description: Pyo vs. DMSO, 8 h Timepoint, Replicate 2. A. coluzzii Ngousso third instar larvae incubated with 50 µM Pyo compared to DMSO control.

value: Pyo

value: 50 µM Pyo equivalent volume


title: genomic DNA from blood 9969489137_R06C02

status: Public on Mar 01 2018

type: genomic

city: Barcelona

first: Carolina

last: Soriano-Tarraga

state: Barcelona

address: Calle Doctor Aiguader 88

department: Department of Neurology

country: Spain

institute: Institut Hospital del Mar d’Investigacions Mèdiques (IMIM).Hospital del Mar

description: stroke blood sample

hyb_protocol: The bisulfite converted DNA was processed and hybridized to the HumanMethylation450 BeadChip (Illumina, Inc.), according to the manufacturer's instructions.

scan_protocol: The BeadChip images were scanned on the iScan system and the data was extracted into GenomeStudio software v2011.1, using default analysis settings.

data_processing:
GenomeStudio 2011.1 software and R version 3.1.2. Processed data: raw Average Beta obtained from GenomeStudio, quality controls were done by MINFI Bioconductor package and probe type correction by SWAN bioconductor package.
Average Beta, normalized provided in
betas_normalized_meneas_185.txt
pval_detection_meneas_185.txt
Raw unmethylated and methylated signal intensities data is provided in
meth_raw_meneas_185.txt
unmeth_raw_meneas_185.txt

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: stroke blood sample

label_protocol: Bisulfite conversion was performed using 500 ng genomic DNA input using the EZ DNA Methylation Gold Kit (Zymo Research)

extract_protocol: DNA samples were extracted from whole peripheral blood collected in 10 mL EDTA tubes. The Chemagic Magnetic Separation Module I system (Chemagen)

tag: age

tag: gender

value: Male

tag: stroke subtype

value: cardioembolic

tag: sample type

value: blood

tag: disease state

value: stroke


title: NQ, 2640, Rep 2

type: RNA

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

country: USA

institute: US Army ERDC

hyb_protocol: The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array G4102A, AMADID 365741) was used for transcript expression assays (Agilent Technologies).  The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 200 ng of total RNA was used as the starting material for each exposure replicate.  Four exposure replicates for each treatment (NQ: Control (0 mg/L), 20.7 and 2640 mg/L)  were hybridized to microarrays in a completely randomized design using a random number generator.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: An Agilent Surescan Microarray Scanner (G2505 C, Agilent Technologies Inc.) was used to scan microarrays at 2 μm resolution.

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.5 (Agilent Technologies). GeneSpring was additionally used to conduct differential transcript expression analysis.  Un-corrected one-way ANOVA with p = 0.005 was used to identify transcripts having significant differential expression.  Post-hoc tests for all chemical exposure experiments were conducted using a moderated t-test (p = 0.05) and log2 fold change cutoff of ≥ 1.5 to discern statistically significant differences in transcript expression for each chemical exposure concentration relative to the control.

molecule: total RNA

organism: Pimephales promelas

source_name: whole animal

growth_protocol: Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment. Fish were fed <24-h old Artemia nauplii prior to test initiation.

extract_protocol: All samples were flash frozen in liquid nitrogen to preserve RNA.  A total of 4 larval fish were sampled per exposure replicate.  Samples were homogenized in lysis buffer with a FAST Prep-24 instrument (MP Biomedicals, Santa Ana, CA) before RNA isolation with RNeasy kits (Qiagen, Valencia, CA). Total RNA concentrations were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA). The integrity of total RNA was assessed on an Agilent 2100 Bioanalyzer (Palo Alto, CA).  Criteria for acceptable RNA integrity included a RNA integrity number > 8.0 from the Agilent 2100 Bioanalyzer and a 260/280 spectrophotometric reading > 2.0

treatment_protocol: Fathead minnow larvae were exposed to NQ at 0 (control), 20.7, 41.8, 82.7, 172, 367, 693. 1390, and 2640 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment.

tag: agent

value: NQ

tag: dose

tag: replicate

tag: tissue

value: larvae


title: NQ, 2640, Rep 1

label_protocol: The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 200 ng of total RNA was used as the starting material for each exposure replicate.


