title: CellCulture_Control

description:
Cell_culture_Control-rep1 (CC1)
Cell_culture_Control-rep2 (CC2)
Cell_culture_Control-rep3 (CC3)
Cell suspension cultures (CS4) at Oregon State University were maintained under continuous fluorescent light (~68 μmol m-2 s-1) at 25°C on an orbital shaker (120 rpm). Suspension cultures were subcultured weekly in 250 mL Erlenmeyer flasks containing 50 mL of cell suspension in B5 medium supplemented with 20 g L-1 sucrose, 250 mg L-1 casein hydrolysate, 0.5 mg L-1 1-naphtalene-acetic acid and 0.12 mg L-1 benzylaminopurine, by inoculating the cells at a 1/5 (v/v) ratio into a fresh medium. For experimental purposes, 7-day-old cell suspensions were inoculated into a fresh medium (3:7) and cultured for 3 days before treatment. Control solution spray was distilled-deionized water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com) and 0.002% ethanol that was applied to cell suspension cultures until running off.

source_name: Vitis vinifera L. cv. Cabernet Sauvignon, 7-day old cell suspension cultures incoulated into fresh medium and cultured for 3-days before treatment, harvested from 3-day old treated cultures

value: Oregon State University, USA

value: Cell culture


title: M1

status: Public on Mar 01 2016

type: genomic

city: Beijing

first: Yu

last: Xia

state: Beijing

address: Tsinghua University, Haidian District

department: Environmental school

country: China

institute: Tsinghua Univeristy

description: GeoChip data for activated sludge sample collected at System MBR, Day 1

hyb_protocol: All labeled DNA was resuspended in 10 μl hybridization solution as previously described (Wu et al. 2006) and was hybridized with GeoChip 4.2 on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA) at 42℃ with 40% formamide for 16h.

scan_protocol: Microarrays were scanned by a ScanArray 5000 Microarray Analysis System (PerkinElmer, Wellesley, MA, USA) at 100% laser power.

data_processing: Signal intensities of the spots were measured with ImaGene 6.0 (Biodiscovery Inc., El Segundo, CA, USA). Data pretreatment was performed online (ieg.ou.edu). The percentages of thermophile probes (negative controls) in each sample were made less than 5% by the removal of low quality spots. The genes detected in only one out of three samples from the same system were removed.  The genes detected only in 3 or fewer samples out of 12 samples from the same system were removed to avoid potential noises. For each sample, intensities of the genes were then transformed to the natural logarithmic form and divided by the mean signal intensity.

molecule: genomic DNA

organism: activated sludge metagenome

label_protocol: As previously described (Lu et al. 2012), 1000 ng of each DNA sample was labeled 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) and then dried.

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 1.

extract_protocol: Microbial genomic DNA was extracted from the pellets of activated sludge samples through joint use of freezing and sodium dodecyl sulfate (SDS) for cell lysis (Zhou et al. 1996). The extracted products were then purified employing the Wizard® SV Genomic DNA Purification Kit (Promega, Madison WI). DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

tag: wastewater treatment system

value: Wastewater treatment system of MBR

tag: collection timepoint

value: Day 1


title: phoPR_7H9+ADC_OD600=0.45_rep3.

type: RNA

city: Tainan

first: Jenn-Wei

last: Chen

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

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

scan_protocol: Arrays were then scanned using Agilent G2565BA microarray scanner and data was extracted using Agilent's feature extraction image analysis software v 10.5.1.1.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1 ) was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Mycobacterium avium subsp. paratuberculosis K-10

label_protocol: 3.0 µg of RNA from each sample were reverse-transcribed using SuperScript III reverse transcriptase with random hexamers (Invitrogen) according to the manufacturer’s instructions. The corresponding cDNA was labeled with 25 U of Klenow fragment (New England Biolabs, Ipswich, MA), 7 µg of exo-resistant random primers (Fermentas, Glen Burnie, MD), dNTP mix (0.12 mM each dATP, dTTP, and dGTP and 0.03 mM dCTP), and 0.1 mM of Cy3-dCTP (Amersham Biosciences, Piscataway, NJ) at 37°C for 8 hours. Labeling reaction was cleaned up using a QIAquick PCR Purification Kit (Qiagen).

growth_protocol: Bacterial cells were grown to a cell density of 0.45 at OD600 in 7H9 broth with supplementation of mycobactin J and ADC (7H9-ADC).

extract_protocol: Cell pellets were transferred to a 2 ml sterile screw-cap microcentrifuge tube and 1 ml of TRIzol reagent (Invitrogen, Life Technologies) and 0.5 ml of sterile RNase-free 0.1 mm zirconia beads were added to the tube. Cells were homogenized and lysed by bead beating three times in a Mini Bead-Beater for 2 min with a gap of 1 min. Cell lysate was transferred to a 1.5 ml sterile RNase-free microcentrifuge tube. RNA from the lysate was cleaned up using RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA). Before elution of RNA from the MinElute columns, following manufacturers protocols, possible contaminating DNA was removed using Qiagen RNase-Free DNase Set.

treatment_protocol: The bacterial cultures were treated with twice the volume of RNA protect reagent (Qiagen) for 30 min at room temperature and the bacterial pellets were collected by centrifugation at 3,000 xg for 10 minutes.

tag: genotype/variation

value: phoPR mutant

tag: growth phase

value: Log phase


title: O11

description: GeoChip data for activated sludge sample collected at System OD, Day 11

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 11.

value: Wastewater treatment system of OD

value: Day 11


title: Berry_ABA

city: Reno

first: Grant

last: Cramer

state: Nevada

address: 1664 N. Virginia St

department: Biochemistry & Molecular Biology

country: USA

institute: University of Nevada, Reno

description:
Berry_ABA-rep1 (BA1)
Berry_ABA-rep2 (BA2)
Berry_ABA-rep3 (BA3)
Own-rooted vines of Vitis vinifera (L.) cv. Cabernet Sauvignon were used for the berries (before véraison) assays at UC Davis. These vines were grown from dormancy in 4-L tree pots filled with 1/3 peat, 1/3 sand, 1/3 redwood compost, with 2.4 kg m-2 dolomite lime in a greenhouse (30/20 ºC ± 3 ºC; 40/70% ± 10% RH; and natural light with a daily maximum of 1200 µmol m-2 s-1 PAR). The vines were pruned to two shoots, and the shoots were vertically trained to ~1.5 m. Pots were drip irrigated four times a day (at 06.00, 09.00, 14.00, and 18.00) for 4 min at 7.57 L h-1 (2 L d-1) with dilute nutrient solution (90 ppm calcium, 24 ppm magnesium, 124 ppm potassium, 6 ppm nitrogen as ammonium, 96 ppm nitrogen as nitrate, 26 ppm phosphate, 16 ppm sulfate, 1.6 ppm iron, 0.27 ppm 195 manganese, 0.16 ppm copper, 0.12 ppm zinc, 0.26 ppm boron, and 0.016 ppm molybdenum) at pH 5.5 to 6.0. A 10 µM ABA spray was made by first dissolving ABA ([+]-ABA, A.G. Scientific, Inc., http://www.agscientific.com) to 500 mM in 100% ethanol and then diluting to 10 µM in water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com) that was applied to berry clusters until running off.

hyb_protocol: Labeled cDNA was hybridized to a NimbleGen microarray 090818 Vitis exp HX12 (Roche, NimbleGen Inc., Madison, WI, USA), which contains probes targeted to 29,549 grapevine genes predicted from the V1 annotation of the 12x grapevine genome (http://srs.ebi.ac.uk/), and 19,091 random probes as negative controls.

scan_protocol: Each microarray was scanned using an Axon GenePix 4400A (Molecular Devices, Sunnyvale, CA, USA) at 532 nm (Cy3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.

data_processing:
Images were analyzed using NimbleScan v2.5 software (Roche), which produces pair files containing the raw signal intensity data for each probe and calls files with normalized expression data derived from the average of the intensities of the four probes for each gene.
Background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: Vitis vinifera L. cv. Cabernet Sauvignon, own-rooted vines, harvested berry clusters

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User's Guide (V 3.2).

growth_protocol: Shoot tips and berries samples were collected at the University of California, Davis in 2010; cell culture samples were sampled at Oregon State University in 2010; roots and leaf samples were collected at the University of Nevada, Reno in 2011.  Own-rooted vines of Vitis vinifera (L.) cv. Cabernet Sauvignon were used for the shoot tips and berries (before véraison) assays at UC Davis. These vines were grown from dormancy in 4-L tree pots filled with 1/3 peat, 1/3 sand, 1/3 redwood compost, with 2.4 kg m-2 dolomite lime in a greenhouse (30/20 ºC ± 3 ºC; 40/70% ± 10% RH; and natural light with a daily maximum of 1200 µmol m-2 s-1 PAR). The vines were pruned to two shoots, and the shoots were vertically trained to ~1.5 m. Pots were drip irrigated four times a day (at 06.00, 09.00, 14.00, and 18.00) for 4 min at 7.57 L h-1 (2 L d-1) with dilute nutrient solution (90 ppm calcium, 24 ppm magnesium, 124 ppm potassium, 6 ppm nitrogen as ammonium, 96 ppm nitrogen as nitrate, 26 ppm phosphate, 16 ppm sulfate, 1.6 ppm iron, 0.27 ppm 195 manganese, 0.16 ppm copper, 0.12 ppm zinc, 0.26 ppm boron, and 0.016 ppm molybdenum) at pH 5.5 to 6.0.   Cell suspension cultures (CS4) at Oregon State University were maintained under continuous fluorescent light (~68 μmol m-2 s-1) at 25°C on an orbital shaker (120 rpm). Suspension cultures were subcultured weekly in 250 mL Erlenmeyer flasks containing 50 mL of cell suspension in B5 medium supplemented with 20 g L-1 sucrose, 250 mg L-1 casein hydrolysate, 0.5 mg L-1 1-naphtalene-acetic acid and 0.12 mg L-1 benzylaminopurine, by inoculating the cells at a 1/5 (v/v) ratio into a fresh medium. For experimental purposes, 7-day-old cell suspensions were inoculated into a fresh medium (3:7) and cultured for 3 days before treatment.   Young vines propagated from leaf cuttings were grown in an aeroponic system in a greenhouse at UNR. The rooted cuttings from Cabernet Sauvignon were grown in a growth chamber for 2 to 3 weeks before being carefully transferred to the aeroponic system. Each container (43.2 cm (L) x 27.9 cm (W) x 20.3 cm (H)) had its own aeroponic nebulizer with a fogger head size of 3.8 cm diameter x 4.4 cm height for each experimental replicate (3 containers for control and 3 containers for ABA treatment). There were small holes in the lid of each container large enough for the rooted plant to pass through. Gibeaut’s solution [78] was used to provide the macronutrients and micronutrients to the vines in the aeroponic mist. The pH of the solution was maintained at 6.0. Root and leaf samples were grown for 3 months in this system before treatment.

extract_protocol: Samples were quickly rinsed and rapidly frozen in liquid nitrogen before storage at -80°C. Three independent experimental (and biological) replicates were harvested to compare between the ABA-treated and untreated samples. Each biological replicate was ground in a frozen mortar and pestle. Total RNA was isolated using a cetyltrimethylammonium bromide (CTAB) based method and RNeasy plant mini kit (Quiagen) following the manufacture’s protocol. The total RNA was treated with RNAse-free DNAse I (Qiagen) to eliminate any genomic DNA contamination and then quantified by using a Nanodrop spectrophotometer (Thermo Scientific NanoDrop 2000c). An aliquot of each RNA sample was also analyzed using an Agilent 2100 Bioanalyzer using RNA LabChip® assays according to the manufacturer's instructions.

