title: WT_t90_slow_3_IP vs. WT_t90_slow_3_INPUT

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

data_processing:
Genes nobg, hybset spec. dye, density: Combination of lowess normalization using genes no backgroundcorrection, hybset specific gene specific dye bias correction and density selection.
limma: A software package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. Author(s): Gordon Smyth. The limma R package version 2.12.0 is used. P-values are Benjamini-Hochberg FDR corrected.

label_protocol: ChIP-amplification: Input and ChIP DNA was amplified using a robotically automated double-round T7 RNA polymerase-based amplification procedure [Van Bakel H, van Werven FJ, Radonjic M, Brok MO, van Leenen D, et al. (2008) Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification. Nucleic Acids Res 36]. ChIP samples were hybridised with input DNA to a high-resolution 44K yeast array (Agilent Technologies).

growth_protocol: growth_ChIP-chip: O/N cultures of WT-aa and Hsf1-aa were diluted in synthetic complete (SC) medium containing 2% glucose and grown for two doublings. Subsequently, a low dose of rapamycin (0.15 µM) or the same volume of DMSO (t0) was added to the cells for the indicated amount of time. Additions were staggered so that all the cultures could be crosslinked at the same time and OD (90 minutes after the first additions: 3 doublings). Crosslinking was done with a final concentration of 2% formaldehyde for 30 minutes at 30oC. Crosslinking was quenched with glycine (final concentration = 125 mM) for 5 minutes. The cells were harvested by centrifugation, washed once in MilliQ and subsequently snap frozen in liquid nitrogen.

extract_protocol: ChIP-DNAextraction: Reverse crosslinked DNA samples were incubated with 400 µg proteinase K (Roche) for 2 hours at 37°C. For ChIP-chip, the proteinase K step was preceded by shrimp alkaline phosphatase (SAP) treatment by adding 1 ul of SAP (Roche) for 2 hours at 37°C. DNA was extracted with phenol-chloroform-isoamylalcohol (Sigma), separated using Phaselock tubes and cleaned on PCR purification columns (Qiagen).

treatment_protocol: treatment_ChIP-chip: ChIP was carried out as previously described (van Bakel et al., 2008) with some modifications. Cells were spheroplasted according to the protocol of the Rando lab (Rando, 2010) and then directly sonicated (Bioruptor, Diagenode: ten cycles, 30 sec on/off, medium setting). 200 µL chromatin extract was incubated with 10 µL of anti-GFP antiserum (homemade) (3h, RT) which had been coupled to Protein G agarose beads (Roche 11 243 233 001) overnight at 4oC. After incubation, antibody ChIPs were washed twice in FA lysis buffer (50 mM HEPES KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), twice with FA lysis buffer containing 0.5 M NaCl, and twice with 10 mM Tris at pH 8.0, 0.25 mM LiCl, 1 mM EDTA, 0.5% Nonidet P-40 and 0.5% Na-deoxycholate. Cross-links of the ChIP samples were reversed overnight at 65°C in 150 μL 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% SDS.

value: By4742-aa :tor1-1; fpr1del; RPL13A-FKBP12-NAT

tag: chip antibody

value: anti-GFP


title: WT_t90_slow_5_INPUT vs. WT_t90_slow_5_IP

status: Public on Nov 11 2016

type: genomic

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

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

molecule: genomic DNA

organism: Saccharomyces cerevisiae

tag: strain/background

tag: genotype/variation

tag: treatment


title: sCAD-5

type: RNA

city: Hannover

first: Julia

last: Osipova

address: Carl-Neuberg Str. 1

department: IMTTS

country: Germany

institute: MHH

description:
Test
SAMPLE 9

data_processing:
Data was processed by Exiqon as standard data analysis:
For the normalization of the data it was used the geomean of all assays detected in all 18 samples.   The formula used is:  Normalized Cp = Geomean(n=18) – assay Cp.
The average normalized Cp of the samples in test groups and in a control group has been calculated.
ΔΔCp: The difference in normalized Cps has been calculated between the average normalized Cp of test and control sample groups.
Fold change = 2 ΔΔCp: Difference in normalized Cps (ΔΔCp) has been converted to fold change with  2 ΔΔCp.  A fold change > 1 indicate up-regulation and a fold change < 1 indicate down-regulation in test (sCAD- or STEMI d0- or STEMI d5-) sample group compared to contol (healthy control) sample group.

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood derived CD34+ progenitor cells

label_protocol: RNA sample were sent to Exiqon (Vedbaek, Denmark) for labelling for miRCURYTM LNA Array microRNA profiling.

growth_protocol: CD34+   were isolated directly from the peripheral blood of the patients using CD34-MicroBead-Kit (Miltenyi Biotec) according to the manufacturer’s protocol

extract_protocol: Total RNA was extracted with miRNeasy Kit (Qiagen) following the manufacturer's recommendations

treatment_protocol: no treatment

tag: cell type

value: CD34+ progenitor cells

tag: disease state (patient group)

value: sCAD

tag: time in culture

value: 0 days


title: WT_t90_slow_4_IP vs. WT_t90_slow_4_INPUT


title: WT_t90_slow_2_INPUT vs. WT_t90_slow_2_IP


title: HSF1_t90_slow_4_IP vs. HSF1_t90_slow_4_INPUT

value: Hsf1-aa :tor1-1; fpr1del; RPL13A-FKBP12-NAT; Hsf1-FRB-yEGFP


title: 166s4

city: Glasgow

first: Lisa

last: Hopcroft

address: Paul O'Gorman Leukaemia Research Centre

country: United Kingdom

institute: University of Glasgow

description: Gene expression following 16h treatment

hyb_protocol: As per standard Affymetrix protocols.

scan_protocol: As per standard Affymetrix protocols.

data_processing: .CEL files were read using Bioconductor's ReadAffy() function.  Data were normalised by the rma() function using default settings.

source_name: Patient sample 166

label_protocol: As per standard Affymetrix protocols.

growth_protocol: Cells were cultured in serum free media in the presence of drug for 16hrs.

extract_protocol: RNEasy minikit.

tag: tissue

value: Peripheral blood

value: CD34+ chronic Myeloid leukemia (CML)


title: 166s3

description: Gene expression following 16h treatment

value: 150nM Dasatinib


title: sCAD-4

description:
Test
SAMPLE 8


title: HSF1_t90_slow_5_INPUT vs. HSF1_t90_slow_5_IP


title: 166s1

description: Gene expression following 16h treatment

value: PBS control


title: 166s2

description: Gene expression following 16h treatment

value: 5uM Imatinib


title: sCAD-3

description:
Test
SAMPLE 7


title: sCAD-2

description:
Test
SAMPLE 6


title: HSF1_t90_slow_2_INPUT vs. HSF1_t90_slow_2_IP


title: 111s6

description: Gene expression following 16h treatment

source_name: Patient sample 111

value: 250nM BMS214662 + 150nM Dasatinib


title: AdultLiver_3

city: Berlin

first: Francesca M.

last: Spagnoli

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center for Molecular Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >12.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays (G4858A-028005) for 17 hours at 65°C and 10 rpm 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). The wash buffers contained 0.005% Triton X-102.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using the AgilentG3_GX_1Color scan protocol for 8x60K high densitiy Microarray Formats (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%, the resulting file is a 20bit tiff image).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown on Collagen-I coated plates in William's E medium supplemented with 2mM Glutamax, 10% FBS, 30ng/mL IGF-II, 50ng/mL EGF, 10µg/mL Insulin, 0.1µM dexamethasone and 10µM nicotinamide.

extract_protocol: For RNA isolation, adult and embryonic tissues were dissected and snap-frozen on dry ice and RNA was extracted with RNAzol (Biozol) according to manufacturer’s instructions. The High Pure RNA Isolation Kit (Roche) was used for RNA extraction from cultured cells. RNA was quantified and quality controlled using the RNA 6000 Pico Kit on the Agilent 2100 Bioanalyzer RNA (Agilent Technologies).

treatment_protocol: HEP cells were transduced with a lentivirus expressing TGIF2 at an MOI of 40. Growth conditions were kept the same as for untransduced control cells.

tag: developmental stage

value: adult

value: liver tissue


title: HSF1_t60_slow_4_IP vs. HSF1_t60_slow_4_INPUT


title: AdultPancreas_3

value: pancreatic tissue


title: Healthy-control-4

description:
Control
SAMPLE 4

value: Healthy control


title: AdultLiver_1


title: Healthy-control-3

description:
Control
SAMPLE 3


title: HSF1_t90_slow_3_IP vs. HSF1_t90_slow_3_INPUT


title: HSF1_t60_slow_5_INPUT vs. HSF1_t60_slow_5_IP


title: 111s4

description: Gene expression following 16h treatment


title: AdultLiver_2


title: HSF1_t60_slow_3_IP vs. HSF1_t60_slow_3_INPUT


title: 111s5

description: Gene expression following 16h treatment


title: 111s1

description: Gene expression following 16h treatment


title: sCAD-1

description:
Test
SAMPLE 5


title: Healthy-control-2

description:
Control
SAMPLE 2


title: HSF1_t30_slow_5_INPUT vs. HSF1_t30_slow_5_IP


title: 111s2

description: Gene expression following 16h treatment


title: Healthy-control-1

description:
Control
SAMPLE 1


title: EmbryonicPancreas_E14.5_2

source_name: Pancreas_embryonic (E14.5)

value: embryonic (E14.5)


title: AdultPancreas_2


title: 111s3

description: Gene expression following 16h treatment


title: HSF1_t60_slow_2_INPUT vs. HSF1_t60_slow_2_IP


title: 170s2

description: Gene expression following 16h treatment

source_name: Patient sample 170


title: EmbryonicPancreas_E14.5_1


title: AdultPancreas_1


title: HSF1_t30_slow_3_IP vs. HSF1_t30_slow_3_INPUT


title: EmbryonicPancreas_E14.5_3


title: 110s5

description: Gene expression following 16h treatment

source_name: Patient sample 110


title: HSF1_t30_slow_4_IP vs. HSF1_t30_slow_4_INPUT


title: 110s6

description: Gene expression following 16h treatment


title: HSF1_t30_slow_2_INPUT vs. HSF1_t30_slow_2_IP


title: HepaticCells_ctrl_1

source_name: Hepatic cells_control

tag: cell type origin

value: hepatic cells

tag: tranduced with

value: none (control)

tag: cell subtype

value: hepatic cells (in control conditions)


title: 110s1

description: Gene expression following 16h treatment


title: 110s2

description: Gene expression following 16h treatment


title: 110s3

description: Gene expression following 16h treatment


title: HSF1_t0_slow_3_IP vs. HSF1_t0_slow_3_INPUT

value: anti-GFP


title: HSF1_t15_slow_3_IP vs. HSF1_t15_slow_3_INPUT


title: MH002-FoxO6#3-4 vs. MH002-ref

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

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

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

label_protocol: Robot amplification and labeling v1.0: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrophotometer (Molecular Devices), and a magnetic bead-locator (Beckman).  mRNA amplification protocol description:  * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script.  * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well.  * plate is incubated @ 70C for 10 mins, cooled to 48C.  * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAs Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.  * plate is incubated @ 48C for 2 hours and cooled to room temperature.  * 106 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul Ranse (Promega) is added and mixed in each well.  * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul.  * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems).  * Plate is incubated @37C for 4 hours.  * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.  * Concentration is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.  * Resulting cRNA plates are sampled for Bioanalyzer QC, snap frozen and stored at -80C.  Labeling protocol description:  * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).  All subsequent steps are performed by the robot script :  * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ).  * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.  * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.  * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.  * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.  * RNA concentration and labeling incorporation are measured (SpectraMax 190).  * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.  * Samples are stored at -20C until hybridization.

