshlight (BASH, Bioconductor) was carried out on bead data to remove spatial artifacts from the array. Bead data was log2 transformed and outliers were removed. Arrays were normalised to each other using a robust spline normalisation (rsn) in the Lumi package from Bioconductor.

source_name: Total RNA extracted from WT C57/BL6 mouse E18.5 muscle tissue, 5 samples pooled and labelled with Cy3

label_protocol: Labelling was carried out according to Illimina Whole-Genome Gene Expression Direct Hybridisation Assay Guide. Pools of RNA were amplified using Illumina TotalPrep-96 amplification kit to make biotin-labelled cRNA. cRNA was purified and brought to the same concentration using RNase-free water, then cRNA was hybridised to BeadChips for 14 hours at 58C. Chips were then washed to remove excess RNA and blocked before incubation for 10 minutes at room temperature with Cy3-streptavidin.

extract_protocol: Tissue was snap frozen and homogenised in TRI reagent (Sigma) in a glass homogenizer then extracted according to manufacturer's guidelines. RNA was cleaned up using Qiagen RNEasy Kit and ethanol extracted before QC using an Agilent Bioanalyser. Samples all had RIN of 8.5 or above.

tag: Stage

value: muscle


title: WT muscle biological replicate 2 technical replicate 2

description: Pool of RNA from tissues from 5 individual embryos. Biological replicate (RNA pool) 2 of 3. Technical replicate 2 of 2.


title: WT muscle biological replicate 1 technical replicate 2

description: Pool of RNA from tissues from 5 individual embryos. Biological replicate (RNA pool) 1 of 3. Technical replicate 2 of 2.


title: 06GZ1 map2

description: Mutation mapping 06GZ1

value: China

value: patient


title: GZ2 map2

description: Mutation mapping GZ2

value: high virulent


title: WT muscle biological replicate 3 technical replicate 1

description: Pool of RNA from tissues from 5 individual embryos. Biological replicate (RNA pool) 3 of 3. Technical replicate 1 of 2.


title: SC84 map2

description: Mutation mapping SC84


title: LN1 map2

description: Mutation mapping LN1


title: Folllicle_thecal_small healthy rounded_rep3

source_name: Follicle_small healthy rounded_rep3


title: Folllicle_thecal_small atretic_rep5

source_name: Follicle_small atretic_rep5


title: Folllicle_thecal_small atretic_rep3

source_name: Follicle_small atretic_rep3


title: 92-4172 map1

description: Mutation mapping 92-4172

value: diseased calf


title: 92-1400 map1

description: Mutation mapping 92-1400


title: Folllicle_thecal_small atretic_rep2

source_name: Follicle_small atretic_rep2


title: Folllicle_thecal_small atretic_rep4

source_name: Follicle_small atretic_rep4


title: Folllicle_thecal_small atretic_rep1

source_name: Follicle_small atretic_rep1


title: WT muscle biological replicate 1 technical replicate 1

description: Pool of RNA from tissues from 5 individual embryos. Biological replicate (RNA pool) 1 of 3. Technical replicate 1 of 2.


title: KO muscle biological replicate 3 technical replicate 2

description: Pool of RNA from tissues from 5 individual embryos. Biological replicate (RNA pool) 3 of 3. Technical replicate 2 of 2.

source_name: Total RNA extracted from miR-127 KO C57/BL6 mouse E18.5 muscle tissue, 5 samples pooled and labelled with Cy3


title: KO muscle biological replicate 2 technical replicate 1


title: Gonadal Ridge Epithelial-Like cell_2

description: Gene expression data from bovine fetal tissue

source_name: cultured bovine fetal ovarian polygonal cell

label_protocol: Biotinylated cRNA was prepared according to the 3' IVT Express labelling kit protocol from 250 ng RNA per culture sample

growth_protocol: Ovarian tissues were obtained from freshly slaughtered Bos taurus heifers

extract_protocol: RNA was extracted using Trizol and and  DNAse I treated to remove genomic DNA before purification with Qiagen Rneasy kit columns .

treatment_protocol: The whole ovaries were sliced into smaller pieces and collagenase treated to disperse the cells as much as possible. Cells were resuspended in DMEM/F12 medium containing 5% fetal calf serum with antibiotics and seeded into 6-well plates , then incubated at 39°C in 5% CO2 in air until 70% confluent.  Two fetal polygonal cell cultures were selected and compared with  polygonal cells and fibroblastic cells isolated from an adult bovine ovary.

value: ovarian tissue

tag: estimated age

value: 130 days gestation

tag: morphology

value: polygonal


title: KO muscle biological replicate 3 technical replicate 1


title: 07S3 map2

description: Mutation mapping 07S3


title: KO muscle biological replicate 2 technical replicate 2


title: P1/7 map2

description: Mutation mapping 1/7

value: England


title: cultured bovine adult ovarian fibroblast

value: >1 year adult

value: fibroblastic


title: 89-590 map1

description: Mutation mapping 89-590

value: virulent


title: 92-1191 map1

description: Mutation mapping 92-1191

value: diseased pig


title: Gonadal Ridge Epithelial-Like cell_1


title: KO muscle biological replicate 1 technical replicate 2


title: control mouse kidney glomerulus, biological rep1

source_name: control kidney glomeruli

value: kidney glomeruli

value: 13 months

tag: genotype

value: wild type

tag: genetic background


title: 89-3576-3 map1

description: Mutation mapping 89-3576-3

value: Canada


title: Granulosa FSH rep1

description: Gene expression data from cultured granulosa

source_name: ovarian follicular granulosa

label_protocol: Biotinylated cRNA was prepared according to the 3' IVT Express labelling kit protocol from 2 ug of total RNA

growth_protocol: Small antral follicles (4-6mm) from ovaries of normal cycling heifers were obtained at abbatoir. For each experiment on separate days, the follicles (n=80 approximately) were excised open and the granulosa cells were removed and pooled. The cells were seeded at 100,000 per well in a 24 well plate and cultured for 6 days under serum free conditions.

extract_protocol: Total RNA was isolated from cultured cells using the Ribopure RNA isolation kit (Ambion) according to the manufacturer’s instructions.

treatment_protocol: Each experiment consisted of 4 treatments: (1) FSH alone, (2) TNFα alone, (3) FSH + TNFα and  (4) control - neither drug. Four replicates each which were added from days 4 to 6 of culture, prior to harvesting for RNA.

value: ovarian follicular granulosa

tag: treatment

value: FSH


title: KO muscle biological replicate 1 technical replicate 1

tag: strain

value: muscle


title: 88-5299A map1

description: Mutation mapping 88-5299A

label_protocol: Genomic DNA was labeled with a Random prime reaction. DNA (1 ug) was mixed with 1 O.D. of 5’-fluorescence dye labeled random nonamer (Cy3 for test strains and Cy5 for reference strain) (TriLink Biotechnologies) in 62.5 mM Tris-HCl, 6.25 mM MgCl2 and 0.0875% ß-mercaptoethanol, denatured at 98°C for 5 min, chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each in TE) for 2 h at 37°C. Reactions were terminated with 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water. A fifty-fold amplification was typically achieved.(http://www.nimblegen.com/products/lit/lit.html)

extract_protocol: Genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit (Qiagen)


title: WT muscle biological replicate 3 technical replicate 2

tag: tissue


title: Granulosa TNFα rep2

tag: cell type

value: TNFα


title: Granulosa FSH rep2


title: WT Skin biological replicate 1 technical replicate 2

source_name: Total RNA extracted from WT C57/BL6 mouse E18.5 skin tissue, 5 samples pooled and labelled with Cy3

