title: Macrophage cell, D6 Male, LPS 24 h, 2 CTRL

tag: cell type

value: 2 CTRL


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_1 [Sah-0_ACC_R1]

status: Public on Jan 01 2018

type: RNA

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

country: Germany

institute: MPI of Molecular Plant Physiology

description: Gene expression for 2 weeks cold acclimated Sah-0 rosette leaves at 4 °C. RNA was hybridized on Agilent Arabidopsis expression array

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to a custom Gene Expression Agilent Microarray  (G2514F; DesignID 031554) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for AgilentHD_GX for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%, Tiff 20bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 031554_D_F_20101207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 6-week-old rosette leaves, 2-week cold-acclimated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds of Arabidopsis thaliana accessions were stratified at 4°C for 1 week and grown on soil at 20°C for 3 weeks under 8 hrs light/16 hrs dark cycle at growth chamber. Seedlings plants were continued grown at 20°C for 2 weeks under 16 hrs light/8 hrs dark cycle at greenhouse. Tuva and Yukon seeds were stratified at 4°C for 1 week and grown on soil at 20°C for 8 weeks under 16 hrs light/8 hrs dark cycle at greenhouse.

extract_protocol: Total RNA was isolated and on-column DNA digestion was performed with the RNeasy Plant mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: For cold acclimation, soil grown 6-week-old Arabidopsis plants were cold acclimated at 4°C for 2 weeks. Soil grown 8-week-old Tuva plants were cold acclimated at 4°C for 2 weeks.

tag: accession

tag: tissue

value: rosette leaves


title: microRNA profile of case T530

city: Guangzhou

first: jingye

last: hu

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The labeled RNAs from breast cancer and noncancerous breast were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, BRB ArrayTools v.3.8.0 was used.

organism: Homo sapiens

source_name: breast cancer

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted from the paraffin-embedded breast cancer and noncancerous breast samples, using a modification of the phenol/chloroform extraction method after processing by dimethylbenzene.

tag: survival

value: breast cancer


title: 6W_old_rosette_leaves_non_acclimated_replicate_1 [Sah-0_NA_R1]

description: Gene expression for non acclimated Sah-0 rosette leaves. RNA was hybridized on Agilent Arabidopsis expression array

source_name: 6-week-old rosette leaves, non-acclimated


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_2 [N13_ACC_R2]

description: Gene expression for 2 weeks cold acclimated N13 rosette leaves at 4 °C. RNA was hybridized on Agilent Arabidopsis expression array


title: microRNA profile of case T53


title: 6W_old_rosette_leaves_non_acclimated_replicate_2 [N13_NA_R2]

description: Gene expression for non acclimated N13 rosette leaves. RNA was hybridized on Agilent Arabidopsis expression array


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_3 [N13_ACC_R3]


title: Macrophage cell, D6 Male, LPS 07 h, 6 Indomethacin

city: Midlothian

first: Tim

last: Regan

address: Easter Bush Campus

department: Genetics and genomics

country: United Kingdom

institute: The Roslin Institute, University of Edinburgh

hyb_protocol: Labeled cDNA (3.5 ug) was then hybridized to the GeneChip Human Gene 2.1 ST array (Affymetrix, Inc.) using the Affymetrix GeneTitan® MC Instrument with the   GeneTitan® Hybridization, Wash, and Stain Kit for WT Array Plates.

scan_protocol: Scanning was performed on the Affymetrix GeneTitan® MC Instrument

data_processing: CEL files were assessed for quality using arrayQualityMetrics (AQM), a Bioconductor R package. Samples which failed 2 or more tests were discounted from the dataset. The matrix was then subject to RMA normalisation and probesets were reduced to a single gene. Statistical analysis was performed using lme4, another Bioconductor R package. Each donor was set as a random effect while drug or inflammatory treatments were set as fixed effects for each analysis.

label: biotin

source_name: human monocyte derived macrophage

label_protocol: Total RNA (500 ng) was reverse transcribed and the single stranded cDNA was amplified using the Ambion WT Expression Kit (Life Technologies, Inc.). The purified cDNA (5.5 μg) was subsequently fragmented and labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix Inc., Santa Clara, CA, U.S.A.)

growth_protocol: Freshly isolated CD14+ monocytes were seeded at a density of 4x10E5/well on 12-well NUNC coated plates in RPMI with 10% FCS 1% pen/Strep and rh-CSF-1 for 1 week until they had transformed into macrophage-like cells.

extract_protocol: Following tretment, supernatant was removed and 350 µl of Rneasy buffer RLT (Qiagen, Skelton House, Manchester, UK) was added to each well and plates were frozen at -80C. RNA extraction was performed using the Rneasy column extraction kit with on column DNase digestion according to the manufacturers protocol.

treatment_protocol: For each treatment, cells were supplemented with the inflammatory stimuli +/- drugs at the same time for 7 or 24 h. Cells were subject to inflammatory stimulus with LPS (10 ng/ml) or IFNα (50 U/ml) for 7 or 24 h or incubated for 24 h with no inflammatory stimulus. In each of these 5 conditions, cells were treated for the same amount of time with either vehicle control (DMSO), escitalopram (1 µM, SSRI antidepressant), nortriptyline (100 nM, tricyclic antidepressant), anti-TNFα (5 µg/ml, neutralising antibody anti-inflammatory), indomethacin (100 µM, non-steroidal anti-inflammatory), prednisolone (1 µM, steroidal anti-inflammatory) or left untreated.

value: blood

value: monocyte derived macrophage

tag: donor

tag: Sex

value: M

tag: inflammatory stimulus

value: LPS 07 h

tag: drug treatment

value: 6 Indomethacin


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_1 [N13_ACC_R1]


title: 6W_old_rosette_leaves_non_acclimated_replicate_1 [N13_NA_R1]


title: Macrophage cell, D6 Male, LPS 07 h, 7 Prednisolone

value: 7 Prednisolone


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_3 [Ms-0_ACC_R3]

description: Gene expression for 2 weeks cold acclimated Ms-0 rosette leaves at 4 °C. RNA was hybridized on Agilent Arabidopsis expression array


title: 6W_old_rosette_leaves_non_acclimated_replicate_3 [Ms-0_NA_R3]

description: Gene expression for non acclimated Ms-0 rosette leaves. RNA was hybridized on Agilent Arabidopsis expression array


title: microRNA profile of case T529


title: Macrophage cell, D6 Male, LPS 07 h, 2 CTRL


title: microRNA profile of case T528


title: 6W_old_rosette_leaves_non_acclimated_replicate_2 [Ms-0_NA_R2]


title: Macrophage cell, D6 Male, LPS 07 h, 5 Anti-TNFa

value: 5 Anti-TNFa


title: microRNA profile of case T527


title: 6W_old_rosette_leaves_non_acclimated_replicate_1 [Col-0_NA_R1]

description: Gene expression for non acclimated Col-0 rosette leaves. RNA was hybridized on Agilent Arabidopsis expression array


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_1 [Col-0_ACC_R1]

description: Gene expression for 2 weeks cold acclimated Col-0 rosette leaves at 4 °C. RNA was hybridized on Agilent Arabidopsis expression array


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_1 [Ms-0_ACC_R1]


title: Macrophage cell, D6 Male, IFN 24 h, 7 Prednisolone

value: IFN 24 h


title: 6W_old_rosette_leaves_non_acclimated_replicate_1 [Ms-0_NA_R1]


title: Macrophage cell, D6 Male, IFN 24 h, 5 Anti-TNFa


title: Macrophage cell, D6 Male, LPS 07 h, 1 Untreated

value: 1 UNT


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_2 [Ms-0_ACC_R2]


title: Macrophage cell, D6 Male, IFN 24 h, 6 Indomethacin


title: 6W_old_rosette_leaves_non_acclimated_replicate_1 [Can-0_NA_R1]

description: Gene expression for non acclimated Can-0 rosette leaves. RNA was hybridized on Agilent Arabidopsis expression array


title: microRNA profile of case T525


title: microRNA profile of case T522


title: microRNA profile of case T523


title: CD19+

city: Augusta

first: John

last: Cowell

state: GA

address: 1410 Laney-Walker Blvd

country: USA

institute: Augusta University

description: miRNA profiling

hyb_protocol: Following labeling, RNAs were hybridized for 18 hr at 48C on GeneChip miRNA 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6).

organism: Mus musculus

source_name: sorted CD19+ mouse B cell

label_protocol: Biotinylated RNAs were prepared according to the standard Affymetrix protocol from 250 ng total RNA (The FlashTag Biotin HSR RNA Labeling Kit, Affymetrix).

growth_protocol: BBC2 cell was cultered in RPMI-1640  medium supplemented with 10% FBS, 100U/ml Penicillin G, 100µg/ml Streptomycin sulfate.

extract_protocol: miRNA was prepared using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA) following the user manual.

treatment_protocol: BBC2 Cells were harvested during exponential growth phase, and fresh sorted CD19+ B cells from spleen were used.

value: BBC2 pro-/pre B cell


title: BBC2

description: miRNA profiling

source_name: BBC2 cell line

value: normal B cell


title: microRNA profile of case T526


title: 6W_old_rosette_leaves_non_acclimated_replicate_2 [Can-0_NA_R2]


title: microRNA profile of case T524


title: Macrophage cell, D6 Male, IFN 24 h, 1 Untreated


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_3 [Can-0_ACC_R3]

description: Gene expression for 2 weeks cold acclimated Can-0 rosette leaves at 4 °C. RNA was hybridized on Agilent Arabidopsis expression array


title: HeLa-Noco-8hr

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

hyb_protocol: The biotin-labeled sample were hybridized for 16 hr at 48C and 60 rpm on GeneChip miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fluidics script FS450_0003.

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

data_processing: The data were analyzed with miRNA QC tool 1.0.0.30 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HeLa_8hr after release from thymidine-nocodazole block

label_protocol: Biotin-labeled RNA were prepared according to the FlashTag Biotin HSR Kit Affymetrix protocol from 1 ug total RNA (FlashTag Manual, Affymetrix).

growth_protocol: HeLa cells were grown in RPMI supplemented with 10% FBS.

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

treatment_protocol: Cells were synchronized in G2/M phase by a thymdine-nocodazole block (Petersen 1999). Cells were treated with 2mM thymidine for 18hr and released into fresh media containing 10% FBS for 9hr, and 100ng/ml nocodazole was added for an additional 17hr. Entry into G2/M phase was monitored by cell cycle profiles and FACS analysis. After second block, Nocodazole was removed by washing with 1X PBS two times and cells were released with fresh 10% FBS containing media. And then released cells prepared at the indicated hours.

tag: cell line

value: HeLa

value: Cervical cancer cells

tag: phase

value: S phase


title: microRNA profile of case T521


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_1 [Can-0_ACC_R1]


title: microRNA profile of case T519


title: 6W_old_rosette_leaves_2W_cold_acclimated_replicate_2 [Can-0_ACC_R2]


title: microRNA profile of case T520


title: Macrophage cell, D6 Male, IFN 07 h, 7 Prednisolone

value: IFN 07 h


title: microRNA profile of case T52


title: Macrophage cell, D6 Male, IFN 24 h, 2 CTRL

value: 2 CTRL


title: 6W_old_rosette_leaves_non_acclimated_replicate_3 [Can-0_NA_R3]

value: rosette leaves


title: HeLa-Noco-0hr

source_name: HeLa_immediately after release from thymidine-nocodazole block

value: G2/M phase


title: HeLa-Noco-12hr

source_name: HeLa_12hr after release from thymidine-nocodazole block


title: HeLa-nonsynchronous

description: HeLa-NS

value: mixed (non_synchronized)


title: HeLa-Noco-7hr

source_name: HeLa_7hr after release from thymidine-nocodazole block


title: Macrophage cell, D6 Male, IFN 07 h, 6 Indomethacin

value: blood

value: monocyte derived macrophage

value: M


title: Macrophage cell, D6 Male, IFN 07 h, 2 CTRL


title: Macrophage cell, D6 Male, IFN 07 h, 1 Untreated


title: Macrophage cell, D6 Male, IFN 07 h, 5 Anti-TNFa


title: Macrophage cell, D6 Male, 24 h Untreated, 7 Prednisolone

value: 24 h No inflammation

value: 7 Prednisolone


title: RNL_CTDNA_1

city: Seattle

first: Daniel

middle: B

last: Stetson

state: WA

address: 750 Republican St

department: Immunology

institute: University of Washington

description: replicate 1

hyb_protocol: Biotin-labelled cRNA was hybridized using the standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using an Illumina HiScan scanner.

