title: EnglishCockerSpaniel-Lingaas_481_ARRAY106890


title: EnglishCockerSpaniel-Lingaas_476_ARRAY106858

status: Public on Nov 20 2014

type: genomic

city: Cambridge

first: Hyun Ji

last: Noh

state: MA

address: 7 Cambridge Center

department: Genome Sequencing and Analysis

country: USA

institute: Broad Institute

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from blood using the Puregene DNA purification Kit (Gentra Systems) protocol.

tag: tissue

value: blood


title: EnglishCockerSpaniel-Lingaas_471_ARRAY106842


title: EnglishCockerSpaniel-Lingaas_430_ARRAY106794


title: EnglishCockerSpaniel-Lingaas_441_ARRAY106810


title: EnglishCockerSpaniel-Lingaas_442_ARRAY106826


title: EnglishCockerSpaniel-Lingaas_554_ARRAY106814


title: EnglishCockerSpaniel-Lingaas_429_ARRAY106778


title: DobermanPinscher-BI_20892_ARRAY376100


title: EnglishCockerSpaniel-Lingaas_427_ARRAY106746


title: GoldenRetriever-BI_11648_ARRAY127420


title: EnglishCockerSpaniel-Lingaas_428_ARRAY106762


title: GoldenRetriever-BI_11043_ARRAY127436


title: GoldenRetriever-BI_02970_ARRAY127388


title: EnglishCockerSpaniel-Lingaas_514_ARRAY106828


title: GoldenRetriever-BI_03568_ARRAY127404


title: GoldenRetriever-BI_03886_ARRAY127372


title: EnglishCockerSpaniel-Lingaas_494_ARRAY106780


title: GoldenRetriever-BI_11791_ARRAY127340


title: GoldenRetriever-BI_11848_ARRAY127356


title: GoldenRetriever-BI_11790_ARRAY127324


title: GoldenRetriever-BI_11789_ARRAY127308


title: GoldenRetriever-BI_03684_ARRAY127276


title: GoldenRetriever-BI_09117_ARRAY127418


title: GoldenRetriever-BI_11628_ARRAY127434


title: GoldenRetriever-BI_05076_ARRAY127260


title: GoldenRetriever-BI_11788_ARRAY127292


title: GoldenRetriever-BI_02139_ARRAY127402


title: EnglishCockerSpaniel-BI_13387_ARRAY141310


title: GoldenRetriever-BI_03539_ARRAY127354


title: GoldenRetriever-BI_03686_ARRAY127370


title: GoldenRetriever-BI_01963_ARRAY127386


title: Eurasier-BI_11709_ARRAY127426


title: Eurasier-BI_11710_ARRAY127252


title: Eurasier-BI_11707_ARRAY127394


title: Eurasier-BI_11708_ARRAY127410


title: Eurasier-BI_11704_ARRAY127346


title: Eurasier-BI_11705_ARRAY127362


title: Eurasier-BI_11699_ARRAY127298


title: Eurasier-BI_11660_ARRAY127266


title: Eurasier-BI_11661_ARRAY127282


title: Eurasier-BI_11703_ARRAY127330


title: Eurasier-BI_11658_ARRAY127424


title: Eurasier-BI_11659_ARRAY127250


title: Eurasier-BI_11657_ARRAY127408


title: Eurasier-BI_11655_ARRAY127376


title: Eurasier-BI_11654_ARRAY127360


title: Eurasier-BI_11652_ARRAY127344


title: Boxer-BI_11571_ARRAY127312


title: Boxer-BI_05565_ARRAY127406


title: Boxer-BI_06470_ARRAY127422


title: Boxer-BI_09734_ARRAY127296


title: Boxer-BI_07332_ARRAY127248


title: Boxer-BI_07383_ARRAY127280


title: Boxer-BI_03677_ARRAY127342


title: Boxer-BI_03703_ARRAY127358


title: Boxer-BI_03302_ARRAY127294


title: Eurasier-BI_11706_ARRAY127378


title: Boxer-BI_09385_ARRAY127390


title: Boxer-BI_03208_ARRAY127246


title: Greyhound-BI_15170_ARRAY185956


title: Greyhound-BI_15180_ARRAY186004


title: Boxer-BI_03228_ARRAY127262


title: Greyhound-BI_15174_ARRAY185988


title: Greyhound-BI_15192_ARRAY186036


title: Greyhound-BI_15167_ARRAY185924


title: Greyhound-BI_15166_ARRAY185908


title: Eurasier-BI_11650_ARRAY127328


title: Greyhound-BI_15164_ARRAY185892


title: Greyhound-BI_15163_ARRAY185876


title: Greyhound-BI_14586_ARRAY185986


title: Greyhound-BI_14569_ARRAY185970


title: Boxer-BI_03671_ARRAY127326


title: Greyhound-BI_15162_ARRAY185860


title: Greyhound-BI_14568_ARRAY185954


title: Greyhound-BI_14992_ARRAY185922


title: Greyhound-BI_14994_ARRAY186032


title: Greyhound-BI_14998_ARRAY186000


title: Greyhound-BI_14995_ARRAY185874


title: Greyhound-BI_15173_ARRAY185972


title: Greyhound-BI_15020_ARRAY185984


title: Boxer-BI_07353_ARRAY127264


title: Greyhound-BI_15079_ARRAY185968


title: GoldenRetriever-BI_14705_ARRAY185920


title: Boxer-BI_04911_ARRAY127374


title: GoldenRetriever-BI_14703_ARRAY185888


title: GoldenRetriever-BI_14702_ARRAY185872


title: GoldenRetriever-BI_15648_ARRAY185936


title: GoldenRetriever-BI_14978_ARRAY185950


title: GoldenRetriever-BI_14941_ARRAY185934


title: GoldenRetriever-BI_14940_ARRAY185918


title: GoldenRetriever-BI_14939_ARRAY185902


title: GoldenRetriever-BI_14937_ARRAY185886


title: Greyhound-BI_14981_ARRAY185938


title: GoldenRetriever-BI_14935_ARRAY185870


title: GoldenRetriever-BI_14934_ARRAY185854


title: GoldenRetriever-BI_14933_ARRAY186028


title: GoldenRetriever-BI_14931_ARRAY185996


title: GoldenRetriever-BI_14930_ARRAY185980


title: GoldenRetriever-BI_14929_ARRAY185964


title: GoldenRetriever-BI_03808_ARRAY127338


title: GoldenRetriever-BI_14927_ARRAY185932


title: GoldenRetriever-BI_14928_ARRAY185948


title: GoldenRetriever-BI_14925_ARRAY185900


title: GoldenRetriever-BI_14926_ARRAY185916


title: Greyhound-BI_15062_ARRAY185952


title: GoldenRetriever-BI_14924_ARRAY185884


title: GoldenRetriever-BI_14921_ARRAY185868


title: GoldenRetriever-BI_14920_ARRAY185852


title: GoldenRetriever-BI_14916_ARRAY185978


title: GoldenRetriever-BI_14915_ARRAY185962


title: GoldenRetriever-BI_14914_ARRAY185946


title: GoldenRetriever-BI_14912_ARRAY185914


title: GoldenRetriever-BI_14918_ARRAY186010


title: GoldenRetriever-BI_14913_ARRAY185930


title: GoldenRetriever-BI_14688_ARRAY185882


title: GoldenRetriever-BI_14695_ARRAY185898


title: GoldenRetriever-BI_14241_ARRAY185866


title: GoldenRetriever-BI_09632_ARRAY186008


title: GoldenRetriever-BI_09483_ARRAY185992


title: GoldenRetriever-BI_05036_ARRAY185960


title: GoldenRetriever-BI_03527_ARRAY185912


title: GoldenRetriever-BI_03525_ARRAY185896


title: GoldenRetriever-BI_03232_ARRAY185880


title: GoldenRetriever-BI_02859_ARRAY185848


title: GoldenRetriever-BI_02698_ARRAY185990


title: GoldenRetriever-BI_02739_ARRAY186022


title: GoldenRetriever-BI_02501_ARRAY185958


title: GoldenRetriever-BI_02703_ARRAY186006


title: GoldenRetriever-BI_02394_ARRAY185942


title: GoldenRetriever-BI_02093_ARRAY185894


title: Eurasier-BI_11701_ARRAY127314


title: GoldenRetriever-BI_02366_ARRAY185926


title: GoldenRetriever-BI_13853_ARRAY238734


title: GoldenRetriever-BI_13854_ARRAY238732


title: GoldenRetriever-BI_01990_ARRAY185862


title: GoldenRetriever-BI_13851_ARRAY238736


title: GoldenRetriever-BI_13856_ARRAY238730


title: GoldenRetriever-BI_09739_ARRAY185850


title: GoldenRetriever-BI_13534_ARRAY238728


title: GoldenRetriever-BI_13532_ARRAY238724


title: GoldenRetriever-BI_09480_ARRAY185976


title: GoldenRetriever-BI_13533_ARRAY238726


title: GoldenRetriever-BI_13915_ARRAY238720


title: GoldenRetriever-BI_13923_ARRAY238722


title: GoldenRetriever-BI_12970_ARRAY238716


title: GoldenRetriever-BI_11469_ARRAY238718


title: GoldenRetriever-BI_03685_ARRAY238714


title: GoldenRetriever-BI_12359_ARRAY238712


title: GoldenRetriever-BI_12355_ARRAY238708


title: GoldenRetriever-BI_12358_ARRAY238710


title: GoldenRetriever-BI_12354_ARRAY238706


title: GoldenRetriever-BI_02091_ARRAY185878


title: GoldenRetriever-BI_12348_ARRAY238700


title: GoldenRetriever-BI_01989_ARRAY185846


title: GoldenRetriever-BI_09214_ARRAY238698


title: GoldenRetriever-BI_09191_ARRAY238696


title: GoldenRetriever-BI_09154_ARRAY238694


title: GoldenRetriever-BI_09101_ARRAY238688


title: GoldenRetriever-BI_11590_ARRAY238684


title: GoldenRetriever-BI_09075_ARRAY238686


title: GoldenRetriever-BI_09298_ARRAY238674


title: GoldenRetriever-BI_09448_ARRAY238678


title: GoldenRetriever-BI_09379_ARRAY238676


title: GoldenRetriever-BI_09297_ARRAY238672


title: GoldenRetriever-BI_09294_ARRAY238668


title: GoldenRetriever-BI_05895_ARRAY238664


title: GoldenRetriever-BI_05479_ARRAY238662


title: GoldenRetriever-BI_03269_ARRAY238660


title: GoldenRetriever-BI_03230_ARRAY238658


title: GoldenRetriever-BI_02568_ARRAY238656


title: GoldenRetriever-BI_02487_ARRAY238654


title: NeapolitanMastiff-BI_24078_ARRAY238652


title: GoldenRetriever-BI_12351_ARRAY238704


title: NeapolitanMastiff-BI_24077_ARRAY238650


title: NeapolitanMastiff-BI_24076_ARRAY238648


title: NeapolitanMastiff-BI_24074_ARRAY238646


title: NeapolitanMastiff-BI_24073_ARRAY238644


title: NeapolitanMastiff-BI_24072_ARRAY238642


title: NeapolitanMastiff-BI_24071_ARRAY238640


title: NeapolitanMastiff-BI_24070_ARRAY238638


title: NeapolitanMastiff-BI_24069_ARRAY238636


title: NeapolitanMastiff-BI_24068_ARRAY238634


title: NeapolitanMastiff-BI_24067_ARRAY238632


title: AfghanHound-BI_14951_ARRAY238626


title: AfghanHound-BI_12918_ARRAY238628


title: AfghanHound-BI_14480_ARRAY238624


title: Boxer-BI_03301_ARRAY127278


title: AfghanHound-BI_22392_ARRAY238622


title: GoldenRetriever-BI_05959_ARRAY238666


title: AfghanHound-BI_15872_ARRAY238620


title: Saluki-BI_11074_ARRAY238618


title: Saluki-BI_11054_ARRAY238616


title: Saluki-BI_11153_ARRAY238612


title: Saluki-BI_11076_ARRAY238610


title: Saluki-BI_11062_ARRAY238608


title: Saluki-BI_11069_ARRAY238604


title: Saluki-BI_09692_ARRAY238602


title: Saluki-BI_11075_ARRAY238600


title: Basenji-BI_24059_ARRAY238598


title: Basenji-BI_24056_ARRAY238592


title: Basenji-BI_24057_ARRAY238594


title: Basenji-BI_24058_ARRAY238596


title: Basenji-BI_24055_ARRAY238590


title: Basenji-BI_24053_ARRAY238586


title: Wolf-BI_23916_ARRAY238578

organism: Canis lupus


title: Wolf-BI_22818_ARRAY238576


title: Wolf-BI_23917_ARRAY238580


title: Saluki-BI_11064_ARRAY238614


title: Wolf-BI_22814_ARRAY238570


title: Wolf-BI_22809_ARRAY238562


title: Wolf-BI_22808_ARRAY238560


title: Wolf-BI_22812_ARRAY238566


title: Wolf-BI_22804_ARRAY238554


title: Wolf-BI_22802_ARRAY238552


title: Wolf-BI_22817_ARRAY238574


title: Wolf-BI_22813_ARRAY238568


title: Wolf-BI_22801_ARRAY238550


title: Wolf-BI_22800_ARRAY238548


title: Wolf-BI_22807_ARRAY238558


title: Saluki-BI_11065_ARRAY238606


title: Wolf-BI_22799_ARRAY238546


title: Akita-BI_05477_ARRAY127996


title: Akita-BI_05478_ARRAY127980


title: GoldenRetriever-UTRECHT_1695_ARRAY127964


title: GoldenRetriever-BI_03741_ARRAY127948


title: Wolf-BI_22816_ARRAY238572


title: GoldenRetriever-BI_03726_ARRAY127932