value: skin


title: Granulosa FSH + TNFα rep3

value: FSH + TNFα


title: Granulosa control rep1

value: control


title: Granulosa FSH + TNFα rep1


title: 89-2479 map1

description: Mutation mapping 89-2479


title: Granulosa control rep2


title: Granulosa FSH + TNFα rep2


title: Granulosa TNFα rep1


title: Granulosa FSH rep4


title: Granulosa TNFα rep3


title: 86-5192 map1

description: Mutation mapping 86-5192

value: Unknown

value: United States

value: diseased calf


title: 89-5259 map1

description: Mutation mapping 89-5259


title: Granulosa control rep4


title: KO Skin biological replicate 2 technical replicate 2

source_name: Total RNA extracted from miR-127 KO mouse E18.5 skin tissue, 5 samples pooled and labelled with Cy3


title: Granulosa FSH + TNFα rep4


title: WT Skin biological replicate 1 technical replicate 1


title: NT77 map1

description: Mutation mapping NT77

value: healthy pig

value: unknown


title: KO Skin biological replicate 2 technical replicate 1


title: Granulosa FSH rep3


title: Granulosa TNFα rep4


title: Follicle_small atretic_rep3

description: Gene expression data from granulosa of antral follicles.

hyb_protocol: Following amplification and fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Bovine Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analysed in Partek Genomics Suite (v6.5) using RMA (Robust Multi Array Algorithm, Irizarry et al. 2003) background corrrection with quantile normalization, mean probe set summarization and adjustment for GC content.

source_name: Follicle 4 mm atretic granulosa phenotype

label_protocol: Biotinylated cRNA was prepared according to the 3' IVT Express labelling kit protocol from 1.2-3.8 ug total RNA for the small healthy and large follicles. 250 ng was used for the small atretic follicles (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Ovarian follicles were obtained from freshly slaughtered non-pregnant Bos taurus heifers.

extract_protocol: Large follicle RNA was extracted using Trizol and purified with Qiagen RNeasy kit columns. Small healthy follicle RNA was extracted using Qiagen RNeasy mini kit columns. Small atretic follicle RNA was extracted with RNAqueous Micro kit columns.

treatment_protocol: Follicles were excised from the ovary, and a piece of wall was removed for histological classification. The follicular fluid was released and the granulosa was scraped from the follicle, then washed with PBS twice and frozen before extraction.

tag: type

value: small atretic

tag: size

value: 4 mm


title: 93A map1

description: Mutation mapping 93A

tag: serotype

value: diseased pig

value: virulent


title: NCTC1046 map1

description: Mutation mapping NCTC1046

tag: sequence type

value: Netherland

value: Canada


title: Follicle_small atretic_rep5

value: ovarian follicular granulosa


title: 2726 map1

description: Mutation mapping 2726

tag: site isolated

value: Denmark


title: Follicle_small atretic_rep4

source_name: Follicle 5 mm atretic granulosa phenotype

value: 5 mm


title: WT Brain biological replicate 1 technical replicate 2

source_name: Total RNA extracted from WT C57/BL6 mouse E18.5 whole brain, 5 samples pooled and labelled with Cy3

value: brain


title: WT Brain biological replicate 1 technical replicate 1


title: 13730 map1

description: Mutation mapping 13730

tag: origin

value: patient

source_name: Reference 89/1591 DNA


title: Follicle_large healthy_rep3

source_name: Follicle 14 mm healthy granulosa phenotype

value: large healthy rounded

value: 14 mm


title: Follicle_small atretic_rep1

source_name: Follicle 3 mm atretic granulosa phenotype

value: 3 mm


title: Follicle_small atretic_rep2


title: 10581 map1

description: Mutation mapping 10581

tag: pathogenicity


title: Follicle_large healthy_rep4

source_name: Follicle 15 mm healthy granulosa phenotype

value: 15 mm


title: WT Brain biological replicate 2 technical replicate 1


title: WT Brain biological replicate 2 technical replicate 2


title: Follicle_large healthy_rep2

source_name: Follicle 16 mm healthy granulosa phenotype

value: 16 mm


title: WT Brain biological replicate 3 technical replicate 2


title: Follicle_large healthy_rep1


title: Follicle_small healthy columnar_rep2

source_name: Follicle 4 mm healthy columnar granulosa phenotype

value: small healthy columnar


title: Follicle_small healthy columnar_rep3

source_name: Follicle 2/2 mm healthy columnar granulosa phenotype


title: WT Brain biological replicate 3 technical replicate 1


title: 8830 map1

description: Mutation mapping 8830


title: KO Brain biological replicate 3 technical replicate 2

source_name: Total RNA extracted from miR-127 KO mouse E18.5 whole brain, 5 samples pooled and labelled with Cy3


title: Follicle_small healthy columnar_rep5

source_name: Follicle 3 mm healthy columnar granulosa phenotype


title: Follicle_small healthy columnar_rep1


title: Follicle_small healthy rounded_rep5

source_name: Follicle 2.5 mm healthy rounded granulosa phenotype

value: small healthy rounded


title: Follicle_small healthy columnar_rep4


title: 4417 map1

description: Mutation mapping 4417


title: Follicle_small healthy rounded_rep2

source_name: Follicle 4 mm healthy rounded granulosa phenotype

value: 4 mm


title: Follicle_small healthy rounded_rep4

source_name: Follicle 3/2.5 mm healthy rounded granulosa phenotype


title: 22083 map1

description: Mutation mapping 22083

value: diseased pig


title: Follicle_small healthy rounded_rep3

source_name: Follicle 2.5/3 mm healthy rounded granulosa phenotype


title: Follicle_small healthy rounded_rep1

source_name: Follicle 3 mm healthy rounded granulosa phenotype


title: 12814 map1

description: Mutation mapping 12814

value: virulent


title: KO Brain biological replicate 1 technical replicate 2


title: KO Brain biological replicate 3 technical replicate 1


title: 2524 map1

description: Mutation mapping 2524


title: KO Brain biological replicate 1 technical replicate 1


title: KO Brain biological replicate 2 technical replicate 2


title: 8074 map1

description: Mutation mapping 8074


title: 11538 map1

description: Mutation mapping 11538


title: GYY4137 85% O2 24 h rep2

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

country: Germany

institute: MPI für Herz- und Lungenforschung

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (GPL10787) for 18 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20121126 for RS-284 samples or Grid: : 028005_D_F_ 20120201 for RS-266 samples) to obtain background subtracted and spatially detrended Processed Signal intensities. Features which were not positive and significant, not above background or were population outliers were flagged as “Compromised”. If features were flagged “Compromised” in all samples of either one of the experiments RS-266 or RS-284, than they were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick-Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Following the isolation protocol of Corti et al. 1996, primary murine alveolar type II cells were isolated. The cells were cultured in an air-liquid interface six well plate and kept in the incubator during three days until a monolayer of cells was formed.

extract_protocol: RNA isolation of the cells was performed, using a peqlab total RNA extraction kit

treatment_protocol: Afterwards, either vehicle (DMEM) or a fast hydrogen sulfide donor (NaHS) was added to the cells at a concentration of 100 µM for 6h and 24 h for samples belonging to the group RS-266. For samples of the group RS-284, either vehicle (DMEM) or a slow hydrogen sulfide donor (GYY4137) was added to the cells at a concentration of 100 µM for 24 h, the cells were put in normoxia (21% O2) and hyperoxia (85% O2) conditions for 24 h.

