title: Expt. db/db eWAT Replicate 1

description: Biological replicate 1 of 3 db/db eWAT

label_protocol: 100 ng-input two-round RT/IVT RNA amplification protocol

source_name: db/db 10 week #1


title: WD44 H3K4me3 ES_genome tiling

status: Public on Mar 22 2013

type: genomic

city: Seattle

first: Joel

last: Berletch

state: WA

address: 1959 NE Pacific St.

department: Pathology

country: USA

institute: University of Washington

description: NimbleGen genome tiling array 2007-07-27_MM8_TILE_ChIP_10_HX1 was used.

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed. The supplementary GFF files contain the bi-weight mean adjusted log base 2 ratios in MM8 coordinates

molecule: genomic DNA

organism: Mus musculus

source_name: H3K4me3 ChIP DNA from mouse male WD44 ES cells

label_protocol: Amplified ChIP or input DNA were labeled by Cy5 or Cy3 respectively using standard NimbleGen protocol.

growth_protocol: ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for experiments and cell collection.

extract_protocol: 1x10E7 cells were fixed with 1% formaldehyde and lysed in 1 ml of IP buffer (150mM NaCl, 50 mM Tris pH7.5, 5 mM EDTA, 0.5% NP-40, 1.0% Triton X-100). The nuclear pellet was sheared to an average size of 0.5-1 kb by sonication. A 10% of chromatin was saved as the input fraction. ChIP was performed using 5ug antibody . Pull-down chromatin by protein A sepharose beads and input were treated with 0.2M NaCl at 65°C overnight to remove crosslinks. DNA was purified using Qiaquick® PCR purification kit (Qiagen) and amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma) prior to labeling.

treatment_protocol: No treatment

tag: genotype

value: Wild type XY

tag: cell line

value: WD44 ES cell line

tag: strain

value: Derived from male blastocysts from C57B/6J

tag: chip antibody

tag: chip antibody manufacturer

value: Abcam

source_name: ChIP input DNA


title: Recipient cells, no exosomes replicate2

type: RNA

city: Utrecht

first: Bas

middle: van

last: Balkom

address: Heidelberglaan 100

department: Nephrology and Hypertension

country: Netherlands

institute: UMC Utrecht

description: Gene expression not exposed to exosomes

hyb_protocol: cRNA was hybridized using the Agilent Gene Expression Hybridization Kit (5188-5242) according to the manufacturer's guidelines

scan_protocol: Slides were scanned using an Agilent Microarray Scanner (G2565BA).

data_processing: Image analysis was performed using feauture extraction software version 9.5 (Agilent Technologies). The Agilent GE2-v5_95 protocol was applied (default settings)

molecule: total RNA

organism: Homo sapiens

source_name: Recipient cells, no exosomes replicate2

label_protocol: Samples were labeled using the Agilent Low RNA Input Linear Amplification Kit Plus (5188-5340) according to the manufacturer's guidelines

growth_protocol: HMEC were cultured for 6h in medium containing HMEC derived exosomes, HMEC derived exosomes depleted of miR-214 or no exosomes

extract_protocol: RNA was isolated using the MirVana isolation kit (Life Technologies) according to the manufacturer's guidelines

tag: cell type

value: HMEC endothelial cell


title: irs_HZ_8253_MST1_32049

city: Houston

first: Peng

last: Yu

state: TX

address: 1 Baylor Plaza

institute: BCM

description: biological rep 1

hyb_protocol: An 80 uL hybridization cocktail containing Affymetrix spike-in controls and the fragmented, labeled cDNA was loaded onto the GeneChip® Mouse Gene 1.0 ST array. The arrays were hybridized for 17 hours at 45°C, with rotation at 60 rpm on the GeneChip® Hybridization Oven 640. The arrays were then washed and stained with a Streptavidin, R-phycoerythrin conjugate stain on the GeneChip® Fluidics Station 450. Signal amplification was assessed using biotinylated antistreptavidin.

scan_protocol: The stained arrays were scanned on the Affymetrix GeneChip® Scanner 3000.

data_processing: The images were analyzed and quality control metrics recorded using Affymetrix Expression Console software version 3.0.

label: biotin

source_name: WT

label_protocol: The Baylor College of Medicine Genomic and RNA Profiling Core Facility used the Ambion WT Expression Kit protocol and reagents to convert total RNA into sense-strand cDNA. The cDNA is then fragmented and labeled using the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671)

growth_protocol: mouse hippocampus dissected at either 4 weeks of age or 9 weeks of age

extract_protocol: tissue was idssected over ice and snap frozen in liquid nitrogen. Tissue was homogenized in PureZOL and RNA was purified using an Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio Rad).

tag: age

value: 4 weeks

tag: genotype/variation

tag: tissue

value: Hippocampus


title: Con4

city: Munich

first: Karin

last: Weber

address: Veterinärstr. 13

department: Medizinische Kleintierklinik

country: Germany

institute: Zentrum für klinische Tiermedizin

description: miRNA expression profile in the serum of a healthy Doberman Pinscher

hyb_protocol: Microarray analysis was performed using custom-made Agilent miRNA microarrays. Cy3-labeled miRNA was hybridized to the microarrays according the manufacturer’s instructions (User Manual G4170-90011_miRNA_complete_2.3).

scan_protocol: Hybridized and washed slides were scanned at 2 µm resolution with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies).

data_processing: Image processing was performed with Feature Extraction Software 10.7.3.1 (Agilent Technologies).

organism: Canis lupus familiaris

source_name: Serum

label_protocol: Labeling of miRNAs with Cy3-CTP was performed with the miRNA Complete Labeling and Hybridization Kit (Cat.-No. 5190-1934; Agilent Technologies) according the manufacturer’s instructions.

growth_protocol: All dogs were client-owned adult Dobermann Pinschers (Age 7 -11 years) that were presented as patients or for health checks to the clinic of Small Animal Veterinary Medicine, LMU University of Munich, Germany

extract_protocol: Total RNA was isolated from  8 serum samples using Qiazol® Reagent (Qiagen, Hilden Germany) and the miRNeasy Mini Kit (QIAGEN, Valencia, CA, USA) according to the supplementary protocol “Purification of total RNA, including small RNAs, from serum or plasma". Quantity and purity of RNA were measured with a NanoDrop 1000 (PEQLAB Biotechnologie GMBH, Erlangen, Germany).

treatment_protocol: Blood was collected by venipuncture in serum tubes and left to clot for 20 min. The blood was centrifuged at 600g for 5 min and the serum was stored at -80°C until RNA extraction.

tag: sample type

value: serum

tag: disease state

value: healthy


title: PGK12.1ES_Control treated_genome tiling

source_name: KDM6A ChIP DNA from mouse female PGK12.1 ES cells treated with control siRNA

treatment_protocol: Treated with scrambled control siRNA oligos

value: Wild type XX

value: PGK12.1 ES cell line

value: Derived from female blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

value: UTX

value: Bethyl labs


title: Recipient cells with anti-miR-214-exosomes replicate1

description: Gene expression after exposure to miR-214 low exosomes


title: Recipient cells with anti-miR-214-exosomes replicate2


title: PGK12.1 H3K27me3_ES_genome tiling

source_name: H3K27me3 ChIP DNA from mouse female PGK12.1 ES cells


title: WD44 H3K27me3 ES_genome tiling

source_name: H3K27me3 ChIP DNA from mouse male WD44 ES cells


title: Con1


title: PGK12.1 KDM6A_Day15_genome tiling

source_name: KDM6A ChIP DNA from mouse female PGK12.1 ES cells after 15 days of differentiation

growth_protocol: ES cells were differentiated by embryoid body formation and removal of LIF for 15 days. Cells were plated in bacterial dishes for 7 days then were replated onto standard cell culture dishes and grown for 8 days. Cells were collected for ChIP.

value: αUTX (K. Ge)


title: Aged Gastroc Muscle Replicate 5

city: West Point

first: I-Ming

last: Wang

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck Research Lab

description: Aged Muscle Replicate 5

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin

organism: Rattus norvegicus

source_name: Diseased

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

growth_protocol: Five 24-month old male Sprague-Dawley rats served as the aged group to compare with five 6-month old male Sprague-Dawley rats as young controls.  All animals were housed in a 12:12 hour light cycle with ad lib food and water for at least a month (Age at necropsy was 28 months and 7 months for old and young, respectively). Animals were euthanized with CO2 and exanguination and the whole hind limb lateral gastrocnemius muscle from the left leg was dissected and snap frozen in liquid nitrogen.

extract_protocol: Total RNA was extracted from muscle using Qiagen RNeasy Midi kit as described by the manufacturer. Samples were treated with DNaseI on-column (Qiagen) for 30 minutes. RNA concentration was measured using a NanoDrop ND-1000 and RNA integrity was determined with a 2100 Bioanalyzer.

value: Muscle

value: Sprague Dawley

value: 24 mo


title: PGK12.1 KDM6A_Day2_genome tiling

source_name: KDM6A ChIP DNA from mouse female PGK12.1 ES cells after 2 days of differentiation

growth_protocol: ES cells were differentiated by embryoid body formation and removal of LIF for 2 days. Cells were plated in bacterial dishes without LIF to form embryoid bodies. Cells were collected for ChIP.


title: Expt. db/db islet Replicate 1

description: Biological replicate 1 of 5 db/db islet

hyb_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

scan_protocol: Scanned on an Agilent G2565AA scanner. 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: Control 9 Weeks

growth_protocol: Pancreatic islets were isolated from the db/db and the lean control (db/+) mice at 9-week of age. The db/db mice are obese, mildly hyperglycemic and severely hyperinsulinemic at 6 week, representing the compensating stage.  Whereas at 9 week of age, the db/db mice become severely hyperglycemic and only modestly hyperinsulinemic (significantly declined from the 6-wk levels), indicating the de-compensation of beta-cell to the insulin resistant state.