data_processing: Data were normalized using quantile normalization with Illumina Genome Studio software

source_name: BMDM, calf thymus DNA, 6 hours

label_protocol: Biotin-labelled cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Bone marrow-derived macrophages (BMDMs) were generated and cultured as described (Lau et al., 2015, PMID 26405230).

extract_protocol: RNA was extracted using RNA-Bee reagent, followed by clean-up using a Qiagen RNeasy kit.

treatment_protocol: BMDMs were seeded  in a 12-well plate and transfected with 5 μg calf thymus DNA, or 1 μg RIG-I ligand per well using Lipofectamine 2000 (Life Technologies) for 6 hours.

tag: strain

tag: genotype

value: Rnasel-/-


title: microRNA profile of case T518

value: breast cancer


title: RNL_RIGI_3

description: replicate 3

source_name: BMDM, RIG-I ligand, 6 hours


title: RNL_CTDNA_3

description: replicate 3


title: RNL_RIGI_2

description: replicate 2


title: RNL_NoTX_3

description: replicate 3

source_name: BMDM, untreated


title: RNL_RIGI_1

description: replicate 1


title: microRNA profile of case T516


title: RNL_CTDNA_2

description: replicate 2


title: microRNA profile of case T515


title: microRNA profile of case T514


title: Macrophage cell, D6 Male, 24 h Untreated, 2 CTRL


title: Macrophage cell, D6 Male, 24 h Untreated, 6 Indomethacin

value: 6 Indomethacin


title: Macrophage cell, D6 Male, 24 h Untreated, 5 Anti-TNFa

value: 5 Anti-TNFa


title: WT_CTDNA_1

description: replicate 1

value: wild-type


title: RNL_NoTX_2

description: replicate 2


title: microRNA profile of case T517


title: WT_RIGI_2

description: replicate 2


title: microRNA profile of case T513


title: WT_CTDNA_2

description: replicate 2


title: Macrophage cell, D6 Male, 24 h Untreated, 1 Untreated

value: 1 UNT


title: WT_RIGI_1

description: replicate 1


title: WT_RIGI_3

description: replicate 3


title: RNL_NoTX_1

description: replicate 1


title: WT_CTDNA_3

description: replicate 3


title: microRNA profile of case T512


title: microRNA profile of case T511


title: microRNA profile of case T510


title: microRNA profile of case T51


title: microRNA profile of case T508


title: Macrophage cell, D5 Female, LPS 24 h, 6 Indomethacin

value: F

value: LPS 24 h


title: microRNA profile of case T509


title: Macrophage cell, D5 Female, LPS 24 h, 7 Prednisolone


title: WT_NoTX_1

description: replicate 1


title: 25mo Callus, 20dpf, biological rep3

city: Philadelphia

first: Jaimo

last: Ahn

state: PA

department: Orthopaedic Surgery

institute: University of Pennsylvania

description:
25mo_20d_42
Gene expression data from 25mo Mus musculus bone callus harvested 20dpf

hyb_protocol: The microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal. Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters.

data_processing: Partek Genomics Suite was used for normalization of microarrays; Partek’s Combat feature was used to adjust for batch effects as samples were run in two batches using an identical protocol.  ANOVA and pairwise comparisons (Partek “contrasts”) were computed within Partek (provided in the 'complete_data.txt' file).

label_protocol: 50ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated an RNA priming region.  Second-strand cDNA synthesis was followed by ribo-SPIA linear amplification of each transcript using an isothermal reaction with RNase, RNA primer and DNA polymerase, and the resulting ssDNA was assessed by Bioanalyzer, fragmented and biotinylated by terminal transferase end labeling. Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645.

growth_protocol: All mice were obtained from the NIH aged rodent colony at 5 months and 25 months

extract_protocol: For RNA extraction, after the mouse was euthanized the samples (either whole bone or just callus) were lysed in TriZOL (ThermoFisher, Waltham, MA) then homogenized via tissue tearor, and, finally, frozen to release RNA. RNA quality was assed via Agilent Bioanalyzer 2100.

treatment_protocol: mice were administered buprenorphine and isoflurane, their legs were prepared aseptically, prestabilized with an intramedullary pin (the same sized pin was used for all animals), and a traumatic closed  fracture  was  created  with  a blunt guillotine  (three-point  bend  mechanism).  The mice were allowed to move freely and given buprenorphine/Nutella ® (Ferrero USA, Inc, Somerset, NJ, USA) for 3 additional days and euthanized via CO2 inhalation and cervical dislocation.

tag: age

tag: dpf (days post fracture)

value: Bone fracture callus


title: WT_NoTX_3

description: replicate 3


title: WT_NoTX_2

description: replicate 2


title: Macrophage cell, D5 Female, LPS 24 h, 2 CTRL

value: 2 CTRL


title: Macrophage cell, D5 Female, LPS 07 h, 6 Indomethacin

value: LPS 07 h


title: 25mo Callus, 20dpf, biological rep4

description:
25mo_20d_44
Gene expression data from 25mo Mus musculus bone callus harvested 20dpf


title: 25mo Callus, 20dpf, biological rep2

description:
25mo_20d_41
Gene expression data from 25mo Mus musculus bone callus harvested 20dpf


title: 25mo Callus, 20dpf, biological rep5

description:
25mo_20d_45
Gene expression data from 25mo Mus musculus bone callus harvested 20dpf


title: 25mo Callus, 10dpf, biological rep4

description:
25mo_10d_97L
Gene expression data from 25mo Mus musculus bone callus harvested 10dpf


title: Macrophage cell, D5 Female, LPS 24 h, 5 Anti-TNFa


title: microRNA profile of case T507


title: 25mo Callus, 10dpf, biological rep3

description:
25mo_10d_38L
Gene expression data from 25mo Mus musculus bone callus harvested 10dpf


title: Macrophage cell, D5 Female, LPS 24 h, 1 Untreated


title: Macrophage cell, D5 Female, LPS 07 h, 5 Anti-TNFa


title: 25mo Callus, 20dpf, biological rep1

description:
25mo_20d_40
Gene expression data from 25mo Mus musculus bone callus harvested 20dpf


title: 25mo Callus, 5dpf, biological rep4

description:
25mo_5d_H194L
Gene expression data from 25mo Mus musculus bone callus harvested 5dpf


title: 25mo Callus, 10dpf, biological rep5

description:
25mo_10d_99L
Gene expression data from 25mo Mus musculus bone callus harvested 10dpf


title: 25mo Callus, 5dpf, biological rep5

description:
25mo_5d_H195L
Gene expression data from 25mo Mus musculus bone callus harvested 5dpf


title: 25mo Callus, 10dpf, biological rep1

description:
25mo_10d_095R
Gene expression data from 25mo Mus musculus bone callus harvested 10dpf


title: 25mo Callus, 5dpf, biological rep3

description:
25mo_5d_H193R
Gene expression data from 25mo Mus musculus bone callus harvested 5dpf


title: 25mo Callus, 5dpf, biological rep2

description:
25mo_5d_H192R
Gene expression data from 25mo Mus musculus bone callus harvested 5dpf


title: Macrophage cell, D5 Female, LPS 07 h, 7 Prednisolone


title: 25mo Callus, 10dpf, biological rep2

description:
25mo_10d_37L
Gene expression data from 25mo Mus musculus bone callus harvested 10dpf


title: 25mo Callus, 5dpf, biological rep1

description:
25mo_5d_67L
Gene expression data from 25mo Mus musculus bone callus harvested 5dpf


title: microRNA profile of case T506


title: Macrophage cell, D5 Female, LPS 07 h, 2 CTRL


title: microRNA profile of case T505


title: microRNA profile of case T504


title: microRNA profile of case T503


title: Macrophage cell, D5 Female, LPS 07 h, 1 Untreated


title: microRNA profile of case T501


title: 25mo Callus, 0dpf, biological rep6

description:
25mo_0d_NON71
Gene expression data from 25mo Mus musculus bone callus harvested 0dpf


title: microRNA profile of case T50


title: Macrophage cell, D5 Female, IFN 24 h, 5 Anti-TNFa

value: IFN 24 h


title: 25mo Callus, 0dpf, biological rep4

description:
25mo_0d_NO69
Gene expression data from 25mo Mus musculus bone callus harvested 0dpf


title: 25mo Callus, 0dpf, biological rep3

description:
25mo_0d_79R
Gene expression data from 25mo Mus musculus bone callus harvested 0dpf


title: 25mo Callus, 0dpf, biological rep2

description:
25mo_0d_78L
Gene expression data from 25mo Mus musculus bone callus harvested 0dpf


title: Macrophage cell, D5 Female, IFN 24 h, 6 Indomethacin

value: blood


title: Macrophage cell, D5 Female, IFN 24 h, 7 Prednisolone

value: monocyte derived macrophage


title: 5mo Callus, 20dpf, biological rep5

description:
5mo_20d_36
Gene expression data from 5mo Mus musculus bone callus harvested 20dpf


title: 25mo Callus, 0dpf, biological rep5

description:
25mo_0d_NO70
Gene expression data from 25mo Mus musculus bone callus harvested 0dpf


title: 25mo Callus, 0dpf, biological rep1

description:
25mo_0d_47L
Gene expression data from 25mo Mus musculus bone callus harvested 0dpf


title: microRNA profile of case T502


title: microRNA profile of case T499


title: 5mo Callus, 20dpf, biological rep1

description:
5mo_20d_30
Gene expression data from 5mo Mus musculus bone callus harvested 20dpf


title: 5mo Callus, 20dpf, biological rep4

description:
5mo_20d_35
Gene expression data from 5mo Mus musculus bone callus harvested 20dpf


title: 5mo Callus, 10dpf, biological rep5

description:
5mo_10d_93L
Gene expression data from 5mo Mus musculus bone callus harvested 10dpf


title: Macrophage cell, D5 Female, IFN 24 h, 2 CTRL


title: Macrophage cell, D5 Female, IFN 07 h, 7 Prednisolone

value: IFN 07 h


title: 5mo Callus, 20dpf, biological rep3

description:
5mo_20d_34
Gene expression data from 5mo Mus musculus bone callus harvested 20dpf


title: 5mo Callus, 10dpf, biological rep3

description:
5mo_10d_90L
Gene expression data from 5mo Mus musculus bone callus harvested 10dpf


title: 5mo Callus, 10dpf, biological rep4

description:
5mo_10d_92R
Gene expression data from 5mo Mus musculus bone callus harvested 10dpf


title: Macrophage cell, D5 Female, IFN 24 h, 1 Untreated


title: 5mo Callus, 20dpf, biological rep2

description:
5mo_20d_33
Gene expression data from 5mo Mus musculus bone callus harvested 20dpf


title: 5mo Callus, 10dpf, biological rep2

description:
5mo_10d_29L
Gene expression data from 5mo Mus musculus bone callus harvested 10dpf


title: microRNA profile of case T498


title: Macrophage cell, D5 Female, IFN 07 h, 6 Indomethacin


title: microRNA profile of case T497


title: 5mo Callus, 5dpf, biological rep5

description:
5mo_5d_P46L
Gene expression data from 5mo Mus musculus bone callus harvested 5dpf


title: microRNA profile of case T495


title: microRNA profile of case T494


title: microRNA profile of case T493


title: 5mo Callus, 5dpf, biological rep4

description:
5mo_5d_H191L
Gene expression data from 5mo Mus musculus bone callus harvested 5dpf