treatment_protocol: A 10 µM ABA spray was made by first dissolving ABA ([+]-ABA, A.G. Scientific, Inc., http://www.agscientific.com) to 500 mM in 100% ethanol and then diluting to 10 µM in water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com).  Control solution spray was distilled-deionized water containing 0.05% adjuvant and 0.002% ethanol.  Shoot tips, berry clusters, and cell culture were sprayed with the 10 µM ABA treatment until running off. Roots were treated with 10 µM ABA in the aeroponic system by adding the ABA to the nutrient solution in the nebulizer for 2 hours; roots and leaves of root-treated vines were harvested. Samples were quickly rinsed and rapidly frozen in liquid nitrogen before storage at -80°C. Three independent experimental (and biological) replicates were harvested to compare between the ABA-treated and untreated samples.

tag: cultivar

value: Cabernet Sauvignon

tag: treatment

value: 10 µM ABA + 0.05% adjuvant, Treatment

tag: year

tag: location

value: University of California, Davis, USA

tag: tissue

value: Berry


title: 182_09B

city: Oslo

first: Linda

last: Ferrante

address: Gaustadalle 30

country: Norway

institute: Norwegian institute of public health

description: Tissue from left central lobe of the brain

hyb_protocol: The assay probe sets consist of an upstream oligo containing a gene-spesific sequence and a universal PCR primer sequence at the 5’ end, and a downstream oligo containing a gene-specific sequence and a universal PCR primer sequence at the 3’. The upstream oligo hybridizes to the targeted cDNA site, and then extends and ligates to its corresponding downstream oligonucleotide to create a PCR template that can be amplified with universal PCR primers.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe.

data_processing: After scanning, the iScan software extracts signal intensities and saves all files for each BeadChip. Raw data is imported to Illumina’s GenomeStudio software V2011.1, Gene Expression module v. 1.9.0. Background correction with bgAdjust.affy in lumi R/Bioconductor package. Quantile normalization, where the three tissue types where quantile normalized separately.

label: biotin

organism: Homo sapiens

source_name: Brain tissue

label_protocol: The Whole-Genome DASL HT Assay begins with conversion of total RNA to cDNA using biotinylated oligo dT and random nonamer primers. The cDNA is then annealed to the DASL Assay Pool probe groups. Probe groups contain oligonucleotides specifically designed to interrogate each target sequence in the transcripts. These probes span about 50 bases, making it possible to profile partially degraded RNA

extract_protocol: Total RNA from 10-20 mg fresh frozen tissues were prepared using the RNeasy mini kits (Qiagen, Valencia, CA) following manufacturer’s instructions. The concentrations of the samples were measured using the NanoDrop Spectrophotometer. The integrity of the samples was assessed using the Agilent 2100 Bioanalyzer. For each sample, 400 ng of total RNA was amplified and labeled. Samples were distributed and processed in a 96-well format and were hybridized to Illumina HumanHT-12 v4 Expression BeadChips. Some samples were up-concentrated using vacuum drying to achieved required concentration/volume.

treatment_protocol: Tissue was harvested during autopsy and stored in RNA later in -70C untill analysis.

tag: condition

value: SIDS

value: left central lobe of the brain


title: O7

description: GeoChip data for activated sludge sample collected at System OD, Day 7

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 7.

value: Day 7


title: UCSF4_hESC-derived NPCs_3

city: SAN FRANCISCO

first: Joshua

middle: F

last: Robinson

state: CA

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

description:
Neural precursor cells (NPCs) were grown on CellStart. RNA was isolated from an independent well of p5 NPCs. The hESC line UCSF4 with a normal 46XX karyotype was derived from a blastocyst-stage embryo on human foreskin fibroblasts. NIH registration number - NIHhESC-10-0044.
NPC_3

hyb_protocol: Hybridization was conducted by the UCSF Gladstone (NHLBI) Genomics Core Facility. The labeled cDNA was hybridized to Human GeneChip Gene 2.0 ST microarrays (Affymetrix, Santa Clara, CA).

scan_protocol: Array scanning was completed by the UCSF Gladstone (NHLBI) Genomics Core Facility. The signal intensity fluorescent images produced during Affymetrix GeneChip hybridizations were read using the Affymetrix Model 3000 Scanner and converted into GeneChip probe results files (CEL) using Command and Expression Console software (Affymetrix).

data_processing: CEL files were imported into Affymextrix Expression Console and RMA normalized on the gene level using Affymetrix default settings

source_name: UCSF4 hESC line

label_protocol: Sample processing was conducted by the UCSF Gladstone (NHLBI) Genomics Core Facility. The NuGEN Pico V2, based on Ribo-SPIA technology, was used for amplification, fragmentation and biotin-labeling.

growth_protocol: Pluripotent hESCs (UCSF4, NIH registry code 0044) were maintained in mTESR defined medium (Stemcell Technologies) on Matrigel-coated plates (BD Biosciences) and passaged every 3-5 days (passage number <60) via dispase (Stemcell Technologies) and manual dissection. hESCs were differentiated into neural precursor cells (NPCs) following a protocol (Swistowski et al., 2009) with modifications.  Briefly, pluripotent hESCs were directed to form embryoid bodies (EB) by culturing hESCs in suspension of KSR medium (Life Technologies) (supplemented with 10% fetal bovine serum (FBS) and ROCK inhibitor (1µl/mL)) for 24h and KSR medium (without ROCK inhibitor) for an additional 48h. Neuroectodermal induction was initiated by culturing EBs in low attachment plates (Corning, Costar) for 6 days in Neural Induction Media, consisting of DMEM/F12 w/Glutamax, NEAA (1X), N2 (1X) and FGF2 (20ng/mL). Neural rosettes were generated, dissected, and transferred to CellStart (Life Technologies) coated plates with Neurobasal medium (Gibco),  supplemented with NEAA (2mM), L-Glut (2mM), B27, LIF (10ng/mL),  PenStrep, and FGF2 (20ng/mL). hESC-derived NPCs were grown in supplemented Neurobasal medium (Gibco) on Cellstart-coated plates and passaged via Accutase (Life Technologies). Stemness of hESCs were monitored via morphology and expression of pluripotency markers (NANOG and POU5F1). Cells were grown at 37C in 5% CO2 and 8% O2.

extract_protocol: Total RNA extraction was performed using the RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions. Purified RNA was analyzed for quality using chip-based capillary electrophoresis (Bioanalyzer, Agilent, Inc) and quantity and purity was determined with a NanoDrop spectrometer.

tag: cell line

value: UCSF4 human embryonic stem cell line

tag: in vitro stage

value: neural precursor


title: 617_12B


title: O3

description: GeoChip data for activated sludge sample collected at System OD, Day 3

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 3.

value: Day 3


title: 403_11B


title: Berry_Control

description:
Berry_Control-rep1 (BC1)
Berry_Control-rep2 (BC2)
Berry_Control-rep3 (BC3)
Own-rooted vines of Vitis vinifera (L.) cv. Cabernet Sauvignon were used for the berries (before véraison) assays at UC Davis. These vines were grown from dormancy in 4-L tree pots filled with 1/3 peat, 1/3 sand, 1/3 redwood compost, with 2.4 kg m-2 dolomite lime in a greenhouse (30/20 ºC ± 3 ºC; 40/70% ± 10% RH; and natural light with a daily maximum of 1200 µmol m-2 s-1 PAR). The vines were pruned to two shoots, and the shoots were vertically trained to ~1.5 m. Pots were drip irrigated four times a day (at 06.00, 09.00, 14.00, and 18.00) for 4 min at 7.57 L h-1 (2 L d-1) with dilute nutrient solution (90 ppm calcium, 24 ppm magnesium, 124 ppm potassium, 6 ppm nitrogen as ammonium, 96 ppm nitrogen as nitrate, 26 ppm phosphate, 16 ppm sulfate, 1.6 ppm iron, 0.27 ppm 195 manganese, 0.16 ppm copper, 0.12 ppm zinc, 0.26 ppm boron, and 0.016 ppm molybdenum) at pH 5.5 to 6.0. Control solution spray was distilled-deionized water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com) and 0.002% ethanol that was applied to berry clusters until running off.

value: 0 µM ABA + 0.05% adjuvant + 0.002% ethanol, Control


title: CellCulture_ABA

description:
Cell_culture_ABA-rep1 (CA1)
Cell_culture_ABA-rep2 (CA2)
Cell_culture_ABA-rep3 (CA3)
Cell suspension cultures (CS4) at Oregon State University were maintained under continuous fluorescent light (~68 μmol m-2 s-1) at 25°C on an orbital shaker (120 rpm). Suspension cultures were subcultured weekly in 250 mL Erlenmeyer flasks containing 50 mL of cell suspension in B5 medium supplemented with 20 g L-1 sucrose, 250 mg L-1 casein hydrolysate, 0.5 mg L-1 1-naphtalene-acetic acid and 0.12 mg L-1 benzylaminopurine, by inoculating the cells at a 1/5 (v/v) ratio into a fresh medium. For experimental purposes, 7-day-old cell suspensions were inoculated into a fresh medium (3:7) and cultured for 3 days before treatment. A 10 µM ABA spray was made by first dissolving ABA ([+]-ABA, A.G. Scientific, Inc., http://www.agscientific.com) to 500 mM in 100% ethanol and then diluting to 10 µM in water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com) that was applied to cell suspension cultures until running off.

value: Oregon State University, USA

value: Cell culture


title: UCSF4_hESCs_3

description:
hESCs were grown and passaged on Matrigel and in MTESR. RNA was isolated from an independent well containing p22 hESC undifferentiated colonies. The hESC line UCSF4 with a normal 46XX karyotype was derived from a blastocyst-stage embryo on human foreskin fibroblasts. NIH registration number - NIHhESC-10-0044.
ESC_3

value: pluripotent


title: GE iPS 3 day

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65oC for 17 hours with a rotational speed of 10 rpm.  Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; room temperature) for 1 minute each.  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.  The scanner can perform simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide.  Data captured from the scanned microarray image is saved as a TIF file.

data_processing: TIF files generated from the scanned microarray image are loaded into Agilent Feature Extraction Software version 10.5.  The software automatically positions a grid and finds the centroid positions of each feature on the microarray.  This information is used to perform calculations that include feature intensities, background measurements and statistical analyses.  Data generated by the software is recorded as a tab-delimited text file.

source_name: GE iPS 3 day

label_protocol: The Agilent One-Color Quick Amp Labeling Kit is used to generate fluorescently labeled cRNA for one-color microarray hybridizations.  Agilent RNA spike-in controls are combined with input total RNA samples (50 to 1000 ng).  The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT.  Following cDNA synthesis, T7 RNA polymerase and cyanine 3-CTP nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate cyanine 3-CTP.  Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit.  The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer.

extract_protocol: Total RNA was prepared from each sample using Qiagen RNeasy kit according to manufacturer’s protocol.

treatment_protocol: IMR90 cells were transduced with Ad-SOcMK or Ad-GFP. Adenoviruses were removed at 12 hrs post-transduction and cells were sampled at every 6 hrs.

