title: mono-DC + Dex + vitD3 4

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

institute: Singapore Immunology Network

description: Tolerogenic Mono-DC phenotype

hyb_protocol: Hybridization to the Illumina Human HT-12 v4 Beadchips for 17 h at 58°C

scan_protocol: Scanned using BeadArray Scanner 500GX

data_processing:
Array data were extracted at the probe level with no background correction using Illumina's GenomeStudio software. These raw data were quantile normalized. Statistical analysis and differential gene expression were carried out using the limma package in R 2.12.2/Bioconductor. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate.
non-normalized matrix contains Illumina Bead Studio raw signal intensity.  Normalized matrix contains quantile normalized log2 signal intensity.

source_name: CD14+ monocytes from healthy donor (number 4)

label_protocol: Total RNA samples were amplified using TargetAmp™ and biotinilated cRNA was prepared Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

growth_protocol: Monocytes were cultured in presence of GM-CSF and IL-4 (both 1000U/mL, Miltenyi Biotec). At days 4 and 6, cells were refreshed with cytokines. Monocyte-derived dendritic cells were harvested at day 7 of differentaition and cell count/viability was assessed by trypan blue exclusion.

extract_protocol: Total RNA was extracted by Trizol (Invitrogen)

treatment_protocol: To obtain tolerogenic moDCs, cells were treated at day 5 with 10nM dexamethasone and 100nM vitamin D3 (Sigma-Aldrich). Cells were then either treated with LPS (E. coli O128-B12, 1μg/mL, Sigma-Aldrich) at day 6 or left untreated. At day 7, immature (untreated), mature (LPS-treated), tolerogenic and LPS-tolerogenic moDCs were harvested, washed and finally cell count/viability was assessed by trypan blue exclusion.

tag: modc type

value: Tolerogenic

value: IL-4 + GM-CSF + Dexamethasone + Vitamin D3 treatment

value: Tolerogenic Mono-DC phenotype


title: MCF7 100nmoles/l FA rep5

status: Public on May 08 2015

type: RNA

city: Southampton

first: Graham

middle: C

last: Burdge

address: IDS Building (Mailpoint 887), Southampton General Hospital, Tremona Road

department: Human Development and Health

country: United Kingdom

institute: University of Southampton

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quintile normalisation with Illumina BeadStudio

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Breast cancer cell line

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

growth_protocol: All cell lines were cultured at 37oC in an atmosphere containing 5% (v/v) CO2, in Dulbecco’s Modified Eagle Medium without FA (Sigma), supplemented with 10% (v/v) fetal bovine serum (FBS), 2mM glutamine, 10U/ml penicillin and 100µg/ml streptomycin. The media for the MCF10a cell line was further supplemented with 20ng/ml epidermal growth factor and 100µg/ml hydrocortisone.

extract_protocol: Total RNA was extracted using TRI reagent (Sigma), followed by clean-up with RNeasy MinElute Cleanup kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyser.

treatment_protocol: Cultures were treated with 0 or 100 nmoles/l folic acid for 72 hours (n=6 replicates/treatment). Background folate concentration derived from FBS in the medium was 1.5 nmoles/l.

tag: cell line

tag: folic acid

value: 100 nmoles/l


title: T2 vs GT21_cy5_Biorep 3

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

description:
Biological replicate 3 of 3
T2_5_BR3

hyb_protocol: Two-colour hybridizations were performed using the samples from all cold treatments as “test” samples and the N33 room temperature sample as the “reference”. Dye-flip hybridizations were performed for each sample combination with three biological replicates for a total of 42 hybridizations. The labelled probes were combined with a solution containing 2 μl of calf thymus ss-DNA (10mg/ml, Sigma), 2 μl Yeast tRNA (10mg/ml, Invitrogen) and 61 μl of DIG easy hybridization buffer (Roche),  denatured at 70°C for 2 minutes and hybridized with the arrays at 37°C for 8-18 hrs. Following incubation, the arrays were washed three times at 50°C for 15 min in 1X SSC-0.1% SDS, rinsed in 1x SSC and spun 5 min (1000 rpm) at room temperature.

scan_protocol: The slides were scanned sequentially at 532 and 635 nm using a Genepix 4200A microarray scanner (Molecular Devices, Sunnyvale, CA). Features were aligned in Genepix Pro 6.0 using the Irregular Features Spot Finder application and local background subtraction. Low quality features were flagged and filtered from further analysis. The raw data files were named using strain abbreviation, hybridization time date and slide number (i.e. MrN33-080326-13723296.gpr). The complete set of data for the N33 gene expression microarray experiment is available on the GEO.

data_processing: Features were aligned in Genepix Pro 6.0 using the Irregular Features Spot Finder application and local background subtraction. Low quality features were flagged and filtered from further analysis. The raw data files were named using strain abbreviation, hybridization time date and slide number (i.e. MrN33-080326-13723296.gpr). Arrays were imported into Acuity 4 (Molecular Devices, Sunnyvale, CA Axon Instruments Inc.) for data normalization and analysis. The arrays were re-named by test treatment, test dye and biological replicate (i.e. B_3_BR1). LOWESS normalization was applied to each array. Data filtering steps were performed by removing features flagged in Genepix as low quality, removing spike-in controls and ribosomal RNA clones and removing negative control features. Furthermore, we removed substances with “LOWESS A” intensities ≤8 in at least 32 of the arrays (75%). As well, substances were removed from the dataset if they were not present in at least 80% of the arrays. Data processing and filtering resulted in the removal of low intensity features and the preservation of the strong signal subsets. The data type was changed to Lowess M log2 ratio. After subtraction and the filtering steps, 4603 substances remained in the dataset. Pearson centered hierarchical clustering analysis was carried out on the dataset and supported strong reproducibility of the technical and biological replicates across all treatments

organism: Mesorhizobium sp. N33

source_name: T2=test sample cells, grown at 21°C, then cold shock at 4°C for 4 minutes

label_protocol: cDNA synthesis, labelling, purification and hybridization were performed based on a protocol from The Institute for Genomic Research (TIGR, now the J. Craig Venter Institute) (ftp://ftp.jcvi.org/pub/data/PFGRC/MAIN/pdf_files/protocols/M007.pdf). Labelled probes were quantified on the NanoDrop ND-1000 Spectrophotometer and yields were calculated in picomoles of cDNA synthesized and Cy-dye incorporation. The labelled cDNA was dried in a vacuum centrifuge with medium heat for 45-60 min and stored at 4°C in the dark. Human clones (~300bp in length), purchased from Michigan State University were used as internal spike-in controls for hybridization.

growth_protocol: Mesorhizobium sp. strain N33 was grown in 100 ml of yeast mannitol broth (YMB) media at 150 rpm at room temperature (~21°C) to mid-log phase (OD600= 0.4-0.6). The purity of colonies was checked by cultivation on yeast extract mannitol agar (YMA) supplemented with 200 μg ml-1 streptomycin and 25 μg ml-1 Congo red. Subsequent purity tests of the strain were followed by performing a nodulation test on Onobrychis viciifolia (sainfoin), and by 16S-rDNA sequencing.

extract_protocol: After each treatment, before harvest of cells, transcription activity was halted by adding a stop solution. The samples were immediately centrifuged (10,000 g) at 4°C for 5 minutes. The pellets were washed once with cold TES buffer (100 mM NaCl, 1 mM EDTA, 10 mM Tris hydrochloride [pH 7.4]), re-centrifuged, and cells frozen in liquid nitrogen and stored at -85°C. Total RNA was purified using the Epicenter Kit (Cat. #MC89010) according to the manufacturer's protocol with additional modifications: i) Small RNAs, proteins, carbohydrates, and DNA were precipitated with 5M LiCl (Ambion). ii) DNA was also removed from RNA samples using DNase I (Ambion). Lack of DNA contamination of RNA samples was verified by standard PCR using one pair of primers from the OrfZ gene of strain N33. RNA concentration was determined using the NanoDrop ND-1000 Spectrophotometer at 260 nm. RNA purity and integrity were assessed by electrophoresis on a density gradient 1% agarose/formaldehyde gel and using the Experion automated electrophoresis system (Biorad).

treatment_protocol: The N33 cells were grown in YMB medium at three steady state temperature conditions (GT21°C= room temperature [21°C] as control, GT4= growth at 4°C in water bath, and GT10= growth at 10°C), and also the room temperature grown cells were downshifted for various times (T1= 2 min, T2= 4 min, T3= 8 min, T4= 60 min, T5= 240 min) at 4°C in water bath under constant agitation. A total of 8 conditions with 3 biological replicates were screened in this experiment. The pellets were collected at mid-log phase (OD600=0.4-0.6) for RNA purification, cDNA synthesis and labelling.

tag: sample type

source_name: GT21= reference cells grown at 21°C

value: GT21= reference cells grown at 21°C


title: T3 vs GT21_cy3_Biorep 1

description:
Biological replicate 1 of 3.
T3_3_BR1

source_name: T3=test sample cells, grown at 21°C, then cold shock at 4°C for 8 minutes


title: V6-5-L9

city: Bunkyo-Ku

first: tomomi

last: hishinuma

state: Tokyo

country: Japan

institute: juntendo university

hyb_protocol: Labeled samples were hybridized onto the microarray at 50°C for 16-20 hr. After hybridization, the arrays were washed in the following buffers, and dry by spin slide.   2X SSC/0.05% SDS, for 15 min  0.2X SSC/0.05% SDS, for 15 min  0.5X SSC, for 3 min  0.2X SSC, for 3 min

scan_protocol: Nimblegen MS200

data_processing: Software: NimbleScan   Algorithm: Robust Multi-Array Analysis (Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Biostatistics. 2003 Apr;4(2):249-64 (PMID 12925520)).   Normalize: global normalization

organism: Staphylococcus aureus

label_protocol: SuperScript Indirect cDNA Labeling System (Invitrogen Life Technologies, Carlsbad, California).

extract_protocol: See reference:Neoh HM, et al.: Mutated response regulator graR is responsible for phenotypic conversion of Staphylococcus aureus from heterogeneous vancomycin-intermediate resistance to vancomycin-intermediate resistance. Antimicrob Agents Chemother. 2008 Jan;52(1):45-53.