title: microRNA profile of case T491


title: 5mo Callus, 5dpf, biological rep3

description:
5mo_5d_H190L
Gene expression data from 5mo Mus musculus bone callus harvested 5dpf


title: microRNA profile of case T492


title: Macrophage cell, D5 Female, IFN 07 h, 2 CTRL


title: 5mo Callus, 10dpf, biological rep1

description:
5mo_10d_27L
Gene expression data from 5mo Mus musculus bone callus harvested 10dpf


title: microRNA profile of case T496


title: Macrophage cell, D5 Female, 24 h Untreated, 7 Prednisolone

value: 24 h No inflammation


title: 5mo Callus, 0dpf, biological rep2

description:
5mo_0d_76R
Gene expression data from 5mo Mus musculus bone callus harvested 0dpf


title: 5mo Callus, 0dpf, biological rep5

description:
5mo_0d_H199
Gene expression data from 5mo Mus musculus bone callus harvested 0dpf


title: Macrophage cell, D5 Female, IFN 07 h, 1 Untreated


title: 5mo Callus, 0dpf, biological rep3

description:
5mo_0d_77R
Gene expression data from 5mo Mus musculus bone callus harvested 0dpf


title: 5mo Callus, 0dpf, biological rep4

description:
5mo_0d_H198
Gene expression data from 5mo Mus musculus bone callus harvested 0dpf


title: Macrophage cell, D5 Female, 24 h Untreated, 6 Indomethacin


title: Macrophage cell, D5 Female, IFN 07 h, 5 Anti-TNFa


title: 5mo Callus, 0dpf, biological rep1

description:
5mo_0d_081L
Gene expression data from 5mo Mus musculus bone callus harvested 0dpf


title: 5mo Callus, 5dpf, biological rep2

description:
5mo_5d_H189L
Gene expression data from 5mo Mus musculus bone callus harvested 5dpf


title: Macrophage cell, D5 Female, 24 h Untreated, 5 Anti-TNFa


title: 5mo Callus, 5dpf, biological rep1

description:
5mo_5d_H188R
Gene expression data from 5mo Mus musculus bone callus harvested 5dpf


title: GFP-CXCR5+PD1-_3

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: Fragmented cRNAs were hybridized to the standard arrays for 17 hours at 45°C, the arrays were then washed and stained using the fluidics station according to genechip array manufacturer's protocol

scan_protocol: The chips were scanned using GeneChip Scanner 3000. The images were analyzed using Expression Console and standard array quality controls analyses were carried out according to the instructions provided by Affymetrix.

data_processing: Data was analyzed with RMA/quantile normalization in r v 2.13.0 in bioconductor using the oligo package

source_name: CD4+ from Payers patches

label_protocol: cDNA were prepared according to the Ambion® WT Expression Kit's protocol from 100ng Total RNA. 5.5ug of cDNA were fragmented and labelled according to Affymetrix GeneChip® WT Terminal Labeling and Hybridization kit's protocol.

growth_protocol: Primary isolates from mouse

extract_protocol: Total RNA was extracted using miRNeasy Mini Kits (Qiagen). RNA Integrity Number (RIN) was assessed by Agilent Bioanalyzer (Agilent Technologies). All RNA samples were RIN≥9.2.

treatment_protocol: Single cell suspensions were prepared from Peyer’s Patches of IL-21eGFP mice. The cells were first incubated with unlabelled anti-CD16/32 antibodies, and subsequently with fluorescently labelled antibodies to CD4, CXCR5, PD-1, Epcam, and MHC II. An MHCII-negative Epcam-negative CD4+ gate was used to sort CXCR5+PD-1+GFP+Tfh, CXCR5+PD-1+GFP-Tfh and CXCR5-PD-1-  cell populations using an LSRII 4-laser cell sorter.

value: T follicular helper

value: Peyer's  patches

tag: gfp


title: Macrophage cell, D5 Female, 24 h Untreated, 2 CTRL


title: GFP-CXCR5-PD1-_3


title: GFP-CXCR5+PD1+_3


title: GFP-CXCR5+PD1-_2


title: GFP-CXCR5-PD1-_2


title: GFP+CXCR5+PD1+_3


title: Macrophage cell, D4 Male, LPS 24 h, 7 Prednisolone

value: M

value: 7 Prednisolone


title: microRNA profile of case T490

value: breast cancer


title: Macrophage cell, D5 Female, 24 h Untreated, 1 Untreated


title: GFP-CXCR5+PD1+_2


title: microRNA profile of case T489


title: microRNA profile of case T49


title: microRNA profile of case T487


title: microRNA profile of case T486


title: microRNA profile of case T485


title: microRNA profile of case T484


title: Macrophage cell, D4 Male, LPS 24 h, 4 Nortriptyline

value: 4 Nortriptyline


title: Macrophage cell, D4 Male, LPS 24 h, 3 Escitalopram

value: 3 Escitalopram


title: GFP-CXCR5+PD1-_1


title: microRNA profile of case T483


title: GFP+CXCR5+PD1+_2


title: Macrophage cell, D4 Male, LPS 24 h, 6 Indomethacin

value: 6 Indomethacin


title: GFP-CXCR5+PD1+_1


title: microRNA profile of case T481


title: skin 24h post treatment, biological rep2

city: Tuebingen

first: Regina

last: Heidenreich

address: Paul-Ehrlich-Str 15

institute: CureVac GmbH

description: Gene expression data from murine skin collected 24h after intradermal injection of RNAdjuvant.

hyb_protocol: Following fragmentation, 2 ug of cDNA were hybridized for 18 h on Affymetrix GeneChip® Mouse Gene 1.0 Arrays in the GeneChip® Hybridization Oven 450. Washing and staining of the arrays was done in the GeneChip® Fluidics Station 450.

scan_protocol: Scanning was done using Affymetrix GeneChip® Scanner 3000.

data_processing: Data generation was controlled by the Affymetrix GeneChip® Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application. The data of the two experiments have been normalized individually using the RMA method as integrated in the transcriptomics analysis software Mayday. Log fold change was calculated according following equation: Log fold change= ((Average log expression values time 1.5h or 6h or 24h) – (Average log expression values reference time point with no treatment)).

source_name: Mus musculus skin 24h upon RNAdjuvant treatment

label_protocol: For biotin labelling 2.0 μg of each amplified cDNA was processed with the NuGEN Encore Biotin Module. All sample processing procedures were performed according the user manuals.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit according to the user manual including DNase treatment. 50 ng of total RNA was used for the amplification which was performed with the Ovation™ Pico SL WTA System.

treatment_protocol: Mice were injected intradermally with 25mg RNAdjuvant, control mice were left untreated. Skin biopsies were isolated 1.5, 6 or 24h post treatment with RNAdjuvant and the tissue was immediately preserved in RNAlater.

value: skin

tag: time

tag: treatment

value: RNAdjuvant

tag: gender

value: female

value: Balb/c


title: skin 6h post treatment, biological rep2

description: Gene expression data from murine skin collected 6h after intradermal injection of RNAdjuvant.

source_name: Mus musculus skin 6h upon RNAdjuvant treatment

value: 6 h


title: GFP+CXCR5+PD1+_1

tag: cell type


title: GFP-CXCR5-PD1-_1

tag: tissue


title: skin 1.5h post treatment, biological rep2

description: Gene expression data from murine skin collected 1.5h after intradermal injection of RNAdjuvant.

source_name: Mus musculus skin 1.5h upon RNAdjuvant treatment


title: skin 24h post treatment, biological rep3


title: Macrophage cell, D4 Male, LPS 24 h, 2 CTRL

value: blood

value: LPS 24 h

value: 2 CTRL


title: skin 1.5h post treatment, biological rep3


title: Macrophage cell, D4 Male, LPS 24 h, 1 Untreated

value: monocyte derived macrophage

value: 1 UNT


title: Macrophage cell, D4 Male, LPS 24 h, 5 Anti-TNFa

value: 5 Anti-TNFa


title: skin 24h post treatment, biological rep1


title: Macrophage cell, D4 Male, LPS 07 h, 7 Prednisolone

value: M

value: LPS 07 h


title: skin 1.5h post treatment, biological rep1


title: skin not treated, biological rep3

description: Gene expression data from murine skin not treated with RNAdjuvant.

source_name: Mus musculus skin without treatment

value: control

value: untreated


title: skin 6h post treatment, biological rep3


title: skin 6h post treatment, biological rep1


title: microRNA profile of case T478

source_name: breast cancer

tag: survival

value: breast cancer


title: microRNA profile of case T480


title: microRNA profile of case T48


title: Macrophage cell, D4 Male, LPS 07 h, 6 Indomethacin

tag: donor

value: 6 Indomethacin


title: Macrophage cell, D4 Male, LPS 07 h, 4 Nortriptyline

tag: Sex

value: 4 Nortriptyline


title: skin not treated, biological rep1

value: skin


title: Macrophage cell, D4 Male, LPS 07 h, 5 Anti-TNFa

tag: inflammatory stimulus


title: microRNA profile of case T475


title: Patient 202 -skin - Placebo - Day28

city: Boston

first: Julio

middle: C

last: Mantero

state: MA

address: 72 E Concord St

department: Rheumatology

institute: Boston University School of Medicine

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip HG-U133A 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: processed using affy package for R, using MAS5 normalization

source_name: human skin

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: Skin bioeise placed in RNAlater at bedside were stored at -80 degrees C until processing. RNA was exrtacted by homogenization in RLT Buffe and purifying over Rneasy columns

treatment_protocol: Each subject forearm was randomized to either treatment or placebo and treated for 28 days.