extract_protocol: Trizol v1.0 RNA isolation of tissue sections:  1. After sectioning, store sections in ice-cold RNAlater (~10 ml RNAlater per 20-mm section). Make sure that the sections do not thaw before they are in ice-cold RNAlater. 50 ml RNAlater.  2. Add X ml Trizol (10x volume of RNAlater) and mix by inverting the tube several times. 500 ml Trizol.  3. Incubate 5 min at room temperature.  4. Pre-incubate Proteinase K (10 mg/ml) at 37 C for at least 10 minutes.  5. Add 10 ml of the pre-heated Proteinase K solution to Trizol mixture. 10 ml Prot-K.  6. Incubate 30 min at 55 C.  7. Add X ml chloroform (20 ml per 100 ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature. 100 ml chloroform.  8. Centrifuge 20 min at 14000 rpm without brake at 4 C. After centrifugation, transfer the water-phase to a new 1.5 ml micro centrifuge tube (~300 ml).  9. Continue with RNeasy columns (Qiagen) for clean-up of RNA.  10. Adjust each sample to a volume of 300 ml with sterile MilliQ water. Add 160 ml buffer RLT to the samples, and mix (= lysis buffer).  11. Add 240 ml ethanol (100% stored at -20 C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipette and work as quickly as possible). Next lysate, and so on.  12. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flow-through and collection tube.  13. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 ml buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in step 5.  14. Pipette 500 ml buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.  15. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).  16. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipette 100 ml milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute.  17. Pipette the eluate of step 7 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute.

treatment_protocol: Treatment of E14 cortex: C57/BL6 mice at 14 days of gestation were anesthetized by injecting a mixture of ketamine/medetomidin/atropine intraperitoneal. The uterus of these mice were exposed and a mixture containing 1 ug/ul siRNA (FoxO6 or Scrambled), 1ug/ul expression vector containing GFP and 0.01% Fast Green dissolved in 20mM Tris-HCl pH 8 was injected through pulled glass capillaries, using a microinjector, into one lateral ventricle of each embryo. We used custom-made siRNAs (Thermo Scientific) to silence FoxO6 (siFoxO6-2, NNACAUGCCAGUGACGACUAC; siFoxO6-3, NNCCAUCAGCCUUAUGACGCU) and a Non-Targeting siRNA ( D-001210-03-20). Next, electric pulses were generated by an ECM830 Square Wave Electroporation System and applied to the cerebral wall at five repeats of 33V for 50 ms with an interval of 950 ms. After the electroporation, the uterus is placed back, and the mouse is taken care of. At E16.5, embryos were harvested, cortex was isolated and dissociated using papain kit according to manufacturer's protocol (Worthington Biochemical Corp.) followed by FAC sorting. Sorted cells were subjected to RNA isolation using the Phenol-Chloroform extraction method. Cortices were pooled to minimize effects due to electroporation differences.

value: FACS-sorted cortex cells

tag: sirna

value: scrambled


title: MH002-ref vs. MH002-FoxO6#3-3


title: TiPPCells_d14_1

source_name: TGIF2-induced pancreatic progenitor cells_d14

value: TGIF2-expressing lentivirus

value: reprogrammed pancreatic cells

tag: time point

value: 14 days after transduction


title: MH002-ref vs. MH002-FoxO6#2-1


title: TiPPCells_d30_1

source_name: TGIF2-induced pancreatic progenitor cells_d30

value: 30 days after transduction


title: HSF1_t15_slow_4_IP vs. HSF1_t15_slow_4_INPUT

value: Hsf1-aa :tor1-1; fpr1del; RPL13A-FKBP12-NAT; Hsf1-FRB-yEGFP


title: HSF1_t0_slow_5_INPUT vs. HSF1_t0_slow_5_IP


title: MH002-ref vs. MH002-FoxO6#3-1


title: TiPPCells_d14_3


title: TiPPCells_d30_3


title: HSF1_t15_slow_2_INPUT vs. HSF1_t15_slow_2_IP


title: FMDV_OA_Chimera

status: Public on Nov 10 2016

city: Greenport

first: Roger

middle: William

last: Barrette

state: NY

address: Plum Island Animal Disease Center

department: Diagnostic Services

country: USA

institute: USDA/APHIS/FADDL

description: Algorithm based sequence assembly

hyb_protocol: Hybridization and washing of Agilent arrays was performed in Agilent HI-RPM hybridization and blocking buffer for 16 hr at 57 °C in an Agilent rotating hybridization incubator.  After hybridization, arrays were washed at room temperature for 5 min in 200 ml of Agilent CGH buffer 1 with mixing.  Arrays were then transferred directly to another slide tray containing 200 ml of Agilent CGH wash buffer 2 and incubated at 37 °C for 1 min.  Finally arrays were transferred to a phosphate buffered saline solution at pH 8.0 (Sigma Aldrich) and incubated with mixing for 5 min, dried by centrifugation at 700 x g  for 1 min in a 50 ml conical tube with a Kimwipe inserted into the bottom of the tube to act as a wick.  Upon completion of drying, slides were scanned and analyzed for fluorescence intensity of features.

scan_protocol: Microarray scanning was performed using a GenePix® 4400A at 532 nm wavelength using a standard green filter, 3 line averaging, and 5 µM resolution.  GenePix® Pro 7.1 was used for data capture.

data_processing: Data analysis was performed using the 'feature and template assisted assembler' written in the Python programming language (Python 2.7.5, Python Software Foundation).  The FASTA output from the FAT assembler is provided as a supplementary file for each sample.

label: Alexa-Fluor 555

organism: Foot-and-mouth disease virus

source_name: Cell culture

label_protocol: BioPrime® Array CGH Genomic Labeling Module (Cat# 18095012).  Incorporation of Alexa Fluor® 555-aha-dUTP (Cat# A32762) as per mfg instructions.

extract_protocol: Qiagen Rneasy extraction of RNA as per mfg instructions, without DNAse.

tag: genbank accession

tag: isolate


title: MH002-FoxO6#2-4 vs. MH002-ref


title: HSF1_t15_slow_5_INPUT vs. HSF1_t15_slow_5_IP


title: HepaticCells_ctrl_2


title: MH002-FoxO6#2-2 vs. MH002-ref


title: FMDV_SAT2

description: Algorithm based sequence assembly

value: SAT2 Zimbabwe


title: FMDV_SAT3

description: Algorithm based sequence assembly

value: SAT3-2 South Africa


title: TiPPCells_d14_2


title: HepaticCells_ctrl_3

value: adult


title: FMDV_Asia1

description: Algorithm based sequence assembly

value: Asia1 Lebanon


title: HSF1_t0_slow_4_IP vs. HSF1_t0_slow_4_INPUT


title: HSF1_t0_slow_2_INPUT vs. HSF1_t0_slow_2_IP


title: FMDV_A

description: Algorithm based sequence assembly

value: A23 Kenya


title: FMDV_C

description: Algorithm based sequence assembly

value: C1 Ober


title: FMDV_O

description: Algorithm based sequence assembly

value: O3 Venezuela


title: MH002-ref vs. MH002-FoxO6#2-3


title: 110s4

description: Gene expression following 16h treatment

value: Peripheral blood

value: CD34+ chronic Myeloid leukemia (CML)


title: MH002-FoxO6#3-2 vs. MH002-ref


title: TiPPCells_d30_2

value: hepatic cells


title: FMDV_SAT1

description: Algorithm based sequence assembly

value: SAT1 Rhodesia


title: DO-32

city: Pittsburgh

first: Guang

last: Li

state: PA

address: 530 45th St. 8116 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

data_processing: Only cells with a Ct value < 25 in any two of the three housekeeping genes (GAPDH, Actb, Hprt) were further analyzed (Fig S4C, Table S5C). Expression level (Log2EX value) was calculated by subtracting the Ct value from the limit of detection (LoD) (previously defined as 35 for the experiments described). Expression levels < 0 are displayed as 0.

label: FAM

source_name: distal outflow tract, single cell

label_protocol: Single cell derived cDNA were pre-amplified in regulat PCR machine (Biorad) with the superscrip III (Direct one step qPCR kit) and Taqman assays (Life technology), then the pre-amplified cDNA were used to quantify the expression level of each taqman assay with 96x96 Fluidigm chips in the Biomark machine.

growth_protocol: e10.5 murine cardiac cells were dissected into 9 zones in PBS, dissociated into single cells, and subjected to single cell RT-PCR

extract_protocol: Single cells were sorted to single well of 96-well strips, and lysated and reverse transcribed with the direct one step qPCR kits (Life technology).