tag: genotype

value: relQ mutation (Q94*)


title: V6-5-L8

value: murZ mutation (G10V)


title: GT10 vs GT21_cy3_Biorep 2

description:
Biological replicate 2 of 3.
GT10_3_BR2

source_name: GT10=test sample cells grown at 10°C

value: GT10=test sample cells grown at 10°C


title: T3 vs GT21_cy3_Biorep 2

description:
Biological replicate 2 of 3.
T3_3_BR2

value: T3=test sample cells, grown at 21°C, then cold shock at 4°C for 8 minutes


title: V6-5-L7

value: glmM mutation (F5I)


title: V6-5-L5

value: relQ mutation (Y29*)


title: T2 vs GT21_cy5_Biorep 2

description:
Biological replicate 2 of 3.
T2_5_BR2

value: T2=test sample cells, grown at 21°C, then cold shock at 4°C for 4 minutes


title: T2 vs GT21_cy5_Biorep 1

description:
Biological replicate 1 of 3.
T2_5_BR1


title: mono-DC + Dex + vitD3 + LPS 3 E

country: Singapore

description: Tolerogenic-LPS Mono-DC phenotype (FACS analysis)

source_name: CD14+ monocytes from healthy donor (number 3)

value: LPS-Tolerogenic

tag: treatment

value: IL-4 + GM-CSF + Dexamethasone + Vitamin D3 + LPS treatment

tag: cell type


title: mono-immDC 4 E

description: Immature Mono-DC phenotype (FACS analysis)

value: Immature

value: IL-4 + GM-CSF treatment


title: mono-DC + Dex + vitD3 + LPS 4 E

value: Tolerogenic-LPS Mono-DC phenotype (FACS analysis)


title: V6-5-L3

value: rpoC mutation (P440L,D645E, R646L)


title: T2 vs GT21_cy3_Biorep 2

description:
Biological replicate 2 of 3.
T2_3_BR2


title: V6-5-L2

value: rpoC mutation (L440V)


title: mono-DC + Dex + vitD3 3 E

description: Tolerogenic Mono-DC phenotype

value: Tolerogenic

value: IL-4 + GM-CSF + Dexamethasone + Vitamin D3 treatment

value: Tolerogenic Mono-DC phenotype


title: mono-maDC + LPS 3 E

description: Mature Mono-DC phenotype (FACS analysis)

value: Mature

value: IL-4 + GM-CSF + LPS treatment treatment


title: mono-maDC + LPS 4 E

value: IL-4 + GM-CSF + LPS treatment

value: Mature Mono-DC phenotype (FACS analysis)


title: T2 vs GT21_cy3_Biorep 1

description:
Biological replicate 1 of 3.
T2_3_BR1

value: GT21= reference cells grown at 21°C


title: T2 vs GT21_cy3_Biorep 3

description:
Biological replicate 3 of 3
T2_3_BR3


title: V6-5-L1

value: rpoC mutation (P440L,F652L)


title: mono-DC + Dex + vitD3 2 E

description: Tolerogenic Mono-DC phenotype

source_name: CD14+ monocytes from healthy donor (number 2)


title: mono-immDC 3 (hybridization replicate)

value: Immature Mono-DC phenotype (FACS analysis)


title: mono-immDC 3


title: mono-DC + Dex + vitD3 + LPS 2 (hybridization replicate)

value: LPS-Tolerogenic


title: Mu3fdh2*

value: wild type


title: mono-maDC + LPS 2


title: mono-DC + Dex + vitD3 + LPS 2

value: IL-4 + GM-CSF + Dexamethasone + Vitamin D3 + LPS treatment


title: V6-5

value: rpoC mutation (P440L)


title: T1 vs GT21_cy5_Biorep 2

description:
Biological replicate 2 of 3.
T1_5_BR2

source_name: T1= test sample cells, grown at 21°C, then cold shock at 4°C for 2 minutes


title: T1 vs GT21_cy5_Biorep 3

description:
Biological replicate 3 of 3
T1_5_BR3

value: T1= test sample cells, grown at 21°C, then cold shock at 4°C for 2 minutes


title: EAE 16 day

city: Shanghai

last: Shen

address: 145 Shan  Dong  Middle Road

country: China

institute: Renji Hospital, JiaoTong University School of Medicine

description: Test

data_processing:
TLDA were run in the 7900 HT Sequence Detection system. The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. Automatic baseline and manual CT were set to 0.2 for all samples. Input data for class comparison, permutations and prediction analysis consisted of the raw miR expression CT values normalized to the average of RNU24 and RNU6B value. [delta]CT = CTsample - CTreference.
[delta]CT = CTsample - Ctreference. Fold Change file reports test/control

label: FAM

organism: Mus musculus

source_name: C57BL/6 mice with the induction of EAE for 16 days

label_protocol: Individual TaqMan® MicroRNA Assays cards were performed for miRNA profiling following the Manufacturer’s instructions .Reverse transcription was performed from 50ng total RNA per sample using Megaplex™ RT Pools(Applied Biosystems). Then add Megaplex™ PreAmp Primers(Applied Biosystems) for additional assay sensitivity. Quantitative real-time PCR were performed on an AbiPrism 7900 HT cycler (Applied Biosystems) with 1 cycle at 50℃ for 2 minutes and 95℃ for 10 minutes and 40 cycles at 94℃ for 15 seconds and 60℃ for 60 seconds.

extract_protocol: Total RNA was extracted with Trizol

tag: strain

value: Splenic CD4+T cells


title: T1 vs GT21_cy5_Biorep 1

description:
Biological replicate 1 of 3.
T1_5_BR1


title: T1 vs GT21_cy3_Biorep 3

description:
Biological replicate 3 of 3
T1_3_BR3


title: mono-DC + Dex + vitD3 E

description: Tolerogenic Mono-DC phenotype

source_name: CD14+ monocytes from healthy donor (number 1)


title: EAE 0 day

description: Control

source_name: healthy C57BL/6 mice


title: T1 vs GT21_cy3_Biorep 1

description:
Biological replicate 1 of 3.
T1_3_BR1


title: GT4 vs GT21_cy5_Biorep 3

description:
Biological replicate 3 of 3
GT4_5_BR3

source_name: GT4=test sample cells grown at 4°C

value: GT4=test sample cells grown at 4°C


title: GT4 vs GT21_cy5_Biorep 2

description:
Biological replicate 2 of 3.
GT4_5_BR2


title: 22d-P23-W

first: Keh-Weei

last: Tzung

address: 1 Research Link National University of Singapore

institute: Temasek Life Sciences Laboratory

description: 22 dpf developing trunk of WT, thirteenth of 14 biological replicates.

hyb_protocol: Hybridization was performed for 16 to 20 hours using MAUI hybridization system (BioMicro Systems) according to Roche NimbleGen expression array protocol.

scan_protocol: Prior to scanning the microarray chip was washed with NimbleGen Wash Buffer Kit (Roche NimbleGen) according to manufacturer's protocol. Then the chip was scanned at 5 um resolution with Axon GenePix 4000B Microarray Scanner (Molecular Devices) according to Roche NimbleGen expression array protocol.

data_processing: The raw data(.pair file) was subjected to RMA (Robust-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan version 2.6 software package.

organism: Danio rerio

source_name: 22 dpf_wild type_High

label_protocol: Amplified double stranded cDNA was labeled using NimbleGen One-Color DNA Labelling Kit (Roche NimbleGen) according to manufacturer's protocol.

growth_protocol: Standard conditions.

extract_protocol: Total RNA was extracted using Ambion RNAqueous-Micro kit (Life Technologies) according to manufacturer's protocol. To obtain sufficient amounts of RNA, whole transcriptome amplification was performed using Ovation RNA Amplificiation System V2 (NuGen).

treatment_protocol: Zebrafish embryos were injected with dnd morpholino, then screened for morphants with different number of PGCs at 24 hpf.  After screening, embryos were reared at 28 °C until sampling at 14 dpf or 22 dpf.

tag: genotype/variation

tag: developmental stage

value: 22 dpf

tag: pgc number

value: High(WT)

tag: tissue

value: developing trunk regions


title: mono-DC + Dex + vitD3 + LPS

value: Tolerogenic-LPS Mono-DC phenotype (FACS analysis)


title: T1 vs GT21_cy3_Biorep 2

description:
Biological replicate 2 of 3.
T1_3_BR2


title: mono-maDC + LPS

value: Mature


title: EAE 32 day

description: Test

source_name: C57BL/6 mice with the induction of EAE for 32 days


title: mono-immDC 2

value: Immature

value: IL-4 + GM-CSF treatment


title: mono-immDC


title: mono-maDC + LPS (hybridization replicate)

value: IL-4 + GM-CSF + LPS treatment

value: Mature Mono-DC phenotype (FACS analysis)


title: 22d-P22-W

description: 22 dpf developing trunk of WT, twelfth of 14 biological replicates.


title: 22d-P24-W

description: 22 dpf developing trunk of WT, fourteenth of 14 biological replicates.


title: 22d-P19-W

description: 22 dpf developing trunk of WT, ninth of 14 biological replicates.


title: GT4 vs GT21_cy5_Biorep 1

description:
Biological replicate 1 of 3.
GT4_5_BR1

value: GT21= reference cells grown at 21°C


title: GT4 vs GT21_cy3_Biorep 3

description:
Biological replicate 3 of 3
GT4_3_BR3


title: 22d-P21-W

description: 22 dpf developing trunk of WT, eleventh of 14 biological replicates.


title: 22d-P18-L

description: 22 dpf developing trunk of dnd morphant, tenth of 10 biological replicates.

source_name: 22 dpf_dnd morphants_Low

value: dnd morphants


title: EBI3

city: Kumamoto

first: Hideo

last: Kudo

address: Chuo-ku, Honjo, 1-1-1

department: Dermatology

institute: Kumamoto University

hyb_protocol: The first-strand cDNA was synthesized from the RNA using RT2 First Strand Kit (Qiagen). The cDNA was mixed with RT2 SYBR Green/Rox qPCR Master Mix (Qiagen), and the mixture was added to 96-well Extracellular Matrix and Adhesion Molecules PCR Array (Qiagen).

scan_protocol: PCR was performed on Takara Thermal Cycler Dice (TP800) (Takara Bio, Shiga, Japan).

data_processing:
The threshold cycle (Ct) for each RNA was determined using Thermal Cycler Dice Real Time System version 2.10B (Takara Bio).The raw Ct (SDM) was normalized using the average value of housekeeping genes (B2M, HPRT1, RPL13A, GAPDH, ACTB).
Relative expression level for the EBI3 sample was calculated as 1/2^(the raw Ct (SDM) of each mRNA – average Ct (SDM) of housekeeping genes). These data are available on the series record.

label: SYBR Green

source_name: dermal fibroblast_stimulated

label_protocol: not applicable

growth_protocol: Human dermal fibroblasts were obtained by skin biopsies from affected dorsal forearm of seven healthy human subjects. Monolayer cultures independently isolated from different individuals were maintained at 37°C in 5% CO2 in air.

extract_protocol: Total RNA was extracted from cultured cells with ISOGEN (Nippon Gene, Tokyo, Japan).

treatment_protocol: Fibroblasts were serum-starved for 24 hours, then were treated with EBI3 (100ng/ml) for 12 hours.

value: skin

value: fibroblast

value: the presence of EBI3


title: 22d-P17-L

description: 22 dpf developing trunk of dnd morphant, ninth of 10 biological replicates.


title: No stimulation

description: The cDNA was mixed with RT2 SYBR Green/Rox qPCR Master Mix (Qiagen), and the mixture was added to 96-well Extracellular Matrix and Adhesion Molecules PCR Array (Qiagen).