value: primary alveolar type II cells

tag: time


title: GYY4137 21% O2 24 h rep2


title: GYY4137 21% O2 24 h rep4


title: 6407 map1

description: Mutation mapping 6407

hyb_protocol: Labeled genomic DNA was hybridized to arrays in the NimbleGen Hybridization Buffer for 16 hours at 42 ℃ using a MAUI hybridization system (BioMicro Systems, Inc. Salt Lake City, Utah). Labeled genomic DNA (5ug) from the reference strain Streptococcus suis 89/1591 and from each test strain were co-hybridized to each array. Arrays were washed with NimbleGen wash buffer, and then were spun dry in a microarray high-speed centrifuge (TeleChem International, Inc., Sunnyvale, CA) and stored until scanned.(http://www.nimblegen.com/products/lit/lit.html)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 CGS data extraction.

treatment_protocol: test strain

value: Canada


title: 4961 map1

description: Mutation mapping 4961

treatment_protocol: Reference


title: GYY4137 85% O2 24 h rep4


title: NaHS 24 h rep4

source_name: NaHS 24 h

value: NaHS


title: 14636 map1

description: Mutation mapping 14636

value: Denmark


title: WT Skin biological replicate 2 technical replicate 2

source_name: Total RNA extracted from WT C57/BL6 mouse E18.5 skin tissue, 5 samples pooled and labelled with Cy3

tag: Stage

value: skin


title: WT Skin biological replicate 2 technical replicate 1


title: KO Brain biological replicate 2 technical replicate 1

value: brain


title: GYY4137 21% O2 24 h rep1


title: NaHS 24 h rep3


title: NaHS 24 h rep1


title: GYY4137 21% O2 24 h rep3


title: vehicle 24 h rep4

source_name: vehicle 24 h

value: vehicle


title: 2651 map1

description: Mutation mapping 2651

value: Netherland

source_name: Reference 89/1591 DNA


title: KO Skin biological replicate 3 technical replicate 2

source_name: Total RNA extracted from miR-127 KO mouse E18.5 skin tissue, 5 samples pooled and labelled with Cy3


title: KO Skin biological replicate 3 technical replicate 1


title: NaHS 24 h rep2


title: WT Skin biological replicate 3 technical replicate 2


title: 5428 map1

description: Mutation mapping 5428


title: NaHS 6 h rep4

source_name: NaHS 6 h

value: 6 h


title: vehicle 24 h rep1


title: KO Skin biological replicate 1 technical replicate 2


title: NaHS 6 h rep3


title: vehicle 24 h rep2


title: GYY4137 85% O2 24 h rep3


title: KO Skin biological replicate 1 technical replicate 1


title: GX407 map1

description: Mutation mapping GX407

value: China

value: patient

value: high virulent


title: TD10 map1

description: Mutation mapping TD10

value: United Kingdom

value: Diseased pig


title: 94-3037 map1

description: Mutation mapping 94-3037

value: low virulent


title: NaHS 6 h rep1


title: LS174T_NET_3

hyb_protocol: Labeled cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA

source_name: LS174T colorectal cancer cells

label_protocol: 25 ng total RNA per sample were processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.) 3.75 mg cDNA were fragmented and biotin-labelled following the Nugen protocol.

growth_protocol: Cells were grown under standard culture conditions. Briefly, all cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with L-Glutamine (Invitrogen 41966, Paisley, Scotland) and 10% FBS (Invitrogen 10270) at 37ºC and 5% CO2. 4-OHT (1uM) was used to activate the tamoxigfen inducible contructs (see treatment protocol for more details).

extract_protocol: Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies). Briefly, CRC cell lines were scraped from cell culture dishes (Costar) and homogenized by pipetting in TRIzol solution (Life Technologies, 15596-018). After phase separation with chloroform, the upper aqueous phase was then mixed with 70% ethanol and bound to RNA columns (PureLink™ RNA Mini kit, Life Technologies) according to the protocol provided by the manufacturer. RNA was quantified using a Nanodrop spectrophotometer.

treatment_protocol: Total RNA was collected from biological replicates of LS174T colorectal cancer cells transduced with  a 4-hydoxy tamoxifen (4-OHT) inducible system used to inducibly block beta-catenin/TCF activity. Cells were treated with 4-OHT  for a period of 36h befroe collecting total RNA. Briefly, the ERT2 domain from the pCMV-CRE-ERT2 (Feil et al., 1996) was amplified by PCR and cloned into a modified FUGW lentiviral vector backbone (Lois et al., 2002). NTCF was then amplified byPCR from the pCDNA3.1-NTCF-NLS (van de Wetering et al., 2002) and cloned in frame upstream of the ERT2 from the FUW-CMV-ERT2 (ET) to create the FUW-CMV-NTCF-ERT2 (NET).

tag: cell line

value: colorectal cancer


title: LS174T_NET_2


title: NaHS 6 h rep2


title: A375 cells 24h Vemurafenib rep3

city: East Melbourne

first: Tiffany

middle: Joy

last: Parmenter

address: 1 St Andrews Pl

institute: Peter MacCallum Cancer Centre

description: Gene expression data from A375 melanoma cells treated with 10 μM vemurafenib

hyb_protocol: 5μg of fragmented, labeled cRNA was hybridized at 45°C for 16h onto GeneChip® 1.0 ST human gene arrays then washed and stained using the Affymetrix GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using an Affymetrix 3000 7G scanner

data_processing: Raw data were RMA normalized after which differentially expressed genes were detected using a 2-way ANOVA using Partek software. The batch date of the different replicates was controlled for and the log fold change between control and Vem-treated samples was estimated. Normalized data was also subjected to gene set enrichment analysis (provided online by the Broad Institute) using c2 curated gene sets (Molecular signatures database v3.1) to identify enrichment of entire gene sets in either the control of Vem-treated samples

source_name: A375 melanoma cells treated with vemurafenib

label_protocol: Biotinylated cRNA was prepared from an input of 250ng RNA using an Ambion WT kit followed by the Affymetrix terminal labelling kit according to the manufacturer's instructions.

growth_protocol: A375 human melanoma cells grown in a monolayer in a 37°C humidified 5%CO2 incubator. Cells were grown in RPMI 1640 + HEPES containing 10% FBS, 2 mM L-alanyl-L-glutamine, 1% penicillin/streptomycin and 250 ng/ml amphotericin B

extract_protocol: Total RNA was extracted using a Qiagen miRNeasy Mini kit according to the manufacturer's protocol.

treatment_protocol: Cells were seeded in dup[licate 10cm dishes at 1,000,000 cells per dish and incubated for 24h then cells were treated with vehicle (0.1% DMSO) or Vemurafenib (Vem; PLX4032) for a further 24h.

value: Melanoma cell line


title: vehicle 6 h rep4

source_name: vehicle 6 h

value: primary alveolar type II cells


title: A375 cells 24h Vemurafenib rep1


title: WT Skin biological replicate 3 technical replicate 1


title: 9801 map1

city: Beijing

first: Xiao

last: Zheng

address: Liuzi five hao

institute: China CDC

description: Mutation mapping 9801

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol

value: diseased pig

value: Canada

value: virulent


title: LS174T_NET_1

hyb_protocol: Labeled cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 400 (Affymetrix, Santa Clara, CA

scan_protocol: Arrays were scanned in Genechip Scanner 3000

label_protocol: 5 mg total RNA were processed using the One-cycle target labeling and control reagents kit(Affymetrix, Santa Clara, CA) to synthesize dscDNA. Biotin-labeled cRNA was synthesized from dscDNA and fragmented using the IVT labeling kit of Affymetrix.