value: distal outflow tract


title: RS-32

source_name: right septum, single cell

value: right septum


title: DO-24


title: PO-32

source_name: proximal outflow tract, single cell

value: proximal outflow tract


title: PO-40


title: DO-47


title: DO-40


title: RS-40


title: RS-24


title: RS-48


title: PO-48


title: PO-24


title: DO-31


title: DO-23


title: PO-47


title: PO-39


title: RS-39


title: RS-31


title: RS-23


title: DO-39


title: PO-23


title: PO-46


title: PO-38


title: DO-46


title: DO-30


title: DO-38


title: RS-47


title: PO-31


title: PO-30


title: PO-22


title: RS-46


title: DO-22


title: RS-30


title: RS-22


title: PO-29


title: RS-38


title: RS-45


title: DO-29


title: DO-37


title: RS-37


title: RS-29


title: PO-37


title: DO-21


title: PO-45


title: PO-21


title: RS-21


title: PO-44


title: DO-20


title: RS-44


title: PO-28


title: RS-36


title: DO-45


title: DO-28


title: DO-36


title: DO-44


title: DO-43


title: RS-20


title: RS-28


title: DO-35


title: DO-27


title: PO-36


title: PO-20


title: DO-42


title: RS-19


title: RS-35


title: PO-35


title: PO-19


title: PO-43


title: PO-27


title: DO-26


title: DO-34


title: DO-18


title: PO-42


title: PO-34


title: RS-43


title: RS-26


title: RS-34


title: RS-18


title: PO-18


title: DO-19


title: PO-26


title: RS-27


title: RS-42


title: PO-41


title: PO-33


title: DO-17


title: DO-41


title: DO-25


title: PO-17


title: PO-25


title: RS-41


title: RS-25


title: DO-33


title: LS-40

source_name: left septum, single cell

value: left septum


title: LS-48


title: LS-24


title: LV-48

source_name: left ventricle, single cell

value: left ventricle


title: LS-32


title: RV-24

source_name: right ventricle, single cell

value: right ventricle


title: RV-40


title: RS-17


title: RV-32


title: RV-31


title: RV-39


title: LV-24


title: RV-47


title: LS-39


title: LS-47


title: LS-31


title: RS-33


title: LS-23


title: LV-40


title: LV-31


title: LV-39


title: LV-23


title: LV-32


title: RV-23


title: RV-46


title: RV-38


title: RV-30


title: RV-22


title: LS-46


title: LV-47


title: LV-30


title: LV-22


title: RV-45


title: LS-30


title: LS-38


title: LS-22


title: LV-29


title: LV-21


title: LS-21


title: LV-45


title: LV-37


title: LS-29


title: RV-44


title: RV-36


title: RV-28


title: LS-45


title: LS-37


title: LV-46


title: LV-38


title: LV-20


title: LS-36


title: LV-28


title: RV-20


title: LV-36


title: LS-44


title: RV-35


title: RV-43


title: RV-19


title: LS-43


title: LS-35


title: LS-19


title: LV-27


title: LV-35


title: LV-43


title: RV-27


title: LS-27


title: LS-42


title: LV-19


title: LS-34


title: LV-34


title: LV-42


title: RV-18


title: LS-18


title: RV-34


title: RV-26


title: RV-42


title: LS-26


title: RV-25


title: RV-17


title: LS-41


title: RV-41


title: LV-26


title: LV-18


title: RV-33


title: LS-17


title: LS-33


title: LS-25


title: LV-33


title: LV-41


title: LV-17


title: LV-25


title: AVC-32

source_name: atrioventricular canal, single cell

value: atrioventricular canal


title: AVC-24


title: RA-40

source_name: right atrium, single cell

value: right atrium


title: RA-24


title: RA-32


title: LA-40

source_name: left atrium, single cell

value: left atrium


title: LA-24


title: LA-48


title: AVC-47


title: AVC-40


title: RA-47


title: RA-48


title: AVC-23


title: AVC-31


title: AVC-39


title: LA-32


title: RA-23


title: LA-47


title: LA-39


title: LA-31


title: RA-31


title: RA-39


title: LA-23


title: AVC-30


title: AVC-38


title: AVC-46


title: AVC-22


title: RA-46


title: RA-38


title: RA-30


title: RA-22


title: LA-46


title: LA-30


title: LA-22


title: LA-38


title: AVC-45


title: AVC-37


title: AVC-29


title: RA-45


title: AVC-21


title: RA-29


title: LNDBB_subject_53_striatum

city: Exeter

first: Jonathan

last: Mill

address: RD&E NHS Foundation, Trust Campus, Barrack Rd

department: Medical School, RILD Building

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization).   Probes containing a SNP with minor allele frequency (MAF) >5% within 10bp of the single base extension site based on   Illumina’s database and probes identified by Chen et al. (n=34,548) * were removed. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: biotin

source_name: striatum (putamen)

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: Genomic DNA was isolated from ~50 mg of each dissected brain region using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.

tag: diagnosis

value: control

tag: age

tag: gender

value: M


title: RA-37


title: RA-21


title: LNDBB_subject_54_striatum


title: LA-37


title: LA-45


title: LA-29


title: LNDBB_subject_50_striatum


title: LNDBB_subject_52_striatum


title: LA-21


title: AVC-36


title: AVC-28


title: LNDBB_subject_47_striatum


title: LNDBB_subject_41_striatum

value: F


title: RA-44


title: AVC-20


title: LNDBB_subject_42_striatum


title: LNDBB_subject_49_striatum


title: RA-28


title: LNDBB_subject_43_striatum


title: LNDBB_subject_44_striatum


title: RA-20


title: LNDBB_subject_37_striatum


title: LA-36


title: LA-44


title: LNDBB_subject_51_striatum


title: LNDBB_subject_39_striatum


title: LNDBB_subject_38_striatum


title: LA-20


title: AVC-43


title: AVC-35


title: LNDBB_subject_35_striatum


title: LNDBB_subject_36_striatum


title: LNDBB_subject_45_striatum


title: LNDBB_subject_33_striatum


title: LNDBB_subject_34_striatum


title: AVC-27


title: LNDBB_subject_40_striatum


title: RA-43


title: AVC-44


title: LNDBB_subject_32_striatum


title: AVC-19


title: RA-35


title: LNDBB_subject_29_striatum


title: RA-19


title: RA-27


title: LA-43


title: LA-35


title: LA-27


title: LNDBB_subject_30_striatum


title: LA-19


title: LNDBB_subject_31_striatum


title: RA-36


title: LNDBB_subject_27_striatum


title: LA-28


title: AVC-42


title: AVC-34


title: AVC-26


title: RA-42


title: AVC-18


title: RA-34


title: RA-26


title: LNDBB_subject_26_striatum


title: LNDBB_subject_25_striatum


title: LA-42


title: LA-34


title: RA-18


title: AVC-33


title: AVC-25


title: AVC-41


title: LNDBB_subject_28_striatum


title: RA-41


title: AVC-17


title: LNDBB_subject_22_striatum

value: schizophrenia


title: LNDBB_subject_19_striatum


title: RA-33


title: LA-26


title: LNDBB_subject_18_striatum


title: LA-18


title: RA-17


title: LNDBB_subject_23_striatum


title: LA-41


title: LA-33


title: LA-25


title: LA-17


title: LNDBB_subject_16_striatum


title: LNDBB_subject_20_striatum


title: AVC-16


title: LV-16


title: PO-8


title: LNDBB_subject_15_striatum


title: DO-8


title: LNDBB_subject_12_striatum


title: LNDBB_subject_8_striatum


title: RV-8


title: LNDBB_subject_13_striatum


title: LS-8


title: LNDBB_subject_14_striatum


title: RA-25


title: LV-8


title: RA-8


title: AVC-8


title: LA-8


title: LNDBB_subject_10_striatum


title: LS-15


title: LV-15


title: AVC-15


title: LNDBB_subject_9_striatum


title: DO-7


title: RS-8


title: LNDBB_subject_6_striatum


title: PO-7


title: RS-7


title: RV-7


title: LNDBB_subject_4_striatum


title: LNDBB_subject_5_striatum


title: DBCBB_subject_4_striatum


title: LS-7


title: LNDBB_subject_3_striatum


title: LV-7


title: DBCBB_subject_6_striatum


title: DBCBB_subject_9_striatum


title: LNDBB_subject_2_striatum


title: GFPminus CD103 - REP3

city: New York

first: Julie Magarian

last: Blander

address: 1425 Madison Avenue, 12-20D

institute: The Icahn School of Medicine at Mount Sinai

description: Live CD45+ CD11c+ MHCII+ CD103+ CD24+ GFP-

hyb_protocol: labeled cDNA was hybridized to Affymetrix mouse Gene 2.0 ST arrays using standard Affymetrix protocols.

scan_protocol: These arrays were then washed, stained with SAPE on a FS450 station, and scanned on a GeneChip 3000 7G scanner using Affymetric GeneChip Command Console Software (AGCC).

data_processing: The signals are quantile normalized using PLIER16 algorithm and base line transformed to the median of all samples

source_name: Intestinal dendritic cell  - i.p. injection DT 4hrs

label_protocol: 1 ng of total RNA was processed using WT Ovation Pico RNA Amplification System (NuGEN). RNA was reverse transcribed and sense target cDNAs were biotin labeled using the standard NuGEN WT pico protocol

extract_protocol: Following cell sorting into TRIzol LS reagent, a sample cleanup step was performed using RNeasy columns (Qiagen) that included DNase treatment.  The isolated RNA was checked for quality using a nanodrop and a Bioanalyzer.

treatment_protocol: Mice were injected I.P. with diphtheria toxin @ 2 ng/kg in PBS and sacrificed 4 hours later.

tag: n value

value: male/female

tag: strain

value: VDTR

value: small intestine

value: intestinal dendritic cells

tag: gfp plus or minus

value: GFPminus


title: DBCBB_subject_8_striatum


title: DBCBB_subject_35_striatum


title: LNDBB_subject_1_striatum


title: LA-7


title: LNDBB_subject_11_striatum


title: DBCBB_subject_7_striatum


title: LNDBB_subject_7_striatum


title: DBCBB_subject_3_striatum


title: DBCBB_subject_33_striatum


title: GFPminus CD103 - REP2

tag: cell type


title: DBCBB_subject_34_striatum


title: DBCBB_subject_32_striatum


title: DBCBB_subject_30_striatum


title: DBCBB_subject_31_striatum


title: RA-7


title: AVC-7


title: DBCBB_subject_27_striatum


title: DBCBB_subject_28_striatum


title: AVC-14


title: LS-14


title: DBCBB_subject_22_striatum


title: DBCBB_subject_23_striatum


title: DBCBB_subject_26_striatum


title: PO-6


title: DBCBB_subject_25_striatum


title: RS-6

value: right septum


title: RV-6


title: DBCBB_subject_24_striatum


title: GFPplus CD103CD11bCD64 - REP2

description: Live CD45+ CD11c+ MHCII+ CD103+ CD11b+ CD64+ GFP+

source_name: Intestinal macrophages - i.p. injection DT 4hrs

value: intestinal macrophages

value: GFPplus


title: LV-14

value: left ventricle


title: GFPminus CD103 - REP1


title: GFPplus CD11bCD64 - REP2

description: Live CD45+ CD11c+ MHCII+ CD11b+ CD64+ GFP+


title: LS-6

value: left septum


title: GFPplus CD103 - REP3

description: Live CD45+ CD11c+ MHCII+ CD103+ CD24+ GFP+


title: GFPplus CD11bCD64 - REP1


title: GFPplus CD103 - REP1


title: DO-6

value: distal outflow tract


title: DBCBB_subject_2_striatum


title: GFPplus CD103CD11bCD64 - REP1


title: GFPplus CD103 - REP2


title: LV-6


title: GFPminus CD11bCD64 - REP3

description: Live CD45+ CD11c+ MHCII+ CD11b+ CD64+ GFP-


title: GFPplus CD11bCD64 - REP3


title: GFPminus CD11bCD64 - REP2


title: RA-6

value: right atrium


title: AVC-6

value: atrioventricular canal


title: DBCBB_subject_21_striatum


title: LA-6

value: left atrium


title: DBCBB_subject_18_striatum

value: M


title: AVC-13


title: LV-13


title: GFPminus CD11bCD64 - REP1


title: DBCBB_subject_5_striatum

value: control


title: GFPminus CD103CD11bCD64 - REP3

description: Live CD45+ CD11c+ MHCII+ CD103+ CD11b+ CD64+ GFP-


title: GFPminus CD103CD11bCD64 - REP2


title: GFPplus CD103CD11bCD64 - REP3


title: DO-5


title: GFPminus CD103CD11bCD64 - REP1


title: WT_5

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

department: UMR7216 "Epigenetics and Cell Fate"

country: France

institute: CNRS-Université Paris Diderot - Sorbonne Paris Cité

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: R, Bioconductor, affy Package, rma()  normalization

source_name: MEF

label_protocol: Affymetrix protocol

growth_protocol: Mouse embryonic fibroblasts were isolated from dorsal skin of E13.5 embryos. Following removal of the head and organs, embryos were rinsed with phosphate-buffered saline, minced, and digested with trypsin-EDTA (LifeTech 25300-054) 30 min at 37°C. Trypsin was inactivated by addition of DMEM containing 10% FBS.

