title: normal skin sample 1

first: Adam

last: Dupuy

address: 51 Newton Road

description: normal skin from a K14-Cre;Zmiz1 double transgenic mouse

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Mouse Gene 1.0 ST Arrays  [probe set (exon) version], and incubated at 45C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. Following hybridization, the arrays will be washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing:
Data were processed using Partek Genomics Suite software. Corrected intensities were RMA normalized.
probe group file: MoEx-1_0-st-v1.r2
meta-probeset file: MoEx-1_0-st-v1.na27.mm9.transcript

source_name: normal

label_protocol: Four ug of SPIA amplified DNA was then used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five micrograms of this product was fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer's recommended protocol.

extract_protocol: Total RNA was extracted from snap-frozen tissues using the PerfectPure RNA Tissue kit with on-column Dnase I treatment (5-PRIME). Extracted total RNA was then quality verified by Agilent Bioanalyzer

tag: histology

value: normal

tag: genotype/variation

value: K14-Cre;Zmiz1 double transgenic mouse


title: keratoacanthoma sample 3

status: Public on Oct 01 2012

type: RNA

city: Iowa City

country: USA

institute: University of Iowa

description: keratoachanthoma from a K14-Cre;Zmiz1 double transgenic mouse

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: tumor

value: tumor


title: normal skin sample 6

description: normal skin from a Zmiz1 transgenic mouse

value: Zmiz1 transgenic mouse


title: normal skin sample 2


title: keratoacanthoma sample 5


title: Twelve hour after the infection replicate 3

city: New Haven

first: Juilee

last: Thakar

state: CT

address: 300 George street

department: Pathology

institute: Yale medical school

description: Green 12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R [R2.12.1 and lumi 2.2.1].

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

label_protocol: Double stranded cDNA and biotin-labeled cRNA was synthesized and purified from 500 ng of total RNA.  Purification of the cRNA and integrity of the cRNA was be assessed by running aliquots on the Bioanalyzer prior to hybridization.   Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip.  The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.  After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.  The BeadChips were scanned on the Illumina Iscan.

growth_protocol: The recent seasonal H1N1 influenza virus A/New Caledonia/20/1999 (NC) was kindly provided by Dr. Peter Palese and grown 10- to 11-day-old embryonated chickens eggs as described previously

extract_protocol: Cells were homogenized by using QIAshredder microcentrifuge spin-columns (Qiagen,  Duesseldorf Germany) and RNA was isolated from cells using Qiagen Micro RNeasy plus kit following the  manufactures protocol (Qiagen, Duesseldorf Germany). RNA quality was assayed by determination of the  RNA integrity number using the 2100 Bioanalyzer (Agilent).

treatment_protocol: The Virus was titrated by immunofluorescence 18  11 hours after infection of MDCK cell plates using monoclonal antibodies specific for Influenza-NP protein  generated by the Mount Sinai Hybridoma Core Facility followed by addition of anti-mouse IgG-FITC and  visualization using fluorescent microscopy.

tag: cell type

value: monocyte-derived dendritic cells

tag: time

value: Twelve hour after the infection


title: keratoacanthoma sample 4


title: normal skin sample 3

description: normal skin from a K14-Cre transgenic mouse

value: K14-Cre transgenic mouse


title: keratoacanthoma sample 1


title: SD.HVC replicate 5

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

institute: University of Illinois

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides in Corning Hybridization Chambers, and incubated O/N at 42C. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

scan_protocol: Scanned on an Axon GenePix 4000B scanner Images were quantified using Axon GenePix 6.0.

data_processing: The R/Bioconductor package limma was used with print-tip loess for within array normalization and the Aquantile method for the between array normalization. Data were not background-adjusted.

organism: Taeniopygia guttata

source_name: universal SoNG reference

label_protocol: 1 µg of aRNA was primed with 3 µl of 100 µM random hexamer primers at 70C for 10 min, then reversed transcribed at 42C for 16 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM dATP, dCTP, dGTP, 60µM dTTP and 40µM aa-dUTP; RNA was hydrolyzed in the presence of NaOH and EDTA and samples were cleaned up on a spin column. Finally, Cy3 and Cy5 dye esters (GE Healthcare) were coupled to aa-dUTP residues in NaCO3 buffer for 2 hrs at room temp, then neutralized and cleaned on spin columns.

extract_protocol: Experimental samples: Total RNA was extracted using Absolutely RNA Microprep kit (Stratagene). 200ng total RNA was double-amplified using MessageAmp II aRNA kit (Ambion). Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Birds were castrated and synchronized to a Short Day (SD) state to ensure regressed song nuclei, basal levels of Testosterone (T) typical of the non-breeding season, low song rates and unstereotyped song structure, and a low intrinsic spontaneous firing rate in the robust nucleus of the arcopalluim (RA). Then, on Day 0 of the experiment we sacrificed 6 birds. This group of birds, referred to as SD long-term, represents the steady-state of the regressed song control system and served as a baseline for all other groups. We implanted the rest of the birds with a subcutaneous Silastic capsule of T, and shifted them to Long Day (LD) photoperiod. To measure gene expression while the song control system was actively changing from a nonbreeding to a breeding phenotype, 6 birds were sacrificed on each of days 3, 7, and 21 (3LD+T, 7LD+T, and 21LD+T, respectively). By day 21, the song control system has reached its full breeding phenotype, and this time point represents the breeding-state song control system. On Day 21, the subcutaneous T capsules were removed from the remaining birds and they were shifted overnight to SD photoperiod to induce regression of the song control system back to the non-breeding state. On each of days 22 and 23 we sacrificed 6 birds (1SD-T and 2SD-T, respectively) to measure gene expression while the song control system is actively regressing. To control for circadian patterns of gene expression, all birds were sacrificed during the three hour period following their subjective dawn (i.e., lights on).

tag: gender

value: male and female

tag: tissue

value: telencephalon

tag: light

value: Dark cycle:NA

tag: testosterone at sacrifice

tag: treatment protocol

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country

organism: Zonotrichia leucophrys gambelii

value: male

value: HVC

value: Dark cycle:8:16

value: No

value: Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.


title: Ten hour after the infection replicate 3

description: Green 10

value: Ten hour after the infection


title: keratoacanthoma sample 2


title: normal skin sample 5

value: normal


title: normal skin sample 4


title: Six hour after the infection replicate 3

description: Green 6

value: Six hour after the infection


title: Two hour after the infection replicate 3

description: Green 2

value: Two hour after the infection


title: control replicate 2

description: White 0

value: control


title: Ten hour after the infection replicate 1

description: Yellow 10

value: monocyte-derived dendritic cells


title: Four hour after the infection replicate 2

description: White 4

value: Four hour after the infection


title: Six hour after the infection replicate 2

description: White 6


title: One hour after the infection replicate 2

description: White 1

value: One hour after the infection


title: Two hour after the infection replicate 2

description: White 2


title: Two hour after the infection replicate 1

description: Yellow 2


title: Eight hour after the infection replicate 2

description: White 8

value: Eight hour after the infection


title: Eight hour after the infection replicate 1

description: Yellow 8


title: control replicate 3

description: Green 0


title: Eight hour after the infection replicate 3

description: Green 8


title: Four hour after the infection replicate 3

description: Green 4


title: Twelve hour after the infection replicate 2

description: White 12

value: Twelve hour after the infection


title: SD.RA replicate 5

value: male and female

value: telencephalon

value: Dark cycle:NA

value: RA


title: Six hour after the infection replicate 1

description: Yellow 6


title: One hour after the infection replicate 1

description: Yellow 1


title: Twelve hour after the infection replicate 1

description: Yellow 12


title: Four hour after the infection replicate 1

description: Yellow 4


title: control replicate 1

description: Yellow 0


title: One hour after the infection replicate 3

description: Green 1


title: active TB 2 weeks post treatment [404/0.5]

city: London

first: Chloe

last: Bloom

address: The Ridgeway

country: United Kingdom

institute: MRC National Institute for Medical Research

description: South Africa patient blood

data_processing:
The data were normalised using 75th percentile normalisation in GeneSpring 11.5
Background subtracted, normalised and log2 transformed for normalised values and non-normalised values have only had background subtraction

source_name: Peripheral blood

label_protocol: Biotinylated, amplified cRNA were prepared using the Illumina CustomPrep RNA amplification kit

extract_protocol: RNA was extracted using the MagMAX-96 Blood RNA Isolation Kit and globin reduced using GLOBINclear

tag: disease

value: PTB

tag: time point (months)

value: Whole blood

tag: geographical location

value: South Africa patient blood

tag: status

value: active TB 2 weeks post treatment


title: Ten hour after the infection replicate 2

description: White 10

value: Ten hour after the infection


title: active TB 6 months post treatment [431/06]

description: South Africa patient blood

value: active TB 6 months post treatment


title: active TB 6 months post treatment [430/06]

description: South Africa patient blood


title: active TB 12 months post treatment [413/12]

description: South Africa patient blood

value: active TB 12 months post treatment


title: active TB 2 months post treatment [436/02]

description: South Africa patient blood

value: active TB 2 months post treatment


title: active TB 12 months post treatment [414/12]

description: South Africa patient blood


title: active TB 6 months post treatment [438/06]

description: South Africa patient blood


title: untreated latent TB  [575/0]

description: South Africa patient blood

value: LTB

value: untreated latent TB


title: active TB 6 months post treatment [405/06]

description: South Africa patient blood


title: active TB pre-treatment [405/0]

description: South Africa patient blood

value: active TB pre-treatment


title: active TB pre-treatment [416/0]

description: South Africa patient blood


title: active TB pre-treatment [432/0]

description: South Africa patient blood


title: untreated latent TB  [520/0]

description: South Africa patient blood


title: active TB 2 months post treatment [404/02]

description: South Africa patient blood


title: untreated latent TB  [573/0]

description: South Africa patient blood


title: active TB 2 weeks post treatment [424/0.5]

description: South Africa patient blood


title: active TB 2 months post treatment [430/02]

description: South Africa patient blood


title: active TB pre-treatment [415/0]

description: South Africa patient blood


title: active TB pre-treatment [436/0]

description: South Africa patient blood


title: active TB 2 months post treatment [413/02]

description: South Africa patient blood


title: active TB 12 months post treatment [402/12]

description: South Africa patient blood


title: active TB 6 months post treatment [440/06]

description: South Africa patient blood


title: active TB 6 months post treatment [407/06]

description: South Africa patient blood


title: untreated latent TB  [539/0]

description: South Africa patient blood


title: active TB 12 months post treatment [425/12]

description: South Africa patient blood


title: active TB 2 weeks post treatment [407/0.5]

description: South Africa patient blood


title: active TB 6 months post treatment [415/06]

description: South Africa patient blood


title: active TB 12 months post treatment [416/12]

description: South Africa patient blood


title: untreated latent TB  [561/0]

description: South Africa patient blood


title: active TB 12 months post treatment [429/12]

description: South Africa patient blood


title: active TB 2 weeks post treatment [418/0.5]

description: South Africa patient blood


title: active TB 12 months post treatment [420/12]

description: South Africa patient blood


title: untreated latent TB  [533/0]

description: South Africa patient blood


title: active TB 2 weeks post treatment [435/0.5]

description: South Africa patient blood


title: active TB 12 months post treatment [437/12]

description: South Africa patient blood


title: active TB 2 months post treatment [422/02]