title: 07S3 map1

description: Mutation mapping 07S3


title: SC84 map1

description: Mutation mapping SC84


title: LS174T_ET_3


title: 11611 map1

description: Mutation mapping 11611

value: Germany

value: Unknown


title: vehicle 6 h rep3

value: vehicle


title: A375 cells 24h Vemurafenib rep2


title: GYY4137 85% O2 24 h rep1


title: vehicle 6 h rep2


title: 31533 map1

description: Mutation mapping 31533

value: France


title: 06GZ1 map1

description: Mutation mapping 06GZ1


title: vehicle 6 h rep1

value: 6 h


title: LS174T_ET_2


title: A375 cells 24h Control rep1

description: Gene expression data from A375 melanoma cells treated with vehicle control (0.1% DMSO)

source_name: A375 melanoma cells treated with vehicle (0.1% DMSO) batch A


title: KatoII PHA 8 130

status: Public on May 19 2014

city: Montreal

first: Sean

last: Cory

state: QC

address: 3649 Promenade Sir William Osler

department: Bioinformatics

country: Canada

institute: McGill University

description: KatoII PHA 8

hyb_protocol: 825 ng of Cy3-labelled aRNA samples were co-hybridised with 825 ng of Cy5-labelled reference aRNA (Universal Human Reference RNA, La Jolla, California, USA) to Agilent 4x44K whole human genome arrays (Agilent Technologies, Mississauga, Ontario). Slides were washed according to the manufacturer’s instructions and scanned using an Agilent dual-laser scanner (P/ N: G2505B).

scan_protocol: Slides were washed according to the manufacturer’s instructions and scanned using an Agilent dual-laser scanner (P/ N: G2505B).  Feature extraction was performed using Agilent Feature Extraction software (FE 9.5.3.1).

data_processing: The arrays were normalized using normexp (RMA) background correction and quantile between array normalization.

source_name: KatoII cell line

label_protocol: 500 ng of total RNA was subjected to a single round of amplification using the Amino Allyl MessageAmpTM II aRNA kit (Ambion/Life Technologies,  Burlington, Ontario, Canada) according to the manufacturer's instructions, and the amplified product was labeled using a CyDye Post-Labeling Reactive Dye Pack (GE Healthcare Bio-Sciences Inc., Baie d'Urfé, Quebec, Canada).

extract_protocol: Total RNA was isolated with Qiazol (Qiagen, Toronto, Ontario) as per the manufacturer’s instructions (Qiagen RNeasy Mini Kit)

value: KatoII

tag: time (hours)

value: PHA

source_name: Human Universal reference

tag: reference

value: Human Universal reference


title: KatoII PHA 24 132

description: KatoII PHA 24


title: GZ2 map1

description: Mutation mapping GZ2

value: China

value: patient

value: high virulent


title: KatoII PHA 16 131

description: KatoII PHA 16


title: KatoII PHA 16 125

description: KatoII PHA 16


title: LS174T_ET_1

value: colorectal cancer


title: KatoII DMSO 4 126

description: KatoII DMSO 4

value: DMSO


title: KatoII DMSO 24 121

description: KatoII DMSO 24


title: KatoII DMSO 8 123

description: KatoII DMSO 8


title: A375 cells 24h Control rep2

source_name: A375 melanoma cells treated with vehicle (0.1% DMSO)