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

value: 9 weeks

value: pancreatic islet

value: db/+

tag: genetic background

source_name: db/db 9 week #1

value: db/db


title: Expt. db/db islet Replicate 3

description: Biological replicate 3 of 5 db/db islet

source_name: db/db 9 week #3


title: DoCM8

description: miRNA expression profile in the serum of a Doberman Pinscher suffering from dilated cardiomyopathy

value: diseased


title: DoCM5


title: Con3


title: Control db/+ eWAT Replicate 2

description: Biological replicate 2 of 3 db/+ eWAT

source_name: Control 10 Weeks

growth_protocol: Adipose tissues (eWAT) were isolated from the db/db and the lean control (db/+) mice at 10-week of age. The db/db mice are obese, severely hyperglycemic and only modestly hyperinsulinemic at 10 weeks of age.

value: 10 weeks

value: eWAT

source_name: db/+ 10 week #2


title: Aged Gastroc Muscle Replicate 2

description: Aged Muscle Replicate 2


title: Aged Gastroc Muscle Replicate 4

description: Aged Muscle Replicate 4


title: DoCM7

value: serum


title: Aged Gastroc Muscle Replicate 1

description: Aged Muscle Replicate 1


title: Control db/+ islet Replicate 5

description: Biological replicate 5 of 5 db/+ islet

source_name: db/+ 9 week #5


title: DoCM6


title: Control db/+ eWAT Replicate 1

description: Biological replicate 1 of 3 db/+ eWAT

source_name: db/+ 10 week #1


title: Expt. db/db islet Replicate 2

description: Biological replicate 2 of 5 db/db islet

source_name: db/db 9 week #2


title: PGK12.1ES_Kdm6a siRNA treated_genome tiling

source_name: KDM6A ChIP DNA from mouse female PGK12.1 ES cells treated with Kdm6a specific siRNA

treatment_protocol: Treated with Kdm6a specific siRNA oligos

value: Wild type XX

tag: treatment

value: Kdm6a siRNA

source_name: ChIP input DNA


title: Control db/+ islet Replicate 4

description: Biological replicate 4 of 5 db/+ islet

source_name: db/+ 9 week #4


title: Control Young Gastrocnemius Muscle Replicate 5

description: Control Young Muscle Replicate 5

source_name: Control

value: 6 mo


title: Expt. db/db islet Replicate 4

description: Biological replicate 4 of 5 db/db islet

source_name: db/db 9 week #4


title: Control Young Gastrocnemius Muscle Replicate 4

description: Control Young Muscle Replicate 4


title: Control db/+ islet Replicate 3

description: Biological replicate 3 of 5 db/+ islet

source_name: db/+ 9 week #3


title: Control db/+ islet Replicate 1

description: Biological replicate 1 of 5 db/+ islet

source_name: db/+ 9 week #1


title: Control Young Gastrocnemius Muscle Replicate 2

description: Control Young Muscle Replicate 2


title: Control Young Gastrocnemius Muscle Replicate 3

description: Control Young Muscle Replicate 3


title: Expt. db/db islet Replicate 5

description: Biological replicate 5 of 5 db/db islet

source_name: db/db 9 week #5


title: Expt. ob/ob eWAT Replicate 1

description: Expt. ob/ob eWAT Replicate 1

source_name: Control ob/+ eWAT Replicates combined

growth_protocol: Adipose tissues (eWAT) were isolated from the ob/ob obese and the lean control (ob/+) mice at 9-week of age.

value: ob/+

source_name: Expt. ob/ob eWAT Replicate 1

value: ob/ob


title: CGN-treated skin Replicate 2

description: CGN-treated skin replicate 2

source_name: Diseased

growth_protocol: Four rats were treated with carrageenan (CGN) at 30 mg/kg body weight (mpk) and then compared to 5 control animals without CGN treatment. 3 hrs post-CGN paw edema and hyperalgesia to mechanical pressure were measured. Rats were euthanized 4 hr post-CGN for skin tissue harvesting.

extract_protocol: Total RNA was extracted from skin using Qiagen RNeasy Midi kit as described by the manufacturer. Samples were treated with DNaseI on-column (Qiagen) for 30 minutes. RNA concentration was measured using a NanoDrop ND-1000 and RNA integrity was determined with a 2100 Bioanalyzer.

value: Skin

value: Carrageenan


title: Control non-treated skin Replicate 5

description: Control non-treated skin Replicate 5

value: Sprague Dawley

value: control


title: Control ob/+ eWAT Replicate 1

description: Control ob/+ eWAT Replicate 1

value: 9 weeks

source_name: Control ob/+ eWAT Replicate 1


title: Control db/+ islet Replicate 2

description: Biological replicate 2 of 5 db/+ islet

source_name: Control 9 Weeks

value: pancreatic islet

source_name: db/+ 9 week #2


title: TGFb1-Tg lung Replicate 3

description: TGFb1-Tg lung Replicate 3

source_name: Control B6J WT Replicates combined

growth_protocol: 8-10 week old transgenic (Tg) mice and wild-type (WT) littermate controls were used in all experiments. To induce expression of active hTGF-β1 in the lungs of transgenic mice, doxycycline (DOX) was added to the drinking water at 1 mg/ml.  Lungs were harvested at various time points, ranging from 2 to 14 days, following the addition of DOX to the drinking water (i.e. hTGF-β1 induction).

value: wild type

value: Lung

source_name: TGFb1-Tg lung Replicate 3

value: TGFb1-Tg overexpression


title: TGFb1-Tg lung Replicate 4

description: TGFb1-Tg lung Replicate 4

value: 10 weeks

source_name: TGFb1-Tg lung Replicate 4


title: Expt. ob/ob eWAT Replicate 2

description: Expt. ob/ob eWAT Replicate 2

value: eWAT

source_name: Expt. ob/ob eWAT Replicate 2


title: Control ob/+ eWAT Replicate 2

description: Control ob/+ eWAT Replicate 2

source_name: Control ob/+ eWAT Replicate 2


title: Control non-treated skin Replicate 4

description: Control non-treated skin Replicate 4


title: Control Young Gastrocnemius Muscle Replicate 1

description: Control Young Muscle Replicate 1

value: Muscle


title: Expt. ob/ob eWAT Replicate 3

description: Expt. ob/ob eWAT Replicate 3

source_name: Expt. ob/ob eWAT Replicate 3


title: CGN-treated skin Replicate 3

description: CGN-treated skin replicate 3


title: CGN-treated skin Replicate 1

description: CGN-treated skin replicate 1


title: TGFb1-Tg lung Replicate 2

description: TGFb1-Tg lung Replicate 2

source_name: TGFb1-Tg lung Replicate 2


title: Control B6J WT Replicate 4

description: Control B6J WT Replicate 4

source_name: Control B6J WT Replicate 4


title: PGK12.1 H3K4me3 ES_genome tiling

source_name: H3K4me3 ChIP DNA from mouse female PGK12.1 ES cells

value: Wild type XX

value: PGK12.1 ES cell line

value: Derived from female blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

value: Abcam

source_name: ChIP input DNA


title: wt (ACY044)+Rapamycin 200nM: 251632210103-1

city: tucson

first: jeremy

last: worley

state: az

address: 1007 e. lowell st.

department: MCB

institute: university of arizona

description: Sample 55

hyb_protocol: as described in capaldi et al (2008). Nature Genetics 40, 1300 - 1306 (2008). doi:10.1038/ng.235

scan_protocol: scanned on genepix 4000b

data_processing:
images were quantified with genepix pro software version 6.1.
background subtraction, loess normalization, and primary filtering performed using stanford microarray database version 2.14 (Nucl. Acids Res. (2007) 35 (suppl 1): D766-D770. doi: 10.1093/nar/gkl1019).  Secondary filtering using Cluster 3.0. Filtered: 1) regression correlation >0.6 AND mean intensity/median background intensity is >1.5-fold in EITHER channel. 2) at least 1 observation with abs(val) >=1.6 (3-fold)
normalized log2 ratio (cy5/cy3). Unless otherwise stated (in the Description column), arrays are test/reference.

organism: Saccharomyces cerevisiae

source_name: 200nM rap_20min


title: TGFb1-Tg lung Replicate 1

description: TGFb1-Tg lung Replicate 1

source_name: TGFb1-Tg lung Replicate 1


title: Control ob/+ eWAT Replicate 3

description: Control ob/+ eWAT Replicate 3

source_name: Control ob/+ eWAT Replicates combined

value: ob/+

source_name: Control ob/+ eWAT Replicate 3


title: CGN-treated skin Replicate 4

description: CGN-treated skin replicate 4

source_name: Diseased

value: Skin


title: Control non-treated skin Replicate 3

description: Control non-treated skin Replicate 3

source_name: Control


title: Aged Gastroc Muscle Replicate 3

description: Aged Muscle Replicate 3

value: 24 mo


title: Control non-treated skin Replicate 2

description: Control non-treated skin Replicate 2

value: Sprague Dawley


title: Control non-treated skin Replicate 1

description: Control non-treated skin Replicate 1

value: control


title: Vip1D487A+Osmotic Stress KCl 0.375: 251632210637-8

description:
251632210637-8 is a dye swap
Sample 54

source_name: KCl stress 0.375M_20min

label_protocol: as described in capaldi et al (2008). Nature Genetics 40, 1300 - 1306 (2008). doi:10.1038/ng.235


title: Vip1D487A: 251632210637-7

description:
251632210637-7 is a dye swap
Sample 53

extract_protocol: as described in capaldi et al (2008). Nature Genetics 40, 1300 - 1306 (2008). doi:10.1038/ng.235


title: 2hours_rph1D_untreated_biologicalreplicateB

city: New Haven

first: Elizabeth

middle: Anne

last: Schroeder

state: CT

address: 310 Cedar St. BML 369

department: Genetics

institute: Yale University

description: This sample is from DBY2006 rph1Δ collected at OD 1.0. It is the second of two biological replicates

hyb_protocol: Performed according to the manufacturer’s protocol

data_processing: Raw data were RMA normalized using Nimblescan software. Probe expression values were used to determine fold-change and filtered to significantly induced and repressed probe lists (p≤0.01 as determined by student’s t- test). Gene lists were generated based on the occurrence of at least two probes for a particular gene present exclusively in induced or repressed probe lists.

source_name: Saccharomyces cerevisiae rph1Δ, OD 1.0, treated with 100% ethanol for 2 hours

extract_protocol: RNA extraction and purification were performed as described (Bonawitz et al., 2008) from wild-type DBY2006 and rph1Δ cultures grown for 24 hours after addition of 50 μM menadione or ethanol. RNA quality bioanalysis, cDNA synthesis, and hybridization to a Roche/NimbleGen 12x135K array were performed in collaboration with the Yale University W.M. Keck Foundation Biotechnology Resource Laboratory according to the manufacturer’s protocol. Two independent biological replicates were prepared for each sample, and hybridization was performed in duplicate to generate technical replicates.

value: DBY2006, rph1::URA3

tag: phenotype

value: does not adapt to mtROS


title: Control B6J WT Replicate 2

description: Control B6J WT Replicate 2

source_name: Control B6J WT Replicates combined

value: wild type

source_name: Control B6J WT Replicate 2


title: 2hours_rph1D_menadione_biologicalreplicateA

description: This sample is from DBY2006 rph1Δ collected at OD 1.0. It is the first of two biological replicates

scan_protocol: Performed according to the manufacturer’s protocol

source_name: Saccharomyces cerevisiae rph1Δ, OD 1.0, treated with 50 μM menadione for 2 hours


title: Rpd3ibs+Osmotic Stress 0.375M KCl: 251632210533-4

description: Sample 52


title: Control B6J WT Replicate 1

description: Control B6J WT Replicate 1

value: Lung

source_name: Control B6J WT Replicate 1


title: 2hours_rph1D_menadione_biologicalreplicateB

label_protocol: Performed according to the manufacturer’s protocol


title: Rpd3ibs: 251632210533-3

description: Sample 51


title: snt1+Osmotic Stress KCl 0.375M: 251632210533-2

description: Sample 50

value: snt1 mutant


title: Vip1D487A+Osmotic Stress KCl 0.375: 251632210531-8

description: Sample 46


title: Rpd3ibs+Osmotic Stress 0.375M KCl: 251632210532-8

description: Sample 48


title: Rpd3ibs: 251632210532-7

description: Sample 47


title: OVA-challenged lung Replicate 5

description: OVA-challenged lung Replicate 5

source_name: Control PBS-treated lung Replicates combined

growth_protocol: Lungs were harvested from PBS- or OVA-challenged mice at ~12-week of age. The OVA-challenged mice showed increased inflammation in lung with airway hyperresponsiveness and increased IgE in sera.