description: South Africa patient blood


title: active TB pre-treatment [435/0]

description: South Africa patient blood


title: active TB 2 months post treatment [419/02]

description: South Africa patient blood


title: active TB 12 months post treatment [424/12]

description: South Africa patient blood


title: active TB 6 months post treatment [435/06]

description: South Africa patient blood


title: active TB 2 weeks post treatment [421/0.5]

description: South Africa patient blood


title: active TB 2 weeks post treatment [403/0.5]

description: South Africa patient blood


title: untreated latent TB  [540/0]

description: South Africa patient blood


title: active TB 6 months post treatment [416/06]

description: South Africa patient blood


title: active TB 12 months post treatment [440/12]

description: South Africa patient blood


title: active TB 12 months post treatment [404/12]

description: South Africa patient blood


title: active TB pre-treatment [437/0]

description: South Africa patient blood


title: active TB 6 months post treatment [413/06]

description: South Africa patient blood


title: active TB 2 weeks post treatment [437/0.5]

description: South Africa patient blood


title: untreated latent TB  [574/0]

description: South Africa patient blood


title: active TB 12 months post treatment [419/12]

description: South Africa patient blood


title: active TB 12 months post treatment [432/12]

description: South Africa patient blood


title: untreated latent TB  [543/0]

description: South Africa patient blood


title: active TB 2 months post treatment [433/02]

description: South Africa patient blood


title: active TB 2 weeks post treatment [433/0.5]

description: South Africa patient blood


title: active TB pre-treatment [424/0]

description: South Africa patient blood


title: active TB 2 weeks post treatment [440/0.5]

description: South Africa patient blood


title: active TB 12 months post treatment [433/12]

description: South Africa patient blood


title: active TB 6 months post treatment [414/06]

description: South Africa patient blood


title: active TB 2 months post treatment [415/02]

description: South Africa patient blood


title: active TB 2 weeks post treatment [432/0.5]

description: South Africa patient blood


title: active TB pre-treatment [421/0]

description: South Africa patient blood


title: active TB 6 months post treatment [436/06]

description: South Africa patient blood


title: untreated latent TB  [567/0]

description: South Africa patient blood


title: active TB 2 weeks post treatment [429/0.5]

description: South Africa patient blood


title: active TB 2 months post treatment [429/02]

description: South Africa patient blood


title: active TB 6 months post treatment [429/06]

description: South Africa patient blood


title: active TB 2 weeks post treatment [436/0.5]

description: South Africa patient blood


title: active TB pre-treatment [438/0]

description: South Africa patient blood


title: active TB 12 months post treatment [422/12]

description: South Africa patient blood


title: active TB pre-treatment [430/0]

description: South Africa patient blood


title: active TB 12 months post treatment [435/12]

description: South Africa patient blood


title: untreated latent TB  [571/0]

description: South Africa patient blood


title: active TB pre-treatment [413/0]

description: South Africa patient blood


title: active TB pre-treatment [401/0]

description: South Africa patient blood


title: active TB 6 months post treatment [437/06]

description: South Africa patient blood


title: active TB 2 months post treatment [420/02]

description: South Africa patient blood


title: untreated latent TB  [502/0]

description: South Africa patient blood


title: untreated latent TB  [532/0]

description: South Africa patient blood


title: active TB 12 months post treatment [412/12]

description: South Africa patient blood


title: active TB pre-treatment [402/0]

description: South Africa patient blood


title: active TB pre-treatment [404/0]

description: South Africa patient blood


title: untreated latent TB  [524/0]

description: South Africa patient blood


title: active TB 6 months post treatment [425/06]

description: South Africa patient blood


title: active TB 12 months post treatment [403/12]

description: South Africa patient blood


title: active TB 2 weeks post treatment [413/0.5]

description: South Africa patient blood


title: active TB 2 weeks post treatment [438/0.5]

description: South Africa patient blood


title: active TB 2 weeks post treatment [415/0.5]

description: South Africa patient blood


title: active TB pre-treatment [425/0]

description: South Africa patient blood


title: [429/0]

description: South Africa patient blood


title: active TB pre-treatment [427/0]

description: South Africa patient blood


title: untreated latent TB  [558/0]

description: South Africa patient blood


title: active TB 6 months post treatment [421/06]

description: South Africa patient blood


title: active TB 2 weeks post treatment [425/0.5]

description: South Africa patient blood


title: active TB 2 weeks post treatment [420/0.5]

description: South Africa patient blood


title: active TB 12 months post treatment [418/12]

description: South Africa patient blood


title: active TB 2 months post treatment [425/02]

description: South Africa patient blood


title: untreated latent TB  [513/0]

description: South Africa patient blood


title: untreated latent TB  [544/0]

description: South Africa patient blood


title: active TB 2 months post treatment [421/02]

description: South Africa patient blood


title: active TB 6 months post treatment [422/06]

description: South Africa patient blood


title: active TB 6 months post treatment [432/06]

description: South Africa patient blood


title: active TB 2 weeks post treatment [430/0.5]

description: South Africa patient blood


title: untreated latent TB  [552/0]

description: South Africa patient blood


title: active TB 12 months post treatment [405/12]

description: South Africa patient blood


title: active TB pre-treatment [440/0]

description: South Africa patient blood


title: active TB 2 months post treatment [438/02]

description: South Africa patient blood


title: active TB pre-treatment [403/0]

description: South Africa patient blood


title: active TB 12 months post treatment [421/12]

description: South Africa patient blood


title: active TB 2 months post treatment [418/02]

description: South Africa patient blood


title: active TB pre-treatment [420/0]

description: South Africa patient blood


title: untreated latent TB  [536/0]

description: South Africa patient blood


title: active TB 2 weeks post treatment [419/0.5]

description: South Africa patient blood


title: active TB pre-treatment [422/0]

description: South Africa patient blood


title: untreated latent TB  [547/0]

description: South Africa patient blood


title: untreated latent TB  [572/0]

description: South Africa patient blood


title: untreated latent TB  [521/0]

description: South Africa patient blood


title: untreated latent TB  [559/0]

description: South Africa patient blood


title: untreated latent TB  [568/0]

description: South Africa patient blood


title: active TB 6 months post treatment [402/06]

description: South Africa patient blood


title: untreated latent TB  [522/0]

description: South Africa patient blood


title: active TB 2 months post treatment [435/02]

description: South Africa patient blood


title: active TB 2 months post treatment [432/02]

description: South Africa patient blood


title: active TB 12 months post treatment [436/12]

description: South Africa patient blood


title: active TB 12 months post treatment [430/12]

description: South Africa patient blood


title: active TB 2 months post treatment [437/02]

description: South Africa patient blood


title: active TB 2 weeks post treatment [412/0.5]

description: South Africa patient blood


title: active TB 2 months post treatment [431/02]

description: South Africa patient blood


title: untreated latent TB  [557/0]

description: South Africa patient blood


title: active TB 2 weeks post treatment [431/0.5]

description: South Africa patient blood


title: active TB 2 weeks post treatment [414/0.5]

description: South Africa patient blood


title: active TB 12 months post treatment [438/12]

description: South Africa patient blood


title: untreated latent TB  [569/0]

description: South Africa patient blood


title: active TB 6 months post treatment [403/06]

description: South Africa patient blood


title: active TB 12 months post treatment [431/12]

description: South Africa patient blood


title: untreated latent TB  [545/0]

description: South Africa patient blood


title: active TB 6 months post treatment [412/06]

description: South Africa patient blood


title: active TB 6 months post treatment [427/06]

description: South Africa patient blood


title: active TB pre-treatment [431/0]

description: South Africa patient blood


title: active TB 12 months post treatment [427/12]

description: South Africa patient blood


title: active TB pre-treatment [407/0]

description: South Africa patient blood


title: active TB 12 months post treatment [401/12]

description: South Africa patient blood


title: active TB 2 months post treatment [440/02]

description: South Africa patient blood


title: active TB 6 months post treatment [420/06]

description: South Africa patient blood


title: untreated latent TB  [546/0]

description: South Africa patient blood


title: active TB 2 months post treatment [427/02]

description: South Africa patient blood


title: active TB pre-treatment [433/0]

description: South Africa patient blood


title: untreated latent TB  [577/0]

description: South Africa patient blood


title: active TB pre-treatment [412/0]

description: South Africa patient blood


title: untreated latent TB  [515/0]

description: South Africa patient blood


title: active TB 2 months post treatment [412/02]

description: South Africa patient blood


title: active TB 2 weeks post treatment [427/0.5]

description: South Africa patient blood


title: active TB 12 months post treatment [415/12]

description: South Africa patient blood


title: untreated latent TB  [579/0]

description: South Africa patient blood


title: untreated latent TB  [531/0]

description: South Africa patient blood


title: active TB pre-treatment [418/0]

description: South Africa patient blood


title: active TB 12 months post treatment [407/12]

description: South Africa patient blood


title: untreated latent TB  [562/0]

description: South Africa patient blood


title: untreated latent TB  [529/0]

description: South Africa patient blood


title: active TB pre-treatment [414/0]

description: South Africa patient blood


title: active TB 2 months post treatment [424/02]

description: South Africa patient blood


title: untreated latent TB  [537/0]

description: South Africa patient blood


title: active TB 2 weeks post treatment [422/0.5]

description: South Africa patient blood


title: active TB 2 months post treatment [414/02]

description: South Africa patient blood


title: active TB pre-treatment [419/0]

description: South Africa patient blood


title: active TB 6 months post treatment [404/06]

description: South Africa patient blood


title: untreated latent TB  [542/0]

description: South Africa patient blood


title: untreated latent TB  [555/0]

description: South Africa patient blood


title: 2009-3

description: UK patient blood

value: UK patient blood


title: active TB 2 months post treatment [416/02]

description: South Africa patient blood


title: 2009-2

description: UK patient blood


title: 2004-5

description: UK patient blood


title: 2083-1

description: UK patient blood


title: 2030-2

description: UK patient blood


title: 2098-5

description: UK patient blood


title: 2030-1

description: UK patient blood


title: 2065-4

description: UK patient blood


title: 2065-5

description: UK patient blood


title: 2004-1

description: UK patient blood


title: 2098-4

description: UK patient blood


title: active TB 6 months post treatment [419/06]

description: South Africa patient blood


title: 2065-3

description: UK patient blood


title: 2009-4

description: UK patient blood


title: 2030-4

description: UK patient blood


title: 2098-1

description: UK patient blood


title: 2074-4

description: UK patient blood


title: 2074-2

description: UK patient blood


title: 2083-5

description: UK patient blood


title: 2055-2

description: UK patient blood


title: 2004-2

description: UK patient blood


title: 2009-5

description: UK patient blood


title: 2098-3

description: UK patient blood


title: 2074-5

description: UK patient blood


title: 2083-3

description: UK patient blood


title: 2009-1

description: UK patient blood


title: 2065-2

description: UK patient blood


title: 2074-1

description: UK patient blood


title: 2074-3

description: UK patient blood


title: Sample B4A

city: Oslo

first: Tommy

middle: Aleksander

last: Karlsen

address: Sognsvannsveien

department: Norwegian center for stem cell research

country: Norway

institute: Oslo University Hospital, Rikshospitalet

description: MSC donor 2

data_processing: The data was vst transformed and normalised using quantile normalisation in R

source_name: Transfected using electroporation and synthetic miR-145

label_protocol: The assay was performed at the Norwegian Microarray Consortium (NMC), Oslo, Norway, using the manufacturers protocols. Briefly, biotin labeled cRNA was synthesized from 500 ng ng total RNA using the Illumina®TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX). 750 ng of this cRNA was used to hybridize onto Illumina HumanHT-12 v4 Expression Beadchips (Illumina Inc., San Diego, CA) containing 48000 transcripts at 58°C overnight, according to the standard protocol. The hybridized chip was stained with streptavidin-Cy3 using FluoroLinkTMCyTM3 (AmershamTM, PA43001, Buckinghampshire, UK) and scanned with an Illumina beadarray reader.