value: Melanoma cell line


title: A375 cells 24h Control rep3


title: KatoII DMSO 4 120

description: KatoII DMSO 4


title: P1/7 map1

description: Mutation mapping 1/7

value: England

value: diseased pig


title: KatoII DMSO 0.5 116

description: KatoII DMSO 0.5


title: KatoII DMSO 2 124

description: KatoII DMSO 2


title: LN1 map1

description: Mutation mapping LN1

value: Canada

value: virulent


title: KatoII DMSO 0 117

description: KatoII DMSO 0


title: KatoII DMSO 16 122

description: KatoII DMSO 16


title: KatoII PHA 4 127

description: KatoII PHA 4


title: KatoII PHA 0 119

description: KatoII PHA 0


title: vehicle 24 h rep3

value: primary alveolar type II cells


title: KatoII PHA 0.5 118

description: KatoII PHA 0.5


title: RC4716 map1

description: Mutation mapping RC4716


title: okajima PHA 16 110

description: okajima PHA 16

source_name: okajima cell line

value: okajima


title: KatoII PHA 8 113

description: KatoII PHA 8


title: KatoII DMSO 2 114

description: KatoII DMSO 2


title: okajima DMSO 16 105

description: okajima DMSO 16


title: okajima DMSO 8 103

description: okajima DMSO 8


title: okajima PHA 0.5 104

description: okajima PHA 0.5


title: okajima DMSO 4 100

description: okajima DMSO 4


title: KatoII PHA 2 115

description: KatoII PHA 2


title: okajima DMSO 2 96

description: okajima DMSO 2


title: KatoII PHA 4 129

description: KatoII PHA 4


title: okajima PHA 16 97

description: okajima PHA 16


title: okajima PHA 8 93

description: okajima PHA 8


title: okajima PHA 0.5 108

description: okajima PHA 0.5


title: okajima DMSO 0 94

description: okajima DMSO 0


title: okajima PHA 2 91

description: okajima PHA 2


title: okajima DMSO 8 111

description: okajima DMSO 8


title: okajima DMSO 24 107

description: okajima DMSO 24


title: okajima PHA 4 89

description: okajima PHA 4


title: okajima PHA 24 90

description: okajima PHA 24


title: okajima DMSO 24 101

description: okajima DMSO 24


title: okajima PHA 0 112

description: okajima PHA 0


title: Snu-5 DMSO 0.5 87

description: Snu-5 DMSO 0.5

source_name: Snu-5 cell line


title: okajima DMSO 4 98

description: okajima DMSO 4


title: Snu-5 PHA 24 88

description: Snu-5 PHA 24


title: okajima PHA 4 95

description: okajima PHA 4


title: Snu-5 PHA 0 86

description: Snu-5 PHA 0


title: okajima PHA 8 99

description: okajima PHA 8


title: okajima PHA 24 102

description: okajima PHA 24


title: Snu-5 PHA 4 81

description: Snu-5 PHA 4


title: Snu-5 PHA 16 80

description: Snu-5 PHA 16


title: Snu-5 DMSO 2 79

description: Snu-5 DMSO 2


title: okajima DMSO 16 109

description: okajima DMSO 16


title: okajima PHA 2 106

description: okajima PHA 2


title: Snu-5 PHA 24 84

description: Snu-5 PHA 24


title: Snu-5 PHA 24 82

description: Snu-5 PHA 24


title: Snu-5 DMSO 2 74

description: Snu-5 DMSO 2


title: Snu-5 DMSO 4 76

description: Snu-5 DMSO 4


title: Snu-5 DMSO 0 72

description: Snu-5 DMSO 0


title: Snu-5 DMSO 4 78

description: Snu-5 DMSO 4


title: Snu-5 DMSO 8 85

description: Snu-5 DMSO 8


title: Snu-5 PHA 4 73

description: Snu-5 PHA 4


title: okajima DMSO 0.5 92

description: okajima DMSO 0.5


title: Snu-5 PHA 8 71

description: Snu-5 PHA 8


title: Snu-5 PHA 16 75

description: Snu-5 PHA 16


title: Snu-5 PHA 8 77

description: Snu-5 PHA 8


title: Snu-5 PHA 2 69

description: Snu-5 PHA 2


title: Snu-5 DMSO 16 68

description: Snu-5 DMSO 16


title: Snu-5 DMSO 16 63

description: Snu-5 DMSO 16


title: mkn45 PHA 0 60

description: mkn45 PHA 0

source_name: mkn45 cell line


title: Snu-5 DMSO 24 66

description: Snu-5 DMSO 24


title: Snu-5 DMSO 0.5 70

description: Snu-5 DMSO 0.5


title: KatoII PHA 24 128

description: KatoII PHA 24


title: mkn45 PHA 0.5 59

description: mkn45 PHA 0.5


title: Snu-5 PHA 0.5 62

description: Snu-5 PHA 0.5


title: mkn45 PHA 8 52

description: mkn45 PHA 8


title: mkn45 PHA 24 53

description: mkn45 PHA 24


title: Snu-5 PHA 2 64

description: Snu-5 PHA 2


title: mkn45 DMSO 16 54

description: mkn45 DMSO 16


title: mkn45 DMSO 24 56

description: mkn45 DMSO 24


title: mkn45 PHA 16 49

description: mkn45 PHA 16


title: Snu-5 DMSO 24 65

description: Snu-5 DMSO 24


title: Snu-5 DMSO 8 61

description: Snu-5 DMSO 8


title: mkn45 DMSO 8 50

description: mkn45 DMSO 8


title: mkn45 PHA 0 57

description: mkn45 PHA 0


title: mkn45 PHA 0 46

description: mkn45 PHA 0


title: mkn45 PHA 2 55

description: mkn45 PHA 2


title: mkn45 PHA 24 48

description: mkn45 PHA 24


title: mkn45 DMSO 0.5 47

description: mkn45 DMSO 0.5


title: mkn45 DMSO 2 43

description: mkn45 DMSO 2


title: mkn45 PHA 16 44

description: mkn45 PHA 16


title: mkn45 DMSO 8 45

description: mkn45 DMSO 8


title: mkn45 PHA 24 42

description: mkn45 PHA 24


title: mkn45 PHA 0.5 51

description: mkn45 PHA 0.5


title: mkn45 PHA 8 40

description: mkn45 PHA 8


title: mkn45 PHA 8 34

description: mkn45 PHA 8


title: mkn45 DMSO 2 37

description: mkn45 DMSO 2


title: mkn45 DMSO 0 35

description: mkn45 DMSO 0


title: mkn45 PHA 16 38

description: mkn45 PHA 16


title: mkn45 DMSO 0.5 33

description: mkn45 DMSO 0.5


title: mkn45 PHA 4 28

description: mkn45 PHA 4


title: mkn45 DMSO 0 29

description: mkn45 DMSO 0


title: mkn45 PHA 2 27

description: mkn45 PHA 2


title: mkn45 PHA 4 30

description: mkn45 PHA 4


title: mkn45 PHA 24 31

description: mkn45 PHA 24


title: mkn45 PHA 4 36

description: mkn45 PHA 4


title: mkn45 PHA 2 32

description: mkn45 PHA 2


title: mkn45 PHA 16 25

description: mkn45 PHA 16


title: mkn45 DMSO 4 23

description: mkn45 DMSO 4


title: mkn45 DMSO 8 26

description: mkn45 DMSO 8


title: mkn45 DMSO 4 39

description: mkn45 DMSO 4


title: mkn45 PHA 8 22

description: mkn45 PHA 8


title: mkn45 DMSO 16 24

description: mkn45 DMSO 16


title: mkn45 DMSO 2 20

description: mkn45 DMSO 2


title: mkn45 PHA 0.5 21

description: mkn45 PHA 0.5


title: mkn45 DMSO 0 19

description: mkn45 DMSO 0


title: mkn45 PHA 24 18

description: mkn45 PHA 24


title: Snu-5 PHA 4 83

description: Snu-5 PHA 4


title: mkn45 PHA 0 17

description: mkn45 PHA 0


title: mkn45 DMSO 0.5 15

description: mkn45 DMSO 0.5


title: mkn45 DMSO 24 16

description: mkn45 DMSO 24


title: mkn45 DMSO 4 12

description: mkn45 DMSO 4


title: mkn45 PHA 0 13

description: mkn45 PHA 0


title: mkn45 PHA 24 8

description: mkn45 PHA 24


title: mkn45 PHA 4 11

description: mkn45 PHA 4


title: mkn45 DMSO 24 10

description: mkn45 DMSO 24


title: mkn45 DMSO 2 9

description: mkn45 DMSO 2


title: mkn45 DMSO 0.5 5

description: mkn45 DMSO 0.5


title: EOS from OVA lung_rep1

city: Cincinnati

first: Marc

last: Rothenberg

state: OH

address: 3333 Burnet Ave. MLC-7028

department: Allergy

institute: Cincinnati Children's Hospital Medical Center

description:
Gene expression data from sorted eosinophils
SAMPLE 5

hyb_protocol: Hybridization chamber: a standard Probe Array Cartidge (GeneChip Mouse Gene 1.0 ST Array Affymetrix). Hybridization cocktail for a single probe array that contains 2.5 ug of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99C for 2 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 90 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 90 uL of the hybridization cocktail. Incubate at 45C for 18 hrs in the Hybridization Oven rotating at 60 rpm.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G, Scanning software: Genechip Operating Software (Affymetrix)

data_processing: Raw data were analyzed by Genespring GX 11 using RMA

source_name: eosinophils sorted from OVA challenged lung

label_protocol: The WT- Ovation Pico RNA Amplification System Version 1.0 (Nugen) is used to prepare target cDNA. Then the WT-Ovation Exon Module v1.0 (NuGEN) is used to create target sense transcript cDNA. Finally the FL-Ovation cDNA Biotin Module V2 (NuGEN) chemically fragments and labels the target sense cDNA

extract_protocol: Following the QIAGEN RNeasy kit procedures

value: BALB/c

value: lung

value: eosinophil


title: mkn45 DMSO 0 1

description: mkn45 DMSO 0


title: mkn45 PHA 2 7

description: mkn45 PHA 2

value: PHA


title: mkn45 PHA 8 14

description: mkn45 PHA 8

value: Human Universal reference


title: mkn45 DMSO 16 6

description: mkn45 DMSO 16


title: mkn45 PHA 0.5 3

description: mkn45 PHA 0.5


title: mkn45 DMSO 4 41

description: mkn45 DMSO 4


title: EOS from OVA lung_rep2

description:
Gene expression data from sorted eosinophils
SAMPLE 6


title: EOS from saline lung_rep4

description:
Gene expression data from sorted eosinophils
SAMPLE 4

source_name: eosinophils sorted from saline challenged lung


title: mkn45 DMSO 8 2

description: mkn45 DMSO 8


title: Lung-10WK-10

city: Bethesda

first: WeiPing

last: Chen

state: MD

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

department: GCL

institute: NIDDK/NIH

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

data_processing: RMA by software Partek

organism: Ovis aries

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

growth_protocol: All animal studies were approved by the NICHD/NIH Animal Care and Use Committee.