value: PBS

value: 12 weeks

value: BALB/c

source_name: OVA-challenged lung Replicate 5

tag: gennetic background

value: ovalbumin


title: OVA-challenged lung Replicate 4

description: OVA-challenged lung Replicate 4

source_name: OVA-challenged lung Replicate 4


title: Control B6J WT Replicate 3

description: Control B6J WT Replicate 3

value: 10 weeks

source_name: Control B6J WT Replicate 3


title: OVA-challenged lung Replicate 1

description: OVA-challenged lung Replicate 1

source_name: OVA-challenged lung Replicate 1


title: OVA-challenged lung Replicate 3

description: OVA-challenged lung Replicate 3

source_name: OVA-challenged lung Replicate 3


title: Control PBS-treated lung Replicate 4

description: Control PBS-treated lung Replicate 4

source_name: Control PBS-treated lung Replicate 4


title: Vip1D487A: 251632210531-7

description: Sample 45


title: Control PBS-treated lung Replicate 3

description: Control PBS-treated lung Replicate 3

source_name: Control PBS-treated lung Replicate 3


title: 24hours_rph1D_menadione_biologicalreplicateA_technicalreplicate2

description: This sample is from DBY2006 rph1Δ collected at OD 3.5. It is the first of two biological and second of two techical replicates

source_name: Saccharomyces cerevisiae rph1Δ, OD 3.5, treated with 50 μM menadione from OD 0.5-2.0


title: 2hours_wildtype_untreated_biologicalreplicateA

description: This sample is from wild-type DBY2006 collected at OD 1.0. It is the first of two biological replicates

source_name: Saccharomyces cerevisiae DBY2006, OD 1.0, treated with 100% ethanol for 2 hours

value: wild-type DBY2006

value: wild-type


title: 2hours_rph1D_untreated_biologicalreplicateA


title: 24hours_rph1D_menadione_biologicalreplicateA_technicalreplicate1

description: This sample is from DBY2006 rph1Δ collected at OD 3.5. It is the first of two biological and first of two techical replicates


title: snt1+Osmotic Stress KCl 0.375M: 251632210531-6

description: Sample 44


title: 2hours_wildtype_untreated_biologicalreplicateB

description: This sample is from wild-type DBY2006 collected at OD 1.0. It is the second of two biological replicates


title: 24hours_rph1D_menadione_biologicalreplicateB_technicalreplicate1

description: This sample is from DBY2006 rph1Δ collected at OD 3.5. It is the second of two biological and first of two techical replicates


title: kcs1/vip1+H2O2 v. kcs1/vip1: 251632210465-2

description: Sample 40

value: kcs1/vip1 mutant


title: kcs1/vip1+KCl+Rap v. kcs1/vip1+KCl: 251632210465-3

description: Sample 41

source_name: 200nM Rapamycin +KCl 0.375M_20min


title: kcs1: 251632210465-4

description: Sample 42

value: kcs1 mutant


title: snt1: 251632210531-5

description: Sample 43


title: 2hours_wildtype_menadione_biologicalreplicateA

source_name: Saccharomyces cerevisiae DBY2006, OD 1.0, treated with 50 μM menadione for 2 hours


title: 24hours_rph1D_untreated_biologicalreplicateB_technicalreplicate2

description: This sample is from DBY2006 rph1Δ collected at OD 3.5. It is the second of two biological and second of two techical replicates

source_name: Saccharomyces cerevisiae rph1Δ, OD 3.5, treated with 100% ethanol from OD 0.5-2.0


title: C57BL6 control Replicate 3

description: Biological replicate 3 of 3 C57BL6 WT aorta

source_name: 16 Week HFD C57BL6 Control

growth_protocol: Aortas were isolated from the ApoE KO and control C57BL6 mice 16 weeks after feeding with HFD (HFD started at 8-week of age). The aorta of the ApoE KO mice showed atheroslerotic lesions whereas no lesion was observed with C57BL6 mice.

value: high fat diet

value: 24 weeks

value: aorta

source_name: db/+ 9 week #5

value: C57BL6 db/+


title: C57BL6 control Replicate 1

description: Biological replicate 1 of 3 C57BL6 WT aorta

source_name: db/+ 9 week #4


title: 24hours_rph1D_menadione_biologicalreplicateB_technicalreplicate2

value: DBY2006, rph1::URA3

value: does not adapt to mtROS


title: 24hours_rph1D_untreated_biologicalreplicateB_technicalreplicate1


title: wt+Oxidative Stress 0.4mM H2O2: 251632210465-1

description: Sample 39

value: wild type


title: kcs1/vip1+Heat Shock 42C: 251632210462-8

description: Sample 37

source_name: heat shock 42C_20min


title: 24hours_rph1D_untreated_biologicalreplicateA_technicalreplicate1


title: 24hours_rph1D_untreated_biologicalreplicateA_technicalreplicate2


title: C57BL6 control Replicate 2

description: Biological replicate 2 of 3 C57BL6 WT aorta


title: wt+Heat Shock 42C: 251632210464-5

description: Sample 38


title: Control PBS-treated lung Replicate 1

description: Control PBS-treated lung Replicate 1

source_name: Control PBS-treated lung Replicates combined

value: Lung

source_name: Control PBS-treated lung Replicate 1


title: ApoE KO aorta Replicate 3

description: Biological replicate 3 of 3 ApoE KO aorta

source_name: db/+ 9 week #3

value: ApoE KO

value: 32 weeks


title: ApoE KO aorta Replicate 2

description: Biological replicate 2 of 3 ApoE KO aorta

source_name: db/+ 9 week #2


title: 2hours_wildtype_menadione_biologicalreplicateB


title: ApoE KO aorta Replicate 1

description: Biological replicate 1 of 3 ApoE KO aorta

source_name: db/+ 9 week #1


title: 24hours_wildtype_menadione_biologicalreplicateB_technicalreplicate2

description: This sample is from wild-type DBY2006 collected at OD 3.5. It is the second of two biological and second of two techical replicates

source_name: Saccharomyces cerevisiae DBY2006, OD 3.5, treated with 50 μM menadione from OD 0.5-2.0


title: 24hours_wildtype_menadione_biologicalreplicateB_technicalreplicate1

description: This sample is from wild-type DBY2006 collected at OD 3.5. It is the second of two biological and first of two techical replicates


title: 24hours_wildtype_menadione_biologicalreplicateA_technicalreplicate2

description: This sample is from wild-type DBY2006 collected at OD 3.5. It is the first of two biological and second of two techical replicates


title: 24hours_wildtype_menadione_biologicalreplicateA_technicalreplicate1

description: This sample is from wild-type DBY2006 collected at OD 3.5. It is the first of two biological and first of two techical replicates


title: kcs1/vip1+Oxidative Stress 0.4mM H2O2: 251632210462-7

description: Sample 36


title: kcs1/vip1+Osmotic Stress v. kcs1/vip1: 251632210462-5

description: Sample 35

source_name: KCl stress 0.375M_20min


title: kcs1/vip1: 251632210394-5

description: Sample 34


title: Expt. Ipsi DRG Replicate 3

description: Biological replicate 3 of 4 spinal nerve-ligated DRG

source_name: Control Contra DRG Pool

growth_protocol: Rat dorsal root ganglia (DRG) at 7 days following spinal nerve ligation that elicits neuropathic pain or sham-operation were profiled. 4 DRG samples per group each pooled from 2 animals were included in the analysis.

extract_protocol: Total RNA was extracted from DRG using Qiagen RNeasy Midi kit as described by the manufacturer. Samples were treated with DNaseI on-column (Qiagen) for 30 minutes. RNA concentration was measured using a NanoDrop ND-1000 and RNA integrity was determined with a 2100 Bioanalyzer.

value: control

value: Dorsal root ganglion (DRG)

value: Sprague Dawley

source_name: Expt. Ipsi DRG Replicate 3

value: spinal nerve ligation


title: Expt. Ipsi DRG Replicate 1

description: Biological replicate 1 of 4 spinal nerve-ligated DRG

source_name: Expt. Ipsi DRG Replicate 1


title: 5LO KO atherogenic Liver Replicate 4

description: 5LO KO Athero Liver Replicate 4

source_name: B6 Liver Athero Pool (n=4)

growth_protocol: Wild type B6 and 5-lipoxygenase knockout mice that have been on a chow and high fat/cholesterol/cholate diet for 16 weeks.  Wild type controls on normal and atherogenic chow were also sacrificed.

value: atherogenic chow

value: 20 weeks

value: Liver

value: B6 WT

source_name: 5LO KO Athero Liver Replicate 4

value: B6 5LO KO


title: kcs1+Osmotic Stress KCl 0.375M: 251632210393-6

description: Sample 30

value: kcs1 mutant


title: Control Contra DRG Replicate 3

description: Biological replicate 3 of 4 sham-operated DRG

source_name: Control Contra DRG Replicate 3


title: 24hours_wildtype_untreated_biologicalreplicateB_technicalreplicate2

source_name: Saccharomyces cerevisiae DBY2006, OD 3.5, treated with 100% ethanol from OD 0.5-2.0

value: wild-type DBY2006

value: wild-type


title: Expt. Ipsi DRG Replicate 2

description: Biological replicate 2 of 4 spinal nerve-ligated DRG

source_name: Expt. Ipsi DRG Replicate 2


title: kcs1/vip1+Osmotic Stress: 251632210393-7

description: Sample 31

value: kcs1/vip1 mutant


title: vip1+osmotic stress KCl 0.375M: 251632210394-4

description: Sample 33

value: wild type

value: vip1 mutant


title: Control Contra DRG Replicate 4

description: Biological replicate 4 of 4 sham-operated DRG

source_name: Control Contra DRG Replicate 4


title: Expt. Ipsi DRG Replicate 4

description: Biological replicate 4 of 4 spinal nerve-ligated DRG

source_name: Expt. Ipsi DRG Replicate 4


title: ipk1+Osmotic Stress KCl 0.375M: 251632210393-8

description: Sample 32

value: ipk1 mutant


title: 5LO KO atherogenic Liver Replicate 3

description: 5LO KO Athero Liver Replicate 3

source_name: 5LO KO Athero Liver Replicate 3


title: Control Contra DRG Replicate 2

description: Biological replicate 2 of 4 sham-operated DRG

source_name: Control Contra DRG Replicate 2


title: 5LO KO atherogenic Liver Replicate 1

description: 5LO KO Athero Liver Replicate 1

source_name: 5LO KO Athero Liver Replicate 1


title: 5LO KO atherogenic Liver Replicate 2

description: 5LO KO Athero Liver Replicate 2

source_name: 5LO KO Athero Liver Replicate 2


title: 24hours_wildtype_untreated_biologicalreplicateB_technicalreplicate1


title: 5LO KO atherogenic Liver Replicate 5

description: 5LO KO Athero Liver Replicate 5

source_name: 5LO KO Athero Liver Replicate 5


title: 24hours_wildtype_untreated_biologicalreplicateA_technicalreplicate2


title: 24hours_wildtype_untreated_biologicalreplicateA_technicalreplicate1


title: Untreated PBMC - repeat 4

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: No additional information.