title: GoldenRetriever-BI_03724_ARRAY127900


title: GoldenRetriever-BI_12342_ARRAY127852


title: GoldenRetriever-BI_05893_ARRAY127836


title: GoldenRetriever-BI_03744_ARRAY127884


title: GoldenRetriever-BI_03725_ARRAY127916


title: GoldenRetriever-BI_12341_ARRAY128010


title: RNA_DU-145 cells

type: RNA

city: Fort Worth

first: Smrithi

last: Rajendiran

state: TX

address: 3500 Camp Bowie Blvd

institute: UNT Health Science Center

description:
4 technical replicates during hybridization
T01

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193]. A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level. t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric. All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

molecule: total RNA

organism: Homo sapiens

source_name: Prostate adenocarcinoma cells

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started with isolation of 1 to 2 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

growth_protocol: DU-145 cells were grown in RPMI 1640 media supplemented with FBS. PWR-1E were grown in Keratinocyte Serum Free media supplemented with human recombinant epidermal growth factor and Bovine Pitutary Extract.

extract_protocol: DU-145 and PWR-1E cells were trypsinized, spun down, washed with sterile PBS and frozen immediately at -80°C. The samples were de-identified and shipped to LC Sciences (Houston, TX) for microarray hybridization.

treatment_protocol: Neither cells were treated in any way before isolation of RNA.

tag: cell line

tag: cell type

value: Prostate adenocarcinoma cells from 69 year-old Caucasian male deposited to ATCC


title: RNA_PWR-1E cells

description:
4 technical replicates during hybridization
T02

source_name: Normal prostate epithelial cells

value: Normal prostate epithelial cells from 67 year-old Caucasian male deposited to ATCC


title: GoldenRetriever-BI_12340_ARRAY127994


title: muscle of 3 eels [ LP_M4]

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: muscle of 3 eels

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized seaprately for each tissue by quantile normalization  of gPRocessed signalusing R2.6.1 statistical software

label: Cyanine 3

organism: Anguilla anguilla

source_name: Pool of RNA  extracted  from muscle of 3 eels

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to Absolutely RNA RT-PCR Miniprep kit (Agilent) according to the manufacturer’s instructions.

treatment_protocol: Eels were collected using electric fishing under similar climatic and hydrological conditions.

tag: sample location

value: segment 2 (Langouarde) of the Canal des Etangs

value: muscle

tag: collection method

value: Individuals were sampled below the obstacle, close to the fishway entry.


title: GoldenRetriever-BI_03427_ARRAY127866


title: GoldenRetriever-BI_02658_ARRAY127850


title: muscle of 3 eels [ LP_M3]

description: muscle of 3 eels

value: segment 1 (Pas du Bouc) of the Canal des Etangs


title: muscle of 3 eels [ LP_M5]

description: muscle of 3 eels


title: Leonberger-BI_03448_ARRAY127992


title: Leonberger-BI_03446_ARRAY127960


title: Leonberger-BI_03447_ARRAY127976


title: muscle of 3 eels [ LP_M6]

description: muscle of 3 eels


title: muscle of 3 eels [ LP_M1]

description: muscle of 3 eels


title: Leonberger-BI_03445_ARRAY127944


title: liver of 3 eels [ LP_F9]

description: liver of 3 eels

source_name: Pool of RNA  extracted  from liver of 3 eels

value: segment 3 (Joncru) of the Canal des Etangs

value: liver

value: Individuals were sampled on the fishway, as water depth before the obstacle, approximately 2 meters, precluded the use of electro-fishing technique.


title: liver of 3 eels [ LP_F8]

description: liver of 3 eels


title: Greyhound-BI_15001_ARRAY185906


title: Leonberger-BI_03444_ARRAY127928


title: Leonberger-BI_03443_ARRAY127912


title: liver of 3 eels [ LP_F7]

description: liver of 3 eels


title: muscle of 3 eels [ LP_M2]

description: muscle of 3 eels


title: liver of 3 eels [ LP_F6]

description: liver of 3 eels


title: GoldenRetriever-BI_03882_ARRAY127978


title: Leonberger-BI_03442_ARRAY127896


title: Greyhound-BI_15168_ARRAY185940


title: Leonberger-BI_03821_ARRAY127880


title: Leonberger-BI_03818_ARRAY127864


title: Leonberger-BI_03791_ARRAY128006


title: Leonberger-BI_03792_ARRAY127832


title: liver of 3 eels [ LP_F3]

description: liver of 3 eels


title: liver of 3 eels [ LP_F1]

description: liver of 3 eels


title: liver of 3 eels [ LP_F4]

description: liver of 3 eels


title: Leonberger-BI_03789_ARRAY127990


title: Leonberger-BI_03718_ARRAY127974


title: liver of 3 eels [ LP_F5]

description: liver of 3 eels


title: liver of 3 eels [ LP_F2]

description: liver of 3 eels


title: brain of 3 eels [ LP_C9]

description: brain of 3 eels

source_name: Pool of RNA  extracted  from brain of 3 eels

value: brain


title: brain of 3 eels [ LP_C8]

description: brain of 3 eels


title: brain of 3 eels [ LP_C7]

description: brain of 3 eels


title: Leonberger-BI_03711_ARRAY127926


title: Damaged interstitium 2

city: Houston

first: Frank

last: McKeon

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

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

hyb_protocol: Hybridization was done using standard Affymetrix protocols

scan_protocol: GeneChip® Scanner 3000,Affymetrix

data_processing: The intensity values were Log2-transformed and imported into the Partek Genomics Suite 6.6 (Partek Inc, USA). Exons were summarized to genes and 1-way ANOVA was performed to identify differentially expressed genes. P values and fold-change were calculated for each analysis.

label: biotin

organism: Mus musculus

source_name: Laser capture microdissection

label_protocol: RNA was amplified and labelled using WT Pico RNA Amplification System, WT-Ovation Exon Module and Encore Biotin Module (NuGEN Technologies)

extract_protocol: RNA was extracted using Pico pure RNA isolation kit from Arcturus.

value: distal lung

tag: state

value: damage from influenza infected mice


title: brain of 3 eels [ LP_C5]

description: brain of 3 eels


title: brain of 3 eels [ LP_C6]

description: brain of 3 eels


title: Leonberger-BI_03710_ARRAY127910


title: Damaged interstitium 1


title: Leonberger-BI_03709_ARRAY127894


title: Leonberger-BI_03702_ARRAY127878


title: Tracheal epithelium 2

value: trachea

value: healthy


title: brain of 3 eels [ LP_C1]

description: brain of 3 eels


title: Alveoli 1


title: brain of 3 eels [ LP_C2]

description: brain of 3 eels


title: brain of 3 eels [ LP_C4]

description: brain of 3 eels


title: Tracheal epithelium 1


title: brain of 3 eels [ LP_C3]

description: brain of 3 eels


title: Leonberger-BI_03700_ARRAY127846


title: Leonberger-BI_03701_ARRAY127862


title: Alveoli 2


title: Cells_NARA_T48hrs_biological rep4

city: Indianapolis

first: James

middle: G

last: MacKrell

state: IN

address: 355 East Merrill St

department: Musculoskeletal

institute: Eli Lilly & Company

hyb_protocol: The cRNA was hybridized to Affymetrix Rat Genome 230_2.0 microarrays according to Affymetrix protocols.  Each microarray was washed and stained using an Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Affymetrix confocal GeneArray scanner

data_processing: Affymetrix MAS5.0 software was used to scale data to a target intensity of 1500 and calculate transcript abundance (signal).

organism: Rattus norvegicus

source_name: LASCs, NARA (10nM) treatment, 48 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: LASCs were maintained in DMEM/F-12 (1:1) (Invitrogen, 21041-025) supplemented with 10% fetal bovine serum, 1% Pen/Strep, and 2.4 ug/ml sodium bicarbonate.

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

treatment_protocol: Treatments (Vehicle or NARA) were performed in growth media with fetal bovine serum replaced with charcoal stripped serum (10%).

value: Levator Ani muscle

value: muscle satellite cell

tag: cell passage

value: passage number 5


title: Cells_NARA_T48hrs_biological rep1


title: Transplanted1

source_name: Transplanted cells incorporated into lung by LCM

growth_protocol: LacZ labeled DASC stem cells are grown on irradiated mouse fibroblast feeder layer and then transplanted into Influenza-injured mouse lung.

value: lung

tag: sample type

value: transplated cells


title: Cells_NARA_T48hrs_biological rep2


title: Cells_NARA_T48hrs_biological rep3


title: Cells_Vehicle_T48hrs_biological rep3

source_name: LASCs, vehicle (DMSO, 0.2%) treatment, 48 hours


title: Leonberger-BI_03699_ARRAY127830

value: blood


title: ndr1-1, V. longisporum-inoculated, 48 hpi, replicate 3

city: Uppsala

first: Jonas

last: Roos

address: PO Box 7080

department: Dept. Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description: Ndr1 +V1(3)

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to Arabidopsis GeneChip ATH1/GPL198 Genome Array, and washed and stained using the Affymetrix Model 450 Fluidics Station.

scan_protocol: GeneChips were scanned on the Affymetrix Model 3000 scanner using the manufacturer's protocol.

data_processing: Normalization of the microarray data was performed using the Robust Multichip Average (RMA) method as implemented by the “quantile normalization” function in the Bioconductor 1.3 software.

organism: Arabidopsis thaliana

source_name: ndr1-1_V. longisporum-inoculated_48 hpi

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis Col-0 and ndr1-1 seeds were grown in petri dishes with liquid MS medium supplemented with 0.2% sucrose, on a horizontal shaker (40 rpm). The light intensity was 100 µmol E m-2 s-1 and the temperature  21°C (light) and 16°C (dark). The light/dark regime was 16/h/8h.

extract_protocol: At 48 hours post inoculation, root materials were harvested in biological replicates (>50 plant roots) and immediately frozen in liquid nitrogen. RNA was extracted with Aurum Total RNA Mini Kit (Bio-Rad).

treatment_protocol: After two weeks, plants were rinsed twice in sterile distilled water and transferred to liquid 0.5xMS medium without sucrose, supplemented with 200 conidia ml-1 of V. longisporum isolate VL1 (CBS110220). Control plants were grown in 0.5x MS only.