data_processing:
The threshold cycle (Ct) for each RNA was determined using Thermal Cycler Dice Real Time System version 2.10B (Takara Bio).The raw Ct (SDM) was normalized using the average value of housekeeping genes (B2M, HPRT1, RPL13A, GAPDH, ACTB).
Relative expression level for the EBI3 sample was calculated as 1/2^(the raw Ct (SDM) of each mRNA –  average Ct (SDM) of housekeeping genes). These data are available on the series record.

source_name: dermal fibroblast_not_stimulated

value: the absence of EBI3


title: GT4 vs GT21_cy3_Biorep 2

description:
Biological replicate 2 of 3.
GT4_3_BR2


title: mouse liver at P9 [71-Liver]

city: Durham,

first: Tomasa

last: Barrientos

state: NC

address: 308 Research Drive, LSRC C127

department: Pharmacology and Cancer Biology

country: USA

institute: Duke University Medical Center

hyb_protocol: Targets were hybridized to the Mouse430 2.0 GeneChip (Affymetrix, Santa Clara, CA).  Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0  Array in the Affymetrix Hybridization Oven.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Partek Genomics Suite 6.5 (Partek Inc., St. Louis, MO) was used to perform data analysis. Robust multi-chip analysis (RMA) normalization was done on the entire data set. Multi-way ANOVA and fold change were performed to identify target genes that were differentially expressed between WT and Tfr1 skeletal muscle KO mice.

source_name: Liver from Tfr1 muscle KO mouse at P9

label_protocol: The labeling, hybridization, scanning, and data processing was performed by the Duke University Genomics Microarray facility. Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX).

growth_protocol: Skeletal muscle and liver from neonate mice at 5 and 9 days of age

extract_protocol: Total RNA was extracted from the gastrocnemius muscle and liver using the Qiagen Rneasy isolation kit according to the manufacturer’s instructions.

treatment_protocol: Gastrocnemius muscle and liver tissues were collected immediately after decapitaion of the mice

tag: strain background

value: mixed C57BL/6 and 129/SvEv

value: Tfr1 muscle KO

tag: age

value: 9-day old

value: Liver


title: mouse liver at P9 [73-Liver]

source_name: Liver from wild type mouse at P9

value: Wild type


title: 22d-P20-W

description: 22 dpf developing trunk of WT, tenth of 14 biological replicates.

value: wild type

value: 22 dpf

value: High(WT)

value: developing trunk regions


title: mouse liver at P9 [52-Liver]


title: 22d-P16-L

description: 22 dpf developing trunk of dnd morphant, eighth of 10 biological replicates.


title: 22d-P12-W

description: 22 dpf developing trunk of WT, eighth of 14 biological replicates.

value: High (WT)


title: 22d-P15-L

description: 22 dpf developing trunk of dnd morphant, seventh of 10 biological replicates.


title: mouse liver at P9 [40-Liver]


title: mouse liver at P9 [57-Liver]


title: 22d-P9-W

description: 22 dpf developing trunk of WT, fifth of 14 biological replicates.


title: 22d-P13-L

description: 22 dpf developing trunk of dnd morphant, fifth of 10 biological replicates.


title: GT4 vs GT21_cy3_Biorep 1

description:
Biological replicate 1 of 3.
GT4_3_BR1

source_name: GT21= reference cells grown at 21°C

value: GT4=test sample cells grown at 4°C


title: 22d-P14-L

description: 22 dpf developing trunk of dnd morphant, sixth of 10 biological replicates.


title: 22d-P8-W

description: 22 dpf developing trunk of WT, fourth of 14 biological replicates.


title: mouse liver at P9 [60-Liver]


title: 22d-P11-W

description: 22 dpf developing trunk of WT, seventh of 14 biological replicates.


title: 22d-P6-W

description: 22 dpf developing trunk of WT, second of 14 biological replicates.


title: 22d-P7-W

description: 22 dpf developing trunk of WT, third of 14 biological replicates.


title: mouse skeletal muscle at P9 [57-G-P]

source_name: Skeletal muscle from wild type mouse at P9

value: Skeletal muscle


title: mouse skeletal muscle at P9 [71-G-P]

source_name: Skeletal muscle from Tfr1 muscle KO mouse at P9


title: mouse liver at P9 [41-Liver]


title: mouse skeletal muscle at P9 [60-G-P]


title: mouse skeletal muscle at P9 [73-G-P]


title: 22d-P5-W

description: 22 dpf developing trunk of WT, first of 14 biological replicates.


title: mouse skeletal muscle at P9 [40-G-P]


title: mouse skeletal muscle at P5 [215-SK-Muscle]

source_name: Skeletal muscle from Tfr1 muscle KO mouse at P5

value: 5-day old


title: 22d-P4-L

description: 22 dpf developing trunk of dnd morphant, fourth of 10 biological replicates.

value: dnd morphants


title: mouse skeletal muscle at P9 [52-G-P]


title: 22d-P2-L

description: 22 dpf developing trunk of dnd morphant, second of 10 biological replicates.


title: mouse skeletal muscle at P9 [41-G-P]


title: mouse skeletal muscle at P5 [213-SK-Muscle]

source_name: Skeletal muscle from wild type mouse at P5


title: 14d-P23-W

description: 14 dpf developing trunk of WT, fourteenth of 14 biological replicates.

source_name: 14 dpf_wild type_High

value: 14 dpf


title: mouse skeletal muscle at P5 [205-SK-Muscle]


title: 22d-P10-W

description: 22 dpf developing trunk of WT, sixth of 14 biological replicates.


title: 14d-P22-W

description: 14 dpf developing trunk of WT, thirteenth of 14 biological replicates.


title: 14d-P18-W

description: 14 dpf developing trunk of WT, ninth of 14 biological replicates.


title: mouse liver at P5 [215-Liver]

source_name: Liver from Tfr1 muscle KO mouse at P5


title: 22d-P1-L

description: 22 dpf developing trunk of dnd morphant, first of 10 biological replicates.


title: 22d-P3-L

description: 22 dpf developing trunk of dnd morphant, third of 10 biological replicates.


title: 14d-P20-W

description: 14 dpf developing trunk of WT,eleventh of 14 biological replicates.


title: mouse skeletal muscle at P5 [214-SK-Muscle]


title: mouse skeletal muscle at P5 [206-SK-Muscle]


title: 14d-P17-W

description: 14 dpf developing trunk of WT, eighth of 14 biological replicates.


title: 14d-P19-W

description: 14 dpf developing trunk of WT, tenth of 14 biological replicates.


title: 14d-P21-W

description: 14 dpf developing trunk of WT, twelfth of 14 biological replicates.


title: mouse liver at P5 [205-Liver]

source_name: Liver from wild type mouse at P5


title: mouse liver at P5 [213-Liver]


title: mouse liver at P5 [207-Liver]


title: mouse liver at P5 [214-Liver]


title: mouse liver at P5 [206-Liver]


title: 14d-P16-L

description: 14 dpf developing trunk of dnd morphant, ninth of 10 biological replicates.

source_name: 14 dpf_dnd morphants_Low


title: mouse skeletal muscle at P5 [207-SK-Muscle]


title: 14d-P15-L

description: 14 dpf developing trunk of dnd morphant, eighth of 10 biological replicates.


title: Lira drug treated-5

city: Toronto

first: Mansoor

last: Husain

address: Room TMDT-3-910, 101 College St.

department: Toronto Gen. Hosp. Res Institute

institute: University Health Network

description:
Lira-5
Gene expression from drug treated mice

hyb_protocol: Affymetrix hybridization protocol EukGE-WS2v4

scan_protocol: Affymetrix GeneChip Scanner 3000 scanning protocol

data_processing: Raw data acquired by using GCOS 1.4 software with output as GCOS DTT Archive Files. The global gene-expression pattern of AL and CR mice (three replicates in each group) were compared using mouse MOE 430.2 Affymetrix Gene Chip Array.  Statistical analysis and visualization was performed using Partek Genomics Suite 6.5 and GX11 software.   Data analysis and visualization was performed using Partek version 6.5 [Partek Inc] and GX11 [Agilent] software.

source_name: heart, Left ventricle_Lira_drug-treated

label_protocol: Biotinylated cRNA were prepared with the Invitrogen SuperScript kit and In Vitro Transcription by the Enzo IVT kit

growth_protocol: Mice for CR and AL were individually caged and their food intake was measured everyday between 10-11 am for 1 wk to calculate the average daily food intake.  AL mice had free access to food and water and were not disturbed.  CR mice were fed 30% less than their calculated mean daily AL food consumption. Liraglutide-treated mice (200 μg/kg i.p. twice daily  for 7 days)  had free access to food and water.

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

treatment_protocol: Mice were subjected to ligation of left anterior descending (LAD) coronary artery ligation or sham surgery.At 2d post-MI, mice were harvested, hearts extracted, and atria were discarded before sectioning the LV with a mouse heart slicer matrix (Zivic Insruments, Pittsburgh, PA, USA). Each 2mm thick slice was incubated in 2% triphenyl tetrazolium chloride (TTC, Sigma-Aldrich), at 37oC to differentiate viable from infarcted myocardium, followed by fixation in 4% paraformaldehyde for 30 min at room temperature.

tag: gender

value: male

value: heart

tag: heart compartment

value: left ventricle


title: Lira drug treated-4

description:
Lira-4
Gene expression from drug treated mice


title: 14d-P13-L

description: 14 dpf developing trunk of dnd morphant, sixth of 10 biological replicates.


title: 14d-P12-W

description: 14 dpf developing trunk of WT, seventh of 14 biological replicates.


title: Lira drug treated-1

description:
Lira-1
Gene expression from drug treated mice


title: 14d-P11-W

description: 14 dpf developing trunk of WT,sixth of 14 biological replicates.


title: Caloric restriction 3

description:
CR-3
Gene expression from caloric restricted mice

source_name: heart, Left ventricle_CR


title: Control 5 (placebo/ad libitum diet)

description:
AL-5
Gene expression from control mice

source_name: heart, Left ventricle_control_ad libitum diet


title: 14d-P8-W

description: 14 dpf developing trunk of WT,third of 14 biological replicates.


title: 14d-P6-W

description: 14 dpf developing trunk of WT, first of 14 biological replicates.


title: Lira drug treated-2

description:
Lira-2
Gene expression from drug treated mice


title: Caloric restriction 1

description:
CR-1
Gene expression from caloric restricted mice


title: 14d-P10-W

description: 14 dpf developing trunk of WT, fifth of 14 biological replicates.


title: 14d-P2-L

description: 14 dpf developing trunk of dnd morphant, second of 10 biological replicates.


title: 14d-P1-L

description: 14 dpf developing trunk of dnd morphant, first of 10 biological replicates.


title: 14d-P4-L

description: 14 dpf developing trunk of dnd morphant, fourth of 10 biological replicates.


title: 14d-P7-W

description: 14 dpf developing trunk of WT,second of 14 biological replicates.