tag: timepoint

value: Placebo


title: microRNA profile of case T476


title: Patient 203 -skin - C82 - Day28


title: Macrophage cell, D4 Male, LPS 07 h, 3 Escitalopram

source_name: human monocyte derived macrophage

tag: drug treatment

value: 3 Escitalopram


title: Patient 203 -skin - C82 - Baseline

value: Baseline


title: microRNA profile of case T479


title: microRNA profile of case T477


title: skin not treated, biological rep2

value: female

value: Balb/c


title: Patient 202 -skin - Placebo - Baseline


title: Patient 202 -skin - C82 - Day28


title: Patient 203 -skin - Placebo - Day28


title: Patient 203 -skin - Placebo - Baseline


title: Macrophage cell, D4 Male, IFN 24 h, 7 Prednisolone

value: blood

value: IFN 24 h

value: 7 Prednisolone


title: Patient 201 -skin - C82 - Day28


title: Patient 201 -skin - Placebo - Day28


title: Macrophage cell, D4 Male, IFN 24 h, 6 Indomethacin

value: monocyte derived macrophage


title: Macrophage cell, D4 Male, LPS 07 h, 1 Untreated

value: M

value: 1 UNT


title: Macrophage cell, D4 Male, LPS 07 h, 2 CTRL

value: LPS 07 h

value: 2 CTRL


title: Patient 201 -skin - Placebo - Baseline


title: Patient 201 -skin - C82 - Baseline


title: microRNA profile of case T474

value: breast cancer


title: Patient 202 -skin - C82 - Baseline


title: Patient 303 -skin - Placebo - Day28


title: microRNA profile of case T471


title: microRNA profile of case T473


title: microRNA profile of case T470


title: microRNA profile of case T47


title: Patient 303 -skin - C82 - Day28


title: microRNA profile of case T472


title: microRNA profile of case T469


title: Patient 306 -skin - Placebo - Baseline


title: Macrophage cell, D4 Male, IFN 24 h, 4 Nortriptyline


title: Patient 305 -skin - C82 - Day28


title: Patient 306 -skin - C82 - Day28


title: Patient 302 -skin - Placebo - Day28


title: Macrophage cell, D4 Male, IFN 07 h, 7 Prednisolone

value: IFN 07 h


title: Patient 303 -skin - C82 - Baseline


title: Patient 305 -skin - Placebo - Baseline


title: Macrophage cell, D4 Male, IFN 24 h, 2 CTRL


title: Macrophage cell, D4 Male, IFN 24 h, 3 Escitalopram


title: microRNA profile of case T468


title: Patient 302 -skin - C82 - Day28


title: Macrophage cell, D4 Male, IFN 07 h, 6 Indomethacin

value: 6 Indomethacin


title: Patient 306 -skin - C82 - Baseline


title: Patient 306 -skin - Placebo - Day28


title: Patient 302 -skin - Placebo - Baseline


title: Patient 305 -skin - C82 - Baseline


title: Macrophage cell, D4 Male, IFN 24 h, 5 Anti-TNFa

value: 5 Anti-TNFa


title: Patient 303 -skin - Placebo - Baseline

value: Placebo


title: Macrophage cell, D4 Male, IFN 07 h, 5 Anti-TNFa


title: microRNA profile of case T467


title: Patient 305 -skin - Placebo - Day28


title: Macrophage cell, D4 Male, IFN 24 h, 1 Untreated


title: Patient 302 -skin - C82 - Baseline


title: Patient 301 -skin - C82 - Day28


title: microRNA profile of case T466


title: Patient 304 -skin - C82 - Day28


title: Patient 304 -skin - Placebo - Day28


title: Macrophage cell, D4 Male, IFN 07 h, 4 Nortriptyline

value: 4 Nortriptyline


title: Macrophage cell, D4 Male, IFN 07 h, 2 CTRL


title: Patient 301 -skin - Placebo - Baseline

value: Baseline


title: Patient 304 -skin - C82 - Baseline


title: microRNA profile of case T462


title: microRNA profile of case T460


title: microRNA profile of case T464


title: microRNA profile of case T463


title: Macrophage cell, D4 Male, 24 h Untreated, 7 Prednisolone

value: 24 h No inflammation


title: Macrophage cell, D4 Male, 24 h Untreated, 6 Indomethacin


title: Patient 304 -skin - Placebo - Baseline


title: Patient 104 -skin - Placebo - Day28


title: Patient 104 -skin - Placebo - Baseline


title: Patient 301 -skin - Placebo - Day28


title: Patient 108 -skin - C82 - Day28


title: microRNA profile of case T46


title: Macrophage cell, D4 Male, IFN 07 h, 3 Escitalopram

value: 3 Escitalopram


title: Patient 104 -skin - C82 - Day28


title: Macrophage cell, D4 Male, IFN 07 h, 1 Untreated

value: blood


title: Patient 108 -skin - Placebo - Baseline


title: Patient 108 -skin - Placebo - Day28


title: Patient 104 -skin - C82 - Baseline


title: microRNA profile of case T459


title: Patient 108 -skin - C82 - Baseline


title: microRNA profile of case T461


title: Patient 103 -skin - Placebo - Day28


title: Macrophage cell, D4 Male, 24 h Untreated, 4 Nortriptyline


title: Macrophage cell, D4 Male, 24 h Untreated, 3 Escitalopram


title: Patient 103 -skin - C82 - Day28


title: Patient 107 -skin - C82 - Baseline


title: Macrophage cell, D4 Male, 24 h Untreated, 5 Anti-TNFa


title: microRNA profile of case T457


title: Patient 107 -skin - Placebo - Day28


title: Patient 103 -skin - Placebo - Baseline


title: microRNA profile of case T456


title: Patient 103 -skin - C82 - Baseline


title: Patient 107 -skin - Placebo - Baseline


title: microRNA profile of case T455


title: microRNA profile of case T453


title: microRNA profile of case T454


title: Patient 102 -skin - Placebo - Day28


title: Macrophage cell, D4 Male, 24 h Untreated, 1 Untreated


title: Patient 106 -skin - C82 - Day28


title: Patient 106 -skin - Placebo - Day28


title: Patient 102 -skin - Placebo - Baseline


title: Macrophage cell, D3 Female, LPS 24 h, 7 Prednisolone

value: F

value: LPS 24 h


title: microRNA profile of case T451


title: microRNA profile of case T452


title: Patient 102 -skin - C82 - Day28


title: microRNA profile of case T45


title: Patient 106 -skin - Placebo - Baseline


title: Macrophage cell, D3 Female, LPS 24 h, 5 Anti-TNFa

value: monocyte derived macrophage


title: Patient 106 -skin - C82 - Baseline


title: Patient 101 -skin - C82 - Day28


title: Patient 102 -skin - C82 - Baseline


title: Macrophage cell, D4 Male, 24 h Untreated, 2 CTRL

value: M


title: Macrophage cell, D3 Female, LPS 24 h, 3 Escitalopram


title: Patient 101 -skin - Placebo - Day28


title: Patient 101 -skin - C82 - Baseline


title: Macrophage cell, D3 Female, LPS 24 h, 2 CTRL


title: Patient 105 -skin - Placebo - Day28


title: microRNA profile of case T449


title: Patient 105 -skin - C82 - Day28


title: microRNA profile of case T448


title: Macrophage cell, D3 Female, LPS 07 h, 7 Prednisolone

value: 7 Prednisolone


title: Patient 105 -skin - C82 - Baseline


title: Patient 105 -skin - Placebo - Baseline


title: microRNA profile of case T447


title: Macrophage cell, D3 Female, LPS 24 h, 1 Untreated

value: 1 UNT


title: Macrophage cell, D3 Female, LPS 07 h, 6 Indomethacin

value: LPS 07 h


title: zebrafish, anterior intestine, fasted

type: SAGE

anchor: NlaIII

city: Talence

first: Patrick

middle: J.

last: BABIN

address: Avenue des facultés

department: UFR Biologie

country: France

institute: Université Bordeaux

description: 50 micrograms of total RNAs of the pool of 6 animals were used to generate the SAGE library using the I-SAGE kit (Invitrogen, Cergy Pointoise, France).

data_processing: SAGE-tag extraction, counting and quality control were undertaken by Skuld-Tech (Montpellier, France, http://www.skuldtech.com)

organism: Danio rerio

source_name: anterior intestine, fasted

extract_protocol: The anterior intestine was isolated from 6 animals. Total RNA were extracted from the intestines with the Nucleospin RNAII kit (Machery-Nagel, Hoerdt, France).

treatment_protocol: Adult zebrafish were deprived of food during 22 hours.

value: wild type

tag: developmental stage

value: adult

value: anterior intestine

value: fasted


title: Macrophage cell, D3 Female, LPS 07 h, 5 Anti-TNFa

value: 5 Anti-TNFa


title: microRNA profile of case T440

value: breast cancer


title: microRNA profile of case T441


title: microRNA profile of case T437


title: Macrophage cell, D3 Female, LPS 07 h, 3 Escitalopram


title: microRNA profile of case T443


title: microRNA profile of case T436


title: Macrophage cell, D3 Female, LPS 07 h, 2 CTRL

value: 2 CTRL


title: hiPSC_Clone-HD2-EXCGC_R1

city: Kiel

first: Franz-Josef

last: Müller

address: Niemannsweg 147

department: Klinik für Psychiatrie und Psychotherapie

institute: Zentrum für Integrative Psychiatrie Kiel

description:
replicate 1
Fibroblasts_IMR90

hyb_protocol: standard protocol according to vendor guidlines (www.illumina.com)

data_processing: data was extracted with GenomeStudio 2010 with no background correction, VST transformation and RSN normalization (both as provided by the lumi R/Bioconductor package)

source_name: induced pluripotent stem cells

growth_protocol: pluripotent stem cells: WiCell protocol; fibroblast cell lines: DMEM, 10% serum, Pen/Strep

extract_protocol: mRNA extraction kit (Quiagen)

treatment_protocol: steady state proliferating cultures, no additional treatment,

value: induced pluripotent stem cells

tag: tag

value: transgene excised hiPSC


title: Fibroblasts_MRC5

description:
replicate 2
hiPSC_CloneHD2EXCGC_R2

scan_protocol: standard protocol according to vendor guidlines (www.illumina.com)

source_name: fibroblast cell line

tag: cell line

value: fibroblast cell line

value: control Fibroblasts


title: hiPSC_Clone-HD2-EXCGC_R2

description:
replicate 2
Fibroblasts_MRC5

label_protocol: standard protocol according to vendor guidlines (www.illumina.com)


title: Macrophage cell, D3 Female, LPS 07 h, 1 Untreated

value: blood

value: F


title: Fibroblasts_IMR90

description:
replicate 1
hiPSC_CloneHD2EXCGC_R1


title: MOOH48-rep1

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

hyb_protocol: RNA samples were hybridized to the Illumina HumanHT-12 v4 Expression BeadChip using standard protocols per the manufacturer's specifications.

scan_protocol: Chips were scanned using standard protocols per the manufacturer's specifications.

data_processing: Data were analyzed with R language and Bioconductor packages. Microarray data normalization, background correction and quality control were carried out with the Bioconductor package “lumi”. The R package “limma” was used to perform differential gene expression analysis of the normalized microarray data.

label_protocol: RNA samples were labelled using standard protocols per the manufactuerer's specifications.

growth_protocol: U266 cells were grown in media (per ATCC specifications) supplemented with heat-inactivated fetal bovine serum (FBS), glutamine and penicillin-streptomycin at 37 °C and 5% CO2.

extract_protocol: RNA was extracted using Qiagen RNAEasy kit per the manufacturer's specifications.

treatment_protocol: U266 cells were treated with solvent control (DMSO), MOOH-Nap, or SAHA or 24 or 48 hours.

value: multiple myeloma cell line

tag: treated with

value: MO-OH-Nap for 48 hours


title: Patient 101 -skin - Placebo - Baseline

value: Baseline

value: Placebo


title: Macrophage cell, D3 Female, LPS 07 h, 4 Nortriptyline

value: monocyte derived macrophage

value: LPS 07 h

value: 4 Nortriptyline


title: hESC_WA09_R2

description:
replicate 2
hESC_WA09_R2

source_name: embryonic stem cells

value: embryonic stem cells

value: control hESC


title: hESC_WA09_R1

description:
replicate 1
hESC_WA09_R1


title: MOOH48-rep2


title: MOOH24-rep2

value: MO-OH-Nap for 24 hours


title: Macrophage cell, D3 Female, IFN 24 h, 6 Indomethacin

value: IFN 24 h

value: 6 Indomethacin


title: MOOH24-rep3


title: Macrophage cell, D3 Female, IFN 24 h, 7 Prednisolone

value: 7 Prednisolone


title: MOOH24-rep1


title: Macrophage cell, D3 Female, IFN 24 h, 5 Anti-TNFa

value: 5 Anti-TNFa


title: SAHA24-rep2

value: SAHA for 24 hours


title: microRNA profile of case T434

value: breast cancer


title: MOOH48-rep3


title: SAHA24-rep1


title: SAHA24-rep3


title: microRNA profile of case T433


title: Macrophage cell, D3 Female, IFN 24 h, 4 Nortriptyline

value: blood

value: F


title: microRNA profile of case T435


title: Macrophage cell, D3 Female, IFN 24 h, 1 Untreated

value: 1 UNT


title: Con-rep1

value: multiple myeloma cell line

value: DMSO for 24 hours


title: microRNA profile of case T432


title: Con-rep2


title: microRNA profile of case T430


title: Con-rep3


title: microRNA profile of case T43


title: microRNA profile of case T429


title: microRNA profile of case T431


title: Macrophage cell, D3 Female, IFN 24 h, 3 Escitalopram

value: monocyte derived macrophage

value: 3 Escitalopram


title: Treatment 2

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

hyb_protocol: Hybridization using standard hybridization protocols from Illumina for 14h at 58°C

scan_protocol: Standard Illumina protocols for HumanHT-12 V4 chips from Illumina using the Illumina iScanner

data_processing: Background signal was removed using the Detection P value algorithm. Signals were normalized using the cubic spline algorithm. Differential expression was determined using the Illumina Custom Algorithm. Ratios were determined as the fraction between the treatments and the Control group

source_name: Primary effusion lymphoma cell-line BCBL1

label_protocol: cRNA was labeled with the TargetAmp-Nano Labeling kit for Illumina Expression BeadChip (Epicentre),

growth_protocol: The cells were cultured in RPMI 1640 medium (ATCC) supplemented with 20% FBS. All cells were cultured at 37°C in 5% CO2. All experiments were carried out using cells harvested at low (< 20) passages.