extract_protocol: Total RNA was extracted using Tri reagent (Sigma) according to the manufacturer's instructions.

value: MEF

tag: genotype/variation

value: wild type


title: DBCBB_subject_19_striatum

value: F


title: DBCBB_subject_16_striatum

value: schizophrenia


title: PO-5

tag: tissue

value: proximal outflow tract


title: LS-13


title: DBCBB_subject_15_striatum


title: RS-5


title: DBCBB_subject_14_striatum


title: RV-5

value: right ventricle


title: WT_3


title: WT_4


title: DBCBB_subject_13_striatum


title: LS-5


title: LV-5


title: KO_5

value: Zbtb4 knock-out


title: AVC-5


title: DBCBB_subject_17_striatum


title: RA-5


title: 085 - D17 1Ba

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

address: 61 Biopolis Drive, Proteos, #06-07

country: Singapore

institute: Institute of Molecular and Cell Biology

description: D17_Mut+ Dia-

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol using Illumina Beadarray Reader

data_processing: The data were normalised using cubic spline with Illumina Genome Studio v2011.1

source_name: MODY5 hiPSC_day17differentiated

label_protocol: Total RNA was amplified with the Illumina TotalPrep RNA Amplification Kit p/n AMIL1791 made by Ambion and labelled with Cy3

growth_protocol: Undifferentiated hiPSCs were maintained in DMEM/F12 20 % KOSR + 10 ng/ml FGF2

extract_protocol: Total RNA was extracted with RNeasy Mini Kit from Qiagen. DNase I treatment was included.

treatment_protocol: Day 12 and 17 differentiated hiPSCs were differentiated with growth factors and chemical compounds in RPMI 2 % B-27

value: female

value: hiPSC from N805-1 skin fibroblast

tag: cell state


title: WT_1


title: KO_3


title: LA-5


title: 085 - D17 2Bb

description: D17_Mut+ Dia+

value: male

value: hiPSC from N805-2 skin fibroblast


title: KO_4


title: DBCBB_subject_12_striatum


title: DBCBB_subject_11_striatum


title: DBCBB_subject_10_striatum


title: LNDBB_subject_53_hippocampus

source_name: hippocampus


title: KO_2


title: LS-12

value: left septum


title: LNDBB_subject_54_hippocampus


title: KO_1


title: LNDBB_subject_51_hippocampus


title: DBCBB_subject_1_striatum


title: LNDBB_subject_49_hippocampus


title: 085 - D17 1da

description: D17_Non Fam Ctr

source_name: control hiPSC_day17differentiated

value: hiPSC from AG16102 skin fibroblast


title: 085 - 2B D12c

description: D12_Mut+ Dia+

source_name: MODY5 hiPSC_day12differentiated


title: LV-12

value: left ventricle


title: LNDBB_subject_40_hippocampus


title: LNDBB_subject_50_hippocampus


title: DO-4

source_name: distal outflow tract, single cell

value: distal outflow tract


title: WT_2


title: 085 - 6C D12a

description: D12_Fam Ctr

source_name: control hiPSC_day12differentiated

value: hiPSC from N805-6 skin fibroblast


title: LNDBB_subject_42_hippocampus

value: control

value: M


title: 085 - 1B D12a

description: D12_Mut+ Dia-


title: LNDBB_subject_38_hippocampus


title: PO-4

source_name: proximal outflow tract, single cell


title: RS-4

source_name: right septum, single cell

value: right septum


title: RV-4


title: 085 - 2B D0b

description: UD_Mut+ Dia+

source_name: MODY5 hiPSC_undifferentiated

value: undifferentiated


title: LS-4

source_name: left septum, single cell


title: LNDBB_subject_34_hippocampus


title: 085 - 1d D12a

description: D12_Non Fam Ctr


title: LNDBB_subject_30_hippocampus

value: F


title: LV-4

source_name: left ventricle, single cell


title: 085 - D17 6Cc

description: D17_Fam Ctr


title: 085 - 6C D0c

description: UD_Fam Ctr

source_name: control hiPSC_undifferentiated


title: 085 - 1d D0a

description: UD_Non Fam Ctr


title: AVC-4

source_name: atrioventricular canal, single cell

value: atrioventricular canal


title: hiPSC_day10differentiation_rep2

treatment_protocol: Day 10 differentiated hiPSCs were differentiated with growth factors and chemical compounds in RPMI 2 % B-27


title: 085 - 1B D0a

description: UD_Mut+ Dia-


title: hiPSC_day10differentiation_rep1


title: Thy-1-CD24medCD49fhigh, replicate 2_FVB

city: Palo Alto

first: Neethan

middle: Amit

last: Lobo

state: CA

address: 265 Campus Drive

department: Institute for Stem Cell and Regenerative Medicine

institute: Stanford University

description: Gene expression data from FACS enriched cell populations from mammary tissue of 6-8 week old virgin female FVB mice

hyb_protocol: Hybridized to Mouse Genome 430 2.0 Arrays (Affymetrix) following manufacturer's instructions.

scan_protocol: Standard scanning protocols from Stanford PAN facility.

data_processing: MIDAS: log2-RMA followed by Cluster 3.0 for probe trimming and mean centering. Visualized and statistically analyzed by TIGR's TM4 MeV software. log2 GC-RMA, probes selected for which at least 2 arrays have greater than 6.229 probe signal, maxValue-minValue of a probe is greater than 2.0, probe signals are mean centered across arrays from a specific mouse genotype.

source_name: Thy-1-CD24medCD49fhigh cells from 6-8 week old FVB mammary glands

label_protocol: Affymetrix 3' IVT two-cycle target labeling was performed according to the manufacturer's instructions.

growth_protocol: Virgin 6-8 week old FVB were euthanized and mammary glands were freshly dissociated into single cells with Collagenase/Hyaluronidase followed by dispase and a short trypsin treatment.

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

treatment_protocol: Cells were stained with antibodies against CD45, CD31, Ter119, CD49f, CD24 and Thy-1 and were double sorted for the indicated phenotypes. Cells were pelleted ans stored at -80C until processed for RNA extraction.

value: Mammary epithelium

value: FVB

value: 6-8 weeks

tag: cell markers


title: LNDBB_subject_33_hippocampus


title: RA-4

source_name: right atrium, single cell

value: right atrium


title: LNDBB_subject_25_hippocampus


title: LNDBB_subject_23_hippocampus

value: schizophrenia


title: LNDBB_subject_27_hippocampus


title: LA-4

source_name: left atrium, single cell

value: left atrium


title: Thy-1-CD24medCD49fhigh, replicate 1_FVB


title: Thy-1+CD24medCD49fhigh, replicate 2_FVB

source_name: Thy-1+CD24medCD49fhigh cells from 6-8 week old FVB mammary glands


title: LS-11

value: left septum


title: Thy-1+CD24medCD49fhigh, replicate 1_FVB


title: hiPSC_undifferentiated_rep1

value: male

value: hiPSC from AG16102 skin fibroblast


title: AVC-12


title: Sox6KO_P60_rep3

city: Davis

first: Chung-Il

last: An

address: One Shields Ave.

institute: University of California, Davis

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Hybridization signals below background levels in each array were removed using a mean+2s of negative control values calculated using negative control probes on the beadchip arrays as an intensity cutoff.  Next, “Bad” and “No match” probes which do not match with the most recent gene annotation database were removed using the information from illuminaMousev2PROBEQUALITY in the illuminaMousev2.db.  Probe annotations were then updated using the information from illuminaMousev2SYMBOLREANNOTATED in the illuminaMousev2.db and Mouse Genome Informatics.  For time course data analysis, data from all arrays were combined and the probes missing at one or more time points were eliminated.  When one gene was represented by multiple probes, a probe with the highest intensity at P1 was selected for the following analyses.  Quantile normalization was then applied using the normalizeBetweenArrays function in the limma package.

source_name: Mouse cardiac ventricle

label_protocol: Biotinylated cRNA were prepared using Illumina TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacture’s instruction and then further purified using RNA Clean & Concentrator-5 (Zymo Research).  The integrity of RNA was confirmed using Bioanalyzer 2100 (Agilent Technologies).