tag: ecotype background

tag: genotype

value: Defense signaling mutant ndr1-1

tag: age

value: 16 days old

value: Pool of >50 individual roots

tag: inoculated with

value: V. longisporum isolate VL1 (CBS110220)

tag: time point

value: 48 hpi


title: ndr1-1, V. longisporum-inoculated, 48 hpi, replicate 2

description: Ndr1 +V1(2)


title: DTR2

source_name: DASC ablated lung, 75pfu H1N1 infected, 30dpi, Dtox treated

treatment_protocol: Mice were infected by 75pfu H1N1 Influenza virus and treated by 5ug/kg Diphtheria Toxin (Dtox) at 8dpi. Lungs were harvested at 30dpi.

tag: genotype/variation


title: Transplanted2


title: Leonberger-BI_03697_ARRAY127988


title: Damaged1

source_name: Damaged lung tissue by LCM

value: damaged


title: AfghanHound-BI_05153_ARRAY238630


title: Leonberger-BI_03638_ARRAY127956


title: Damaged2


title: Leonberger-BI_03698_ARRAY128004


title: WT1

source_name: Control lung, 75pfu H1N1 infected, 30dpi, Dtox treated

value: wild type


title: Cells_Vehicle_T48hrs_biological rep4


title: DTR1


title: Leonberger-BI_03628_ARRAY127940


title: TBSC-ALI2

source_name: primary cell culture

growth_protocol: Mouse upper airways and distal lungs were disossciated enzymatically and stem cells are grown on irradiated mouse fibroblast feeder layer. Differentiation of stem cells are performed in 3D Matrigel (MAT) system and Air-Liquid Interface (ALI) system respectively.

value: upper airway

tag: culture condition

value: on ALI in upper airway differentiation medium


title: Cells_Vehicle_T48hrs_biological rep2


title: ndr1-1, mock treatment, 48 hpi, replicate 3

description: Ndr1 (3)

source_name: ndr1-1_mock treatment_48 hpi

value: none (mock control)


title: ndr1-1, V. longisporum-inoculated, 48 hpi, replicate 1

description: Ndr1 +V1(1)


title: Leonberger-BI_03626_ARRAY127924


title: TBSC-ALI1


title: Cells_NARA_T4hrs_biological rep4

source_name: LASCs, NARA (10nM) treatment, 4 hours


title: Basenji-BI_24054_ARRAY238588

source_name: blood


title: Cells_NARA_T4hrs_biological rep2


title: ndr1-1, mock treatment, 48 hpi, replicate 2

description: Ndr1 (2)


title: ndr1-1, mock treatment, 48 hpi, replicate 1

description: Ndr1 (1)


title: Leonberger-BI_03332_ARRAY127876


title: Col-0, V. longisporum-inoculated, 48 hpi, replicate 3

source_name: Col-0_V. longisporum-inoculated_48 hpi

value: Wild-type


title: Cells_NARA_T4hrs_biological rep3

value: Levator Ani muscle


title: Col-0, V. longisporum-inoculated, 48 hpi, replicate 2


title: TBSC-MAT1

value: on 3D Matrigel in distal airway differentiation medium


title: TBSC-MAT2


title: TBSC2

value: on feeder cell in cFAD growth medium


title: Cells_Vehicle_T48hrs_biological rep1

value: muscle satellite cell

value: passage number 5


title: Cells_Vehicle_T4hrs_biological rep4

source_name: LASCs, vehicle (DMSO, 0.2%) treatment, 4 hours


title: Cells_NARA_T4hrs_biological rep1


title: Leonberger-BI_02872_ARRAY127844

value: blood


title: Leonberger-BI_03331_ARRAY127860


title: TBSC1


title: DASC-ALI2

value: distal lung


title: Col-0, mock treatment, 48 hpi, replicate 3

source_name: Col-0_mock treatment_48 hpi

value: 16 days old


title: Leonberger-BI_02694_ARRAY127828


title: Col-0, V. longisporum-inoculated, 48 hpi, replicate 1

value: Pool of >50 individual roots


title: Col-0, mock treatment, 48 hpi, replicate 2


title: Cells_Vehicle_T4hrs_biological rep1


title: DASC-ALI1


title: Col-0, mock treatment, 48 hpi, replicate 1


title: DASC-MAT1


title: Cells_Vehicle_T4hrs_biological rep2


title: DASC-MAT2


title: DASC2


title: Increased ALP_K9OSATissue5

status: Public on Nov 19 2014

city: Madison

first: Timothy

last: Stein

state: WI

address: 2015 Linden Drive

department: Medical Sciences

institute: University of Wisconsin-Madison

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: Increased ALP, K9OSATissue5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Canine OSA tissue was snap frozen at the time of surgery, biopsy, or necropsy from patients with differing serum ALP concentration

treatment_protocol: All tissue was treated inidentical fashion and RNA was collected from snap frozen tumor tissue samples

tag: alp concentration

value: increased ALP

value: primary osteosarcoma tumor sample


title: Increased ALP_K9OSATissue9

source_name: Increased ALP, K9OSATissue9


title: Normal ALP_K9OSATissue9

source_name: Normal ALP, K9OSATissue9

value: normal ALP


title: Increased ALP_K9OSATissue4

source_name: Increased ALP, K9OSATissue4


title: Normal ALP_K9OSATissue2

source_name: Normal ALP, K9OSATissue2


title: Normal ALP_K9OSATissue6

source_name: Normal ALP, K9OSATissue6


title: Normal ALP_K9OSATissue8

source_name: Normal ALP, K9OSATissue8


title: Normal ALP_K9OSATissue3

source_name: Normal ALP, K9OSATissue3


title: WT2

value: wild type

value: lung


title: Normal ALP_K9OSATissue5

source_name: Normal ALP, K9OSATissue5


title: Increased ALP_K9OSATissue6

source_name: Increased ALP, K9OSATissue6


title: Increased ALP_K9OSATissue2

source_name: Increased ALP, K9OSATissue2


title: Increased ALP_K9OSATissue1

source_name: Increased ALP, K9OSATissue1


title: Normal ALP_K9OSATissue4

source_name: Normal ALP, K9OSATissue4


title: Normal ALP_K9OSATissue1

source_name: Normal ALP, K9OSATissue1


title: Increased ALP_K9OSATissue3

source_name: Increased ALP, K9OSATissue3


title: Normal ALP_K9OSATissue7

source_name: Normal ALP, K9OSATissue7


title: Twin with type 2 diabetes, pair 12

city: Copenhagen

first: jette

last: bork-jensen

address: Tagensvej 20

department: the department of endocrionlogy (diabetes and metabolism)

country: Denmark

institute: Rigshospitalet

hyb_protocol: The HS-400-Pro microarray hybridization station (Tecan, Grödig, Austria) was used for hybridization to miRCURY LNA miRNA arrays (Exiqon, Vedbaek, Denmark) representing version 9.2 of the Sanger miRBase, according to Exiqon's protocol.

scan_protocol: Scanning was performed using the ArrayWoRx white-light CCD-based scanner (Applied Precision, Issaquah, WA). ImaGene 8.0 (BioDiscovery, El Segundo, CA) was used for image analysis including flagging of bad-quality spots.

data_processing: Data was processed in R using Limma. Background correction was performed using the normexp method with an offset of 0. Between array normalization was performed using quantiles.

source_name: vastus lateralis muscle, type 2 diabetes

label_protocol: 1 µg total RNA was labeled with Hy3 using the miRCURY labeling kit according to the manufacturer's instructions.

extract_protocol: Total RNA from human muscle biopsies were extracted with TRI reagent (Sigma-Aldrich, St. Louis, MO).

value: vastus lateralis muscle

tag: disease state

value: type 2 diabetes

tag: twin pair


title: 18B_C_2.5h

first: Peter

last: Schjerling

address: Bispebjerg Bakke 23, M81

department: Institute of Sports Medicine Copenhagen, ISMC

institute: Bispebjerg Hospital

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The CEL files were analyzed using Partek Genomic Suite v6.6 (Partek), using the default Partek settings (GC content pre-adjustment, RMA background correction, quantile normalizetion, mean probe set summarization) to generate transcript expression.

source_name: Muscle, Control, 2.5h, Subj18

label_protocol: RNA was amplified and labeled using the Ambion WT Expression Kit (Applied Biosystems) according to manufacturer's instructions. 100 ng total RNA was used as input.

extract_protocol: TriReagent (MRCgene) extraction followed by RNeasy MinElute Cleanup (Qiagen).

treatment_protocol: Biopsies were taken from muscle Vastus lateralis with a Bergström needle and frozen in liquid nitrogen.

tag: tissue

value: Vastus lateralis

tag: exercise state

value: 2.5 hours, sedentary control

tag: gender

value: Male


title: 19C_E_5h

source_name: Muscle, Endurance, 5h, Subj19

value: 5 hours after last endurance training session


title: 19A_E_Pre

source_name: Muscle, Endurance, Pre, Subj19

value: before training


title: 18A_C_Pre

source_name: Muscle, Control, Pre, Subj18


title: Increased ALP_K9OSATissue8

source_name: Increased ALP, K9OSATissue8


title: Twin without type 2 diabetes, pair 12

source_name: vastus lateralis muscle, no type 2 diabetes

value: no type 2 diabetes


title: 19B_E_2.5h

source_name: Muscle, Endurance, 2.5h, Subj19

value: 2.5 hours after last endurance training session


title: Twin without type 2 diabetes, pair 11


title: Twin with type 2 diabetes, pair 11


title: 18C_C_5h

source_name: Muscle, Control, 5h, Subj18

value: 5 hours, sedentary control


title: 17C_E_5h

source_name: Muscle, Endurance, 5h, Subj17


title: DASC1

source_name: primary cell culture

value: distal lung

value: on feeder cell in cFAD growth medium


title: Increased ALP_K9OSATissue7

source_name: Increased ALP, K9OSATissue7

value: increased ALP


title: Twin with type 2 diabetes, pair 10


title: 17B_E_2.5h

source_name: Muscle, Endurance, 2.5h, Subj17


title: Twin without type 2 diabetes, pair 10


title: Twin with type 2 diabetes, pair 9


title: Twin without type 2 diabetes, pair 9


title: Twin without type 2 diabetes, pair 8


title: Twin with type 2 diabetes, pair 8


title: Twin without type 2 diabetes, pair 7


title: 16B_E_2.5h

source_name: Muscle, Endurance, 2.5h, Subj16


title: 16A_E_Pre

source_name: Muscle, Endurance, Pre, Subj16


title: Twin with type 2 diabetes, pair 7


title: Twin without type 2 diabetes, pair 4


title: Twin with type 2 diabetes, pair 6


title: Twin without type 2 diabetes, pair 6


title: 15C_C_5h

source_name: Muscle, Control, 5h, Subj15


title: Twin with type 2 diabetes, pair 4


title: Twin without type 2 diabetes, pair 2


title: Twin with type 2 diabetes, pair 1


title: 16C_E_5h

source_name: Muscle, Endurance, 5h, Subj16


title: 17A_E_Pre

source_name: Muscle, Endurance, Pre, Subj17


title: 15A_C_Pre

source_name: Muscle, Control, Pre, Subj15


title: Leonberger-BI_03337_ARRAY127892

source_name: blood

value: blood


title: 14B_E_2.5h

source_name: Muscle, Endurance, 2.5h, Subj14


title: Twin with type 2 diabetes, pair 2

source_name: vastus lateralis muscle, type 2 diabetes


title: Twin without type 2 diabetes, pair 3


title: 15B_C_2.5h

source_name: Muscle, Control, 2.5h, Subj15


title: Twin without type 2 diabetes, pair 1

source_name: vastus lateralis muscle, no type 2 diabetes


title: 14C_E_5h

source_name: Muscle, Endurance, 5h, Subj14


title: Twin with type 2 diabetes, pair 3


title: 14A_E_Pre

source_name: Muscle, Endurance, Pre, Subj14


title: 8WG16_rep2-T6

city: Singapore

first: Mark

middle: Stephen

last: Featherstone

state: Singapore

address: 60, Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

hyb_protocol: The microarray hybridization was carried at 63.50 C or 650 C in an automated hybridization station (Maui, USA) for ChIP DNA or cDNA respectively as described previously in Bozdech Z et al., 2003.

