title: genomic DNA_leukocytes 6

description:
leukocytes DNA from health individual 6
leuko.6


title: genomic DNA_leukocytes 4

status: Public on Sep 26 2017

type: genomic

city: São Paulo

first: Ana

last: Krepischi

state: São Paulo

address: Rua do Matão, 277

country: Brazil

institute: University of São Paulo

description:
leukocytes DNA from health individual 4
leuko.4

hyb_protocol: Bisulphite converted DNA (EZ DNA methylation kit; Zymo Research) was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan according to standard recommended Illumina scanner setting

data_processing: Only experiments exhibiting call rate >0.98 of probes with detection p-value ≤0.01 were considered for data analysis. Microarray data were extracted using the GenomeStudio software (v.2011.1) with the methylation module (v.1.9.0) (Illumina). DNA methylation level of each CpG was obtained in β values (β= intensity of the methylated allele (M)/ intensity of the unmethylated allele (U) + intensity of the M + 100) ranging from 0 to 1, with 0 indicating unmethylated sites and 1, fully methylated sites. Background subtraction and normalization of data were performed using the Illumina default protocol with internal controls. CpG sites with detection p-value ≥0.01 as well as those mapped at X and Y chromosomes were excluded from further analysis.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from leukocytes using Gentra Puregene Blood Core Kit (Qiagen) or QIAmp DNA Blood Mini QIACUBE kit (Quiagen)

tag: gender

value: female

tag: cell type

value: leukocytes


title: DO mouse on HFCA Diet DO2.449

type: RNA

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: Cornell University

country: USA

institute: Cornell University

description: Gene expression in homogenized liver of DO mouse

hyb_protocol: Done according to Affymetrix MoGene 2.1 ST Array Protocol

data_processing: Probes containing known SNPs from the founder strains were masked. Affymetrix Expression Console was used for QC and identifying low quality samples, which were removed. Several samplers were run in duplicate on at least 2 plates. Control, reporter, and normalizing probes were removed.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Adult mouse liver

growth_protocol: 4-week old DO mice were put on AIN-76 diet for 2 weeks. Then one of each sibling pair was put on either HFCA or HP diet for 18 weeks.

extract_protocol: RNA was harvested using Norgen Total RNA Purification Kit (Cat# 24300).

treatment_protocol: Livers were removed, flash frozen in liquid nitrogen, and homogenized.

tag: sibling pair


title: genomic DNA_leukocytes 5

description:
leukocytes DNA from health individual 5
leuko.5


title: genomic DNA_leukocytes 8

description:
leukocytes DNA from health individual 8
leuko.8

value: male


title: DO mouse on HFCA Diet DO2.448

scan_protocol: Done according to Affymetrix MoGene 2.1 ST Array Protocol


title: genomic DNA_leukocytes 2

description:
leukocytes DNA from health individual 2
leuko.2


title: genomic DNA_leukocytes 7

description:
leukocytes DNA from health individual 7
leuko.7


title: DO mouse on HFCA Diet DO2.446

label_protocol: Done according to Affymetrix MoGene 2.1 ST Array Protocol


title: genomic DNA_leukocytes 3

description:
leukocytes DNA from health individual 3
leuko.3


title: genomic DNA_breast 2

description:
breast DNA from normal human tissue 2
breast2

source_name: breast tissue

tag: tissue

value: breast


title: genomic DNA_leukocytes 1

description:
leukocytes DNA from health individual 1
leuko.1


title: genomic DNA_breast 7

description:
breast DNA from normal human tissue 7
breast7


title: genomic DNA_breast 6

description:
breast DNA from normal human tissue 6
breast6


title: genomic DNA_breast 1

description:
breast DNA from normal human tissue 1
breast1


title: genomic DNA_breast 3

description:
breast DNA from normal human tissue 3
breast3


title: genomic DNA_breast 5

description:
breast DNA from normal human tissue 5
breast5


title: DO mouse on HFCA Diet DO2.447


title: DO mouse on HFCA Diet DO2.442


title: DO mouse on HFCA Diet DO2.444


title: DO mouse on HFCA Diet DO2.439


title: genomic DNA_liver 9

description:
liver DNA from normal human tissue 9
liver9

source_name: liver tissue

value: liver


title: genomic DNA_liver 10

description:
liver DNA from normal human tissue 10
liver10


title: DO mouse on HFCA Diet, Sample 441 replicate on plate 2 DO2.441


title: DO mouse on HFCA Diet DO2.436


title: DO mouse on HFCA Diet DO2.445


title: DO mouse on HFCA Diet, Sample 434 replicate on plate 2 DO2.434


title: DO mouse on HFCA Diet DO2.440


title: DO mouse on HFCA Diet DO2.435


title: genomic DNA_breast 4

description:
breast DNA from normal human tissue 4
breast4


title: DO mouse on HFCA Diet DO2.430


title: DO mouse on HFCA Diet DO2.429


title: DO mouse on HFCA Diet DO2.424


title: DO mouse on HFCA Diet DO2.431


title: DO mouse on HFCA Diet DO2.423


title: DO mouse on HFCA Diet DO2.438


title: DO mouse on HFCA Diet DO2.443


title: DO mouse on HFCA Diet DO2.425


title: DO mouse on HFCA Diet DO2.433


title: DO mouse on HFCA Diet DO2.432


title: DO mouse on HFCA Diet DO2.428


title: DO mouse on HFCA Diet DO2.437


title: E12.5 Heart

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Mouse hearts

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

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Heart

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

growth_protocol: 24 h after transduction, the medium was replaced with StemPro-34 SF medium (Gibco 10639-011)/GlutaMAX, 35050-061)/ascorbic acid (Sigma Aldrich, A-4544)/recombinant human VEGF165 (5 ng/mL, R&D Systems, 293-VE-050)/recombinant human FGF basic146 aa (10 ng/mL, R&D Systems, 233-FB-025)/recombinant human FGF10 (50 ng/mL, R&D Systems, 345-FG-025). The medium was changed every 2-3 days.

extract_protocol: RNA samples were extracted from cells using ReliaPrep RNA Cell Miniprep System (Promega, Z6012).

treatment_protocol: pMX-GMT, pMX-GHMT retroviruses were used for transduction with Polybrene (Miilopore).

tag: treatment

value: Heart tissue witout any treatment


title: genomic DNA_temporal cortex 7

description:
temporal cortex DNA from normal human tissue 7
TC7

source_name: brain tissue

value: temporal cortex brain


title: 2W-GHMT-iCMs

description: a-MHC-GFP+ cells induced by GHMT transduction were sorted at 2W

source_name: MEF

value: GHMT transduced-MEFs at 2W


title: genomic DNA_liver 5

description:
liver DNA from normal human tissue 5
liver5


title: 4W-GHMT-iCMs

description: a-MHC-GFP+ cells induced by GHMT transduction were sorted at 4W

value: GHMT transduced-MEFs at 4W


title: DO mouse on HFCA Diet DO2.426

description: Gene expression in homogenized liver of DO mouse


title: genomic DNA_temporal cortex 8

description:
temporal cortex DNA from normal human tissue 8
TC8


title: 4W-GMT-iCMs

description: a-MHC-GFP+ cells induced by GMT transduction were sorted at 4W

value: GMT transduced-MEFs at 4W


title: DO mouse on HFCA Diet DO2.420


title: DO mouse on HFCA Diet DO2.422


title: DO mouse on HFCA Diet DO2.421


title: genomic DNA_temporal cortex 4

description:
temporal cortex DNA from normal human tissue 4
TC4


title: genomic DNA_temporal cortex 5

description:
temporal cortex DNA from normal human tissue 5
TC5


title: DO mouse on HFCA Diet DO2.419


title: 2W-GMT-iCMs

description: a-MHC-GFP+ cells induced by GMT transduction were sorted at 2W

value: GMT transduced-MEFs at 2W


title: DO mouse on HFCA Diet DO2.417


title: genomic DNA_liver 8

description:
liver DNA from normal human tissue 8
liver8


title: D7 MEF

description: Mouse fibroblasts

value: MEFs without any treatment


title: genomic DNA_liver 6

description:
liver DNA from normal human tissue 6
liver6


title: genomic DNA_liver 7

description:
liver DNA from normal human tissue 7
liver7


title: genomic DNA_temporal cortex 6

description:
temporal cortex DNA from normal human tissue 6
TC6


title: DO mouse on HFCA Diet DO2.414


title: DO mouse on HFCA Diet DO2.415


title: DO mouse on HFCA Diet DO2.416


title: genomic DNA_liver 2

description:
liver DNA from normal human tissue 2
liver2


title: genomic DNA_temporal cortex 9

description:
temporal cortex DNA from normal human tissue 9
TC9


title: genomic DNA_temporal cortex 1

description:
temporal cortex DNA from normal human tissue 1
TC1


title: Placenta HLA-DRhi 4

city: St. Louis

first: Marco

last: Colonna

state: Missouri

address: 509 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

description: immune subset

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Human 1.0 ST Array in the GeneChip Hypridization Oven 640 for 18hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Sation 450

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

data_processing: Data were processed using the AffySTExpressionFileCreator function of GenePattern from the Broad Institute using quantile normalization and background correction. Data were analzyed using Multiplot Studio from the Broad Institute.

source_name: placenta

label_protocol: Biotyinylated cDNA were prepared according to the standard NuGEN WT-Ovation PicoSL RNA Amplification system from 2 ng of total RNA.

extract_protocol: Qiagen RNAeasy Plus Micro kit was used to extract RNA from freshly sorted human myeloid cell subsets.

value: placenta

value: immune

tag: cell subtype

value: HLA-DRhi


title: genomic DNA_liver 4

description:
liver DNA from normal human tissue 4
liver4


title: Blood NK 3

source_name: blood

value: blood

value: NK


title: Placenta HLA-DRlo 2

description: immune subset

value: HLA-DRlo


title: genomic DNA_liver 3

description:
liver DNA from normal human tissue 3
liver3


title: genomic DNA_liver 1

description:
liver DNA from normal human tissue 1
liver1


title: genomic DNA_temporal cortex 2

description:
temporal cortex DNA from normal human tissue 2
TC2


title: DO mouse on HFCA Diet DO2.407

description: Gene expression in homogenized liver of DO mouse


title: DO mouse on HFCA Diet DO2.412


title: genomic DNA_temporal cortex 3

description:
temporal cortex DNA from normal human tissue 3
TC3

value: female


title: Placenta HLA-DRlo 3

description: immune subset


title: DO mouse on HFCA Diet DO2.406


title: Blood NK 2


title: DO mouse on HFCA Diet DO2.411


title: DO mouse on HFCA Diet DO2.409


title: DO mouse on HFCA Diet DO2.413


title: DO mouse on HFCA Diet DO2.410


title: DO mouse on HFCA Diet DO2.404


title: Placenta HLA-DRhi 3

description: immune subset


title: DO mouse on HFCA Diet DO2.401


title: Placenta HLA-DRhi 1

description: immune subset


title: DO mouse on HFCA Diet DO2.408


title: Placenta HLA-DRlo 1

description: immune subset


title: DO mouse on HFCA Diet, Sample 403 replicate on plate 3 DO2.403


title: DO mouse on HFCA Diet DO2.405


title: c-kit Positivie Globose Cells_3

city: Miami

first: Lina

middle: A

last: Shehadeh

state: FL

department: Medicine

institute: University of Miami

hyb_protocol: Affymetrix FlashTag Biotin HSR RNA Labeling Kit (P/N 901910)

scan_protocol: Command ConsoleTM User Guide (P/N 702569); GeneChip Scanner 3000 7G system; GeneChip Command Console Software (AGCC)

data_processing: Expression ratios were calculated in Genespring 13.0 as the power-2 exponential of the log2 differences. The acceptance criteria for gene array expression changes was a minimum 2 fold change in log2 (equivalent to 4 fold) and a one-way Analysis of Variance (ANOVA) t-test with Benjamini-Hochberg multiple testing correction p-value of <0.05.

label: FlashTag™ Biotin HSR RNA Labeling Reagent

source_name: Mouse Lesioned Nose

extract_protocol: Total RNA from sorted c-Kit (+) and (-) fractions was extracted using Quick-RNA MicroPrep kit (Zymo Research, Irvine, CA) to yield a 260–280 nm absorbance ratio of 2.0. RNA concentration and integrity was confirmed using an Agilent Bioanalyzer. Briefly, 500ng total RNA was prepared using the Affymetrix FlashTag Biotin HSR RNA Labeling Kit (Part# 901910) according to manufacturer’s protocol (3 samples per group; 2 groups per experiment). Fragmented and labeled products were hybridized to the Affymetrix GeneChip miRNA 4.0 Array. Washing and staining of arrays took place on the GeneChip Fluidics Station 450 and scanning was done on the GeneChip Scanner 3000 7G system.

treatment_protocol: 10 days following methimazole lesion, adult mice were deeply anesthetized, decapitated, and nasal tissue was harvested, enzymatically dissociated into a single cell suspension, and washed. Immunomagnetic selection was performed using the EasySep Mouse APC Positive Selection kit (Stemcell Technologies, Vancouver, BC) to label cells with APC-conjugated antibody against c-Kit (eBiosciences 17-1171; RRID:AB_469430).

value: olfactory epithelium

tag: cell population

value: c-Kit (+)


title: DO mouse on HFCA Diet DO2.402


title: c-kit Positivie Globose Cells_2

label_protocol: Affymetrix FlashTag Biotin HSR RNA Labeling Kit (P/N 901910)


title: c-kit Positivie Globose Cells_1


title: 68-7 ATRA (gene-level)

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

description:
Sample name: 247-349
Gene-level analysis in Transcriptome Analysis Console

hyb_protocol: 5.15 ug fragmented and end-labeled sample was hybridized for 16 hr at 45 C and 60 rpm to Rat Transcriptome Array (RTA) 1.0 microarrays (Affymetrix) and scanned at the Brown University Genomics Core.