growth_protocol: Human bone marrow derived MSCs were cultured in DMEM-F12 containing 10%FBS and 1% P/S until reaching 70% confluency. Processed by Trypsination until passage 3-6.

extract_protocol: Total RNA was isolated using the RNAqueous Micro Kit following protocols from the manufacturer (Ambion). Following DNase treatment (Ambion), RNA was quantified by spectrophotometry

treatment_protocol: Lipofectamine 2000 was used for liposomal transfection according to the reverse transfection protocol from the manufacturer (Invitrogen, Carlsbad, CA). Briefly, for each reaction 500.000 cells were transfected using 50 nM Pre-miR-negative control no.1 and Pre-miR-145 (Ambion, Austin, TX) (table 1), 8 ul Lipofectamine 2000 and were seeded out in a total volume of 2.5 ml culture medium (without antibiotics). The next day the medium was changed and the following day (2 days after transfection) cells were harvested using trypsin-EDTA and washed in PBS before total RNA was isolated. The Amaxa Nucleofection system was used according to the protocols from the manufacturer (Lonza). For both hBM-MSCs and hACs the Human Chondrocyte Nucleofector Kit and the U-23 program was used as these conditions were shown to give the best transfection efficiency for both cell types. Briefly, 1 x106 cells were used for each nucleofection reaction using 3 µM Pre-negative control and Pre-miR-145 in a total volume of 100 µl nucleofector solution. Directly after transfection the cells were seeded out in culture medium (without antibiotics) containing 20% FBS. The next day the medium was changed and the following day (2 days after electroporation) cells were harvested using trypsin-EDTA and washed in PBS before total RNA was isolated.

value: mesenchymal stem cells


title: Sample C4A

description: MSC donor 3


title: 2065-1

description: UK patient blood


title: 2083-2

description: UK patient blood


title: 2030-5

description: UK patient blood


title: 2055-1

description: UK patient blood


title: 2055-5

description: UK patient blood


title: Sample B5

description: MSC donor 2

source_name: Transfected using lipofectamine and synthetic miR-145


title: Sample A3A

description: MSC donor 1

source_name: Transfected using electroporation and synthetic negative control miR


title: Sample A4A

description: MSC donor 1


title: Sample C3A

description: MSC donor 3


title: Sample B3A

description: MSC donor 2


title: 2083-4

description: UK patient blood


title: Sample C5

description: MSC donor 3


title: GM19239_treated_1hr

city: Chicago

first: Athma

middle: A

last: Pai

address: 920 E. 58th Street

institute: University of Chicago

hyb_protocol: mRNA was amplified from the total RNA and hybridized to the Illumina HT-12 v4.0 expression beadchip using standard Illumina protocols.

scan_protocol: Arrays were imaged using an iScan reader using standard recommended Illumina scanner settings and intensity values were compiled using BeadArray software.

data_processing: Raw intensity values were log-transformed and robust-spline normalized using the lumi package in R. For the final study, genes with low detection p-values in either the 0hr or 4hr timepoints were considered not expressed and thus not used the following analyses.

source_name: HapMap lymphoblastoid cell line, treated with ActD, 1hr timepoint

label_protocol: Standard Illumina protocols.

growth_protocol: Cell lines were cultured at 37C in RPMI 1640 media (supplemented with 2mM L-glutamine and 15% fetal bovine serum) and maintained at a density of between 2-5x10^5 viable cells/ml as per Coriell recommendations.

extract_protocol: Cells were pelleted and then total RNA was extracted with an Rneasy Mini Kit (Qiagen). RNA quality was assessed using an Agilent Bioanalyzer.

treatment_protocol: Cells were treated with Actinomycin D (ActD) to arrest transcription. The treatment was done at a concentration of 750,000 cells/ml with 7.5ug/ml of ActD.

value: male

tag: hapmap population

value: YRI

tag: ethnicity

value: Yoruba

tag: cell line

tag: treatment

value: ActD

tag: time point


title: GM19257_treated_0.5hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 0.5hr timepoint

value: female


title: GM19239_untreated_0hr

source_name: HapMap lymphoblastoid cell line, untreated, 0hr timepoint


title: 110spc4 aerobic 10 micromolar BCS plus 1 millimolar ascorbic acid 3

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

description: B. japonicum strain 110spc4 grown aerobically with 10 micromolar bathocuproine disulfonate (BCS) plus 1 millimolar ascorbic acid

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2–2.5 µg of labeled cDNA from culture-grown bacteria were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich, St. Louis, USA) in addition to the described composition. Hybridization was done overnight at 48°C.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with MAS 5 statistical algorithm (http://www.affymetrix.com).

organism: Bradyrhizobium japonicum

source_name: B. japonicum strain 110spc4 grown aerobically in BVM medium with 10 micromolar bathocuproine disulfonate (BCS) plus 1 millimolar ascorbic acid

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix). The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: Cells were grown to mid-exponential phase under aerobic conditions in buffered Vincent's minimal medium (BVM)

extract_protocol: RNA was extracted as described by Hauser et al. (2007) and Pessi et al. (2007)

treatment_protocol: BVM medium contained either "no", 5 nanomolar or 2 micromolar copper

tag: growth condition

value: aerobiosis

tag: medium

value: BVM

value: 10 micromolar bathocuproine disulfonate (BCS) plus 1 millimolar ascorbic acid added

tag: strain


title: Sample B4

description: MSC donor 2

source_name: Transfected using lipofectamine and synthetic negative control miR

tag: cell type


title: GM19239_treated_4hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 4hr timepoint

tag: gender


title: GM19238_treated_2hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 2hr timepoint


title: GM19225_treated_1hr


title: 110spc4 aerobic 2 micromolar CuSO4 2

description: B. japonicum strain 110spc4 grown aerobically with 2 micromolar CuSO4 added

source_name: B. japonicum strain 110spc4 grown aerobically in BVM medium with 2 micromolar CuSO4

value: microaerobiosis

value: 2 micromolar CuSO4 added


title: GM19238_untreated_0hr


title: 110spc4 aerobic 10 micromolar BCS plus 1 millimolar ascorbic acid 1


title: 110spc4 aerobic 2 micromolar CuSO4 1


title: 110spc4 aerobic 10 micromolar BCS plus 1 millimolar ascorbic acid 2


title: GM19239_treated_2hr


title: GM19257_treated_4hr


title: 110spc4 aerobic 2 micromolar CuSO4 3


title: GM19238_treated_1hr


title: GM19225_treated_2hr


title: GM19239_treated_0.5hr


title: 110spc4 aerobic BVM minus copper 2

description: B. japonicum 110spc4 strain  grown aerobically without added copper

source_name: B. japonicum strain 110spc4 grown aerobically in BVM medium without copper

value: no copper added (corresponds to 5 nanomolar Cu)


title: 110spc4 aerobic BVM minus copper 3


title: Sample C4

description: MSC donor 3


title: GM19238_treated_4hr


title: Sample A5

description: MSC donor 1


title: GM19257_untreated_0hr


title: GM19257_treated_2hr


title: GM19257_treated_1hr


title: GM19225_treated_4hr


title: GM19238_treated_0.5hr


title: Girl_5_Post_DTP_Vaccination

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

hyb_protocol: Affymetrix hybridization kit, hybridize 16 hours at 45° at 60rpm

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneSpring GX 10. iterPLIER16 algorithm was used for normalization
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v1.r2.dt1.hg18.core.mps

source_name: Venous full blood, Post-DTP-vaccination

label_protocol: Gene-Chip Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix)

growth_protocol: not applicable

extract_protocol: RNAeasy kit (Qiagen)

treatment_protocol: not applicable

tag: age

value: 18 to 19 months

tag: tissue

value: Blood


title: Girl_7_Pre_DTP_Vaccination

source_name: Venous full blood, Pre-DTP-vaccination


title: Girl_7_Post_DTP_Vaccination


title: Girl_8_Post_DTP_Vaccination


title: Girl_6_Pre_DTP_Vaccination


title: Girl_6_Post_DTP_Vaccination


title: Girl_4_Pre_DTP_Vaccination


title: Girl_4_Post_DTP_Vaccination


title: GM19225_treated_0.5hr


title: 110spc4 aerobic BVM minus copper 1


title: GM19223_treated_1hr


title: GM19223_treated_4hr


title: Girl_3_Pre_DTP_Vaccination


title: Girl_2_Pre_DTP_Vaccination


title: Girl_2_Post_DTP_Vaccination


title: Girl_3_Post_DTP_Vaccination


title: Girl_8_Pre_DTP_Vaccination


title: Girl_5_Pre_DTP_Vaccination


title: GM19225_untreated_0hr


title: GM19222_treated_4hr


title: GM19223_treated_2hr


title: GM19222_treated_2hr


title: GM19222_untreated_0hr


title: GM19222_treated_1hr


title: GM19223_treated_0.5hr


title: GM19222_treated_0.5hr


title: GM19223_untreated_0hr


title: GM19210_treated_4hr


title: GM19210_treated_2hr


title: Girl_1_Post_DTP_Vaccination


title: Girl_1_Pre_DTP_Vaccination


title: GM19209_treated_2hr


title: GM19210_treated_0.5hr


title: GM19209_treated_4hr


title: GM19209_untreated_0hr


title: GM19209_treated_0.5hr


title: GM19207_treated_4hr


title: GM19210_treated_1hr


title: GM19207_treated_2hr


title: GM19210_untreated_0hr


title: GM19207_untreated_0hr


title: GM19207_treated_0.5hr


title: GM19209_treated_1hr


title: GM19207_treated_1hr


title: GM19206_treated_2hr


title: M2_7

city: Bonn

first: Andrea

last: Nino Castro

state: NRW

address: Carl Troll str. 31

country: Germany

institute: Life and Medical Sciences institute

data_processing: R, quantile-normalization

source_name: human monocyte derived macrophages

label_protocol: Biotinylated cRNA were prepared with the Epicentre TargetAmp Biotin labelling kit for Illumina arrays

extract_protocol: Cells were lysed in Qiazol and Total RNA was extracted using  miRN easy kit from Qiagen. Quality control was perform by visualization in Agarose gel

value: M2 macrophages


title: GM19206_treated_4hr


title: GM19206_treated_1hr


title: M0_2

value: M0 macrophages


title: M1_7

value: M1 macrophages


title: Sample A4

description: MSC donor 1

value: mesenchymal stem cells


title: GM19204_treated_4hr


title: GM19206_untreated_0hr


title: GM19204_treated_2hr


title: M2_6


title: GM19204_treated_1hr


title: M0_6


title: M0_7


title: GM19206_treated_0.5hr


title: GM19203_treated_0.5hr

value: male


title: M1_5


title: M1_6


title: M1_4


title: M0_3


title: GM19203_treated_2hr

value: YRI


title: GM19204_untreated_0hr

value: Yoruba


title: GM19201_treated_4hr

value: ActD


title: GM19201_treated_1hr

value: female


title: GM19201_treated_0.5hr


title: GM19200_treated_4hr


title: M2_4


title: M2_5


title: M0_4


title: GM19200_treated_2hr


title: GM19203_treated_1hr


title: GM19203_treated_4hr


title: M0_1


title: GM19203_untreated_0hr


title: M2_1


title: M2_2


title: GM19204_treated_0.5hr


title: M0_5


title: M1_1


title: M2_3


title: M1_3


title: GM19201_treated_2hr


title: GM19201_untreated_0hr


title: M1_2


title: GM19200_treated_0.5hr


title: GM19200_untreated_0hr


title: PAHM4 LB-37C tech03

city: Atlanta

first: John

last: Varga

state: GA

address: 1510 Clifton Road

department: Pediatrics

institute: Emory University

hyb_protocol: aRNA was fragmented using 5x fragmentation buffer and the total amount of fragmented biotinylated aRNA used per chip was 6.5 µg. Biotinylated aRNA was then spotted in triplicate on P. aeruginosa GeneChips® (Affymetrix) following the procedure established by the manufacturer. The hybridization and washing steps were performed in the Affymetrix Array facility at the Helmoltz Center for Infection Research (HZI) in Braunschweig, Germany (Dr. Roberts Geffers).