scan_protocol: The microarrays were scanned using the GenePix scanner 400b and GenePix pro 6.0 software (Axon Laboratory).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed green signal. Limma Package of R was used.

organism: Plasmodium falciparum

source_name: Plasmodium falciparum in culture fixed for ChIP at TP6

label_protocol: For expression analsysis, samples for individual time points (labeled with Cy5, red) were hybridized against a reference pool (labeled with Cy3, green) which consisted of a mixture of RNA from all the six time points in equal amounts. Amplified ChIP and input DNA were labeled with Cy5 and Cy3 respectively.

growth_protocol: P. falciparum  T996 strain was cultured following standard methods.

extract_protocol: RNA from each time point was isolated by trizol method.The chromatin immunoprecipitation assay was performed as described in Gupta AP et.al. 2013.

tag: antibody

value: Anti-8WG16 ChIP DNA from TP6

tag: timepoint (hours post invasion)

value: TP6=48 hpi

tag: strain

source_name: Input DNA from pooled TP1-6

value: Anti-8WG16 pooled Input DNA from TP1-6


title: 13C_S_5h

source_name: Muscle, Strength, 5h, Subj13

value: 5 hours after last strength training session


title: Cells_Vehicle_T4hrs_biological rep3

source_name: LASCs, vehicle (DMSO, 0.2%) treatment, 4 hours

value: Levator Ani muscle

tag: cell type

value: muscle satellite cell

tag: cell passage

value: passage number 5


title: 8WG16_rep1-T5

source_name: Plasmodium falciparum in culture fixed for ChIP at TP5

value: Anti-8WG16 ChIP DNA from TP5

value: TP5=40 hpi


title: 8WG16_rep1-T6


title: 13B_S_2.5h

source_name: Muscle, Strength, 2.5h, Subj13

value: Vastus lateralis

value: 2.5 hours after last strength training session

value: Male


title: 8WG16_rep2-T5


title: 8WG16_rep2-T4

source_name: Plasmodium falciparum in culture fixed for ChIP at TP4

value: Anti-8WG16 ChIP DNA from TP4

value: TP4=32 hpi


title: 12C_C_5h

source_name: Muscle, Control, 5h, Subj12

value: 5 hours, sedentary control


title: 8WG16_rep1-T4


title: 12B_C_2.5h

source_name: Muscle, Control, 2.5h, Subj12

value: 2.5 hours, sedentary control


title: 8WG16_rep2-T3

source_name: Plasmodium falciparum in culture fixed for ChIP at TP3

value: Anti-8WG16 ChIP DNA from TP3

value: TP3=24 hpi


title: 12A_C_Pre

source_name: Muscle, Control, Pre, Subj12

value: before training


title: 8WG16_rep1-T3

value: Anti-8WG16 pooled Input DNA from TP1-6


title: 13A_S_Pre

source_name: Muscle, Strength, Pre, Subj13


title: 8WG16_rep2-T1

source_name: Plasmodium falciparum in culture fixed for ChIP at TP1

value: Anti-8WG16 ChIP DNA from TP1

value: TP1=8 hpi


title: 8WG16_rep1-T2

source_name: Plasmodium falciparum in culture fixed for ChIP at TP2

value: Anti-8WG16 ChIP DNA from TP2

value: TP2=16 hpi


title: 8WG16_rep1-T1


title: 11B_S_2.5h

source_name: Muscle, Strength, 2.5h, Subj11


title: 11A_S_Pre

source_name: Muscle, Strength, Pre, Subj11


title: 11C_S_5h

source_name: Muscle, Strength, 5h, Subj11

value: 5 hours after last strength training session


title: 8WG16_rep2-T2


title: Fumarate hydratase WT, biological rep2

city: Glasgow

first: Leon

last: zheng

address: Garscube Estate

country: United Kingdom

institute: Beatson Institute

description: Normoxic conditions.

hyb_protocol: Samples were hybridised to GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) according to the Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay protocol. Arrays were washed and stained in the Affymetrix GeneChip Fluidics Station 450 using protocol FS450_0001. User-prepared reagents were used in the hybridisation cocktail and for Fluidics washes and stains.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G with AGCC software.

data_processing:
RMA using Partek software.
Core exons were used for the analysis.
Transcript assignments are based on genome build mm9.

source_name: kidney epithelial cells, FH WT

label_protocol: Total RNA samples were amplified, fragmented and biotinylated according to the Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay protocol, using a 1µg input.

growth_protocol: FH wild type and knock out cells were cultured in DMEM supplemented with 10% FBS and 2 mM glutamine.

extract_protocol: Qiagen RNeasy Mini Kit # 74104 according to the manufacturer's instructions.

treatment_protocol: No treatment.

tag: strain/background

value: Fh1fl/fl; C57BL/6

value: fumarate hydratase (FH) wild type

value: kidney epithelial cells


title: Ser2-5-P_rep1-T6

hyb_protocol: The microarray hybridization was carried at 63.50 °C or 65.0 °C in an automated hybridization station (Maui, USA) for ChIP DNA or cDNA respectively as described previously in Bozdech Z et al., 2003.

source_name: Plasmodium falciparum in culture fixed for ChIP at TP6

source_name: Input DNA from pooled TP1-6

tag: control type

value: Anti-Ser2-5-P pooled Input DNA from TP1-6


title: Ser2-5-P_rep1-T5


title: Ser2-5-P_rep2-T5


title: Ser2-5-P_rep3-T5


title: Ser2-5-P_rep3-T4


title: Fumarate hydratase WT, biological rep1

description: Normoxic conditions.


title: Ser2-5-P_rep2-T4


title: 10C_S_5h

source_name: Muscle, Strength, 5h, Subj10

value: Vastus lateralis

value: Male


title: Fumarate hydratase KO, biological rep2

description: Normoxic conditions.

source_name: kidney epithelial cells, FH KO

value: fumarate hydratase (FH) knock out


title: 10B_S_2.5h

source_name: Muscle, Strength, 2.5h, Subj10

value: 2.5 hours after last strength training session


title: Ser2-5-P_rep3-T6


title: Ser2-5-P_rep2-T6


title: Fumarate hydratase KO, biological rep1

description: Normoxic conditions.


title: 10A_S_Pre

source_name: Muscle, Strength, Pre, Subj10


title: 9C_C_5h

source_name: Muscle, Control, 5h, Subj9

value: 5 hours, sedentary control


title: Ser2-5-P_rep1-T4

source_name: Plasmodium falciparum in culture fixed for ChIP at TP4


title: Ser2-5-P_rep3-T3

source_name: Plasmodium falciparum in culture fixed for ChIP at TP3


title: abh1-plus ABA-rep2 [slide #462 technical rep2]

city: Lubbock

first: Christopher

middle: Dale

last: Rock

address: Flint and Main Sts.

department: Biological Sciences

institute: Texas Tech University

description:
slide #462 technical rep2
abh1-plus ABA-rep2

hyb_protocol: A pair of Cy5- and Cy3-labeled samples were mixed in equimolar proportions (~70 pmoles per sample) and hybridized on a Nimblegen station with appropriate accessory gaskets (Roche cat# 05223539001) to duplicate slides in parallel.  After competitive hybridization for 20 hrs, the slides were washed according to manufacturer’s specifications (Roche cat #05223512001 HYB SAMPLE TRACKING CONTROL KIT, #005583683001 NIMBLEGEN HYBRIDIZATION KIT, #005584507001 NIMBLEGEN WASH BUFFER KIT).

scan_protocol: Axon GenePix 4000B 2 μm scanner at wavelengths (550 nm or 650 nm) that excite Cy3 or Cy5 dyes, respectively.  Fluorescence measurements were recorded separately for each dye emission at each spot on the array.

data_processing: The RMA (Robust Microarray Average) method (NimbleScan 2.6.0, Roche-Nimblegen) was used to normalize the signal intensities of 48 datasets at the probe level.

source_name: 7 days old whole seedings, sprayed with 30 micromolar ABA 3 hr before harvesting

label_protocol: ~2.5 µg of total RNA was used per sample per labeling reaction for reverse transcription into cDNA.  Strand-specific cRNA was labeled according to manufacturer's specifications (Agilent Technologies, Santa Clara, CA; cat# 5188-5340 Two-Color Low RNA input Linear Amplification Kit PLUS).

growth_protocol: Arabidopsis thaliana seeds were soaked in water and kept in the dark at 4°C for 3 days before being placed in rows and germinated on Petri plates containing 0.5x Murashige & Skoog salts (Research Products International, Mt. Prospect, IL), 1% sucrose, 0.5% phytagel (SIGMA-ALDRICH, St. Louis, MO). Plates were kept vertically under continuous light (~ 100 µE/m-2s-1) at 21°C for one week before spraying with 30 µM ABA solution or water.  After a three hr treatment with ABA or water, seedlings were collected in microfuge tubes, frozen in liquid nitrogen and stored at -80°C before RNA extraction.  The accessions used in this study are listed as follows: Col-0 [CS60000], abh1-285 [SALK_024285c], sgs3-14 [SALK_001394], available from the Arabidopsis Biological Resource Center (Ohio State University; http://abrc.osu.edu/).

extract_protocol: For each of three biological replicates, ten seedlings (~70 mg plant material) each genotype were ground in a mortar and pestle with liquid nitrogen.  Total RNA was extracted using RNAqueous Kit (Ambion, Austin, TX) according to manufacturer’s specification.  Total RNA was eluted sequentially with three washes of 50 µL, 50 µL and 30 µL from the columns and collected in separate tubes.  10 µg RNA from the first elution were diluted to 20 µL in elution buffer and treated with TURBO DNase (Ambion) (1 µL DNase and 20 min reaction time).  After DNase treatment, 2 µL of each sample was run on a Bioanalyzer (Agilent Technologies, Santa Clara, CA) before and after labeling.

treatment_protocol: spraying 7 day old vertically grown seedings with a 30 µM (±) solution of abscisic acid (ACROS Organics, New Jersey), or control treatment of water spray.