tag: transduction

value: Ad-SOcMK

value: iPS

tag: time

value: 3 days


title: UCSF4_hESC-derived NPCs_1

description:
Neural precursor cells (NPCs) were grown on CellStart. RNA was isolated from an independent well of p5 NPCs. The hESC line UCSF4 with a normal 46XX karyotype was derived from a blastocyst-stage embryo on human foreskin fibroblasts. NIH registration number - NIHhESC-10-0044.
NPC_1


title: UCSF4_hESC-derived NPCs_2

description:
Neural precursor cells (NPCs) were grown on CellStart. RNA was isolated from an independent well of p5 NPCs. The hESC line UCSF4 with a normal 46XX karyotype was derived from a blastocyst-stage embryo on human foreskin fibroblasts. NIH registration number - NIHhESC-10-0044.
NPC_2


title: GE iPS 2.5 day

source_name: GE iPS 2.5 day

value: 2.5 days


title: phoPR_7H9+ADC_OD600=0.45_rep1.

value: phoPR mutant

value: Log phase


title: phoPR_7H9+ADC_OD600=0.45_rep2.


title: SK-N-BE(2) Non-silencing control #1

city: Barcelona

first: Miguel

last: Segura

state: Barcelona

address: Passeig Vall d'Hebron 119-129. Collserola. Lab 207

department: Pediatric Oncology

country: Spain

institute: Vall d'Hebron Research Institute

hyb_protocol: Chips were hybridized for 16h to 45ºC with rotation (60rpm).

scan_protocol: Chips were scanned in the Affymetrix GCS3000 7G.

data_processing: Data were processed using the limma (v3.19) and oligo (v1.27) packages in the R (v3.1.0) environment. Probeset level expression was derived using Robust Multi-array Average normalization. Non-specific filtering of 50% less intense and variable data was applied. Data were limited to core probe set only, and summarized at the gene expression level.

label: Biotin+Phycoerythrin

label_protocol: 200 ng of total RNA were hybridized to the arrays with the GeneChip WT Terminal Labeling and Hybridization Kit (Affymetrix, Santa Clara, CA)

growth_protocol: SK-N-BE(2) cells were obtained from ATCC and grown in grown in Iscove's Modified Dulbecco's Medium supplemented with 20% heat-inactivated FBS, 1% of Insulin-Transferrin-Selenium supplement

extract_protocol: Total RNA was extracted using miRNAeasy RNA extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: pLKO-NSC and  pLKO-shBRG1 were purchased from Sigma-Aldrich, Madrid, Spain. Lentiviruses were propagated using standard methods.

tag: lentivirus

value: non-silencing control


title: K-10_7H9+ADC_OD600=0.45_rep1.

value: wildtype


title: K-10_7H9+ADC_OD600=0.45_rep3.


title: K-10_7H9+ADC_OD600=0.45_rep2.


title: UCSF4_hESCs_2

description:
hESCs were grown and passaged on Matrigel and in MTESR. RNA was isolated from an independent well containing p22 hESC undifferentiated colonies. The hESC line UCSF4 with a normal 46XX karyotype was derived from a blastocyst-stage embryo on human foreskin fibroblasts. NIH registration number - NIHhESC-10-0044.
ESC_2


title: UCSF4_hESCs_1

description:
hESCs were grown and passaged on Matrigel and in MTESR. RNA was isolated from an independent well containing p22 hESC undifferentiated colonies. The hESC line UCSF4 with a normal 46XX karyotype was derived from a blastocyst-stage embryo on human foreskin fibroblasts. NIH registration number - NIHhESC-10-0044.
ESC_1


title: Leaf_ABA

description:
Leaf_ABA-rep1 (LA1)
Leaf_ABA-rep2 (LA2)
Leaf_ABA-rep3 (LA3)
Young vines propagated from leaf cuttings were grown in an aeroponic system in a greenhouse at UNR. The rooted cuttings from Cabernet Sauvignon were grown in a growth chamber for 2 to 3 weeks before being carefully transferred to the aeroponic system. Each container (43.2 cm (L) x 27.9 cm (W) x 20.3 cm (H)) had its own aeroponic nebulizer with a fogger head size of 3.8 cm diameter x 4.4 cm height for each experimental replicate (3 containers for control and 3 containers for ABA treatment). There were small holes in the lid of each container large enough for the rooted plant to pass through. Gibeaut’s solution [78] was used to provide the macronutrients and micronutrients to the vines in the aeroponic mist. The pH of the solution was maintained at 6.0. Root and leaf samples were grown for 3 months in this system before treatment. A 10 µM ABA spray was made by first dissolving ABA ([+]-ABA, A.G. Scientific, Inc., http://www.agscientific.com) to 500 mM in 100% ethanol and then diluting to 10 µM in water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com). Roots were treated with 10 µM ABA in the aeroponic system by adding the ABA to the nutrient solution in the nebulizer for 2 hours; roots and leaves of root-treated vines were harvested.

source_name: Vitis vinifera L. cv. Cabernet Sauvignon, propagated leaf cuttings grown in an aeroponic system, harvested leaf tissue

value: Cabernet Sauvignon

value: 10 µM ABA + 0.05% adjuvant, Treatment

value: University of Nevada, Reno, USA

value: Leaf


title: FFPE histological sample of resected hepatocellular carcinoma; group NR (non-recurrent HCC), NR10

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

description:
NR10
microRNA

hyb_protocol: GeneChip® miRNA 3.0 arrays (Affymetrix) were hybridized with 200 ng labelled microRNA. Hybridisation time was 18 hours.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Microarray preprocessing: Probe level normalization was conducted using the robust multichip average method (RMA) from Bolstad et al. Affymetrix Expression Console with RMA+DABG normalization and default export options was used.
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest) were taken from the Bioconductor project.
UnsupportedGeneChip® miRNA 3.0 Array CDF Files.
miRNA 3.0 Annotations, Unsupported, CSV format from Affymetrix.

source_name: macrodissected hepatocellular carcinoma, non-recurrent HCC

label_protocol: miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit.

extract_protocol: miRNA was extracted with the miRNeasy FFPE Kit from Qiagen.

treatment_protocol: 2-5 x 5µm macrodissected slices.

value: resected hepatocellular carcinoma (HCC)

tag: group

value: non-recurrent HCC after liver transplantation


title: FFPE histological sample of resected hepatocellular carcinoma; group NR (non-recurrent HCC), NR8

description:
NR8
microRNA


title: FFPE histological sample of resected hepatocellular carcinoma; group NR (non-recurrent HCC), NR7

description:
NR7
microRNA


title: FFPE histological sample of resected hepatocellular carcinoma; group NR (non-recurrent HCC), NR4

description:
NR4
microRNA


title: FFPE histological sample of resected hepatocellular carcinoma; group NR (non-recurrent HCC), NR9

description:
NR9
microRNA


title: FFPE histological sample of resected hepatocellular carcinoma; group NR (non-recurrent HCC), NR1

description:
NR1
microRNA


title: FFPE histological sample of resected hepatocellular carcinoma; group R (recurrent HCC), R8

description:
R8
microRNA

source_name: macrodissected hepatocellular carcinoma, recurrent HCC

value: recurrent HCC after liver transplantation


title: FFPE histological sample of resected hepatocellular carcinoma; group NR (non-recurrent HCC), NR6

description:
NR6
microRNA


title: FFPE histological sample of resected hepatocellular carcinoma; group R (recurrent HCC), R6

description:
R6
microRNA


title: FFPE histological sample of resected hepatocellular carcinoma; group NR (non-recurrent HCC), NR3

description:
NR3
microRNA


title: FFPE histological sample of resected hepatocellular carcinoma; group NR (non-recurrent HCC), NR2

description:
NR2
microRNA


title: FFPE histological sample of resected hepatocellular carcinoma; group R (recurrent HCC), R5

description:
R5
microRNA


title: FFPE histological sample of resected hepatocellular carcinoma; group R (recurrent HCC), R7

description:
R7
microRNA


title: FFPE histological sample of resected hepatocellular carcinoma; group NR (non-recurrent HCC), NR5

description:
NR5
microRNA


title: GE GFP 1 day

source_name: GE GFP 1 day

value: Ad-GFP

value: GFP

value: 1 day


title: FFPE histological sample of resected hepatocellular carcinoma; group R (recurrent HCC), R4

description:
R4
microRNA


title: GE iPS 2 day

source_name: GE iPS 2 day

value: Ad-SOcMK

value: iPS

value: 2 days


title: GE GFP 0 day

source_name: GE GFP 0 day

value: 0 day


title: FFPE histological sample of resected hepatocellular carcinoma; group R (recurrent HCC), R1

description:
R1
microRNA


title: GE iPS 1 day

source_name: GE iPS 1 day


title: GE iPS 1.7 day

source_name: GE iPS 1.7 day

value: 1.7 days


title: GE iPS 0 day

source_name: GE iPS 0 day


title: GE iPS 3.5 day

source_name: GE iPS 3.5 day

value: 3.5 days


title: GE iPS 1.5 day

source_name: GE iPS 1.5 day

value: 1.5 days


title: FFPE histological sample of resected hepatocellular carcinoma; group R (recurrent HCC), R2

description:
R2
microRNA


title: GE iPS 1.2 day

source_name: GE iPS 1.2 day

value: 1.2 days


title: GE iPS 2.7 day

source_name: GE iPS 2.7 day

value: 2.7 days


title: GE iPS 0.5 day

source_name: GE iPS 0.5 day

value: 0.5 day


title: GE iPS 0.7 day

source_name: GE iPS 0.7 day

value: 0.7 day


title: GE iPS 2.2 day

source_name: GE iPS 2.2 day

value: 2.2 days


title: GE GFP 3 day

source_name: GE GFP 3 day

value: 3 days


title: FFPE histological sample of resected hepatocellular carcinoma; group R (recurrent HCC), R3

description:
R3
microRNA

value: resected hepatocellular carcinoma (HCC)

value: recurrent HCC after liver transplantation


title: SJSC LBH2

city: Clayton

first: Jason

last: Cain

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

description:
SAMPLE 17
replicate 2

hyb_protocol: A total hybridization volume of 15ul was prepared for each sample and 15ul loaded into a single array on the Ilumina humanHT 12 Expression Beadchip. A total of 12 different labelled samples can be loaded into 12 individual arrays per beadchip.  The chip was then hybridized at 58C for 16 hours in an oven with a rocking platform.  After hybridization, the chip was washed using the appropriate protocols as outlined in the Illumina manual.  Upon completion of the washing, the chips were then coupled with Cy3 and scanned in the Illumina iScan Reader.

scan_protocol: Standard Illumina scanning protocol in the Illumina iScan Reader

data_processing: GenomeStudio V2011.1 - Gene Expression Module 1.9.0

source_name: SJSC Human malignant rhabdoid tumor cell line treated for 21 days with low-dose Panobinostat

label_protocol: A total of 500ng of total RNA was prepared for hybridization to the Ilumina humanHT 12 Expression Beadchip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridization Buffer (supplied with the beadchip).

extract_protocol: RNA and DNase I treatment was performed using the QIAGEN Rneasy Mini Kit,, in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: SJSC malignant rhabdoid tumor cell line

tag: cell origin

value: Liver tumor

value: Panobinostat


title: BC_SQ_OP_25_R4

city: Las Vegas

first: Allen

middle: G.

last: Gibbs

address: 4505 S Maryland Parkway

department: School of Life Sciences

institute: University of Nevada

description: This sample is of wild-type Drosophila mojavensis originally from San Quintin, Baja California. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 25 °C temperature.

hyb_protocol: Hybridizations with custom NimbleGen 12-plex microarrays were performed with a NimbleGen Hybridization System 4.