value: FVB/B6 hybrid

value: Heart

tag: genotype

value: Sox6loxp/loxp; MCK-Cre

value: postnatal day 60


title: Sox6KO_P60_rep2

description: replicate 2


title: LV-11

value: left ventricle


title: CD24medCD49fmed, replicate 3_FVB

source_name: CD24medCD49fmed cells from 6-8 week old FVB mammary glands


title: AVC-11


title: CD24medCD49fmed, replicate 2_FVB


title: LNDBB_subject_19_hippocampus

source_name: hippocampus

value: M


title: LNDBB_subject_13_hippocampus


title: Sox6KO_P60_rep1

description: replicate 1


title: DO-3

value: distal outflow tract


title: Sox6KO_P30_rep3

description: replicate 3

value: postnatal day 30


title: Sox6KO_P30_rep2

description: replicate 2


title: LNDBB_subject_11_hippocampus


title: CD24highCD49fmed, replicate 2_FVB

source_name: CD24highCD49fmed cells from 6-8 week old FVB mammary glands

value: Mammary epithelium


title: LNDBB_subject_16_hippocampus

value: F


title: LNDBB_subject_12_hippocampus


title: RS-3

value: right septum


title: hiPSC_undifferentiated_rep2

value: undifferentiated


title: CD24medCD49f-/low, replicate 2_FVB

source_name: CD24medCD49f-/low cells from 6-8 week old FVB mammary glands

value: FVB

value: 6-8 weeks


title: PO-3

value: proximal outflow tract


title: CD24highCD49fmed, replicate 1_FVB


title: CD24medCD49f-/low, replicate 1_FVB


title: LNDBB_subject_18_hippocampus

value: schizophrenia


title: Sox6KO_P14_rep2

description: replicate 2

value: postnatal day 14


title: Sox6KO_P14_rep3

description: replicate 3

value: FVB/B6 hybrid


title: Sox6KO_P30_rep1

description: replicate 1

value: Heart


title: LNDBB_subject_6_hippocampus


title: LNDBB_subject_2_hippocampus


title: LNDBB_subject_9_hippocampus


title: LS-3

value: left septum


title: RV-3

source_name: right ventricle, single cell

value: right ventricle


title: LV-3

value: left ventricle


title: LNDBB_subject_3_hippocampus


title: LNDBB_subject_1_hippocampus

value: M


title: LNDBB_subject_4_hippocampus


title: Thy-1+CD24medCD49fhigh, replicate 1_BL6

description: Gene expression data from FACS enriched cell populations from mammary tissue of 6-8 week old virgin female BL6 mice

source_name: Thy-1+CD24medCD49fhigh cells from 6-8 week old BL6 mammary glands

growth_protocol: Virgin 6-8 week old C57BL6/J were euthanized and mammary glands were freshly dissociated into single cells with Collagenase/Hyaluronidase followed by dispase and a short trypsin treatment.


title: Sox6KO_P14_rep1

description: replicate 1

value: Sox6loxp/loxp; MCK-Cre


title: LNDBB_subject_10_hippocampus


title: DBCBB_subject_9_cerebellum

source_name: cerebellum

value: control


title: Thy-1+CD24medCD49fhigh, replicate 3_BL6

value: Mammary epithelium


title: Thy-1-CD24medCD49fhigh, replicate 1_BL6

source_name: Thy-1-CD24medCD49fhigh cells from 6-8 week old BL6 mammary glands


title: LA-3

value: left atrium


title: AVC-3

value: atrioventricular canal


title: RA-3

value: right atrium


title: Thy-1+CD24medCD49fhigh, replicate 2_BL6


title: Thy-1-CD24medCD49fhigh, replicate 2_BL6


title: Sox6KO_P7_rep3

description: replicate 3

value: postnatal day 7


title: Sox6KO_P7_rep2

description: replicate 2


title: Sox6KO_P7_rep1

description: replicate 1


title: LS-10

source_name: left septum, single cell


title: LV-10

source_name: left ventricle, single cell


title: CD24medCD49fmed, replicate 3v_BL6

source_name: CD24medCD49fmed cells from 6-8 week old BL6 mammary glands

value: 6-8 weeks


title: AVC-10

source_name: atrioventricular canal, single cell


title: DBCBB_subject_8_cerebellum


title: Thy-1-CD24medCD49fhigh, replicate 3_BL6


title: DO-2

source_name: distal outflow tract, single cell

value: distal outflow tract


title: PO-2

source_name: proximal outflow tract, single cell

value: proximal outflow tract


title: DBCBB_subject_7_cerebellum

value: schizophrenia


title: Sox6KO_P1_rep3

description: replicate 3

value: FVB/B6 hybrid

value: postnatal day 1


title: RS-2

source_name: right septum, single cell

value: right septum


title: RV-2

value: right ventricle


title: CD24highCD49fmed, replicate 2_BL6

source_name: CD24highCD49fmed cells from 6-8 week old BL6 mammary glands


title: CD24medCD49fmed, replicate 1_BL6


title: CD24highCD49fmed, replicate 3_BL6


title: Sox6KO_P1_rep2

description: replicate 2

source_name: Mouse cardiac ventricle

value: Heart


title: Control_P60_rep1

description: replicate 1

value: MCK-Cre

value: postnatal day 60


title: CD24medCD49fmed, replicate 2_BL6


title: LS-2

value: left septum


title: Control_P60_rep2

description: replicate 2


title: Sox6KO_P1_rep1

description: replicate 1

value: Sox6loxp/loxp; MCK-Cre


title: CD24highCD49fmed, replicate 1_BL6

value: Mammary epithelium


title: Control_P60_rep3

description: replicate 3


title: Control_P30_rep3

description: replicate 3

value: postnatal day 30


title: Control_P30_rep2

description: replicate 2


title: DBCBB_subject_4_cerebellum

value: control

value: M


title: DBCBB_subject_33_cerebellum


title: DBCBB_subject_34_cerebellum


title: Control_P14_rep2

description: replicate 2

value: postnatal day 14


title: DBCBB_subject_6_cerebellum


title: Control_P14_rep3

description: replicate 3


title: Control_P30_rep1

description: replicate 1


title: DBCBB_subject_5_cerebellum


title: DBCBB_subject_31_cerebellum


title: RA-2

source_name: right atrium, single cell

value: right atrium


title: LS-9


title: LA-2

source_name: left atrium, single cell

value: left atrium


title: LV-2

value: left ventricle


title: Control_P7_rep2

description: replicate 2

value: FVB/B6 hybrid

value: postnatal day 7


title: DBCBB_subject_30_cerebellum

value: schizophrenia


title: Control_P14_rep1

description: replicate 1


title: LV-9


title: Control_P7_rep3

description: replicate 3


title: AVC-2

value: atrioventricular canal


title: AVC-9


title: DBCBB_subject_32_cerebellum


title: DBCBB_subject_35_cerebellum

value: F


title: CD24medCD49f-/low, replicate 2_BL6

source_name: CD24medCD49f-/low cells from 6-8 week old BL6 mammary glands

value: 6-8 weeks


title: Striatum, KO animal 3

city: Ulm

first: Hanna

last: Bayer

address: Helmholtzstrasse 8/1

institute: Ulm University

hyb_protocol: according to Affymetrix

scan_protocol: according to Affymetrix; GeneChip Fluidics Station 450 and GeneChip Scanner 3000  were used for washing and scanning

data_processing: BRB Array Tools

label: Biotin

source_name: Striatum of homozygous B6.129-Ppargc1atm1Brsp/J

label_protocol: One Cycle Target Labelling Protocol

extract_protocol: Rneasy Mini Kit, Qiagen

value: homozygous B6.129-Ppargc1atm1Brsp/J

value: Striatum


title: Control_P7_rep1

description: replicate 1

value: Heart

value: MCK-Cre


title: Striatum, WT animal 1

source_name: Striatum of wild type littermate of B6.129-Ppargc1atm1Brsp/J

value: wild type littermate


title: Striatum, WT animal 3


title: DO-1

value: distal outflow tract


title: PO-1

value: proximal outflow tract


title: Control_P1_rep2

description: replicate 2

value: postnatal day 1


title: Control_P1_rep3

description: replicate 3


title: CD24medCD49f-/low, replicate 1_BL6

value: Mammary epithelium


title: Striatum, WT animal 2


title: Striatum, KO animal 1


title: DBCBB_subject_29_cerebellum

value: M


title: Striatum, KO animal 2


title: EH70 Control

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description: Control

data_processing:
QuantStudio™ run files from GS (n=4) and control macaques (n=5) were analyzed simultaneously using ExpressionSuite software v1.0.3 (Thermo-Fisher). Since Expression Suite software is not equipped to perform non-parametric analysis, the output file containing five columns (well, sample, detector, task and CT values) were saved as a tab-delimited text file, imported and analyzed by non-parametric Wilcoxon’s rank sum test for independent samples using RealTime STATMINER™ package (Integromics on Spotfire DecisionSite) designed to compare samples using the DDCT method for relative quantification of gene expression.
miRNA expression data was analyzed by normalizing to two endogenous controls (RNU44 and RNU48)
In all experiments, the CT upper limit was set to 28 meaning that all miRNA detectors with a CT value greater than or equal to 28 were excluded.
Due to the small sample size and exploratory nature of the study multiple comparisons correction was not applied.
RealTime STATMINER software calculates all deltadeltaCT based fold-change calculations and provides p values using the wilcoxon's rank sum test.
fold-change.txt reports test/control (i.e., GS vs Control) ratios.

organism: Macaca mulatta

source_name: Intact Jejunum

label_protocol: microRNA profiling was performed using the TaqMan® OpenArray® Human microRNA panels (Life Tech) following the manufacturer’s instructions. Reverse transcription was first performed from 100 ng of total RNA using the microRNA reverse transcription kit. 2.5 µL of cDNA was preamplified using the TaqMan® PreAmp Master Mix kit. Preamplified products were first diluted and then loaded onto to TLDA plates. TLDA plates were run on the ABI 7900 HT Fast PCR system following the manufacturer’s recommended thermal cycling conditions.

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

treatment_protocol: 4 gluten sensitive rhesus macaques were fed gluten containing chow and 5 were normal healthy controls

value: intact jejunum

tag: phenotype

value: healthy control


title: RS-1

value: right septum


title: EL66 Control

description: Control


title: DBCBB_subject_27_cerebellum

source_name: cerebellum

value: control


title: DBCBB_subject_28_cerebellum

value: schizophrenia


title: RV-1

source_name: right ventricle, single cell

value: right ventricle


title: HR84 Control

description: Control


title: DBCBB_subject_3_cerebellum


title: Control_P1_rep1

description: replicate 1

value: FVB/B6 hybrid


title: LS-1

source_name: left septum, single cell

value: left septum


title: HA09 Control

description: Control


title: FH45 GS

description: GS

value: gluten-sensitive


title: LV-1

source_name: left ventricle, single cell

value: left ventricle


title: AVC-1

value: atrioventricular canal


title: FH09 GS

description: GS


title: FB97 GS

description: GS


title: DE87 GS

description: GS


title: DBCBB_subject_25_cerebellum


title: LA-1

value: left atrium


title: RA-1

value: right atrium


title: DBCBB_subject_2_cerebellum


title: DBCBB_subject_23_cerebellum


title: DBCBB_subject_21_cerebellum


title: DBCBB_subject_20_cerebellum


title: DBCBB_subject_17_cerebellum


title: DBCBB_subject_16_cerebellum


title: DBCBB_subject_18_cerebellum


title: cold-treated leaves rep2

status: Public on Nov 09 2016

city: Qingdao

last: Chen

address: wannianquan road

country: China

institute: Shandong Peanut Research Institute

description: This sample is of cold treated leaves of peanut huayu19. It is the second of three wild-type biological replicates used in this experiment.