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

data_processing:
Raw data were processed in Affymetrix Gene Chip Command Console software to produce .cel files and Affymtrix Expresion Console for gene-level .chp files using the SST-RMA process.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0

organism: Rattus norvegicus

source_name: fetal testis, ATRA

label_protocol: Labeling was performed using GeneChip WT Terminal Labeling reagents (Agilent). 100 ng input RNA was converted to cDNA and amplified by in vitro transcription (IVT) over night.  15 ug purified IVT cRNA was reverse transcribed and labeled with dUTP. 5.5 ug purified cDNA was fragmented and 5.15 ug cDNA were end-labeled with biotin. All steps were done according to the manufacturer's protocol.

growth_protocol: Gestational day (GD) 15 fetal rat testes were cultured in supplemented DMEM/F-12 media on Millicell CM cell culture inserts for 24 h.

extract_protocol: Total RNA was isolated from fetal testes after 24 h of culture, using the Qiagen AllPrep DNA/RNA Micro Kit, per manufacturer's instructions, including the on-column DNase digestion.

treatment_protocol: Samples were treated by addition of 10^-6 M ATRA in 1:4000 DMSO vehicle or vehicle only to the culture media. Treatment design was paired so that each fetus (individual) had one testis cultured in treatment media and one in vehicle.

value: fetal testis

tag: strain

value: SAS SD (Charles River #400)

value: 10^-6 M all-trans retinoic acid

tag: individual (pairing)


title: 40-8 vehicle (gene-level)

description:
Sample name: 249-218
Gene-level analysis in Transcriptome Analysis Console

source_name: fetal testis, vehicle

value: vehicle (DMSO)


title: Blood NK 1


title: c-kit Negative Olfactory Epithelium_3

value: c-Kit (-)


title: 36-8 vehicle (gene-level)

description:
Sample name: 247-214
Gene-level analysis in Transcriptome Analysis Console


title: 48-10 ATRA (gene-level)

description:
Sample name: 251-264
Gene-level analysis in Transcriptome Analysis Console


title: 35-8 ATRA (gene-level)

description:
Sample name: 247-225
Gene-level analysis in Transcriptome Analysis Console


title: c-kit Negative Olfactory Epithelium_2


title: Blood NK 4


title: 36-8 ATRA (gene-level)

description:
Sample name: 255-226
Gene-level analysis in Transcriptome Analysis Console


title: 43-12 vehicle (gene-level)

description:
Sample name: 259-242
Gene-level analysis in Transcriptome Analysis Console


title: Placenta HLA-DRhi 2

description: immune subset


title: 48-10 vehicle (gene-level)

description:
Sample name: 253-258
Gene-level analysis in Transcriptome Analysis Console


title: 40-8 ATRA (gene-level)

description:
Sample name: 253-228
Gene-level analysis in Transcriptome Analysis Console


title: 68-7 vehicle (gene-level)

description:
Sample name: 257-343
Gene-level analysis in Transcriptome Analysis Console


title: 43-12 ATRA (gene-level)

description:
Sample name: 251-263
Gene-level analysis in Transcriptome Analysis Console


title: IL17RC_EPG02P1_WT mouse_colon_AOM-DSS_D15_r2

status: Public on Sep 25 2017

city: Cleveland

first: Junjie

last: Zhao

state: Ohio

address: 9500 Euclid Avenue, NE4256

department: Immunology

institute: Cleveland Clinic Lerner Research Institute

hyb_protocol: GeneTitan

scan_protocol: GeneTitan

data_processing: GeneTitan

label: Biotin

source_name: WT mouse_colon_AOM-DSS_D15

label_protocol: GeneChip HT 39 IVT Express Kit

growth_protocol: 6-8 weeks old WT and IL-17RC KO mice

extract_protocol: Mice were sacrificed and colons were taken. Colon tissues were minced and homogenized and then lysed in TRIZol.

treatment_protocol: Mice were either left untreated or injected with 12g/KG of AOM followed by three cycles of 5-day oral 3% DSS water and 14 day regular water

tag: genotype

value: AOM+DSS

tag: time

value: 15 days

tag: disease state

value: Developing

value: colon


title: IL17RC_EPH01P1_WT mouse_colon_AOM-DSS_D15_r1


title: IL17RC_EPF01P1_KO mouse_colon_AOM-DSS_D7_r3

source_name: KO mouse_colon_AOM-DSS_D7

value: 7 days


title: c-kit Negative Olfactory Epithelium_1


title: IL17RC_EPF03P1_KO mouse_colon_AOM-DSS_D7_r1


title: IL17RC_EPF04P1_WT mouse_colon_AOM-DSS_D7_r3

source_name: WT mouse_colon_AOM-DSS_D7


title: IL17RC_EPE04P1_KO mouse_colon_AOM-DSS_D15_r4

source_name: KO mouse_colon_AOM-DSS_D15


title: 35-8 vehicle (gene-level)

description:
Sample name: 261-211
Gene-level analysis in Transcriptome Analysis Console


title: IL17RC_EPE02P1_WT mouse_colon_AOM-DSS_D7_r1


title: IL17RC_EPF02P1_WT mouse_colon_AOM-DSS_D7_r4


title: IL17RC_EPB02P1_KO mouse_colon_AOM-DSS_D15_r2


title: IL17RC_EPD04P1_WT mouse_colon_AOM-DSS_D15_r3


title: IL17RC_EPC01P1_KO mouse_colon_AOM-DSS_D15_r3


title: IL17RC_EPE01P1_KO mouse_colon_AOM-DSS_D7_r4


title: IL17RC_EPD05P1_KO mouse_colon_AOM-DSS_D7_r2


title: IL17RC_EPA03P1_KO mouse_colon_AOM-DSS_D15_r1


title: IL17RC_EPC02P1_WT mouse_colon_AOM-DSS_D15_r4


title: IL17RC_EPG04P1_KO mouse_colon_tumor_r4

description: Tumor

source_name: KO mouse_colon_tumor

value: 63 days

value: Terminal


title: IL17RC_EPH02P1_KO mouse_colon_tumor_r5

description: Tumor


title: IL17RC_EPA01P1_WT mouse_colon_AOM-DSS_D7_r2


title: IL17RC_EPG03P1_KO mouse_colon_tumor_r2

description: Tumor


title: IL17RC_EPH03P1_WT mouse_colon_tumor_r2

description: Tumor

source_name: WT mouse_colon_tumor


title: IL17RC_EPE03P1_KO mouse_colon_tumor_r6

description: Tumor


title: IL17RC_EPD02P1_KO mouse_colon_tumor_r3

description: Tumor


title: IL17RC_EPD01P1_WT mouse_colon_tumor_r3

description: Tumor


title: IL17RC_EPC03P1_WT mouse_colon_tumor_r6

description: Tumor


title: IL17RC_EPB03P1_WT mouse_colon_tumor_r4

description: Tumor


title: IL17RC_EPB01P1_KO mouse_colon_tumor_r1

description: Tumor


title: IL17RC_EPC05P1_KO mouse_colon_untreated_r2

description: Untreated

source_name: KO mouse_colon_untreated

value: 0 day

value: Healthy


title: IL17RC_EPB05P1_WT mouse_colon_untreated_r1

description: Untreated

source_name: WT mouse_colon_untreated


title: IL17RC_EPC04P1_WT mouse_colon_tumor_r5

description: Tumor


title: IL17RC_EPD03P1_KO mouse_colon_untreated_r3

description: Untreated


title: IL17RC_EPA05P1_WT mouse_colon_untreated_r4

description: Untreated


title: IL17RC_EPA04P1_WT mouse_colon_untreated_r2

description: Untreated


title: IL17RC_EPA02P1_KO mouse_colon_untreated_r1

description: Untreated


title: IL17RC_EPG01P1_KO mouse_colon_untreated_r4

description: Untreated


title: IL17RC_EPH04P1_WT mouse_colon_tumor_r1

description: Tumor


title: IL17RC_EPB04P1_WT mouse_colon_untreated_r3

description: Untreated


title: ExVivoBlood-control [150932E_N5]

status: Public on Sep 23 2017

city: Beijing

first: Tong

last: Liu

address: Anzhen road 2#, Chaoyang district

department: Department of Cardiology

country: China

institute: Bejing Anzhen Hospital,Capital Medical University

description: MicroRNA expression of control group

hyb_protocol: Purified labeled RNAs were hybridized onto a microarray chip (Release 19.0, Agilent) containing 2006 human miRNA probes. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

scan_protocol: The arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: The scanned images were analyzed by Agilent Feature Extraction Software (Agilent Technologies)

source_name: Peripheral Blood-control

label_protocol: Total RNA was dephosphorylated, denatured and then labeled with Cyanine-3-CTP.