title: Caloric restriction 2

description:
CR-2
Gene expression from caloric restricted mice


title: Control 4 (placebo/ad libitum diet)

description:
AL-4
Gene expression from control mice


title: Control 2 (placebo/ad libitum diet)

description:
AL-2
Gene expression from control mice


title: 14d-P14-L

description: 14 dpf developing trunk of dnd morphant, seventh of 10 biological replicates.


title: 14d-P3-L

description: 14 dpf developing trunk of dnd morphant, third of 10 biological replicates.


title: Control 1 (placebo/ad libitum diet)

description:
AL-1
Gene expression from control mice


title: Caloric restriction 4

description:
CR-4
Gene expression from caloric restricted mice


title: Caloric restriction 5

description:
CR-5
Gene expression from caloric restricted mice


title: late-stage primary mouse T-ALL, rep. 2

city: Lausanne

first: Fabian

last: Junker

state: VD

address: EPFL SV ISREC - UPRAD, SV2533, Station 19

department: ISREC

country: Switzerland

institute: Ecole polytechnique fédérale de Lausanne

description: miRbase v18.0

hyb_protocol: Performed at Lausanne Genomic Technologies Facility according to standard protocol (F. Consales)

scan_protocol: Agilent Feature Extraction, Version 10.7.3.1

data_processing: Expression values are measured using RMA algorithm from the BioConductor affy package. RMA is a measure of expression comprising background correction, quantile normalization and probe set summary by robust regression.  Unlike the MAS 5.0/GCOS algorithm of Affymetrix, the resulting expression values are on the log 2 scale and range from 0 to 16.

source_name: BL-6 spleen, N1ICD-transformed BM chimera, late-stage T-ALL, FACS-sorted (CD4+CD8+)

extract_protocol: Cells were FACS-sorted from spleens, thymuses or culture dish, respectively, and total RNA was extracted using miRNeasy microRNA kit (Qiagen).

tag: disease status

value: late-stage T-ALL

tag: cell markers

value: spleen


title: Mouse T-ALL cell line M295

description: miRbase v18.0

source_name: T-ALL cell culture, M295 mouse cell line (from BL-6)

label_protocol: Performed at Lausanne Genomic Technologies Facility according to standard protocol (F. Consales)

tag: cell line

value: T-ALL


title: early-stage primary mouse T-ALL, rep. 2

description: miRbase v18.0

source_name: BL-6 spleen, N1ICD-transformed BM chimera, early-stage T-ALL, FACS-sorted (CD4+CD8+)

value: early-stage T-ALL


title: late-stage primary mouse T-ALL, rep. 3

description: miRbase v18.0


title: late-stage primary mouse T-ALL, rep. 1

description: miRbase v18.0


title: early-stage primary mouse T-ALL, rep. 1

description: miRbase v18.0


title: 14d-P5-L

description: 14 dpf developing trunk of dnd morphant, fifth of 10 biological replicates.


title: CD4+CD8+ primary mouse thymus cells, rep. 3

description: miRbase v18.0

source_name: BL-6 thymus, FACS-sorted (CD4+CD8+)

value: thymus


title: CD4+CD8+ primary mouse thymus cells, rep. 2

description: miRbase v18.0


title: early-stage primary mouse T-ALL, rep. 3

description: miRbase v18.0


title: WT Treg

description: Gene expression data on Treg cells isolated from wildtype mice

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

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

data_processing: 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: Treg cells isolated from different WT mice and equal amounts of RNA were pooled

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

treatment_protocol: Mouse CD4+T cells were first enriched by magnetic isolation, then were stained by anti-mouse CD4 and anti-mouse CD25 antibodies.CD4+CD25hi population were further sorted by flow cytometry.

value: CD4+CD25hi Treg cells

value: wild type


title: CD4-CD8- primary mouse thymus cells, rep. 3

description: miRbase v18.0

source_name: BL-6 thymus, FACS-sorted (CD4-CD8-)


title: CD4-CD8- primary mouse thymus cells, rep. 2

description: miRbase v18.0


title: MiR-125a KO Treg

description: Gene expression data on Treg cells isolated from miR-125a deficient mice

source_name: Treg cells isolated from different miR-125a KO mice and equal amounts of RNA were pooled

value: miR-125a KO


title: 14d-P9-W

description: 14 dpf developing trunk of WT, fourth of 14 biological replicates.

value: High (WT)

value: developing trunk regions


title: Lira drug treated-3

description:
Lira-3
Gene expression from drug treated mice


title: Control 3 (placebo/ad libitum diet)

description:
AL-3
Gene expression from control mice


title: colon tissue_case_rep2

city: Guangzhou

first: Yanfen

last: Xing

address: No.1. Panfu Rd

institute: Guangzhou First People’s Hospital

description: Gene expression in IBD rat after MSC transplantation

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.6) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.5.1).

organism: Rattus norvegicus

source_name: case 2

label_protocol: For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: Mesenchymal stem cells were cultured in L-DMEM medium

extract_protocol: Total RNA was extracted by Trizol following the manufacturer's recommendations. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers.ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000.

treatment_protocol: MSCs were cultured in L-DMEM medium and then transfected into IBD rats

value: colon tissue

tag: msc transplantation

value: yes


title: Control_03

city: Chengdu

first: Haixiang

last: Wu

address: No. 55, People’s South Road

department: Department of Ultrasonics

institute: the Second Hospital of Sichuan

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.9.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.

hyb_protocol: The Array was prehybridized for 30 min at 45℃ with 2X Hybridization Mix (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 16 h at 45℃. Finally, the array was washed twice with wash buffer A (Invitrogen).

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.

source_name: Myocardial tissues from healthy individuals

label_protocol: Three  mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions.

extract_protocol: RNA was extracted by TriZol

tag: viability status

value: dead

value: no disease

value: Heart

tag: Sex

value: M


title: Control_02

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.8.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.

value: F


title: Control_04

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.10.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.


title: Control_05

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.11.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.


title: CD4-CD8- primary mouse thymus cells, rep. 1

description: miRbase v18.0


title: CUTLL1 T-ALL cells, DAPT-treated, replicate 3

description:
Agilent-021827
miRbase v12.0

source_name: CUTLL1, 3d culture_DAPT

extract_protocol: Cells cultured in standard culture medium in vitro, and total RNA was extracted using miRNeasy microRNA kit (Qiagen).

treatment_protocol: DAPT treatment: 10µM, 3d in vitro. DMSO serves as control


title: HCM_03

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.2.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.

source_name: Myocardial tissues from HCM patients

value: Alive

value: Hypertrophic Cardiomyopathy


title: HCM_06

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.5.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.


title: HCM_05

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.4.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.


title: HCM_02

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.1.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.


title: colon tissue_control_rep1

description: Gene expression in normal rat

source_name: control 1

value: male

value: no


title: HCM_01

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.0.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.


title: colon tissue_case_rep1

source_name: case 1


title: rosette_line3.1_rep3

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

description:
pool of rosette leaves from eight transgenic plants (line 3.1)
3.1C

hyb_protocol: Pre-hybridization, RNA fragmentation, hybridization, washings and imaging were performed as indicated in CustomArray™ 90K Microarray Hybridization and Imaging Protocol (PTL020).

scan_protocol: The slides were scanned at 5 μm resolution, using a GenePix 4300A microarray scanner with Gene Pix Pro 7 software. Laser power was set at 30% while PMT gain was adjusted in order to get a fraction of saturated pixels equal to 1E-06.

data_processing: Densitometric quantification of the spots using the Microarray Imager 5.8 software. Data were normalized using quantile normalization and signals below the background (calculated as the average of the signals of negative controls plus 2 times their standard deviation) were filtered out.

organism: Arabidopsis thaliana

source_name: rosette leaves_line3.1

label_protocol: Amino allyl aRNA synthesis and dye Cy5-ULS labeling were performed using the RNA ampULSe: Amplification and Labeling Kit for CombiMmatrix arrays (KREATECH Biotechnology, Amsterdam, The Netherlands).

growth_protocol: Plants were grown in soil under a short day (10/14 h light/dark) photoperiod, at 70% relative humidity, 24/22°C day/night temperature and 100-120 μE m-2 s-1 irradiance.

extract_protocol: RNA was extracted from lyophilized plant material using the Spectrum Plant TotalRNA kit (Sigma-Aldrich). Contaminating DNA was removed with RQ1 RNase-Free DNase (Promega).

tag: ecotype

value: Wassilewskjia

value: overexpressing GmENOD40 gene

tag: transgenic line

tag: transformed with

value: soybean ENOD40 driven by 35S constitutive promoter

value: rosette leaves


title: Control_01

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.7.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.


title: rosette_line4.4_rep1

description:
pool of rosette leaves from eight transgenic plants (line 4.4)
4.4A

source_name: rosette leaves_line4.4

tag: genotype/variation


title: HCM_04

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.3.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.


title: rosette_line4.4_rep2

description:
pool of rosette leaves from eight transgenic plants (line 4.4)
4.4B


title: CUTLL1 T-ALL cells, DAPT-treated, replicate 2

description:
Agilent-021827
miRbase v12.0

tag: cell type

value: T-ALL


title: rosette_line1.1_rep3

description:
pool of rosette leaves from eight transgenic plants (line 1.1)
1.1C

source_name: rosette leaves_line1.1


title: colon tissue_control_rep2

description: Gene expression in normal rat

source_name: control 2


title: rosette_line1.1_rep2

description:
pool of rosette leaves from eight transgenic plants (line 1.1)
1.1B


title: rosette_line4.4_rep3

description:
pool of rosette leaves from eight transgenic plants (line 4.4)
4.4C


title: CUTLL1 T-ALL cells, DMSO-treated, replicate 1

description:
Agilent-021827
miRbase v12.0

source_name: CUTLL1, 3d culture_DMSO


title: rosette_line3.1_rep2

description:
pool of rosette leaves from eight transgenic plants (line 3.1)
3.1B


title: HCM_07

description: Approximately 30,000 probes (60 mer of length) for detection of lncRNA and mRNA were spotted on CapitalBio Human LncRNA Microarray v2.6.The database resource included Refseq, ENSEMBL, UCSC, NRED, ENCODE, and other relevant database.


title: CUTLL1 T-ALL cells, DAPT-treated, replicate 1

description:
Agilent-021827
miRbase v12.0


title: CUTLL1 T-ALL cells, DMSO-treated, replicate 3

description:
Agilent-021827
miRbase v12.0


title: CUTLL1 T-ALL cells, DMSO-treated, replicate 2

description:
Agilent-021827
miRbase v12.0


title: rosette_wt_rep2

description:
pool of rosette leaves from eight wt plants
WTB

source_name: rosette leaves_wt

value: wild type


title: rosette_line1.1_rep1

description:
pool of rosette leaves from eight transgenic plants (line 1.1)
1.1A


title: rosette_wt_rep1

description:
pool of rosette leaves from eight wt plants
WTA


title: Huh7 U6 20 Cre 16 P2

status: Public on May 07 2015

city: Heidelberg

first: Tobias

last: Bauer

address: Im Neuenheimer Feld 280

department: Theoretical Bioinformatics

country: Germany

institute: German Cancer Research Center

description: miRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and knock out of miR-122

hyb_protocol: Labeled miRNA sample were hybridized for at least 20 hr at 55C on Agilent human miRNA Microarray Release 19.0, 8x60k.