extract_protocol: Total RNA was extracted with TriZol

treatment_protocol: The cells were treated with vehicle control or RR inhibitor 3-AP (2.5 µM) for 48 h

tag: agent


title: microRNA profile of case T428


title: Treatment 1

source_name: Primary effusion lymphoma cell-line BCP1


title: Control 2

value: vehicle control


title: Control 1


title: microRNA profile of case T427


title: Macrophage cell, D3 Female, IFN 07 h, 5 Anti-TNFa

value: IFN 07 h


title: Macrophage cell, D3 Female, IFN 24 h, 2 CTRL

value: 2 CTRL


title: Macrophage cell, D3 Female, IFN 07 h, 7 Prednisolone


title: Control 3

source_name: Primary effusion lymphoma cell-line BC1


title: microRNA profile of case T426


title: blood-sublinical tb-10

city: Cape Town

first: Hanif

last: Esmail

address: Anzio Road

country: South Africa

institute: University of Cape Town

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw background subtracted expression data was normalised using GeneSpring GX version 12.6 (Agilent).  Raw signal values <1 were then set to a threshold of 1 and all values were log2 transformed.  Each sample was then normalised using a 75th percentile shift algorithm.  Baseline transformation was then carried out to rescale intensity values to the median of all samples

label: Biotin

source_name: Whole Blood

label_protocol: Globin-reduced RNA was used to prepare and amplify biotinylated, antisense complementary RNA (cRNA) with the TotalPrep RNA Amplification Kit

extract_protocol: Blood was drawn into Tempus Blood RNA tubes and stored between -20C and -80C for no longer than 21 months before RNA extraction.  RNA was extracted using the PerfectPure™ Blood RNA Kit (5 PRIME)  according to maufacturer’s instructions

value: whole blood

tag: hiv status

value: HIV-1 infected

tag: anti-retroviral therapy

value: NO

tag: tb status

value: Subclinical

value: Pre-treatment

tag: study number

value: PET0-037 DO


title: blood-sublinical tb-7

value: PET0-023 DO


title: blood-sublinical tb-8

value: PET0-026 DO


title: blood-sublinical tb-6

value: PET0-013 DO


title: blood-sublinical tb-3

value: PET0-006 DO


title: Macrophage cell, D3 Female, IFN 07 h, 1 Untreated

value: blood

tag: cell type

value: F

value: 1 UNT


title: Macrophage cell, D3 Female, IFN 07 h, 4 Nortriptyline

tag: tissue

value: monocyte derived macrophage

value: 4 Nortriptyline


title: blood-sublinical tb-2

value: PET0-005 DO


title: blood-sublinical tb-9

value: PET0-028 DO


title: blood-sublinical tb-5

value: whole blood

value: PET0-009 DO


title: blood-sublinical tb-4

value: HIV-1 infected

value: NO

value: PET0-007 DO


title: Macrophage cell, D3 Female, IFN 07 h, 3 Escitalopram

value: IFN 07 h

value: 3 Escitalopram


title: microRNA profile of case T425

tag: survival

value: breast cancer


title: blood-sublinical tb-1

value: Subclinical

value: Pre-treatment

value: PET0-001 DO


title: microRNA profile of case T423


title: microRNA profile of case T424


title: Macrophage cell, D3 Female, 24 h Untreated, 7 Prednisolone

value: blood

tag: donor

value: F

value: 24 h No inflammation

value: 7 Prednisolone


title: microRNA profile of case T421


title: blood-latent tb-24

value: Latent

value: PET0-034 DO


title: Macrophage cell, D3 Female, 24 h Untreated, 6 Indomethacin

value: monocyte derived macrophage

tag: Sex

value: 6 Indomethacin


title: blood-latent tb-25

value: whole blood

value: HIV-1 infected

value: PET0-035 DO


title: microRNA profile of case T420


title: blood-latent tb-23

value: NO

value: PET0-033 DO


title: blood-latent tb-20

value: PET0-030 DO


title: blood-latent tb-22

value: PET0-032 DO


title: Macrophage cell, D3 Female, 24 h Untreated, 4 Nortriptyline

tag: inflammatory stimulus

value: 4 Nortriptyline


title: blood-latent tb-19

tag: timepoint

value: Pre-treatment

value: PET0-029 DO


title: microRNA profile of case T42

value: breast cancer


title: microRNA profile of case T419


title: blood-latent tb-17

value: PET0-025 DO


title: blood-latent tb-21

value: PET0-031 DO


title: Macrophage cell, D3 Female, 24 h Untreated, 3 Escitalopram

value: blood

value: F

value: 24 h No inflammation

tag: drug treatment

value: 3 Escitalopram


title: microRNA profile of case T417


title: Macrophage cell, D3 Female, 24 h Untreated, 5 Anti-TNFa

value: monocyte derived macrophage

value: 5 Anti-TNFa


title: Macrophage cell, D3 Female, 24 h Untreated, 2 CTRL

value: 2 CTRL


title: Macrophage cell, D3 Female, 24 h Untreated, 1 Untreated

value: 1 UNT


title: blood-latent tb-15

value: whole blood

value: HIV-1 infected

value: NO

value: Latent

value: PET0-022 DO


title: blood-latent tb-13

value: Pre-treatment

value: PET0-020 DO


title: blood-latent tb-16

value: PET0-024 DO


title: Macrophage cell, D2 Male, LPS 24 h, 6 Indomethacin

value: M

value: LPS 24 h

value: 6 Indomethacin


title: Macrophage cell, D2 Male, LPS 24 h, 7 Prednisolone

value: blood

value: 7 Prednisolone


title: blood-latent tb-18

value: PET0-027 DO


title: blood-latent tb-14

value: PET0-021 DO


title: blood-latent tb-12

value: PET0-019 DO


title: blood-latent tb-11

value: PET0-018 DO


title: microRNA profile of case T415

value: breast cancer


title: microRNA profile of case T414


title: Macrophage cell, D2 Male, LPS 24 h, 5 Anti-TNFa

value: monocyte derived macrophage

value: 5 Anti-TNFa


title: Macrophage cell, D2 Male, LPS 24 h, 4 Nortriptyline

value: 4 Nortriptyline


title: blood-latent tb-10

value: whole blood

value: HIV-1 infected

value: NO

value: Latent

value: PET0-017 DO


title: Macrophage cell, D2 Male, LPS 24 h, 3 Escitalopram

value: M

value: LPS 24 h

value: 3 Escitalopram


title: blood-latent tb-9

value: Pre-treatment

value: PET0-015 DO


title: microRNA profile of case T411


title: blood-latent tb-6

value: PET0-011 DO


title: blood-latent tb-8

value: PET0-014 DO


title: microRNA profile of case T41


title: blood-latent tb-4

value: PET0-008 DO


title: blood-latent tb-7

value: PET0-012 DO


title: blood-latent tb-2

value: PET0-003 DO


title: blood-latent tb-3

value: PET0-004 DO


title: blood-latent tb-1

value: PET0-002 DO


title: microRNA profile of case T408

value: breast cancer


title: Macrophage cell, D2 Male, LPS 24 h, 1 Untreated

value: blood

value: monocyte derived macrophage

value: 1 UNT


title: microRNA profile of case T413


title: blood-active tb-15

value: whole blood

value: HIV-1 infected

value: NO

value: Active

value: PET0-921 DO


title: blood-latent tb-5

value: Latent

value: Pre-treatment

value: PET0-010 DO


title: microRNA profile of case T406


title: blood-active tb-13

value: PET0-919 DO


title: microRNA profile of case T404


title: microRNA profile of case T401


title: microRNA profile of case T402


title: blood-active tb-12

value: PET0-918 DO


title: Macrophage cell, D2 Male, LPS 07 h, 7 Prednisolone

value: M

value: LPS 07 h

value: 7 Prednisolone


title: blood-active tb-14

value: PET0-920 DO


title: Macrophage cell, D2 Male, LPS 07 h, 4 Nortriptyline

value: blood

value: 4 Nortriptyline


title: microRNA profile of case T4

value: breast cancer


title: blood-active tb-10

value: whole blood

value: PET0-916 DO


title: blood-active tb-11

value: HIV-1 infected

value: NO

value: PET0-917 DO


title: Treatment 3


title: Macrophage cell, D2 Male, LPS 07 h, 5 Anti-TNFa

value: monocyte derived macrophage

value: 5 Anti-TNFa


title: microRNA profile of case T399


title: blood-active tb-6

value: Active

value: Pre-treatment

value: PET0-911 DO


title: Macrophage cell, D2 Male, LPS 07 h, 3 Escitalopram

value: M

value: 3 Escitalopram


title: blood-active tb-7

value: PET0-912 DO


title: blood-active tb-9

value: PET0-915 DO


title: blood-active tb-8

value: PET0-913 DO


title: microRNA profile of case T40


title: blood-active tb-5

value: PET0-910 DO


title: blood-active tb-4

value: PET0-905 DO


title: blood-active tb-3

value: whole blood

value: PET0-904 DO


title: Macrophage cell, D2 Male, LPS 07 h, 2 CTRL

value: blood

value: LPS 07 h

value: 2 CTRL


title: Macrophage cell, D2 Male, LPS 07 h, 1 Untreated

value: monocyte derived macrophage

value: 1 UNT


title: microRNA profile of case T398

value: breast cancer


title: Macrophage cell, D2 Male, IFN 24 h, 7 Prednisolone

value: IFN 24 h

value: 7 Prednisolone


title: blood-active tb-2

value: HIV-1 infected

value: NO

value: Active

value: Pre-treatment

value: PET0-903 DO


title: blood-active tb-1

value: PET0-901 DO


title: microRNA profile of case T394


title: microRNA profile of case T396


title: Macrophage cell, D2 Male, LPS 24 h, 2 CTRL

value: M

value: LPS 24 h


title: microRNA profile of case T393


title: microRNA profile of case T391


title: microRNA profile of case T392


title: LNTP_pTfh_CFSEneg [9287078050_F]

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

institute: Case Western Reserve University

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R (v.2.15.2) statistical language and various software packages from Bioconductor (v.2.11) by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: PBMCs from EC and CA subjects were labeled with CFSE and both CFSE+ circulating memory Tfh cells and memory B cells were sorted and placed in coculture at equal numbers in the presence of 100ng/ml of SEB. After 5 days the CFSElo and CFSEhi memory Tfh cells population was sorted for gene array analysis.

extract_protocol: After 5 days in coculture CFSElo and CFSEhi circulating memory Tfh cells were sorted into 2X buffer for RNA extraction. Reverse transcription reactions were performed to obtain cDNAs which were hybridized to the Illumina Human HT-12 version 4 Expression BeadChip according to the manufacturer’s instruction, and quantified using an Illumina iScan System. The data were collected with Illumina GenomeStudio software. Analysis of the genome array output data was conducted using the R statistical language and the Limma statistical package from Bioconductor.

treatment_protocol: CFSE labeled and sorted (FACSAria) circulating memory Tfh cells and memory B cells were cocultured for 5 days in the presence of SEB.