extract_protocol: The quantity and quality of RNA were determined using NanoDrop ND-2000 (Thermo Scientific). The integrity of RNA was assessed by Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: diagnosis

value: healthy control

value: plasma

value: male

tag: age (years)


title: 36-8 vehicle (exon-level)

description:
Sample name: 247-214
Alt-Splice analysis in Transcriptome Analysis Console

data_processing:
Raw data were processed in Affymetrix Gene Chip Command Console software to produce .cel files and Affymtrix Expresion Console for .chp files for alt-splice analysis.
affymetrix-algorithm-name = sst-rma-alt-splice : sst-dabg
affymetrix-algorithm-version = 1.0

value: fetal testis


title: #48-SU223-B3 iPSC

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University

hyb_protocol: Bisulphite converted DNA was amplified, fragemtned and hybridized to Infinium Methylation 450 arrays using standard Illumina protocol

scan_protocol: Arrays were scanned using recommened Illumina settings

data_processing: Beta values were calculated with Minfi v 1.12.0 (Aryee et al 2014)

label: Cy3 and Cy5

label_protocol: Standard Ilumina protocol

extract_protocol: Genomic DNA was isolated from the indicated populations using standard protocols (Qiagen Inc)

tag: sample  group

value: Undiff iPS from AML

tag: subject


title: #47-SU223-A4 iPSC


title: ExVivoBlood-control [150932E_N7]

description: MicroRNA expression of control group

value: female


title: ExVivoBlood-control [150932E_N6]

description: MicroRNA expression of control group


title: ExVivoBlood-control [150932E_N4]

description: MicroRNA expression of control group


title: #46-SU042-3 iPSC


title: 43-12 vehicle (exon-level)

description:
Sample name: 259-242
Alt-Splice analysis in Transcriptome Analysis Console

value: SAS SD (Charles River #400)

value: vehicle (DMSO)


title: 35-8 vehicle (exon-level)

description:
Sample name: 261-211
Alt-Splice analysis in Transcriptome Analysis Console


title: #45-SU042-2 iPSC


title: ExVivoBlood-control [150932E_N3]

description: MicroRNA expression of control group


title: 68-7 vehicle (exon-level)

description:
Sample name: 257-343
Alt-Splice analysis in Transcriptome Analysis Console


title: ExVivoBlood-control [150932E_N2]

description: MicroRNA expression of control group


title: ExVivoBlood-case [150932A_C7]

description: MicroRNA expression of  case group

source_name: Peripheral Blood-case

value: heart failure


title: 43-12 ATRA (exon-level)

description:
Sample name: 251-263
Alt-Splice analysis in Transcriptome Analysis Console

value: 10^-6 M all-trans retinoic acid


title: #41-TKDA3-4 iPSC diff-1

source_name: TKDA3 cell line

value: Diff normal iPS

value: TKDA3 cell line


title: #44-WT3 iPSC diff-2

source_name: WT3 cell line

value: WT3 cell line


title: #38-H7 ES diff-2

source_name: H7 cell  line

value: Diff normal ES

value: H7 cell  line


title: #40-JMC1 iPSC diff-2

source_name: JMC1 cell line

value: JMC1 cell line


title: #37-H7 ES diff-1


title: ExVivoBlood-case [150932A_C3]

description: MicroRNA expression of  case group


title: #43-WT3 iPSC diff-1


title: 40-8 ATRA (exon-level)

description:
Sample name: 253-228
Alt-Splice analysis in Transcriptome Analysis Console


title: #39-JMC1 iPSC diff-1


title: #42-TKDA3-4 iPSC diff-2


title: 35-8 ATRA (exon-level)

description:
Sample name: 247-225
Alt-Splice analysis in Transcriptome Analysis Console


title: 68-7 ATRA (exon-level)

description:
Sample name: 247-349
Alt-Splice analysis in Transcriptome Analysis Console


title: 48-10 vehicle (exon-level)

description:
Sample name: 253-258
Alt-Splice analysis in Transcriptome Analysis Console


title: ExVivoBlood-case [150932A_C8]

description: MicroRNA expression of  case group


title: ExVivoBlood-case [150932A_C9]

description: MicroRNA expression of  case group


title: ExVivoBlood-case [150932A_C6]

description: MicroRNA expression of  case group


title: ExVivoBlood-case [150932A_C4]

description: MicroRNA expression of  case group


title: 48-10 ATRA (exon-level)

description:
Sample name: 251-264
Alt-Splice analysis in Transcriptome Analysis Console


title: ExVivoBlood-case [150932A_C5]

description: MicroRNA expression of  case group


title: 40-8 vehicle (exon-level)

description:
Sample name: 249-218
Alt-Splice analysis in Transcriptome Analysis Console


title: ExVivoBlood-case [150932A_C1]

description: MicroRNA expression of  case group


title: 36-8 ATRA (exon-level)

description:
Sample name: 255-226
Alt-Splice analysis in Transcriptome Analysis Console


title: NGB-007

city: Heidelberg

first: Justo

last: Lorenzo Bermejo

address: Im Neuenheimer Feld, 130.3

department: Statistical Genetics

country: Germany

institute: Institute of Medical Biometry and Informatics, University of Heidelberg

description:
miRNA
Agilent-046064 Unrestricted_Human_miRNA_V19.0_Microarray

hyb_protocol: 200ng labeled miRNA sample were hybridized for at least 20 hr at 55°C on Agilent human miRNA Microarray Release 19.0, 8x60k.

scan_protocol: Gene Expression Microarrays were scanned using the Agilent Scanner G2505C.  The scanned images were analyzed with Feature Extraction Software (Agilent technologies) using default settings.

data_processing: The miRNA data analysis was performed using R package limma available at the Bioconductor (www.bioconductor.org). The algorithms were implemented in the R programming language (www.r-project.org). Expression levels of the 8 non-neoplastic gallbladder tissues and 40 GBC tumour samples were normalized together using quantile normalization and were subsequently log2 transformed.

source_name: FFPE tissue block, normal gallbladder

label_protocol: Fluorescently-labeled miRNA were prepared according to Agilent protocol miRNA Complete Labeling and Hyb Kit. For miRNA profiling of normal gallbladder tissues and human GBC tumour samples, Agilent SurePrint Human miRNA Microarray (G4872A, miRBase Release 19.0, Agilent Technologies, Santa Clara, CA) representing 2006 human miRNAs were used. Quality control as well as labeling and hybridization were performed in the Core Facility of the DKFZ Heidelberg.

extract_protocol: MiRNA samples for microarray hybridization were purified from microdissected FFPE material using the miRNeasy FFPE Kit (Qiagen, Hilden, Germany), according to the manufacturer's instructions.

treatment_protocol: All tissue samples were formalin-fixed and paraffin-embedded (FFPE) tissue blocks.

tag: survival

value: normal

value: gallbladder


title: NGB-008


title: NGB-005


title: NGB-003


title: GBC-038

source_name: FFPE tissue block, gallbladder carcinoma

value: short survival

value: gallbladder carcinoma


title: NGB-002


title: GBC-039


title: GBC-040


title: GBC-036


title: NGB-001


title: GBC-037


title: NGB-004


title: ExVivoBlood-control [150932E_N1]

description: MicroRNA expression of control group

value: healthy control

value: plasma

tag: gender

value: male


title: ExVivoBlood-case [150932A_C2]

description: MicroRNA expression of  case group

value: female


title: NGB-006


title: GBC-035


title: GBC-029


title: GBC-027


title: GBC-032


title: GBC-033


title: GBC-030


title: GBC-034


title: GBC-026


title: GBC-025


title: GBC-028


title: GBC-031


title: GBC-024


title: GBC-021


title: GBC-022


title: GBC-020

value: long survival


title: GBC-019


title: GBC-023


title: GBC-018


title: GBC-012


title: GBC-009


title: GBC-011


title: GBC-017


title: GBC-008


title: GBC-010


title: GBC-006


title: GBC-014


title: GBC-016


title: GBC-005


title: GBC-013


title: GBC-015


title: GBC-002


title: GBC-003


title: GBC-007


title: GBC-001


title: GBC-004


title: DMPC_80 µg/cm²_48h_repl biol1

city: Bagnols sur Cèze

first: Odette

last: Prat

address: Site de Marcoule

department: Life Science

country: France

institute: CEA

description:
DMPC_80µg/cm²_48h
Gene expression after 48h exposure to NPs

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 5 µL of 10x GE Blocking agent and 1 µL of 25 x Fragmentation buffer according to the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of  2X GE Hybridization Buffer Hi-RPM was added to the fragmentation mixture and 40 µL of this mix was hybridized to Human V3 Sure Print oligo microarrays 8x60K (Agilent) for 17 hours at 65°C in a rotating hybridization oven (Agilent).  After hybridization, microarrays were sequentially washed with GE Wash Buffers (Agilent) following the manufacturers instructions, then dried at room temperature.

scan_protocol: Microarrays were scanned immediately after drying on the Agilent Scanner using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent technologies) using one-color treatment to obtain background subtracted and spatially detrended Processed Signal intensities.  Non-uniform outliers were excluded. Data were statistically analyzed with Genespring GX13 software (Agilent technologies).

source_name: HepaRG cells exposed to DMPC M-MSN_80 µg/cm²_48h

label_protocol: RNA samples were amplified and labeled with cyanine-3 fluorophore using the One-Color Low Input Quick Amp Labeling Kit (Agilent), according to the supplier’s protocol. The efficiency of fluorescent labelling was controlled by UV spectroscopy (Nanodrop 2000c).

growth_protocol: Cryopreserved differenciated HepaRG™ cells were obtained from Biopredic International (Rennes, France). Cells were thawed in William E medium (Biopredic International) supplemented with additives (Biopredic International) composed of essential elements for the culture such as fetal bovine serum and antibiotics, according to the supplier procedure. Cells were seeded into flat-bottom multi-well plate at 480,000 cells per well. The medium was renewed as recommended. Cells were incubated at 37°C and 5% CO2 for 7 days in order to constitute a monolayer with active CYP activities before exposure to nanoparticles.

extract_protocol: Total RNAs were extracted using the RNeasy Mini Kit (Qiagen). RNAs were quantified with the NanoDrop 2000c spectrophotometer and their qualities were assessed with the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: For microarray experiments, 480,000 HepaRG cells per well were seeded in 24-well plates. Three different cultures were exposed to three concentrations of pristine , PEG- and DMPC M-MSNs (1,6, 16, and 80 µg/cm²) and  medium (control cells) for 24h and 48h. Each experimental condition of exposure to M-MSNs was compared with control cells.