scan_protocol: Gene Expression Microarrays were scanned using the Agilent Scanner G2505C.

data_processing: Background correction was applied with "normexp"-method following quantile normalization on the probe level and log2-transformation. Probes were then averaged i) by duplicates ii) per gene target. Quantile normalization was re-applied (all Bioconductor software package limma), and finally ComBat batch-effect removal (Bioconductor package sva).

label: Cyanine 3-pCp

source_name: Huh7 cell line, shmiRNA integration and miR-122 ko, passage 2

label_protocol: Agilent protocol "miRNA Complete Labeling and Hyb Kit"

growth_protocol: Huh7 cells were culture with DMEM supplemented with 10% FCS, 1% P/S and 1% NEAA

extract_protocol: To extract the total RNA the cells were harvested from one confluent 10 cm dish and resuspended in 5 ml of QIAzol Lysis Reagent (QIAGEN, Hilden, Germany). The QIAzol RNA extraction protocol recommended by QIAGEN was used for RNA purification.

tag: passage

tag: origin

value: Hepatocellular carcinoma

value: Male


title: rosette_line3.1_rep1

description:
pool of rosette leaves from eight transgenic plants (line 3.1)
3.1A

tag: tissue


title: Huh7 T2 31 Cre 3

description: miRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells

source_name: Huh7 cell line, shmiRNA integration, passage 1


title: Huh7 TS 30 Cre 20 P3

description: miRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and mutation of miR-122

source_name: Huh7 cell line, shmiRNA integration and miR-122 mutation, passage 3


title: Huh7 U6 20 Cre 16 P3

source_name: Huh7 cell line, shmiRNA integration and miR-122 ko, passage 3

value: integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and knock out of miR-122


title: rosette_wt_rep3

description:
pool of rosette leaves from eight wt plants
WTC


title: Huh7 wt P2

description: miRNA expression profile of Huh7 wild-type cells

source_name: Huh7 cell line, wild type, passage 2


title: Huh7 T2 31 Cre 3 P2

source_name: Huh7 cell line, shmiRNA integration, passage 2

value: integration of a an anti-HCV shmiRNA in the hcr locus of Huh7


title: Huh7 TS 30 Cre 20

source_name: Huh7 cell line, shmiRNA integration and miR-122 mutation, passage 1

value: integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and mutation of miR-122


title: Huh7 wt

source_name: Huh7 cell line, wild type, passage 1


title: Huh7 wt P3

source_name: Huh7 cell line, wild type, passage 3


title: Huh7 TS 30 Cre 20 P2

source_name: Huh7 cell line, shmiRNA integration and miR-122 mutation, passage 2


title: Huh7 U6 20 Cre 16

source_name: Huh7 cell line, shmiRNA integration and miR-122 ko, passage 1


title: shHES1_2

city: New York

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

hyb_protocol: hybridized to the Illumina HumanT-12v4 Expression BeadChip  Expression BeadChip  according to manufacturer’s protocol

scan_protocol: Standard scan according to manufacturer's protocol

data_processing: Raw gene expression data were log2 transformed and quantile-normalized using MATLAB.

label_protocol: 10 ng of RNA from each sample was amplified using the Ovation PicoSL WTA System (NuGen), labeled by the Encore BiotinIL Module (NuGen)

growth_protocol: CUTLL1 cells were cultured in standard conditions in RPMI 1640 media supplemented with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol: RNA isolation from mice tumors was performed in triplicate using the RNeasy Micro kit (QIAGEN) according to manufacturer’s protocol.

treatment_protocol: CUTLL1 cells infected with shRNA LUC and shHES1 were collected 72 hours post puromycin selection

tag: shRNA


title: shHES1_1


title: shRNA LUC_2

value: shRNA LUC


title: shRNA LUC_1


title: CD4+CD8+ primary mouse thymus cells, rep. 1

description: miRbase v18.0

source_name: BL-6 thymus, FACS-sorted (CD4+CD8+)

tag: strain

value: thymus


title: Intercaruncular_SUI_en3 26

type: genomic

city: Auckland

first: Caroline

middle: Gwendolyn

last: Walker

state: Outside the US or Canada

address: 3A symonds st

department: University of Auckland

country: New Zealand

institute: DairyNZ Ltd

description:
en3 26
Affinity-enriched DNA vs. input DNA.

hyb_protocol: All of the labeled IP DNA (~3-4 µg) and 4 µg of labeled Input DNA were hybridized onto the 400K custom-designed Agilent-027994 microarray (2 x 400K array format, AMADID and Part no. are 027994 and G4820A, respectively) for 40 hours at 65°C. Microarray was washed using aCGH wash buffer 1 and 2 for five minutes and 1 minute, respectively.

scan_protocol: Hybridized arrays were scanned at 2μm resolution on an Agilent Technologies Scanner G2505C. Data extraction from Images was done using Feature Extraction software v 10.5.1.1 of Agilent.

data_processing:
Normalization of the data was done using the centralization method (Centralization adds or subtracts a constant value from each log ratio measurement. This recenters the log ratio values, and makes sure that the zero- point reflects the most common ploidy state). Methylation states were obtained using the BATMAN Algorithm. BATMAN is a visualization and report analysis that determines the absolute methylation level for CpG dinucleotides contained within DNA fragments queried by probes across the microarray. The algorithm begins with a calibration step, which uses a regression to fit a trend between local CpG density and either probe logratios, or Z- scores (Methylation Status Detection Algorithm). This was followed by a modeling step, which used the calibration results to construct the conditional probability of the log- ratios (or Z- scores) given the methylation state. A sampling step occurs to generate a large number of possible methylation states. Bayesian methodology is used to invert the conditional probability and summarize the methylation state per probe. Finally, a methylation call step fits a distribution to the scores on a per- chromosome basis.
Methylation Status Detection Algorithm: The methylation status detection algorithm is designed for two-color assays, where the green (Cy3) channel is comprised of input DNA, and the red (Cy5) channel is comprised of the affinity-enriched DNA. As a result of constraints imposed on the array design, the probes that target genomic regions with varying CG content do not share a uniform melting temperature (Tm), which can result in compression of the log-ratios. The methylation detection algorithm allows normalizing the log- ratios for each probe, based on its Tm, and returns the methylation status of a probe. The algorithm first bins the probes by their melting temperature. For each bin, it applies Gaussian fits using one of three models. It fits the probe log- ratios to Gaussians, using a local searching algorithm called random hill climbing. Z-Scores and p-values derived from the Gaussian data give probabilities and confidence values for methylated and unmethylated probe populations. The algorithm then calculates a methylation logOdds, which gives the relative probability that a probe is more likely, methylated than unmethylated.

molecule: genomic DNA

organism: Bos taurus

source_name: Intercaruncular, SUI, input

label_protocol: Input DNA was labeled with Cy3 and IP DNA with Cy5 using Agilent's Genomic DNA labeling kit (Cat. no. 5190-0453). Labeled samples were cleaned and concentrated using Microcon YM-30 columns (Millipore Cat. no. 42410).

extract_protocol:
5 ug of DNA were sonicated and the efficiency of sonication was tested on the Agilent Bioanalyser. An ideal smear size ranged between 100-700 bp. The sonicated DNA was then immunoprecipitated using anti-5-methylcytidine antibody (Cat. no: Eurogentec Ref: MECY_0500) bound to Pan Mouse IgG Dynabeads (Invitrogen Cat no: 110.41). DNA was eluted in 1% SDS solution at 65 C. Input DNA (whole cell extract-genomic DNA) and IP DNA were precipitated with 3M Acetate after a Phenol:chloroform (25:24:1) clean up using heavy phase lock gels Cat. No. Eppendorf (ref # 2302830).
DNA was extracted from endometrial tissue using a Qiagen DNeasy blood and tissue kit (QIAGEN catalogue# 69506). DNA quantity was determined by spectrophotometry using a Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE). Genomic DNA integrity was assessed by running it on a 0.8% Agarose Gel. Genomic DNA purity was assessed by the NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop Technologies, Rockland, USA). Genomic DNA with OD260/OD280>1.8 and OD260/OD230 ≥ 1.8 was used for microarray experiments. We considered DNA to be good quality when a single clear band was seen when run against a reference genomic DNA sample.

treatment_protocol: Endometrial tissues were obtained at 29 days post-partum (n=12) and Agilent two-colour microarrays were used to characterize DNA methylation profiles. Cows with subclinical endometritis (SUI, n=6) were compared with control cows (NUI, n=6). Sub-clinical endometritis was diagnosed by uterine cytology. Cows with PMN% above 18 were diagnosed with sub-clinical endometritis. Control cows had 0 PMN%.

tag: breed

value: Holstein Friesian

value: intercaruncular endometrium

tag: developmental stage

value: 29 days post-partum

tag: disease state

value: subclinical endometritis

tag: ip antibody

tag: animal identifier

source_name: Intercaruncular, SUI, IP


title: Intercaruncular_SUI_en3 34

description:
en3 34
Affinity-enriched DNA vs. input DNA.

tag: disease status


title: Huh7 T2 31 Cre 3 P3

source_name: Huh7 cell line, shmiRNA integration, passage 3

tag: cell line

tag: gender


title: Intercaruncular_NUI_en3 14

description:
en3 14
Affinity-enriched DNA vs. input DNA.

source_name: Intercaruncular, NUI, input

value: control

source_name: Intercaruncular, NUI, IP


title: Intercaruncular_SUI_en3 18

description:
en3 18
Affinity-enriched DNA vs. input DNA.


title: Caruncular_NUI_en3 45

description:
en3 45
Affinity-enriched DNA vs. input DNA.

source_name: Caruncular, NUI, input

value: caruncular endometrium

source_name: Caruncular, NUI, IP


title: Caruncular_NUI_en3 31

description:
en3 31
Affinity-enriched DNA vs. input DNA.


title: Intercaruncular_NUI_en3 32

description:
en3 32
Affinity-enriched DNA vs. input DNA.


title: LNA-tRF-Tyr2_shYBX1_8hr

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: Amanitin-treatement

hyb_protocol: Per manufacturer's instruction

scan_protocol: Per manufacturer's instruction

data_processing: Data were quantile-normalized and processed using the Lumi package. Futher processed values are the difference between the average normalized and corrected transcripts stability in LNA-tranfected cells in control cells relative to YBX1-knockdown background.

label_protocol: Samples were biotin-labeled using the TargetAmp-Nano Labeling Kit for Ilumina Expression BeadChip

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol: 48hr post-transfection, total RNA was extracted and on-column Dnase treated using Norgen Biotek total RNA extraction kit (per manufacturer instructions).

treatment_protocol: tRF antisense LNA oligonucleotides (Exiqon) were transfected using Lipofectamine 2000 in Reduced Serum Media (Life Technologies) consisting of equal parts of each tRF decoy or anti-tRF LNA. After six hours incubation, transfection media was replaced with fresh media. Cells are then collected at 0hr or 8hr upon treatment with Amanitin.