title: NQ, 2640, Rep 3


title: CON, Rep 3

hyb_protocol: The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array G4102A, AMADID 365741) was used for transcript expression assays (Agilent Technologies).  The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 200 ng of total RNA was used as the starting material for each exposure replicate.  Four exposure replicates for each treatment (IMX-101: Control (0 mg/L), 2.0 and 61.7 mg/L)  were hybridized to microarrays in a completely randomized design using a random number generator.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.5 (Agilent Technologies). GeneSpring was additionally used to conduct differential transcript expression analysis.  One-way ANOVA with Benjamini-Hochberg multiple-test corrected p = 0.05 was used to identify transcripts having significant differential expression.  Post-hoc tests for all chemical exposure experiments were conducted using a moderated t-test (p = 0.05) and log2 fold change cutoff of ≥ 1.5 to discern statistically significant differences in transcript expression for each chemical exposure concentration relative to the control.

treatment_protocol: Fathead minnow larvae were exposed to IMX-101 at 0 (control),1.9, 3.8, 7.6, 15.2, 30.2, 85.2, and 121.9 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment.

value: 0 (control)


title: genomic DNA from blood 9969489137_R06C01

description: stroke blood sample


title: genomic DNA from blood 9969489154_R02C02

description: stroke blood sample

value: Female

value: small-vessel disease


city: Berlin

first: Philip

middle: Adrian

last: Huegli

state: Berlin

address: Charitéplatz 1

department: Vector Biology

country: Germany

institute: Max Planck Institute for Infection Biology

description: Pyo vs. DMSO, 4 h Timepoint, Replicate 2. A. coluzzii Ngousso third instar larvae incubated with 50 µM Pyo compared to DMSO control.

hyb_protocol: Microarray experiments were performed as dual-color hybridizations with color-swap dye-reversal.

scan_protocol: Scanning of microarrays was performed at 5 μm resolution using a G2565CA high-resolution laser microarray scanner (Agilent Technologies) with XDR extended range.

data_processing: Microarray image data were analyzed and extracted with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings.

organism: Anopheles coluzzii

source_name: Pooled A. coluzzii Ngousso third instar larvae

label_protocol: RNA was labeled with a two-color Low Input Quick Amp Labeling Kit according the supplier’s recommendations (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7 primer, and labeled with Cyanine 3-CTP or Cyanine 5-CTP. After precipitation, purification, and quantification, 1.25 μg of each labeled cRNA was fragmented and hybridized to A. gambiae whole genome 4x44K multipack microarrays (Design ID 020449) according to the manufacturer’s protocol (Agilent Technologies).

growth_protocol: Anopheles coluzzii Ngousso strain was maintained at 28 ± 2°C, 85 ± 5% humidity and 12 h day/night cycle. Larvae were reared in 0.1% NaCl/ddH2O and fed with generic cat food pellets.

extract_protocol: Total RNA was isolated with TRIzol (Life Technologies) according the supplier’s protocol using Glycogen RNA carrier. Quality control and quantification of total RNA was assessed using an Agilent 2100 Bioanalyzer with a RNA Nano 6000 microfluidics kit (Agilent Technologies).

treatment_protocol: Fifteen third instar larvae (ca. 6 days old) were incubated with 1-HP, Pyo (50 µM) or an equivalent volume of DMSO in single wells of 6-well tissue culture plates for 4 h or 8 h.

value: mixed

tag: strain

value: Ngousso

value: whole-body

tag: developmental stage

value: third instar larvae

tag: exposure time

value: 4 h

tag: exposure compound

tag: exposure compound concentration

value: 50 µM

value: DMSO


title: NQ, 20.7, Rep 4


title: DMSO vs. Pyo, 4 h Timepoint, Replicate 2

description: Pyo vs. DMSO, 4 h Timepoint, Replicate 2. A. coluzzii Ngousso third instar larvae incubated with 50 µM Pyo compared to DMSO control. Color-swap dye-reversal.

value: 50 µM Pyo equivalent volume

value: Pyo


description: Pyo vs. DMSO, 8 h Timepoint, Replicate 1. A. coluzzii Ngousso third instar larvae incubated with 50 µM Pyo compared to DMSO control.

value: 8 h


title: DMSO vs. Pyo, 8 h Timepoint, Replicate 1

description: Pyo vs. DMSO, 8 h Timepoint, Replicate 1. A. coluzzii Ngousso third instar larvae incubated with 50 µM Pyo compared to DMSO control. Color-swap dye-reversal.