tag: microarray number

tag: block

value: Liver

tag: cell type

value: Differentiated hepatocyte and primitive biliary cells

tag: cell line

value: HepaRG cells


title: Pristine_80 µg/cm²_48h_repl biol2

description:
Pristine_80 µg/cm²_48h
Gene expression after 48h exposure to NPs

source_name: HepaRG cells exposed to Pristine M-MSN_80µg/cm²_48h

tag: tissue


title: Pristine_80 µg/cm²_48h_repl biol3


title: DMPC_80 µg/cm²_24h_repl biol1

description:
DMPC_80µg/cm²_24h
Gene expression after 24h exposure to NPs

source_name: HepaRG cells exposed to DMPC M-MSN_80 µg/cm²_24h


title: Pristine_80 µg/cm²_48h_repl biol1


title: DMPC_80 µg/cm²_24h_repl biol2


title: DMPC_80 µg/cm²_48h_repl biol3


title: Pristine_80 µg/cm²_24h_repl biol2

description:
Pristine_80 µg/cm²_24h
Gene expression after 24h exposure to NPs

source_name: HepaRG cells exposed to Pristine M-MSN_80µg/cm²_24h


title: DMPC_80 µg/cm²_48h_repl biol2


title: Pristine_80 µg/cm²_24h_repl biol1


title: DMPC_80 µg/cm²_24h_repl biol3


title: HepaRG_CTRL 48h_repl biol3_257236310469

description:
CTRL_48H
Gene expression after 48h

source_name: HepaRG cells, 48h, no treatment


title: PEG_80 µg/cm²_24h_repl biol2

description:
PEG_80 µg/cm²_24h
Gene expression after 24h exposure to NPs

source_name: HepaRG cells exposed to PEG M-MSN_80 µg/cm²_24h


title: HepaRG_CTRL 48h_repl biol2_257236310468

description:
CTRL_48H
Gene expression after 48h


title: Pristine_80 µg/cm²_24h_repl biol3


title: HepaRG_CTRL 24h_repl biol2_257236310468

description:
CTRL_24H
Gene expression after 24h

source_name: HepaRG cells, 24h, no treatment


title: PEG_80 µg/cm²_48h_repl biol1

description:
PEG_80 µg/cm²_48h
Gene expression after 48h exposure to NPs

source_name: HepaRG cells exposed to PEG M-MSN_80 µg/cm²_48h


title: PEG_80 µg/cm²_48h_repl biol2


title: HepaRG_CTRL 48h_repl biol4

description:
CTRL_48H
Gene expression after 48h


title: PEG_80 µg/cm²_24h_repl biol1


title: DMPC_1.6 µg/cm²_24h_repl biol4

description:
DMPC_1.6 µg/cm²_24h
Gene expression after 24h exposure to NPs

source_name: HepaRG cells exposed to DMPC M-MSN_1.6 µg/cm²_24h


title: PEG_80 µg/cm²_48h_repl biol3


title: HepaRG_CTRL 24h_repl biol1_257236310467

description:
CTRL_24H
Gene expression after 24h


title: HepaRG_CTRL 48h_repl biol1_257236310467

description:
CTRL_48H
Gene expression after 48h


title: DMPC_1.6 µg/cm²_48h_repl biol1

description:
DMPC_1.6 µg/cm²_48h
Gene expression after 48h exposure to NPs

source_name: HepaRG cells exposed to DMPC M-MSN_1.6 µg/cm²_48h


title: DMPC_1.6 µg/cm²_48h_repl biol2


title: DMPC_16 µg/cm²_48h_repl biol3

description:
DMPC_16 µg/cm²_48h
Gene expression after 48h exposure to NPs

source_name: HepaRG cells exposed to DMPC M-MSN_16 µg/cm²_48h


title: PEG_80 µg/cm²_24h_repl biol3


title: DMPC_1.6 µg/cm²_48h_repl biol3


title: HepaRG_CTRL 24h_repl biol3_257236310469

description:
CTRL_24H
Gene expression after 24h


title: PEG_16 µg/cm²_48h_repl biol2

description:
PEG_16 µg/cm²_48h
Gene expression after 48h exposure to NPs

source_name: HepaRG cells exposed to PEG M-MSN_16 µg/cm²_48h


title: DMPC_16 µg/cm²_48h_repl biol1


title: PEG_16 µg/cm²_48h_repl biol1


title: Pristine_1.6 µg/cm²_48h_repl biol3

description:
Pristine_1.6 µg/cm²_48h
Gene expression after 48h exposure to NPs

source_name: HepaRG cells exposed to Pristine  M-MSN_1.6 µg/cm²_48h


title: DMPC_16 µg/cm²_48h_repl biol2


title: Pristine_1.6 µg/cm²_48h_repl biol2


title: PEG_1.6 µg/cm²_48h_repl biol1

description:
PEG_1.6 µg/cm²_48h
Gene expression after 48h exposure to NPs

source_name: HepaRG cells exposed to PEG M-MSN_1.6 µg/cm²_48h


title: PEG_1.6 µg/cm²_48h_repl biol3


title: Pristine_1.6 µg/cm²_48h_repl biol1


title: Pristine_16 µg/cm²_48h_repl biol2

description:
Pristine_16 µg/cm²_48h
Gene expression after 48h exposure to NPs

source_name: HepaRG cells exposed to Pristine M-MSN_16 µg/cm²_48h


title: HepaRG_CTRL 48h_repl biol3_257236310432

description:
CTRL_48H
Gene expression after 48h


title: PEG_16 µg/cm²_48h_repl biol3


title: PEG_1.6 µg/cm²_48h_repl biol2


title: Pristine_16 µg/cm²_48h_repl biol3


title: CPZ_24H_repl biol3

description:
CPZ_24H
Gene expression after 24h exposure to Chlorpromazine

source_name: HepaRG cells exposed to Chlorpromazine 100 µM_24h


title: PEG_1.6 µg/cm²_24h_repl biol3

description:
PEG_1.6 µg/cm²_24h
Gene expression after 24h exposure to NPs

source_name: HepaRG cells exposed to PEG M-MSN_1.6 µg/cm²_24h


title: CPZ_24H_repl biol1


title: Pristine_16 µg/cm²_48h_repl biol1


title: HepaRG_CTRL 48h_repl biol1_257236310470

description:
CTRL_48H
Gene expression after 48h


title: HepaRG_CTRL 48h_repl biol2_257236310431

description:
CTRL_48H
Gene expression after 48h


title: DMPC_16 µg/cm²_24h_repl biol1

description:
DMPC_16 µg/cm²_24h
Gene expression after 24h exposure to NPs

source_name: HepaRG cells exposed to DMPC M-MSN_16 µg/cm²_24h


title: DMPC_1.6 µg/cm²_24h_repl biol3


title: DMPC_1.6 µg/cm²_24h_repl biol2


title: DMPC_16 µg/cm²_24h_repl biol3


title: PEG_16 µg/cm²_24h_repl biol3

description:
PEG_16 µg/cm²_24h
Gene expression after 24h exposure to NPs

source_name: HepaRG cells exposed to PEG M-MSN_16 µg/cm²_24h


title: PEG_1.6 µg/cm²_24h_repl biol2


title: CPZ_24H_repl biol2


title: DMPC_1.6 µg/cm²_24h_repl biol1


title: PEG_1.6 µg/cm²_24h_repl biol1


title: Pristine_1.6 µg/cm²_24h_repl biol3

description:
Pristine_1.6 µg/cm²_24h
Gene expression after 24h exposure to NPs

source_name: HepaRG cells exposed to Pristine  M-MSN_1.6 µg/cm²_24h


title: Pristine_16 µg/cm²_24h_repl biol2

description:
Pristine_16 µg/cm²_24h
Gene expression after 24h exposure to NPs

source_name: HepaRG cells exposed to Pristine  M-MSN_16 µg/cm²_24h


title: Pristine_1.6 µg/cm²_24h_repl biol1


title: Pristine_1.6 µg/cm²_24h_repl biol2


title: PEG_16 µg/cm²_24h_repl biol1


title: Pristine_16 µg/cm²_24h_repl biol1

source_name: HepaRG cells exposed to Pristine M-MSN_16 µg/cm²_24h


title: PEG_16 µg/cm²_24h_repl biol2


title: Pristine_16 µg/cm²_24h_repl biol3


title: HepaRG_CTRL 24h_repl biol1_257236310382

description:
CTRL_24H
Gene expression after 24h


title: gtr mutant (Cy5) vs wild-type (Cy3)_2

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

description: Candida albicans gtr1/gtr1 homozygous mutant in YEPD at 37˚C versus Candida albicans wild-type parent in YEPD at 37˚C

hyb_protocol: Hybridization and washing of the arrays was carried out using the Agilent Gene Expression Hybridization Kit and Gene Expression Wash Pack according the manufacturer’s instructions.

scan_protocol: Slides were scanned using the GenePix personal 4100A scanner (Axon) and data was extracted with GenePix Pro 6.1 (Axon).

data_processing: Spots were flagged absent if the signal was less than background +1 standard deviation in both fluorescent channels. Raw data was exported to GeneSpring GX10 and signals for each replicate spot were background corrected and normalized using Loess normalization. Log fluorescence ratios were generated for each replicate spot and averaged. Oligonucleotides were excluded from analysis if >50% of replicates in each condition were flagged absent.

molecule: polyA RNA

organism: Candida albicans

source_name: Candida albicans homozygous gtr1 null mutant grown to OD600nm 0.8 in YEPD at 37˚C

label_protocol: Total RNA was labelled with Cy5 or Cy3 using the Agilent Two-Color Low RNA input Linear Amplification Kit PLUS

growth_protocol: Strains were growm overnight in liquid YEPD at 37˚C with shaking. These were used to inoculate new cultures which were grown to OD600nm 0.8 in YEPD broth at 37˚C

extract_protocol: Total RNA was extracted using Tri-reagent (Sigma) using a microdismembrator (Braun, Melsungen,Germany).

treatment_protocol: Cell pellets were snap frozen in liquid N and disrupted using a Mikro-Dismembrator S (Sartorius Stedim Biotech, Göttingen, Germany) and RNA was purified using the RNeasy Mini-kit (Qiagen). Extracted RNA was treated with the TURBO DNase kit (Applied BioSystems, Life Technologies Corporation, California, USA).

source_name: Candida albicans wild-type grown to OD600nm 0.8 in YEPD at 37˚C

value: wildtype


title: HepaRG_CTRL 24h_repl biol2_257236310383

description:
CTRL_24H
Gene expression after 24h

source_name: HepaRG cells, 24h, no treatment


title: gtr mutant (Cy3) vs wild-type (Cy5)_3


title: HepaRG_CTRL 24h_repl biol3_257236310384

description:
CTRL_24H
Gene expression after 24h


title: gtr mutant (Cy5) vs wild-type (Cy3)_4


title: Pml wt_fasted 6h 3

status: Public on Sep 22 2017

city: Paris

first: Michiko

last: Kawakita

address: 1 av. Claude-Vellefaux

institute: INSERM

description: gene expression data from mouse liver sample using Affymetrix Mouse Gene 2.1 ST

hyb_protocol: Samples were hybridized onto  GeneChip Mouse Gene 1.1 ST Arrays (Affymetrix) using the GeneTitan platform at the Genomics platform, Translational Resarch Dept, Institut Curie , Paris, France. 3.3µg of targets were hybridized according Affymetrix recommendations.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with Expression Console from Affymetrix. A RMA normlisation was applied to control to data.

source_name: Pml wt liver, fasted 6h

label_protocol: 100ng of total RNA were amplified to generate cRNA; 10µg of cRNA were converted into single stranded DNA, based on the WT cDNA Synthesis Kit (Affymetrix).  5,5µg of cDNA were fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Pml wt and Pml KO mice with BALB/cByJ mice are maintained in a 12-hour light/dark cycle animal facility under SPF conditions, with free access to water and food.

extract_protocol: total RNA were extracted from using miRNeasy kit (Qiagen)

treatment_protocol: The food were removed.  Free access to water. Six hours later, mice are sacrificed by cervical dislocation. Liver samples are collected and stabilized in RNAlater solution and kept in -20.

value: liver

tag: age (months)

value: BALB/cByJ


title: Pml wt_ad libitum 2

source_name: Pml wt liver, ad libitum

tag: strain


title: Pml wt_fasted 6h 2


title: gtr mutant (Cy3) vs wild-type (Cy5)_1


title: Pml KO_fasted 6h 2

source_name: Pml KO liver, fasted 6h


title: Pml KO_fasted 6h 3


title: Pml wt_fasted 6h 1


title: Pml ko_ad libitum 2

source_name: Pml KO liver, ad libitum


title: Pml KO_fasted 6h 1


title: Pml wt_ad libitum 1


title: Pml ko_ad libitum 1


title: AML_NPM1wt_pat27

city: Ulm

first: Lars

last: Bullinger

address: Albert-Einstein-Allee 23

department: Internal Medicine III

institute: University of Ulm

description: Gene expression data from AML with normal karyotype

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with Partek® Genomics Suite® 6.6 using RMA, which includes normalization and log2 transformation of intensity values.

source_name: enriched leukemic blast cells

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

extract_protocol: The total RNA was purified with AllPrep DNA/RNA kits (QIAGEN).

value: AML

tag: genotype/variation

value: NPM1 wildtype

tag: relative hsa_circ_0075001 expression

value: low

value: enriched leukemic blast cells


title: AML_NPM1wt_pat25


title: AML_NPM1wt_pat11


title: AML_NPM1wt_pat26


title: AML_NPM1wt_pat18

value: high


title: AML_NPM1wt_pat21


title: AML_NPM1wt_pat20


title: AML_NPM1wt_pat15


title: AML_NPM1wt_pat17


title: AML_NPM1wt_pat12


title: AML_NPM1wt_pat22


title: AML_NPM1wt_pat19


title: AML_NPM1wt_pat9


title: AML_NPM1wt_pat23


title: AML_NPM1wt_pat13


title: AML_NPM1wt_pat7


title: AML_NPM1wt_pat6


title: AML_NPM1wt_pat5


title: AML_NPM1mut_pat25

value: NPM1 mutated


title: AML_NPM1wt_pat4


title: DMPC_16 µg/cm²_24h_repl biol2


title: AML_NPM1mut_pat18


title: AML_NPM1mut_pat20


title: AML_NPM1mut_pat29


title: AML_NPM1mut_pat21


title: AML_NPM1wt_pat3


title: AML_NPM1mut_pat27


title: AML_NPM1mut_pat22


title: AML_NPM1mut_pat30


title: AML_NPM1mut_pat26


title: AML_NPM1mut_pat17


title: AML_NPM1mut_pat14


title: AML_NPM1wt_pat1


title: AML_NPM1mut_pat13


title: AML_NPM1mut_pat6


title: AML_NPM1mut_pat7


title: AML_NPM1mut_pat2


title: AML_NPM1mut_pat5


title: AML_NPM1mut_pat3


title: human_control_rep5

city: Suzhou

first: Tongtong

last: Zhang

address: shizi street 188

institute: the First Affiliated Hospital of Soochow University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Affymetrix GeneChip Command Console (version4.0, Affymetrix), Gene Spring Software (version 13.1; Agilent Technologies).

source_name: MDS patients with -7/7q-

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted from bone marrow mononuclear cells of MDS patients with Trizol (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: The bone marrow mononuclear cells were isolated from the patients.