scan_protocol: Array scanning was performed with a GenePix 4000B scanner (Molecular Devices) and associated software at 532 nm, with photomultiplier gain settings that resulted in less than one in 105 normalized counts at saturation.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Drosophila mojavensis

source_name: Drosophila mojavensis SQ08

label_protocol: cDNA samples were labeled with Cy3 using a NimbleGen (Roche Diagnostics) One Color DNA Labeling kit.

growth_protocol: Bottle cultures were established at moderate larval densities to minimize nutritionally caused maternal/environmental effects from the vial cultures and maintained in an incubator programmed on a 14:10 LD photoperiod that cycled from 27° to 17° C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). Invitrogen Superscript Double-Stranded cDNA Synthesis kits were used to synthesize double-stranded cDNA.  Each cDNA sample was quantified using a NanoDrop spectrophotometer (NanoDrop Technologies).

tag: genotype

value: Wild-type

tag: phenotype

value: normal

tag: accession

tag: populations

value: San Quintin, Baja California

tag: gender

value: females

tag: temperature

value: 25 °C temperature


title: SJSC DMSO3

description:
SAMPLE 15
replicate 3

source_name: SJSC Human malignant rhabdoid tumor cell line treated for 21 days with DMSO vehicle

tag: treatment

value: control


title: BC_SQ_OP_35_R1

description: This sample is of wild-type Drosophila mojavensis originally from San Quintin, Baja California. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 35 °C temperature.

value: 35 °C temperature


title: BC_SQ_OP_35_R4


title: SJSC LBH1

description:
SAMPLE 16
replicate 1


title: SJSC DMSO2

description:
SAMPLE 14
replicate 2


title: STM91-01 LBH2

description:
SAMPLE 11
replicate 2

source_name: STM91-01 Human malignant rhabdoid tumor cell line treated for 21 days with low-dose Panobinostat

value: STM91-01 malignant rhabdoid tumor cell line

value: Lung metastasis


title: SJSC DMSO1

description:
SAMPLE 13
replicate 1


title: SJSC LBH3

description:
SAMPLE 18
replicate 3


title: BC_SQ_OP_35_R3


title: STM91-01 LBH3

description:
SAMPLE 12
replicate 3


title: BC_SQ_OP_35_R2


title: BC_SQ_OP_25_R3


title: STM91-01 LBH1

description:
SAMPLE 10
replicate 1


title: BC_SQ_OP_25_R1


title: BC_SQ_OP_25_R2


title: STM91-01 DMSO2

description:
SAMPLE 8
replicate 2

source_name: STM91-01 Human malignant rhabdoid tumor cell line treated for 21 days with DMSO vehicle


title: STM91-01 DMSO1

description:
SAMPLE 7
replicate 1


title: BC_SQ_OP_15_R3

description: This sample is of wild-type Drosophila mojavensis originally from San Quintin, Baja California. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 15 °C temperature.

value: 15 °C temperature


title: G401t2

description:
SAMPLE 5
replicate 2

source_name: G401 Human malignant rhabdoid tumor cell line treated for 21 days with low-dose Panobinostat

value: G401 malignant rhabdoid tumor cell line

value: Renal tumor


title: G401c3

description:
SAMPLE 3
replicate 3

source_name: G401 Human malignant rhabdoid tumor cell line treated for 21 days with DMSO vehicle


title: G401t1

description:
SAMPLE 4
replicate 1


title: STM91-01 DMSO3

description:
SAMPLE 9
replicate 3


title: G401c1

description:
SAMPLE 1
replicate 1


title: BC_SQ_OP_15_R2


title: BC_SQ_AG_25_R4

description: This sample is of wild-type Drosophila mojavensis originally from San Quintin, Baja California. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 25 °C temperature.


title: G401t3

description:
SAMPLE 6
replicate 3


title: BC_SQ_OP_15_R1


title: BC_SQ_AG_35_R3

description: This sample is of wild-type Drosophila mojavensis originally from San Quintin, Baja California. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 35 °C temperature.


title: BC_SQ_AG_35_R4


title: BC_SQ_OP_15_R4


title: BC_SQ_AG_35_R2


title: BC_SQ_AG_25_R1


title: BC_SQ_AG_25_R2


title: BC_SQ_AG_15_R3

description: This sample is of wild-type Drosophila mojavensis originally from San Quintin, Baja California. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 15 °C temperature.


title: BC_SQ_AG_15_R4


title: BC_SQ_AG_35_R1


title: BC_SQ_AG_25_R3


title: Hep3B shCav1

city: Hong Kong

first: Judy

middle: Wai Ping

last: Yam

address: Pokfulam

department: Department of Pathology

country: Hong Kong

institute: The University of Hong Kong

description: Gene Expression

hyb_protocol: Service by the Centre for Genomic Sciences, The University of Hong Kong

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method

source_name: Hep3B shCav1

growth_protocol: Hep3B shCav1 and Hep3B shCtl cells grown in DMEM-HG

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

tag: cell type

value: HCC


title: PBS-1

city: ShiJiaZhuang

first: Qi

last: Wang

address: DuJuan Road

institute: EpiGenoMine

description: Gene expression data from HELF cells treated with PBS

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

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

growth_protocol: Human embray lung fibroblast (HELF) cells grown in MEM with 10% FBS and 1% amp.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004, QIAGEN, GmBH, Germany) following the manufacturer’ s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

treatment_protocol: HELFs in MEM with 2% FBS and 1% amp were infected with BAC HAN and BAC HAN^RNA2.7, then incubated by 72 hours. HELF treated with PBS was used as control.

tag: cell

value: HELF cells

tag: protocol

value: PBS


title: Hep3B shCtl

description: Gene Expression

scan_protocol: Service by the Centre for Genomic Sciences, The University of Hong Kong

source_name: Hep3B shCtl

tag: cell line


title: G401c2

description:
SAMPLE 2
replicate 2


title: RNA2.7-1

description: Gene expression data from HELF cells infected by HCMV

source_name: Human embray lung fibroblast (HELF) cells

value: BAC HAN^RNA2.7


title: BC_SQ_AG_15_R1


title: PBS-2


title: BC_PP_OP_35_R4

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 35 °C temperature.

source_name: Drosophila mojavensis PP08

value: Punta Prieta, Baja California


title: 4CB_MK

city: Hinxton

first: Louella

last: Vasquez

address: Genome Campus

country: United Kingdom

institute: Wellcome Trust Sanger Institute

description: megakaryocytes from cord blood individual 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Microarray signal intensities from Genome Studio version 1.9 were variance stabilized transformed and robust spline normalized using R package lumi.

source_name: human megakaryocytes

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

extract_protocol: DNA free total RNA was extracted, using RNeasy kits (Qiagen) according to the manufacturer’s instructions including DNase treatment, from sorted CD42+ cell fractions.   Quality control was performed with Agilent Bioanalyzer.

tag: tissue

value: blood (primary)

value: megakaryocytes from cord blood


title: 1CB_MK

description: megakaryocytes from cord blood individual 1


title: 3CB_MK

description: megakaryocytes from cord blood individual 3


title: BC_SQ_AG_15_R2

value: Wild-type

value: normal

value: San Quintin, Baja California


title: 3A1ATD1_MK_DD

description: megakaryocytes from directed differentiated hiPSC (A1ATD1) replicate 3

value: blood


title: Fermentor 4

city: Delft

first: Claire

last: Price

address: Alexander Fleminglaan

department: DFS

country: Netherlands

institute: DSM

description:
Fermentor 4_342637
Fermentor 4_342639
Fermentor 4_342641
Fermentor 4_342643
averaged data from 4 replicates of Fermentor4
Analysis used RNA from Generation 0 as control samples for comparison to the evolved strains from Fermentors 4

hyb_protocol: Superamin glass slides (ArrayIt, Sunnyvale, CA) were spotted with duplicates of approximately 2500 ORF amplicons of L. lactis subsp. MG1363.  Hybridization was performed in Ambion Slidehyb #1 hybridisation buffer (Ambion Biosystems, Foster City, CA) for 16 h at 45°C in a microarray hybridization incubator ISO20 (Grant Boekel, Cambridgeshire, UK).  Slides were washed in 2x SSC (+0.5 % SDS), 1x SSC (+0.25% SDS) and 1x SSC (+0.1% SDS), prior to drying and scanning.

scan_protocol: Slides were scanned using a GenePix Autoloader 4200AL scanner (Molecular Devices Corporation, Sunnyvale, CA)

data_processing:
Data analysis was carried out using ArrayPro 4.5 (Media Cybernetics, Silver Spring, MD) for image analysis and processed using a lowess normalization assuming that at least 50% of the genes will show no change in expression.  Data was compiled from two anaerobic cultures each with a dye-swap replicate, providing two biological repeats within four technical repeats.
Lowess normalized log2 ratio (experiment/control). Genes were considered significantly changes based on a Bayes p-value and a Benjamini Hochberg multiple testing corrections.
Raw data files: A=Cy3 and B=Cy5.

organism: Lactococcus cremoris

source_name: control strain

label_protocol: cDNA  was synthesized using Superscript III Reverse Transcriptase (Invitrogen, Carlsbad, CA) and allyl-modified dUTPs to allow indirect Cy-3/Cy-5 labelling according to manufacturers instructions (Amersham Biosciences, Piscataway, NJ).

growth_protocol: Cultures were grown in closed vessles at 30°C in chemically defined medium containing 0.5% glucose as a carbon source.

extract_protocol: As described in Marredy et al., 2011.  Cells were harvested immediately upon reaching the required optical density, snap frozen in liquid nitrogen and stored at -80°C.  Cells were lysed by bead beating and chromosomal DNA was removed by Macaloid suspension (Bentone MA, Hightstown, NJ).  Proteins were removed from the cell lysate by chloroform/phenol extraction and total RNA was isolated from the water phase using the Pure RNA Isolation Kit (Roche Molecular Biochemicals, Mannheim, Germany).

treatment_protocol: Cultures were grown to mid-exponential phase.

tag: strain

value: control MG1363

tag: fermentor

source_name: evolved 309F4

value: evolved 309F4


title: Fermentor 3

description:
Fermentor 3_343080
Fermentor 3_343081
Fermentor 3_343082
Fermentor 3_343083
averaged data from 4 replicates of Fermentor3
Analysis used RNA from Generation 0 as control samples for comparison to the evolved strains from Fermentors 3

source_name: evolved 309F3

value: evolved 309F3


title: 4A1ATD1_MK_DD

description: megakaryocytes from directed differentiated hiPSC (A1ATD1) replicate 4


title: 2A1ATD1_MK_DD

description: megakaryocytes from directed differentiated hiPSC (A1ATD1) replicate 2


title: 1BBHX_MK_FoP

description: megakaryocytes from forward programmed hiPSC (BBHX8) replicate 1


title: Fermentor 2

description:
Fermentor 2_343844
Fermentor 2_343845
Fermentor 2_343846
Fermentor 2_343860
averaged data from 4 replicates of Fermentor2
Analysis used RNA from Generation 0 as control samples for comparison to the evolved strains from Fermentors 2

source_name: evolved 309F2

value: evolved 309F2


title: RNA2.7-2


title: BC_PP_OP_35_R2

value: females

value: 35 °C temperature


title: BC_PP_OP_35_R3


title: Fermentor 1

description:
Fermentor 1_343685
Fermentor 1_343836
Fermentor 1_343840
Fermentor 1_343841
averaged data from 4 replicates of Fermentor1
Analysis used RNA from Generation 0 as control samples for comparison to the evolved strains from Fermentors 1

source_name: evolved 309F1

value: evolved 309F1


title: 2CB_MK

description: megakaryocytes from cord blood individual 2


title: 1A1ATD1_MK_DD

description: megakaryocytes from directed differentiated hiPSC (A1ATD1) replicate 1


title: HAN-2

value: HELF cells

value: BAC HAN


title: BC_PP_OP_35_R1


title: 2BBHX_MK_FoP

description: megakaryocytes from forward programmed hiPSC (BBHX8) replicate 2


title: HAN-1


title: 3A1ATD1_MK_FoP

description: megakaryocytes from forward programmed hiPSC (A1ATD1) replicate 3


title: 4A1ATD1_MK_FoP

description: megakaryocytes from forward programmed hiPSC (A1ATD1) replicate 4


title: BC_PP_OP_25_R4

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 25 °C temperature.