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

value: Lung

tag: age

value: postnatal 10 wk


title: Lung-10WK-11


title: EOS from OVA lung_rep3

description:
Gene expression data from sorted eosinophils
SAMPLE 7


title: EOS from saline lung_rep1

description:
Gene expression data from sorted eosinophils
SAMPLE 1


title: mkn45 PHA 16 4

description: mkn45 PHA 16

tag: treatment


title: mkn45 DMSO 24 58

description: mkn45 DMSO 24


title: Lung-10WK-7


title: Lung-10WK-12


title: Lung-FD90-80B

value: fetal day 90


title: EOS from saline lung_rep2

description:
Gene expression data from sorted eosinophils
SAMPLE 2

tag: strain


title: Lung-10WK-8

tag: tissue


title: Snu-5 PHA 0.5 67

description: Snu-5 PHA 0.5


title: Kidney-AD-444

source_name: AD

value: Kidney

value: adult


title: Lung-FD90-14A


title: Lung-FD90-26B


title: CD138low RPMI-8226 rep 1

city: Salamanca

first: Teresa

last: Paíno

address: Campus Miguel de Unamuno

institute: Centro de investigación del cáncer

hyb_protocol: Labeled RNA was hybridized to Human Gene 1.0 ST Array

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

data_processing:
Expression value for each probe set was calculated using Affymetrix Expression Console that uses RMA (Robust Multi-Array Average) algorithm.
probe_group_file: HuGene-1_0-st-v1.r4.pgf
meta-probeset_file HuGene-1_0-st-v1.r4.mps

source_name: RPMI-8226 cell line

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA)

growth_protocol: cells were cultured in RPMI-1640 medium supplemented with 2 mM L-glutamine, 100 U/mL penicillin, 100 mg/mL streptomycin and 10% fetal bovine serum at 37°C and 5% CO2/95% air

extract_protocol: RNA was isolated from CD138++ (n=3) and CD138low (n=3) RPMI-8226 cells using an RNeasy Mini Kit (Qiagen, Valencia, USA) following the manufacturer’s protocol

treatment_protocol: not applicable

tag: disease

value: multiple myeloma

tag: subpopulation


title: EOS from saline lung_rep3

description:
Gene expression data from sorted eosinophils
SAMPLE 3

tag: cell type


title: CD138low RPMI-8226 rep 3


title: CD138++ RPMI-8226 rep 3


title: CD138++ RPMI-8226 rep 2


title: Kidney-10WK-10


title: Kidney-10WK-11


title: Kidney-AD-432


title: Kidney-10WK-9


title: CD138low RPMI-8226 rep 2


title: Kidney-AD-442


title: Kidney-10WK-8


title: Kidney-10WK-7


title: KO.C2

city: New Haven

first: Qin

last: Yan

state: CT

address: 310 Cedar St

department: Pathology

institute: Yale University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The unnormalized data were exported from Illumina Genome Studio, and then normalized using lumi package in R

source_name: Mammary Epithelial Cells, KO

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

extract_protocol: Total RNA samples were isolated from 3 pairs of 80% confluent Jarid1b+/+ and Jarid1b-/- early-passage MECs using RNeasy Plus Mini Kit (74134, Qiagen).

tag: genotype/variation

value: Jarid1B Knock Out

value: Mammary Epithelial Cells

tag: sample id


title: Kidney-FD90-19A


title: WT.C2

source_name: Mammary Epithelial Cells, WT

value: Wild type


title: Lung-AD-287


title: Lung-AD-204


title: KO.B3

value: MEC 72


title: Lung-FD90-10A


title: Kidney-FD90-10A


title: Kidney-FD90-14A


title: Lung-AD-299


title: WT.B1

value: MEC 70


title: Lung-AD-286


title: Kidney-FD90-26A


title: Kidney-FD90-80B


title: Lung-AD-297


title: KO.A1

value: MEC 69


title: SA_RF122, rep3

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

hyb_protocol: Each hybridization mixture was made up from 1 µg test material (Cy3) and 1 µg reference material (Cy5). The S. aureus experiments were performed according to a common reference design, with all eleven strains as test samples in triplicates, and MRSA252 as common reference. The combined samples were dried and 1.98 µl of water was added. The hybridization cocktail was made according to the manufacturer's instructions (NimbleGen microarrays User's Guide - Gene Expression microarrays Version 5.0, Roche NimbleGen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min. at 95°C and 5 min. at 42°C prior to loading. Hybridization samples were loaded onto the microarray and hybridized for 20 h. at 42°C with the NimbleGen Hybridization System 4 (Roche NimbleGen).

scan_protocol: Afterwards, the slides were washed according to the NimbleGen microarrays User's Guide - Gene Expression microarrays Version 5.0 and scanned in an ozone-free room with an Agilent DNA microarray scanner G2565CA (Agilent Technologies). Feature extraction was performed with NimbleScan v2.6 (Roche NimbleGen).

data_processing: Sequence-based normalization is generally recommended for high density aCGH analysis and was performed according to Naef and Magnasco.

organism: Staphylococcus aureus

label_protocol: Genomic DNA was amplified and labeled by strand displacement amplification. 200 ng genomic DNA was combined with 5 µg random octamers (Biolegio). The DNA was partly fragmented by heat at 99°C for 10 min. and allowed to cool on an ice/water bath for 5 min. The DNA/octamer mix was made on ice to 50 mM Tris-Cl (pH 7.5), 5 mM MgCl2, 1 mM DTT, 1 mM dGAC (GE Healthcare), 0.6 mM dTTP (GE Healthcare), 0.4 mM aminoallyl dUTP (TriLink Biotechnologies) and finally 10U Klenow exo- (Jena Bioscience) was added. After gentle vortexing, the samples were place at 37°C for 8h. and subsequently incubated for 15 min. at 75°C to inactivate the enzyme. Each reaction was made to 1.5M sodium acetate (pH 5.2) and the amplified DNA was purified with the QIAquick PCR Purification Kit (Qiagen) according to the manufacturer's instructions with the exception that 7 volumes of buffer PB were used instead of 5 to increase the recovery of smaller fragments. Concentrations of amplified products were measured on the NanoDrop ND-1000 (Thermo Scientific) and quality assessed on the BioAnalyzer (Agilent Technologies) with the DNA 1000 Kit (Agilent Technologies). From each sample, 5 µg was taken, dried down and dissolved in 50 mM carbonate buffer (pH 8.5). Individual vials of Cy3/Cy5 from the mono-reactive dye packs (GE Healthcare) were dissolved in 200 µl DMSO. To each sample, 10 µl of the appropriate CyDye dissolved in DMSO was added and the mixture was incubated for 1h. Reactions were quenched with the addition of 5 µl 4M hydroxylamine (Sigma-Aldrich). This mixture was made to 0.75M Ammonium acetate and 0.2 µg/µl glycogen (Ambion). After mixing 2.5 vol. of 100% EtOH was added and mixed. All samples were incubated for at least 60 min. at -20°C to enhance precipitation and centrifuged for 30 min. at 13.000xg. The supernatants were carefully removed by pipetting and 1 vol. of 80% EtOH was added to the pellets. After brief vortexing, the labeled DNA was pelleted once more by centrifugation for 10 min. at 13.000xg. The supernatants were removed by pipetting and the pellets were dried by vacuum concentrating. Final labeled pellets were dissolved in 30 µl H2O and the yield and CyDye incorporation were measured with the NanoDrop ND-1000.

extract_protocol: The PTD method was validated with aCGH analyses on the bacterium Staphylococcus aureus (S. aureus). Eleven S. aureus strains were used: MRSA252 (NCBI Reference Sequence: NC_002952.2), MSSA476 (NC_002953.3), Mu50 (NC_002758.2), MW2 (NC_003923.1), N315 (NC_002745.2), NCTC8325 (NC_007795.1), Newman (NC_009641.1), RF122 (NC_007622.1), S0385, USA300, WKZ1. The strains were grown overnight in Iscove's Modified Dulbecco's Medium (IMDM) (Invitrogen, Carlsbad, CA, USA). The overnight cultures were diluted (1:7) in fresh pre-warmed IMDM and grown twice to mid-log phase culture (a A660nm of 0.5). The second mid-log phase culture was diluted to an A660nm of 0.3 with pre-warmed IMDM and directly transferred to fresh pre-warmed IMDM to obtain an A660nm of 0.03. Samples for DNA extraction were taken at 4h post-inoculation.