value: bone marrow

tag: karyotype


title: human_control_rep6


title: AML_NPM1mut_pat11

tag: disease state


title: AML_NPM1mut_pat4


title: AML_NPM1mut_pat12


title: AML_NPM1mut_pat10


title: human_control_rep4


title: human_control_rep1


title: human_experiment_rep4

source_name: MDS patients with der(1;7)(q10;p10)


title: Pml KO_apap6h_2

description: gene expression data from mouse liver sample using Affymetrix Mouse Gene 1.1 ST

source_name: Pml KO liver, 6h after apap ip

treatment_protocol: The mice were i.p. injected with Acetaminophen (Sigma) 300mg/kg solved in warmed PBS. They were sacrificed by cervical dislocation at indicated time.   Untreated mice were sacrificed as a control. Liver samples are collected and stabilized in RNAlater solution and kept in -20.   .


title: human_experiment_rep5


title: human_experiment_rep2


title: human_experiment_rep3


title: human_control_rep2


title: Pml KO_apap6h_1


title: Pml wt_apap6h_2

source_name: Pml wt liver, 6h after apap ip


title: human_experiment_rep6


title: human_experiment_rep7


title: Pml KO_apap2h_2

source_name: Pml KO liver, 2h after apap ip


title: Pml KO_ctrl_1

source_name: Pml KO liver, untreated


title: human_control_rep3


title: Pml wt_ctrl_2

source_name: Pml wt liver, untreated


title: Pml wt_apap2h_1

source_name: Pml wt liver, 2h after apap ip


title: Pml w_apap2h_2


title: 7. MSC (30 years)

first: Nidhi

last: Bhutani

address: 300 Pasteur Drive

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Data were processed using dChip software. Background correction was applied and normalization to the median array intensity was performed, gene level expression were summarized from the corrected intensities.

source_name: Human Bone marrow derived MSC

label_protocol: Ambion WT Expression kit  was used to generate ssDNA performed using Afymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: Chondrocytes were cultured for limited passages in high-density monolayers, as described in manuscript.MSC were purchased from Lonza and cultured according to instructions.

extract_protocol: QIAGEN RNeasy.

tag: group

value: Adult

value: Stem cells


title: Pml KO_ctrl_2

value: female


title: Pml wt_ctrl_1


title: 5.Adult Chondrocytes (34 years)

source_name: Human  chondrocyte

value: chondrocyte


title: AML_NPM1mut_pat9


title: PML 4 18h-exp2

description: Gene expression data from transduced human primary cells using Affy Human Gene v2.1

hyb_protocol: Samples were hybridized onto GeneChip Human Gene 2.1 ST Arrays (Affymetrix) using the GeneTitan platform at the Genomics platform, Translational Resarch Dept, Institut Curie , Paris, France. 3.3µg of targets were hybridized according Affymetrix recommendations.

data_processing:
Raw data were processed with Expression Console from Affymetrix. A RMA normlization was applied to control to data.
Filtering details no longer available.

source_name: Human primary fibroblasts transduced by PML4 expressing viruses for 18h

label_protocol: 100ng of total RNA were amplified to generate cRNA; 10µg of cRNA were converted into single stranded DA, based on the WT cDNA Synthesis Kit (Affymetrix). 5,5µg of cDNA were fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA samples were extracted from fresh transduced cells, with Rneasy Mini Kit, according to the manufacturer’s instructions. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

value: human lung normal fibroblast, ATCC CCL-75

tag: developmental stage

value: 3 months gestation fetus

tag: ethnicity

value: Caucasian

tag: time


title: 3.Juvenile chondrocytes (18 months)

value: Juvenile


title: 1.Juvenile chondrocytes (24 weeks)


title: 6. MSC (19years)


title: control 18h-exp2

source_name: Human primary fibroblasts transduced by empty viruses for 18h

value: control


title: 4. Adult Chondrocytes (27 years)


title: control 24h-exp2

source_name: Human primary fibroblasts transduced by empty viruses for 24h


title: 2.Juvenile chondrocytes (6months)


title: human_experiment_rep1


title: PML 4 24h-exp2

source_name: Human primary fibroblasts transduced by PML4 expressing viruses for 24h


title: PML 4 24h-exp1


title: Pml KO_apap2h_1

value: Liver

value: BALB/cByJ


title: M7_PC_24

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description: SAMPLE 17

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with R-Bioconductor packages using RMA algorithm.

source_name: macrophages + CFNA (PC)

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

extract_protocol: RNA extraction kit (Qiagen)

value: macrophage

tag: treated with

value: PC

tag: culture


title: control 24h-exp1

tag: gender


title: PML 4 18h-exp1


title: DC7_PC_4

description: SAMPLE 19

source_name: dendritic cells + CFNA (PC)

value: dendritic cell


title: DC7_RBC_2

description: SAMPLE 12

source_name: dendritic cells +CFNA(RBC)

value: RBC


title: DC8_FFP_7

description: SAMPLE 22

source_name: dendritic cells + CFNA (FFP)

value: FFP


title: DC8_PBS_5

description: SAMPLE 20

source_name: dendritic cells + control

value: PBS


title: DC8_PC_8

description: SAMPLE 23


title: DC7_FFP_3

description: SAMPLE 18


title: M6_FFP_19

description: SAMPLE 11

source_name: macrophages+CFNA (FFP)


title: M7_FFP_23

description: SAMPLE 16


title: DC8_RBC_6

description: SAMPLE 21


title: M6_PC_20

description: SAMPLE 13


title: AML_NPM1mut_pat1

source_name: enriched leukemic blast cells

value: AML

value: NPM1 mutated

value: high

value: enriched leukemic blast cells


title: M7_RBC_22

description: SAMPLE 15

source_name: macrophages+CFNA(RBC)


title: M6_RBC_18

description: SAMPLE 10


title: DC9_PC_12

description: SAMPLE 4


title: control 18h-exp1

value: human lung normal fibroblast, ATCC CCL-75

value: female


title: M1_RBC_14

description: SAMPLE 6


title: M1_PBS_13

description: SAMPLE 5

source_name: macrophages + control


title: DC9_PBS_9

description: SAMPLE 24


title: M7_PBS_21

description: SAMPLE 14


title: M6_PBS_17

description: SAMPLE 9


title: Pml wt_apap6h_1

source_name: Pml wt liver, 6h after apap ip


title: M1_PC_16

description: SAMPLE 8


title: M1_FFP_15

description: SAMPLE 7


title: DC9_FFP_11

description: SAMPLE 3


title: DC9_RBC_10

description: SAMPLE 2


title: M-MØ_control_donor3

city: Madrid

first: Ángel

middle: L

last: Corbí

state: Madrid

address: Ramiro de Maeztu, 9

department: Molecular Microbiology and Infection Biology

country: Spain

institute: Consejo Superior de Investigaciones Científicas

description: Gene expression in monocyte-derived M-CSF macrophages

hyb_protocol: 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays. Images provided by the scanner were analyzed using Feature Extraction software (Agilent Technologies).

data_processing: Data files from Feature Extraction were imported into GeneSpring® GX software version 9.0. (Agilent Technologies). Quantile normalization was performed and expression values (log2 transformed) were obtained for each probe.

source_name: Control M-MØ Donor 3

label_protocol: For each sample, we have generated cyanine 3-labeled cRNA from one microgram of total RNA, using the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color. Briefly, total RNA is reverse-transcribed using T7-oligo (dT) primer; after first and second strand cDNA synthesis, cRNA is synthesized from the double-stranded cDNA using T7 RNA polymerase, which simultaneously incorporates cyanine 3.

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of  M-CSF or GM-CSF to generate M-CSF- or GM-CSF-polarized macrophages (M-MØ and GM-MØ, respectively).

extract_protocol: Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Macrophages were either left untreated or stimulated for 4h with 10ng/ml LPS.

value: Monocyte-derived M-CSF macrophages

tag: treatment

value: Untreated


title: M-MØ+LPS_donor3

description: Gene expression in monocyte-derived M-CSF macrophages after 4h of treatment with 10ng/ml LPS

source_name: LPS M-MØ Donor 3

tag: cell type

value: 10ng/ml LPS for 4h


title: M-MØ_control_donor2

source_name: Control M-MØ Donor 2


title: GM-MØ+LPS_donor3

description: Gene expression in monocyte-derived GM-CSF macrophages after 4h of treatment with 10ng/ml LPS

source_name: LPS GM-MØ Donor 3

value: Monocyte-derived GM-CSF macrophages


title: PBMC+CFNA(RBC)_8

description: SAMPLE 22

source_name: PBMC+CFNA(RBC)

extract_protocol: RNA extraction  kit (Qiagen)

value: peripheral mononuclear cells (PBMCs)

value: CFNA (RBC)


title: M-MØ+LPS_donor1

source_name: LPS M-MØ Donor 1


title: PMC+CFNA(FFP)_5

description: SAMPLE 19

source_name: PMC+CFNA(FFP)

value: CFNA (FFP)


title: GM-MØ+LPS_donor2

source_name: LPS GM-MØ Donor 2


title: M-MØ+LPS_donor2

source_name: LPS M-MØ Donor 2


title: GM-MØ_control_donor3

description: Gene expression in monocyte-derived GM-CSF macrophages

source_name: Control GM-MØ Donor 3


title: PBMC+LPS_20

description: SAMPLE 12

source_name: PBMC+LPS

value: LPS


title: DC7_PBS_1

description: SAMPLE 1

source_name: dendritic cells + control

value: dendritic cell


title: PBMC_24

description: SAMPLE 15

source_name: PBMC


title: PBMC+LPS_7

description: SAMPLE 21


title: GM-MØ_control_donor2

source_name: Control GM-MØ Donor 2


title: PBMC+CFNA(PBS)_6

description: SAMPLE 20

source_name: PBMC+CFNA(PBS)

value: CFNA (PBS)


title: PMC+CFNA(FFP)_9

description: SAMPLE 23


title: PMC+CFNA(FFP)_23

description: SAMPLE 14


title: PBMC+LPS_3

description: SAMPLE 17


title: PBMC_19

description: SAMPLE 10


title: GM-MØ+LPS_donor1

source_name: LPS GM-MØ Donor 1


title: PBMC+CFNA(PBS)_25

description: SAMPLE 16


title: M-MØ_control_donor1

source_name: Control M-MØ Donor 1


title: PBMC+CFNA(RBC)_4

description: SAMPLE 18


title: PMC+CFNA(FFP)_18

description: SAMPLE 9


title: GM-MØ_control_donor1

source_name: Control GM-MØ Donor 1


title: PBMC+CFNA(RBC)_22

description: SAMPLE 13


title: PBMC+CFNA(PBS)_2

description: SAMPLE 11


title: PBMC+CFNA(RBC)_17

description: SAMPLE 8


title: miRNA_RectalCancer_rep134

status: Public on Sep 21 2017

city: Koto

first: Akihisa

last: Takahara

state: Tokyo

institute: Japanese Foundation For Cancer Research

description: miRNA

hyb_protocol: After fragmentation, RNA was hybridized with Affymetrix Hybridization,Wash, and Stain Kit on Affymetrix miRNA 3.0 Arrays following manufactuer's instruction.