title: DMSO vs. Pyo, 4 h Timepoint, Replicate 1

description: Pyo vs. DMSO, 4 h Timepoint, Replicate 1. A. coluzzii Ngousso third instar larvae incubated with 50 µM Pyo compared to DMSO control. Color-swap dye-reversal.


title: NQ, 20.7, Rep 2


title: NQ, 20.7, Rep 1


title: NTO, Con, Rep 4

hyb_protocol: The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array G4102A, AMADID 365741) was used for transcript expression assays (Agilent Technologies).  The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 200 ng of total RNA was used as the starting material for each exposure replicate.  Four exposure replicates for each treatment (NTO: Control (0 mg/L), 68, and 1040 mg/L)  were hybridized to microarrays in a completely randomized design using a random number generator.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

treatment_protocol: Fathead minnow larvae were exposed to NTO at 0 (control), 68, 130, 265, 528, and 1040 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment.

value: NTO


title: genomic DNA from blood 9969489137_R04C02

description: stroke blood sample

value: cardioembolic

value: blood

value: stroke


title: NTO, Con, Rep 3

value: 0 (control)

value: larvae


title: NQ, 20.7, Rep 3

value: NQ


title: DMSO vs. Pyo, 8 h Timepoint, Replicate 2

description: Pyo vs. DMSO, 8 h Timepoint, Replicate 2. A. coluzzii Ngousso third instar larvae incubated with 50 µM Pyo compared to DMSO control. Color-swap dye-reversal.

value: mixed


title: genomic DNA from blood 9969489137_R05C02

description: stroke blood sample

value: Female


description: Pyo vs. DMSO, 4 h Timepoint, Replicate 1. A. coluzzii Ngousso third instar larvae incubated with 50 µM Pyo compared to DMSO control.

value: Ngousso

value: whole-body


title: genomic DNA from blood 9969489137_R04C01

description: stroke blood sample

value: Male


title: genomic DNA from blood 9969489137_R05C01

description: stroke blood sample


title: B9_base

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description: Tissue Sample

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to 8 plex Whole Human Genome microarrays

scan_protocol: Scanned on Agilent Scanner

data_processing: Images were quantified using Agilent Feature Extraction Software

source_name: Sample: Human Tissue Biopsy

label_protocol: 100ng of total RNA was reversed transcribed using Agilent Low Input Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted using RNeasy Fibrous Tissue Mini following manufacturers protocol

treatment_protocol: Storage of human tissue in RNAlater

tag: case/control

value: case

tag: biopsy site

value: base

tag: batch

tag: ssc subtype

value: dcSSc

source_name: Universal Human Reference

value: Universal Human Reference


title: NTO, Con, Rep 2


title: B9_12mo

description: Tissue Sample

value: post


title: B5_base

description: Tissue Sample


title: HFs after 6h (HF10-003)

city: Jerusalem

first: Yuval

last: Ramot

address: Kiryat Hadassah, POB 12000

country: Israel

institute: Hadassah - Hebrew University Medical Center

description: Gene expression data from GMG-43AC-treated HFs in comparison to vehicle-treated HFS

hyb_protocol: The hybridization procedure was performed according to the Two-color MicroarrayBased Gene Expression Analysis (Quick Amp Labeling) protocol using the Agilent Gene Expression Hybridization Kit. Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome 4x44K Oligo Microarrays using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of Microarrays were detected by Agilent’s Microarray Scanner.

data_processing:
Analysis was performed using an Agilent Human Whole Genome Oligo Microarray (44K) by ChromoMed Ltd. (Budapest, Hungary)
normalized log10 ratio (Cy5/Cy3) representing test/reference, representing LogRatio column from Agilent Feature Extraction files

source_name: GMG-43AC-treated HFs from a female patient

label_protocol: To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: The hair follicles were cultured in serum-free Williams’ E medium supplemented with glutamine, insulin, hydrocortisone, and an antibiotic/antimycotic mixture.