tag: genotype

value: seedlings


title: Ser2-5-P_rep2-T3


title: Ser2-5-P_rep3-T2


title: 9B_C_2.5h

source_name: Muscle, Control, 2.5h, Subj9

value: 2.5 hours, sedentary control


title: double mutant-ABA-rep2 [slide #462 technical rep2]

description:
slide #462 technical rep2
double mutant-ABA-rep2

value: abh1 sgs3 double


title: 9A_C_Pre

source_name: Muscle, Control, Pre, Subj9

value: before training


title: Ser2-5-P_rep3-T1

source_name: Plasmodium falciparum in culture fixed for ChIP at TP1


title: Ser2-5-P_rep1-T2

source_name: Plasmodium falciparum in culture fixed for ChIP at TP2


title: sgs3-ABA-rep2 [slide #462 technical rep2]

description:
slide #462 technical rep2
sgs3-ABA-rep2


title: Col-0-ABA-rep2 [slide #462 technical rep2]

description:
slide #462 technical rep2
Col-0-ABA-rep2

value: wild type Col-0


title: Ser2-5-P_rep2-T2


title: Ser2-5-P_rep2-T1


title: Ser5-P_rep2-T6

value: Anti-Ser5-P pooled Input DNA from TP1-6


title: sgs3-ABA-rep1 [slide #462 technical rep2]

description:
slide #462 technical rep2
sgs3-ABA-rep1


title: Ser2-5-P_rep1-T1


title: Ser5-P_rep3-T5

source_name: Plasmodium falciparum in culture fixed for ChIP at TP5


title: double mutant-ABA-rep3 [slide #462 technical rep2]

description:
slide #462 technical rep2
double mutant-ABA-rep3


title: Ser2-5-P_rep1-T3


title: 7C_C_5h

source_name: Muscle, Control, 5h, Subj7


title: Ser5-P_rep1-T6


title: Ser5-P_rep2-T5


title: 8B_S_2.5h

source_name: Muscle, Strength, 2.5h, Subj8


title: Ser5-P_rep3-T6

source_name: Plasmodium falciparum in culture fixed for ChIP at TP6


title: sgs3-ABA-rep3 [slide #462 technical rep2]

description:
slide #462 technical rep2
sgs3-ABA-rep3


title: 8A_S_Pre

source_name: Muscle, Strength, Pre, Subj8


title: Ser5-P_rep1-T5

source_name: Input DNA from pooled TP1-6


title: 8C_S_5h

source_name: Muscle, Strength, 5h, Subj8


title: Ser5-P_rep2-T4


title: 7B_C_2.5h

source_name: Muscle, Control, 2.5h, Subj7


title: Ser5-P_rep3-T4


title: Ser5-P_rep1-T4


title: Ser5-P_rep3-T3


title: Ser5-P_rep1-T3


title: abh1-plus ABA-rep1 [slide #462 technical rep2]

description:
slide #462 technical rep2
abh1-plus ABA-rep1


title: Col-0-ABA-rep3 [slide #462 technical rep2]

description:
slide #462 technical rep2
Col-0-ABA-rep3


title: abh1-plus ABA-rep3 [slide #462 technical rep2]

description:
slide #462 technical rep2
abh1-plus ABA-rep3


title: Ser5-P_rep1-T2


title: Ser5-P_rep3-T1


title: Ser5-P_rep2-T2


title: Ser5-P_rep2-T1


title: 6B_E_2.5h

source_name: Muscle, Endurance, 2.5h, Subj6

value: 2.5 hours after last endurance training session


title: Ser5-P_rep2-T3


title: 7A_C_Pre

source_name: Muscle, Control, Pre, Subj7


title: double mutant-ABA-rep1 [slide #462 technical rep2]

description:
slide #462 technical rep2
double mutant-ABA-rep1


title: Ser5-P_rep1-T1


title: CTD_rep3-T6

value: Anti-CTD

value: Anti-CTD pooled Input DNA from TP1-6


title: 4C_S_5h

source_name: Muscle, Strength, 5h, Subj4

value: 5 hours after last strength training session


title: double mutant-water-rep2 [slide #462 technical rep2]

description:
slide #462 technical rep2
double mutant-water-rep2

source_name: 7 days old whole seedings, sprayed with water 3 hr before harvesting


title: Col-0-ABA-rep1 [slide #462 technical rep2]

description:
slide #462 technical rep2
Col-0-ABA-rep1

source_name: 7 days old whole seedings, sprayed with 30 micromolar ABA 3 hr before harvesting


title: 6A_E_Pre

source_name: Muscle, Endurance, Pre, Subj6


title: CTD_rep2-T6


title: abh1-water-rep2 [slide #462 technical rep2]

description:
slide #462 technical rep2
abh1-water-rep2


title: sgs3-water-rep2 [slide #462 technical rep2]

description:
slide #462 technical rep2
sgs3-water-rep2


title: CTD_rep1-T6


title: 4A_S_Pre

source_name: Muscle, Strength, Pre, Subj4


title: CTD_rep2-T5


title: CTD_rep3-T5


title: 3C_C_5h

source_name: Muscle, Control, 5h, Subj3


title: CTD_rep2-T4

source_name: Plasmodium falciparum in culture fixed for ChIP at TP4


title: CTD_rep1-T5

source_name: Plasmodium falciparum in culture fixed for ChIP at TP5


title: CTD_rep3-T4


title: abh1-water-rep1 [slide #462 technical rep2]

description:
slide #462 technical rep2
abh1-water-rep1


title: 3B_C_2.5h

source_name: Muscle, Control, 2.5h, Subj3


title: Col-0-water-rep2 [slide #462 technical rep2]

description:
slide #462 technical rep2
Col-0-water-rep2


title: sgs3-water-rep1 [slide #462 technical rep2]

description:
slide #462 technical rep2
sgs3-water-rep1


title: CTD_rep2-T3

source_name: Plasmodium falciparum in culture fixed for ChIP at TP3


title: 3A_C_Pre

source_name: Muscle, Control, Pre, Subj3


title: 2C_S_5h

source_name: Muscle, Strength, 5h, Subj2


title: CTD_rep1-T2

source_name: Plasmodium falciparum in culture fixed for ChIP at TP2

source_name: Input DNA from pooled TP1-6


title: sgs3-water-rep3 [slide #462 technical rep2]

description:
slide #462 technical rep2
sgs3-water-rep3


title: double mutant-water-rep3 [slide #462 technical rep2]

description:
slide #462 technical rep2
double mutant-water-rep3


title: CTD_rep1-T4


title: 1C_E_5h

source_name: Muscle, Endurance, 5h, Subj1

value: 5 hours after last endurance training session


title: 2A_S_Pre

source_name: Muscle, Strength, Pre, Subj2


title: RNA_T6

source_name: TP6 Plasmodium falciparum in culture

source_name: total RNA from pooled TP1-6

value: cDNA from pooled total RNA


title: 2B_S_2.5h

source_name: Muscle, Strength, 2.5h, Subj2

value: Vastus lateralis


title: CTD_rep3-T1

source_name: Plasmodium falciparum in culture fixed for ChIP at TP1


title: 4B_S_2.5h

source_name: Muscle, Strength, 2.5h, Subj4

value: Male


title: CTD_rep3-T3


title: CTD_rep3-T2


title: Col-0-water-rep1 [slide #462 technical rep2]

description:
slide #462 technical rep2
Col-0-water-rep1

source_name: 7 days old whole seedings, sprayed with water 3 hr before harvesting


title: CTD_rep2-T2


title: CTD_rep1-T3


title: CTD_rep1-T1


title: CTD_rep2-T1


title: RNA_T5

source_name: TP5 Plasmodium falciparum in culture


title: Col-0-water-rep3 [slide #462 technical rep2]

description:
slide #462 technical rep2
Col-0-water-rep3


title: double mutant-water-rep1 [slide #462 technical rep2]

description:
slide #462 technical rep2
double mutant-water-rep1


title: abh1-water-rep3 [slide #462 technical rep2]

description:
slide #462 technical rep2
abh1-water-rep3


title: double mutant-ABA-rep2 [slide #250 technical rep1]

description:
slide #250 technical rep1
double mutant-ABA-rep2

source_name: 7 days old whole seedings, sprayed with 30 micromolar ABA 3 hr before harvesting


title: 1A_E_Pre

source_name: Muscle, Endurance, Pre, Subj1


title: THC-SIV 60DPI [HN56-60DPI]

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description: Test

data_processing:
QuantStudio run files representing all treatment groups and timepoints were analyzed using ExpressionSuite Software (Life Tech)
miRNA expression data was analyzed by normalizing to three endogenous controls (RNU44, RNU48 and snoU6)
In all experiments, the CT upper limit was set to 28 meaning that all miRNA detectors with a CT value greater than or equal to 28 were excluded.
Due to the small sample size and exploratory nature of the study multiple comparisons correction was not applied.
ExpressionSuite software automatically calculates all deltadeltaCT based fold-change calculations and provides p values from the uploaded QuantStudio files.
Fold Change worksheet reports test/control (i.e., THC or VEH/SIV, THC/SIV vs uninfected control) ratios.

organism: Macaca mulatta

source_name: THC-SIV 60DPI

label_protocol: microRNA profiling was performed using the TaqMan® OpenArray® Human microRNA panels (Life Tech) following the manufacturer’s instructions. Reverse transcription was first performed from 350 ng of total RNA using the microRNA reverse transcription kit. 2.5 µL of cDNA was preamplified using the TaqMan® PreAmp Master Mix kit. Preamplified products were first diluted and then loaded onto to TLDA plates. TLDA plates were run on the ABI 7900 HT Fast PCR system following the manufacturer’s recommended thermal cycling conditions.

extract_protocol: Total RNA (small and large) was extracted using the miRNeasy Mini kit (Qiagen). On-column DNase digestion was also performed to eliminate contaminating genomic DNA.

treatment_protocol: 8 animals were infected intravenously with 100 TCID50 SIVmac251 and 4 (3 THC only and 1 vehicle only) remained uninfected

value: Intact Duodenum

tag: days post siv infection (dpi)

value: 60 DPI


title: THC-SIV 60DPI [HV47-60DPI]

description: Test


title: THC-SIV 60DPI [GP68-60DPI]

description: Test


title: RNA_T4

source_name: TP4 Plasmodium falciparum in culture


title: THC-SIV 60DPI [FT59-60DPI]

description: Test


title: THC-SIV 30DPI [HV47-30DPI]

description: Test

source_name: THC-SIV 30DPI

value: 30 DPI


title: 6C_E_5h

source_name: Muscle, Endurance, 5h, Subj6


title: THC-SIV 30DPI [HN56-30DPI]

description: Test


title: RNA_T3

source_name: TP3 Plasmodium falciparum in culture


title: THC-SIV 30DPI [GP68-30DPI]

description: Test


title: THC-SIV 14DPI [HV47-14DPI]

description: Test

source_name: THC-SIV 14DPI

value: 14 DPI


title: endometrial tissue 1 on gestational day 50 in Yorkshire pig

city: wuhan

first: su

last: lijie

state: Hubei

address: shizishan street

department: animal science college

country: China

institute: Huazhong (Central China) Agricultural University

description: miRNA expression data of endometrium on gestational day 50 in Yorkshire pig

hyb_protocol: Biotin labeled samples were mixed with the eukaryotic hybridization controls (Affymetrix) and hybridized to Affymetrix miRNA arrays. Arrays were subsequently washed and stained in the GeneChip fluidics station 450 (Affymetrix).

scan_protocol: To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).

data_processing: RMA normalization and probe summarization was carried out on the probe sets.

organism: Sus scrofa

source_name: endometrium: gestational day 50: Yorkshire

label_protocol: Samples were spiked with RNA spike control oligos (Genisphere) and labeled according to the Genisphere solution using the Genisphere FlashTag™ Biotin RNA Labeling Kit.

treatment_protocol: the uterus is opened anti-mesometrially and the endometrial tissue is collected from the healthy attachment site

value: endometrium

tag: age

value: gestational day 50

tag: breed

value: Yorkshire


title: endometrial tissue 2 on gestational day 26 in Yorkshire pig

description: miRNA expression data of endometrium on gestational day 26 in Yorkshire pig

source_name: endometrium: gestational day 26: Yorkshire

value: gestational day 26


title: RNA_T2

source_name: TP2 Plasmodium falciparum in culture


title: endometrial tissue 2 on gestational day 50 in Yorkshire pig


title: endometrial tissue 3 on gestational day 50 in Yorkshire pig


title: endometrial tissue 3 on gestational day 26 in Yorkshire pig


title: RNA_T1

source_name: TP1 Plasmodium falciparum in culture

source_name: total RNA from pooled TP1-6


title: sgs3-ABA-rep2 [slide #250 technical rep1]

description:
slide #250 technical rep1
sgs3-ABA-rep2

value: seedlings


title: Col-0-ABA-rep2 [slide #250 technical rep1]

description:
slide #250 technical rep1
Col-0-ABA-rep2

value: wild type Col-0


title: endometrial tissue 1 on gestational day 26 in Yorkshire pig


title: abh1-plus ABA-rep1 [slide #250 technical rep1]

description:
slide #250 technical rep1
abh1-plus ABA-rep1


title: abh1-plus ABA-rep2 [slide #250 technical rep1]

description:
slide #250 technical rep1
abh1-plus ABA-rep2


title: sgs3-ABA-rep1 [slide #250 technical rep1]

description:
slide #250 technical rep1
sgs3-ABA-rep1


title: THC-SIV 14DPI [HN56-14DPI]

description: Test


title: THC-SIV 14DPI [GP68-14DPI]

description: Test


title: 1B_E_2.5h

source_name: Muscle, Endurance, 2.5h, Subj1

value: 2.5 hours after last endurance training session


title: resistant sample_D

city: La Jolla

first: Paul

last: Mischel

state: California

address: 9500 Gilman Drive, CMME, room 2021

department: Pathology

institute: LICR, UCSD

description:
RNA-D.CEL.pimg
4_RNA sample D

hyb_protocol: As per manufacturer (Affymetrix); test run by the Clinical Microarray Core of the University of California Los Angeles.