hyb_protocol: Labeled samples were dried and redissolved in the hybridization solution, DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Hybridization was performed at 42℃ for 14h with NimbleGen Hybridization System, Array were washed in wash buffer I and II and III supplied by NimbleGen,and dried in NimbleGen Microarray Dryer.

scan_protocol: After hybridizations, microarrays were scanned using the Roche NimbleGen MS200 scanner and the data of obtained images were extracted with NimbleScan software at CapitalBio Corporation.

data_processing: Normalization was performed using RMA (Robust Multichip Analysis) method and further analysis was performed with SAM (Significance Analysis of Microarrays) software (Tusher et al. 2001).

organism: Arachis hypogaea

source_name: cold-treated leaves

label_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription using CbcScript Ⅱ reverse transcriptase. Briefly, 2 µg amplified RNA was mixed with 4 µg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 µL of 4×first-strand buffer, 2 µL of 0.1M DTT, and 1.5 µL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 µL. The cDNA was mixed with 4 µg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 µL Klenow buffer, dNTP, and Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 µM dATP, 240 µM dGTP, 240 µM dTTP, 120 µM dCTP, and 40 µM Cy-dCTP. 1.2 µL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

growth_protocol: Peanut seeds were germinated in a mixture of nutrient-rich soil and vermiculite (2:1) and grown under conditions of 16/8 h and 28/22°C of light/dark.

extract_protocol: Total RNA was isolated from samples using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA samples were purified with a NucleoSpin® RNA clean-up kit (MACHEREY-NAGEL, Germany). RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantified spectrophotometrically. All RNA was stored at –80°C until further analysis.

treatment_protocol: Seedlings at the trefoil leaf stage were maintained at 4°C in a light incubator. The leaves were collected after 48 h of cold treatment and untreated leaves were used as controls. All the samples were immediately frozen in liquid nitrogen and then stored at -80℃ until required.

tag: cultivar

value: huayu 19


title: untreated leaves rep2

description: This sample is of untreated leaves of peanut huayu19. It is the second of three wild-type biological replicates used in this experiment.

source_name: untreated leaves


title: AA-CJ/CC-CJ Replicate 1

city: Amsterdam

first: Mark

last: Verheijen

address: De Boelelaan 1085

institute: CNCR, Vrije University Amsterdam

hyb_protocol: Arrays were hybridized with Cy5 and Cy3 solution for 18h at 60°C in a rotating hybridization chamber, using 1x hybridization solution (Agilent technologies).

scan_protocol: Arrays were scanned using an Agilent scanner.

data_processing: Normalization of the raw data was performed, after feature extraction by Agilent software, by Optimized Local Intensity-dependent Normalization (OLIN) and Optimized Scaled Local Intensity-dependent Normalization (OSLIN) (Futschik and Crompton, 2005) using the R project for statistical computing (version 6.0; r-project)

organism: Rattus norvegicus

source_name: Astrocytes from co-cultures purified by cold jet treatment

label_protocol: oligo dT primers were used and Cy3 and Cy5 labeling was done using the Agilent Two-color RNA Spike-In Kit instructions

growth_protocol: Primary rat astrocytes were obtained from Wistar rat pups (P1) and cultured in DMEM + Glutamax containing 10% fetal bovine serum and cultured in non-coated plastic flasks. For co-plating of neurons, hippocampi of E18 mouse embryos were collected and cultured in Neurobasal medium supplemented with 2% B-27, 1.8% HEPES, 1% glutamax, 1% Pen/Strep (Invitrogen), and 0.2% beta-mercaptoethanol on the astrocyte monolayers in 12 well plates. Cultures were maintained in 5% CO2 at 37°C, and half of the medium was changed at 1 day and 7 days after plating. Control conditions (astrocytes alone) were kept under similar tissue culture conditions as neuron-astrocyte co-cultures.

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

treatment_protocol: For removal of neurons from the co-cultured astrocytes, we modified a method previously used for removal of Schwann cells from co-cultured fibroblasts (Jirsova et al., 1997). 12-well tissue culture plates were placed on ice and the medium was gently aspirated. The cells were carefully rinsed once with ice-cold PBS (pH 7.4). Next, using a 1 mL pipette tip, 1mL of ice-cold PBS was pipetted onto the cocultures using a concentric circular motion, ensuring the force of the stream contacted the entire well surface area, which was repeated 3 times. This resulted in specific detachment of neurons  which were aspirated, leaving purified astrocytes, which were harvested for molecular analysis

tag: background strain

value: Wistar

value: Astrocytes

source_name: Astrocyte alone with cold jet treatment


title: DBCBB_subject_19_cerebellum

value: F


title: untreated leaves rep1

description: This sample is of untreated leaves of peanut huayu19. It is the first of three wild-type biological replicates used in this experiment.


title: AA-CJ/CC-CJ Replicate 2


title: CC/CC-CJ Replicate 2

source_name: Co-cultures neurons and astrocytes

value: Astrocytes and neurons


title: cold-treated leaves rep3

description: This sample is of cold treated leaves of peanut huayu19. It is the third of three wild-type biological replicates used in this experiment.


title: DBCBB_subject_24_cerebellum


title: Normal Cervical Tissue  [Experimento 342]

city: México

first: MAURICIO

middle: SALCEDO

last: VARGAS

address: Cuauhtemoc 300

department: UIMEO

country: Mexico

institute: Mexican Institute for Social Security

hyb_protocol: Labeled cRNA was hybridized to Human Gene 1.0 ST arrays (Affymetrix) at 45°C for 16 h. The probe arrays were washed ans stained on a Affymetrix GeneChip Fluidics-450 following the manufacturer´s instructions.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G System.

data_processing: Microarrays analysis was carried out using the software Partek Genomic Suite v6.5 ((Partek, St. Louis, MO). Probe sets were summarized by means of Median Polish, Quantile normalization, with no probe sets excluded from the analysis. Background correction was achieved by means Robust Multi-chip Average (RMA) and data were log2 transformed

source_name: Normal cervical tissues were from women who underwent hysterectomy

label_protocol: 100 ng of RNA in each sample with RNA integrity number >7 was  reverse transcribed, amplified and labeled with the Ambion WT Express kit (Ambion)

extract_protocol: Total RNA was obtained with the miRVana Isolation Kit (Ambion, Life Technologies, CA, USA) according to the manufacturer’s instructions.

value: Normal Cervical Tissue


title: Cervical Cell Line Inbl [Experimento 340 ]

source_name: Inbl HPV18

tag: cell line

value: Cervical Cell Line Inbl


title: KO HZ5

city: Bethesda

first: Julian

middle: CK

last: Lui

state: MD

address: 10 Center Drive

institute: NICHD, NIH

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

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

data_processing: The data were nomanized by RMA with Parteck Genomic Suit 6.6

source_name: Ezh2 KO proximal tibia HZ

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

growth_protocol: growth plate zones dissected from proximal tibia using laser capture microdissection

extract_protocol:
tissue microdissected from 30-40 sections from a single animal were combined and RNA were isolated by picopure RNA isolation kit
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: tissues from Proliferative zone (PZ) and Hypertrophic zones (HZ) of proximal tibial growth plate from KO and wild type were dissected from 3-day old mice by laser capture microdissection for microarray experiments

value: Ezh2 KO

value: tibia

tag: growth plate zone

value: Hypertrophic zone (HZ)

value: 3 days old


title: KO HZ4


title: KO HZ3


title: DBCBB_subject_14_cerebellum

tag: diagnosis

value: control

value: M


title: KO HZ2

tag: age


title: DBCBB_subject_12_cerebellum

tag: gender


title: KO HZ6


title: Cervical Cell Line C-33A [Experimento 339]

source_name: C-33A negative for HPV

value: Cervical Cell Line C-33A


title: DBCBB_subject_13_cerebellum


title: Keratinocyte Cell Line Hacat [Experimento 337]

source_name: Hacat negative for HPV

value: Keratinocyte Cell Line Hacat


title: CC/CC-CJ Replicate 1


title: DBCBB_subject_15_cerebellum

value: schizophrenia


title: HB72 Control

description: Control

value: intact jejunum

value: healthy control


title: Cervical Cell Line Vipa [Experimento 174]

source_name: Vipa HPV18

value: Cervical Cell Line Vipa


title: WT HZ6

source_name: WT proximal tibia HZ

value: wildtype


title: Cervical Cancer [Experimento 164]

source_name: Squamous cell carcinoma

value: Cervical Cancer


title: Cervical Cancer [Experimento 163]


title: WT HZ5


title: Cervical Cancer [Experimento 162]


title: Cervical Cancer [Experimento 165]


title: WT HZ4


title: Cervical Cell Line ROVA [Experimento 151]

source_name: ROVA HPV18

value: Cervical Cell Line ROVA


title: cold-treated leaves rep1

description: This sample is of cold treated leaves of peanut huayu19. It is the first of three wild-type biological replicates used in this experiment.

value: huayu 19


title: KO HZ1


title: Normal Cervical Tissue  [Experimento 154]

value: Normal Cervical Tissue


title: Cervical Cell Line HeLa [Experimento 153]

source_name: HeLa HPV18

value: Cervical Cell Line HeLa


title: Cervical Cell Line SiHa [Experimento 152]

source_name: SiHa HPV16

value: Cervical Cell Line SiHa


title: Cervical Cell Line Caski [Experimento 119]

source_name: Casky HPV16

value: Cervical Cell Line Caski


title: WT HZ1

value: tibia

value: Hypertrophic zone (HZ)

value: 3 days old


title: WT HZ3


title: DBCBB_subject_1_cerebellum

source_name: cerebellum

value: control

value: M


title: DBCBB_subject_11_cerebellum

value: schizophrenia

value: F


title: DBCBB_subject_10_cerebellum


title: 600uM_FA_15G_rep3

city: Gainesville

first: Chris

last: Vulpe

state: FL

address: 2187 Mowry Drive, Building 470, Room 113, PO Box 110885

institute: University of Florida

hyb_protocol: Arrays were incubated overnight and then stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix). Please see Jo et al., 2009, PMID: 19635755

data_processing: Raw TAG4 array data were log2 transformed, corrected for signal saturation as previously described (Pierce et al., 2006), and corrected for mean chip background using robust location and scale estimators for log2-transformed intensities of null features (total of 18,000 equally distributed on the array). Please see Jo et al., 2009, PMID: 19635755

label_protocol: The strain-specific barcodes in the DNA were amplified by PCR using a set of biotinylated primers. Please see Jo et al., 2009, PMID: 19635755

extract_protocol: Cells were collected and genomic DNA was extracted using the YDER kit (Pierce Biotechnology, Rockford, IL). Please see Jo et al., 2009, PMID: 19635755

tag: treatment

value: 600uM FA


title: KO PZ6

source_name: Ezh2 KO proximal tibia PZ

value: Ezh2 KO

value: proliferative zone (PZ)


title: Huh7.5 cells stimulated with IL10 for 72 hrs 4

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

institute: University of  Oxford

hyb_protocol: Hybridization protocol Fragmented labeled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). A 200µl of this hybridization cocktail was used on the chip and incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v5, Affymetrix) of double-staining and post-hybridisations washes.