extract_protocol: RNA was isolated by standard protocols (TRIzol; InvitrogenLife Technologies)

treatment_protocol: 25 HFs from two individuals were treated for 6 hours with 0.01 mM N-Acetyl-GED or vehicle

value: Scalp hair follicles

tag: gender

tag: treatment

source_name: Vehicle-treated HFs from a female patient

value: control


title: B5_12mo

description: Tissue Sample

tag: sample type


title: 24h.7

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Cy3- and Cy5-labeled RNAs were hybridized overnight to 4×44K 60mer oligonucleotide spotted microarray slides (Mouse Whole Genome 4×44K; Agilent Technologies, P/N G4122F). Hybridization and subsequent washing and drying of the slides were performed following the Agilent hybridization protocol.

scan_protocol: The dried slides were scanned using the GenePix 4100A scanner (Axon Instruments, Downingtown, PA).

data_processing: Image analysis was performed with GenePix Pro 5.1 software and calculated values for all spots were saved as GenePix results files. Data were evaluated using the R software and the limma package from BioConductor. MA-values were loess-normalized.

organism: Mus musculus

source_name: N 24h

label_protocol: Purified total RNA was amplified and Cy-dye-labeled using the dual-color QuickAmp labeling kit (Agilent, P/N 5190-0444) following the kit instructions. Per reaction, 1 µg of total RNA was used. The samples were labeled with either Cy3 or Cy5 to match a balanced dye-swap design

growth_protocol: Murine alveolar MLE12 cells (ATCC CRL 2110) were maintained in DMEM/F12 medium (Gibco) supplemented with 2 % (v/v) fetal bovine serum (FBS, PAA), 10 nM hydrocortisone (Sigma), 10 nM hydro-beta-estradiole (Sigma), 5 µg/mL insulin (PAN Biotech), 10 µg/ml transferrin (PAN Biotech), 30 nM Na-selenite (PAN Biotech), 10 mM HEPES (Sigma), 2 mM L-Glutamine (Gibco) and 1% (v/v) penicillin/streptomycin (Gibco). Cells were grown at 37°C, 5 % CO2.

extract_protocol: Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen)

treatment_protocol: To overexpress NICD1 in MLE12 cells, the NICD1-pIRES-DsRed2 construct or empyt vector were transfected using Lipofectamine2000 (Invitrogen) according to the manufacturer's instruction. Cells were harvested 12, 24, and 48h after transfection

tag: cell line

value: lung epithelial cell line MLE12

tag: transfection

tag: time

source_name: EV 24h

value: Empty vector


title: NTO, Con, Rep 1

tag: agent

value: NTO

tag: dose

value: 0 (control)

tag: replicate


title: genomic DNA from blood 9969489137_R03C01

description: stroke blood sample

tag: age

tag: stroke subtype

value: cardioembolic

value: blood

tag: disease state

value: stroke


title: HFs after 6h (HF09-111)