tag: strain/background

source_name: Common reference MRSA252

tag: sample type

value: reference


title: Adult mouse right ventricle tissue AdltR.3

city: Rochester

first: XING

last: LI

state: MN

address: 200 1st street SW

department: Health Sciences Research

institute: Mayo Clinic

description: Right ventricle tissue from adult mouse heart

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 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 R/Bioconductor using RMA.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Wild type CD1 strain mouse embryos were harvested at defined stages from timed mating pairs. Morphology and somite count were used as inclusion criteria for each developmental time point.

extract_protocol: RNA was extracted using the Qiagen RNeasy kit.

treatment_protocol: For the first developmental stage, embryonic day (E) 7.5, whole embryos were collected. For later stages cardiac structures were micro-dissected including E8.5 heart tubes and left and right ventricles corresponding to E9.5, E12.5, E14.5, E18.5, newborn and adult mice. All samples were harvested in biological triplicates, with approximately 30-50 embryos/hearts included per replicate corresponding to E7.5, E8.5 and E9.5; 10-20 hearts for each E12.5 or E14.5 sample; 3-5 hearts pooled for each E18.5 replicate and one used for newborn and adult samples. Embryonic stem cells (ESC) from the R1 line were used as pluripotent gold standard. To avoid interference due to high protein content newborn and adult hearts were fast-frozen and pulverized prior to RNA extraction.

value: Right ventricle tissue


title: Kidney-AD-441


title: SA_N315, rep3


title: SA_Mu50, rep3


title: WT.A1

value: MEC 68


title: Adult mouse left ventricle tissue AdltL.3

description: Left ventricle tissue from adult mouse heart

value: Left ventricle tissue


title: Mouse right ventricle tissue at 3 days after birth D3R.2

description: Right ventricle tissues from mouse at 3 days after birth

value: Right ventricle tissues

value: 3 days after birth


title: SA_Newman, rep3

value: Newman


title: SA_WKZ1, rep3


title: Mouse left ventricle tissue at 3 days after birth D3L.1

description: Left ventricle tissues from mouse at 3 days after birth

value: Left ventricle tissues


title: Mouse right ventricle tissue at 3 days after birth D3R.1

source_name: Right ventricle tissues from mouse at 3 days after birth


title: Adult mouse left ventricle tissue AdltL.2

source_name: Left ventricle tissue from adult mouse heart


title: Mouse left ventricle tissue at 3 days after birth D3L.2

source_name: Left ventricle tissues from mouse at 3 days after birth


title: Mouse left ventricle tissue at 3 days after birth D3L.3


title: Adult mouse left ventricle tissue AdltL.1


title: Mouse right ventricle tissue at 3 days after birth D3R.3


title: Adult mouse right ventricle tissue AdltR.1

source_name: Right ventricle tissue from adult mouse heart


title: Adult mouse right ventricle tissue AdltR.2


title: SA_USA300, rep3


title: SA_MW2, rep3


title: Mouse E18.5 right ventricle tissue E18R.3

description: Right ventricle tissues from mouse embryo at E18.5


title: SA_NCTC8325, rep3


title: Mouse E18.5 right ventricle tissue E18R.2

source_name: Right ventricle tissues from mouse embryo at E18.5


title: Lung-FD90-14B

value: Lung

value: fetal day 90


title: SA_MSSA476, rep3


title: SA_MSSA476, rep2


title: SA_MRSA252, rep3


title: Mouse E18.5 right ventricle tissue E18R.1


title: Kidney-AD-434

value: Kidney

value: adult


title: CD138++ RPMI-8226 rep 1

value: multiple myeloma


title: SA_RF122, rep2


title: Mouse E18.5 left ventricle tissue E18L.3

description: Left ventricle tissues from mouse embryo at E18.5


title: Mouse E14.5 left ventricle tissue E14L.2

description: Left ventricle tissues from mouse embryo at E14.5


title: Mouse E18.5 left ventricle tissue E18L.1

source_name: Left ventricle tissues from mouse embryo at E18.5


title: Mouse E14.5 right ventricle tissue E14R.3

description: Right ventricle tissues from mouse embryo at E14.5


title: Mouse E14.5 right ventricle tissue E14R.2

source_name: Right ventricle tissues from mouse embryo at E14.5


title: Mouse E18.5 left ventricle tissue E18L.2


title: SA_MRSA252, rep2


title: SA_MW2, rep2


title: Mouse E14.5 right ventricle tissue E14R.1


title: Mouse E12.5 right ventricle tissue E12R.3

description: Right ventricle tissues from mouse embryo at E12.5


title: Mouse E14.5 left ventricle tissue E14L.3

source_name: Left ventricle tissues from mouse embryo at E14.5


title: Mouse E14.5 left ventricle tissue E14L.1


title: SA_Mu50, rep2


title: SA_USA300, rep2


title: Mouse E12.5 right ventricle tissue E12R.2

source_name: Right ventricle tissues from mouse embryo at E12.5


title: SA_NCTC8325, rep2


title: SA_N315, rep2


title: Mouse E12.5 right ventricle tissue E12R.1


title: SA_S0385, rep2


title: SA_RF122, rep1


title: SA_Newman, rep2


title: SA_S0385, rep3


title: SA_WKZ1, rep2


title: SA_N315, rep1


title: SA_Mu50, rep1


title: Mouse E9.5 right ventricle tissue E9R.3

description: Right ventricle tissues from mouse embryo at E9.5


title: Mouse E9.5 right ventricle tissue E9R.2

source_name: Right ventricle tissues from mouse embryo at E9.5


title: Mouse E12.5 left ventricle tissue E12L.3

description: Left ventricle tissues from mouse embryo at E12.5


title: Mouse E12.5 left ventricle tissue E12L.1

source_name: Left ventricle tissues from mouse embryo at E12.5


title: Mouse E12.5 left ventricle tissue E12L.2


title: Mouse E9.5 left ventricle tissue E9L.3

description: Left ventricle tissues from mouse embryo at E9.5


title: Mouse E9.5 right ventricle tissue E9R.1


title: Mouse E9.5 left ventricle tissue E9L.2

source_name: Left ventricle tissues from mouse embryo at E9.5


title: SA_USA300, rep1


title: SA_MRSA252, rep1


title: Mouse E9.5 left ventricle tissue E9L.1


title: SA_Newman, rep1


title: Mouse E8.5 whole heart tissue (heart tube) E8.1

description: Whole heart tube tissues from mouse embryo at E8.5

value: Whole heart tube tissues


title: Mouse E8.5 whole heart tissue (heart tube) E8.2

source_name: Whole heart tube tissues from mouse embryo at E8.5


title: Mouse E8.5 whole heart tissue (heart tube) E8.3


title: Mouse E7.5 whole embryo tissue E7.3

description: Mouse whole embryo tissues at E7.5

source_name: Mouse whole embryo tissues at E7.5

value: Mouse whole embryo tissues at E7.5


title: SA_MW2, rep1


title: SA_NCTC8325, rep1


title: SA_S0385, rep1


title: SA_MSSA476, rep1


title: SA_WKZ1, rep1


title: Mouse E7.5 whole embryo tissue E7.2

description: Mouse whole embryo tissues at E7.5


title: REH attached_21% Oxygen_s3

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: REH attached_21% Oxygen

label_protocol: 200 ng total RNA was amplified and biotin-labeled through a Eberwine procedure using Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: BM-MSC isolated from BM of healthy donors, expanded with pooled human platelet lysate and cryopreserved, were thawed and plated for triplicate cultures in RPMI with 10% FBS at 37°C in 5% CO2/air. After 24 hours, medium was replaced with RPMI/FBS alone, for BM-MSC alone, or with RPMI/FBS containing pre-B REH cells for REH/BM-MSC co-cultures, at an REH/BM-MSC ratio of ~2. In parallel, monocultures of REH cells and BM-MSC were similarly prepared and seeded at the same density as co-cultures.