scan_protocol: standard Affymetrix

data_processing: The analyses of the arrays were performed using Bioconductor microarray analysis suite (Gentleman, 2004). The quality of all chips was assessed by fitting a linear model to the probe level data using the fitPLM function from the affyPLM package. Expression values were computed using the Robust Multichip Average algorithm. As the number of replicates was low, differentially expressed genes were identified using the Rank Products algorithm (Irizarry, 2003). The value of 0.05 was accepted as a cut-off for pfp.

organism: Pseudomonas aeruginosa PAHM4

source_name: PAHM4 grown at 37C in LB

label_protocol: Biotinylated dUTP was incorporated during the cDNA synthesis step.

growth_protocol: All bacteria were grown to mid-exponential phase in lysogeny broth with shaking at 37C

extract_protocol: Cells were stabilized with RNA protect (Qiagen) and total RNA was purified using the RNeasy mini-kit (Qiagen).  Purified total RNA was amplified using the MessageAmpII Bacteria kit (Ambion).


title: GM19200_treated_1hr


title: PAHM4 LB-37C tech02


title: PAO1 LB-37C tech02

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 grown at 37C in LB


title: PAO1 LB-37C tech03


title: Diseased individual (ulcerative colitis) of twinpair #3

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

description: Gene expression data from whole biopsies, primary mucosal tissue

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133 2.0 Plus Array (Affymetrix GeneChipHybridization Oven 640). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Sample data was processed using GCOS 1.3.0 (Affymetrix default settings) and normalized using GCRMA (R Bioconductor, gcrma package).

source_name: primary mucosal tissue,  colon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

extract_protocol: RNA extracted using RNEasy (Qiagen) according to the manufacturers guidelines

tag: twin pair

tag: individual

value: diseased individual, inflamed

value: primary mucosal tissue,  colon

tag: mean age


title: GM19193_treated_2hr


title: GM19193_treated_0.5hr


title: Healthy individual of twinpair #2

value: healthy individual, non-inflamed


title: GM19192_treated_4hr


title: Diseased individual (ulcerative colitis) of twinpair #2


title: Healthy individual of twinpair #3


title: GM19193_treated_1hr


title: GM19193_treated_4hr


title: GM19193_untreated_0hr


title: GM19192_treated_0.5hr


title: GM19190_treated_2hr


title: GM19192_treated_1hr


title: PAO1 LB-37C tech01


title: NHBE_day28_3 [mRNA]

city: Bethesda

first: Steven

last: Kern

state: MD

address: 10 Center Drive

department: Critical Care Medicine Department

institute: National Institutes of Health

description: CCL100408_ALI_day 28_3

hyb_protocol: Following fragmentation, labeled RNA was hybridized to the Affymetrix U133 plus 2.0 microarray chip at 46 ⁰C and 60 rpm for 16h. The microarrays were washed and stained in the Affymetrix Fluidics Station 450 using the standard format as describe by Affymetrix.

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

data_processing: Gene expression was pre-processed by the Robust Multichip Analysis (RMA) algorithm using Affymetrix Expression Console. All statistical analysis were performed using the Mathematical and Statistical Computing Laboratory (MSCL) Analyst's Toolbox (http://abs.cit.nih.gov/MSCLtoolbox/).

label: Biotin

source_name: NHBE cells_Day 28

label_protocol: Total RNA (100ng) was processed and labeled using the 3’ IVT Express kit following manufacturer's instructions.

growth_protocol: Normal human bronchial epithelial cells were grown in 6.5-mm transwell-clear membrane supports coated with rat tail collagen inserted in 24-well plates. Undifferentiated cells were grown under submerged conditions until they reached confluence. At that point, an air-liquid interface culture was created by removing the apical medium and replacing the medium of the basal compartment with B-ALI differentiation medium. Medium was changed every 48h throughout the ALI culture period (4 weeks).

extract_protocol: Trizol extraction of total RNA combined with spin column extraction was performed according to manufacturer's instructions (miRNeasy  Mini kit, Qiagen).

treatment_protocol: Cells were harvested for total RNA extraction when they were subconfluent or confluent, and after 28 days of ALI culture.

value: normal human bronchial epithelial (NHBE) cells

tag: culture stage

value: Day 28


title: NHBE_day28_2 [mRNA]

description: CCL100408_ALI_day 28_2


title: GM19192_treated_2hr


title: GM19192_untreated_0hr


title: NHBE_Confluent_3 [mRNA]

source_name: NHBE cells_Confluent stage

value: Confluent


title: HEPG2, EtOH treated

city: Innsbruck

first: Oliver

middle: Alexander

last: Wrulich

address: Innrain 80-82

department: Medical Biochemistry

country: Austria

institute: Medical University Innsbruck

description: Gene expression data from EtOH (solvent control)-treated HepG2 cells.

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: GCRMA using R 2.15.1 with the gcrma 2.28.0 package.

source_name: HepG2 cells treated with EtOH (solvent control)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA.

growth_protocol: HepG2 cells were seeded into a 25cm cell culture flask in DMEM growth medium supplemented with 10% FCS (w/o antibiotics).

extract_protocol: Cell culture flasks were placed on ice for 15 min, and then washed with PBS (4°C) and scraped off in 3ml of PBS (4°C). Total RNA was extracted with the Qiagen RNeasy Mini Kit according to the manufacturer's protocol.

treatment_protocol: 6 hrs after seeding, the medium was replaced by fresh growth medium containing PADMA28 aqueous ethanolic solution (218ug/ml) or 0.9% EtOH (solvent control). Treatment time was 18 hrs.

value: EtOH

tag: treatment duration


title: GM19190_untreated_0hr

tag: hapmap population


title: GM19190_treated_0.5hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 0.5hr timepoint

tag: ethnicity


title: NHBE_Confluent_2 [mRNA]


title: GM19190_treated_4hr

tag: cell line


title: NHBE_day28_1 [mRNA]

description: CCL100408_ALI_day 28_1


title: HEPG2, PADMA28 treated

description: Gene expression data from PADMA28-treated HepG2 cells.

source_name: HepG2 cells treated with PADMA28

tag: treatment


title: NHBE_Confluent_1 [mRNA]


title: GM19171_treated_4hr

tag: time point


title: GM19190_treated_1hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 1hr timepoint


title: NHBE_Subconfluent_1 [mRNA]

source_name: NHBE cells_Subconfluent stage

value: Subconfluent


title: GM19171_treated_0.5hr


title: Control, donor 5

first: Markus

middle: H

last: Kuehn

state: IA

address: 375 Newton Road

department: Ophthalmology and Visual Sciences

description: Gene expression of trabecular meshwork and scleorcorneal tissue maintaned in perfusion organ culture, control eye without dexamethasome

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

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

data_processing: Data were normalized using RMAExpress software and PLM .

source_name: trabecular meshwork and corneoscleral tissue

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

growth_protocol: Human donor eyes were obtained from the local eye bank between five and six hours postmortem. Following removal of the lens, Iris, and ora serrata, anterior segments were maintained in a profusion organ culture system. Eyes were perfused at 2 µL per minute with DMEN and the pressure inside the perfusion chamber was continuously monitored with a blood pressure transducer.

extract_protocol: After 10 days in culture the trabecular meshwork and the underlying corneoscleral tissue would dissected along Schwalbe's line and the scleral spur. RNA was extracted using Rneasy minipreps (Qiagen).

treatment_protocol: One eye from each pair was perfused with culture medium containing 100 nM dexamethasone while the fellow I was maintained in culture media only as a control. Both eyes were maintained under these conditions for 10 days.

value: 73 years

tag: Sex


title: GM19171_untreated_0hr

source_name: HapMap lymphoblastoid cell line, untreated, 0hr timepoint


title: GM19160_treated_0.5hr


title: NHBE_Subconfluent_2 [mRNA]


title: NHBE_Subconfluent_3 [mRNA]


title: Dex treatment, donor 4

description: Gene expression of trabecular meshwork and scleorcorneal tissue maintaned in perfusion organ culture, Study  eye with dexamethasome

value: 100 nM dexamethasone

value: 90 years


title: Control, donor 4


title: GM19160_treated_2hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 2hr timepoint


title: Dex treatment, donor 3

value: 51 years


title: GM19171_treated_1hr

value: male


title: GM19160_treated_4hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 4hr timepoint

value: YRI


title: GM19160_untreated_0hr

value: Yoruba


title: Control, donor 3


title: Dex treatment, donor 5


title: GM19171_treated_2hr

value: ActD


title: GM19160_treated_1hr


title: Dex treatment, donor 2

value: 69 years


title: Dex treatment, donor 1

value: 77 years


title: GM19159_treated_0.5hr

value: female


title: GM19159_treated_1hr


title: GM19159_treated_4hr


title: Control, donor 1


title: GM19159_treated_2hr


title: Control, donor 2


title: GM19153_treated_4hr


title: PAHM4 LB-37C tech01


title: GM19159_untreated_0hr


title: GM19152_treated_4hr


title: GM19153_treated_2hr


title: GM19152_treated_2hr


title: GM19152_treated_0.5hr


title: GM19153_untreated_0hr


title: GM19153_treated_1hr


title: Microvascular endothelial cells from healthy subject 2

city: Florence

first: Betti

last: Giusti

address: viale Morgagni, 85

department: Dpt. of Medical and Surgical Critical Care

country: Italy

institute: University of Florence

description: Biological replicate 2/3

hyb_protocol: Biotinylated cRNA was then purified and fragmented before hybridization. After an over-night hybridization, GeneChips were washed and stained with streptoavidin-phycoerythrin conjugate and biotinylated anti-streptavidin antibody. RNA from individual N-MVECs was hybridized to each chip.