value: 25 °C temperature


title: 2A1ATD1_MK_FoP

description: megakaryocytes from forward programmed hiPSC (A1ATD1) replicate 2


title: BC_PP_OP_25_R3

value: Punta Prieta, Baja California


title: 1A1ATD1_MK_FoP

description: megakaryocytes from forward programmed hiPSC (A1ATD1) replicate 1


title: 2A1ATD1

description: A1ATD1 hiPSC replicate 2

source_name: hiPSC

value: hiPSC


title: 1A1ATD1

description: A1ATD1 hiPSC replicate 1


title: BC_PP_OP_25_R1


title: BC_PP_OP_25_R2


title: stool_142B

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description: Gene expression data of stool RNAs from study subject

data_processing:
Quantasoft software for the QX100 system reports absolute quantity of each target (copies/ul in reaction).  These data are then uploaded into MS Access where all data are analyzed for average target, average GAPDH, and then the ratio of these values.  Final  output is target/GAPDH ratio (average target/ average GAPDH).
Matrix normalized worksheet reports normalized target/GAPDH ratios.  Matrix non-normalized worksheet reports the copies/ul in the ddPCR reaction.  Fold change data were not calculated or reported in the manuscript, and are therefore not included.

label: duplex VIC/FAM

source_name: stool total RNA

label_protocol: Quantitative PCR (qPCR) was performed using commercially available duplexed Taqman  assays in a droplet digital PCR (ddPCR) system (QX100 - Bio-Rad Laboratories Inc., Hercules, CA). Reactions of 20 µL were prepared using 7.76 µL RNA, 10 µL ddPCR Supermix for Probes (BioRad), 0.08 µL SuperScript III Reverse Transcriptase (200 U/µL, Invitrogen Corporation, Carlsbad, CA), 0.16 µL RNase OUT (40 U/µL, Invitrogen), and 1 µL each of two 20× TaqMan Gene Expression Assay (Applied Biosystems, Carlsbad, CA), one VIC-labeled and one FAM-labeled. Droplets were generated according to manufacturer guidelines with the QX100 Droplet generator (BioRad) before cycling in a C1000 Touch thermal cycler (BioRad) at 50°C (30:00), 95°C (10:00), 40 cycles of 94°C (0:30) followed by 60°C (1:00), 98°C (10:00). Each assay was performed in replicate with GAPDH assays on the same plate.  Plates were held at 4°C between amplification and droplet reading. Data from the QX100 Droplet Reader were analyzed with QuantaSoft software (Kosice, Slovakia).

extract_protocol: Total nucleic acids were extracted using “Specific A” protocol on the NucliSENS EasyMAG system (bioMérieux, Durham, NC) )

treatment_protocol: Fresh stools were collected prior to the dual sugar absorption testing using a small, clean non-absorbant, plastic diaper. The stools were immediately transferred to cryovials and flash frozen in liquid nitrogen. Samples were transferred to a -80°C freezer and transported to Washington University (St. Louis, MO), where they were then processed for nucleic acid extraction.

value: F

tag: age (month)

tag: percent lactulose in urine

tag: disease state

value: environmental enteric dysfunction


title: Exosome_29 or 30 month_pooling 7 samples_High-meat yield cattle

city: Daejeon

first: Jinjong

last: Bong

address: Daehak-ro

country: South Korea

institute: NEXBIO

description: exosomal miRNA expression pattern in high-meat yield grade cattle

hyb_protocol: Cyanine3-labeled cRNA was incubated with 10X GE Blocking Agent and 2X Hi-RPM Hybridization Buffer for 5 min at 100℃. The reaction mixtures were hybridized with bovine miRNA array (8x60K, Agilent) for 20 hours at 55 ℃. The hybridized array was washed with Gene Expression wash buffer 1 and buffer 2.

scan_protocol: Array image was scanned in Agilent Scanner B.

data_processing:
Signal density of array was extracted in Feature extraction software. Signal density was normalized by Genespring ver 13.0 (Agilent, USA).
The unique miRNA was considered that normalized value was above 1.

organism: Bos taurus

source_name: Exosomal miRNA, pooling 7 samples, high-meat yield cattle

label_protocol: 100ng RNA was incubated with 10x Calf Intestinal Phosphatase Buffer, Labeling Spike-In and Calf Intestinal Phosphatase for 30 min at 37℃. The reaction mixture was denatured and chilled with 100% DMSO for 5 min at 100℃. The ligation reaction was performed with 10x T4 RNA Ligase Buffer, Cyanine3-pCp and T4 RNA ligase for 2 hours at 16℃. The unlabeled Cyanine3-pCp was removed from ligation mixtures using Micro Bio-Spin6 column (Bio-Rad, USA).

extract_protocol: Serum or plasma exosome was precipitated by miRCURYTM exosome precipitation kit (Exiqon, Denmark). LM tissue removed from adipose tissue and Allprotect solution was grinded in liquid nitrogen. Total RNA was extracted from the precipitated pellet and a grinding tissue by Tri-zol LS reagent (MCB, USA). Total RNA was stored at -70℃ before miRNA analysis.

treatment_protocol: 20 ml bloods were collected from the jugular vein of Hanwoo steer (29 or 30 months) in National Agricultural Cooperative Ferderation, Gyeonggi-do. 5 ml bloods were transferred to Serum BD Vacutainer (TUBE SST II PLH 16X100 8.5 PLBL CE GLD) and plasma BD Vacutainer (TUBE PST II PLH 16X100 8.0 PLBL L/GN). Vacutainer tube was incubated at room temperature for 20 min. Vacutainer tube was centrifuged at 1500 x g for 10 min. The supernants were transferred to a 15 ml tube. Longissimus dorsi (LM) muscle tissue was collected 24 hours after slaughter in an Agricultural Cooperative's joint market, Eunseong, Chungcheongbuk-do. The LM tissue was preserved at Allprotect solution (Qiagen, USA).

tag: breed

value: Korean cattle

value: male

value: Whole blood

tag: age

value: 29 or 30 month


title: Exosome_29 or 30 month_pooling 4 samples_Middle-meat yield cattle

description: exosomal miRNA expression pattern in middle-meat yield grade cattle

source_name: Exosomal miRNA, pooling 4 samples, middle-meat yield cattle


title: Longissimus dorsi muscle_29 or 30 month_pooling 7 samples_High-meat yield cattle

description: Longissimus dorsi muscle miRNA expression pattern in high-meat yield grade cattle

source_name: Longissimus dorsi muscle miRNA, pooling 7 samples, high-meat yield cattle

value: Longissimus dorsi muscle


title: Exosome_29 or 30 month_pooling 4 samples_Low-meat yield cattle

description: exosomal miRNA expression pattern in low-meat yield grade cattle

source_name: Exosomal miRNA, pooling 4 samples, low-meat yield cattle


title: Longissimus dorsi muscle_29 or 30 month_pooling 4 samples_Low-meat yield cattle

description: Longissimus dorsi muscle miRNA expression pattern in low-meat yield grade cattle

source_name: Longissimus dorsi muscle miRNA, pooling 4 samples, low-meat yield cattle


title: Longissimus dorsi muscle_29 or 30 month_pooling 4 samples_Middle-meat yield cattle

description: Longissimus dorsi muscle miRNA expression pattern in middle-meat yield grade cattle

source_name: Longissimus dorsi muscle miRNA, pooling 4 samples, middle-meat yield cattle


title: BC_PP_AG_35_R5

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 35 °C temperature.

tag: genotype

value: Wild-type

tag: phenotype

value: normal

tag: accession


title: BC_PP_OP_15_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 15 °C temperature.

tag: populations

tag: gender

value: females

tag: temperature

value: 15 °C temperature


title: PFC PolyI:C offspring, biological replicate 1

city: Zurich

first: Juliet

last: Richetto

address: Winterthurerstrasse 260

department: Institute for Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich - Vetsuisse

description:
Gene expression data in PolyI:C offspring
sample 25 GD17 PF

hyb_protocol: Labelled cDNA (10ug) was then fragmented and 5.5µg were hybridized onto Mouse Gene 1.1 ST Array Strips. The reactions of hybridation, fluidics and imaging were performed on the Affymetrix Gene Atlas instrument according to the manufacturer’s protocol.

scan_protocol: GeneChips were scanned using theGeneAtlas Platform following the manufacturers' instructions.

data_processing: Affymetrix CEL files were imported into Partek Genomics Suite version 6.6 for data visualization and statistical testing. Quality control assessment was performed using Partek Genomic Suite 6.6. All samples passed the criteria for hybridization controls, labelling controls and 3’/5’ Metrics. Background correction was conducted using Robust Multi-strip Average (RMA) (Irizarry et al, 2003) to remove noise from auto fluorescence. After background correction, normalization was conducted using Quantiles normalization (Bolstad et al, 2003) to normalize the distribution of probe intensities among different microarray chips. Subsequently, a summarization step was conducted using a linear median polish algorithm (Tukey, 1977) to integrate probe intensities in order to compute the expression levels for each gene transcript. Upon data upload, pre-processing of CEL data for the complete data set [total of twelve samples; six biological replicates per sample for vehicle, six biological replicates for GD17 Poly(I:C)] was performed using ANOVA to assess treatment effects.

organism: Mus musculus

source_name: C57BL/6 mouse Prefrontal Cortex - frozen brain tissue - POLYI:C

label_protocol: Gene expression microarray assays were performed using Mouse Gene 1.1 ST Array Strips on GeneAtlas platform (Affymetrix), following the 3’IVT one cycle labeling and amplification protocol described in the Affymetrix GeneChip Expression Analysis Technical Manuals and in the GeneAtlas™ WT Expression Kit User Manual. In detail, to synthesize First-Strand cDNA, 250ng RNA were reverse-transcribed with the Gene Atlas 3’IVT Express Kit or WT Expression Kit (Affymetrix, Santa Clara, CA, USA) using T7 oligo(dT) primer. Second-Strand cDNA synthesis was carried out using DNA polymerase and RNase H to simultaneously degrade RNA and synthesize second-strand cDNA. This step was followed by the in vitro transcription using IVT Labelling Master Mix to generate multiple copies of biotin-modified antisense-RNA (aRNA) from the double-stranded cDNA templates. Subsequently strand DNA was purified to remove unincorporated NTPs, salts, enzymes and inorganic phosphate.