hyb_protocol: Hybridization Protocol Other: n/a

scan_protocol: Scanning Protocol Other: n/a

data_processing:
Data Processing Protocol
Calculation Method: Data was processed using the software RQ Manager 1.2 from Applied Biosystems. The endogenous control was small non-coding RNA (SNO) RNAU48. (delta)Ct = normalized Ct = Ctsample - CtRNAU48. For statistical analysis, (delta)Ct was log2 transformed. The RQ (relative quantification) was calculated as follows: RQ = (delta)(delta)Ct = (delta)Cttreated sample - (delta)Ctuntreated sample, followed by -log2 transformation (2-(delta)(delta)Ct).

label: FAM

source_name: Untreated PBMC

label_protocol:
Sample Labeling Protocol
Label amount: 100 ng
Other: 100 ng of total RNA was reverse transcribed according to ABI microRNA TLDA Reverse Transcription Reaction protocol. Samples were diluted 62.5 fold and loaded onto each port of the TLDA.

extract_protocol:
Sample Extraction Protocol
Other: Total RNA (with microRNA) was isolated using the miRNeasy mini kit (Qiagen, Valencia, CA).

treatment_protocol:
Treatment time: 48 hours
In-vitro treatment: Human PBMC (peripheral blood mononuclear cells) were left untreated for 48hrs.

value: Blood

value: peripheral blood mononuclear cells (PBMC)

tag: pbmc treatment

value: Untreated


title: Untreated PBMC - repeat 3

description: No additional information.


title: Control Contra DRG Replicate 1

description: Biological replicate 1 of 4 sham-operated DRG

value: control

value: Dorsal root ganglion (DRG)

value: Sprague Dawley

source_name: Control Contra DRG Replicate 1


title: arg82+Osmotic Stress KCl 0.375M: 251632210393-5

description: Sample 29

source_name: KCl stress 0.375M_20min

value: arg82 mutant


title: Untreated PBMC - repeat 2

description: No additional information.


title: Untreated PBMC - repeat 1

description: No additional information.


title: snt1: 251632210533-1

description: Sample 49

value: snt1 mutant


title: MEF HMGB1+/+ Treated PBMC - repeat 4

description: No additional information.

source_name: MEF HMGB1+/+ Treated PBMC

treatment_protocol:
Treatment type: stress
Treatment time: 48 hours
In-vitro treatment: Human PBMC (peripheral blood mononuclear cells) were exposed to conditioned media from serum-starved and glucose-deprived and heat shocked HMGB1+/+ MEF cells (mouse embryonic fibroblast cells). 2-3x(10)6 of MEF cells (HMGB1+/+) were seeded in 20 cm diameter plates in 10% FBS in IMDM (supplemented with Pen/Strep) 2 days before adding RPMI without glucose. This resulted in about 9 million cells/cell type/plate after 2 days. Two days later, the plates were washed twice with 1xPBS and 20ml of RPMI without glucose was added to each plate. The cells were incubated for 24hrs. After 24hrs, the RPMI without glucose from each plate was collected, and centrifuged at 400g for 5 minutes. To 20 ml of RPMI without glucose, 10% FBS (v/v) (2ml of stock serum), 0.2ml of glucose solution (from 100mg/ml stock) as well as 0.2ml of Penicillin/Streptomycin stock solution was added. The conditioned media were stored on ice until it was added to 2 million of freshly isolated human PBMCs per well in a 6-well plate for 48hrs. Heat shock was carried out at 42C for an additional 2hrs after incubation of MEF cells in serum and glucose-free RPMI. PBMCs were pre-treated for 30 minutes with 50uM of glybenclamide (Glyb) before incubation with conditioned media.


title: MEF HMGB1+/+ Treated PBMC - repeat 3

description: No additional information.

value: conditioned media from serum-starved and glucose-deprived and heat shocked HMGB1+/+ MEF cells


title: rpd3+Osmotic Stress 0.375M KCl: 251632210393-4

description: Sample 28


title: rpd3: 251632210393-3

description: Sample 27


title: MEF HMGB1+/+ Treated PBMC - repeat 2

description: No additional information.


title: kcs1/vip1+KCl v. kcs1/vip1, osmotic stress 0.375M KCl: 251632210288-2

description: Sample 22


title: MEF HMGB1+/+ Treated PBMC - repeat 1

description: No additional information.


title: ipk1: 251632210288-5

description: Sample 23


title: kcs1/vip1+Osmotic Stress: 251632210288-8

description: Sample 26


title: ipk1+Osmotic Stress KCl 0.375M: 251632210288-6

description: Sample 24


title: kcs1/vip1: 251632210288-7

description: Sample 25


title: kcs1/vip1+0.375M KCl + Rapamycin 200nM: 251632210288-1

description: Sample 21

source_name: 200nM Rapamycin + KCl 0.375M_20min


title: 5LO KO Chow Liver Replicate 2

description: 5LO KO Chow Liver Replicate 2

source_name: B6 Liver Chow Pool (n=5)

value: normal chow

value: 20 weeks

value: Liver

value: B6 WT

source_name: 5LO KO Chow Liver Replicate 2

value: B6 5LO KO


title: MEF HMGB1-/- Treated PBMC - repeat 4

description: No additional information.

source_name: MEF HMGB1-/- Treated PBMC

treatment_protocol:
Treatment type: stress
Treatment time: 48 hours
In-vitro treatment: Human PBMC (peripheral blood mononuclear cells) were exposed to conditioned media from serum-starved and glucose-deprived and heat shocked HMGB1-/- MEF cells (mouse embryonic fibroblast cells). 2-3x(10)6 of MEF cells (HMGB1-/-) were seeded in 20 cm diameter plates in 10% FBS in IMDM (supplemented with Pen/Strep) 2 days before adding RPMI without glucose. This resulted in about 9 million cells/cell type/plate after 2 days. Two days later, the plates were washed twice with 1xPBS and 20ml of RPMI without glucose was added to each plate. The cells were incubated for 24hrs. After 24hrs, the RPMI without glucose from each plate was collected, and centrifuged at 400g for 5 minutes. To 20 ml of RPMI without glucose, 10% FBS (v/v) (2ml of stock serum), 0.2ml of glucose solution (from 100mg/ml stock) as well as 0.2ml of Penicillin/Streptomycin stock solution was added. The conditioned media were stored on ice until it was added to 2 million of freshly isolated human PBMCs per well in a 6-well plate for 48hrs. Heat shock was carried out at 42C for an additional 2hrs after incubation of MEF cells in serum and glucose-free RPMI. PBMCs were pre-treated for 30 minutes with 50uM of glybenclamide (Glyb) before incubation with conditioned media.


title: Control B6 atherogenic Liver Replicate 3

description: Control B6 Athero Liver Replicate 3

source_name: B6 Liver Athero Pool (n=4)

value: atherogenic chow

source_name: Control B6 Athero Liver Replicate 3


title: wt+Oxidative Stress 0.4mM H2O2: 251632210259-6

description: Sample 20

value: wild type


title: 5LO KO Chow Liver Replicate 3

description: 5LO KO Chow Liver Replicate 3

source_name: 5LO KO Chow Liver Replicate 3


title: 5LO KO Chow Liver Replicate 5

description: 5LO KO Chow Liver Replicate 5

source_name: 5LO KO Chow Liver Replicate 5


title: 5LO KO Chow Liver Replicate 1

description: 5LO KO Chow Liver Replicate 1

source_name: 5LO KO Chow Liver Replicate 1


title: Control B6 atherogenic Liver Replicate 4

description: Control B6 Athero Liver Replicate 4

source_name: Control B6 Athero Liver Replicate 4


title: kcs1/vip1+Oxidative Stress 0.4mM H2O2: 251632210259-5

description: Sample 19

value: kcs1/vip1 mutant


title: 5LO KO Chow Liver Replicate 4

description: 5LO KO Chow Liver Replicate 4

source_name: 5LO KO Chow Liver Replicate 4


title: kcs1/vip1+ KCl + Rap v. kcs1/vip1+KCl : 251632210259-2

description: Sample 18

source_name: 200nM Rapamycin +KCl 0.375M_20min


title: Control B6 Chow Liver Replicate 5

description: Control B6 Chow Liver Replicate 5

source_name: Control B6 Chow Liver Replicate 5


title: MEF HMGB1-/- Treated PBMC - repeat 2

description: No additional information.

value: Blood

value: conditioned media from serum-starved and glucose-deprived and heat shocked HMGB1-/- MEF cells


title: MEF HMGB1-/- Treated PBMC - repeat 1

description: No additional information.

value: peripheral blood mononuclear cells (PBMC)


title: LPS-Treated PBMC - repeat 4

description: No additional information.

source_name: LPS-Treated PBMC

treatment_protocol:
Treatment type: compound
Agent: Lipopolysaccharide (LPS)
Treatment dose: 100 ng/ml
Treatment time: 48 hours
In-vitro treatment: Human PBMC (peripheral blood mononuclear cells) were stimulated with LPS (Lipopolysaccharide) (LPS, Serotype O55:B5, Sigma) at 100ng/ml for 48 hours.

value: LPS


title: kcs1+Osmotic Stress KCl 0.375M: 251632210250-8

description: Sample 17

value: kcs1 mutant


title: Control B6 Chow Liver Replicate 3

description: Control B6 Chow Liver Replicate 3

source_name: Control B6 Chow Liver Replicate 3


title: OVA-challenged lung Replicate 2

description: OVA-challenged lung Replicate 2

source_name: Control PBS-treated lung Replicates combined

value: PBS

value: 12 weeks

value: Lung

value: BALB/c

source_name: OVA-challenged lung Replicate 2

value: ovalbumin


title: Control B6 atherogenic Liver Replicate 2

description: Control B6 Athero Liver Replicate 2

value: 20 weeks

source_name: Control B6 Athero Liver Replicate 2


title: kcs1: 251632210250-7

description: Sample 16


title: LPS-Treated PBMC - repeat 2

description: No additional information.