scan_protocol: Scanned with Affymetrix GeneChip Scanner 3000

data_processing:
After the scanning procedure, data files were checked for quality parameters (such as scale factor, background noise, corner and central fluorescent intensities, GAPDH and Actin 3'/5' ratio values and percentage of expressed probe sets).
MAS 5.0

source_name: microvascular endothelial cells from healthy subject

label_protocol: Double-stranded cDNA was synthesized by reverse transcriptase reaction from total RNA extracted from the N-MVECs (siDSG2-treated  and control N-MVECs). cDNA was then used to obtain biotin-labeled cRNA by in vitro transcription reaction.

growth_protocol: Isolated cells were isolated  from apparently healthy subject and were identified as microvascular endothelial cells (MVECs) by labeling with anti-factor VIII-related antigen, anti-CD105 (endoglin), and re-probing with anti-CD31 antibodies.

extract_protocol: Total RNA was isolated from cultured N-MVEC and siDSG2-N-MVECs using RNeasy Qiagen Kit (QIAGEN, Germany), as suggested by the manufacturer. The presence of RNA degradation was assessed by evaluation of 28S and 18S band sharpness after denaturing electrophoresis. Quantification and purity of RNA samples was performed by 260 and 280 spectrophotometer analysis; a 260/280 absorbance ratio ranging between 1.8 and 2.1 being acceptable.

treatment_protocol: siRNAs for down-regulation of DSG2 expression and irrelevant control siRNA were obtained from DharmaFECT (DHARMACON RNA Technologies, Euroclone, Pero, Milan, Italy; siGENOME SMARTpool M-017765-0005, Human DSG2, NM_002852). To favour internalization into N-MVEC, siRNA constructs were incorporated into cationic liposomes, utilizing DharmaFECT transfection reagent and following the instructions of the manufacturer. Briefly, N-MVEC were grown to 70-80% confluence and maintained over-night in antibiotic-free culture medium, supplemented with 2% FBS. Solutions of siRNA (2μM) and DarmaFECT transfection reagent were separately diluted in serum-free culture medium (1:2 and 1:200, respectively) and incubated 5 min at room temperature. Solutions were mixed and incubated 20 min at room temperature. Serum-free culture medium was then added to reach a final concentration of 100 nM siRNA. Culture medium was then removed, cells were rinsed with PBS and incubated with transfection mix (24-48 hours for mRNA analysis, and 72 hours for protein and phenotypic analysis, respectively). The silenced gene was analyzed by RT-PCR, utilizing previously described primers and cycling conditions (5, 7).

value: microvascular endothelial cells

tag: protocol

value: control


title: Microvascular endothelial cells from healthy subject 1

description: Biological replicate 1/3


title: DSG2 silenced microvascular endothelial cells from healthy subject 3

description: Biological replicate 3/3

value: DSG2 knockdown


title: DSG2 silenced microvascular endothelial cells from healthy subject 2

description: Biological replicate 2/3


title: Microvascular endothelial cells from healthy subject 3

description: Biological replicate 3/3


title: GM19152_treated_1hr


title: GM19153_treated_0.5hr


title: DSG2 silenced microvascular endothelial cells from healthy subject 1

description: Biological replicate 1/3


title: GM19147_treated_2hr


title: P1636 WM plasma cells_GPL570

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

description: human peripheral blood B cells  P1636 WM plasma cells_GPL570

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

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

source_name: P1636 WM plasma cells_GPL570

label_protocol: Biotinylated cRNA were prepared according to the standard affymetrix protocol

extract_protocol: RNeasy Mini Kit(50)

tag: P1636 WM plasma cells_GPL570


title: P2060 WM plasma cells_GPL570

description: human peripheral blood B cells  P2060 WM plasma cells_GPL570

source_name: P2060 WM plasma cells_GPL570

tag: P2060 WM plasma cells_GPL570


title: P1578 WM plasma cells_GPL570

description: human peripheral blood B cells  P1578 WM plasma cells_GPL570

source_name: P1578 WM plasma cells_GPL570

tag: P1578 WM plasma cells_GPL570


title: P1642 MM plasma cells_GPL570

description: human peripheral blood B cells  P1642 MM plasma cells_GPL570

source_name: P1642 MM plasma cells_GPL570

tag: P1642 MM plasma cells_GPL570


title: W01 WM plasma cells_GPL570

description: human peripheral blood B cells  W01 WM plasma cells_GPL570

source_name: W01 WM plasma cells_GPL570

tag: W01 WM plasma cells_GPL570


title: GM19147_treated_1hr

tag: gender


title: GM19147_treated_4hr


title: W02 WM plasma cells_GPL570

description: human peripheral blood B cells  W02 WM plasma cells_GPL570

source_name: W02 WM plasma cells_GPL570

tag: W02 WM plasma cells_GPL570


title: GM19147_treated_0.5hr


title: GM19152_untreated_0hr


title: P1809 MM plasma cells_GPL570

description: human peripheral blood B cells  P1809 MM plasma cells_GPL570

source_name: P1809 MM plasma cells_GPL570

tag: P1809 MM plasma cells_GPL570


title: P1641 MM plasma cells_GPL570

description: human peripheral blood B cells  P1641 MM plasma cells_GPL570

source_name: P1641 MM plasma cells_GPL570

tag: P1641 MM plasma cells_GPL570


title: P1360 WM plasma cells_GPL570

description: human peripheral blood B cells  P1360 WM plasma cells_GPL570

source_name: P1360 WM plasma cells_GPL570

tag: P1360 WM plasma cells_GPL570


title: P1411 SMM plasma cells_GPL570

description: human peripheral blood B cells  P1411 SMM plasma cells_GPL570

source_name: P1411 SMM plasma cells_GPL570

tag: P1411 SMM plasma cells_GPL570


title: P1577 WM plasma cells_GPL570

description: human peripheral blood B cells  P1577 WM plasma cells_GPL570

source_name: P1577 WM plasma cells_GPL570

tag: P1577 WM plasma cells_GPL570


title: GM19144_treated_4hr

tag: hapmap population

tag: ethnicity

tag: cell line


title: P1294 WM plasma cells_GPL570

description: human peripheral blood B cells  P1294 WM plasma cells_GPL570

source_name: P1294 WM plasma cells_GPL570

tag: P1294 WM plasma cells_GPL570


title: GM19144_treated_0.5hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 0.5hr timepoint

tag: treatment

tag: time point


title: GM19144_treated_1hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 1hr timepoint


title: GM19144_treated_2hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 2hr timepoint


title: GM19144_untreated_0hr

source_name: HapMap lymphoblastoid cell line, untreated, 0hr timepoint


title: GM19147_untreated_0hr


title: GM19143_treated_2hr


title: GM19143_treated_4hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 4hr timepoint


title: P1287 WM plasma cells_GPL570

description: human peripheral blood B cells  P1287 WM plasma cells_GPL570

source_name: P1287 WM plasma cells_GPL570

tag: P1287 WM plasma cells_GPL570


title: P1280-02 WM plasma cells_GPL570

description: human peripheral blood B cells  P1280-02 WM plasma cells_GPL570

source_name: P1280-02 WM plasma cells_GPL570

tag: P1280-02 WM plasma cells_GPL570


title: P1288 WM plasma cells_GPL570

description: human peripheral blood B cells  P1288 WM plasma cells_GPL570

source_name: P1288 WM plasma cells_GPL570

tag: P1288 WM plasma cells_GPL570


title: P1293 WM plasma cells_GPL570

description: human peripheral blood B cells  P1293 WM plasma cells_GPL570

source_name: P1293 WM plasma cells_GPL570

tag: P1293 WM plasma cells_GPL570


title: P1018 MGUS plasma cells_GPL570

description: human peripheral blood B cells  P1018 MGUS plasma cells_GPL570

source_name: P1018 MGUS plasma cells_GPL570

tag: P1018 MGUS plasma cells_GPL570


title: P1280-01 WM plasma cells_GPL570

description: human peripheral blood B cells  P1280-01 WM plasma cells_GPL570

source_name: P1280-01 WM plasma cells_GPL570

tag: P1280-01 WM plasma cells_GPL570


title: P0950 MM plasma cells_GPL570

description: human peripheral blood B cells  P0950 MM plasma cells_GPL570

source_name: P0950 MM plasma cells_GPL570

tag: P0950 MM plasma cells_GPL570


title: P1285 WM plasma cells_GPL570

description: human peripheral blood B cells  P1285 WM plasma cells_GPL570

source_name: P1285 WM plasma cells_GPL570

tag: P1285 WM plasma cells_GPL570


title: P0925 WM plasma cells_GPL570

description: human peripheral blood B cells  P0925 WM plasma cells_GPL570

source_name: P0925 WM plasma cells_GPL570

tag: P0925 WM plasma cells_GPL570


title: GM19143_treated_0.5hr

tag: gender


title: GM19141_treated_4hr


title: P0829 WM plasma cells_GPL570

description: human peripheral blood B cells  P0829 WM plasma cells_GPL570

source_name: P0829 WM plasma cells_GPL570

tag: P0829 WM plasma cells_GPL570


title: GM19143_untreated_0hr

tag: hapmap population


title: GM19143_treated_1hr

tag: ethnicity


title: GM19141_treated_2hr

tag: cell line


title: GM19141_treated_0.5hr


title: GM19141_treated_1hr


title: P1026 MGUS plasma cells_GPL570

description: human peripheral blood B cells  P1026 MGUS plasma cells_GPL570

source_name: P1026 MGUS plasma cells_GPL570

tag: P1026 MGUS plasma cells_GPL570


title: GM19140_treated_4hr

tag: treatment


title: P0699-02 WM plasma cells_GPL570

description: human peripheral blood B cells  P0699-02 WM plasma cells_GPL570

source_name: P0699-02 WM plasma cells_GPL570

tag: P0699-02 WM plasma cells_GPL570


title: P0697 MM plasma cells_GPL570

description: human peripheral blood B cells  P0697 MM plasma cells_GPL570

source_name: P0697 MM plasma cells_GPL570

tag: P0697 MM plasma cells_GPL570


title: P0714 WM plasma cells_GPL570

description: human peripheral blood B cells  P0714 WM plasma cells_GPL570

source_name: P0714 WM plasma cells_GPL570

tag: P0714 WM plasma cells_GPL570


title: P0699-01 WM plasma cells_GPL570

description: human peripheral blood B cells  P0699-01 WM plasma cells_GPL570

source_name: P0699-01 WM plasma cells_GPL570

tag: P0699-01 WM plasma cells_GPL570


title: P0624 WM plasma cells_GPL570

description: human peripheral blood B cells  P0624 WM plasma cells_GPL570

source_name: P0624 WM plasma cells_GPL570

tag: P0624 WM plasma cells_GPL570


title: P0771-02 WM plasma cells_GPL570

description: human peripheral blood B cells  P0771-02 WM plasma cells_GPL570

source_name: P0771-02 WM plasma cells_GPL570

tag: P0771-02 WM plasma cells_GPL570


title: GM19141_untreated_0hr

source_name: HapMap lymphoblastoid cell line, untreated, 0hr timepoint

tag: time point


title: P0771-03 WM plasma cells_GPL570

description: human peripheral blood B cells  P0771-03 WM plasma cells_GPL570

source_name: P0771-03 WM plasma cells_GPL570

tag: P0771-03 WM plasma cells_GPL570


title: GM19140_treated_1hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 1hr timepoint


title: GM19140_untreated_0hr


title: GM19140_treated_0.5hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 0.5hr timepoint


title: GM19140_treated_2hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 2hr timepoint


title: P0652 MGUS plasma cells_GPL570

description: human peripheral blood B cells  P0652 MGUS plasma cells_GPL570

source_name: P0652 MGUS plasma cells_GPL570

tag: P0652 MGUS plasma cells_GPL570


title: GM19138_treated_4hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 4hr timepoint


title: P0514 WM plasma cells_GPL570

description: human peripheral blood B cells  P0514 WM plasma cells_GPL570

source_name: P0514 WM plasma cells_GPL570

tag: P0514 WM plasma cells_GPL570


title: GM19138_treated_1hr

tag: gender


title: P0450 SMM plasma cells_GPL570

description: human peripheral blood B cells  P0450 SMM plasma cells_GPL570

source_name: P0450 SMM plasma cells_GPL570

tag: P0450 SMM plasma cells_GPL570


title: P0445 WM plasma cells_GPL570

description: human peripheral blood B cells  P0445 WM plasma cells_GPL570

source_name: P0445 WM plasma cells_GPL570

tag: P0445 WM plasma cells_GPL570


title: P0488 WM plasma cells_GPL570

description: human peripheral blood B cells  P0488 WM plasma cells_GPL570

source_name: P0488 WM plasma cells_GPL570

tag: P0488 WM plasma cells_GPL570


title: Intestinal vs. control SmedArray1-Biorep4

first: Noelle

last: James

address: 601 S. Goodwin Ave.