extract_protocol:
[Tissue extraction protocol] The brains from adult offspring (12 weeks) were rapidly extracted from the skull (within < 20 s) and placed on an ice-chilled plate. This was followed by preparing 1-mm coronal brain sections using razorblade cuts and subsequent micro-dissection of the brain areas of interest. We dissected  We dissected the medial prefrontal cortex (mPFC, including anterior cingulate, prelimbic and dorsal parts of the infralimbic cortices; bregma: +2.3 to +1.3 mm) . Brain specimens were collected in 96-well microtiter plates kept on dry ice and allowed to freeze before storage at −80°C until further use. Total DNA and RNA were isolated using the Qiagen AllPrep DNA and RNA Mini kit. Genome-wide gene expression analyses were performed using Affymetrix microarray assays (Mouse Gene 1.1 ST Array Strips on GeneAtlas platform), following the 3’IVT one cycle labelling.
Total DNA and RNA were isolated using the Qiagen AllPrep DNA and RNA Mini kit following the manufacturers' instructions

treatment_protocol: C57BL/6 mice were treated with the synthetic viral mimetic poly(I:C) (5 mg/kg, i.v.) or control (saline, i.v.) solution on  gestation day 17. Offspring were subjected to cognitive and behavioral testing in adulthood, and then whole genome gene expression analysis with Affymetrix Microarray and subsequent q-PCR validation were performed on the Prefrontal Cortex.

tag: prenatal exposure

value: 12 weeks

value: brain

tag: tissue region

value: medial prefrontal cortex (mPFC)


title: BC_PP_OP_15_R2


title: PFC PolyI:C offspring, biological replicate 2

description:
Gene expression data in PolyI:C offspring
sample 27 GD17 PF


title: BC_PP_OP_15_R4


title: BC_PP_OP_15_R1


title: PFC control offspring, biological replicate 2

description:
Gene expression data in control offspring
sample 3 CON PF

source_name: C57BL/6 mouse Prefrontal Cortex - frozen brain tissue - CONTROL

value: control


title: PFC PolyI:C offspring, biological replicate 6

description:
Gene expression data in PolyI:C offspring
sample 33 GD17 PF


title: PFC PolyI:C offspring, biological replicate 4

description:
Gene expression data in PolyI:C offspring
sample 30 GD17 PF


title: PFC PolyI:C offspring, biological replicate 3

description:
Gene expression data in PolyI:C offspring
sample 28 GD17 PF


title: PFC control offspring, biological replicate 4

description:
Gene expression data in control offspring
sample 7 CON PF


title: PFC control offspring, biological replicate 3

description:
Gene expression data in control offspring
sample 5 CON PF


title: stool_LNS68

description: Gene expression data of stool RNAs from study subject

value: M


title: Nac PolyI:C offspring, biological replicate 4

description:
Gene expression data in PolyI:C offspring
sample 30 gd17 nac

hyb_protocol: Labelled cDNA (10ug) was then fragmented and 5.5ug were hybridized onto Mouse Gene 1.1 ST Array Strips. The reactions of hybridation, fluidics and imaging were performed on the Affymetrix Gene Atlas instrument according to the manufacturer’s protocol.

scan_protocol: GeneChips were scanned using the GeneAtlas Platform following the manufacturers' instructions.

source_name: C57BL/6 Nucleus Accumbens - frozen brain tissue - POLYI:C

extract_protocol:
[Tissue extraction protocol] The brains from adult offspring (12 weeks) were rapidly extracted from the skull (within < 20 s) and placed on an ice-chilled plate. This was followed by preparing 1-mm coronal brain sections using razorblade cuts and subsequent micro-dissection of the brain areas of interest. We dissected  the nucleus accumbens (NAc, including core and shell subregions; bregma +1.5 to +0.5 mm). Brain specimens were collected in 96-well microtiter plates kept on dry ice and allowed to freeze before storage at −80°C until further use. Total DNA and RNA were isolated using the Qiagen AllPrep DNA and RNA Mini ki. Genome-wide gene expression analyses were performed using Affymetrix microarray assays (Mouse Gene 1.1 ST Array Strips on GeneAtlas platform), following the 3’IVT one cycle labelling
Total DNA and RNA were isolated using the Qiagen AllPrep DNA and RNA Mini kit following the manufacturers' instructions

treatment_protocol: CC57BL/6 mice were treated with the synthetic viral mimetic poly(I:C) (5 mg/kg, i.v.) or control (saline, i.v.) solution on  gestation day 17. Offspring were subjected to cognitive and behavioral testing in adulthood, and then whole genome gene expression analysis with Affymetrix Microarray and subsequent q-PCR validation were performed on the nucleus accumbens.

value: Nucleus Accumbens (NAc)


title: PFC control offspring, biological replicate 6

description:
Gene expression data in control offspring
sample12 con PF


title: PFC control offspring, biological replicate 5

description:
Gene expression data in control offspring
sample 9 CON PF


title: Nac PolyI:C offspring, biological replicate 6

description:
Gene expression data in PolyI:C offspring
sample 33 gd17 nac


title: Nac PolyI:C offspring, biological replicate 5

description:
Gene expression data in PolyI:C offspring
sample 32 gd17 nac


title: PFC PolyI:C offspring, biological replicate 5

description:
Gene expression data in PolyI:C offspring
sample 32 GD17 PF


title: PFC control offspring, biological replicate 1

description:
Gene expression data in control offspring
sample 1 CON PF


title: stool_LNS225

value: F


title: stool_021B

value: environmental enteric dysfunction


title: stool_023A


title: stool_180B


title: stool_294B


title: stool_LNS24


title: stool_142A


title: stool_LNS188


title: BC_PP_AG_35_R2

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 35 °C temperature.

source_name: Drosophila mojavensis PP08

value: Punta Prieta, Baja California

value: 35 °C temperature


title: stool_LNS229


title: Nac PolyI:C offspring, biological replicate 2

description:
Gene expression data in PolyI:C offspring
sample 27 gd17 nac


title: BC_PP_AG_25_R4

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 25 °C temperature.

value: 25 °C temperature


title: BC_PP_AG_25_R2


title: BC_PP_AG_35_R1


title: stool_LNS122


title: stool_186A


title: BC_PP_AG_25_R3


title: BC_PP_AG_15_R4

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 15 °C temperature.


title: stool_LNS235


title: BC_PP_AG_25_R1


title: Nac PolyI:C offspring, biological replicate 3

description:
Gene expression data in PolyI:C offspring
sample 28 gd17 nac


title: BC_PP_AG_35_R3


title: BC_PP_AG_35_R4


title: stool_168B


title: stool_LNS102


title: BC_PP_AG_15_R2


title: BC_PP_AG_15_R1


title: stool_309A


title: BC_PP_AG_15_R3


title: stool_LNS52


title: SO_OPNM_OP_35_R4

description: This sample is of wild-type Drosophila mojavensis originally from Organ Pipe National Monument, Sonora. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 35 °C temperature.

source_name: Drosophila mojavensis OPNM08

value: Organ Pipe National Monument, Sonora


title: stool_LNS133


title: stool_LNS210


title: stool_LNS67


title: Nac control offspring, biological replicate 6

description:
Gene expression data in control offspring
sample 12 con nac

source_name: C57BL/6 Nucleus Accumbens - frozen brain tissue - CONTROL


title: stool_LNS35


title: SO_OPNM_OP_35_R3


title: Nac control offspring, biological replicate 2

description:
Gene expression data in control offspring
sample 3 con nac


title: Nac control offspring, biological replicate 3

description:
Gene expression data in control offspring
sample 5 con nac


title: SO_OPNM_OP_25_R2

description: This sample is of wild-type Drosophila mojavensis originally from Organ Pipe National Monument, Sonora. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 25 °C temperature.


title: SO_OPNM_OP_35_R1


title: Nac control offspring, biological replicate 4

description:
Gene expression data in control offspring
sample 7 con nac


title: Nac control offspring, biological replicate 5

description:
Gene expression data in control offspring
sample 9 con nac


title: stool_LNS40

description: Gene expression data of stool RNAs from study subject


title: Nac control offspring, biological replicate 1

description:
Gene expression data in control offspring
sample 1 con  Nac


title: stool_LNS189


title: stool_LNS38


title: SO_OPNM_OP_15_R4

description: This sample is of wild-type Drosophila mojavensis originally from Organ Pipe National Monument, Sonora. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 15 °C temperature.


title: SO_OPNM_OP_25_R1


title: SO_OPNM_OP_25_R3


title: SO_OPNM_OP_25_R4


title: stool_273A


title: 47 SO_OPNM_OP_35_R3


title: SO_OPNM_OP_15_R3


title: SO_OPNM_OP_15_R2


title: SO_OPNM_AG_35_R4

description: This sample is of wild-type Drosophila mojavensis originally from Organ Pipe National Monument, Sonora. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 35 °C temperature.


title: stool_248A


title: SO_OPNM_OP_15_R1


title: stool_311A


title: stool_LNS196


title: stool_314A


title: stool_079A


title: stool_258A


title: stool_112A


title: stool_088A


title: SO_OPNM_AG_25_R4

description: This sample is of wild-type Drosophila mojavensis originally from Organ Pipe National Monument, Sonora. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 25 °C temperature.


title: SO_OPNM_AG_35-R3


title: SO_OPNM_AG_35_R2


title: SO_OPNM_AG_35_R1


title: stool_126B


title: stool_060B


title: SO_OPNM_AG_15_R2

description: This sample is of wild-type Drosophila mojavensis originally from Organ Pipe National Monument, Sonora. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 15 °C temperature.


title: stool_152B


title: SO_OPNM_AG_25_R3


title: SO_OPNM_AG_15_R1


title: SO_OPNM_AG_25_R2


title: SKBrM3-2

city: Winston-Salem

first: fei

last: xing

state: North Carolina

address: 1 Medical Center Blvd

department: cancer biology

institute: wake forest baptist health

description: gene expression data from SKBrM3

hyb_protocol: standard Affymetrix protocol

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

data_processing: RMA

source_name: SKBrM3 control

label_protocol: standard Affymetrix protocol

growth_protocol: cells were cultured in DMEM with 10%FBS

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

treatment_protocol: 100ng doxycycline for 48hrs

tag: cell type

value: breast cancer cell line

tag: cell line


title: SO_OPNM_AG_15_R4

value: Wild-type


title: stool_206A


title: stool_117A


title: SKBrM3+DOX-2

description: gene expression data from SKBrM3 treated with doxycycline

source_name: SKBrM3 treated with doxycycline


title: SO_OPNM_AG_15_R3

value: normal


title: SO_OPNM_AG_25_R1

value: females


title: SO_PO_OP_35_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Onah, Sonora. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 35 °C temperature.

source_name: Drosophila mojavensis PO07

value: Punta Onah, Sonora


title: 231BrM+DOX-2

description: gene expression data from 231BrM with doxycycline treatment

source_name: 231BrM treated with doxycycline


title: SKBrM3+DOX-1


title: SKBrM3-1

description: gene expression data from SKBrM3


title: SO_PO_OP_35_R4


title: stool_049B

source_name: stool total RNA


title: 231BrM+DOX-1


title: SO_PO_OP_35_R2


title: stool_243B


title: stool_106B


title: stool_238A


title: 231BrM-2

description: gene expression data from 231BrM

source_name: 231BrM control


title: stool_157A


title: 231BrM-1

description: gene expression data from 231BrM


title: stool_LNS243


title: stool_203B


title: stool_LNS94


title: SO_PO_OP_25_R4

description: This sample is of wild-type Drosophila mojavensis originally from Punta Onah, Sonora. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 25 °C temperature.


title: SO_PO_OP_25_R2


title: SO_PO_OP_35_R1


title: SO_PO_OP_25_R1


title: SO_PO_OP_25_R3


title: stool_LNS27


title: SO_PO_OP_15_R4

description: This sample is of wild-type Drosophila mojavensis originally from Punta Onah, Sonora. These adults were raised on lab media prepared from Organ Pipe cactus. These females were exposed to 15 °C temperature.