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

data_processing: Data was processed with RMA-dabg using Affymetrix Expression Console software.

source_name: Rectal Cancer tissue

label_protocol: Biotinylated RNA was prepared with FrashTag Biotin HSR RNA Labeling Kit according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN miRNeasy Mini Kit following manufacturer's instruction.

value: Rectal Cancer tissue

value: M

tag: age


title: miRNA_RectalCancer_rep133

description: miRNA

tag: tissue


title: miRNA_RectalCancer_rep131

description: miRNA

value: F


title: miRNA_RectalCancer_rep136

description: miRNA


title: miRNA_RectalCancer_rep130

description: miRNA


title: miRNA_RectalCancer_rep132

description: miRNA


title: miRNA_RectalCancer_rep129

description: miRNA


title: PBMC+LPS_11

description: SAMPLE 2


title: PBMC+CFNA(PBS)_15

description: SAMPLE 6


title: PBMC_14

description: SAMPLE 5


title: PBMC+CFNA(PBS)_10

description: SAMPLE 1


title: PBMC+LPS_16

description: SAMPLE 7


title: PMC+CFNA(FFP)_13

description: SAMPLE 4


title: PBMC+CFNA(RBC)_12

description: SAMPLE 3


title: miRNA_RectalCancer_rep137

description: miRNA


title: miRNA_RectalCancer_rep117

description: miRNA


title: miRNA_RectalCancer_rep122

description: miRNA


title: miRNA_RectalCancer_rep119

description: miRNA


title: miRNA_RectalCancer_rep118

description: miRNA


title: miRNA_RectalCancer_rep121

description: miRNA


title: miRNA_RectalCancer_rep116

description: miRNA


title: miRNA_RectalCancer_rep126

description: miRNA


title: miRNA_RectalCancer_rep123

description: miRNA


title: miRNA_RectalCancer_rep127

description: miRNA


title: miRNA_RectalCancer_rep135

description: miRNA


title: miRNA_RectalCancer_rep124

description: miRNA


title: miRNA_RectalCancer_rep125

description: miRNA


title: miRNA_RectalCancer_rep120

description: miRNA


title: miRNA_RectalCancer_rep128

description: miRNA


title: miRNA_RectalCancer_rep110

description: miRNA


title: miRNA_RectalCancer_rep109

description: miRNA


title: miRNA_RectalCancer_rep115

description: miRNA


title: miRNA_RectalCancer_rep113

description: miRNA


title: miRNA_RectalCancer_rep111

description: miRNA


title: miRNA_RectalCancer_rep112

description: miRNA


title: miRNA_RectalCancer_rep114

description: miRNA


title: miRNA_RectalCancer_rep107

description: miRNA


title: miRNA_RectalCancer_rep102

description: miRNA


title: miRNA_RectalCancer_rep103

description: miRNA


title: miRNA_RectalCancer_rep104

description: miRNA


title: miRNA_RectalCancer_rep99

description: miRNA


title: miRNA_RectalCancer_rep105

description: miRNA


title: miRNA_RectalCancer_rep98

description: miRNA


title: miRNA_RectalCancer_rep101

description: miRNA


title: miRNA_RectalCancer_rep96

description: miRNA


title: miRNA_RectalCancer_rep100

description: miRNA


title: miRNA_RectalCancer_rep91

description: miRNA


title: miRNA_RectalCancer_rep95

description: miRNA


title: miRNA_RectalCancer_rep106

description: miRNA


title: miRNA_RectalCancer_rep94

description: miRNA


title: miRNA_RectalCancer_rep108

description: miRNA


title: miRNA_RectalCancer_rep93

description: miRNA


title: miRNA_RectalCancer_rep92

description: miRNA


title: miRNA_RectalCancer_rep90

description: miRNA


title: miRNA_RectalCancer_rep97

description: miRNA


title: miRNA_RectalCancer_rep88

description: miRNA


title: miRNA_RectalCancer_rep89

description: miRNA


title: miRNA_RectalCancer_rep87

description: miRNA


title: miRNA_RectalCancer_rep86

description: miRNA


title: miRNA_RectalCancer_rep85

description: miRNA


title: miRNA_RectalCancer_rep83

description: miRNA


title: miRNA_RectalCancer_rep84

description: miRNA


title: miRNA_RectalCancer_rep80

description: miRNA


title: miRNA_RectalCancer_rep79

description: miRNA


title: miRNA_RectalCancer_rep77

description: miRNA


title: miRNA_RectalCancer_rep78

description: miRNA


title: miRNA_RectalCancer_rep76

description: miRNA


title: miRNA_RectalCancer_rep75

description: miRNA


title: miRNA_RectalCancer_rep67

description: miRNA


title: miRNA_RectalCancer_rep71

description: miRNA


title: miRNA_RectalCancer_rep68

description: miRNA


title: miRNA_RectalCancer_rep69

description: miRNA


title: miRNA_RectalCancer_rep73

description: miRNA


title: miRNA_RectalCancer_rep74

description: miRNA


title: miRNA_RectalCancer_rep72

description: miRNA


title: miRNA_RectalCancer_rep65

description: miRNA


title: miRNA_RectalCancer_rep81

description: miRNA


title: miRNA_RectalCancer_rep66

description: miRNA


title: miRNA_RectalCancer_rep64

description: miRNA


title: miRNA_RectalCancer_rep82

description: miRNA


title: miRNA_RectalCancer_rep61

description: miRNA


title: miRNA_RectalCancer_rep60

description: miRNA


title: miRNA_RectalCancer_rep63

description: miRNA


title: miRNA_RectalCancer_rep62

description: miRNA


title: miRNA_RectalCancer_rep57

description: miRNA


title: miRNA_RectalCancer_rep58

description: miRNA


title: miRNA_RectalCancer_rep70

description: miRNA


title: miRNA_RectalCancer_rep55

description: miRNA


title: miRNA_RectalCancer_rep54

description: miRNA


title: miRNA_RectalCancer_rep59

description: miRNA


title: miRNA_RectalCancer_rep53

description: miRNA


title: miRNA_RectalCancer_rep52

description: miRNA


title: miRNA_RectalCancer_rep48

description: miRNA


title: miRNA_RectalCancer_rep49

description: miRNA


title: miRNA_RectalCancer_rep42

description: miRNA


title: miRNA_RectalCancer_rep50

description: miRNA


title: miRNA_RectalCancer_rep56

description: miRNA


title: miRNA_RectalCancer_rep46

description: miRNA


title: miRNA_RectalCancer_rep44

description: miRNA


title: miRNA_RectalCancer_rep47

description: miRNA


title: miRNA_RectalCancer_rep39

description: miRNA


title: miRNA_RectalCancer_rep45

description: miRNA


title: miRNA_RectalCancer_rep38

description: miRNA


title: miRNA_RectalCancer_rep40

description: miRNA


title: miRNA_RectalCancer_rep35

description: miRNA


title: miRNA_RectalCancer_rep36

description: miRNA


title: miRNA_RectalCancer_rep37

description: miRNA


title: miRNA_RectalCancer_rep34

description: miRNA


title: miRNA_RectalCancer_rep41

description: miRNA


title: miRNA_RectalCancer_rep51

description: miRNA


title: miRNA_RectalCancer_rep30

description: miRNA


title: miRNA_RectalCancer_rep32

description: miRNA


title: miRNA_RectalCancer_rep31

description: miRNA


title: miRNA_RectalCancer_rep29

description: miRNA


title: miRNA_RectalCancer_rep27

description: miRNA


title: miRNA_RectalCancer_rep33

description: miRNA


title: miRNA_RectalCancer_rep26

description: miRNA


title: miRNA_RectalCancer_rep25

description: miRNA


title: miRNA_RectalCancer_rep28

description: miRNA


title: miRNA_RectalCancer_rep43

description: miRNA


title: miRNA_RectalCancer_rep19

description: miRNA


title: miRNA_RectalCancer_rep22

description: miRNA


title: miRNA_RectalCancer_rep17

description: miRNA


title: miRNA_RectalCancer_rep18

description: miRNA


title: miRNA_RectalCancer_rep24

description: miRNA


title: miRNA_RectalCancer_rep16

description: miRNA


title: miRNA_RectalCancer_rep12

description: miRNA


title: miRNA_RectalCancer_rep13

description: miRNA


title: miRNA_RectalCancer_rep15

description: miRNA


title: miRNA_RectalCancer_rep10

description: miRNA


title: miRNA_RectalCancer_rep8

description: miRNA


title: miRNA_RectalCancer_rep6

description: miRNA


title: miRNA_RectalCancer_rep14

description: miRNA


title: miRNA_RectalCancer_rep7

description: miRNA


title: miRNA_RectalCancer_rep5

description: miRNA


title: miRNA_RectalCancer_rep2

description: miRNA


title: miRNA_RectalCancer_rep23

description: miRNA


title: miRNA_RectalCancer_rep4

description: miRNA


title: miRNA_RectalCancer_rep21

description: miRNA


title: miRNA_RectalCancer_rep3

description: miRNA


title: miRNA_RectalCancer_rep9

description: miRNA


title: miRNA_RectalCancer_rep20

description: miRNA


title: miRNA_RectalCancer_rep11

description: miRNA


title: miRNA_RectalCancer_rep1

description: miRNA


title: NCSTN transgenic model

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

description: Transgenic model

hyb_protocol: The labelled RNA were hybridized to a microarray (Agilent Mouse whole genome 44K, Agilent Technologies) containing approximately 44,000 probes (~26,600 unique genes) in accordance with the manufacturer's instructions.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner.

data_processing: Signal intensities of genes were normalized by the quantile method.

source_name: brain tissues

label_protocol: The isolated RNA was amplified and labeled using a Low RNA Input Linear Amplification kit PLUS following manufacturer’s instructions (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: All animals were housed individually in polycarbonate cages at a controlled temperature of 23 ± 3 ᴼC with 60% humidity and a 12-hour light/dark cycle. Standard chow diet and water were provided ad libitum throughout the experiment. All mice were fasted overnight and anesthetized using 5% isoflurane before sacrifice.

extract_protocol: Total RNA was purified from brain tissues of mice by using an RNeasy kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany). The quality of isolated RNA was measured using Agilent’s Bio-analyzer 2100 RNA Nano kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Brain tissues were prepared 14 days after i.c.v. injection of Aβ or streptozotocin. Scopolamine was administered by intraperitoneal (i.p.) injection 30 minutes before isolation of brain tissues.

value: hippocampus


title: Ab-injected model_10µM

description: Amyloid-b (10µM) injected model

value: ICR


title: MAPT overexpression model

description: Transgenic model


title: PSEN2 transgeinc model

description: Transgenic model


title: Mice of 4 month-old

description: Aging model

value: prefrontal cortex


title: Scopolamine_1mg/kg_model

description: Pharmacological model (treatment of Scopolamine_1mg/kg)


title: Streptozotocin_2.5mg/kg_model

description: Pharmacological model (treatment of Streptozotocin_2.5mg/kg)


title: Streptozotocin_3mg/kg_model

description: Pharmacological model (treatment of Streptozotocin_3mg/kg)


title: Mice of 22 month-old

description: Aging model


title: 5xFAD

description: Transgenic model


title: Ab-injected model_5µM

description: Amyloid-b (5µM) injected model


title: Mice of 17 month-old

description: Aging model


title: Mice of 1.5 month-old

description: Aging model


title: WT_BCR_24hr_3

city: Sendai

first: Akihiko

last: Muto

state: Miyagi

address: Seiryou-machi 2-1

department: Biochemistry

institute: Tohoku University Graduate School of Medicine

description: Splenic Follicular Zone B cells from WT mice were stimulated with BCR for 24hrs.

hyb_protocol: A sureprint G3 mouse GE microarray slide was used for hybridization according to the manufacturer's protocols (Agilent)

scan_protocol: After hybridization, a slide was washed adequately and scanned immediately by using an Agilent DNA Microarray Scanner with one color scan setting

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep9 and Grid: 028005_D_F_20101029) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Spleen, Follicular Zone B cells, WT, BCR stimulation 24hr, replicate3

label_protocol: Purified RNA samples were labeled with indocarbocyanine by using a Cy3 post-labeling reactive dye pack (Amersham)

growth_protocol: Purified Follicular Zone B cells were cultured in 24 well plates at 1.0 x 10^6 cells/well in RPMI1640 medium (Sigma).

extract_protocol: Total RNA was extracted by using RNeasy Plus Micro Kit (QIAGEN).

treatment_protocol: Cells were stimulated with 10 micro-g/mL anti-mouse IgM (Fab’) (115-006-020; Jackson ImmunoResearch Laboratories) for 24 hours.

value: Spleen

value: Follicular Zone B cells

value: WT

tag: Sex

value: Male


title: Bach2-/-_BCR_24hr_3

description: Splenic Follicular Zone B cells from Bach2-/- mice were stimulated with BCR for 24hrs.