department: Cell and Developmental Biology

institute: U of IL / HHMI

description: This is the fourth of four biological replicates used in this experiment, each prepared separately.

hyb_protocol: Labeled aRNA targets were hydrolyzed using RNA Fragmentation Reagents (Ambion/Applied Biosystems) according to the manufacturerʼs instructions.  Combimatrix arrays were hydrated, prehybridized, hybridized, and washed according to the manufacturerʼs protocols.

scan_protocol: Arrays were covered with Imaging Solution and a LifterSlip, and imaged using a GenePix 4000B Scanner and GenePix Pro 6.0 software (Axon Instruments/Molecular Devices).

data_processing: GenePix “.gpr” files were processed using the limma package in Bioconductor (Gentleman et al., 2004; Smyth, 2004). Within-array loess normalization was conducted with the normexp background correction method (Ritchie et al., 2007) and an offset value of 25; the scale method was utilized for between-array normalization. Normalized values for each spot were fitted to a linear model, and moderated t-statistics and adjusted p-values were calculated for each probe on the array.

label: Alexa Fluor 647

organism: Schmidtea mediterranea

source_name: Intestine

label_protocol: ~12 μg aminoallyl-labeled aRNA were coupled to Alexa Fluor 555 or Alexa Fluor 647 succinimidyl ester dyes (Molecular Probes) and purified according to the MessageAmp II protocol. Labeling efficiency was calculated using a NanoDrop spectrophotometer.

growth_protocol: Asexual Schmidtea mediterranea were maintained in 1X Montjuic salts at 21°C (Cebrià  et al., 2005)

extract_protocol: All intestinal cells (2-5 x 10^5) and ~10% of non-intestinal cells (1-3 x 10^6)  were lysed in Trizol (Invitrogen). RNA was isolated according to the manufacturerʼs instructions, using the high-salt step for RNA precipitation. RNA was DNAse-treated, purified, and concentrated using the DNA-free RNA kit (Zymo Research). 500 ng of total RNA were amplified using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion).

treatment_protocol: One hundred large planarians were fed a mixture of liver homogenate, food coloring, and Feridex (AMAG Pharmaceuticals). Forty-eight hours later, animals were dissociated into single cell suspensions essentially as described (Reddien et al., 2005), with the exception that dispase (Worthington Biochemical, final 0.6U/mL) was substituted for trypsin. Intestinal phagocytes were purified on Miltenyi magnetic columns.

tag: cell type

value: Intestinal phagocytes

tag: strain

value: asexual

label: Alexa Fluor 555

source_name: Control

value: non-intestinal cells (column flow-through)


title: Intestinal vs. control SmedArray1-Biorep3

description: This is the third of four biological replicates used in this experiment, each prepared separately.


title: GM19137_treated_4hr

tag: hapmap population

tag: ethnicity

tag: cell line

tag: treatment


title: P0542 WM plasma cells_GPL570

description: human peripheral blood B cells  P0542 WM plasma cells_GPL570

source_name: P0542 WM plasma cells_GPL570

tag: P0542 WM plasma cells_GPL570


title: GM19137_treated_1hr


title: GM19138_untreated_0hr


title: GM19138_treated_0.5hr


title: GM19138_treated_2hr


title: P0485 WM plasma cells_GPL570

description: human peripheral blood B cells  P0485 WM plasma cells_GPL570

source_name: P0485 WM plasma cells_GPL570

tag: P0485 WM plasma cells_GPL570


title: GM19137_treated_0.5hr


title: GM19131_treated_4hr


title: GM19131_treated_2hr


title: Intestinal vs. control SmedArray1-Biorep1

description: This is the first of four biological replicates used in this experiment, each prepared separately.


title: GM19131_treated_1hr


title: GM19131_treated_0.5hr


title: GM19137_untreated_0hr


title: GM19137_treated_2hr


title: GM19131_untreated_0hr


title: GM19130_treated_1hr


title: Intestinal vs. control SmedArray1-Biorep2

description: This is the second of four biological replicates used in this experiment, each prepared separately.


title: GM19130_treated_4hr


title: 474867A10 - Col0+NAA_BR2 vs Col0_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: study the role of AtNSRs proteins in the regulation of gene expression

hyb_protocol: Col0_BR2 Cy5 / Col0+NAA_BR2 Cy3 : 40pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media=1/2 MS 0%sucrose Temperature=24C° Light=long days

extract_protocol: Col0_BR2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

tag: genotype

value: wildtype

tag: developmental stage

value: (boyes et al. plant cell 2001):boyes:1.0

extract_protocol: Col0+NAA_BR2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Auxin - hormone treatment - hormone addition,auxin:quantity 1uM time 24hour . 10days plants growing in 1/2MS 0%sucrose are transfered in auxin plates during 24h before harvest.


title: GM19130_treated_2hr

tag: time point


title: 474913A06 - Col0+NAA_BR3 vs nsra-b+NAA_BR3

hyb_protocol: nsra-b+NAA_BR3 Cy5 / Col0+NAA_BR3 Cy3 : 40pmol.

value: mutant

extract_protocol: Col0+NAA_BR3:10ug. (Qiagen_RNeasy.pdf)


title: GM19130_untreated_0hr

value: male


title: 474913A02 - nsra-b_BR3 vs Col0_BR3

hyb_protocol: Col0_BR3 Cy5 / nsra-b_BR3 Cy3 : 40pmol.

extract_protocol: Col0_BR3:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: nsra-b_BR3:10ug. (Qiagen_RNeasy.pdf)


title: 474912A05 - nsra-b+NAA_BR2 vs Col0+NAA_BR2

hyb_protocol: Col0+NAA_BR2 Cy5 / nsra-b+NAA_BR2 Cy3 : 40pmol.


title: GM19130_treated_0.5hr

extract_protocol: Cells were pelleted and then total RNA was extracted with an Rneasy Mini Kit (Qiagen). RNA quality was assessed using an Agilent Bioanalyzer.

value: YRI


title: 474913A09 - nsra-b+NAA_BR3 vs Col0+NAA_BR3

hyb_protocol: Col0+NAA_BR3 Cy5 / nsra-b+NAA_BR3 Cy3 : 40pmol.


title: 474867A06 - Col0_BR2 vs Col0+NAA_BR2

hyb_protocol: Col0+NAA_BR2 Cy5 / Col0_BR2 Cy3 : 40pmol.


title: 474912A01 - Col0+NAA_BR2 vs nsra-b+NAA_BR2

hyb_protocol: nsra-b+NAA_BR2 Cy5 / Col0+NAA_BR2 Cy3 : 40pmol.


title: GM19128_treated_4hr

hyb_protocol: mRNA was amplified from the total RNA and hybridized to the Illumina HT-12 v4.0 expression beadchip using standard Illumina protocols.

value: Yoruba


title: 474871A01 - Col0_BR2 vs nsra-b+NAA_BR2

hyb_protocol: nsra-b+NAA_BR2 Cy5 / Col0_BR2 Cy3 : 40pmol.


title: GM19128_treated_2hr

value: ActD


title: 474896A05 - Col0_BR2 vs nsra-b_BR2

hyb_protocol: nsra-b_BR2 Cy5 / Col0_BR2 Cy3 : 40pmol.

extract_protocol: nsra-b_BR2:10ug. (Qiagen_RNeasy.pdf)


title: 474912A09 - Col0_BR3 vs nsra-b_BR3

hyb_protocol: nsra-b_BR3 Cy5 / Col0_BR3 Cy3 : 40pmol.


title: GM19128_treated_1hr


title: 474871A05 - nsra-b+NAA_BR2 vs Col0_BR2

hyb_protocol: Col0_BR2 Cy5 / nsra-b+NAA_BR2 Cy3 : 40pmol.


title: GM19128_treated_0.5hr


title: GM19127_treated_1hr


title: 474874A06 - nsra-b_BR1 vs Col0_BR1

hyb_protocol: Col0_BR1 Cy5 / nsra-b_BR1 Cy3 : 40pmol.

extract_protocol: Col0_BR1:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: nsra-b_BR1:10ug. (Qiagen_RNeasy.pdf)


title: GM19128_untreated_0hr


title: GM19127_treated_4hr


title: GM19127_treated_2hr


title: 474896A02 - nsra-b+NAA_BR1 vs Col0+NAA_BR1

hyb_protocol: Col0+NAA_BR1 Cy5 / nsra-b+NAA_BR1 Cy3 : 40pmol.

extract_protocol: Col0+NAA_BR1:10ug. (Qiagen_RNeasy.pdf)


title: 474896A10 - nsra-b_BR2 vs Col0_BR2

hyb_protocol: Col0_BR2 Cy5 / nsra-b_BR2 Cy3 : 40pmol.


title: 474873A10 - nsra-b+NAA_BR3 vs Col0_BR3

hyb_protocol: Col0_BR3 Cy5 / nsra-b+NAA_BR3 Cy3 : 40pmol.


title: 474874A01 - Col0_BR1 vs nsra-b_BR1

hyb_protocol: nsra-b_BR1 Cy5 / Col0_BR1 Cy3 : 40pmol.


title: GM19127_untreated_0hr


title: 474874A10 - Col0+NAA_BR1 vs nsra-b+NAA_BR1

hyb_protocol: nsra-b+NAA_BR1 Cy5 / Col0+NAA_BR1 Cy3 : 40pmol.


title: GM19127_treated_0.5hr


title: GM19119_treated_2hr


title: GM19119_treated_4hr


title: GM19119_treated_0.5hr


title: GM19119_treated_1hr


title: 474867A01 - nsra-b+NAA_BR1 vs Col0_BR1

hyb_protocol: Col0_BR1 Cy5 / nsra-b+NAA_BR1 Cy3 : 40pmol.


title: 474873A06 - Col0_BR3 vs nsra-b+NAA_BR3

hyb_protocol: nsra-b+NAA_BR3 Cy5 / Col0_BR3 Cy3 : 40pmol.