title: LPS-Treated PBMC - repeat 3

description: No additional information.


title: LPS-Treated PBMC - repeat 1

description: No additional information.


title: Control PBS-treated lung Replicate 2

description: Control PBS-treated lung Replicate 2

source_name: Control PBS-treated lung Replicate 2


title: Control B6 Chow Liver Replicate 2

description: Control B6 Chow Liver Replicate 2

source_name: B6 Liver Chow Pool (n=5)

value: normal chow

value: Liver

source_name: Control B6 Chow Liver Replicate 2


title: arg82: 251632210250-5

description: Sample 14

value: arg82 mutant


title: MEF HMGB1-/- Treated PBMC - repeat 3

description: No additional information.

source_name: MEF HMGB1-/- Treated PBMC


title: arg82+Osmotic Stress KCl 0.375M: 251632210250-6

description: Sample 15

source_name: KCl stress 0.375M_20min


title: Control B6 Chow Liver Replicate 1

description: Control B6 Chow Liver Replicate 1

value: B6 WT

source_name: Control B6 Chow Liver Replicate 1


title: Control B6 atherogenic Liver Replicate 1

description: Control B6 Athero Liver Replicate 1

source_name: B6 Liver Athero Pool (n=4)

value: atherogenic chow

source_name: Control B6 Athero Liver Replicate 1


title: vip1+Osmotic Stress KCl 0.376: 251632210250-2

description: Sample 12

value: wild type

value: vip1 mutant


title: wt (ACY044)+Osmotic Stress 0.375MKCl: 251632210250-3

description: Sample 13


title: vip1: 251632210250-1

description: Sample 11


title: Patient5

city: Paris

first: Danièle

last: Lacasa

address: 15 rue de l'Ecole de Médecine

country: France

institute: INSERM

description: Analysis used preadipocytes with normal breeding ground as control samples for comparison to preadipocytes with inflammatory breeding ground.Biological replicate 5 of 5.

hyb_protocol: Samples were hybridized with Agilent Gene Expression Hybridization Kit and then hybridized for 17 hours at 65°C in a 4 rpm rotary oven. Slides were then washed in buffer 1 and 2, according to manufacturer’s specification.

scan_protocol: Arrays scanned using an GenePix 4000B scanner and GenePix Pro 6.0.1.00 software

data_processing: Data analysis was carried out using the limma package of R software. The mean values from each channel were log2 transformed and normalized using the LOESS algorithm to remove intensity dependent effects within the calculated values. For each patient, dye-swap replicates were combined.

source_name: Normal breeding ground

label_protocol: Total RNA samples were labelled using Agilent low RNA input linear amplification Kit, according to the manufacturer's protocols. 200ng of  total RNA were reversed transcribed by MMLV reverse transcriptase. Amplification and labelling were done by T7-polymerase transcription.  cRNA were labelled with cyanine Cy5 or Cy3-CTP dyes.

growth_protocol: Preadipocytes were cultured in DMEM/F12 medium with 50nm Insulin and 100 nM Rosiglitazone

extract_protocol: Total RNA extracted using Rneasy Mini Kit following manufacturer's instructions (Qiagen,Coutaboeuf, France)

treatment_protocol: Preadipocytes were treated by secreted factors of macrophages for 10 days

value: adipose tissue

value: preadipocytes

tag: protocol

value: control

source_name: Inflammatory breeding ground

value: macrophage treatment


title: vip1: 251632210249-7

description: Sample 9


title: vip1+Osmotic Stress KCl 0.375: 251632210249-8

description: Sample 10


title: Patient1

description: Analysis used preadipocytes with normal breeding ground as control samples for comparison to preadipocytes with inflammatory breeding ground.Biological replicate 1 of 5.


title: arg82+Osmotic Stress KCl 0.375M: 251632210249-6

description: Sample 8


title: Control B6 Chow Liver Replicate 4

description: Control B6 Chow Liver Replicate 4

source_name: Control B6 Chow Liver Replicate 4


title: Expt. LPS-treated liver Replicate 4

description: Biological replicate 4 of 4 LPS-treated liver

source_name: Liver Control Pool

growth_protocol: Four Sprague Dawley rats received either an i.p. injection of lipopolysaccharides (LPS) of 3 mg/kg body weight (n = 4) or vehicle control sodium chloride (SC) 0.9% (n = 4). Animals were sacrificed 24 h after LPS or SC injection.

extract_protocol: Total RNA was extracted from liver using Qiagen RNeasy Midi kit as described by the manufacturer. Samples were treated with DNaseI on-column (Qiagen) for 30 minutes. RNA concentration was measured using a NanoDrop ND-1000 and RNA integrity was determined with a 2100 Bioanalyzer.

value: Not known

value: liver

value: Sprague Dawley

value: control pool

source_name: Expt. LPS-treated liver Replicate 4

value: LPS


title: human iPS cell AD3E211

city: Kyoto

first: Haruhisa

last: Inoue

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

description:
gene expression data
SAMPLE 11

hyb_protocol: We used Gene Expression Hybridization Kit (Agilent) and GE Wash Pack (Agilent), according to the manufacturer's instructions.

scan_protocol: We used G2565BA Microarray Scanner System (Agilent), according to the manufacturer's instructions.

data_processing: Data were analyzed by default analysis settings and global scaling as normalization method of GeneSpring GX7.3.1 software (Agilent)

source_name: iPS cell line

label_protocol: We used Low Inpurt Quick Amp Labeling Kit, One-color (Agilent), according to the manufacturer's instructions.

growth_protocol: human ES or iPS cells were cultivated in Primate ES cell medium (ReproCELL Inc. Japan) with 4 ng/ml basic FGF (Wako Pure Chemicals Industries, Ltd, Japan)

extract_protocol: We used Rneasy (Quiagen) total RNA extraction kit, according to the manufacturer's instructions.

treatment_protocol: Cells were scraped in PBS, and collected by centrifugation of 200 G, 5 minutes.

value: iPS cell line AD3E211


title: Expt. LPS-treated liver Replicate 3

description: Biological replicate 3 of 4 LPS-treated liver

source_name: Expt. LPS-treated liver Replicate 3


title: human iPS cell APP2E22

description:
gene expression data
SAMPLE 9

value: iPS cell line APP2E22


title: human iPS cell AD8K213

description:
gene expression data
SAMPLE 12

value: iPS cell line AD8K213


title: Patient4

description: Analysis used preadipocytes with normal breeding ground as control samples for comparison to preadipocytes with inflammatory breeding ground.Biological replicate 4 of 5.


title: Patient3

description: Analysis used preadipocytes with normal breeding ground as control samples for comparison to preadipocytes with inflammatory breeding ground.Biological replicate 3 of 5.


title: Expt. LPS-treated liver Replicate 2

description: Biological replicate 2 of 4 LPS-treated liver

source_name: Expt. LPS-treated liver Replicate 2


title: arg82: 251632210249-5

description: Sample 7

value: arg82 mutant


title: Patient2

description: Analysis used preadipocytes with normal breeding ground as control samples for comparison to preadipocytes with inflammatory breeding ground.Biological replicate 2 of 5.


title: kcs1/vip1+Osmotic Stress: 251632210246-8

description: Sample 6

value: kcs1/vip1 mutant


title: Expt. LPS-treated liver Replicate 1

description: Biological replicate 1 of 4 LPS-treated liver

source_name: Expt. LPS-treated liver Replicate 1


title: Control non-treated liver Replicate 4

description: Biological replicate 4 of 4 control non-treated liver

source_name: Control non-treated liver Replicate 4


title: kcs1/vip1: 251632210246-7

description: Sample 5


title: wt (ACY044)+Osmotic Stress 0.375MKCl: 251632210246-2

description: Sample 2


title: ipk1: 251632210246-5

description: Sample 3

value: ipk1 mutant


title: ipk1+Osmotic Stress KCl 0.375M: 251632210246-6

description: Sample 4

value: wild type


title: Control non-treated liver Replicate 3

description: Biological replicate 3 of 4 control non-treated liver

source_name: Control non-treated liver Replicate 3


title: Control non-treated liver Replicate 2

description: Biological replicate 2 of 4 control non-treated liver

source_name: Control non-treated liver Replicate 2


title: human iPS cell APP1E311

description:
gene expression data
SAMPLE 8

value: iPS cell line APP1E311


title: human iPS cell 409B2

description:
gene expression data
SAMPLE 5

value: iPS cell line 409B2


title: Control non-treated liver Replicate 1

description: Biological replicate 1 of 4 control non-treated liver

source_name: Control non-treated liver Replicate 1


title: human iPS cell APP1E111

description:
gene expression data
SAMPLE 6

value: iPS cell line APP1E111


title: wt (ACY044)+Osmotic Stress 0.375MKCl: 251632210087-5

description:
251632210087-5 is a dye swap
Sample 1

source_name: KCl stress 0.375M_20min


title: human iPS cell APP1E211

description:
gene expression data
SAMPLE 7

value: iPS cell line APP1E211


title: human iPS cell N117322

description:
gene expression data
SAMPLE 4

value: iPS cell line N117322


title: human iPS cell APP2E26

description:
gene expression data
SAMPLE 10

value: iPS cell line APP2E26


title: human iPS cell N116213

description:
gene expression data
SAMPLE 3

value: iPS cell line N116213


title: Fibroblast

description:
gene expression data
SAMPLE 1

source_name: fibroblast

value: skin fibroblasts


title: human ES cell

description:
gene expression data
SAMPLE 2

source_name: ES cell line

value: ES cells


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB5hr_rep1

status: Public on Mar 21 2013

city: Martinsried/Munich

first: Jörg

last: Renkawitz

address: Am Klopferspitz 18

department: Molecular Cell Biology

institute: Max Planck Institute of Biochemistry

hyb_protocol: standard NimbleGen protocol

scan_protocol: standard NimbleGen protocol

data_processing: Raw signals of all channels in all replicate arrays were normalized and log2 transformed using the 'vsn' package in R/Bioconductor as described ((Prestel et al., 2010) and Tobias Straub Epigenome project PROT43, http://www.epigenesys.eu/).