scan_protocol: Fluorescent images were captured using gene Array Scanner 3000 and GCOS1.2 software (Affymetrix).

data_processing: We have used the genechip robust multi-array average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 32,321 probe sets (transcripts) on each array.

source_name: Cell line Human hepatocyte Huh7.5

label_protocol: 8 microgram total RNA used in Affymetrix one cycle target labeling kit cat. no. 900493.

growth_protocol: Human hepatocyte cell line Huh7.5 cells were grown in DMEM media, supplemented with 10% FCS, Penicillin/Streptomycin and MEM nonessential aminoacids

extract_protocol: Cellular RNA was extracted from cells using Rneasy Mini kit (Qiagen) following manufacturers protocol

treatment_protocol: Huh7.5 cells were cultured in DMEM media and treated with 100ng/ml of IL-27 for 72 hrs at 37oC 5% CO2 in culture media.

tag: stimulation

value: IL10 for 72 hrs


title: Cervical Cell Line C-4 I [Experimento 175]

source_name: C-4 I HPV18

value: Cervical Cell Line C-4 I


title: Cervical Cell Line MS-751 [Experimento 338]

value: Cervical Cell Line MS-751


title: KO PZ5


title: Huh7.5 cells stimulated with IFNA for 72 hrs 4

value: IFNA for 72 hrs


title: Huh7.5 cells stimulated with IL17 for 24 hrs 4

value: IL17 for 24 hrs


title: Huh7.5 cells stimulated with IL22 for 72 hrs 2

value: IL22 for 72 hrs


title: 600uM_FA_15G_rep2

scan_protocol: Arrays were incubated overnight and then stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix). Please see Jo et al., 2009, PMID: 19635755


title: 300uM_FA_15G_rep3

growth_protocol: Please see Jo et al., 2009, PMID: 19635755

value: 300uM FA


title: untreated leaves rep3

description: This sample is of untreated leaves of peanut huayu19. It is the third of three wild-type biological replicates used in this experiment.

source_name: untreated leaves

value: huayu 19


title: Huh7.5 cells stimulated with IL22 for 72 hrs 3


title: Huh7.5 cells stimulated with IL17 for 24 hrs 3


title: KO PZ4

value: tibia


title: 600uM_FA_15G_rep1

treatment_protocol: Please see Jo et al., 2009, PMID: 19635755


title: Normal Cervical Tissue  [Experimento 120]

source_name: Normal cervical tissues were from women who underwent hysterectomy

value: Normal Cervical Tissue


title: Huh7.5 cells stimulated with IL22 for 72 hrs 4


title: Huh7.5 cells stimulated with IFNA for 72 hrs 2


title: Huh7.5 cells stimulated with IL22 for 72 hrs 1


title: 150uM_FA_15G_rep3

value: 150uM FA


title: 300uM_FA_15G_rep1


title: KO PZ1

value: 3 days old


title: Huh7.5 cells stimulated with IFNA for 72 hrs 1


title: KO PZ3


title: KO PZ2


title: Huh7.5 cells stimulated with IL22 for 24 hrs 3

value: IL22 for 24 hrs


title: Mock Stimulated Huh7.5 cells 4

value: mock


title: WT HZ2

value: wildtype

value: Hypertrophic zone (HZ)


title: 300uM_FA_15G_rep2


title: Huh7.5 cells stimulated with IFNA for 72 hrs 3


title: WT PZ6

source_name: WT proximal tibia PZ

value: proliferative zone (PZ)


title: Huh7.5 cells stimulated with IL27 for 72 hrs 3

value: IL27 for 72 hrs


title: Huh7.5 cells stimulated with IL28 for 72 hrs 3

value: IL28 for 72 hrs


title: Huh7.5 cells stimulated with IL28 for 72 hrs 1


title: Mock Stimulated Huh7.5 cells 3


title: Huh7.5 cells stimulated with IL28 for 72 hrs 2


title: WT PZ5


title: WT PZ4


title: WT PZ3


title: Huh7.5 cells stimulated with IL27 for 72 hrs 2


title: 600uM_FA_5G_rep3

value: 600uM FA


title: 150uM_FA_15G_rep2


title: Huh7.5 cells stimulated with IL27 for 72 hrs 1


title: Huh7.5 cells stimulated with IL22 for 24 hrs 2


title: 150uM_FA_15G_rep1


title: Huh7.5 cells stimulated with IL10 for 72 hrs 2

value: IL10 for 72 hrs


title: 600uM_FA_5G_rep1


title: WT PZ2


title: 600uM_FA_5G_rep2


title: Mock Stimulated Huh7.5 cells 2


title: Mock Stimulated Huh7.5 cells 1


title: 300uM_FA_5G_rep3


title: Huh7.5 cells stimulated with IL22 for 24 hrs 1


title: 300uM_FA_5G_rep2


title: P4N-treated 12 h-2

city: Hsinchu City

first: Yu-Ling

last: Lin

address: Po-Ai street

department: Department of Biological Science and Technology

country: Taiwan

institute: National Chiao Tung University

description: Sample name: SAMPLE 6

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: THP-1 cell_P4N-treated

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

growth_protocol: THP-1 cells were cultured in in a RPMI-1640 culture medium supplemented with 4.5 g/L glucose (MP Biomedicals, Santa Ana, OH), 10 mM HEPES (MP Biomedicals), 1.0 mM sodium pyruvate (MP Biomedicals), 0.05 mM 2-mercaptoethanol (AMRESCO, OH, USA), 10% fetal calf serum (Invitrogen), and 1% penicillin-streptomycin (Invitrogen).

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

treatment_protocol: THP-1 cells (5 x10^5 cells/ml) in 1 ml of culture medium were seeded in each well of a 24-well microplate and treated with 3 uM of P4N for 12 h.

value: monocyte


title: 300uM_FA_5G_rep1


title: Huh7.5 cells stimulated with IL17 for 24 hrs 1

value: IL17 for 24 hrs


title: P4N-treated 12 h-3

description: Sample name: SAMPLE 7


title: Cervical Cell Line CaLo [Experimento 176]

source_name: CaLo HPV18

value: Cervical Cell Line CaLo


title: P4N-treated 12 h-4

description: Sample name: SAMPLE 8


title: Untreat-2

description: Sample name: SAMPLE 2

source_name: THP-1 cell_untreated


title: P4N-treated 12 h-1

description: Sample name: SAMPLE 5


title: WT PZ1


title: A1105C

city: Beijing

first: yang

last: sihang

address: Haidian district Shuangqing road #30

institute: Tsinghua University

description: GeoChip data for organic soil sample at control condition, replicate 2

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

organism: soil metagenome

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: Soil DNA was extracted by freeze-grinding mechanical lysis as previously described (Zhou et al 1996). Freshly extracted DNA was purified twice using 0.5% low melting point agarose gel followed by phenol-chloroform-butanol extraction. DNA quality and quantity were assessed by the ratios of 260 nm/280 nm and 260 nm/230 nm, and final DNA contents were quantified with a PicoGreen method using a FLUO star Optima .

value: Soil microbes

tag: geographical location

value: USA:Barrow, Alaska

tag: layer

value: organic

tag: temperature

value: 0℃

tag: day


title: Huh7.5 cells stimulated with IL10 for 72 hrs 3


title: Huh7.5 cells stimulated with IL10 for 72 hrs 1


title: A1104C

description: GeoChip data for organic soil sample at control condition, replicate 3

tag: tissue


title: A2107C

description: GeoChip data for organic soil sample incubated at warmest month condition for 34 day, replicate 3


title: 150uM_FA_5G_rep3

value: 150uM FA


title: Untreat-4

description: Sample name: SAMPLE 4

tag: cell type


title: Untreat-3

description: Sample name: SAMPLE 3


title: A2108C

description: GeoChip data for organic soil sample incubated at warmest month condition for 34 day, replicate 2


title: A1106C

description: GeoChip data for organic soil sample at control condition, replicate 1


title: Treatment with IL-4 for 72 hours, biological rep3

city: Pozzuoli

first: Diego

last: Carrella

state: NAPOLI

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

description: Gene expression data in human bronchial epithelial cells from cystic fibrosis patients treated with IL-4 for 72 hours

hyb_protocol: Hybridization and scanning was performed on the Affymetrix platform.

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: bronchus

label_protocol: Oligo(dT)-primed cDNAs were synthesized using the SuperScript III First-Strand Synthesis SuperMix (Invitrogen, Irvine, CA) following manufacturer’s instructions. For microarray analysis, double-stranded cDNAs were synthesized using the Custom SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and extracted with phenol-chloroform isoamyl alcohol (25:24:1), ethanol precipitated, and used to prepare cRNAs using the Bioarray High Yield RNA Transcription Kit (Affymetrix, Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: Primary bronchial epithelial cells were first grown in LHC9/RPMI 1640 serum-free medium and then plated on porous Snapwell inserts.  Differentiation was obtained in serum-containing medium enriched with hormones and supplements (Scudieri et al., J Physiol 590: 6141-6145, 2012).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions.

treatment_protocol: Six days after plating, the medium on the apical side was removed (air liquid culture, ALC) to further promote mucociliary differentiation.  After two weeks under ALC condition, cells were treated with and without  IL-4 for 6, 12, 24, or 72 hours.

value: primary bronchial epithelial cells


title: Treatment with IL-4 for 72 hours, biological rep2

scan_protocol: Hybridization and scanning was performed on the Affymetrix platform.