extract_protocol: Total RNA was isolated by using TRIzol reagent (life Technologies), then further purified using the RNeasy plus Mini kit (Qiagen).

treatment_protocol: All cultures were maintained for 48 hours. To harvest co-cultured cells for analysis, medium and nonattached REH cells were removed and discarded, and attached REH cells and BM-MSC were mobilized with EDTA and collected. Monocultured BM-MSC were similarly harvested, and all cells from REH monocultures were collected. All cell suspensions were stained with anti-human CD90 (Thy-1) antibody as the BM-MSC marker, and anti-human CD45 antibody as the REH cell marker, and then separated with a FACSAria II flow cytometer. Sorted cells were pelleted and lysed with QIAzol lysis reagent for total RNA extraction.

value: REH

value: pre-B acute lymphoblastic leukaemia cells

tag: culture type

value: attached


title: REH attached_21% Oxygen_s2


title: Mouse R1 Stem Cells R1.2

description: mouse stem cell line

source_name: Mouse stem cell lines, R1


title: D3196_Saliva_Unaffected_rep1

first: Philippe

last: Lemay

state: Quebec

address: 3175 Chemin de la Côte-Sainte-Catherine

institute: Université de Montréal

description:
Genotyping batch2
raw data file: Batch2_RAW.txt

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a iScan Autoloader 2X (Illumina).

data_processing: Genomic DNA extracted from saliva was genotyped using Infinium CanineHD Genotyping BeadChips (Illumina).

label: Cy3 and Cy5

organism: Canis lupus familiaris

source_name: saliva (mouth swap)_unaffected (control)

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-MA1, WG-MA2) and primer/neutralization mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: DNA was extracted from blood or saliva using the ORAGENE Animal kit (DNAgenotek)

tag: breed

value: Griffon Bruxellois

tag: Sex

value: Male

tag: diameter f

tag: line ab

tag: angle 1 (abc)

tag: line bc

tag: line cd

tag: line bd

tag: line be

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)

tag: line fg


title: Mouse R1 Stem Cells R1.1

description: mouse stem cell line

tag: cell line


title: Mouse R1 Stem Cells R1.3

description: mouse stem cell line


title: Mouse E7.5 whole embryo tissue E7.1

description: Mouse whole embryo tissues at E7.5

tag: tissue

tag: age

tag: strain


title: REH alone_21% Oxygen_s2

source_name: REH alone_21% Oxygen

tag: cell type

tag: culture type

value: cultured alone (monoculture)


title: REH alone_21% Oxygen_s1


title: Endothelial cells TAC, Biological Replicate 1

city: La Jolla

first: thomas

last: moore-morris

state: CA

address: 9500 Gilman Drive #0613C

department: SSPPS

institute: University of California San Diego

description: Gene expression data from cells sorted from left ventricle

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using the affymetrix Gene Chip Scanner 3000 7G.

data_processing: Affymetrix expression values were generated and normalized with RMA using AltAnalyse

source_name: left ventricle, TAC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were maintained in a vivarium under normal conditions.

extract_protocol: RNA was extracted from cell pellets using the Zymo Quick RNA microprep according to the manufacturer's instructions.

treatment_protocol: Mice were subjected to transaortic contriction or sham operated.

value: cardiac endothelial cell

value: black swiss

tag: gender

value: male

value: 8-10 weeks


title: Endothelial cells SHAM, Biological Replicate 1

source_name: left ventricle, sham operated


title: Tie2cre non-lineage traced fibroblast TAC, Biological Replicate 1

value: cardiac fibroblasts

tag: lineage

value: Tie2cre non-lineage


title: D3175_Saliva_Affected_rep1

source_name: saliva (mouth swap)_affected

tag: breed

tag: Sex

tag: diameter f

tag: line ab

tag: angle 1 (abc)

tag: line bc

tag: line cd

tag: line bd


title: MSC alone_21% Oxygen_s3

source_name: MSC alone_21% Oxygen

tag: tissue source

value: BM of healthy donors

value: Human bone marrow mesenchymal stromal cells (BM-MSCs)


title: REH alone_21% Oxygen_s3

tag: cell line


title: MSC coculture_21% Oxygen_s3

source_name: MSC coculture_21% Oxygen

value: co-cultured with the pre-B ALL REH cells


title: D3052_Saliva_Unaffected_rep1

tag: line be

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)

tag: line fg


title: D3054_Saliva_Unaffected_rep1

tag: breed

tag: Sex

value: Female

tag: age


title: D3061_Saliva_Unaffected_rep1

tag: diameter f

tag: line ab

tag: angle 1 (abc)


title: REH attached_21% Oxygen_s1

tag: cell type

tag: culture type


title: Tie2cre non-lineage traced fibroblast SHAM, Biological Replicate 1

tag: strain

tag: gender

tag: lineage


title: Tie2cre lineage traced fibroblast TAC, Biological Replicate 1

value: Tie2cre lineage traced


title: MSC coculture_21% Oxygen_s2

tag: tissue source


title: mock

first: Beile

last: Gao

address: 295 Congress Ave

department: Microbial Pathogenesis

description: Gene expression data from RNA extracted from mock-treated cells

hyb_protocol: The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 according to Affymetrix standard protocols.

data_processing: The images were processed with Affymetrix Microarray Suite version 5.0, scaled to a target intensity of 500

source_name: HeLa229 cells untransfected

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: HeLa229 cells were grown in DMEM supplemented with 10%FBS.

extract_protocol: HeLa229 cells were lysed in 1ml of TRIzol. Phase separation was carried with 0.5ml chloroform. Total RNA was precipitated with 0.5ml 100% isopropanol. RNA pellet was resuspended in 50ul RNAase-free water and further purified with RNeasy kit form Qiagen.

treatment_protocol: HeLa229 cells were transfected with siRNA duplexes targeting FLASH or ZEB1 or left untreated. Transfections were carried with Dharmafect 1 transfection reagent for 3 days before samples were collected.

tag: treatment

value: mock

tag: tissue

value: cervix

tag: cell line

value: HeLa 229

value: 31 years


title: D3051_Saliva_Unaffected_rep1

value: Griffon Bruxellois

tag: line bc

tag: line cd

tag: line bd

tag: line be

tag: line ae

tag: angle 2(caf)

tag: angle 3 (dla)

tag: line ag

tag: angle 4 (ahg)

tag: angle 5 (afh)


title: Tie2cre lineage traced fibroblast SHAM, Biological Replicate 1

tag: cell type

tag: strain

tag: age


title: flash knockdown

description: Gene expression data from RNA extracted from FLASH-depleted cells

source_name: HeLa229 cells siRNA transfected

value: flash knockdown


title: MSC alone_21% Oxygen_s1

tag: tissue source

tag: culture type

value: cultured alone (monoculture)


title: D2931_Saliva_Affected_rep1

tag: breed

tag: Sex

tag: diameter f

tag: line ab

tag: angle 1 (abc)

tag: line fg


title: zeb knock down

description: Gene expression data from RNA extracted from ZEB1-depleted cells

tag: treatment

value: zeb knock down

tag: tissue

tag: cell line