tag: tissue

value: Female


title: 48h.7

source_name: N 48h

source_name: EV 48h


title: NTO, 1040, Rep 3

value: larvae


title: NTO, 1040, Rep 4


title: B4_base

description: Tissue Sample

tag: case/control


title: B4_12mo

description: Tissue Sample

tag: biopsy site


title: genomic DNA from blood 9969489137_R02C02

description: stroke blood sample

value: Male


title: 12h.6

source_name: N 12h

source_name: EV 12h


title: B26_base

description: Tissue Sample

value: case

tag: batch


title: NTO, 1040, Rep 1


title: genomic DNA from blood 9969489137_R03C02

description: stroke blood sample

value: small-vessel disease


title: 48h.6


title: genomic DNA from blood 9969489137_R02C01

description: stroke blood sample


title: genomic DNA from blood 9969489116_R06C02

description: stroke blood sample


title: genomic DNA from blood 9969489154_R03C02

description: stroke blood sample


title: genomic DNA from blood 9969489116_R06C01

description: stroke blood sample


title: genomic DNA from blood 9969489116_R05C01

description: stroke blood sample


title: B26_12mo

description: Tissue Sample

tag: ssc subtype

value: dcSSc


title: 24h.6


title: NTO, 68, Rep 4


title: NTO, 1040, Rep 2


title: 48h.5


title: 12h.5


title: B25_12mo

description: Tissue Sample

value: Universal Human Reference


title: genomic DNA from blood 9969489116_R03C02

description: stroke blood sample

tag: gender


title: B25_base

description: Tissue Sample

value: base


title: NTO, 68, Rep 3


title: NTO, 68, Rep 1


title: NTO, 68, Rep 2


title: B24_base

description: Tissue Sample


title: genomic DNA from blood 9969489116_R03C01

description: stroke blood sample


title: genomic DNA from blood 9969489116_R04C01

description: stroke blood sample


title: B22_base

description: Tissue Sample


title: 24h.3


title: B24_12mo

description: Tissue Sample

value: post


title: B22_12mo

description: Tissue Sample


title: genomic DNA from blood 9969489092_R06C01

description: stroke blood sample


title: DNAN, CON, Rep 2

hyb_protocol: The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array G4102A, AMADID 365741) was used for transcript expression assays (Agilent Technologies).  The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 200 ng of total RNA was used as the starting material for each exposure replicate.  Four exposure replicates for each treatment (DNAN: Control (0 mg/L), 0.81, and 26.5 mg/L)  were hybridized to microarrays in a completely randomized design using a random number generator.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

treatment_protocol: Fathead minnow larvae were exposed to DNAN at 0 (control), 0.37, 0.81, 1.6, 3.3, 6.6, 13.2, 26.5, 53.0 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment.

value: DNAN


title: 24h.5

value: lung epithelial cell line MLE12


title: DNAN, CON, Rep 1


title: DNAN, CON, Rep 4


title: DNAN, CON, Rep 3


title: B20_base

description: Tissue Sample


title: 24h.4

value: Empty vector


title: 12h.4


title: genomic DNA from blood 9969489092_R05C02

description: stroke blood sample


title: DNAN, 26.5, Rep 4


title: genomic DNA from blood 9969489092_R06C02

description: stroke blood sample


title: 48h.4


title: genomic DNA from blood 9969489092_R04C02

description: stroke blood sample


title: 48h.3


title: B20_12mo

description: Tissue Sample


title: genomic DNA from blood 9969489092_R03C01

description: stroke blood sample


title: 12h.3


title: B19_base

description: Tissue Sample


title: B2_12mo

description: Tissue Sample


title: genomic DNA from blood 9969489092_R02C01

description: stroke blood sample


title: B2_base

description: Tissue Sample


title: 12h.2


title: DNAN, 26.5, Rep 3


title: genomic DNA from blood 9969489092_R01C02

description: stroke blood sample

value: atherotrombotic


title: B19_12mo

description: Tissue Sample


title: 48h.1


title: DNAN, 26.5, Rep 2


title: genomic DNA from blood 9969489092_R01C01

description: stroke blood sample


title: DNAN, 0.81, Rep 4


title: genomic DNA from blood 9969489065_R06C02

description: stroke blood sample


title: 48h.2


title: 12h.1


title: B18_base

description: Tissue Sample


title: DNAN, 26.5, Rep 1


title: genomic DNA from blood 9969489065_R06C01

description: stroke blood sample


title: B18_12mo

description: Tissue Sample


title: genomic DNA from blood 9969489065_R05C02

description: stroke blood sample


title: DNAN, 0.81, Rep 2


title: DNAN, 0.81, Rep 1


title: 24h.2


title: DNAN, 0.81, Rep 3


title: B17_base

description: Tissue Sample


title: genomic DNA from blood 9969489065_R05C01

description: stroke blood sample


title: spt16-1_Aerial_DAS10, biological rep3

city: Regensburg

first: Alexander

last: Pfab

address: Universitätsstraße 31

department: Cell Biology & Plant Biochemistry

institute: University of Regensburg

description: Gene expression data from Arabidopsis spt16-1 (DAS10)

hyb_protocol: 3.5 µg of fragmented and labeled ss-cDNA were hybridized for 16hr at 45C in a GeneChip hybridization oven 640.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using the RMA algorithm as implemented in the Affymetrix GeneChip Expression Console v1.3 software.

label: biotin

organism: Arabidopsis thaliana

source_name: Aerial parts of spt16-1 (DAS10)

label_protocol: The Affymetrix GeneChip WT PLUS Reagent Kit Protocol was used for the preparation of biotinylated ss-cDNA from 200ng of total RNA.

growth_protocol: Arabidopsis wild type and mutants plants were grown for 10 days on 0.5xMS plates under standard growth conditions

extract_protocol: Total RNA was extracted with the RNeasy Mini Plant kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Aerial parts of 10-days old plants were harvested and immediately frozen in liquid nitrogen.

tag: ecotype

tag: genotype

value: Aerial parts

tag: light


title: 24h.1

tag: cell line

tag: transfection


title: GF-IEC

city: Tianjin

first: Rongcun

last: Yang

address: Weijin Road 94

department: Immunology

country: China

institute: Nankai university

description: Gene expression data from germ-free mice intestinal epithelial cells

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: GF mice intestinal epithelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: Mice were maintained in vinyl isolators within the gnotobiotic facility.