title: A4123C

description: GeoChip data for organic soil sample incubated at a near-freezing condition for 60 day, replicate 1

value: 8℃


title: A3119C

description: GeoChip data for organic soil sample incubated at warmest month condition for 122 day, replicate 2


title: Treatment with IL-4 for 72 hours, biological rep1


title: Control 72hr, biological rep3

description: Gene expression data in human bronchial epithelial cells from cystic fibrosis patients


title: A2109C

description: GeoChip data for organic soil sample incubated at warmest month condition for 34 day, replicate 1


title: A3118C

description: GeoChip data for organic soil sample incubated at warmest month condition for 122 day, replicate 3


title: Control 72hr, biological rep2


title: A4121C

description: GeoChip data for organic soil sample incubated at a near-freezing condition for 60 day, replicate 3


title: A3120C

description: GeoChip data for organic soil sample incubated at warmest month condition for 122 day, replicate 1


title: A5114C

description: GeoChip data for organic soil sample incubated at a near-freezing condition for 122 day, replicate 3


title: Control 24hr, biological rep3


title: B1204C

description: GeoChip data for mineral soil sample at control condition, replicate 3

value: mineral


title: 150uM_FA_5G_rep2


title: 150uM_FA_5G_rep1


title: Treatment with IL-4 for 24 hours, biological rep3

description: Gene expression data in human bronchial epithelial cells from cystic fibrosis patients treated with IL-4 for 24 hours


title: B1206C

description: GeoChip data for mineral soil sample at control condition, replicate 2


title: A5116C

description: GeoChip data for organic soil sample incubated at a near-freezing condition for 122 day, replicate 1


title: Control 24hr, biological rep2


title: Treatment with IL-4 for 24 hours, biological rep2


title: A5115C

description: GeoChip data for organic soil sample incubated at a near-freezing condition for 122 day, replicate 2


title: Untreat-1

description: Sample name: SAMPLE 1


title: A4122C

description: GeoChip data for organic soil sample incubated at a near-freezing condition for 60 day, replicate 2


title: Treatment with IL-4 for 12 hours, biological rep3

description: Gene expression data in human bronchial epithelial cells from cystic fibrosis patients treated with IL-4 for 12 hours


title: B1201A

description: GeoChip data for mineral soil sample at control condition, replicate 1


title: Control 24hr, biological rep1


title: Treatment with IL-4 for 12 hours, biological rep2


title: B3210A

description: GeoChip data for mineral soil sample incubated at warmest month condition for 122 day, replicate 1


title: B3218C

description: GeoChip data for mineral soil sample incubated at warmest month condition for 122 day, replicate 3


title: Control 72hr, biological rep1


title: Control 12hr, biological rep2


title: Control 12hr, biological rep3


title: Treatment with IL-4 for 24 hours, biological rep1


title: B2208C

description: GeoChip data for mineral soil sample incubated at warmest month condition for 34 day, replicate 2


title: Treatment with IL-4 for 12 hours, biological rep1


title: Treatment with IL-4 for 6 hours, biological rep3

description: Gene expression data in human bronchial epithelial cells from cystic fibrosis patients treated with IL-4 for 6 hours


title: B2203A

description: GeoChip data for mineral soil sample incubated at warmest month condition for 34 day, replicate 1


title: Control 6hr, biological rep1

description: Gene expression data in human bronchial epithelial cells from cystic fibrosis patients


title: Control 12hr, biological rep1


title: B4221C

description: GeoChip data for mineral soil sample incubated at a near-freezing condition for 60 day, replicate 3


title: B3220C

description: GeoChip data for mineral soil sample incubated at warmest month condition for 122 day, replicate 2


title: Control 6hr, biological rep3


title: Treatment with IL-4 for 6 hours, biological rep1


title: Treatment with IL-4 for 6 hours, biological rep2


title: B4322C

description: GeoChip data for mineral soil sample incubated at a near-freezing condition for 60 day, replicate 1


title: Control 6hr, biological rep2


title: B4222C

description: GeoChip data for mineral soil sample incubated at a near-freezing condition for 60 day, replicate 2


title: B2207C

description: GeoChip data for mineral soil sample incubated at warmest month condition for 34 day, replicate 3


title: B5215C

description: GeoChip data for mineral soil sample incubated at a near-freezing condition for 122 day, replicate 3


title: Non-Pregnant control ID 357_set2

status: Public on Nov 08 2016

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

hyb_protocol: Following fragmentation, 5 micrograms of cDNA were diluted into 220 microlitres of hybridization cocktail, with 200 microlitres hybridized for 18 hr at 45 C on Human U133 Plus 2 Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data Processiing performed with TIBCO Spotfire and OmicsOffice

source_name: PBMC

label_protocol: Biotinylated cDNAs were prepared using Nugen Ovation WTA protocol from 25 ng total RNA.

extract_protocol: RNA was extracted using the Rneasy RNA Isolation Kit according to manufacturer's instructions.

tag: source

value: human

tag: condition

value: Non-Pregnant


title: Post-partum 12 weeks ID8_set1

value: Post-partum 12 weeks


title: Post-partum 24 weeks ID8_set1

value: Post-partum 24 weeks


title: Post-partum 2 weeks ID12_set2

value: Post-partum 2 weeks


title: B5216C

description: GeoChip data for mineral soil sample incubated at a near-freezing condition for 122 day, replicate 2


title: B5214C

description: GeoChip data for mineral soil sample incubated at a near-freezing condition for 122 day, replicate 1


title: Post-partum 24 weeks ID7_set1


title: Non-Pregnant control ID 354_set2


title: Post-partum 2 weeks ID10_set2


title: Post-partum 4 weeks ID8_set1

value: Post-partum 4 weeks


title: Post-partum 2 weeks ID7_set1


title: Post-partum 12 weeks ID7_set1


title: Post-partum 4 weeks ID7_set1


title: Non-Pregnant control ID 357_set1


title: liver_SS_HLD-50

city: Toronto

first: Johane

middle: P.

last: Allard

state: Ontario

address: 585 University Ave, 9-NU-973

department: Medicine

country: Canada

institute: University Health Network

data_processing: Data was checked for overall quality using R (v2.15.1) with the lumi Bioconductor package. Nine outliers (4 NASH, 5 SS), which fell below the threshold for one or more of the quality metrics  calculated with this package, were excluded from further analysis. The data were imported in GeneSpring v12.5 (Agilent) and normalized using a quantile normalization followed by a “per  probe” median centered normalization.

source_name: liver

label_protocol: 200 ng of RNA were labelled and amplified following Illumina Whole Genome Expression - DASL assay kit for partially degraded and FFPE derived RNA.

extract_protocol: Total RNA was extracted from liver biopsies using the mirVana miRNA Isolation kit (Life Technologies Corp., Carlsbad, CA, USA). RNA concentration and purity were assessed with a Thermo Scientific's NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

tag: array ^sample

value: SS

tag: steatosis (%)

tag: fibrosis (stage)

tag: ballooning (intensity)

tag: age (y)

value: male

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c

tag: diabetes

value: no

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: day7_HNT_NKG2+_biolrep1

city: Worcester

first: Allen

middle: Minh

last: Vong

state: MA

address: 368 Plantation Street

department: Pathology

institute: University of Massachusetts Medical School

description: gene expression of CD4 T cells expressing NKG2ACE in the lung 7 days post influenza A infection

hyb_protocol: Following fragmentation, 3.5ug of ss-cDNA were hybridized for 16hr at 45C on GeneChip Mouse Gene 2.0ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using Affymetrix Transcriptome Console 3.0. Data was normalized using RMA algorithm.

source_name: NKG2+ CD4 T cell day 7 post infection

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from total RNA [GeneChip WT Plus Reagent Kit User Manual, 2013 Affymetrix].

extract_protocol: Cells were kept in RNA cell protect [Qiagen] then total RNA extracted using RNA extraction kit based on manufacturer's protocol [Qiagen]

treatment_protocol: Transferred T cells of interested into mice, then infected mice intranasally with influenza A virus [A/PR8 strain], harvested lungs at day 7 post infection, mechanically disrupted lung for single cell suspensions, magnetically enriched for T cells, isolated cells of indicated phenotype using flow cytometry based sorting

tag: tissue

value: lung

tag: nkg2 status

value: positive

tag: cell type

value: CD4 T cell

tag: background strain

value: BALB/cByJ


title: day7_HNT_NKG2neg_biolrep1

description: gene expression of CD4 T cells not expressing NKG2ACE in the lung 7 days post influenza A infection

source_name: NKG2neg CD4 T cell day 7 post infection

value: negative


title: Post-partum 2 weeks ID8_set1

tag: source

tag: condition


title: liver_HC_HLD-41

tag: array ^sample

tag: diagnosis

value: HC

tag: age (y)

tag: gender

value: female

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)


title: liver_HC_HLD-23

tag: waist (cm)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c

tag: diabetes

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: Non-Pregnant control ID 354_set1

tag: source

tag: condition


title: day7_HNT_NKG2+_biolrep2

tag: tissue

tag: nkg2 status

tag: cell type

tag: background strain


title: liver_HC_HLD-53

tag: array ^sample

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: ballooning (intensity)

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)


title: liver_HC_HLD-51

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c

tag: diabetes

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: day7_HNT_NKG2neg_biolrep2

tag: tissue

tag: nkg2 status

tag: cell type

tag: background strain


title: liver_HC_HLD-13

tag: array ^sample

tag: diagnosis

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)


title: liver_HC_HLD-36

tag: steatosis (%)

tag: fibrosis (stage)

tag: ballooning (intensity)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c

tag: diabetes


title: liver_HC_HLD-35

tag: array ^sample

tag: diagnosis

tag: lobular inflammation (severity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_HC_HLD-14

tag: steatosis (%)

tag: fibrosis (stage)

tag: ballooning (intensity)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)


title: liver_HC_HLD-55

tag: array ^sample

tag: diagnosis

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c

tag: diabetes


title: liver_HC_HLD-47

tag: steatosis (%)

tag: fibrosis (stage)

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_HC_HLD-43

tag: ballooning (intensity)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)


title: liver_HC_HLD-10

tag: array ^sample

tag: diagnosis

tag: fasting glucose (mmol/l)

tag: hemoglobin a1c

tag: diabetes


title: liver_HC_HLD-21

tag: age (y)

tag: gender

tag: body mass index (kg/m2)


title: liver_SS_HLD-38

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: nafld activity score

tag: hdl cholesterol (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_HC_HLD-66

tag: array ^sample

tag: diagnosis

tag: ballooning (intensity)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)


title: liver_HC_HLD-26

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: hemoglobin a1c

tag: diabetes


title: liver_HC_HLD-56

tag: steatosis (%)

tag: fibrosis (stage)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_HC_HLD-11

tag: array ^sample

tag: diagnosis

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: hdl cholesterol (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance


title: liver_NASH_CL-167

value: NASH

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)


title: liver_SS_CL-161

tag: steatosis (%)

tag: fibrosis (stage)

tag: waist (cm)

tag: diabetes

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_NASH_CL-155

tag: array ^sample

tag: diagnosis

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c


title: liver_HC_HLD-7

tag: steatosis (%)

tag: ballooning (intensity)

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)


title: liver_HC_HLD-2

tag: array ^sample

tag: diagnosis

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: nafld activity score

tag: waist (cm)

tag: diabetes

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_SS_CL-142

tag: steatosis (%)

tag: ballooning (intensity)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: fasting insulin (pmol/l)

tag: hemoglobin a1c


title: liver_NASH_CL-132

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: homa-insulin resistance