title: GM19116_treated_2hr


title: GM19116_treated_4hr


title: mut neural crest cell at E10.5, biological rep1

city: shanghai

first: yunfu

last: sun

state: shanghai

address: 150 jimo road, pudong new district

department: school of medicine

country: China

institute: tongji university

description:
Gene expression data from cardiac neural crest at E10.5
Mut1 OFT

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

data_processing: program-name = Expression Console; affymetrix-algorithm-name = plier-mm

source_name: ILK mutant neural crest cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: embryos at E10.5 were dissected and genotyped

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

treatment_protocol: The OFTs of NKO mutant and control embryos at E10.5 were digested with collagenase/dispase (1mg/ml)/trypsin (0.1%) for 10 minutes (x3). The cell suspension was filtered through a 40um filter unit, centrifuged and resuspended in up to 0.5ml staining medium, and stained with FDG using FluoReporter LacZ Flow Cytometry kits (Molecular Probes, F-1930). The treated cell suspensions were FACS sorted (BD FACSAria) and stored at 80°C.

tag: tissue

value: outflow tract (OFT)

value: cardiac neural crest cell

tag: genotype/variation

value: ILK deletion

value: embryo

tag: age


title: GM19119_untreated_0hr

tag: gender


title: 474852A10 - Col0_BR1 vs nsra-b+NAA_BR1

hyb_protocol: nsra-b+NAA_BR1 Cy5 / Col0_BR1 Cy3 : 40pmol.


title: control neural crest cell at E10.5, biological rep2

description:
Gene expression data from cardiac neural crest at E10.5
Wt2 OFT

source_name: control neural crest cells


title: 474873A02 - Col0+NAA_BR3 vs Col0_BR3

hyb_protocol: Col0_BR3 Cy5 / Col0+NAA_BR3 Cy3 : 30pmol.


title: mut neural crest cell at E10.5, biological rep2

description:
Gene expression data from cardiac neural crest at E10.5
Mut2 OFT


title: control neural crest cell at E10.5, biological rep1

description:
Gene expression data from cardiac neural crest at E10.5
Wt1 OFT


title: reverted nurse thorax vs. typical-aged nurse thorax

city: Las Vegas

first: Joseph

last: Margotta

address: 4505 S. Maryland Parkway

department: SOLS

institute: University of Nevada, Las Vegas

description: Reversion comparison

hyb_protocol: Arrays were hybridized with 120 picomoles of each labeled tissue’s probes.

scan_protocol: Arrays were then scanned with a GenePix scanner (Molecular Devices, Sunnyvale, CA, USA) and visualized using GenePix software (Agilent Technologies, Santa Clara, CA, USA).  Prior to data analysis, each array was visually inspected for any inconsistencies in dye incorporation.

data_processing:
Analysis was implemented in R version 2.8.  Data was normalized using the Limma package in R.  Spots were log transformed and within-slide normalization was conducted using a print-tip Loess to correct for differences between print-tips on the array printer and variation during the print run.  No background correction was used for within-slide normalization.  For between-slide normalization, a quantile normalization method was used.  Pre and post normalization MA plots were generated to ensure each array was of acceptable quality to use.
The log2 lowess normalized (average of all replicates) data is available on a Series records ('average_normalized_data.txt")

organism: Apis mellifera

source_name: Reverted nurse 'RN' (25 to 26 days old; 7 to 9 days flight experience)

label_protocol: For each individual, 4 micrograms of brain RNA were labeled with cy3 and 4 micrograms of thorax RNA were labeled with cy5 using a Kreatech Labeling Kit (Applied Biosystems, Salt Lake City, UT, USA).  The directionality of the dye labeling was switched between replicates to avoid a dye bias.

growth_protocol: Honey bees (Apis mellifera L.) used for this project were reared at the University of Nevada, Las Vegas apiary. 4 source colonies headed by a single drone inseminated queen (Glenn Apiaries, Fallbrook, CA,USA) carrying the Minnesota (MN) varroa sensitive hygienic (VSH) genotype were used to obtain age/genotype matched workers to start single-cohort colonies (SCCs).  From these source colonies, eight SCCs were created using a frame of pollen, an open frame for the SCC’s queen to lay on and a frame of honey.

extract_protocol: RNA was extracted from dissected brains and thoraces using PicoPure RNA Isolation kits according to the manufacturer’s protocol (Molecular Devices, Sunnyvale, CA, USA).

treatment_protocol: Whole bee heads and thoraces were partially lyophilized at -70°C to facilitate dissection.  Heads and thoraces were then dissected on dry ice to prevent RNA degradation.

tag: behavioral group

value: European honey bee in nurse behavioral stage

value: thorax

source_name: Typical aged nurse 'YN' (8-10 days old; <1 day flight experience)


title: 474871A09 - Col0_BR3 vs Col0+NAA_BR3

hyb_protocol: Col0+NAA_BR3 Cy5 / Col0_BR3 Cy3 : 40pmol.


title: old forager thorax vs. reverted nurse thorax

description: Reversion comparison

source_name: Forager - old 'OF' (25 to 26 days old; 10 to 12 days flight experience)

value: European honey bee in forager behavioral stage


title: GM19116_untreated_0hr

hyb_protocol: mRNA was amplified from the total RNA and hybridized to the Illumina HT-12 v4.0 expression beadchip using standard Illumina protocols.

source_name: HapMap lymphoblastoid cell line, untreated, 0hr timepoint

value: female


title: GM19116_treated_1hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 1hr timepoint


title: 10T1/2, both_treatment

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

description: Gene expression data from 10T1/2 with both MAL overexpression and MED23 deficiency

hyb_protocol: The Affymetrix GeneChip arrays were hybridized and washed using the manufacturer's protocol.

scan_protocol: Affymetrix GeneChip arrays were scanned using the Affymetrix GeneArray scanner.

data_processing: The microarray data were normalized using the Robust Multichip Average (RMA) method. We discarded probe sets that did not have signals above background in more than 75% of the arrays for all samples using the Affymetrix MAS5 present/absent calls.

source_name: 10T1/2 cell, both MAL overexpression and Med23 deficiency

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: WT and Med23 KO MEFs were isolated from 9.5-day embryos and self-immortalized from standard protocol (Balamotis et al. 2009; Wang et al. 2009). MEF and 10T1/2 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% FBS (Hyclone) in 5% CO2.

treatment_protocol: No treatment prior to experiment was applied.

tag: cell type

value: embryonic fibroblast

value: cell line derived from embryo

value: MAL overexpression and MED23 deficiency


title: 10T1/2, control

description: Gene expression data from 10T1/2 control

source_name: 10T1/2 cell, control


title: MEF, Med23KO_serum_90min

description: Gene expression data from Med23 KO cultured with serum for 90min

source_name: MEF cell, Med23 deficiency , 90min serum

value: 9.5-day embryos

value: serum for 90min


title: GM19116_treated_0.5hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 0.5hr timepoint


title: 474852A02 - Col0_BR1 vs Col0+NAA_BR1

hyb_protocol: Col0+NAA_BR1 Cy5 / Col0_BR1 Cy3 : 40pmol.

value: columbia

value: wildtype

value: (boyes et al. plant cell 2001):boyes:1.0


title: GM19114_untreated_0hr

value: YRI

value: Yoruba


title: 10T1/2, MAL_overexpression

description: Gene expression data from 10T1/2 with MAL overexpression

source_name: 10T1/2 cell, MAL overexpression

value: MAL overexpression


title: typical-aged nurse thorax vs. old forager thorax

description: Behavioral comparison

source_name: Typical-aged nurse 'YN' (8-10 days old; <1 day flight experience)


title: 10T1/2, Med23_knockdown

description: Gene expression data from 10T1/2 with MED23 deficiency

source_name: 10T1/2 cell, Med23 deficiency

value: MED23 deficiency


title: GM19114_treated_4hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 4hr timepoint

value: ActD


title: GM19114_treated_1hr


title: GM19114_treated_0.5hr


title: MEF, Med23KO_serum_30min

description: Gene expression data from Med23 KO cultured with serum for 30min

source_name: MEF cell, Med23 deficiency , 30min serum

value: serum for 30min


title: precocious forager thorax vs. typical-aged nurse thorax

description: Behavioral comparison

source_name: Precocious forager 'PF' (8 to 10 days old; 2 to 3 days flight experience)

value: thorax

value: European honey bee in nurse behavioral stage


title: overage nurse thorax vs. forager - low flight thorax

description: Behavioral comparison

source_name: Overaged nurse 'ON' (19 to 22 days old; < 1 day flight experience)

source_name: Forager - low flight 'TFL' (19 to 22 days old; 2 to 3 days flight experience)

value: European honey bee in forager behavioral stage


title: 474852A05 - Col0+NAA_BR1 vs Col0_BR1

hyb_protocol: Col0_BR1 Cy5 / Col0+NAA_BR1 Cy3 : 40pmol.


title: GM19108_treated_4hr

value: female


title: forager low flight thorax vs. precocious forager thorax

description: Flight comparison


title: GM19114_treated_2hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 2hr timepoint


title: MEF, Med23KO_serum_0min

description: Gene expression data from Med23 KO MEF

source_name: MEF cell, Med23 deficiency , no serum

value: embryonic fibroblast

value: no serum


title: GM19108_treated_1hr


title: GM19108_untreated_0hr


title: MEF, WT_serum_90min

description: Gene expression data from WT MEF cultured with serum for 90min

source_name: MEF cell, control, 90min serum

value: wild type

value: 9.5-day embryos


title: GM19108_treated_0.5hr


title: GM19108_treated_2hr


title: reverted nurse thorax vs. forager - high flight thorax

description: Behavioral comparison

source_name: Reverted nurse 'RN' (25 to 26 days old; 7 to 9 days flight experience)

source_name: Forager - high flight 'TFH' ( 19 to 22 days old; 7 to 9 days flight experience)


title: GM19102_treated_4hr


title: overage nurse thorax vs. reverted nurse thorax

description: Reversion comparison


title: MEF, WT_serum_30min

description: Gene expression data from WT MEF cultured with serum for 30min

source_name: MEF cell, control, 30min serum


title: forager - high flight thorax vs. forager low flight thorax

description: Flight comparison


title: typical-aged nurse thorax  vs. overage nurse thorax

description: Age comparison


title: reverted nurse brain vs. typical-aged nurse brain

description: Reversion comparison

value: brain

source_name: Typical aged nurse 'YN' (8-10 days old; <1 day flight experience)


title: embryonic stem cells

city: guangzhou

first: zhenwei

last: song

address: beisan road

institute: sun yat-sen university

description: primary cell

hyb_protocol: Hybridization Control Kit (Affymetrix, P/N 900454).  Hybridization Oven 640. Affymetrix Gene Chip Mouse Genome 430 2.0 Array (GEO accession number: platform GPL1261, Affymetrix, Santa Clara, CA, USA) was used for microarray hybridizations to examine global gene expression of samples at Capital biochip Corp. (Beijing, China) in which the gene chip microarray service was certified by Affymetrix.

scan_protocol: GeneChip® Scanner 3000

data_processing: The normalization method in our data processing is according to the RMA (based on log (PM/MM)) with s series of calculation with some default set supplied by Affymetrix company.