source_name: Input DNA

label_protocol: standard NimbleGen protocol

growth_protocol: YP lactate

extract_protocol: Chromatin extract preparation and chromatin immunoprecipitation were performed as described in (Kalocsay et al., 2009). Briefly, 200ml cultures of every time point were cross-linked by the addition of 1% (final concentration) formaldehyde for 16 min, and subsequent quenching with 375 mM (final concentration) glycine for at least 10 min. Cells were lysed using Silica beads, the chromatin was enriched by centrifugation and sonicated (water bath sonification: Bioruptor UCD-200, Diagenode) to shear the DNA to an average size of 250-500 bp. After RNase treatment and ligation of linker oligonucleotides, DNA was amplified two times for 14 PCR cycles (using the GenomePlex Whole Genome Amplification (WGA) and reamplifications kits (Sigma)), as described in the Farnham Lab protocol for WGA amplification of DNA (O'Geen et al., 2006). Subsequent labeling of input and IP samples (either Cy3 or Cy5), hybridization to custom-made high-density whole S. cerevisiae genome NimbleGen arrays, array scanning and raw data extraction was done by imaGenes (www.imaGenes-bio.de).

treatment_protocol: Addition of 2% Galactose (Gal-driven HO endonuclease expression) at 0hr; addition of 2% Glucose to shutoff HO endonuclease expression

value: Input DNA

source_name: Rad51 ChIP DNA


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB5hr_rep2

value: Addition of 2% Galactose (Gal-driven HO endonuclease expression) at 0hr; addition of 2% Glucose to shutoff HO endonuclease expression


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB2hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB1hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB2hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB30min_rep2


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATa_DSB5hr_rep1

treatment_protocol: Addition of 2% Galactose (Gal-driven HO endonuclease expression) at 0hr

source_name: Myc ChIP DNA

value: Myc


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATa_DSB2hr_rep2

value: Addition of 2% Galactose (Gal-driven HO endonuclease expression) at 0hr


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATa_DSB5hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB0hr_rep2

treatment_protocol: Without addition of 2% Galactose

value: Without addition of 2% Galactose


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB45min_rep2


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB30min_rep1


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB1hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB45min_rep1


title: Rad51_ChIP_HoChromosomeIII_MATa_DonorProf_DSB0hr_rep1


title: Rad51_ChIP_Sce720kbChromosomeIV_DSB0hr_rep2

growth_protocol: SC-ADE lactate


title: Rad51_ChIP_Sce720kbChromosomeIV_DSB5hr_rep2


title: Rad51_ChIP_Sce720kbChromosomeIV_DSB5hr_rep1


title: Rad51_ChIP_Sce720kbChromosomeIV_DSB0hr_rep1


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATa_DSB0hr_rep2


title: gammaH2A_ChIP_HoChromosomeIII_MATaDeltaRE_DSB5hr_rep2

source_name: gamma-H2A ChIP


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_REchrV_DSB0hr_rep1


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATa_DSB2hr_rep1


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATa_DSB0hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_REchrV_DSB2hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_REchrV_DSB0hr_rep2


title: gammaH2A_ChIP_HoChromosomeIII_MATaDeltaRE_DSB0hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_REchrV_DSB2hr_rep2


title: gammaH2A_ChIP_HoChromosomeIII_MATaDeltaRE_DSB1hr_rep1


title: gammaH2A_ChIP_HoChromosomeIII_MATaDeltaRE_DSB5hr_rep1


title: gammaH2A_ChIP_HoChromosomeIII_MATaDeltaRE_DSB1hr_rep2


title: gammaH2A_ChIP_HoChromosomeIII_MATaDeltaRE_DSB0hr_rep2


title: gammaH2A_ChIP_HoChromosomeIII_MATa_DSB5hr_rep2


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB0hr_DeltaRad54Rdh54_rep2


title: gammaH2A_ChIP_HoChromosomeIII_MATa_DSB1hr_rep2


title: gammaH2A_ChIP_HoChromosomeIII_MATa_DSB5hr_rep1


title: gammaH2A_ChIP_HoChromosomeIII_MATa_DSB1hr_rep1


title: gammaH2A_ChIP_HoChromosomeIII_MATa_DSB0hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB4hr_DeltaRad54Rdh54_rep1


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB4hr_DeltaRad54Rdh54_rep2


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB4hr_DeltaRad54Rdh54_rep1


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB4hr_DeltaRad54Rdh54_rep2


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB0hr_DeltaRad54Rdh54_rep1


title: gammaH2A_ChIP_HoChromosomeIII_MATa_DSB0hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB4hr_DeltaRdh54_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB1hr_DeltaRad54Rdh54_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB0hr_DeltaRdh54_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB1hr_DeltaRdh54_rep1


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB1hr_DeltaRdh54_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB0hr_DeltaRdh54_rep1


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB0hr_DeltaRad54Rdh54_rep1


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB0hr_DeltaRad54Rdh54_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB1hr_DeltaRad54_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB1hr_DeltaRad54Rdh54_rep1


title: iMAIT_day4

city: Kobe

first: Kei

last: Enomoto

state: Hyogo

address: Chuo-ku, Minatojima-Minamimachi

institute: ASUBIO PHARMA CO., LTD.

description: Gene expression of iMAIT cells derived from 1-3D at 4 days after the beginnig of induction

hyb_protocol: 1.65 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 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray 4x44K v2 (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 026652_D_F_20100115) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

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

extract_protocol: RNA was prepared using the RNAeasy column purification (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were harvested with TRIzol (Invitrogen, Carlsbad, CA) and proceeded to RNA purification.


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB1hr_DeltaRad54_rep1


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB4hr_DeltaRad54_rep1


title: iMAIT_day8

description: Gene expression of iMAIT cells derived from 1-3D at 8 days after the beginnig of induction


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB4hr_DeltaRdh54_rep1


title: iMAIT_day0

description: Gene expression of iMAIT cells derived from 1-3D at 0 days after the beginnig of induction


title: iMAIT_day30

description: Gene expression of iMAIT cells derived from 1-3D at 30 days after the beginnig of induction


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB4hr_DeltaRad54_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB0hr_DeltaRad54_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB0hr_DeltaRad54_rep1


title: C4B

description: Gene expression of one of the MAIT-iPSC clones, named C4B

source_name: MAIT-iPS (C4B)

value: MAIT-iPS (C4B)


title: A11

description: Gene expression of one of the MAIT-iPSC clones, named A11

source_name: MAIT-iPS (A11)

value: MAIT-iPS (A11)


title: 4-6D

description: Gene expression of one of the MAIT-iPSC clones, named 4-6D

source_name: MAIT-iPS (4-6D)

value: MAIT-iPS (4-6D)


title: khES3

description: Gene expression of hESC (khES3)

source_name: hESC (khES3)

value: hESC (khES3)


title: 1-3D

description: Gene expression of one of the MAIT-iPSC clones, named 1-3D

source_name: MAIT-iPS (1-3D)

value: MAIT-iPS (1-3D)


title: iMAIT_day20

description: Gene expression of iMAIT cells derived from 1-3D at 20 days after the beginnig of induction


title: C5B

description: Gene expression of one of the MAIT-iPSC clones, named C5B

source_name: MAIT-iPS (C5B)

value: MAIT-iPS (C5B)


title: 2-5D

description: Gene expression of one of the MAIT-iPSC clones, named 2-5D

source_name: MAIT-iPS (2-5D)

value: MAIT-iPS (2-5D)


title: A13

description: Gene expression of one of the MAIT-iPSC clones, named A13

source_name: MAIT-iPS (A13)

value: MAIT-iPS (A13)


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB4hr_ControlForDrad54rdh54_rep2


title: CB-MAIT

description: Gene expression of MAIT cells purified from human cord blood

source_name: CB-MAIT

value: CB-MAIT


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB1hr_ControlForDrad54rdh54_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB1hr_ControlForDrad54rdh54_rep1


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB0hr_ControlForDrad54rdh54_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB4hr_ControlForDrad54rdh54_rep1


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_DSB2hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_DSB5hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATa_DSB2hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_DSB1hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_DSB0hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATa_DSB5hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_DSB5hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATa_DSB5hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_DSB0hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATa_DSB2hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB0hr_ControlForDrad54rdh54_rep1


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_DSB2hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATa_DSB0hr_rep2


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB5hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB5hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATaDeltaRE_DSB1hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATa_DSB0hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB5hr_rep1


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB1hr_rep2


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB2hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATa_DSB1hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB1hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB0hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB1hr_rep1


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB2hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB0hr_rep1


title: Rfa1-9myc_ChIP_HoChromosomeIII_MATalpha_DSB0hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATalpha_DSB2hr_rep1


title: gammaH2A_ChIP_SceChromosomeIV_DSB2hr_rep2


title: gammaH2A_ChIP_SceChromosomeIV_DSB5hr_rep1


title: gammaH2A_ChIP_SceChromosomeIV_DSB2hr_rep1


title: gammaH2A_ChIP_SceChromosomeIV_DSB0hr_rep2


title: Rad51_ChIP_HoChromosomeIII_MATa_DSB1hr_rep2


title: gammaH2A_ChIP_SceChromosomeIV_DSB5hr_rep2


title: gammaH2A_ChIP_SceChromosomeIV_DSB0hr_rep1


title: Rad51_ChIP_Sce491kbChromosomeIV_DSB2hr_rep2


title: Rad51_ChIP_Sce491kbChromosomeIV_DSB5hr_rep2


title: Rfa1-9myc_ChIP_HoChromosomeIV_DSB2hr_rep1


title: Rfa1-9myc_ChIP_HoChromosomeIV_DSB2hr_rep2


title: Rad51_ChIP_HoChromosomeIV_DSB5hr_rep1


title: Rad51_ChIP_Sce491kbChromosomeIV_DSB5hr_rep1


title: Rad51_ChIP_Sce491kbChromosomeIV_DSB2hr_rep1


title: Rfa1-9myc_ChIP_HoChromosomeIV_DSB0hr_rep2


title: Rfa1-9myc_ChIP_HoChromosomeIV_DSB5hr_rep1


title: Rfa1-9myc_ChIP_HoChromosomeIV_DSB0hr_rep1


title: Rad51_ChIP_Sce491kbChromosomeIV_DSB0hr_rep1


title: Rad51_ChIP_Sce491kbChromosomeIV_DSB0hr_rep2


title: Rad51_ChIP_HoChromosomeI_DSB5hr_rep2

treatment_protocol: Addition of 2% Galactose (Gal-driven HO endonuclease expression)


title: Rad51_ChIP_HoChromosomeI_DSB5hr_rep1

value: Addition of 2% Galactose (Gal-driven HO endonuclease expression)


title: Rfa1-9myc_ChIP_HoChromosomeIV_DSB5hr_rep2


title: P. aeruginosa PAO1 LB 1% Streptomyces 230 for 7h biofilm cells

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

description: In the present study, we performed global gene expression analyses using Affymetrix GeneChip® P. aeruginosa Genome arrays. The sample preparation was performed according to the instructions and recommendations provided by the manufacturer. RNA extracted from biofilm cells of P. aeruginosa PAO1 wild type after 7 h of growth in LB at 37oC plus 1% Streptomyces 230

hyb_protocol: Following affymetrix protocol.  Fragmented end-labeled cDNA was hybridized to the GeneChip® P. aeruginosa Genome arrays for 16 hours at 50 ℃ and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: Following affymetrix protocol. After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: MAS 5.0 Expression Analysis Defalut Setting

organism: Pseudomonas aeruginosa

source_name: rna extracted from biofilm cells of p. aeruginosa pao1 grown for 7 h on glass wool in lb at 37C with 1% of streptomyces supernatant 230

label_protocol: Per RNAsample, 300 ng were used as input into the Affymetrix procedure as recommended by protocol (http://www.affymetrix.com). Briefly, 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

extract_protocol: To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia/silica beads (Biospec) were added to the cell pellets. The tubes were closed tightly and vortexed for 50 seconds. The total RNA was isolated by following the protocol of the RNeasy Mini Kit (Qiagen) including an on-column DNase digestion with RNase-free DNase I (Qiagen). RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., DE, USA).