tag: subject group

value: Elite Controller (EC)

tag: subject

value: PBMCs

tag: cell subtype


title: LH_pTfh_CFSEpos [9287078050_L]

value: Healthy Control (HC)


title: ST_pTfh_CFSEneg [9287078042_L]

value: Chronic Aviremic (CA)


title: LNTP_pTfh_CFSEneg [9287078045_F]


title: LH_pTfh_CFSEneg [9287078042_E]


title: LNTP_pTfh_CFSEpos [9287078042_G]


title: Macrophage cell, D2 Male, IFN 24 h, 5 Anti-TNFa

value: blood

value: monocyte derived macrophage

value: 5 Anti-TNFa


title: Macrophage cell, D2 Male, IFN 24 h, 2 CTRL

value: IFN 24 h

value: 2 CTRL


title: ST_pTfh_CFSEpos [9287078042_C]


title: LH_pTfh_CFSEpos [9287078050_K]


title: microRNA profile of case T390

value: breast cancer


title: Macrophage cell, D2 Male, IFN 24 h, 3 Escitalopram

value: 3 Escitalopram


title: Macrophage cell, D2 Male, IFN 24 h, 6 Indomethacin

value: 6 Indomethacin


title: ST_pTfh_CFSEneg [9287078045_B]


title: LNTP_pTfh_CFSEpos [9287078042_D]


title: LNTP_pTfh_CFSEpos [9287078042_H]


title: LNTP_pTfh_CFSEneg [9287078045_C]


title: LNTP_pTfh_CFSEpos [9287078045_A]


title: ST_pTfh_CFSEpos [9287078050_H]


title: LH_pTfh_CFSEneg [9287078050_J]


title: Macrophage cell, D2 Male, IFN 07 h, 7 Prednisolone

value: IFN 07 h

value: 7 Prednisolone


title: Macrophage cell, D2 Male, IFN 24 h, 4 Nortriptyline

value: 4 Nortriptyline


title: microRNA profile of case T39


title: microRNA profile of case T389


title: microRNA profile of case T388


title: ST_pTfh_CFSEpos [9287078045_H]


title: ST_pTfh_CFSEneg [9287078042_J]


title: LNTP_pTfh_CFSEneg [9287078042_K]


title: Macrophage cell, D2 Male, IFN 24 h, 1 Untreated

value: M

value: 1 UNT


title: Macrophage cell, D2 Male, IFN 07 h, 6 Indomethacin


title: LH_pTfh_CFSEneg [9287078042_B]


title: LH_pTfh_CFSEpos [9287078045_J]


title: Macrophage cell, D2 Male, IFN 07 h, 5 Anti-TNFa


title: LH_pTfh_CFSEpos [9287078045_D]


title: microRNA profile of case T384


title: ST_pTfh_CFSEneg [9287078050_C]


title: LH_pTfh_CFSEneg [9287078050_D]


title: microRNA profile of case T387


title: LH_pTfh_CFSEpos [9287078042_A]


title: Macrophage cell, D2 Male, IFN 07 h, 4 Nortriptyline


title: Macrophage cell, D2 Male, 24 h Untreated, 7 Prednisolone

value: 24 h No inflammation


title: Macrophage cell, D2 Male, IFN 07 h, 2 CTRL


title: microRNA profile of case T385


title: microRNA profile of case T386


title: ST_pTfh_CFSEneg [9287078050_E]

value: PBMCs


title: LH_pTfh_CFSEneg [9287078050_G]

value: Healthy Control (HC)


title: Macrophage cell, D2 Male, 24 h Untreated, 6 Indomethacin


title: LNTP_pTfh_CFSEpos [9287078042_I]

value: Elite Controller (EC)


title: Macrophage cell, D2 Male, IFN 07 h, 1 Untreated

value: blood


title: LNTP_pTfh_CFSEneg [9287078045_G]


title: Macrophage cell, D2 Male, 24 h Untreated, 4 Nortriptyline

value: monocyte derived macrophage


title: ST_pTfh_CFSEpos [9287078045_I]

value: Chronic Aviremic (CA)


title: Macrophage cell, D2 Male, 24 h Untreated, 5 Anti-TNFa

value: 5 Anti-TNFa


title: microRNA profile of case T381


title: Macrophage cell, D2 Male, IFN 07 h, 3 Escitalopram


title: microRNA profile of case T382


title: microRNA profile of case T383


title: microRNA profile of case T378


title: microRNA profile of case T380


title: microRNA profile of case T379


title: microRNA profile of case T377


title: WM35_7_Hypoxia_Control_A

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: Human WM35 melanoma cell line

label_protocol: 300 ng total RNA was amplified and biotin-labeled through a Eberwine procedure using Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: WM35 and Mel-624 cell lines were maintained in humidified air/5% CO2 in RPMI 1640 medium with 5% fetal bovine serum and antibiotics, and passaged by trypsinization.

extract_protocol: Total RNA was isolated by using TRIzol reagent (life Technologies), then further purified using the RNeasy plus Mini kit (Qiagen).

treatment_protocol: WM35 cells were plated at 4 x 105 cells/mL and further maintained for 24h in 5% CO2 humidified air with either normoxic (21%) or hypoxic (1%) O2 concentrations, with experimental cultures being stimulated for 6h before harvest with rhIGF1 (100 ng/mL; R and D Systems). Mel-624 cells were plated at 1 x 105 cells/mL and transfected with either control (siGENOME Non-Targeting siRNA Pool #2; Thermo Scientific) or IGF1R-targeting siRNA (SMARTpool siGENOME) as previously described [PMID 20959481] and further maintained for 3 days in either normoxia or hypoxia.

tag: cell line

value: melanoma cell line


title: microRNA profile of case T376

value: breast cancer


title: Macrophage cell, D2 Male, 24 h Untreated, 3 Escitalopram

value: 3 Escitalopram


title: Macrophage cell, D2 Male, 24 h Untreated, 1 Untreated


title: WM35_9_Hypoxia_Control_C


title: Macrophage cell, D2 Male, 24 h Untreated, 2 CTRL

value: 2 CTRL


title: WM35_8_Hypoxia_Control_B


title: WM35_1_Normoxia_Control_A


title: Macrophage cell, D1 Female, LPS 24 h, 6 Indomethacin

value: F

value: LPS 24 h

value: 6 Indomethacin


title: WM35_5_Normoxia_rhIGF1_B


title: WM35_4_Normoxia_rhIGF1_A


title: Macrophage cell, D1 Female, LPS 24 h, 7 Prednisolone

value: 7 Prednisolone


title: WM35_11_Hypoxia_rhIGF1_B


title: WM35_10_Hypoxia_rhIGF1_A


title: WM35_6_Normoxia_rhIGF1_C


title: WM35_3_Normoxia_Control_C


title: Mel624_11_Hypoxia_siIGFR1_B

source_name: Human Mel-624 melanoma cell line


title: Macrophage cell, D1 Female, LPS 24 h, 5 Anti-TNFa


title: Mel624_8_Hypoxia_siControl_B


title: Mel624_10_Hypoxia_siIGFR1_A


title: microRNA profile of case T375


title: Mel624_9_Hypoxia_siControl_C


title: Mel624_12_Hypoxia_siIGFR1_C


title: WM35_2_Normoxia_Control_B


title: Mel624_7_Hypoxia_siControl_A


title: WM35_12_Hypoxia_rhIGF1_C


title: microRNA profile of case T374


title: Mel624_6_Normoxia_siIGF1R_C


title: microRNA profile of case T371


title: microRNA profile of case T373


title: microRNA profile of case T372


title: microRNA profile of case T369


title: Macrophage cell, D1 Female, LPS 24 h, 3 Escitalopram


title: Macrophage cell, D1 Female, LPS 24 h, 2 CTRL


title: microRNA profile of case T370


title: Mel624_5_Normoxia_siIGF1R_B


title: Mel624_4_Normoxia_siIGF1R_A


title: Mel624_2_Normoxia_siControl_B


title: Mel624_3_Normoxia_siControl_C


title: Macrophage cell, D1 Female, LPS 07 h, 7 Prednisolone

value: LPS 07 h


title: Macrophage cell, D1 Female, LPS 07 h, 5 Anti-TNFa


title: microRNA profile of case T37


title: WM35_Ciclopirox_24h_s1

growth_protocol: WM35 cell lines was maintained in humidified air/5% CO2 in RPMI 1640 medium with 5% fetal bovine serum and antibiotics, and passaged by trypsinization.

treatment_protocol: WM35 cell line was plated at 4 x 105 cells/mL overnight and treated with ciclopirox or crizotinib at 75% inhibitory concentrations (IC75, determined previously at 72h of treatment) or DMSO (vehicle) for 8h or 24h before harvest.


title: WM35_Crizotinib_8h_s3


title: WM35_Crizotinib_8h_s2


title: Mel624_1_Normoxia_siControl_A


title: WM35_Ciclopirox_8h_s1


title: Macrophage cell, D1 Female, LPS 07 h, 6 Indomethacin


title: Macrophage cell, D1 Female, LPS 24 h, 1 Untreated

value: 1 UNT


title: WM35_Ciclopirox_8h_s3


title: microRNA profile of case T368


title: WM35_Crizotinib_24h_s1


title: WM35_Ciclopirox_24h_s2


title: Macrophage cell, D1 Female, LPS 24 h, 4 Nortriptyline

value: 4 Nortriptyline


title: WM35_Crizotinib_24h_s2


title: microRNA profile of case T367


title: WM35_Ciclopirox_8h_s2


title: WM35_CONTRL_s2


title: Macrophage cell, D1 Female, LPS 07 h, 4 Nortriptyline


title: WM35_CONTRL_s1


title: microRNA profile of case T364


title: microRNA profile of case T365


title: microRNA profile of case T361


title: microRNA profile of case T362


title: WM35_LTM_24h_s1

growth_protocol: WM35 cell line was maintained in humidified air/5% CO2 in RPMI 1640 medium with 5% fetal bovine serum and antibiotics, and passaged by trypsinization.

treatment_protocol: WM35 cell line was plated at 4 x 105 cells/mL overnight and treated with trifluridine or lactimidomycin at 75% inhibitory concentrations (IC75, determined previously at 72h of treatment) or DMSO (vehicle) for 8h or 24h before harvest.


title: Macrophage cell, D1 Female, LPS 07 h, 2 CTRL


title: Macrophage cell, D1 Female, LPS 07 h, 3 Escitalopram


title: WM35_LTM_24h_s2


title: WM35_LTM_8h_s3


title: WM35_TFT_24h_s2


title: Macrophage cell, D1 Female, LPS 07 h, 1 Untreated


title: microRNA profile of case T36


title: WM35_LTM_8h_s2


title: WM35_TFT_24h_s1


title: WM35_LTM_8h_s1


title: microRNA profile of case T359


title: Macrophage cell, D1 Female, IFN 24 h, 7 Prednisolone

value: IFN 24 h


title: WM35_TFT_8h_s3


title: microRNA profile of case T366


title: WM35_TFT_8h_s1


title: WM35_CTRL_s1


title: WM35_CTRL_s2


title: Macrophage cell, D1 Female, IFN 24 h, 5 Anti-TNFa


title: WM35_TFT_8h_s2


title: Macrophage cell, D1 Female, IFN 24 h, 3 Escitalopram


title: Macrophage cell, D1 Female, IFN 24 h, 4 Nortriptyline


title: A375_Crizotinib_24h_s2

source_name: Human A375 melanoma cell line

growth_protocol: A375 cell lines was maintained in humidified air/5% CO2 in RPMI 1640 medium with 5% fetal bovine serum and antibiotics, and passaged by trypsinization.

treatment_protocol: A375 cell line was plated at 4 x 105 cells/mL overnight and treated with ciclopirox or crizotinib at 75% inhibitory concentrations (IC75, determined previously at 72h of treatment) or DMSO (vehicle) for 8h or 24h before harvest.


title: Macrophage cell, D1 Female, IFN 24 h, 6 Indomethacin

treatment_protocol: For each treatment, cells were supplemented with the inflammatory stimuli +/- drugs at the same time for 7 or 24 h. Cells were subject to inflammatory stimulus with LPS (10 ng/ml) or IFNα (50 U/ml) for 7 or 24 h or incubated for 24 h with no inflammatory stimulus. In each of these 5 conditions, cells were treated for the same amount of time with either vehicle control (DMSO), escitalopram (1 µM, SSRI antidepressant), nortriptyline (100 nM, tricyclic antidepressant), anti-TNFα (5 µg/ml, neutralising antibody anti-inflammatory), indomethacin (100 µM, non-steroidal anti-inflammatory), prednisolone (1 µM, steroidal anti-inflammatory) or left untreated.