source_name: embryonic stem cells

label_protocol: One-cycle target labeling protocol was completed with the reagent MessageAmp II-Biotin (Ambion, #1791) and Poly-A RNA Control Kit (Affymetrix, P/N 900433),

growth_protocol: MEFs were derived from embryonic day 13.5 mice embryos and maintained in Dulbecco’s modified Eagle’s medium (DMEM; high glucose) containing 10% fetal bovine serum (FBS), nonessential amino acids (NEAA), L-glutamate, sodium pyruvate, and penicillin/streptomycin. ESCs and iPSCs were cultured on γ-irradiated MEFs in ES medium containing Knockout DMEM supplemented with 20% KnockOut Serum Replacement, NEAA, L-glutamate, sodium pyruvate, 0.1 mM β-mercaptoethanol, penicillin/streptomycin, and 1000 U/ml leukemia inhibitory factor (Millipore, Billerica, MA, USA). All other reagents were purchased from Invitrogen Corp. (Carlsbad, CA, USA).

extract_protocol: Total RNA was purified using TRIzol reagent (Invitrogen) and reverse transcribed using a reverse transcription system (Promega, Madison, WI, USA) according to the manufacturer’s protocol.

treatment_protocol: MEF cells were plated at 80% conﬂuence and transfected with PMX-based retroviral vectors (Addgene, Cambridge, MA, USA) containing murine Oct4, Sox2, and Klf4 cDNAs using Lipofectamine 2000 (Invitrogen) following the manufacturer’s instructions. The virus supernatant was harvested 48 hours after transfection. MEFs at passage 2 or 3 were seeded at a density of 3500–5000 cells/cm2 and incubated with filtered viral supernatants containing equal parts of the three transcription factors (Oct4, Sox2, Klf4)[88] and 5 μg/ml polybrene. Twelve hours later, the medium was gradually replaced with ESC medium supplemented with 50 μg/ml Vc (Sigma-Aldrich, St. Louis, MO, USA) using a 4-day stepwise process

tag: strain

value: embryonic stem cells

value: male

value: embryo


title: GM19102_treated_2hr

first: Athma

last: Pai

address: 920 E. 58th Street

data_processing: Raw intensity values were log-transformed and robust-spline normalized using the lumi package in R. For the final study, genes with low detection p-values in either the 0hr or 4hr timepoints were considered not expressed and thus not used the following analyses.

label_protocol: Standard Illumina protocols.

tag: hapmap population

value: YRI

value: Yoruba


title: Induced pluripotent stem cells

description: primary cell

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells


title: MEF, WT_serum_0min

description: Gene expression data from WT MEF

source_name: MEF cell, control, no serum


title: GM19102_untreated_0hr

source_name: HapMap lymphoblastoid cell line, untreated, 0hr timepoint

tag: ethnicity


title: GM19101_treated_4hr

tag: cell line

value: ActD


title: GM19099_treated_4hr

tag: treatment


title: GM19101_treated_0.5hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 0.5hr timepoint


title: GM19102_treated_1hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 1hr timepoint


title: mouse embryonic fibroblasts

description: primary cell

source_name: mouse embryonic fibroblasts

value: embryonic fibroblasts


title: GM19099_treated_2hr


title: GM19102_treated_0.5hr


title: old forager brain vs. reverted nurse brain

description: Reversion comparison

source_name: Forager - old 'OF' (25 to 26 days old; 10 to 12 days flight experience)


title: typical-aged nurse brain vs. old forager brain

description: Behavioral comparison

source_name: Typical-aged nurse 'YN' (8-10 days old; <1 day flight experience)


title: GM19101_treated_2hr


title: GM19101_untreated_0hr


title: mouse embryonic fibroblasts day7

description: artificial cell induced by virus

source_name: mouse embryonic fibroblasts_ ay7

value: embryonic fibroblasts day7


title: overage nurse brain vs. forager - low flight brain

description: Behavioral comparison

source_name: Overaged nurse 'ON' (19 to 22 days old; < 1 day flight experience)

value: European honey bee in nurse behavioral stage

source_name: Forager - low flight 'TFL' (19 to 22 days old; 2 to 3 days flight experience)


title: GM19099_treated_1hr


title: precocious forager brain vs. typical-aged nurse brain

description: Behavioral comparison

source_name: Precocious forager 'PF' (8 to 10 days old; 2 to 3 days flight experience)

value: European honey bee in forager behavioral stage


title: GM19099_treated_0.5hr

value: female


title: GM19098_treated_4hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 4hr timepoint


title: GM19099_untreated_0hr


title: GM19098_treated_1hr


title: GM19101_treated_1hr


title: forager low flight brain vs. precocious forager brain

description: Flight comparison


title: forager - high flight brain vs. forager low flight brain

description: Flight comparison

source_name: Forager - high flight 'TFH' ( 19 to 22 days old; 7 to 9 days flight experience)


title: GM19093_treated_4hr


title: GM19098_treated_0.5hr


title: GM19098_untreated_0hr


title: GM19098_treated_2hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 2hr timepoint


title: GM19093_treated_2hr


title: GM19093_treated_1hr


title: overage nurse brain vs. reverted nurse brain

description: Reversion comparison

source_name: Reverted nurse 'RN' (25 to 26 days old; 7 to 9 days flight experience)


title: GM19093_treated_0.5hr


title: GM19092_treated_2hr


title: GM19092_treated_4hr


title: typical-aged nurse brain vs. overage nurse brain

description: Age comparison


title: reverted nurse brain vs. forager - high flight brain

description: Behavioral comparison


title: GM19092_treated_0.5hr


title: GM19092_treated_1hr


title: GM19092_untreated_0hr


title: GM19093_untreated_0hr


title: Heart.Placebo.Norm.6

city: Gold Coast

first: Kevin

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

country: Australia

institute: Bond University

description:
SAMPLE 24
replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were variance stabilized and robust spline normalized using the ‘lumi’ package in R/BioConductor

source_name: ventricular myocardium, 5 days placebo,normoxic

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

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

treatment_protocol: Mature male C57Bl/6 mice were briefly anesthetized with halothane, a small incision made at the base of the neck, and placebo or 75-mg morphine pellets were inserted into the dorsal subcutaneous space before closure with 9-mm wound clips. Pellets were left in place for 5 days before analysis of cardiac I-R tolerance ex vivo. Briefly mice were anesthetized with sodium pentobarbital and hearts excised and perfused in a Langendorff mode. After 30 min stabilization control (placebo) and SLP hearts were subjected to either 25 min of global normothermic ischemia and 45 minutes of aerobic reperfusion, or time-matched normoxic perfusion. Hearts were collected in RNAlater and the left ventricular tissue dissected from the heart.

value: 10-14 weeks

tag: agent

value: placebo

tag: treatment protocol (post-agent)

value: normoxic perfusion

value: ventricular myocardium


title: Heart.Placebo.Norm.4

description:
SAMPLE 22
replicate 4


title: Pediatric diarrheal sample from Mexico, #12

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

description:
Sample12
Amplified cDNA.

hyb_protocol: Microarrays were hybridized overnight at 65C according to the manufacturer's protocol (Agilent Technologies) using the Agilent Gene Expression Hybridization kit.

scan_protocol: Microarrays were scanned at 2 um resolution on an Agilent DNA Microarray Scanner.

data_processing:
Background-subtracted output intensities from Agilent's Feature Extraction software from 37,432 V3/V4 viral probes were sum normalized and then used for cluster and Z-score analysis (Eisen, et al., 1998; Chiu, et al., 2006; Chen, et al., 2011). Samples were declared positive for a diarrheal virus by microarray if positive by both cluster and Z-score analysis.

The background-subtracted output intensities from Agilent's Feature Extraction Software are available in 'GSE40008_raw_matrix.txt', which is linked to the Series record as a supplementary file.
The sum-normalized intensities are in the Sample data tables.

source_name: Diarrheal stool

label_protocol: Randomly amplified cDNA was labelled using a Cy3 fluorescent dye via aa-dNTP incorporation (Wang, et al, 2002; Chiu, et al, 2006; Chiu, et al, 2008).

growth_protocol: Viral particles were purified from stool samples by shaking 1 mL phosphate-buffered saline, 0.1 g glass beads, 100 uL chloroform, and 0.2 g feces using a mechanical shaker, spinning x 20 min x 1000g in a centrifuge, and recovering the supernatant.

extract_protocol: Total nucleic acid was extracted using the PureLink 96 Viral RNA/DNA kit.

treatment_protocol: 500 uL of supernatant were passed through a 0.45 um filter and treated with a cocktail of nucleases (Turbo DNAse, Ambion, and RANseA, Invitrogen)

value: child

tag: disease state

value: acute gastroenteritis

value: diarrhea

tag: polyomavirus (mxpyv) status

value: positive


title: GM18916_untreated_0hr

city: Chicago

institute: University of Chicago

scan_protocol: Arrays were imaged using an iScan reader using standard recommended Illumina scanner settings and intensity values were compiled using BeadArray software.

value: YRI


title: GM18916_treated_4hr

value: Yoruba


title: GM18913_treated_4hr

value: male


title: GM18916_treated_2hr

value: ActD


title: Pediatric diarrheal sample from Mexico, #10

description:
Sample10
Amplified cDNA.

tag: developmental stage


title: Heart.Placebo.Norm.5

description:
SAMPLE 23
replicate 5


title: vU1.8 snRNA knock-down, biological replicate 3

city: Oxford

first: Martin

last: Dienstbier

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

hyb_protocol: Performed by Source Bioscience according to the manufacturer's instructions.

data_processing:
Microarray data from 4 biological repeats (each for vU1.8 knock-down and control) were processed by Affymetrix Power tools (http://www.affymetrix.com) using DABG and RMA algorithms for background correction and quantile normalization. Signal values were expressed in log2-scale.
HuEx-1_0-st-v2.r2.pgf

source_name: HeLa, vU1.8 snRNA knock-down

growth_protocol: HeLa cells were grown in Dulbecco's Modified Eagle Media (Invitrogen) supplemented with 10% fetal calf serum, 50  g of Penicillin per ml and 4 uM L-glutamine.

extract_protocol: Total RNA was isolated from HeLa cells using Trizol (Invitrogen), according to manufacturers’ instructions.

treatment_protocol: Knockdown experiments were performed in HeLa cells with lipofectAMINE 2000 reagent (Invitrogen) according to manufacturers' instructions. Typically, 1 × 107 cells were transfected with 600 pmoles of the 2-OMe oligonucleotide and cells harvested 18 hrs later. The control oligonucleotide is sense to the tU1 at position 11 to 32, the vU1.8-specific oligonucleotide is antisense to vU1.8 at position 11 to 33, where 1 is the first base of the U1/vU1 sequence.

value: HeLa


title: Pediatric diarrheal sample from Mexico, #11

description:
Sample11
Amplified cDNA.


title: GM18913_untreated_0hr

source_name: HapMap lymphoblastoid cell line, untreated, 0hr timepoint

treatment_protocol: Cells were treated with Actinomycin D (ActD) to arrest transcription. The treatment was done at a concentration of 750,000 cells/ml with 7.5ug/ml of ActD.

tag: time point


title: GM18913_treated_0.5hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 0.5hr timepoint


title: GM18913_treated_1hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 1hr timepoint


title: Heart.Placebo.Norm.1

description:
SAMPLE 19
replicate 1

tag: tissue


title: GM18916_treated_0.5hr


title: Pediatric diarrheal sample from Mexico, #9

description:
Sample9
Amplified cDNA.


title: GM18913_treated_2hr