tag: agent

value: streptomyces 230 supernatant


title: P. aeruginosa PAO1 in LB for 7h biofilm cells

description: In the present study, we performed global gene expression analyses using Affymetrix GeneChip® P. aeruginosa Genome arrays. The sample preparation was performed according to the instructions and recommendations provided by the manufacturer. RNA extracted from biofilm cells of P. aeruginosa PAO1 wild type after 7 h of growth in LB at 37oC

source_name: rna extracted from p. aeruginosa pao1 cells grown for 7 h on glass wool in lb at 37C

value: control


title: Rad51_ChIP_HoChromosomeIV_DSB2hr_rep1

value: Input DNA


title: Rad51_ChIP_HoChromosomeIV_DSB2hr_rep2


title: Rad51_ChIP_HoChromosomeIV_DSB5hr_rep2


title: Rad51_ChIP_HoChromosomeIV_DSB0hr_rep2


title: Rad51_ChIP_HoChromosomeI_DSB0hr_rep1


title: Rad51_ChIP_HoChromosomeI_DSB0hr_rep2


title: Rad51_ChIP_HoChromosomeIV_DSB0hr_rep1


title: IL-2 treated (biol repl #1)

city: Debrecen

first: Zsuzsanna

middle: S.

last: Nagy

address: Nagyerdei krt. 98

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: Gene expression data

hyb_protocol: Hybridization, etc was performed by the BCM Microarray Core Facility in Houston, TX.

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

data_processing: The raw data in the .CEL files were normalized by the GCRMA method (GC robust multi-array analysis). It is implemented in Bioconductor (http://www.bioconductor.org/). The raw signal intensity data were normalized, background corrected and summarized based on certain statistical models, and an expression value, in log2-scale, is obtained per chip per probe set.

source_name: Kit225 cells treated with IL-2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol in the Baylor College of Medicine Microarray Core Facility, Houston, TX.

growth_protocol: Cells were maintained in RPMI-1640 medium containing 10% fetal calf serum, 2 mM L-glutamine and penicillin-streptomycin (50 IU/ml and 50 μg/ml, respectively). Kit225 media was supplemented with 20 U/ml human recombinant IL-2 (NCI Preclinical Repository).

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy Kit according to the manufacturer's instructions.

treatment_protocol: Prior to IL-2 stimulation, Kit225 cells were made quiescent for 24 h in their regular medium without IL-2. Cell stimulations were carried out with 10 nM IL-2.

value: Leukemia cell

tag: cell line


title: IL-2 treated (biol repl #2)

description: Gene expression data


title: untreated (biol repl #2)

description: Gene expression data

source_name: Kit225 cells untreated


title: Multiple Myeloma Patient 4

city: Brussels

first: Thibaud

last: André

address: Boulevard de Waterloo, 121

country: Belgium

institute: ULB - Jules Bordet Insitute

description:
MM4
Biological rep4.

hyb_protocol: Following fragmentation, 16 µg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450 according to the Affymetrix protocol (www.affymetrix.com).

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

data_processing: Image analysis and probe quantification were done with Affymetrix software, which produced raw probe intensity data in the Affymetrix CEL files. Normalization was done with the RMA method, which processed a group of CEL files simultaneously using BRB arrays tools.

source_name: bone-marrow mesenchymal stromal cells extracted from myeloma patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (www.affymetrix.com).

growth_protocol:
Bone marrow was harvested from the sternum or iliac crest of patients after informed consent. Mononuclear cells were isolated by density gradient centrifugation (LinfoSep, BiomediCs, Madrid, Spain), washed in Hank’s buffered salt solution (HBSS, Lonza Europe, Verviers, Belgium) and seeded at 20,000 cells/cm2 in Dulbecco’s Modified Eagle’s Medium-low glucose (DMEM-LG, Lonza) supplemented with 15% of fetal bovine serum (FBS) (Sigma-Aldrich, Bornem, Belgium), 2 mM of L-glutamine, 50 U/ml of penicillin, and 50 µg/ml of streptomycin (all from Lonza). Cells were incubated at 37°C in a 5% CO2 and 95% humidified atmosphere.
After 48 hours, nonadherent cells were removed by washing and the medium was changed once a week. When subconfluency (80–90%) was achieved, adherent cells were detached with TrypLE Select solution (Lonza) and expanded by replating at a lower density (± 600 cells/cm2).

extract_protocol: Total RNA from each cell culture was extracted in a single step by the TriPure Isolation Reagent (Roche Applied Science, Vilvoorde, Belgium). We performed the reverse transcription reaction with 2 µg RNA using qScript cDNA SuperMix (Quanta Bioscienes, Gaithersburg, MD, USA).

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

value: multiple myeloma

tag: mm stage

value: IIIa

tag: Sex

value: F


title: 201B7

description: Gene expression of hiPSC (201B7)

source_name: hiPSC (201B7)

value: hiPSC (201B7)


title: Multiple Myeloma Patient 3

description:
MM3
Biological rep3.

growth_protocol:
Bone marrow was harvested from the sternum or iliac crest of patients after informed consent. Mononuclear cells were isolated by density gradient centrifugation (LinfoSep, BiomediCs, Madrid, Spain), washed in Hank’s buffered salt solution (HBSS, Lonza Europe, Verviers, Belgium) and seeded at 20,000 cells/cm2 in Dulbecco’s Modified Eagle’s Medium-low glucose (DMEM-LG, Lonza) supplemented with 15% of fetal bovine serum (FBS) (Sigma-Aldrich, Bornem, Belgium), 2 mM of L-glutamine, 50 U/ml of penicillin, and 50 µg/ml of streptomycin (all from Lonza). Cells were incubated at 37°C in a 5% CO2 and 95% humidified atmosphere.

After 48 hours, nonadherent cells were removed by washing and the medium was changed once a week. When subconfluency (80–90%) was achieved, adherent cells were detached with TrypLE Select solution (Lonza) and expanded by replating at a lower density (± 600 cells/cm2).

value: M


title: untreated (biol repl #1)

description: Gene expression data


title: Multiple Myeloma Patient 2

description:
MM2
Biological rep2.


title: Healthy Donors 2

description:
HD2
Biological rep2.

source_name: bone-marrow mesenchymal stromal cells extracted from healthy donor

value: healthy


title: Healthy Donors 1

description:
HD1
Biological rep1.


title: P53-wildetype without Del17p, biological rep233

city: Basel

first: Giuseppe

last: Palermo

address: wettsteinallee 76

country: Switzerland

institute: F. Hoffman-La Roche Ltd.

hyb_protocol: Hybridization was performed according to Affymetrix-recommended procedures, except that the 20X GeneChip Eukaryotic Hybridization Controls were omitted from the hybridization.

scan_protocol: Imaging and signal extraction were performed according to Affymetrix-recommended procedures. GCOS 1.3 was used

data_processing: The probe intensities of miRNA arrays were background-subtracted, quantile normalized and summarized using the RMA method. All data were log2-transformed

source_name: Patient WITHOUT P53-mutation and WITHOUT Del17p

label_protocol: The 3’ ends of RNA molecules in total RNA samples (400ng total RNA per sample) were labeled with biotin according to the company’s standard protocol

extract_protocol: RNA of CD19 selected B-cells was isolated using Ambion miRVANA total RNA extraction kit

tag: p53 mutation

value: NO


title: P53-wildetype without Del17p, biological rep228


title: P53-wildetype with Del17p, biological rep1

source_name: Patient WITHOUT P53-mutation and WITH Del17p, biological rep1

value: YES


title: P53-wildetype with Del17p, biological rep4

source_name: Patient WITHOUT P53-mutation and WITH Del17p, biological rep4


title: P53-wildetype with Del17p, biological rep3

source_name: Patient WITHOUT P53-mutation and WITH Del17p, biological rep3


title: P53-wildetype with Del17p, biological rep5

source_name: Patient WITHOUT P53-mutation and WITH Del17p, biological rep5


title: P53-wildetype without Del17p, biological rep236


title: P53-wildetype with Del17p, biological rep2

source_name: Patient WITHOUT P53-mutation and WITH Del17p, biological rep2


title: P53-wildetype without Del17p, biological rep229


title: P53-wildetype with Del17p, biological rep8

source_name: Patient WITHOUT P53-mutation and WITH Del17p, biological rep8


title: P53-wildetype without Del17p, biological rep231


title: P53-wildetype without Del17p, biological rep235


title: P53-wildetype without Del17p, biological rep232


title: P53-wildetype with Del17p, biological rep6

source_name: Patient WITHOUT P53-mutation and WITH Del17p, biological rep6


title: P53-wildetype without Del17p, biological rep227


title: P53-wildetype without Del17p, biological rep230


title: P53-wildetype without Del17p, biological rep234


title: P53-wildetype without Del17p, biological rep226


title: R27n_25C_St1

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

description: This sample is of strain SL1344 without plasmid R27 grown at 25oC to stationary growth phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed following NimbleGen's standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed following NimbleGen's standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis), quantile normalization and background correction as implemented in the NimbleScan software package.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella Typhimurium SL1344

label_protocol: Labelling was performed following NimbleGen's standard operating protocol. See www.nimblegen.com.

growth_protocol: wild-type SL1344 and SL1344 (R27) were grown at 25oC and 37oC to mid-exponential growth (OD600 0.6) and early stationary phase (OD600 2.0) in Luria-Bertani (LB) medium (10 g NaCl, 10 g tryptone and 5 g yeast extract per litre).

extract_protocol: Total RNA was purified using an SV Total RNA Isolation System (Promega) according to the manufacturer's directions. The RNA was DNase treated with TURBO DNA-free (Ambion) and purified and concentrated again with RNeasy Minielute Clean-up kit (Qiagen). The purity and quality of the purified RNA was tested by Bionalyser 2100 (Agilent Technologies).