value: MDA

tag: time point

tag: lna


title: LNA-tRF-Tyr3_shYBX1_8hr

description: Amanitin-treatement

tag: genotype/variation


title: Intercaruncular_SUI_en3 38

description:
en3 38
Affinity-enriched DNA vs. input DNA.


title: LNA-tRF-Gly1_shYBX1_8hr

description: Amanitin-treatement

tag: cell type


title: LNA-tRF-Gly3_shYBX1_8hr

description: Amanitin-treatement


title: Caruncular_SUI_en3 11

description:
en3 11
Affinity-enriched DNA vs. input DNA.

source_name: Caruncular, SUI, input

source_name: Caruncular, SUI, IP


title: Caruncular_NUI_en3 21

description:
en3 21
Affinity-enriched DNA vs. input DNA.


title: LNA-tRF-Glu3_shYBX1_8hr

description: Amanitin-treatement


title: LNA-tRF-Tyr1_shYBX1_8hr

description: Amanitin-treatement


title: Intercaruncular_SUI_en3 08

description:
en3 08
Affinity-enriched DNA vs. input DNA.


title: Caruncular_SUI_en3 25

description:
en3 25
Affinity-enriched DNA vs. input DNA.


title: Intercaruncular_NUI_en3 42

description:
en3 42
Affinity-enriched DNA vs. input DNA.


title: Caruncular_SUI_en3 17

description:
en3 17
Affinity-enriched DNA vs. input DNA.


title: Intercaruncular_NUI_en3 46

description:
en3 46
Affinity-enriched DNA vs. input DNA.


title: Intercaruncular_NUI_en3 22

description:
en3 22
Affinity-enriched DNA vs. input DNA.


title: Caruncular_NUI_en3 13

description:
en3 13
Affinity-enriched DNA vs. input DNA.


title: Caruncular_NUI_en3 01

description:
en3 01
Affinity-enriched DNA vs. input DNA.


title: Caruncular_SUI_en3 37

description:
en3 37
Affinity-enriched DNA vs. input DNA.


title: Caruncular_NUI_en3 41

description:
en3 41
Affinity-enriched DNA vs. input DNA.


title: Intercaruncular_NUI_en3 02

description:
en3 02
Affinity-enriched DNA vs. input DNA.


title: Caruncular_SUI_en3 07

description:
en3 07
Affinity-enriched DNA vs. input DNA.


title: Intercaruncular_SUI_en3 12

description:
en3 12
Affinity-enriched DNA vs. input DNA.


title: LNA-tRF-Gly2_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Asp3_shYBX1_8hr

description: Amanitin-treatement


title: Caruncular_SUI_en3 33

description:
en3 33
Affinity-enriched DNA vs. input DNA.


title: LNA-tRF-Tyr3_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Glu3_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Gly1_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Glu1_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Asp3_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Asp1_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Asp1_shYBX1_8hr

description: Amanitin-treatement


title: LNA-tRF-Tyr2_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Asp2_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Gly3_shControl_8hr

description: Amanitin-treatement

source_name: MDA-shControl

value: shControl


title: LNA-tRF-Gly2_shYBX1_8hr

description: Amanitin-treatement


title: LNA-tRF-Gly1_shControl_8hr

description: Amanitin-treatement


title: LNA-tRF-Glu2_shYBX1_8hr

description: Amanitin-treatement


title: LNA-tRF-Tyr1_shControl_8hr

description: Amanitin-treatement


title: LNA-tRF-Tyr1_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Tyr2_shControl_8hr

description: Amanitin-treatement


title: LNA-tRF-Tyr3_shControl_8hr

description: Amanitin-treatement


title: LNA-tRF-Gly2_shControl_8hr

description: Amanitin-treatement


title: LNA-tRF-Glu1_shYBX1_8hr

description: Amanitin-treatement


title: LNA-tRF-Glu2_shControl_8hr

description: Amanitin-treatement


title: LNA-tRF-Glu2_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Asp3_shControl_8hr

description: Amanitin-treatement


title: LNA-tRF-Asp2_shControl_8hr

description: Amanitin-treatement


title: LNA-tRF-Asp1_shControl_8hr

description: Amanitin-treatement


title: LNA-tRF-Tyr2_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Asp2_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Glu3_shControl_8hr

description: Amanitin-treatement


title: LNA-tRF-Gly2_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Gly3_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Tyr1_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Glu3_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Glu1_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Asp2_shYBX1_8hr

description: Amanitin-treatement


title: LNA-tRF-Tyr3_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Gly1_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Glu1_shControl_8hr

description: Amanitin-treatement


title: LNA-tRF-Asp1_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Glu2_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Asp3_shControl_0hr

description: Amanitin-treatement


title: LNA-tRF-Scr2_shYBX1-1

data_processing: Data were quantile-normalized and processed using the Lumi package. Processed values are the difference between the logFC of average normalized signals in LNA-induced changes in control cells relative to YBX1-knockdown cells.

treatment_protocol: tRF antisense LNA oligonucleotides (Exiqon) were transfected using Lipofectamine 2000 in Reduced Serum Media (Life Technologies). After six hours incubation, transfection media was replaced with fresh media.


title: LNA-tRF-Tyr2_shYBX1-2


title: LNA-tRF-Scr3_shYBX1-2


title: LNA-tRF-Scr4_shYBX1-2


title: LNA-tRF-Gly2_shYBX1-2


title: LNA-tRF-Glu2_shYBX1-2


title: IL-2 un-induced,2

city: rasht

first: Najmeh

last: Ranji

state: Guilan

address: iran. rasht. rasht branch , islamic azad university

department: Genetics

country: Iran

institute: islamic azad university

description: Control

data_processing: To analyze Q-RT-PCR data, GenEx software and ΔΔCT method were used. By Normfinder, SNORD49A (snoRNA U49) gene was identified as optimal reference gene for normalization. Fold change of each miRNA was calculated by the equation 2−ΔΔCT and logarithmically transformed (base 2). P-values were adjusted for multiple comparisons using Dunn-Benferroni correction.

label: SYBR Green,

source_name: IL-2 un-induced CD4+T cells,2

label_protocol: cDNA synthesis and Q-RT-PCR were performed with miRCURY LNATM universal RT microRNA PCR kit. Both kits were purchased from Exiqon (Vedbaek, Denmark). According to manufacturer’s instructions, to synthesize cDNA, total RNA was added to enzyme mix, reaction buffer, and RNA spike-in (control RNA). Then, the mixture was incubated 60 min at 42 °C and 5 min at 95 °C. To perform Q-RT-PCR array, cDNA was added to SYBR green master mix and was dispensed into the 384-well plates (by a specific LNATM primer pair/ well); then the reaction was performed using a real-time PCR cycler (Roche LC480, USA) according to this program: 95°C for 10 min, 45 cycles at 95˚C for 10 sec, 60˚C for 1 min. For miRNA profiling, two 384-well plates (human panel I & II) were used and each reaction was performed twice. Each panel contained 6 reference primer sets as well as one control primer set (that targeted a synthetic spike-in RNA) and an inter-plate calibrator in triplicate.

growth_protocol: The heparinized venous blood was diluted with phosphate buffered saline (PBS) and carefully was layered over Ficoll-Paque. Peripheral blood mononuclear cells (PBMC) were isolated according to the manufacturer’s instrument.Then Naïve CD4+T cells were collected negatively by naïve CD4+T cell isolation kit ΙΙ and MS MACS columns.

extract_protocol: For miRNA profiling, total RNA from activated CD4+T cells in the presence and the absence of IL-2 (0.75 n/ml) after 3 days was extracted. RNA isolation was carried out using miRCURYTM RNA isolation kit.

treatment_protocol: Naïve CD4+T cells (1× 105 cells/well) were cultured in 0.2-ml 96-well tissue culture plates and complete medium of DMEM supplemented with 10 % heat-inactivated fetal bovine serum (FBS), 100 U/ml penicillin, 100 μg/ml streptomycin and 10 mM HEPES . Naïve CD4+T cells were treated by anti-CD2,-CD3,-CD28microbeads (bead-to-cell ratio 1:2) during 3 days for full activation. Then,  of IL-2 ( 0.75  ng/ml) were added to half of activated cells for 72 h.

tag: treatment


title: IL-2 un-induced,1

description: Control

source_name: IL-2 un-induced CD4+T cells,1


title: IL-2 induced,2

description: Test

source_name: IL-2 induced CD4+T cells,2


title: IL-2 induced,1

description: Test

source_name: IL-2 induced CD4+T cells,1


title: LNA-tRF-Asp2_shYBX1-2


title: LNA-tRF-Tyr1_shYBX1-1


title: LNA-tRF-Glu1_shYBX1-1


title: LNA-tRF-Asp1_shYBX1-1


title: LNA-tRF-Scr4_shControl


title: LNA-tRF-Scr2_shControl


title: LNA-tRF-Scr1_shYBX1-1


title: MDA-Hypoxia-shYBX1-Scr-2

data_processing: Data were quantile-normalized and processed using the Lumi package. Processed values are the difference between the logFC of average normalized signals in LNA-induced expression changes (tRF-LNA/scr-LNA) in control cells relative to YBX1-knockdown cells.

treatment_protocol: tRF antisense LNA oligonucleotides (Exiqon) were transfected using Lipofectamine 2000 in Reduced Serum Media (Life Technologies). After six hours incubation, transfection media was replaced with fresh media and cells were incubated in a hypoxia chamber (1% oxygen).

value: Hypoxia

tag: transfection

value: scr-LNA


title: LNA-tRF-Gly1_shYBX1-1


title: MDA-Hypoxia-shCtrl-LNA-1

source_name: MDA-shCtrl

value: shCtrl

value: tRF-LNA


title: LNA-tRF-Tyr1_shControl


title: LNA-tRF-Scr3_shControl


title: LNA-tRF-Gly2_shControl


title: LNA-tRF-Glu2_shControl


title: MDA-Hypoxia-shYBX1-Scr-1


title: LNA-tRF-Gly3_shYBX1_0hr

description: Amanitin-treatement


title: LNA-tRF-Asp2_shControl


title: LNA-tRF-Scr1_shControl


title: MDA-Hypoxia-shCtrl-Scr-2


title: MDA-Hypoxia-shCtrl-LNA-2


title: LNA-tRF-Tyr2_shControl


title: LNA-tRF-Asp1_shControl


title: MDA-Hypoxia-shYBX1-LNA-2


title: LM2-Hypoxia-shCtrl-2

data_processing: Data were quantile-normalized and processed using the Lumi package. Futher processed values are the difference between the logFC of average normalized signals changes in hypoxic versus normoxic cells relative to YBX1-knockdown cells.

treatment_protocol: The hypoxia chamber was flushed with 1% oxygen at a rate of 25L/min for 5 minutes. Cells were then incubated at 37C.


title: LNA-tRF-Glu1_shControl


title: MDA-Hypoxia-shCtrl-Scr-1


title: LNA-tRF-Gly1_shControl


title: MDA-Hypoxia-shYBX1-LNA-1


title: LM2-shCtrl-1

value: Normoxia


title: LM2-Hypoxia-shYBX1-2

value: shYBX1 knockdown


title: LM2-shCtrl-2


title: LM2-shYBX1-2


title: MDA-Hypoxia-shYBX1-1


title: CAR_SUI_6

description: En3 37

hyb_protocol: Eight hundred and twenty five nanograms of Cy3- and Cy5-labeled cRNA were added to Agilent-023647 4x44k 60-mer oligonucleotide microarrays (G2519F 023647) and hybridized overnight at 65°C (17 hours). Slides were then washed with Agilent Gene Expression Wash Buffers 1 and 2 according to the manufacturer's instructions, inserted into a slide cover with ozone barrier, and scanned on an Agilent C scanner at 5µm.

scan_protocol: Slides were scanned on an Agilent C scanner at 5µm.