data_processing:
Affymetrix U133 plus 2.0 array data were processed with Partek Genomics Suite 6.6 and RMA was used to normalized the data.
Normalized data were further analysed for differential gene expression by P-value less than 0.05 and fold change greater than 1.5 either direction. A set of 88 genes profiles was significantly different in CC214-2 resistant samples versus control samples.

source_name: GBM39 xenograft_CC214-2 resistant

growth_protocol: GBM39 primary neurospheres were cultured in standard cancer stem cell medium conditions and then were injected in the mice flanks to generate xenograft tissues.

extract_protocol: Total RNA was extracted from GBM39 control and CC214-2 resistant xenografts using the Qiagen RNA micro kit protocol. RNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: Mice carrying CC214-2 resistant xenografts were treated with a solution of CC214-2 once every two days, by gavage, for 40 days.

tag: source cell type

value: GBM39 primary neurospheres

tag: tissue type

value: GBM39 xenograft

tag: tissue subtype

value: CC214-2-treated, CC214-2- resistant


title: control sample_E

description:
RNA-E.CEL.pimg
2_RNA-sample E

scan_protocol: As per manufacturer (Affymetrix); test run by the Clinical Microarray Core of the University of California Los Angeles.

source_name: GBM39 xenograft_control

value: vehicle-treated control


title: resistant sample_C

description:
RNA-C.CEL.pimg
3_RNA-sample C

label_protocol: As per manufacturer (Affymetrix); test run by the Clinical Microarray Core of the University of California Los Angeles.


title: endometrial tissue 3 on gestational day 15 in Yorkshire pig

description: miRNA expression data of endometrium on gestational day 15 in Yorkshire pig

source_name: endometrium: gestational day 15: Yorkshire

tag: tissue

value: gestational day 15


title: double mutant-ABA-rep3 [slide #250 technical rep1]

description:
slide #250 technical rep1
double mutant-ABA-rep3

source_name: 7 days old whole seedings, sprayed with 30 micromolar ABA 3 hr before harvesting

value: abh1 sgs3 double


title: THC-SIV 14DPI [FT59-14DPI]

description: Test

value: Intact Duodenum


title: control sample_A

description:
RNA-A.CEL.pimg
1_RNA-sample A


title: VEH-SIV 60DPI [HN54-60DPI]

description: Test

source_name: VEH-SIV 60DPI

value: 60 DPI


title: endometrial tissue 2 on gestational day 15 in Yorkshire pig


title: endometrial tissue 1 on gestational day 15 in Yorkshire pig


title: endometrial tissue 3 on gestational day 50 in Meishan pig

description: miRNA expression data of endometrium on gestational day 50 in meishan pig

source_name: endometrium: gestational day 50: Meishan

value: Meishan


title: 638315.NCI-H358.EMT

city: South San Francisco

first: Yuting

last: Sun

state: CA

address: 1 DNA Way

department: Discovery Oncology

institute: Genentech

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133P 2.0 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 was normalized with RMA using R/Bioconductor. Various filter steps were applied to only retain one probeset per gene. First, probesets without Entrez Gene ID annotation were filtered out. Secondly, probe sets with the best grade were kept per Entrez Gene ID. Lastly, in case of multiple remaining probe sets per Entrez Gene ID, the most varying probe set was selected using IQR.

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: A549, HCC827 and NCI-H358 cells were cultured in RPMI1640 media containing 10%FBS and 4mM glutamine.

extract_protocol: Qiagen Rneasy kit used for the extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: To induce EMT, the cells were cultured in the presence of 2ng/ml TGFb for 3 weeks, with fresh media replenished every 3-4 days. The day before the cells were lysed, the cells were switched to fresh media without TGFb.

tag: cell line

value: Lung cancer


title: VEH-SIV 60DPI [FE07-60DPI]

description: Test


title: VEH-SIV 60DPI [HH45-60DPI]

description: Test


title: Col-0-ABA-rep3 [slide #250 technical rep1]

description:
slide #250 technical rep1
Col-0-ABA-rep3


title: 638314.NCI-H358.EMT


title: endometrial tissue 2 on gestational day 50 in Meishan pig

value: endometrium


title: sgs3-ABA-rep3 [slide #250 technical rep1]

description:
slide #250 technical rep1
sgs3-ABA-rep3


title: 638313.NCI-H358.EMT


title: endometrial tissue 1 on gestational day 50 in Meishan pig

value: gestational day 50


title: VEH-SIV 30DPI [HT49-30DPI]

description: Test

source_name: VEH-SIV 30DPI

value: 30 DPI


title: 638299.NCI-H358.Parental


title: Col-0-ABA-rep1 [slide #250 technical rep1]

description:
slide #250 technical rep1
Col-0-ABA-rep1


title: endometrial tissue 3 on gestational day 26 in Meishan pig

description: miRNA expression data of endometrium on gestational day 26 in meishan pig

source_name: endometrium: gestational day 26: Meishan

value: gestational day 26


title: 638311.NCI-H358.Parental


title: 638312.NCI-H358.Parental


title: abh1-plus ABA-rep3 [slide #250 technical rep1]

description:
slide #250 technical rep1
abh1-plus ABA-rep3

value: seedlings


title: double mutant-ABA-rep1 [slide #250 technical rep1]

description:
slide #250 technical rep1
double mutant-ABA-rep1


title: double mutant-water-rep2 [slide #250 technical rep1]

description:
slide #250 technical rep1
double mutant-water-rep2

source_name: 7 days old whole seedings, sprayed with water 3 hr before harvesting


title: abh1-water-rep2 [slide #250 technical rep1]

description:
slide #250 technical rep1
abh1-water-rep2


title: endometrial tissue 2 on gestational day 26 in Meishan pig


title: 638310.HCC827.EMT


title: sgs3-water-rep2 [slide #250 technical rep1]

description:
slide #250 technical rep1
sgs3-water-rep2


title: VEH-SIV 30DPI [HN54-30DPI]

description: Test


title: 638309.HCC827.EMT


title: VEH-SIV 30DPI [HH45-30DPI]

description: Test


title: endometrial tissue 1 on gestational day 26 in Meishan pig


title: VEH-SIV 14DPI [HT49-14DPI]

description: Test

source_name: VEH-SIV 14DPI

value: 14 DPI


title: 638308.HCC827.EMT


title: VEH-SIV 14DPI [HH45-14DPI]

description: Test


title: THC only 60D [HE44-60D]

description: Test

source_name: THC only 60D


title: 638307.HCC827.Parental


title: abh1-water-rep1 [slide #250 technical rep1]

description:
slide #250 technical rep1
abh1-water-rep1


title: VEH-SIV 30DPI [FE07-30DPI]

description: Test


title: VEH-SIV 14DPI [FE07-14DPI]

description: Test


title: endometrial tissue 1 on gestational day 15 in Meishan pig

description: miRNA expression data of endometrium on gestational day 15 in meishan

source_name: endometrium: gestational day 15: Meishan


title: Col-0-water-rep2 [slide #250 technical rep1]

description:
slide #250 technical rep1
Col-0-water-rep2

value: wild type Col-0


title: 638306.HCC827.Parental


title: 638297.HCC827.Parental


title: VEH-SIV 14DPI [HN54-14DPI]

description: Test


title: double mutant-water-rep3 [slide #250 technical rep1]

description:
slide #250 technical rep1
double mutant-water-rep3


title: 638305.A549.EMT


title: endometrial tissue 2 on gestational day 15 in Meishan pig


title: endometrial tissue 3 on gestational day 15 in Meishan pig


title: 638302.A549.Parental


title: sgs3-water-rep1 [slide #250 technical rep1]

description:
slide #250 technical rep1
sgs3-water-rep1


title: THC only 60D [HM74-60D]

description: Test


title: Col-0-water-rep1 [slide #250 technical rep1]

description:
slide #250 technical rep1
Col-0-water-rep1


title: 638304.A549.EMT


title: sgs3-water-rep3 [slide #250 technical rep1]

description:
slide #250 technical rep1
sgs3-water-rep3


title: 638303.A549.EMT


title: double mutant-water-rep1 [slide #250 technical rep1]

description:
slide #250 technical rep1
double mutant-water-rep1


title: abh1-water-rep3 [slide #250 technical rep1]

description:
slide #250 technical rep1
abh1-water-rep3


title: THC only 60D [GH61-60D]

description: Test


title: THC only 30D [HM74-30D]

description: Test

source_name: THC only 30D


title: THC only 14D [HM74-14D]

description: Test

source_name: THC only 14D


title: THC only 14D [HE44-14D]

description: Test


title: THC only 30D [GH61-30D]

description: Test


title: THC only 30D [HE44-30D]

description: Test


title: 638298.A549.Parental


title: THC only 14D [GH61-14D]

description: Test


title: 0vs2_rep2

city: Groningen

first: Wout

last: Overkamp

address: Nijenborgh 7

country: Netherlands

institute: Rijksuniversiteit Groningen, Department of Molecular Genetics

hyb_protocol: Hybridization was performed at 65°C as described in the Agilent two-color microarray manual (v1.3).

scan_protocol: Slides were scanned using a confocal laser scanner (Genepix autoloader AL4200, Molecular Devices Ltd., Sunnyvale, USA).

data_processing:
Each slide consists of 8 arrays, which is scanned as one picture and split into separate files. Total 3 slides were used, thus 8x3=24 hybridizations as described in the overall design.
Fluorescent signal intensity data were quantified using GenePix 6.1 (Molecular Devices Ltd., Sunnyvale, USA). A script was used to split 8-array image file of Cy3 intensity into eight separate Cy3 files. A script was used script to split 8-array image file of Cy5 intensity into eight separate Cy5 files. For each indidivual array, a merge file was produced consisting the merged Cy3 and Cy5 intensity files created before. The final merged processed data file is provided as supplementary file. Data sets were Lowess normalized and statistical analysis was performed using LimmaR software package (Smyth, 2004). Following the Limma pipeline, the multiple values of genes with a multi probe design are merged to one value by taking the average ln(ration) and the e(average ln(p-values)).

organism: Bacillus subtilis

source_name: Retentostat culture at timepoint 0. Biological replicate #2

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Dylight 550 or Dylight 650 Dyes (Thermo Scientific Pierce, Rockford, USA) to the dUTP aminoallyl reactive group and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences)

growth_protocol: Cells were grown at 37°C in a 1.4L retentostat culture in M9 media. Samples were taken at various timepoints during biomass accumulation.

extract_protocol: For RNA isolation, cells were broken using 500 mg of glass beads, 500 μl of phenol-chloroform, 30 μl of 3 M sodium acetate, and 15 μl of 20% sodium dodecyl sulfate. RNAs were isolated using the High Pure RNA isolation kit (Roche, Mannheim, Germany) according to the manufacturer's instructions. After a quality check of the isolated RNA using a Agilent Bioanalyzer 2100 with RNA 6000 LabChips (Agilent Technologies, the Netherlands), 20 μg of total RNA was used for cDNA synthesis and incorporation of aminoalyl-dUTP using SuperscriptIII reverse transcriptase  Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from four replicate cultures.

treatment_protocol: Harvested cultures were quickly centrifuged for 2 min at 6,000 × g, and frozen in liquid nitrogen.