value: 15 °C temperature


title: stool_078A


title: stool_LNS165


title: stool_059A


title: SO_PO_OP_15_R2


title: SO_PO_OP_15_R3


title: BRCAX.5

city: London

first: Kirsty

middle: J

last: Flower

address: Du Cane Road

institute: Imperial College London

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
Unmethylated and methylated signal intensities in unprocessedmatrix.txt file

label: Cy5 and Cy3

source_name: tumour genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA samples were extracted from macrodissected FFPE tumour tissue using standard phenol chlorform ethanol precipation protocol.

value: Female

tag: sample type

value: tumour DNA

value: breast cancer

value: BRCAx

tag: variant

tag: er_status (1=postive, 0=negative)

tag: grade

tag: ChIP

tag: sample removed after qc

value: YES


title: stool_319A

value: M

tag: age (month)

tag: percent lactulose in urine

tag: disease state


title: stool_240B

value: environmental enteric dysfunction


title: Nac PolyI:C offspring, biological replicate 1

description:
Gene expression data in PolyI:C offspring
sample 25 gd17 nac

tag: strain

tag: age

value: 12 weeks

tag: tissue

value: brain

value: Nucleus Accumbens (NAc)


title: SO_PO_AG_35_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Onah, Sonora. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 35 °C temperature.

tag: genotype

tag: phenotype

tag: accession

tag: populations

tag: gender

tag: temperature

value: 35 °C temperature


title: stool_304A


title: SO_PO_AG_35_R2


title: SO_PO_AG_35_R4


title: stool_114A

value: F


title: stool_282B


title: stool_LNS29


title: stool_097A


title: SO_PO_AG_25_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Onah, Sonora. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 25 °C temperature.

value: Wild-type

value: 25 °C temperature


title: SO_PO_OP_15_R1

value: normal

value: females


title: SO_PO_AG_25_R2

value: Punta Onah, Sonora


title: SO_PO_AG_25_R1


title: stool_136A


title: S0_PO_AG_25_R4


title: SO_PO_AG_35_R1


title: stool_202A


title: stool_260B


title: SO_PO_AG_15_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Onah, Sonora. These adults were raised on lab media prepared from Agria cactus. These females were exposed to 15 °C temperature.

value: 15 °C temperature


title: stool_014A


title: SO_PO_AG_15_R2


title: BRCAX.55

value: Female

tag: sample type

value: tumour DNA

tag: variant

value: NO


title: SO_PO_AG_15_R4


title: BRCAX.54

value: breast cancer

value: BRCAx

tag: er_status (1=postive, 0=negative)

tag: grade


title: BRCAX.52

tag: ChIP

tag: sample removed after qc


title: stool_LNS28

tag: age (month)

tag: percent lactulose in urine

value: environmental enteric dysfunction


title: SO_PO_AG_15_R1


title: BRCAX.51

tag: disease state


title: BRCAX.50


title: stool_LNS217

value: M


title: Sirt1KO_rep3

city: Sydney

first: Jianmin

last: Wu

state: NSW

address: 370 Victoria Street Darlinghurst

department: Cancer Division

institute: Garvan Institute of Medical Research

description: Total RNA from whole pancreas of 6month old male Sirt1 Knock out mouse, replicate 3

hyb_protocol: Amplified cRNAs were hybridized on Mouse Gene 2.0 ST Arrays (Affymetrix, Santa Clara, CA, USA) according with manufacturer’s procedures. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The arrays were processed using the oligo and pd.mogene.2.0.st packages, and normalized by Robust Multi-array Average (RMA) method and annotated by the mogene20sttranscriptcluster.db package. The limma package was applied to identify differentially expressed genes.

source_name: whole pancreas of 6-month old male animals

label_protocol: Biotinylated cRNAs were prepared according to the Ambion WT kit (Life Technologies, CA, USA) protocol from 250 ng total RNA.

growth_protocol: B6.FVB-Tg(Ipf1-cre)6Tuv/J (Pdx1Cre), B6;129-Sirt1tm1Ygu/J (Sirt1ex4) strains were obtained from Jackson Laboratories and bred to create the strain Pdx1Cre;Sirt1ex4F/F.

extract_protocol: Total RNA from whole pancreas of 6month old male animals was extracted using Purelink RNA Mini Kit (Ambion, Life Technologies, Carlsbad, CA, USA).

treatment_protocol: Standard animal house treatment.

value: pancreas


title: Sirt1KO_rep2

description: Total RNA from whole pancreas of 6month old male Sirt1 Knock out mouse, replicate 2


title: stool_LNS177

description: Gene expression data of stool RNAs from study subject


title: stool_LNS101


title: BRCAX.53


title: stool_LNS71


title: Sirt1KO_rep1

description: Total RNA from whole pancreas of 6month old male Sirt1 Knock out mouse, replicate 1


title: BRCAX.47


title: stool_LNS173


title: Ctrl_rep2

description: Total RNA from whole pancreas of 6month old male PDX1Cre mouse as control, replicate 2


title: BRCAX.49


title: Ctrl_rep3

description: Total RNA from whole pancreas of 6month old male PDX1Cre mouse as control, replicate 3


title: BRCA1.UV.29

value: YES


title: Ctrl_rep1

description: Total RNA from whole pancreas of 6month old male PDX1Cre mouse as control, replicate 1


title: stool_LNS160


title: BRCAX.44


title: stool_LNS191


title: stool_020A


title: BRCAX.45


title: BRCAX.46


title: BRCA1.UV.21


title: BRCAX.43


title: BRCAX.38


title: BRCAX.48


title: BRCAX.42


title: stool_256A


title: BRCAX.41


title: stool_091B


title: Gdap1-null day 4, rep2

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

institute: CIPF

description: Gdap1-null mouse embryonic fibroblast four days after expression of the four reprogramming factors (Oct4, Sox2, Klf4, cMyc)

hyb_protocol: Following fragmentation, 5.5 ug of single-stranded cDNA were hybridized for 18 hr at 45C on GeneChip Mouse Gene 2.0STArray. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console Software using Affymetrix default analysis settings

label_protocol: Biotinylated single-stranded cDNA were prepared according to the standard Ambion protocol  (The Ambion WT Expression manual for Affymetrix Genechip Whole Transcript Expression Arrays, 2009, Applied Biosystems).

growth_protocol: Cells were grown in DMEM 10 % FBS

treatment_protocol: Cells were mock- or OSKM-transduced overnight, and grown during four more days before processing.

tag: group

value: KO

tag: day

tag: replicated


title: Gdap1-null day 0, rep3

description: Gdap1-null mouse embryonic fibroblast before reprogramming


title: Gdap1-null day 0, rep2

source_name: Gdap1-null mouse embryonic fibroblast before reprogramming


title: BRCAX.39


title: Gdap1-null day 4, rep1

source_name: Gdap1-null mouse embryonic fibroblast four days after expression of the four reprogramming factors (Oct4, Sox2, Klf4, cMyc)


title: stool_186C


title: Gdap1-null day 0, rep1


title: Wild type day 4, rep3

description: Wild type mouse embryonic fibroblast four days after expression of the four reprogramming factors (Oct4, Sox2, Klf4, cMyc)

value: WT


title: BRCA1.UV.9

value: IVS

value: BRCA1 IVS 9+16C>G


title: stool_241B

value: F


title: BRCAX.37


title: BRCA1.UV.33


title: stool_087B


title: BRCA1.UV.6


title: Gdap1-null day 4, rep3


title: stool_288A


title: stool_085A


title: stool_019A


title: BRCAX.40


title: stool_LNS246


title: BRCA1.UV.36


title: BRCA1.UV.1


title: stool_LNS141


title: stool_201A


title: stool_LNS49


title: Wild type day 4, rep1

source_name: Wild type mouse embryonic fibroblast four days after expression of the four reprogramming factors (Oct4, Sox2, Klf4, cMyc)


title: BRCA1.UV.27


title: BRCA1.UV.3


title: Wild type day 0, rep2

description: Wild type mouse embryonic fibroblast before reprogramming


title: BRCA1.path.7


title: Wild type day 0, rep1

source_name: Wild type mouse embryonic fibroblast before reprogramming


title: stool_LNS89


title: Wild type day 0, rep3


title: stool_LNS156


title: BRCA1.UV.23


title: BRCA1.UV.22


title: stool_LNS60


title: stool_295B


title: BRCA1.UV.19


title: BRCA1.UV.20


title: SUNE1-NC

city: Guangzhou

first: Yang

middle: Meng

last: Zhao

address: Shiliugang Road

institute: Southern Medical University

description: the negtive SUNE1 control cell

hyb_protocol: After 16 to 18 hours of hybridization, remove the arrays from the oven. Remove the Tough-Spots from the arrays.Wash and stain with Fluidics Station 450 using the appropriate fluidics script for the array format

scan_protocol: The instructions for using the scanner and scanning arrays can be found in the Affymetrix® Command Console® User Manual (P/N 702569).

data_processing:
miRNA QC Tool Version 1.1.1.0/Expression Console 1.2 or higherfor data summarization, normalization, and quality control.
Statistical analysis was carried out using the open source R-software (http://www.r-project.org)

source_name: the negtive SUNE1 control cell

label_protocol: Add 2X Hybridization Mix,27.5% Formamide (Vial 12),DMSO,20X Hybridization Controls,Control Oligo B2, 3nM,Nuclease-free Waterthe 21.5 μL biotin-labeled sample in the order listed, to prepare the array hybridization cocktail:

growth_protocol: SUNE1 cell lines were cultured in RPMI-1640 (Invitrogen) supplemented with 10% fetal calf serum (FCS; Hyclone, Invitrogen) and incubated in a humidiﬁed chamber with 5% CO2 at 37°C

extract_protocol: RNA was extracted from the SUNE1-FOXO1 and SUNE1-NC cell lines using Trizol (Takara, Shiga,Japan).

treatment_protocol: Lentiviral particles carrying pGC-FU-FOXO1-RFP vector and its flanking control sequence transfect SUNE1 cell,the levels of FOXO1 protein were measured using Western blotting.

tag: cell line

tag: cell type

value: Nasopharyngeal carcinoma


title: stool_153A


title: stool_014B


title: stool_308A


title: stool_207B


title: SUNE1-FOXO1

description: FOXO1 gene overexpressed in SUNE1 cell

source_name: FOXO1 gene overexpressed in SUNE1 cell


title: stool_LNS231


title: stool_LNS79


title: BRCA1.UV.16


title: BRCA1.UV.17


title: BRCA1.path.21

value: STOP 1835


title: BRCA1.UV.13

value: BRCA1 IVS 19-12 G>A


title: stool_LNS219


title: stool_169A


title: stool_LNS153


title: stool_LNS111


title: BRCA1.UV.11

value: Female

value: BRCA1 IVS 14+2 ins 8


title: stool_279A


title: BRCA1.UV.14

value: tumour DNA

value: NO


title: stool_182B


title: stool_273B


title: stool_137A


title: BRCA1.path.8

value: breast cancer


title: BRCA1.UV.10

value: BRCA1 IVS 12+9 C>T


title: BRCA1.path.42


title: stool_LNS200

value: M

value: environmental enteric dysfunction


title: BRCA1.path.9


title: stool_LNS112


title: stool_138B


title: BRCA1.path.24

value: c.70_80 del TGTCCCATCTG

value: STOP 36


title: BRCA1.path.28

value: c.2071 del A

value: STOP 700


title: stool_LNS51


title: stool_LNS214


title: BRCA1.path.22

value: c.1018 del G

value: STOP 340


title: stool_LNS36

value: F


title: BRCA1.path.26


title: stool_LNS205


title: BRCA1.path.27


title: stool_LNS110


title: BRCA1.path.2


title: BRCA1.path.30

value: STOP 901


title: Wild type day 4, rep2

value: WT


title: stool_LNS75


title: BRCA1.path.11

value: Female


title: BRCA1.path.15

value: STOP 1087


title: BRCA1.path.18

value: tumour DNA

value: c.4936 del G

value: STOP 1657


title: stool_LNS88


title: stool_LNS242


title: stool_177A


title: stool_LNS12


title: BRCA1.path.12

value: breast cancer

value: NO


title: stool_LNS213

value: environmental enteric dysfunction


title: stool_209A


title: stool_LNS208

value: M


title: stool_LNS241


title: stool_018A


title: genomic DNA from peripheral blood 93

city: Tokushima

first: Makoto

last: Kinoshita

state: Tokushima

address: 3-18-15, Kuramoto

department: Psychiatry

country: Japan

institute: Tokushima University Graduate School

description: normal peripheral blood sample

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

data_processing: GenomeStudio Software v2011.1; The unmethylated (Signal_A) and methylated (Signal_B) signal intensities are found in the files Methylated_and_unmethylated_signal_samples1-93.txt and Methylated_and_unmethylated_signal_samples101-124.txt located on the series record.