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to analyze the scanned Agilent microarray. The 24 scanned microarray image files were uploaded to the Feature Extraction software. Using a design file (023647), the Feature Extraction software locates features and converts the extracted data from each feature into a quantitative log2ratio. This software removes pixel outliers, performs statistical tests on the non-outlier pixels, subtracts background from features and flags any outlier features. The software was then used to perform LOWESS (locally weighted linear regression analysis) dye normalization and to calculate a p-value for each feature.

source_name: Caruncular, SUI

label_protocol: One hundred and fifty nanograms of RNA were amplified using the Agilent Low Input Quick Amp Labeling Kit, two color (Agilent, G2519F) to generate fluorescent complimentary RNA (cRNA) according to the manufacturer's instructions. cRNA quantity was measured by spectrophotometry using a ND-1000 (Nanodrop Technologies, Wilmington, DE).

extract_protocol: Endometrial tissue was homogenised in Qiagen buffer RLT (QIAGEN GmbH, QIAGEN, Hilden, Germany) using a TissueLyser II (Qiagen). Approximately 30 mg of tissue was homogenized for 2 minutes with three ball bearings of 1/8 inch diameter (Farrell Bearings, Hamilton, NZ) in a tube containing RLT lysis buffer (Qiagen). Total RNA was extracted using a Qiagen RNeasy kit (QIAGEN). All samples were DNase treated using the Ambion DNA-free kit (Ambion, Austin, TX) according to the manufacturer's instructions. RNA quantity was determined by spectrophotometry in a Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE). RNA integrity was checked using the Agilent 2100 Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA).

tag: tissue

tag: pmn%

tag: progesterone concentration (ng/ml)

tag: bacteriology score

source_name: Pooled reference

value: caruncular and intercaruncular endometrium

value: subclinical endometritis and control

tag: sample type

value: reference


title: CAR_NUI_5

description: En3 41

source_name: Caruncular, NUI

tag: breed

value: Holstein Friesian

tag: disease state


title: ICAR _NUI_6

description: En3 46

source_name: Intercaruncular, NUI

value: intercaruncular endometrium

tag: animal identifier


title: LM2-Hypoxia-shYBX1-1


title: MDA-shCtrl-2


title: LM2-Hypoxia-shCtrl-1


title: MDA-Hypoxia-shYBX1-2


title: ICAR _NUI_5

description: En3 42


title: MDA-shYBX1-2


title: MDA-shYBX1-1


title: MDA-Hypoxia-shCtrl-1


title: ICAR _NUI_4

description: En3 32


title: LM2-shYBX1-1


title: MDA-Hypoxia-shCtrl-2


title: MDA-shCtrl-1


title: CAR_SUI_5

description: En3 33


title: CAR_NUI_4

description: En3 31


title: ICAR _SUI_5

description: En3 34

source_name: Intercaruncular, SUI


title: ICAR _NUI_3

description: En3 22


title: CAR_NUI_6

description: En3 45


title: CAR_SUI_4

description: En3 25


title: ICAR _SUI_6

description: En3 38


title: CAR_NUI_3

description: En3 21


title: carpt-00469: RA37N

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Prostate Cancer

value: Prostate Cancer

value: Dura

tag: pathological stage

value: non-metastatic tumor

tag: Sex

value: male

value: Normal Dura

source_name: Promega Female Genomic DNA

value: Female


title: carpt-00469: RA45M

scan_protocol: See mage-tab files linked to series entry for additional details

value: Femur

value: metastatic tumor


title: ICAR _SUI_3

description: En3 18

value: subclinical endometritis


title: ICAR _NUI_2

description: En3 14

value: control


title: carpt-00469: RA37T

data_processing: See mage-tab files linked to series entry for additional details


title: carpt-00469: RA45AT2

label_protocol: See mage-tab files linked to series entry for additional details

value: Adrenal


title: carpt-00469: RA48RN

extract_protocol: See mage-tab files linked to series entry for additional details

value: Rib

value: Normal Rib


title: carpt-00469: RA45AN

value: Normal Adrenal


title: carpt-00469: RA53M

value: Lung

value: normal lung


title: CAR_SUI_1

description: En3 07

value: Holstein Friesian

value: caruncular endometrium

value: caruncular and intercaruncular endometrium

value: subclinical endometritis and control

value: reference


title: CAR_SUI_3

description: En3 17


title: DB-1

city: Suzhou

first: Junjie

last: Yang

address: 708 Renmin Road

institute: Institute for cardiovascular science of Soochow University

description: Gene expression data from bone marrow cells of diabetic mice

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix Expression Console default analysis settings and global scaling as normalization method. Normalized signal intensities were transformed to the log base 2 scale.

source_name: bone marrow cells_diabetic

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: The femurs and tibiae of type 2 diabetic mice and wild type mice were excised and the diaphyses flushed using a 25g needle and PBS to get bone marrow cells.

extract_protocol: All samples were prepared using Trizol. Total RNA was isolated using the RNeasy Mini Kit (QIAGEN), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: No further treatment

tag: genotype

value: BKS.Cg-Dock7m -/- Leprdb/JNju

tag: gender

value: male

tag: age

value: 10 weeks

value: bone marrow


title: ICAR _NUI_1

description: En3 02

value: intercaruncular endometrium


title: WT-3

description: Gene expression data from bone marrow cells of wild type mice

source_name: bone marrow cells_wildtype

value: BKS.Cg-Dock7m +/+ Leprdb/JNju


title: CAR_SUI_2

description: En3 11

value: subclinical endometritis


title: Hes1 KO, biological rep2

hyb_protocol: hybridized to the Illumina MouseWG-6 v2.0 Expression BeadChip  according to manufacturer’s protocol

source_name: Hes1-/- NOTCH1 induced leukemias

growth_protocol: To generate NOTCH1-induced T-ALL tumors in mice, we performed retroviral transduction of bone marrow cells enriched in lineage negative cells using magnetic beads (Lineage cell depletion kit by Miltenyi kit #130-090-858 following manufacturer’s guidelines) with an activated form of the NOTCH1 oncogene (ΔE-NOTCH1) and transplanted them via intravenous injection into lethally irradiated NRG immunodeficient mice (JAX: 007799) as previously described26,27. We treated secondary recipients with vehicle only or with tamoxifen (5 mg/mouse) by intra-peritoneal injection to induce deletion of the Hes1 locus.

treatment_protocol: Cells from ΔE-NOTCH1 Rosa26 Cre-ERT2 Hes1flox/flox T-ALL were cultured in vitro and treated for 36 hours with ethanol or 4-hydroxy-tamoxifen

tag: host strain background

value: lethally irradiated NRG immunodeficient mice (JAX:007799)

tag: genotype/variation

tag: treated with

value: 4-hydroxy-tamoxifen for 36hrs

tag: induced genotype

value: Hes1-/- ΔE-NOTCH1


title: DB-3

tag: tissue


title: CAR_NUI_1

description: En3 01

value: control

tag: pmn%


title: Hes1 WT, biological rep3

source_name: Hes1 wild type NOTCH1 induced leukemias

value: ΔE-NOTCH1 Rosa26 Cre-ERT2 Hes1flox/flox T-ALL

value: ethanol for 36hrs

value: Hes1 wild type ΔE-NOTCH1


title: ICAR _SUI_1

description: En3 08

value: Holstein Friesian

tag: progesterone concentration (ng/ml)

value: caruncular and intercaruncular endometrium


title: Hes1 WT, biological rep2


title: CAR_NUI_2

description: En3 13

value: caruncular endometrium

tag: bacteriology score

value: subclinical endometritis and control

value: reference


title: DB-2

value: BKS.Cg-Dock7m -/- Leprdb/JNju

value: male

value: 10 weeks


title: WT-1

value: BKS.Cg-Dock7m +/+ Leprdb/JNju

value: bone marrow


title: carpt-00469: RA48RM

value: Prostate Cancer

value: Rib

value: metastatic tumor

value: Female


title: ICAR _SUI_4

description: En3 26

value: intercaruncular endometrium

value: subclinical endometritis

tag: sample type


title: WT-2


title: Hes1 WT, biological rep1

value: lethally irradiated NRG immunodeficient mice (JAX:007799)