source_name: Spleen, Follicular Zone B cells, Bach2-/-, BCR stimulation 24hr, replicate3

tag: strain


title: Bach2-/-_BCR_24hr_2

source_name: Spleen, Follicular Zone B cells, Bach2-/-, BCR stimulation 24hr, replicate2

tag: genotype/variation


title: WT_BCR_0hr_3

description: Splenic Follicular Zone B cells from WT mice

source_name: Spleen, Follicular Zone B cells, WT, BCR stimulation 0hr, replicate3


title: WT_BCR_24hr_2

source_name: Spleen, Follicular Zone B cells, WT, BCR stimulation 24hr, replicate2


title: WT_BCR_0hr_2

source_name: Spleen, Follicular Zone B cells, WT, BCR stimulation 0hr, replicate2


title: Bach2-/-_BCR_24hr_1

source_name: Spleen, Follicular Zone B cells, Bach2-/-, BCR stimulation 24hr, replicate1


title: WT_BCR_24hr_1

source_name: Spleen, Follicular Zone B cells, WT, BCR stimulation 24hr, replicate1


title: AML_NPM1wt_pat24

source_name: enriched leukemic blast cells

value: AML

value: NPM1 wildtype

tag: relative hsa_circ_0075001 expression

value: high

value: enriched leukemic blast cells


title: HPneuron_TTX_rep4

city: Urbana

first: Hee Jung

last: Chung

state: IL

address: 407 South Goodwin Avenue, 524 Burrill Hall

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana-Champaign

description:
TTX.4
HP neurons TTX #4-blockade of neuronal activity

hyb_protocol: The samples were hybridized to Agilent 4x44k whole genome Rat (014879) microarrays by the Sandler Asthma Basic Research (SABRE) Center Functional Genomics Core Facility at the University of California, San Francisco, using their standard protocols

scan_protocol: The samples were scanned with Agilent Feature Extraction software by the Sandler Asthma Basic Research (SABRE) Center Functional Genomics Core Facility at the University of California, San Francisco, using their standard protocols

data_processing: Quantile normalization was performed on the median feature pixel intensity without background subtraction using R and the limma package (versions unknown, but done in June 2008). 245 probes had replicate spots and were summarized by taking the median intensity

source_name: HP neurons TTX

label_protocol: The samples were labeled with Cy3 by the Sandler Asthma Basic Research (SABRE) Center Functional Genomics Core Facility at the University of California, San Francisco, using their standard protocols

growth_protocol: Primary dissociated hippocampal cultures were prepared from E18.5 Sprague - Dawley rat embryos and plated at high density (330 cells/mm2) onto poly L-lysine-coated (0.1 mg/mL) 12 mm glass coverslips (1.5×10^5 cells/coverslip), or 30 or 60 mm cell culture dishes (6.5 ×10^5 or 2.3×10^6 cells/dish, respectively).

extract_protocol: Total RNA was isolated using an RNeasy kit (Qiagen) and stored at −80°C. Total RNA quality and quantity was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer and Nanodrop ND-100 spectrophotometer.

treatment_protocol: At 10–13 days in vitro (DIV), neurons were treated for 48 h with (CTL-DMSO, 0.1% DMSO), TTX (0.5-1 μM), or BC (20 μM)

value: Sprague-Dawley

tag: tissue type

value: High-density cultures of dissociated hippocampal neurons (330 neurons/cm2)

value: sodium channel blocker tetrodotoxin (TTX) for 48hrs


title: HPneuron_TTX_rep2

description:
TTX.2
HP neurons TTX #2-blockade of neuronal activity


title: WT_BCR_0hr_1

source_name: Spleen, Follicular Zone B cells, WT, BCR stimulation 0hr, replicate1


title: Bach2-/-_BCR_0hr_2

description: Splenic Follicular Zone B cells from Bach2-/- mice

source_name: Spleen, Follicular Zone B cells, Bach2-/-, BCR stimulation 0hr, replicate2


title: HPneuron_TTX_rep3

description:
TTX.3
HP neurons TTX #3-blockade of neuronal activity


title: Bach2-/-_BCR_0hr_1

source_name: Spleen, Follicular Zone B cells, Bach2-/-, BCR stimulation 0hr, replicate1


title: HPneuron_TTX_rep1

description:
TTX.1
HP neurons TTX #1-blockade of neuronal activity


title: Bach2-/-_BCR_0hr_3

source_name: Spleen, Follicular Zone B cells, Bach2-/-, BCR stimulation 0hr, replicate3


title: HPneuron_BC_rep1

description:
BC.1
HP neurons BC #1-enhancement of neuronal activity

source_name: HP neurons BC

value: GABA-A receptor antagonist bicuculine (BC) for 48hrs


title: HPneuron_BC_rep4

description:
BC.4
HP neurons BC #4-enhancement of neuronal activity


title: HPneuron_BC_rep3

description:
BC.3
HP neurons BC #3-enhancement of neuronal activity


title: HPneuron_DMSO_rep1

description:
DMSO.1
HP neurons DMSO #1 - control

source_name: HP neurons DMSO

value: vehicle contrl (DMSO) for 48hrs


title: HPneuron_DMSO_rep2

description:
DMSO.2
HP neurons DMSO #2 - control


title: skbr3_144h_trastuzumab_treatment_rep1

city: Ankara

first: Bala

last: Gur Dedeoglu

address: Dogol cad.

country: Turkey

institute: Ankara University Biotechnology Institute

description:
skbr3_trast1
miRNA profiling after 6 ug/mL trastuzumab treatment for 144h ; SKBR3 cells, rep1

hyb_protocol: Hybridization was performed in Human miRNA Microarray, Release 19.0, 8x60K (G4870A, Agilent Technologies) platform, which was an array designed from miRBase version 19 containing 2006 miRNAs. Each miRNA sequence was represented by probes replicated at least 30 times on the array. Spike-in control solutions were first prepared and total RNA (100 ng) from each sample was dephosphorylated with calf intestine alkaline phosphatase at 37°C for 30 min. It was followed by a denaturation step that includes the incubation of samples in DMSO at 100°C for 10 minutes.

scan_protocol: After the washing step, the arrays were scanned in Roche Nimblegen instrument by using Agilent Scan Control software. The data were acquired using Agilent Feature Extraction software for miRNA microarray, generating a GeneView file that contained summarized signal intensities for each miRNA by subtracting the background after combining the intensities of replicate probes.

data_processing: BRB Array Tools 4.3.2. stable release was used for the normalization and statistical analysis. Bioconductor packages were used for the normalization and statistical comparisons. The data were normalized by Quantile normalization method.

label_protocol: Samples were then labeled with Cyanine3-pCp by using T4 RNA Ligase at 16°C for 2 hours. They were mixed with 10x blocking agent and 2x Hi-RPM hybridization buffer (Agilent Technologies), and hybridizations were performed at 55°C with rotation at 20 rpm.

growth_protocol: HER2+ breast cancer cell lines BT474 (HTB-20)  and SKBR3 (HTB-30) were purchased from the American Type Culture Collection (ATCC). SKBR3 cells were maintained in Mc Coy’s 5A medium (Lonza) with L-glutamine containing 10% fetal bovine serum (FBS), 1% penicillin-streptomycin. BT474 cells were maintained in RPMI 1640 medium with L-glutamine (Lonza) supplemented with 10% FBS, 1% penicillin-streptomycin and 2% bovine insulin. The cell lines were cultured in a humidified air supplemented with 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated with the TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Absorption at 260 nm and 280 nm was measured for the determination of RNA purity.

treatment_protocol: SKBR3 and BT474 cells were plated at a starting density of 2 x 106 in 100 mm cell culture plates. BT474 and SKBR3 cells were treated with 6 µg/mL trastuzumab and/or PBS as control within two biological replicates for 144 hours. The media were changed in every 72 hours.

tag: cell line

value: HER2+ breast cancer cell line

tag: receptor

value: ER-, HER2+, PR+

value: 6 ug/mL trastuzumab for 144 hrs


title: HPneuron_DMSO_rep3

description:
DMSO.3
HP neurons DMSO #3 - control

value: hippocampus


title: HPneuron_DMSO_rep4

description:
DMSO.4
HP neurons DMSO #4 - control


title: skbr3_144h_PBS_treatment_rep2

description:
skbr3_k2
miRNA profiling after PBS treatment for 144h ; SKBR3 cells, rep2

value: PBS for 144 hrs


title: skbr3_144h_trastuzumab_treatment_rep2

description:
skbr3_trast2
miRNA profiling after 6 ug/mL trastuzumab treatment for 144h ; SKBR3 cells, rep2


title: bt474_144h_trastuzumab_treatment_rep1

description:
bt474_trast1
miRNA profiling after 6 ug/mL trastuzumab treatment for 144h ; BT474 cells, rep1

value: ER+, HER2+, PR+


title: HPneuron_BC_rep2

description:
BC.2
HP neurons BC #2-enhancement of neuronal activity


title: bt474_144h_PBS_treatment_rep2

description:
bt474_k2
miRNA profiling after PBS treatment for 144h ; BT474 cells, rep2


title: skbr3_144h_PBS_treatment_rep1

description:
skbr3_k1
miRNA profiling after PBS treatment for 144h ; SKBR3 cells, rep1


title: bt474_144h_PBS_treatment_rep1

description:
bt474_k1
miRNA profiling after PBS treatment for 144h ; BT474 cells, rep1


title: B2-6h-18

city: Toulouse

first: Alice

last: DAVY

address: 118 route de Narbonne

department: CBI

institute: CNRS

description:
replicate 3
7810815037_F

hyb_protocol: Hybridization was performed by Asuragen

scan_protocol: Scanning was performed by Asuragen

data_processing: BeadStudio

source_name: Mouse neural progenitor

label_protocol: Labeling was performed by Asuragen

growth_protocol: Cultures of primary NPCs were obtained as described previously (Chojnacki et al., 2008). Briefly, embryonic day 14.5 (E14.5) cortices were dissected mechanically in phosphate buffered saline solution (PBS). The single-cell suspension was collected, rinsed with DMEM/F12, and cultured with growing medium (DMEM/F12 medium containing 0.6% glucose, 5 mM HEPES, 1 mM putrescine, 5 ng/ml basic fibroblast growth factor 2 [FGF-2], 20 ng/ml epidermal growth factor [EGF], 10 ng/ml insulin-transferrin-sodium selenite supplement and 2% B27 supplement) in a 5% CO2 incubator at 37°C.

extract_protocol: Total RNA was extracted using Tri-Reagent (Molecular Research Center, Inc) using the manufacturer's instructions.

treatment_protocol: Prior to stimulation, neurospheres were dissociated with Trypsin, and aliquots of 12 000 000 cells were placed in growing medium then incubated at 37° with IgG-Fc, EphB2-Fc or ephrin-B1-Fc (1 μg/ml) preclustered with anti-human IgG (0.1 μg/ml). Total RNA was extracted using Tri-reagent at 2 hours and  6 hours poststimulation.

value: neocortex


title: bt474_144h_trastuzumab_treatment_rep2

description:
bt474_trast2
miRNA profiling after 6 ug/mL trastuzumab treatment for 144h ; BT474 cells, rep2


title: B2-6h-17

description:
replicate 2
7810815037_E


title: B2-6h-16

description:
replicate 1
7810815037_D


title: b1-6h-12

description:
replicate 3
7810815012_F


title: B2-2h-13

description:
replicate 1
7810815037_A


title: b1-6h-11

description:
replicate 2
7810815012_E


title: B2-2h-15

description:
replicate 3
7810815037_C


title: b1-2h-8

description:
replicate 2
7810815012_B


title: b1-2h-7

description:
replicate 1
7810815012_A


title: B2-2h-14

description:
replicate 2
7810815037_B


title: b1-2h-9

description:
replicate 3
7810815012_C


title: ctrl-6h-6

description:
replicate 3
7810815042_F


title: b1-6h-10

description:
replicate 1
7810815012_D


title: ctrl-6h-4

description:
replicate 1
7810815042_D


title: ctrl-6h-5

description:
replicate 2
7810815042_E


title: ctrl-2h-1

description:
replicate 1
7810815042_A


title: HREC PEG-GNRs rep2

city: Shanghai

first: Hongyuan

last: Song

state: --- Select One ---

address: Department of Ophthalmoloty, Changhai Hospital, No. 168 Changhai Road, Yangpu District

department: Ophthalmology

institute: Changhai Hospital, Second Military Medical University

description:
Gene expression data from HREC treated with PEG-GNRs
HREC used in 3 to 8 passages

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on AffymetrixPrimeView 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:
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = PrimeView
program-name = Expression Console
program-version = 1.3.1.187
program-company = Affymetrix

source_name: HREC treated with PEG-GNRs

growth_protocol: HREC were cultured in Endothelial Cell Medium (ECM) supplemented with 5% FBS, 1% L-glutamine, 100 U/mL penicillin and 100μg/mL streptomycin.