tag: culture age (days)

tag: specific growth rate (h-1)

source_name: Retentostat culture at timepoint 2. Biological replicate #2


title: 638301.A549.Parental


title: 1vs3_rep2

source_name: Retentostat culture at timepoint 1. Biological replicate #2

source_name: Retentostat culture at timepoint 3. Biological replicate #2


title: Wild Type Rep2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: HeLa cells Wild Type. Biological replicate 2

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip HG-U133plus2 Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

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

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: HeLa cells Wild Type

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Adherent HeLa cell lines expressing stably empty (control) or TIA1 plus TIAR shRNA-pSUPER constructs were cultured under standard conditions as previously reported (Izquierdo JM, Alcalde J, Carrascoso I, Reyes R, Ludeña MD: Knockdown of T-cell intracellular antigens triggers cell proliferation, invasión and tumor growth. Biochem J 2011, 435:337-344).

extract_protocol: Total RNA from above HeLa cell lines was purified by TRIZOL method (Invitrogen). The quality of the total RNA was tested using the Agilent 2100 Bioanalyzer RNA Nano Chip.

value: HeLa

tag: genotype/variation

value: wild type


title: Double KO TIA1-TIAR Rep2

description: HeLa cells KO for TIA1 and TIAR. Biological replicate 2

source_name: HeLa cells KO for TIA1 and TIAR

value: KO for TIA1 and TIAR


title: Double KO TIA1-TIAR Rep3

description: HeLa cells KO for TIA1 and TIAR. Biological replicate 3


title: Wild Type Rep1

description: HeLa cells Wild Type. Biological replicate 1


title: 1vs3_rep1

source_name: Retentostat culture at timepoint 1. Biological replicate #1

tag: strain

source_name: Retentostat culture at timepoint 3. Biological replicate #1


title: Double KO TIA1-TIAR Rep1

description: HeLa cells KO for TIA1 and TIAR. Biological replicate 1


title: Preinfection [HV47-Pre]

description: Control

source_name: Preinfection

value: Uninfected


title: 0vs3_rep1

source_name: Retentostat culture at timepoint 0. Biological replicate #1


title: Preinfection [HM74-Pre]

description: Control


title: Preinfection [HT49-Pre]

description: Control


title: VEH-SIV 60DPI [HT49-60DPI]

description: Test

source_name: VEH-SIV 60DPI


title: Preinfection [HN54-Pre]

description: Control


title: 3vs2_rep1

source_name: Retentostat culture at timepoint 2. Biological replicate #1


title: 0vs2_rep1


title: Preinfection [HN56-Pre]

description: Control


title: Preinfection [HH45-Pre]

description: Control


title: 1vs0_rep1


title: Preinfection [IC52-Pre]

description: Control


title: Preinfection [HE44-Pre]

description: Control


title: 3vs2_rep2


title: clone #17, R140Q, DMSO, 8 days [35]

city: Cambridge

first: Andrew

last: Kernytsky

state: Massachusetts

address: 38 Sidney St

institute: Agios

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2 was used to export data to Partek Genomics Suite Format

label: Cy5 and Cy3

source_name: clone #17, R140Q, DMSO, 8 days

label_protocol: Standard Illumina Protocol

growth_protocol: Cell culture with varying growth times

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Varies

tag: construct

tag: treatment

value: DMSO

tag: days

tag: barcode

tag: cell type

value: TF-1 cells


title: Preinfection [GP68-Pre]

description: Control

value: Intact Duodenum

tag: days post siv infection (dpi)


title: Preinfection [GH61-Pre]

description: Control


title: 0vs3_rep2


title: clone #17, R140Q, DMSO, 8 days [36]


title: Preinfection [FT59-Pre]

description: Control


title: clone #17, R140Q, 1uM 6780, 8 days [31]


title: Col-0-water-rep3 [slide #250 technical rep1]

description:
slide #250 technical rep1
Col-0-water-rep3

source_name: 7 days old whole seedings, sprayed with water 3 hr before harvesting

tag: genotype


title: clone #17, pLVX, DMSO, 8 days [29]

source_name: clone #17, pLVX, DMSO, 8 days

value: pLVX


title: 2vs0_rep1


title: clone #17, R140Q, 1uM 6780, 8 days [33]


title: 3vs0_rep1


title: clone #17, R140Q, 1uM 6780, 8 days [32]


title: Preinfection [FE07-Pre]

description: Control


title: clone #17, R140Q, DMSO, 8 days [34]


title: 3vs1_rep1


title: Wild Type Rep3

description: HeLa cells Wild Type. Biological replicate 3


title: clone #17, pLVX, DMSO, 8 days [28]


title: clone #11, R140Q, DMSO, 28 days [23]

source_name: clone #11, R140Q, DMSO, 28 days


title: 2vs3_rep1


title: clone #17, pLVX, 1uM 6780, 8 days [27]

source_name: clone #17, pLVX, 1uM 6780, 8 days


title: clone #17, pLVX, DMSO, 8 days [30]


title: 2vs1_rep1


title: clone #17, pLVX, 1uM 6780, 8 days [26]


title: 0vs1_rep1


title: 2vs1_rep2


title: clone #11, R140Q, DMSO, 28 days [24]


title: Human Female low BMD [miRNA_D8]

city: Chang sha

first: shishi

last: min

state: Hunan

address: Lu shan  road

department: College of life sciences

institute: Hunan Normal University

hyb_protocol: Hybridization (Affymetrix Genechip Hybridization Oven 640) was carried out on Affymetrix genechip® miRNA 2.0.

scan_protocol: The hybridized chips were washed (Affymetrix Fluidics Station 450), stained with phycoerythrin-streptavidin, and scanned using an Affymetrix GeneChip® Scanner 3000 7G.

data_processing: Scanned images were quantified by GeneChip® Command Console® Software. miRNA QC Tool software was used for data summarization, normalization, and quality control.

source_name: Healthy female

label_protocol: miRNA microarray was performed by Capitalbio Cor. (Beijing, China). Briefly, 1 μg of total RNA from each sample was end-tailed with Poly(A) and ligated to the biotinylated signal molecule (FlashTag™ Biotin RNA Labeling Kit).(dT24) primer to produce biotinylated cRNA. The full-length cRNAs were fragmented to 20 to 200 bp and hybridized to Affymetrix GeneChip Human Exon 1.0 ST Array. 100 ng of total RNA was amplified and labeled using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol without rRNA reduction.

growth_protocol: One hundred and fifty milliliters of peripheral blood were drawn for each selected subject.

extract_protocol: Total RNA from monocytes was extracted using a Qiagen RNeasy Mini Kit .

treatment_protocol: Monocyte isolation ：A monocyte negative isolation kit (Order No. 130-091-153, Miltenyi Biotec Inc., Auburn, CA, USA) was used to isolate circulating monocytes from 150mL whole blood .

value: Peripheral blood monocytes

tag: Sex

value: female


title: 1vs2_rep1


title: Human Female low BMD [miRNA_D9]


title: Human Female low BMD [miRNA_D4]


title: Human Female low BMD [miRNA_D1]


title: 1vs0_rep2

source_name: Retentostat culture at timepoint 0. Biological replicate #2


title: Human Female high BMD [miRNA_G7]


title: clone #17, pLVX, 1uM 6780, 8 days [25]


title: clone #11, R140Q, DMSO, 28 days [22]


title: clone #11, R140Q, 1uM 6780, 28 days [19]


title: Human Female high BMD [miRNA_G6]


title: 3vs0_rep2


title: clone #11, R140Q, DMSO, 7 days [18]

source_name: clone #11, R140Q, DMSO, 7 days


title: clone #11, R140Q, 1uM 6780, 28 days [21]


title: 1vs2_rep2

source_name: Retentostat culture at timepoint 1. Biological replicate #2

source_name: Retentostat culture at timepoint 2. Biological replicate #2


title: 0vs1_rep2


title: 2vs0_rep2


title: 2vs3_rep2

source_name: Retentostat culture at timepoint 3. Biological replicate #2


title: Human Female low BMD [miRNA_D6]


title: Human Female high BMD [miRNA_G1]


title: clone #11, R140Q, DMSO, 7 days [17]


title: 3vs1_rep2


title: WT-ProE replicate 1 vs. KO-ProE replicate 1

status: Public on Nov 18 2014

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

institute: Northwestern University

description: WT ProE replicate 1 and KO ProE replicate 1

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
normalized log10 ratio (Cy5/Cy3) representing test/reference

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

growth_protocol: Bone marrow cells were isolated from WT and Bmi1 -/- mice and ProEs were purified using FACS.

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

value: WT

value: Bone marrow

value: ProE

value: KO


title: WT-MEP replicate 3 vs. KO-MEP replicate 3

description: WT MEP replicate 3 and KO MEP replicate 3

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

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

growth_protocol: Bone marrow cells were isolated from WT and Bmi1 -/- mice and MEPs were purified using FACS.

value: MEP


title: WT-ProE replicate 3 vs. KO-ProE replicate 3

description: WT ProE replicate 3 and KO ProE replicate 3


title: WT-ProE replicate 2 vs. KO-ProE replicate 2

description: WT ProE replicate 2 and KO ProE replicate 2


title: clone #11, R140Q, 1uM 6780, 28 days [20]


title: H11A1

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

description:
5753685039_B
rep1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All data were normalized and scaled by Partek Genomic Suite 6.4.

source_name: HMLE tumors

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

growth_protocol: HMLE cells were cultrured in HUMEC media prior to injection into NOD-SCID mice

extract_protocol: RNA from QIAGEN RNA prep kit

treatment_protocol: Overexpression of BCL11A (DOX inducible)

tag: gender

value: HMLE

value: BCL11A overexpression


title: clone #11, pLVX, DMSO, 28 days [11]

source_name: clone #11, pLVX, DMSO, 28 days


title: H11A3

description:
5753685039_F
rep3


title: H11A2

description:
5753685039_D
rep2


title: COLO 320_xenograt_with/without rat MSCs_rep1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16h at 37C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0 (Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: COLO320 MSC(-)

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: COLO320 cancer cells were maintained in RPMI 1640 with 10% FBS, penicillin (100 U/ml) and streptomycin (100 microgram/ml), in a 5% CO2 environment. Rat MSCs were harvested and cultured as follows. Briefly, rat bone marrow cells were harvested by inserting a needle into the shaft of the femurs and tibias and flushing it with 30 ml of complete alpha-modified Eagle’s medium (alpha MEM) containing 20% fetal bovine serum (FBS). Cell suspensions were filtered through a 70-micrometer nylon filter (Becton Dickinson, Franklin Lakes, NJ) and plated in 75-cm2 flasks. Cells were grown in complete alpha MEM (20% FBS) at 37°C and 5% CO2. After 3 days, the medium was replaced with fresh medium (10% FBS), and the adherent cells were grown to 80% confluency to obtain samples defined as passage 0. Cells in accordance with the criteria defined by International Society for Cellular Therapy (ISCT) [Cytotherapy 2006; 8: 315] between passage 3 and 5 were used for subsequent experiments.

extract_protocol: Total RNA was extracted using RNeasy® Mini Kit (QIAGEN, Hilden, Germany).

treatment_protocol: For xenograft experiments, 1million viable cancer cells were implanted alone, or were mixed with 1 million rat MSCs and injected subcutaneously into recipient 7-week old female NOG mouse® (NOD/Shi-scid, IL-2Rγnull), each of which four injections per mouse were performed at dorsolateral locations. Animals were observed daily whose tumors were measured in two dimensions three times weekly using precision calipers. Tumors were harvested at the end of the experiments or when the tumors reached 1.0 cm3 to avoid central tumor necrosis for microarray analysis.