source_name: peripheral blood 93

extract_protocol: Genomic DNA was prepared from peripheral blood samples.

tag: tissue

value: peripheral blood

value: normal


title: BRCA1.path.14

tag: gender


title: BRCA1.path.10


title: genomic DNA from peripheral blood 90

description: normal peripheral blood sample

source_name: peripheral blood 90

value: Male


title: stool_LNS179


title: BRCA1.UV.12

value: IVS

value: BRCA1 IVS 14-8 C>T


title: stool_LNS105

value: F


title: genomic DNA from peripheral blood 92

description: normal peripheral blood sample

source_name: peripheral blood 92


title: BRCA1.path.23

value: c.70_80 del TGTCCCATCTG

value: STOP 36


title: stool_LNS18


title: DHT-48h_2

city: Cleveland

first: Nima

last: Sharifi

state: OH

address: 9500 Euclid ave

department: Cancer biology

institute: Cleveland CLinic

description: Triplication for DHT

data_processing: Hybrid signal were process with Illumina GenomeStudio software

source_name: LAPC4 cells_DHT-48h

label_protocol: Standard Illumina labeling protocol

growth_protocol: LAPC4 cells were grown in Iscove’s Modified Dulbecco’s Medium with 10% FBS.

extract_protocol: mRNA were extracted with mirVanaTM miRNA isolation kit (Life technologies) following the manufactory protocol.

treatment_protocol: Cells were starved for 2 days with phenol red-free and serum free-medium  and stimulated with 1µM 5α-Abi or 0.1nM DHT for 48h.

tag: treatment

value: 0.1nM DHT treated for 48h


title: stool_196B


title: DHT-48h_1

description: Triplication for DHT


title: 5α-Abi-48h_3

description: Triplication for 5α-Ab

source_name: LAPC4 cells_5α-Abi-48h

value: 1µM 5α-Abi treated for 48h


title: DHT-48h_3

description: Triplication for DHT


title: stool_LNS46


title: genomic DNA from peripheral blood 91

description: normal peripheral blood sample

source_name: peripheral blood 91

value: Female


title: stool_LNS7


title: stool_146B


title: 5α-Abi-48h_2

description: Triplication for 5α-Ab


title: genomic DNA from peripheral blood 80

description: normal peripheral blood sample

source_name: peripheral blood 80


title: Ctrl-48h_3

description: Triplication for Ctrl

source_name: LAPC4 cells_control

value: ethanol treated for 48h


title: genomic DNA from peripheral blood 88

description: normal peripheral blood sample

source_name: peripheral blood 88


title: Ctrl-48h_2

description: Triplication for Ctrl


title: 5α-Abi-48h_1

description: Triplication for 5α-Ab


title: stool_253A

source_name: stool total RNA


title: genomic DNA from peripheral blood 81

description: normal peripheral blood sample

source_name: peripheral blood 81


title: Ctrl-48h_1

description: Triplication for Ctrl


title: stool_103A


title: genomic DNA from peripheral blood 86

description: normal peripheral blood sample

source_name: peripheral blood 86


title: genomic DNA from peripheral blood 83

description: normal peripheral blood sample

source_name: peripheral blood 83


title: genomic DNA from peripheral blood 79

description: normal peripheral blood sample

source_name: peripheral blood 79


title: genomic DNA from peripheral blood 85

description: normal peripheral blood sample

source_name: peripheral blood 85


title: genomic DNA from peripheral blood 78

description: normal peripheral blood sample

source_name: peripheral blood 78


title: genomic DNA from peripheral blood 87

description: normal peripheral blood sample

source_name: peripheral blood 87


title: stool_218B


title: genomic DNA from peripheral blood 77

description: normal peripheral blood sample

source_name: peripheral blood 77


title: stool_182A


title: genomic DNA from peripheral blood 76

description: normal peripheral blood sample

source_name: peripheral blood 76


title: stool_231A


title: genomic DNA from peripheral blood 89

description: normal peripheral blood sample

source_name: peripheral blood 89


title: ES_E14_2 Expression

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

institute: Hubrecht Institute

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Raw array data was processed using limma (Ritchie et al., 2015). We perform “normexp” background correction with an offset of 16. We normalize between arrays using quantile normalization. To identify differently expressed genes we create a contrast matrix in which all pairwise comparisons are made. For each probe an empirical Bayes moderated t-statistic test is performed. An FDR correction is applied to the nominal p-values.

source_name: ES E14

label_protocol: 500ng of total RNA per sample were labeled using Agilent's QuickAmp labeling kit and hybridized to Agilent 8X60K expression arrays.

growth_protocol: ESCs and iPSCs were cultured on Mitomycin-C treated MEFs in KO-DMEM (Invitrogen) supplemented with 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Invitrogen), 1,000 U/ml LIF (Millipore) and 15% fetal bovine serum (FBS, Invitrogen) (ESC medium). Naïve ESCs were cultured in serum-free N2B27 medium on gelatin-coated dishes. N2B27 medium (500ml) was generated by inclusion of the following: 240ml DMEM/F12 (Invitrogen), 240ml Neurobasal (Invitrogen), 5ml N2 supplement (Invitrogen), 10ml B27 supplement (Invitrogen), 1,000 U/ml LIF (Millipore), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Invitrogen), and the small molecules PD0325901 (Stemgent, 1μM) and CHIR (Stemgent, 3μM). CD19+ pre-B cells and Mac1+ macrophages were isolated from bone marrow with monoclonal antibodies to CD19 and Mac-1 (BD Pharmingen) respectively, using MACS sorting (Miltenyi Biotech). B cells were grown in RPMI medium with 10% FBS and 10ng/ml IL-7 (Peprotech); macrophages in DMEM with 10% FBS and 10ng/ml each of CSF1 and IL-3 (Peprotech). MEFs were established from day 13.5 mouse embryos and cultured in DMEM containing 10% FBS. NSC were isolated and cultured as previously described (Di Stefano et al., 2009). All media were supplemented with L-glutamine and penicillin/streptomycin (GIBCO).

extract_protocol: RNA was isolated with the miRNeasy mini kit (Qiagen), eluted with RNase-free water and quantified by Nanodrop. cDNA was produced with the High Capacity RNA-to-cDNA kit (Applied Biosystem). RNA samples with a RIN greater than 9 were analyzed by expression arrays.

treatment_protocol: Reprogramming experiments with B cells were performed as previously described (Di Stefano et al., 2014); with MEFs, macrophages and NSCs were conducted by plating 100.000 cells/well on gelatinized plates seeded with irradiated MEFs, using ESC medium supplemented with 2 µg/ml of doxycycline. For the isolation of iPSC lines, doxycycline was washed out after 15 days of reprogramming and colonies with ESC-like morphology were picked at 20 days before further passaging.  iPSC lines were expanded for an additional 9 days (3 passages) to obtain P3 iPS cell lines or for 20 passages to obtain P20 iPS cell lines.

value: ES E14


title: genomic DNA from peripheral blood 74

description: normal peripheral blood sample

source_name: peripheral blood 74


title: ES_E14_1 Expression


title: genomic DNA from peripheral blood 71

description: normal peripheral blood sample

source_name: peripheral blood 71


title: genomic DNA from peripheral blood 75

description: normal peripheral blood sample

source_name: peripheral blood 75


title: stool_180A


title: stool_LNS15


title: genomic DNA from peripheral blood 84

description: normal peripheral blood sample

source_name: peripheral blood 84


title: genomic DNA from peripheral blood 70

description: normal peripheral blood sample

source_name: peripheral blood 70


title: stool_148B

source_name: stool total RNA


title: stool_289A


title: genomic DNA from peripheral blood 73

description: normal peripheral blood sample

source_name: peripheral blood 73


title: genomic DNA from peripheral blood 82

description: normal peripheral blood sample

source_name: peripheral blood 82


title: stool_LNS212


title: MEF_iPS_p20_2 Expression

source_name: MEF iPS p20

value: MEF iPS p20


title: NSC_iPS_p20_2 Expression

source_name: NSC iPS p20

value: NSC iPS p20


title: stool_200A

value: environmental enteric dysfunction


title: MEF_iPS_p20_1 Expression


title: genomic DNA from peripheral blood 68

description: normal peripheral blood sample

source_name: peripheral blood 68


title: macrophages_iPS_p20_2 Expression

source_name: macrophages iPS p20

value: macrophages iPS p20


title: stool_LNS174

value: M


title: genomic DNA from peripheral blood 67

description: normal peripheral blood sample

source_name: peripheral blood 67

value: peripheral blood

value: normal


title: genomic DNA from peripheral blood 72

description: normal peripheral blood sample

source_name: peripheral blood 72

value: Male


title: NSC_iPS_p20_1 Expression


title: stool_LNS209


title: stool_LNS42


title: preB_iPS_p20_2 Expression

source_name: preB iPS p20

value: preB iPS p20


title: genomic DNA from peripheral blood 69

description: normal peripheral blood sample

source_name: peripheral blood 69


title: genomic DNA from peripheral blood 66

description: normal peripheral blood sample

source_name: peripheral blood 66


title: macrophages_iPS_p3_1 Expression

source_name: macrophages iPS p3

value: macrophages iPS p3


title: genomic DNA from peripheral blood 65

description: normal peripheral blood sample

source_name: peripheral blood 65


title: genomic DNA from peripheral blood 63

description: normal peripheral blood sample

source_name: peripheral blood 63


title: stool_LNS99


title: macrophages_iPS_p3_2 Expression


title: MEF_iPS_p3_2 Expression

source_name: MEF iPS p3

value: MEF iPS p3


title: stool_LNS201

value: F


title: MEF_iPS_p3_1 Expression


title: stool_LNS146


title: genomic DNA from peripheral blood 62

description: normal peripheral blood sample

source_name: peripheral blood 62


title: genomic DNA from peripheral blood 64

description: normal peripheral blood sample

source_name: peripheral blood 64


title: NSC_iPS_p3_2 Expression

source_name: NSC iPS p3

value: NSC iPS p3


title: stool_LNS21

source_name: stool total RNA


title: stool_LNS92


title: BRCA1.path.13

source_name: tumour genomic DNA

tag: sample type

value: tumour DNA

value: breast cancer

value: NO