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

treatment_protocol: GF mice monocolonized with 1*10^8 L.NK2, two weeks later, intestinal epithelial cells and peyer's patches cells were isolated.

value: intestinal epithelial cells


title: L.NK2-IEC

description: Gene expression data from germ-free monocolonized with L.NK2 mice intestinal epithelial cells

source_name: L.NK2-colonized mice intestinal epithelial cells


title: B16_12mo

description: Tissue Sample

tag: sample type


title: Col-0_Aerial_DAS10, biological rep3

description: Gene expression data from Arabidopsis Col-0 (DAS10)

source_name: Aerial parts of Col-0 (DAS10)

value: wildtype


title: B16_base

description: Tissue Sample


title: ssrp1-2_Aerial_DAS10, biological rep3

description: Gene expression data from Arabidopsis ssrp1-2 (DAS10)

source_name: Aerial parts of ssrp1-2 (DAS10)


title: genomic DNA from blood 9969489065_R04C02

description: stroke blood sample

source_name: stroke blood sample

value: blood

value: stroke


title: B17_12mo

description: Tissue Sample


title: B15_base

description: Tissue Sample


title: genomic DNA from blood 9969489065_R04C01

description: stroke blood sample

value: Female

value: cardioembolic


title: genomic DNA from blood 9969489065_R03C02

description: stroke blood sample

value: Male


title: GF-PP

description: Gene expression data from germ-free mice peyer's patches cells

source_name: GF mice Peyer's patches cells

value: Peyer's patches cells


title: L.NK2-PP

description: Gene expression data from germ-free mice monocolonized with L.NK2 mice peyer's patches cells

source_name: L.NK2-colonized mice Peyer's patches cells


title: genomic DNA from blood 9969489065_R02C02

description: stroke blood sample


title: spt16-1_Aerial_DAS10, biological rep2


title: B15_12mo

description: Tissue Sample

source_name: Sample: Human Tissue Biopsy

value: case

value: dcSSc

source_name: Universal Human Reference


title: B14_base

description: Tissue Sample

value: base

value: Universal Human Reference


title: High-fat diet_Bacteria_mouse 5

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

description: Gene expression data from the skin of C. accolens-associated mice under high-fat diet regimen

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

label: Biotin

source_name: Skin (ear) from C. accolens-associated mouse under high-fat diet regimen

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

value: Skin

tag: diet

value: High-Fat diet

tag: bacteria

value: C. accolens


title: B14_12mo

description: Tissue Sample

value: post


title: ssrp1-2_Aerial_DAS10, biological rep2

tag: age

value: Aerial parts


title: Col-0_Aerial_DAS10, biological rep2


title: genomic DNA from blood 9969489065_R02C01

description: stroke blood sample

tag: stroke subtype


title: High-fat diet_Bacteria_mouse 4


title: spt16-1_Aerial_DAS10, biological rep1


title: High-fat diet_Bacteria_mouse 3


title: ssrp1-2_Aerial_DAS10, biological rep1


title: B12_base

description: Tissue Sample


title: genomic DNA from blood 9969489033_R06C01

description: stroke blood sample

tag: disease state


title: genomic DNA from blood 9969489033_R06C02

description: stroke blood sample


title: Col-0_Aerial_DAS10, biological rep1

tag: tissue


title: genomic DNA from blood 9969489033_R05C02

description: stroke blood sample


title: genomic DNA from blood 9969489033_R05C01

description: stroke blood sample

value: small-vessel disease


title: B11_base

description: Tissue Sample

tag: case/control


title: B12_12mo

description: Tissue Sample

tag: biopsy site


title: genomic DNA from blood 9969489033_R04C02

description: stroke blood sample


title: B11_12mo

description: Tissue Sample

tag: batch


title: Control diet_Bacteria_mouse 5

description: Gene expression data from the skin of C. accolens-associated mice under control diet regimen