title: A375_Crizotinib_24h_s1


title: WM35_Crizotinib_8h_s1


title: microRNA profile of case T354


title: Macrophage cell, D1 Female, IFN 24 h, 2 CTRL


title: microRNA profile of case T351


title: A375_Crizotinib_8h_s3


title: microRNA profile of case T350


title: Macrophage cell, D1 Female, IFN 07 h, 7 Prednisolone

value: IFN 07 h


title: A375_Crizotinib_8h_s2


title: A375_Crizotinib_8h_s1


title: A375_Ciclopirox_24h_s2


title: microRNA profile of case T349


title: A375_Ciclopirox_8h_s2


title: A375_Ciclopirox_8h_s3


title: microRNA profile of case T35


title: microRNA profile of case T353


title: TabZIP6-overexpressing Arabidopsis L20, cold treatment for 6h, biological rep1

city: Shijiazhuang

first: Caili

last: Bi

state: Hebei

address: No.20 Road East. 2nd Ring South, Yuhua District

department: College of life sciences

institute: Hebei Normal University

description: Arabidopsis L20-4-1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Arabidopsis GeneChip ATH1-121501. 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: TabZIP6-overexpressed Arabidopsis seedlings, cold treatment for 6h

growth_protocol: Seedlings of wild type and TabZIP6-overexpressing Arabidopsis line L20 were normally-grown at 22 ℃ for 10 days.

treatment_protocol: 10-day seedlings of wild type and TabZIP6-overexpressing Arabidopsis line L20 were treated at 4C for 6 hours. Samples were collected before/after cold treatment.

tag: line

tag: genotype/variation

value: seedlings

tag: age

value: 10 days

tag: treatment

value: cold for 6h


title: Macrophage cell, D1 Female, IFN 07 h, 5 Anti-TNFa

value: blood

value: monocyte derived macrophage

value: 5 Anti-TNFa


title: A375_Ciclopirox_8h_s1

value: melanoma cell line


title: Col-1, cold treatment for 6h, biological rep2

description: Arabidopsis WT-4-2

source_name: wild-type Arabidopsis seedling, cold treatment for 6h

tag: ecotype

value: wild-type


title: A375_CONTROL_s1

tag: cell type


title: Macrophage cell, D1 Female, IFN 07 h, 3 Escitalopram

tag: tissue

value: F

value: 3 Escitalopram


title: Macrophage cell, D1 Female, IFN 07 h, 6 Indomethacin

value: 6 Indomethacin


title: Macrophage cell, D1 Female, IFN 24 h, 1 Untreated


title: Macrophage cell, D1 Female, IFN 07 h, 4 Nortriptyline


title: A375_Ciclopirox_24h_s1


title: TabZIP6-overexpressing Arabidopsis L20, before cold treatment, biological rep2

description: Arabidopsis L20-0-2

source_name: TabZIP6-overexpressed Arabidopsis seedlings, before cold treatment

value: before cold


title: TabZIP6-overexpressing Arabidopsis L20, cold treatment for 6h, biological rep2

description: Arabidopsis L20-4-2


title: Macrophage cell, D1 Female, IFN 07 h, 2 CTRL

value: 2 CTRL


title: microRNA profile of case T345

city: Guangzhou

first: jingye

last: hu

institute: Sun Yat-sen University Cancer Center

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, BRB ArrayTools v.3.8.0 was used.

source_name: breast cancer

tag: survival

value: breast cancer


title: Col-1, cold treatment for 6h, biological rep1

description: Arabidopsis WT-4-1


title: A375_CONTROL_s2


title: Col-1, before cold treatment, biological rep2

description: Arabidopsis WT-0-2

source_name: wild-type Arabidopsis seedling, before cold treatment


title: TabZIP6-overexpressing Arabidopsis L20, before cold treatment, biological rep1

description: Arabidopsis L20-0-1


title: A375_LTM_24h_s2

treatment_protocol: A375 cell line was plated at 4 x 105 cells/mL overnight and treated with trifluridine or lactimidomycin at 75% inhibitory concentrations (IC75, determined previously at 72h of treatment) or DMSO (vehicle) for 8h or 24h before harvest.

value: lactimidomycin

tag: time


title: A375_LTM_24h_s1


title: microRNA profile of case T346


title: Macrophage cell, D1 Female, IFN 07 h, 1 Untreated

city: Midlothian

first: Tim

last: Regan

institute: The Roslin Institute, University of Edinburgh

data_processing: CEL files were assessed for quality using arrayQualityMetrics (AQM), a Bioconductor R package. Samples which failed 2 or more tests were discounted from the dataset. The matrix was then subject to RMA normalisation and probesets were reduced to a single gene. Statistical analysis was performed using lme4, another Bioconductor R package. Each donor was set as a random effect while drug or inflammatory treatments were set as fixed effects for each analysis.

source_name: human monocyte derived macrophage

tag: donor

tag: Sex

value: 1 UNT


title: Macrophage cell, D1 Female, 24 h Untreated, 5 Anti-TNFa

tag: inflammatory stimulus

value: 24 h No inflammation


title: A375_LTM_8h_s2

value: 8 h


title: microRNA profile of case T344


title: Macrophage cell, D1 Female, 24 h Untreated, 6 Indomethacin

tag: drug treatment


title: Macrophage cell, D1 Female, 24 h Untreated, 7 Prednisolone

value: 7 Prednisolone


title: microRNA profile of case T340


title: microRNA profile of case T343


title: microRNA profile of case T34


title: microRNA profile of case T342


title: microRNA profile of case T339


title: Macrophage cell, D1 Female, 24 h Untreated, 1 Untreated


title: Macrophage cell, D1 Female, 24 h Untreated, 4 Nortriptyline

value: 4 Nortriptyline


title: Col-1, before cold treatment, biological rep1

description: Arabidopsis WT-0-1

value: seedlings

value: 10 days


title: Macrophage cell, D1 Female, 24 h Untreated, 3 Escitalopram

value: blood

value: monocyte derived macrophage


title: microRNA profile of case T332


title: microRNA profile of case T331


title: Macrophage cell, D1 Female, 24 h Untreated, 2 CTRL


title: A375_LTM_8h_s3


title: A375_TFT_24h_s2

value: trifluorothymidine


title: microRNA profile of case T33


title: microRNA profile of case T329


title: A375_TFT_24h_s1


title: A375_TFT_8h_s3


title: A375_LTM_8h_s1


title: microRNA profile of case T327


title: A375_CTRL_s1

value: control


title: A375_TFT_8h_s1


title: SCC_2

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Lavage-based self-sample

hyb_protocol: Hybridisation was done as described in the automated protocol of the Infinium HD assay methylation protocol guide.

scan_protocol: Scanning was done as described in the automated protocol of the Infinium HD assay methylation protocol guide.

data_processing: Data were pre-processed, including probe quality control. Probes which, (i) showed a low bead count (<3 in at least 5% of samples), (ii) had a detection p-value of > 0.05 in at least 3% of samples, (iii) contained SNPs at or within 10 bp from the target CpG-site (Chen et al. Epigenetics 2013), (iv) were vulnerable to cross-hybridization (Chen et al. Epigenetics 2013) or (v) were located on allosomes, were removed, leaving 365,620 probes for analysis. Data were normalised using dasen normalisation (Pidsley et al. BMC Genomics 2013), which uses a different background correction and quantile normalisation for type I and type II probes. It returns normalised beta-values, representing methylation percentage at the corresponding CpG-site.

label: Cy3 en Cy5

molecule: genomic DNA

source_name: Self-sample SCC_2

label_protocol: Labelling was done as described in the automated protocol of the Infinium HD assay methylation protocol guide.

extract_protocol: DNA from self-samples was isolated using the NucleoMag 96 Tissue kit (Macherey-Nagel, Düren, Germany) and a Microlab Star robotic system (Hamilton, Martinsried, Germany) according to the manufacturer’s protocol. Isolated DNA was bisulphite-converted using the EZ DNA Methylation kit (Zymo Research, Orange, CA, USA) according to manufacturer's instructions.

tag: disease state

value: Cervical squamous cell carcinoma

tag: sample type

value: Self-sampled cervico-vaginal material (self-sample)


title: A375_CTRL_s2


title: microRNA profile of case T319

address: 651 Dongfeng East Road

hyb_protocol: The labeled RNAs from breast cancer and noncancerous breast were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

extract_protocol: Total RNA was extracted from the paraffin-embedded breast cancer and noncancerous breast samples, using a modification of the phenol/chloroform extraction method after processing by dimethylbenzene.


title: microRNA profile of case T318


title: SCC_4

description: Lavage-based self-sample

source_name: Self-sample SCC_4


title: microRNA profile of case T317


title: microRNA profile of case T323


title: microRNA profile of case T32


title: microRNA profile of case T324


title: A375_TFT_8h_s2


title: microRNA profile of case T320


title: CIN3_36

description: Lavage-based self-sample

source_name: Self-sample CIN3_36

value: CIN3 (precancer)