tag: plasmids

value: pSLT, pRSF, pCOL1B

tag: temperature

tag: growth phase

value: stationary


title: R27p_25C_St3

description: This sample is of strain SL1344 containing plasmid R27 grown at 25oC to stationary growth phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella Typhimurium SL1344 (R27)

value: pSLT, pRSF, pCOL1B, R27


title: R27n_25C_St2

description: This sample is of strain SL1344 without plasmid R27 grown at 25oC to stationary growth phase. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: R27n_25C_St3

description: This sample is of strain SL1344 without plasmid R27 grown at 25oC to stationary growth phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P53-wildetype without Del17p, biological rep223


title: P53-wildetype without Del17p, biological rep222


title: P53-wildetype without Del17p, biological rep224


title: P53-wildetype without Del17p, biological rep225


title: Healthy Donors 3

description:
HD3
Biological rep3.

tag: cell type

tag: age


title: R27p_25C_Exp3

description: This sample is of strain SL1344 containing plasmid R27 grown at 25oC to exponential growth phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

value: exponential


title: R27n_25C_Exp1

description: This sample is of strain SL1344 without plasmid R27 grown at 25oC to exponential growth phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: R27p_25C_Exp2

description: This sample is of strain SL1344 containing plasmid R27 grown at 25oC to exponential growth phase. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P53-wildetype without Del17p, biological rep217


title: P53-wildetype without Del17p, biological rep215


title: R27p_25C_St1

description: This sample is of strain SL1344 containing plasmid R27 grown at 25oC to stationary growth phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P53-wildetype without Del17p, biological rep216


title: R27p_25C_Exp1

description: This sample is of strain SL1344 containing plasmid R27 grown at 25oC to exponential growth phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: R27n_25C_Exp3

description: This sample is of strain SL1344 without plasmid R27 grown at 25oC to exponential growth phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: R27n_37C_St3

description: This sample is of strain SL1344 without plasmid R27 grown at 37oC to stationary growth phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: R27n_37C_St2

description: This sample is of strain SL1344 without plasmid R27 grown at 37oC to stationary growth phase. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P53-wildetype without Del17p, biological rep220


title: P53-wildetype without Del17p, biological rep219


title: R27n_25C_Exp2

description: This sample is of strain SL1344 without plasmid R27 grown at 25oC to exponential growth phase. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P53-wildetype without Del17p, biological rep214


title: P53-wildetype without Del17p, biological rep218


title: P53-wildetype without Del17p, biological rep212


title: R27p_37C_St2

description: This sample is of strain SL1344 containing plasmid R27 grown at 37oC to stationary growth phase. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P53-wildetype without Del17p, biological rep213


title: R27p_37C_St3

description: This sample is of strain SL1344 containing plasmid R27 grown at 37oC to stationary growth phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: R27p_37C_St1

description: This sample is of strain SL1344 containing plasmid R27 grown at 37oC to stationary growth phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P53-wildetype without Del17p, biological rep209


title: P53-wildetype without Del17p, biological rep221


title: P53-wildetype without Del17p, biological rep210


title: R27n_37C_St1

description: This sample is of strain SL1344 without plasmid R27 grown at 37oC to stationary growth phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P53-wildetype without Del17p, biological rep208


title: P53-wildetype with Del17p, biological rep7

source_name: Patient WITHOUT P53-mutation and WITH Del17p, biological rep7


title: P53-wildetype without Del17p, biological rep205


title: P53-wildetype without Del17p, biological rep211


title: R27p_37C_Exp3

description: This sample is of strain SL1344 containing plasmid R27 grown at 37oC to exponential growth phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: R27n_37C_Exp1

description: This sample is of strain SL1344 without plasmid R27 grown at 37oC to exponential growth phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: R27n_37C_Exp3

description: This sample is of strain SL1344 without plasmid R27 grown at 37oC to exponential growth phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: R27n_37C_Exp2

description: This sample is of strain SL1344 without plasmid R27 grown at 37oC to exponential growth phase. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P53-wildetype without Del17p, biological rep204


title: P53-wildetype without Del17p, biological rep207


title: P53-wildetype without Del17p, biological rep202


title: P53-wildetype without Del17p, biological rep201


title: R27p_37C_Exp2

description: This sample is of strain SL1344 containing plasmid R27 grown at 37oC to exponential growth phase. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: R27p_37C_Exp1

description: This sample is of strain SL1344 containing plasmid R27 grown at 37oC to exponential growth phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P53-wildetype without Del17p, biological rep203


title: P53-wildetype without Del17p, biological rep199


title: P53-wildetype without Del17p, biological rep200


title: P53-wildetype without Del17p, biological rep206


title: P53-wildetype without Del17p, biological rep196


title: P53-wildetype without Del17p, biological rep198


title: P53-wildetype without Del17p, biological rep195


title: P53-wildetype without Del17p, biological rep197


title: P53-wildetype without Del17p, biological rep193


title: 9 10% Power

city: Albuquerque

first: shannon

last: bruse

state: New Mexico

address: 2425 ridgecrest drive SE

institute: lovelace respiratory research institute

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
9 10% Power (610-500)

hyb_protocol: Samples were hybridized to the array at 37˚C overnight using the hybridization buffer included with the labeling kit.

scan_protocol: Image analysis was performed on a GenePix 4000B microarray scanner.  A marked difference in pixel intensity was observed between Sanger miRNAs and the novel features exclusively present on the NCode V3 arrays, with many of the latter approaching saturation.  Photomultiplier tube (PMT) settings were adjusted so as to balance signal intensity in the red and green channels, and maximize pixel intensity without saturation at 10% power.  Arrays were then rescanned at 100% power without PMT adjustment.

data_processing: Images were exported and processed using the Acuity 4.0 software package.  Data filtering parameters were established to include only features with (1) at least 70% of pixels greater than 2 standard deviations above background in either the red or green channel, (2) regression R2 greater than 0.5 to ensure feature uniformity, (3) less than 20% of pixels saturated in both the red and the green channels, and (4) no flags upon visual inspection.  Normalization was performed with the LOWESS (locally weighted regression) method, and expression log ratios were used for statistical analysis.

source_name: Brain, cerebral tissue

label_protocol: On each array, a single Cy3 labeled total RNA sample was competitively hybridized against a Cy5 labeled control pool.  The control pool was a mixture of all RNA samples, where each developmental time point was equally represented, and each individual sample was equally represented within a given time point.  For each channel, 1 μg of total RNA was labeled with the Label IT® miRNA Labeling Kit, Version 2 (Mirus Bio, Madison, WI) according to manufacturer’s protocol.

growth_protocol: Frozen brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders, housed at the University of Maryland.  Brain sectioning (described at http://medschool.umaryland.edu/btbank/NICHD-BTB-ProtocolMethods.asp) began with separation of the cerebral hemispheres, followed by removal of the midbrain/pons/cerebellum. The remaining cerebrum (from the left hemisphere) was sectioned coronally at approximately 1 cm intervals.

extract_protocol: Tissue homogenization and RNA extraction procedures were performed using the mirVana PARIS kit (Ambion) according to the manufacturer’s protocol.  RNA yield and quality were determined using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: Brain, cerebral tissue

tag: gestational age, weeks

tag: taqman pool by age

value: female

tag: race

value: African American

tag: post-mortem interval (hours)

source_name: Brain

tag: sample type

value: Control pool (a mixture of all RNA samples, where each developmental time point was equally represented, and each individual sample was equally represented within a given time point)


title: 779 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
779 10% Power (590-520)

tag: age, years

tag: age, days

value: male


title: 66 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
66 10% Power (620-560)


title: 633 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
633 10%


title: First Choice 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
First Choice 10% Power (570-510)

source_name: Total Brain [FirstChoice Human Brain Total RNA (Ambion)]

value: Caucasian


title: Reference Pool 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
Reference Pool 10% Power (590-520)

source_name: Total Brain, multisample [FirstChoice Human Brain Reference RNA (Ambion)]


title: P53-wildetype without Del17p, biological rep194


title: 4934 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4934 10% Power (610-540)


title: 57 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
57 10% (660-490)


title: 4912 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4912 10% Power (610-510)

value: African AmerincaAmerican


title: 4825 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4825 10% Power (610-520)


title: 4889 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4889 10% Power (610-480)


title: P53-wildetype without Del17p, biological rep192


title: P53-wildetype without Del17p, biological rep191


title: P53-wildetype without Del17p, biological rep187


title: P53-wildetype without Del17p, biological rep185


title: P53-wildetype without Del17p, biological rep190


title: P53-wildetype without Del17p, biological rep188


title: 4823 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4823 10% Power (610-520)


title: 4715 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4715 10% Power (600-530)


title: 4799 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4799 10% Power (600-530)


title: 4794 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4794 10% Power (610-570)


title: 4670 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4670 10% Power (620-550)


title: P53-wildetype without Del17p, biological rep186


title: P53-wildetype without Del17p, biological rep189


title: 4573 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4573 10% Power (600-530)


title: 4654 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
4654 10% Power (610-520)

value: unknown


title: P53-wildetype without Del17p, biological rep181


title: P53-wildetype without Del17p, biological rep184


title: P53-wildetype without Del17p, biological rep182


title: P53-wildetype without Del17p, biological rep183


title: P53-wildetype without Del17p, biological rep180


title: 45 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
45 10% Power (600-530)


title: Multiple Myeloma Patient 1

description:
MM1
Biological rep1.

source_name: bone-marrow mesenchymal stromal cells extracted from myeloma patient

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

tag: disease state

value: multiple myeloma

value: IIIb

value: F


title: P53-wildetype without Del17p, biological rep178

value: NO


title: 43 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
43 10% Power (590-490)


title: 42 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
42 10% Power


title: P53-wildetype without Del17p, biological rep176


title: P53-wildetype without Del17p, biological rep179


title: 392 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
392 10% Power


title: 396 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
396 10% Power (590-520)


title: P53-wildetype without Del17p, biological rep177


title: P53-wildetype without Del17p, biological rep175


title: 33 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
33 10% Power (620-490)


title: R27p_25C_St2

description: This sample is of strain SL1344 containing plasmid R27 grown at 25oC to stationary growth phase. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: P53-wildetype without Del17p, biological rep173


title: 31 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
31 10% Power (600-520)


title: 291 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
291 10% Power (620-570)


title: P53-wildetype without Del17p, biological rep170


title: 261 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
261 10% Power (590-520)


title: 279 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
279 10% Power (590-520)


title: 278 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
278 10% Power (600-540)


title: P53-wildetype without Del17p, biological rep172


title: P53-wildetype without Del17p, biological rep169


title: P53-wildetype without Del17p, biological rep171


title: P53-wildetype without Del17p, biological rep166


title: P53-wildetype without Del17p, biological rep168


title: P53-wildetype without Del17p, biological rep165


title: 311 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
311 10% Power (600-450)


title: 391 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
391 10% Power (610-520)


title: 250 10% Power

description:
This is the 10% power scan, as described in Chronological Changes in microRNA Expression in the Developing Human Brain, Moreau et. al.
250 10% Power (620-560)