source_name: Skin (ear) from C. accolens-associated mouse under control diet regimen

value: Control diet


title: High-fat diet_Bacteria_mouse 1


title: High-fat diet_Bacteria_mouse 2


title: Control diet_Bacteria_mouse 4


title: B1_12mo

description: Tissue Sample

tag: ssc subtype


title: PPARg Hom2 lung int pop_10002897010_B.mean

city: Heidelberg

first: Markus

last: Feuerer

address: Im Neuenheimer Feld 280

institute: DKFZ

description:
replicate 2
SAMPLE 8

hyb_protocol: 1.5 µg of cDNA were hybridized for 17hrs at 55.4 °C on Illumina Mouse WG-6-Microarray

scan_protocol: Illumina iSCAN-Scanner according to Std Illumina Scanning Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). Microarray scanning was done using an iScan array scanner

data_processing: Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers are removed when the absolute difference to the median is greater than 2.5 times MAD(2.5 Hampelís method). All remaining bead level data points are than quantile normalized [1]. As test for significance the studentís t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction [2] was applied to the complete set of p-values of all 48107 ProbeIDs on the chip. The average expression value is calculated as mean of the measured expressions of beads together with the standard deviation of the beads. [1] Probe Level Quantile Normalization of High Density Oligonucleotide Array Data, Ben Bolstad, Division of Biostatistics, University of California, Berkeley December 2001  [2] Y. Benjamini and Y. Hochberg (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, Vol. 57, 289ñ300.

source_name: lung tissue

label_protocol: The NuGEN Ovation Pico WTA System (linear isothermal DNA amplification process) was used to generate single-stranded cDNA. Labeled cRNA was prepared according to Nugene Encore BiotinIL Module.

growth_protocol: Cell were isolated from lung via FACS and immediatedly lysed for RNA isolation.

extract_protocol: Total RNA was extracted from sorted cells using the RNEasy Plus Micro Kit (Qiagen)

tag: strain

tag: genotype/variation

tag: gender

value: female

value: lung

tag: cell type

value: Pparg deficient alveolar macrophages


title: B1_base

description: Tissue Sample


title: n2 young adult sample [N2_young_2]

type: SRA

city: Medford

first: David

last: Angeles-Albores

state: MA

address: 61 Locust St

institute: Northwestern University

library_source: transcriptomic

data_processing:
Pseudo-alignment using Kallisto
Differential expression analysis using Sleuth
Genome_build: WBcel235
Supplementary_files_format_and_content: raw reads, fastq; abundance files, tsv; abundance files for sleuth, h5

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: n2 young adult sample

growth_protocol: Synchronized growth at 20C on ample OP50

extract_protocol:
Grow synchronized worms on OP50, wash off plate, extract using trizol
RNA-Seq libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530) following manufacturer’s instructions.

value: wild type

tag: life stage

value: Young Adult (no eggs visible)


title: n2 young adult sample [N2_young_3]


title: PPARg Hom1 lung int pop_10002897010_A.mean

description:
replicate 1
SAMPLE 7


title: PPARg Hom3 lung int pop_10002897010_C.mean

description:
replicate 3
SAMPLE 9


title: PPARg Het2 lung Mph_10002897002_E.mean

description:
replicate 2
SAMPLE 5

value: wild type alveloar macrophages


title: PPARg Het3 lung Mph_10002897002_F.mean

description:
replicate 3
SAMPLE 6


title: genomic DNA from blood 9969489033_R03C01

description: stroke blood sample

value: Male

value: cardioembolic

value: blood

value: stroke


title: genomic DNA from blood 9969489033_R03C02

description: stroke blood sample

value: Female


title: genomic DNA from blood 9969489033_R02C02

description: stroke blood sample


title: PPARg Het1 lung Mph_10002897002_D.mean

description:
replicate 1
SAMPLE 4


title: n2 aged adult sample [N2_aged_2]

source_name: n2 aged adult sample

value: 6th day aged adult


title: Control diet_Bacteria_mouse 3

value: Skin

value: C. accolens


title: n2 aged adult sample [N2_aged_3]


title: n2 young adult sample [N2_young_1]


title: High-fat diet_No Bacteria_mouse 4

description: Gene expression data from the skin of unassociated mice under high-fat diet regimen