title: SCC_3

description: Lavage-based self-sample

source_name: Self-sample SCC_3


title: CIN3_35

description: Lavage-based self-sample

source_name: Self-sample CIN3_35


title: CIN3_33

description: Lavage-based self-sample

source_name: Self-sample CIN3_33


title: SCC_1

description: Lavage-based self-sample

source_name: Self-sample SCC_1


title: microRNA profile of case T315


title: CIN3_31

description: Lavage-based self-sample

source_name: Self-sample CIN3_31


title: CIN3_32

description: Lavage-based self-sample

source_name: Self-sample CIN3_32


title: microRNA profile of case T313


title: microRNA profile of case T311


title: microRNA profile of case T310


title: microRNA profile of case T31


title: microRNA profile of case T316


title: microRNA profile of case T312


title: microRNA profile of case T309


title: microRNA profile of case T308


title: CIN3_30

description: Lavage-based self-sample

source_name: Self-sample CIN3_30


title: CIN3_28

description: Lavage-based self-sample

source_name: Self-sample CIN3_28


title: CIN3_29

description: Lavage-based self-sample

source_name: Self-sample CIN3_29


title: CIN3_23

description: Lavage-based self-sample

source_name: Self-sample CIN3_23


title: CIN3_25

description: Lavage-based self-sample

source_name: Self-sample CIN3_25


title: microRNA profile of case T352

source_name: breast cancer


title: CIN3_26

description: Lavage-based self-sample

source_name: Self-sample CIN3_26


title: microRNA profile of case T314


title: microRNA profile of case T306


title: CIN3_34

description: Lavage-based self-sample

source_name: Self-sample CIN3_34


title: microRNA profile of case T303


title: CIN3_22

description: Lavage-based self-sample

source_name: Self-sample CIN3_22


title: microRNA profile of case T305


title: microRNA profile of case T30


title: microRNA profile of case T301


title: microRNA profile of case T3


title: microRNA profile of case T299


title: microRNA profile of case T296


title: CIN3_17

description: Lavage-based self-sample

source_name: Self-sample CIN3_17


title: microRNA profile of case T293


title: CIN3_18

description: Lavage-based self-sample

source_name: Self-sample CIN3_18


title: CIN3_20

description: Lavage-based self-sample

source_name: Self-sample CIN3_20


title: CIN3_24

description: Lavage-based self-sample

source_name: Self-sample CIN3_24


title: CIN3_16

description: Lavage-based self-sample

source_name: Self-sample CIN3_16


title: CIN3_19

description: Lavage-based self-sample

source_name: Self-sample CIN3_19


title: microRNA profile of case T290


title: microRNA profile of case T291


title: microRNA profile of case T29


title: CIN3_15

description: Lavage-based self-sample

source_name: Self-sample CIN3_15


title: microRNA profile of case T288


title: CIN3_21

description: Lavage-based self-sample

source_name: Self-sample CIN3_21


title: CIN3_27

description: Lavage-based self-sample

source_name: Self-sample CIN3_27


title: microRNA profile of case T289


title: CIN3_14

description: Lavage-based self-sample

source_name: Self-sample CIN3_14


title: microRNA profile of case T287


title: microRNA profile of case T286


title: CIN3_12

description: Lavage-based self-sample

source_name: Self-sample CIN3_12


title: CIN3_10

description: Lavage-based self-sample

source_name: Self-sample CIN3_10


title: microRNA profile of case T285


title: CIN3_9

description: Lavage-based self-sample

source_name: Self-sample CIN3_9


title: microRNA profile of case T283

source_name: breast cancer


title: microRNA profile of case T282


title: CIN3_8

description: Lavage-based self-sample

source_name: Self-sample CIN3_8


title: microRNA profile of case T280


title: CIN3_13

description: Lavage-based self-sample

source_name: Self-sample CIN3_13


title: microRNA profile of case T28


title: microRNA profile of case T279


title: microRNA profile of case T270


title: Normal_28

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_28

value: Normal


title: microRNA profile of case T27

value: breast cancer


title: CIN3_5

description: Lavage-based self-sample

source_name: Self-sample CIN3_5


title: CIN3_6

description: Lavage-based self-sample

source_name: Self-sample CIN3_6


title: microRNA profile of case T273


title: CIN3_7

description: Lavage-based self-sample

source_name: Self-sample CIN3_7


title: CIN3_1

description: Lavage-based self-sample

source_name: Self-sample CIN3_1


title: CIN3_2

description: Lavage-based self-sample

source_name: Self-sample CIN3_2


title: Normal_26

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_26


title: microRNA profile of case T267


title: microRNA profile of case T266


title: microRNA profile of case T265


title: CIN3_3

description: Lavage-based self-sample

source_name: Self-sample CIN3_3


title: microRNA profile of case T264


title: microRNA profile of case T268


title: Normal_24

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_24


title: microRNA profile of case T263


title: microRNA profile of case T262


title: CIN3_4

description: Lavage-based self-sample

source_name: Self-sample CIN3_4


title: microRNA profile of case T261


title: Normal_27

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_27


title: microRNA profile of case T26


title: Normal_25

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_25


title: Normal_22

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_22


title: microRNA profile of case T260


title: Normal_21

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_21


title: microRNA profile of case T259

source_name: breast cancer


title: Normal_19

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_19


title: Normal_23

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_23


title: CIN3_11

description: Lavage-based self-sample

source_name: Self-sample CIN3_11


title: microRNA profile of case T258


title: microRNA profile of case T255


title: Normal_17

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_17


title: Normal_20

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_20


title: microRNA profile of case T25


title: Normal_15

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_15


title: microRNA profile of case T248


title: microRNA profile of case T246


title: Normal_12

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_12


title: Normal_14

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_14


title: Normal_16

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_16


title: Normal_13

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_13


title: Normal_11

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_11


title: Normal_10

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_10


title: microRNA profile of case T244


title: microRNA profile of case T245


title: Normal_9

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_9


title: microRNA profile of case T243


title: microRNA profile of case T242


title: Normal_18

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_18


title: microRNA profile of case T240


title: microRNA profile of case T241


title: Normal_7

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_7


title: microRNA profile of case T239


title: Normal_8

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_8


title: microRNA profile of case T238

source_name: breast cancer


title: microRNA profile of case T237


title: microRNA profile of case T236


title: Normal_4

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_4


title: Normal_1

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_1


title: microRNA profile of case T235


title: Normal_2

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_2


title: microRNA profile of case T23


title: microRNA profile of case T256


title: microRNA profile of case T224


title: SSA/P2

city: Sapporo

first: Eiichiro

last: Yamamoto

address: South-1, West-16, Chuo-ku

country: Japan

institute: Sapporo medical university

description: SSA/P sample

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

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

data_processing: BeadStudio software V2011.1

label: Cy5 and Cy3

source_name: genomic DNA from SSA/P2

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the standard phenol-chloroform method.

value: Sessile serrated adenoma/polyp


title: Normal_5

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_5


title: Normal_3

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_3


title: Normal_6

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_6


title: microRNA profile of case T22

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight


title: microRNA profile of case T226


title: TSA4_protruding portion

description: TSA sample

source_name: genomic DNA from TSA4

value: Traditional serrated adenoma


title: TSA3_flat portion

description: TSA sample

source_name: genomic DNA from TSA3

value: Traditional serrated adenoma precurcer


title: microRNA profile of case T214


title: microRNA profile of case T21


title: microRNA profile of case T206


title: TSA4_flat portion

description: TSA sample


title: microRNA profile of case T205


title: microRNA profile of case T203


title: microRNA profile of case T204


title: SSA/P1

description: SSA/P sample

source_name: genomic DNA from SSA/P1


title: TSA3_protruding portion

description: TSA sample


title: microRNA profile of case T201


title: microRNA profile of case T200


title: TSA2_protruding portion

description: TSA sample

source_name: genomic DNA from TSA2


title: microRNA profile of case T202


title: TSA1_flat portion

description: TSA sample

source_name: genomic DNA from TSA1


title: microRNA profile of case T20


title: microRNA profile of case T2


title: TF-1 N838D rep 2

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

description: SAMPLE 34

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting.

data_processing: GenomeStudio software version V2011.1

source_name: TF-1 cells

label_protocol: Standard Illumina labelling protocol.

growth_protocol: The TF-1 human erythroleukemic cell line was obtained from ATCC and cultivated in the RPMI 1640 base medium (Invitrogen) supplemented with 10% of FBS and 2 ng/ml of recombinant human GM-CSF (R&D Systems).

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen), and 1µg genomic DNA was subject to bisulfite conversion using EZ DNA methylation gold kit (Zymo Research) according to manufacturer's instructions.

treatment_protocol: TF-1 cell lines with stable expression of wild-type (WT) or mutant DNMT3A were established by MSCV-based retrovirus packaged in HEK293 cells.

tag: gene expressed

value: DNMT3A N838D


title: TSA1_protruding portion

description: TSA sample


title: microRNA profile of case T198


title: TSA2_flat portion

description: TSA sample


title: microRNA profile of case T199


title: SSA/P3

description: SSA/P sample

source_name: genomic DNA from SSA/P3


title: microRNA profile of case T196


title: microRNA profile of case T197


title: TF-1 N838D rep 1

description: SAMPLE 33

tag: cell line


title: microRNA profile of case T195


title: microRNA profile of case T194


title: microRNA profile of case T193


title: TF-1 R836W rep 2

description: SAMPLE 28

value: DNMT3A R836W


title: microRNA profile of case T192


title: microRNA profile of case T191


title: TF-1 N838D rep 3

description: SAMPLE 35


title: microRNA profile of case T190


title: TF-1 K841E rep 3

description: SAMPLE 32

value: DNMT3A K841E


title: microRNA profile of case T19


title: TF-1 T835M rep 3

description: SAMPLE 26

value: DNMT3A T835M


title: TF-1 K841E rep 2

description: SAMPLE 31


title: microRNA profile of case T189


title: TF-1 T835M rep 1

description: SAMPLE 24


title: TF-1 R792H rep 3

description: SAMPLE 23

value: DNMT3A R792H


title: TF-1 R836W rep 1

description: SAMPLE 27


title: TF-1 R836W rep 3

description: SAMPLE 29


title: microRNA profile of case T187


title: TF-1 T835M rep 2

description: SAMPLE 25


title: microRNA profile of case T186


title: TF-1 R792H rep 2

description: SAMPLE 22


title: TF-1 K841E rep 1

description: SAMPLE 30


title: microRNA profile of case T188


title: microRNA profile of case T185


title: TF-1 R792H rep 1

description: SAMPLE 21


title: TF-1 P718L rep 1

description: SAMPLE 18

value: DNMT3A P718L


title: microRNA profile of case T184


title: TF-1 P718L rep 2

description: SAMPLE 19


title: microRNA profile of case T182


title: microRNA profile of case T183


title: TF-1 WT rep 5

description: SAMPLE 13

value: DNMT3A WT


title: microRNA profile of case T180


title: TF-1 V716D rep 3

description: SAMPLE 17

value: DNMT3A V716D


title: microRNA profile of case T181


title: TF-1 V716D rep 2

description: SAMPLE 16


title: TF-1 WT rep 6

description: SAMPLE 14


title: microRNA profile of case T18


title: microRNA profile of case T179


title: TF-1 V716D rep 1

description: SAMPLE 15


title: TF-1 WT rep 4

description: SAMPLE 12


title: microRNA profile of case T177


title: microRNA profile of case T175


title: microRNA profile of case T176


title: microRNA profile of case T174


title: TF-1 WT rep 3

description: SAMPLE 11


title: microRNA profile of case T173


title: microRNA profile of case T172


title: TF-1 EV rep 8

description: SAMPLE 8

value: Empty vector (EV)


title: microRNA profile of case T178


title: microRNA profile of case T171


title: TF-1 WT rep 2

description: SAMPLE 10


title: TF-1 EV rep 5

description: SAMPLE 5


title: TF-1 WT rep 1

description: SAMPLE 9


title: TF-1 EV rep 6

description: SAMPLE 6


title: TF-1 EV rep 4

description: SAMPLE 4


title: microRNA profile of case T17


title: microRNA profile of case T170


title: TF-1 EV rep 2

description: SAMPLE 2


title: microRNA profile of case T168


title: microRNA profile of case T167


title: microRNA profile of case T169


title: TF-1 EV rep 7

description: SAMPLE 7


title: TF-1 P718L rep 3

description: SAMPLE 20


title: TF-1 EV rep 1

description: SAMPLE 1


title: microRNA profile of case T166


title: eAML-NGS-S58

city: Berlin

first: Patricia

last: Silva

address: Hindenburgdamm 30

department: Campus Benjamin Franklin, Hematology

institute: Charité Berlin

hyb_protocol: 500 ng bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol. Sample preparation and readout was done by High Throughput sequencing unit at German Cancer Research Center (Heidelberg, Germany).

scan_protocol: Arrays were imaged using iScan SQ instrument (Illumina)  using standard recommended Illumina scanner setting

data_processing:
Data was treated in R, homogenized using the dasen function (minfi package). dbSNP related CpGs with MAF>0.01 were filtered out. Beta values of methylation in sex related positions CpGs were removed.
The non-normalized.txt contains unmethylated and methylated signal intensities

source_name: bone marrow

growth_protocol: Bone marrow aspirates were obtained from eldely AML patients, mononuclear cells were isolated using density centrifugation

extract_protocol: genomic DNA was extracted from the blasts derived from AML patients using AllPrep DNA/RNA Mini Kit (Qiagen)

treatment_protocol: Standard Illumina Protocol

tag: subject status

value: acute myeloid leukemia (AML) patient

tag: tumor stage

value: First diagnosis

value: F

value: bone marrow


title: eAML-NGS-S32


title: microRNA profile of case T165

value: breast cancer


title: eAML-NGS-S48


title: TF-1 EV rep 3

description: SAMPLE 3


title: eAML-NGS-S44

value: M


title: eAML-NGS-S36


title: microRNA profile of case T164


title: microRNA profile of case T161


title: microRNA profile of case T16


title: microRNA profile of case T159


title: eAML-NGS-S47


title: microRNA profile of case T163


title: eAML-NGS-S60


title: microRNA profile of case T162


title: eAML-NGS-S57


title: eAML-NGS-S55


title: microRNA profile of case T156


title: eAML-NGS-S61


title: microRNA profile of case T157


title: eAML-NGS-S59


title: microRNA profile of case T158


title: microRNA profile of case T155


title: eAML-NGS-S34


title: microRNA profile of case T154


title: eAML-NGS-S20


title: microRNA profile of case T152


title: microRNA profile of case T153


title: eAML-NGS-S54


title: eAML-NGS-S56


title: microRNA profile of case T15


title: microRNA profile of case T150


title: eAML-NGS-S30


title: microRNA profile of case T149