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

treatment_protocol: HREC were treated with PEG-GNRs for 3 days.Then the cells were collected and placed on ice in the Trizol solution (Gibco).

value: HREC

tag: passages

value: 3 to 8 passages

tag: agent

value: PEG-GNRs


title: HREC PEG-GNRs rep3


title: HREC PEG-GNRs rep1


title: HREC control rep2

description:
Gene expression data from HREC
HREC used in 3 to 8 passages

source_name: HREC, control

value: control


title: HREC control rep1


title: bli-1_12DAG_cont-light_rep1

status: Public on Sep 20 2017

city: Berlin

first: Daniel

last: Schubert

address: Königin-Luise-Str. 12-16 Raum 105

department: Institut für Biologie

institute: Freie Universität Berlin

hyb_protocol: Array hybridization was performed by the Imagenes Corp. (Berlin, Germany) as described in the “One-Color Microarray-Based Gene Expression Analysis” Protocol (G4140-90040 Version 5.7, March 2008). A oligo dT / T7 RNA-Polymerase based protocol was used for labelling.

scan_protocol: Samples were scanned on an Agilent Technologies Scanner G2505C

data_processing: The scanned array images were analyzed with Feature Extractor 11.0.1.1. Processing of raw data was performed as follows: The microarray was analyzed using background correction and quantile normalization of the limma package in the R environment (Ritchie et al., 2015; R Core Team, 2015). Differential expression was estimated using the empirical Bayes statistics implemented in limma (Ritchie et al., 2015; Smyth, 2004). P-values were adjusted for multiple testing using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). For our evaluation we calculated the mean of all probes belonging to the same gene. Hence, the number of probes was reduced by a third.

organism: Arabidopsis thaliana

source_name: bli-1 whole seedlings 12 DAG continuous light rep1

label_protocol: Cy3 probe labelling was performed by the Imagenes Corp. (Berlin, Germany) as described in the “One-Color Microarray-Based Gene Expression Analysis” Protocol (G4140-90040 Version 5.7, March 2008). A oligo dT / T7 RNA-Polymerase based protocol was used for labelling.

growth_protocol: Seeds were sterilized (10 min 70% Ethanol supplemented with 0.05% Triton X-100, 10 min 96% Ethanol) and sown on ½ MS germination medium (half-strength Murashige and Skoog medium supplemented with 0.5% sucrose and 0.05% MES). Seeds were stratified for two days at 4°C, grown under continuous light conditions (24 h light  at 20 °C), and then harvested.

extract_protocol: RNA from whole seedlings was extracted using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), resuspended in 30 µl RNAse-free water and treated with DNase (Fermentas). The quality was determined using a Bioanalyzer eukaryote total RNA nano chip (in cooperation with BMFZ, HHU Düsseldorf, Germany). RNA samples were processed by imaGenes GmbH (Berlin, Germany) with Agilent technologies using Arabidopsis 44k single colour arrays.

tag: genotype

tag: seedling age

value: 12 days after germination (DAG)


title: Col-0_12DAG_cont-light_rep2

source_name: Col-0 whole seedlings 12 DAG continuous light rep2


title: Col-0_12DAG_cont-light_rep1

source_name: Col-0 whole seedlings 12 DAG continuous light rep1


title: ctrl-2h-2

description:
replicate 2
7810815042_B


title: HREC control rep3


title: ctrl-2h-3

description:
replicate 3
7810815042_C


title: bli-1_12DAG_cont-light_rep2

source_name: bli-1 whole seedlings 12 DAG continuous light rep2


title: U-87_P68 KD_rep3

city: Harbin

first: Rui

last: Wang

address: 157 BaoJian Road Nangang District, Harbin, Heilongjiang, China

institute: Harbin medical university

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16hr at 45C on GeneChip 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA 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: U-87, P68 Knockdown

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

growth_protocol: U-87 MG cells were cultured using complete DMEM(Thermo Fisher Scientific,Ltd.) with 10% fetal bovine serum. Cells were subcultured at split ratios of 1:2~1:3 twice a week.

treatment_protocol: Cells were transfected with siP68 or NC according to the siRNA manufacture's instructions.

value: P68 Knockdown

value: brain


title: U-87_WT_rep1

source_name: U-87, P68 Wild Type

value: P68 Wild Type


title: U-87_WT_rep2


title: U-87_WT_rep3


title: A549 at T1, biological rep3

city: Jinan

first: Xiaoli

last: Ma

address: 105# Jiefang Road

institute: Jinan Central Hospital affiliated to Shandong University

description: Expression data from CHRNA5 knockdown A549 lung cancer cells compared with control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on PrimeView Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: A549 cell treated with Si-CHRNA5

growth_protocol: Human NSCLC cell line A549  cultured in RPMI 1640 supplemented with 10% fetal bovine serum, penicillin (100 units/mL), and streptomycin (100 Ag/mL; Invitrogen Corp.) at 37℃ in a humidified atmosphere with 5% CO2.

treatment_protocol: RNA was isolated from lung cancer A549 cells transfected with scrambled siRNA or α5-nAChR -specific siRNA (3 replicates each).

tag: cell

value: A549 cell

tag: transfection

value: [infinity]5-nAChR -specific siRNA


title: A549 at T1, biological rep1


title: A549 at T1, biological rep2


title: U-87_P68 KD_rep1


title: A549 at T0, biological rep2

source_name: A549 cell treated with Si-NC

value: scrambled siRNA


title: A549 at T0, biological rep3


title: U-87_P68 KD_rep2


title: Colon cancer LoVo-P cells

city: Guangzhou

first: Zhonghua

last: Chu

state: Guangdong

address: 107 Yan Jiang West Road

institute: Sun Yat-sen Memorial Hospital,Sun Yat-sen University

description: LoVo-P cells were stable transfected with pAcGFP-PRL-3 for overexpression PRL-3 and cultured in RPMI 1640 supplemented with 10%FBS 48 h

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: Colon cancer LoVo-P cells

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

growth_protocol: All cells were cultured in RPMI 1640 supplemented with 10%FBS, 100 mg/ml penicillin, and 100 mg/ml streptomycin. All cells were incubated at 37°Cin a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using the GeneJET RNA purification Kit according to the manufacturer’s instructions (Thermo Scientific). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.The concentration of each sample was measured by NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by the Agilent2200 (Agilent, USA).

treatment_protocol: LoVo-P or LoVo-C cells culutred in petri dish, incubated at 37°C in a humidified atmosphere containing 5% CO2. After 48 h, collected cells for subsequent experiments.

value: LoVo

value: colorectal cancer cell line

tag: transfected with

value: pAcGFP-PRL-3 for overexpression PRL-3

value: Expressed hight levels of PRL-3


title: A549 at T0, biological rep1


title: WT vs cyc- stationary growth phase

city: Bloemfontein

first: Walter

middle: Joseph

last: Muller

state: Free state

address: Decan Street

department: Biotechnology

country: South Africa

institute: University of the Free State

description: 1:1 combined, labeled cDNA of the WT and KO strain cultured until stationary growth phase

hyb_protocol: Scanned on an Agilent G2505C US22502585 scanner.

scan_protocol: Image processing was performed using Agilent Feature Extraction software. Data were analyzed using the Agilent microarray data analyzing software GeneSpring version 11.5.1.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization. Analysis was performed in the lab of Shiladitya DasSarma in Baltimore, MD, USA.

organism: Halobacterium salinarum

label_protocol: Labeled cDNA targets of the WT and KO strains were mixed 1:1 and were mixed with hybridization buffer (Agilent) and hybridized to microarray slides, which were assembled into a hybridization chamber (Agilent) for 17 h at 65°C in the dark.

growth_protocol: H. salinarum WT and KO strains were cultured, in triplicate to minimize biological noise, under normal conditions with aeration (200 r.p.m.) in complete medium at 40°C (Oesterhelt & Krippahl (1983). Cultures were grown until logarithmic (OD600 = 0.3) and also until stationary phase (OD600 = 1.3) of growth.

extract_protocol: 6 ug high quality total RNA was combined with 500 ng of random hexamers (Qiagen) and reverse transcribed to Cy3- or Cy5-dCTP (Amersham Pharmacia)-labeled cDNA using SuperScript II RNase H_ reverse transcriptase (Invitrogen).

treatment_protocol: After cell lysis and DNAase treatment (Invitrogen), RNA was extracted using spin columns (Agilent).

value: wildtype

tag: growth phase

value: stationary

value: cyc knockout


title: WT_NonPhagocytic_02

status: Public on Sep 19 2017

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

hyb_protocol: Refer to the NanoString nCounter Assay System Manual.

data_processing: The raw data were normalized using 6 housekeeping genes.

source_name: FACS sorted MG cells

extract_protocol: none provided by the submitter

tag: cells

value: microglia


title: WT_NonPhagocytic_03

scan_protocol: Refer to the NanoString nCounter Assay System Manual.


title: WT_Phagocytic_03

label_protocol: Refer to the NanoString nCounter Assay System Manual.


title: Colon cancer LoVo-C cells

description: LoVo-C cells were stable transfected with pAcGFP vectors for control vectors and cultured in RPMI 1640 supplemented with 10%FBS 48 h

source_name: Colon cancer LoVo-C cells

tag: cell type

value: pAcGFP vectors (control)

value: Expressed low levels of PRL-3


title: WT_Phagocytic_02


title: mock_rep3_vs_ref

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

hyb_protocol: All of the hybridization, washing and drying steps were performed in 2x105K Chambers in an HS 4800 Pro (Tecan) automatic hybridization station according to the manufacturer’s guidelines regarding Agilent microarrays treatment. A Gene Expression Hybridization Kit (Agilent) and Gene Expression Wash Buffer Kit solutions (Agilent) were used for the hybridization and washing steps, respectively.

scan_protocol: The intensity data were collected with 4200AL GenePix scanner and GenePix Pro 6.1 software at 5 µm resolution, at green and red channel.

data_processing: The scans were processed with GenePix Pro 6.1 software using morphological opening background method. Intensity data were analyzed with R/Bioconductor limma package. Background was subtracted. Loess within-array normalization and Aquantile between-array normalization was applied.

organism: Nicotiana benthamiana

source_name: ref

label_protocol: Labeled cRNA samples were prepared from 200 ng RNA each, using Quick Amp Labeling Kit (Agilent). The labeling efficiency was monitored with Nanodrop 2000 spectrophotometer.

growth_protocol: N. benthamiana plants were grown in separate cabins under 14h light/ 10h dark at 21°C day/16°C night.

extract_protocol: Samples from 3 biological replicates per treatment were obtained. Total RNA was extracted from upper parts of plants using spin-columns (RNeasy Plant Mini Kit, QIAGEN) and DNase-digested with TURBO DNA-free kit (Ambion) according to the manufacturers’ standard protocols. RNA quality was determined using Nanodrop 2000 and 2100 Bioanalyzer (Agilent). All of the samples used for the study were pure (A260/A280 ≥ 1.9; A260/A230 ≥ 2) and showed no visible signs of degradation.

treatment_protocol: Plants were inoculated with Peanut stunt virus strain G (PSV-G) or PSV-G and satellite RNA-P (PSV-G+satRNA) infectious copies in 0.5 M phosphate, pH 7.5, after carborund dusting. Mock-inoculated plants were treated as controls. Plants were harvested when first symptoms of infection occurred (20 dpi).

tag: tissue

value: upper part of plant

tag: treatment

value: phosphate buffer


title: mock_rep2_vs_ref


title: mock_rep1_vs_ref


title: PSV-G+satRNA_rep3_vs_ref

value: peanut stunt virus strain G and satellite RNA-P


title: WT_Phagocytic_01


title: MiR155ko_Phagocytic_03