value: COLO 320DM

source_name: COLO320 MSC(+)

value: COLO 320DM co-implanted with 7-week old female SD-TG (CAG-EGFP) rat MSCs harvesed passage 4


title: clone #11, R140Q, 1uM 6780, 7 days [14]


title: clone #11, pLVX, DMSO, 7 days [4]

source_name: clone #11, pLVX, DMSO, 7 days


title: clone #11, R140Q, 1uM 6780, 7 days [15]


title: clone #11, pLVX, 1uM 6780, 28 days [7]

source_name: clone #11, pLVX, 1uM 6780, 28 days


title: clone #11, pLVX, 1uM 6780, 7 days [2]

source_name: clone #11, pLVX, 1uM 6780, 7 days


title: AD.2

city: Baltimore

first: Saraswati

last: Sukumar

address: 1650 Orleans St, CRB 1, Rm 132

department: Breast Cancer Program

institute: Johns Hopkins School of Medicine

description: MDA-MB-231 cells treated with ATRA and doxorubicin

scan_protocol: Standard Illumina scan protocol

data_processing: Data was quantile normalized and minimum values were set to 64 using the limma package in R statistical environment.

source_name: MDA-MB-231_ATRA and Doxorubicin

label_protocol: Biotinylated cRNA were synthesized using Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) following the standard protocol.

growth_protocol: MDA-MB-231 cells grown in DMEM 10% FBS

extract_protocol: RNA was extracted using RNeasy Mini Kit (Qiagen)

treatment_protocol: MDA-MB-231 cells treated with entinostat (2.5 µM), ATRA (1 µM) and doxorubicin (0.2 µM), single and combinations treatments for 48h

value: ATRA and Doxorubicin

tag: replicate


title: clone #11, pLVX, DMSO, 28 days [10]


title: MD.2

description: MDA-MB-231 cells treated with entinostat and doxorubicin

source_name: MDA-MB-231_Entinostat and Doxorubicin

value: Entinostat and Doxorubicin


title: DOX.2

description: MDA-MB-231 cells treated with doxorubicin

value: Doxorubicin


title: clone #11, pLVX, DMSO, 28 days [12]

value: DMSO

value: TF-1 cells


title: Human Female high BMD [miRNA_G3]


title: clone #11, pLVX, 1uM 6780, 28 days [8]

value: pLVX


title: ATRA.2

description: MDA-MB-231 cells treated with ATRA

value: ATRA


title: MS.2

description: MDA-MB-231 cells treated with entinostat

value: Entinostat


title: MA.2

description: MDA-MB-231 cells treated with entinostat and ATRA

source_name: MDA-MB-231_Entinostat and ATRA

value: Entinostat and ATRA


title: clone #11, pLVX, DMSO, 7 days [6]


title: AD.1


title: DMSO.2

description: MDA-MB-231 cells treated with DMSO


title: MAD.1

description: MDA-MB-231 cells treated with entinostat, ATRA, and doxorubicin

source_name: MDA-MB-231_Entinostat and ATRA and Doxorubicin

value: Entinostat and ATRA and Doxorubicin


title: clone #11, R140Q, DMSO, 7 days [16]


title: MAD.2


title: clone #11, R140Q, 1uM 6780, 7 days [13]


title: WT-MEP replicate 1 vs. KO-MEP replicate 1

description: WT MEP replicate 1 and KO MEP replicate 1

value: WT

value: Bone marrow


title: MA.1


title: clone #11, pLVX, 1uM 6780, 7 days [3]


title: ATRA.1

description: MDA-MB-231 cells treated with ATRA


title: clone #11, pLVX, 1uM 6780, 7 days [1]


title: MS.1


title: clone #11, pLVX, 1uM 6780, 28 days [9]


title: DOX.1


title: WT-MEP replicate 2 vs. KO-MEP replicate 2

description: WT MEP replicate 2 and KO MEP replicate 2

value: MEP

value: KO


title: DMSO.1

description: MDA-MB-231 cells treated with DMSO


title: clone #11, pLVX, DMSO, 7 days [5]


title: Human Female high BMD [miRNA_G5]

source_name: Healthy female

value: Peripheral blood monocytes

value: female


title: MO1/veh_3

city: Leiden

first: Marcel

last: Schaaf

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

description: Biological replicate 3 of 3: MO1/veh

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the Microarray Department (MAD) of the University of Amsterdam (Amsterdam, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

source_name: The CR (common reference) was a mixture of all RNA samples from this microarray study.

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Twenty embryos per treatment group were collected in 1 ml of TRIZOL® Reagent (Invitrogen) and stored at -80°C. Embryos were homogenized in TRIZOL® and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Zebrafish embryos were microinjected at the 1-2 cell stage with 1 nl of 0.05 mM SC-MO, 0.05 mM  MO1, 0.05 mM MO2, or 5 ng/ml zGRb mRNA. At 24 hpf, they were treated with 100 mM dex or vehicle. At 30 hpf, twenty embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent. Three individual experiments were performed, yielding triplicate samples per treatment group.

value: embryo

source_name: MO1-injected at 1-2 cell stage, veh-injected at 24 hpf, RNA isolated from 20 embryos at 30 hpf


title: MO1/dex_3

description: Biological replicate 3 of 3: MO1/dex

source_name: MO1-injected at 1-2 cell stage, dex-injected at 24 hpf, RNA isolated from 20 embryos at 30 hpf


title: zGRb mRNA/veh_3

description: Biological replicate 3 of 3: zGRb mRNA/veh

source_name: zGRb mRNA-injected at 1-2 cell stage, veh-injected at 24 hpf, RNA isolated from 20 embryos at 30 hpf


title: MO2/veh_1

description: Biological replicate 1 of 3: MO2/veh

source_name: MO2-injected at 1-2 cell stage, veh-injected at 24 hpf, RNA isolated from 20 embryos at 30 hpf


title: MO1/veh_2

description: Biological replicate 2 of 3: MO1/veh


title: MO2/dex_3

description: Biological replicate 3 of 3: MO2/dex

source_name: MO2-injected at 1-2 cell stage, dex-injected at 24 hpf, RNA isolated from 20 embryos at 30 hpf


title: Tube KO2

description:
5355441031_C
KO rep2

scan_protocol: standard Illumina scan protocol.

source_name: mammary stem cells, KO

extract_protocol: RNA from sorted cells was extracted using PicoPure RNA isolation kit (Molecular Devices) according to the manufacturer’s instructions.

value: 129/C57B6 mixed background

value: mammary gland

value: stem cell

value: Bcl11a KO


title: zGRb mRNA/dex_3

description: Biological replicate 3 of 3: zGRb mRNA/dex

source_name: zGRb mRNA-injected at 1-2 cell stage, dex-injected at 24 hpf, RNA isolated from 20 embryos at 30 hpf


title: Tube WT1

description:
5355441031_E
WT rep1

source_name: mammary stem cells, WT


title: zGRb mRNA/dex_1

description: Biological replicate 1 of 3: zGRb mRNA/dex


title: MO2/veh_2

description: Biological replicate 2 of 3: MO2/veh


title: Tube WT2

description:
5355441031_F
WT rep2


title: zGRb mRNA/veh_2

description: Biological replicate 2 of 3: zGRb mRNA/veh


title: MO1/veh_1

description: Biological replicate 1 of 3: MO1/veh


title: MO2/dex_1

description: Biological replicate 1 of 3: MO2/dex


title: MO1/dex_2

description: Biological replicate 2 of 3: MO1/dex


title: zGRb mRNA/veh_1

description: Biological replicate 1 of 3: zGRb mRNA/veh


title: SC-MO/veh_3

description: Biological replicate 3 of 3: SC-MO/veh

source_name: SC-MO-injected at 1-2 cell stage, veh-injected at 24 hpf, RNA isolated from 20 embryos at 30 hpf


title: MO2/veh_3

description: Biological replicate 3 of 3: MO2/veh


title: MO1/dex_1

description: Biological replicate 1 of 3: MO1/dex


title: MO2/dex_2

description: Biological replicate 2 of 3: MO2/dex


title: PNS.HET.3.INPUT

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: Input stressed 5Htt +/- mice group 3

hyb_protocol: Approximately 7µg of amplified and terminally labeled DNA was hybridized to tiling arrays at 45°C for 16h at 60 rpm. Washing of arrays and staining of bound DNA was achieved with the GeneChipHWS kit in a Fluidics Station 450 (both Affymetrix) using fluidics script FS450_0001.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data from MeDIP and input pairs were loess normalized; log2(MeDIP/input) signal log ratios (SLR) were reported in bedGraph files.  Coordinates of genomic probes were mapped to the M. musculus MMv37 sequence assembly. Analyses were performed in R (http://www.r-project.org) with the Bioconductor package Starr (http://www.bioconductor.org).
Raw data from CEL files of MeDIP and input pairs of the same sample were loess normalized, followed by calculation of the MeDIP-input signal log ratio (SLR). SLRs between samples were quantiles normalized, followed by a 300bp sliding-window median smoothing along the genomically ordered probe signals. The preprocessed array signals are reported in the "_smoothed.bedGraph" files. The CMARRT algorithm was employed to define MeDIP-enriched autosomal regions in smoothed SLRs of each sample; the ".cmarrt.bed" files contain genomic coordinates of MeDIP-enriched regions. Analyses were performed in R (http://www.r-project.org) with the Bioconductor package Starr (http://www.bioconductor.org).

source_name: murine hippocampal input DNA from stressed 5Htt +/- animals

label_protocol: Samples (approximately 7 µg of amplified DNA each) were fragmented and terminally labeled with biotin using the GeneChip Mapping 10K Xba kit (Affymetrix).

growth_protocol: The wt and 5-Htt +/- deficient  mice  ([B6.129(Cg)-Slc6a4tm1Kpl/J]) were housed individually within a temperature-controlled  environment (2161uC) with 12 h light/12 h dark cycle (lights on from 7.00 h) and standard rodent chow and water available ad libitum.

extract_protocol: Genomic DNA was extracted from the tissue using phenol/chloroform/isoamyl alcohol extraction.  300 µl 0.5%-SDS extraction buffer were added to the frozen tissue. The tissue was subsequently homogenized for 30 to 60 sec at 25 Hz at 4°C in the Tissue Lyser (Qiagen, Hilden, Germany) using a metallic bead. After adding 200 µl 0.5%-SDS extraction buffer and 50 µl 10- or 20mg/µl-proteinase K, samples were incubated at 55°C over night/3 h. Following this, samples were incubated with 50 µl 10mg/µl-RNAse A with for 1 h at 37°C and then mixed with 700 µl of phenol/chloroform/isoamyl alcohol mixture (25:24:1). Phases were separated using MaXtract high density tubes (Qiagen) by centrifuging the samples at 14 000 rpm for 5 min at RT. The aqueous phase was then mixed with 700 µl phenol isoamyl alcohol (24:1) and phases were again separated by centrifuging the samples in MaXtract high density tubes as described above. DNA was precipitated with 50 µl sodium acetate and 1000 µl cold absolute ethanol (incubation 10 min at -20°C, centrifugation 20 min at 4°C, 14  000 rpm). The resulting pellet was washed with 500 µl cold 80%-ethanol using the same conditions as for the precipitation, dried at RT for 5 to 30 min and resuspended in 50 µl 1xTE. DNAs of single animals were then pooled, creating 2-3 pools per group. DNA was then  sheared using the BiorupterTM UCD-200 (Diagenode, Liège, Belgium) yielding fragments of 300bp size +/- 200bp.Conditions were 20 KHz, 30 sec ON alternated by 30 sec OFF, for 3 x 5 min at low power

tag: backgroud strain

value: Prenatal stress group (3 x 45 min/ day, E13-17)


title: PNS.HET.2.INPUT

description: Input stressed 5Htt +/- mice group 2


title: PNS.HET.3.MEDIP

description: MeDIP stressed 5Htt +/- mice group 3

source_name: murine hippocampal MeDIP DNA from stressed 5Htt +/- animals


title: PNS.HET.2.MEDIP

description: MeDIP stressed 5Htt +/- mice group 2


title: zGRb mRNA/dex_2

description: Biological replicate 2 of 3: zGRb mRNA/dex

tag: tissue


title: SC-MO/veh_2

description: Biological replicate 2 of 3: SC-MO/veh


title: SC-MO/veh_1

description: Biological replicate 1 of 3: SC-MO/veh


title: Tube KO1

description:
5355441031_B
KO rep1