value: ΔE-NOTCH1 Rosa26 Cre-ERT2 Hes1flox/flox T-ALL

value: ethanol for 36hrs

value: Hes1 wild type ΔE-NOTCH1


title: Hes1 KO, biological rep3

value: 4-hydroxy-tamoxifen for 36hrs

value: Hes1-/- ΔE-NOTCH1


title: dobbi-00100: NCI_U133A_NC 95C

source_name: Sloan Kettering Institute for Cancer Research

tag: cell line

tag: tumor grading

tag: disease stage

tag: organism part

tag: histology


title: dobbi-00100: NCI_U133A_NC Reference-wk2

tag: disease state

tag: Sex


title: Hes1 KO, biological rep1


title: dobbi-00100: NCI_U133A_NC 90C

tag: age


title: dobbi-00100: NCI_U133A_NC 83C


title: dobbi-00100: NCI_U133A_NC Reference


title: dobbi-00100: NCI_U133A_NC 84C


title: dobbi-00100: NCI_U133A_NC 80C


title: dobbi-00100: NCI_U133A_NC 79C


title: dobbi-00100: NCI_U133A_NC 96C


title: cho-00156: UM-OS-009

source_name: Ovary

value: F

value: Ovary cancer

tag: disease location

value: Ovary

value: serous


title: dobbi-00100: NCI_U133A_NC 167T

value: Non neoplastic liver with cirrosis

value: Liver


title: dobbi-00100: NCI_U133A_NC 162T

value: Ovarian Adenocarcinoma

value: Papillary Serous Adenocarcinoma


title: cho-00156: UM-OS-008


title: cho-00156: UM-OS-007


title: dobbi-00100: NCI_U133A_NC 153T

value: Large Cell Lymphoma


title: cho-00156: UM-OS-002


title: cho-00156: UM-OS_E-001

value: serous/endometrioid


title: dobbi-00100: NCI_U133A_NC 161T

value: Metastatic Renal Cell Carcinoma

value: Kidney


title: dobbi-00100: NCI_U133A_NC 172T

value: Squamous Cell Carcinoma

value: Lung


title: dobbi-00100: NCI_U133A_NC 164T

value: Stomach Adenocarcinoma

value: Stomach


title: cho-00156: UM-OS_C-002

value: serous/clear cell


title: cho-00156: UM-OS-011

value: F


title: carpt-00469: RA49NS

value: Prostate Cancer

value: Spleen

tag: pathological stage

value: non-metastatic tumor

value: male

value: normal spleen

value: Female


title: dobbi-00100: NCI_U133A_NC 144T

value: Non neoplastic liver with cirrosis

value: Liver

value: Non neeoplastic liver with cirrosis


title: dobbi-00100: NCI_U133A_NC 143T

value: Recurrent Renal Cell Carcinoma

value: Renal Cell Carcinoma


title: cho-00156: UM-OS_C-001

value: Ovary cancer

value: Ovary


title: cho-00156: UM-OM-003

value: mucinous


title: cho-00156: UM-OE-001

value: endometrioid


title: cho-00156: CU-OS-005

value: serous

value: U


title: dobbi-00100: NCI_U133A_NC 134T

value: Ovarian Adenocarcinoma


title: dobbi-00100: NCI_U133A_NC 127T

value: Metastatic Renal Cell Carcinoma

value: Kidney

value: Metastatic Renal Cell Carcinoma, clear cell type


title: dobbi-00100: NCI_U133A_NC 141T

value: Squamous Cell Carcinoma

value: Lung

value: Squamoous Cell Carcinoma


title: dobbi-00100: NCI_U133A_NC 140T

value: Leiomyoma

value: Uterus


title: cho-00156: CHTN-OS-146

value: F


title: cho-00156: CHTN-OS-141


title: cho-00156: JH-OE-002


title: cho-00156: CHTN-OS-147


title: dobbi-00100: NCI_U133A_NC 123T

value: Malignant G1 Stromal Tumor

value: Stomach


title: dobbi-00100: NCI_U133A_NC 126

value: Stage IB

value: female

value: Lung Adenocarcinoma


title: BBr2-ICM-DMSO-b vs. BBr2-Blastpool

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA    * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan)    * Priming: 5xSSC, 0.1%SDS    * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul    * Hybridization: 45 min at 42C.    * Wash 2x: milliQ    * Wash: 5xSSC, 0.1%SDS    * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul)    * Hybridization: 16 hours at 42C.    * Wash 2x: 1xSSC, 0.2%SDS at 23C    * Wash 2x: 0.1xSSC, 0.2%SDS at 23C    * Wash 2x: 0.1xSSC at 23C    * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009

label_protocol: Double-amplification&labeling (robotic): All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).mRNA amplification protocol description:* 5 ul per RNA is put in a 96-wells plate (4-Titude). All subsequent steps are performed by the robot script.Round1:* mix1 containing 10 ng T7 Mlu VN primer (custom mix) per 5 ul is added and mixed in each well.* plate is incubated @ 70C for 10 mins, cooled to 48C.* mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.* plate is incubated @ 48C for 2 hours and cooled to room temperature.* 106 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH (Promega) is added and mixed in each well.* plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul .* 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems)* Plate is incubated @37C for 4 hours.* cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.Round2:* mix1 containing 100 ng random hexamer primers per 5 ul is added and mixed in each well.* plate is incubated @ 70C for 10 mins, cooled to 48C.* mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.* plate is incubated @ 48C for 2 hours and cooled to room temperature.* 106 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 100ng T7 Mlu VN primer (custom mix), 4 ul E.coli DNA polymerase I and 1 ul RNAseH (Promega) is added and mixed in each well.* plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul .* 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems).* Plate is incubated @37C for 4 hours.* cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.* Concentration of cRNA is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.* Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.Labeling protocol description:* NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).All subsequent steps are performed by the robot script :* 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ).* 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.* 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.* 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.* Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.* RNA concentration and labeling incorporation are measured (SpectraMax 190).* 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.* Samples are stored at -20C until hybridization.

growth_protocol: Bovine in vitro embryo culture: Bovine embryo culture was performed at 39°C in a humidified atmosphere with 5% CO2, unless stated otherwise. Three to eight mm follicles of ovaries, obtained from a local slaughterhouse, were aspirated to retrieve cumulus oocyte complexes (COCs). Groups of 35-60 COCs were incubated for 23 hrs in 500 ml M199 (Life Technologies, Bleiswijk, The Netherlands) supplemented with 0.05 IU/ml recombinant hFSH (Organon, Oss, The Netherlands) and with 1% (v/v) penicillin-streptomycin (Life Technologies). Fertilization was performed as described previously [68] with modifications as described [69]. In short, matured COCs were transferred to fertilization medium (Fert-TALP) supplemented with heparin at a final concentration of 10 mg/ml (Sigma-Aldrich, Zwijndrecht, The Netherlands), 20mM D-penicillamine (Sigma-Aldrich), 10 ?M hypotaurine (Sigma-Aldrich), and 1 uM epinephrine (Sigma-Aldrich). Frozen-thawed sperm from a bull with proven fertility was centrifuged over a Percoll-gradient (GE Healthcare Europe GmbH, Eindhoven, The Netherlands) and added to the COCs at a final concentration of 1.0 E6 spermatozoa/ml. Fertilization day was considered as day 0. After incubation for 20 hrs the COCs were denuded by vortexing for 3 min and the cumulus-free oocytes were placed in synthetic oviduct fluid (SOF) medium. The presumptive zygotes were incubated at 39°C in a humidified atmosphere with 7% O2 and 5% CO2. At day 5 either morulae were collected or embryos were transferred to fresh SOF medium, cultured to blastocyst stage embryos and collected on day 9.

extract_protocol: 1. Add 1 ml Trizol per 5x 106 cells in suspension (1 ml trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube.     2. Incubate 5 min at room temperature.     3. Add chloroform (200 Âµl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature.     4. Centrifuge 20 min at 14000 rpm 4Â°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube.     5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min.     6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 Âµg/column)     7. Adjust each sample to a volume of 300 Âµl with sterile MilliQ water. Add 160 Âµl buffer RLT to the samples, and mix (= lysis buffer).     8. Add 240 Âµl ethanol (100% stored at -20 Â°C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on.     9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at roomtemperature! DNAse treatment: D1. Pipet 350 Âµl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 Âµl/reaction): add 10 Âµl DNase I stock solution to 70 Âµl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 Âµl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30Â°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 Âµl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube.     10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 Âµl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps.    11. Pipet 500 Âµl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.     12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).     13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 Âµl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 Âµl milliQ.     14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 Â°C.

treatment_protocol: bovine embryo-harvest and dissection: Blastocysts collected to obtain inner cell mass and trophectoderm were placed in wash buffer containing 6.67 mg/ml NaCl (Merck, Schiphol-Rijk, The Netherlands), 0.24 mg/ml KCl (Merck), 0.168 mg/ml NaHCO3 (Sigma-Aldrich), 0.047 mg/ml NaH2PO4 (Merck), 0.217%  (v/v) of a 60% sodium lactate solution (Sigma-Aldrich), 2.38 mg/ml HEPES (Sigma-Aldrich), 0.2% (v/v) phenolred (Sigma-Aldrich), 0.39 mg/ml CaCl2 · 2H2O (Sigma-Aldrich), 0.10 mg/ml MgCl2 · 6H2O (Merck), 0.11 mg/ml sodium pyruvate, 100U/ml Penicillin-Streptomycin (Life Technologies) and 6.0 mg/ml bovine serum albumin fraction 5 (MP Biomedicals, Santa Ana, CA, USA), set at an osmolality of 280 osmol/kg and adjusted to pH 7.3. Sharpened tungsten needles were used to manually separate the trophectoderm from the ICM. This procedure was performed in wash medium under a stereo microscope. Collected cells and embryos were harvested per tissue type or treatment and stored in 100 ml extraction buffer (Life Technologies) at -80°C until RNA isolation.

tag: cell type

value: icm-control

value: ref-blastocystpool


title: dobbi-00100: NCI_U133A_NC 129

value: male


title: BBr2-Blastpool vs. BBr2-ICM-PD-a

value: icm-ERK-inhibited


title: BBr2-Blastpool vs. BBr2-ICM-DMSO-a


title: BBr2-ICM-PD-b vs. BBr2-Blastpool


title: cho-00156: CHTN-OS-137

value: Ovary cancer

value: Ovary

value: serous


title: BBr1-M2 vs. BBr1-Blastpool

value: morula


title: dobbi-00100: NCI_U133A_NC 122T

value: Large Cell Lymphoma


title: BBr1-ICM2 vs. BBr1-Blastpool

value: inner cell mass


title: BBr1-Blastpool vs. BBr1-M1


title: BBr1-Blastpool vs. BBr1-TE1

value: trophectoderm


title: BBr1-Blastpool vs. BBr1-ICM1


title: dobbi-00100: NCI_U133A_NC 117

value: Lung


title: BBr1-TE2 vs. BBr1-Blastpool


title: BBr1-Blastpool vs. BBr1-B1

value: blastocyst


title: BBr1-B2 vs. BBr1-Blastpool


title: Tylosin rep3

city: Buffalo

first: Jiho

last: Sohn

state: New York

address: 3435 Main Street, 644 Biomedical Research Building

department: Oral Biology

institute: SUNY Buffalo

hyb_protocol: standard procedures recommended by Affymetrix was used

data_processing: The raw microarray data was normalized by the Robust Multi-Array (RMA) method using Affy package in Bioconductor

source_name: liver

growth_protocol: C57BL/6J mice received three antibiotic courses: at days 10-15, 28-31, and 37-40 of life, amoxicillin or tylosin.Livers were collected at age 22 weeks, RNA was extracted, and transcriptional differences were measured by microarray analysis.

extract_protocol: RNeasy Mini Kit (Qiagen, Valencia CA)

treatment_protocol: Tylosin tartrate and amoxicillin trihydrate (Sigma Aldrich, St. Louis MO) were dissolved in distilled deionized water at concentrations of 0.333 and 0.167 mg/mL, respectively, to provide mice with 50 mg of tylosin or 25 mg of amoxicillin per kg body mass/day, based on an estimated daily water consumption of 150 mL/kg body mass.

value: 24 week

tag: gender

value: Female

tag: strain

value: liver


title: Amoxicillin rep2

scan_protocol: standard procedures recommended by Affymetrix was used

tag: tissue


title: Tylosin rep2

label_protocol: standard procedures recommended by Affymetrix was used


title: dobbi-00100: NCI_U133A_NC 116T

value: Recurrent Renal Cell Carcinoma

value: Kidney

value: Recurrent Renal Cell Carcinoma, chromophobe cell type


title: Amoxicillin rep3


title: cho-00156: CHTN-OS-102

value: F