source_name: Skin (ear) from unassociated mouse under high-fat diet regimen

value: High-Fat diet

value: No bacteria


title: Control diet_Bacteria_mouse 2

value: Control diet


title: High-fat diet_No Bacteria_mouse 5


title: genomic DNA from blood 9969489033_R04C01

description: stroke blood sample


title: Control diet_Bacteria_mouse 1


title: n2 aged adult sample [N2_aged_1]


title: fog-2 young adult sample [JK_young_3]

source_name: fog-2 young adult sample

value: fog-2 mutant


title: genomic DNA from blood 9969489009_R06C02

description: stroke blood sample

value: small-vessel disease


title: genomic DNA from blood 9969489009_R06C01

description: stroke blood sample


title: Control diet_No Bacteria_mouse 5

description: Gene expression data from the skin of unassociated mice under control diet regimen

source_name: Skin (ear) from unassociated mouse under control diet regimen


title: fog-2 young adult sample [JK_young_2]


title: High-fat diet_No Bacteria_mouse 2


title: Control diet_No Bacteria_mouse 4


title: genomic DNA from blood 9969489033_R02C01

description: stroke blood sample


title: PPARg Hom1 lung Mph_10002897002_A.mean

description:
replicate 1
SAMPLE 1

value: female

value: lung


title: PPARg Hom3 lung Mph_10002897002_C.mean

description:
replicate 3
SAMPLE 3


title: genomic DNA from blood 9969489009_R04C02

description: stroke blood sample


title: fog-2 aged sample [JK_aged_3]

source_name: fog-2 aged sample


title: genomic DNA from blood 9969489009_R04C01

description: stroke blood sample


title: genomic DNA from blood 9969489009_R03C01

description: stroke blood sample


title: fog-2 aged sample [JK_aged_1]


title: fog-2 aged sample [JK_aged_2]


title: genomic DNA from blood 9969489009_R02C02

description: stroke blood sample


title: genomic DNA from blood 9969489009_R05C02

description: stroke blood sample


title: fog-2 young adult sample [JK_young_1]

value: Young Adult (no eggs visible)


title: Control diet_No Bacteria_mouse 3


title: High-fat diet_No Bacteria_mouse 1


title: genomic DNA from blood 9969489009_R02C01

description: stroke blood sample


title: genomic DNA from blood 9969489007_R06C02

description: stroke blood sample


title: Patient 17 17N_17T

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

description:
in the raw data file,gProcessedSignal represented Normal
in the raw data file, rProcessedSignal represented Tumor

hyb_protocol: 27.5 μL of labeled samples were dissolved in 82.5 μL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a the CapitalBio circRNA Human Gene Expression Microarray V1.0 (4x90K, CapitalBio, Beijing). Arrays hybridization were performed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: After washing the slides, the arrays were scanned by the Agilent Scanner G2565CA (Agilent, Santa Clara, CA). Acquired array images were analyzed by Agilent Feature Extraction (v10.7) software.

data_processing: Microarray data was extracted using Agilent Feature Extraction software. Data summarization, quantile normalization, quality control and most of the subsequent data processing were executed using GeneSpring software V12.0 (Agilent, Santa Clara, CA) or R software package. Raw and processed files were filtered to remove lncRNA probes.

source_name: cervical tumor

label_protocol: 5ug isolated total RNA was treated with Rnase R (Epicentre, Madison, WI) to remove linear RNA. cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction41, and the procedure has been improved by using CapitalBio circRNA Amplification and Labeling Kit (CapitalBio, Beijing) for producing higher yields of labeled cDNA. In detail, double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 0.2 μg total RNA using the CbcScript reverse transcriptase with cDNA synthesis system according to the manufacturer’s protocol (Capitalbio, Beijing) with the T7 Oligo (dN). After completion of double-stranded cDNA (dsDNA) synthesis using DNA polymerase and RNase H, the dsDNA products about 12.5μL were subjected to 40μL in vitro transcription reactions at 37℃ for 14 h using a T7 Enzyme Mix. The amplified cRNA was purified using the RNA Clean-up Kit (MACHEREY - NAGEL, Germany). Klenow enzyme labeling strategy was adopted after reverse transcription using reverse transcriptase. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MACHEREY - NAGEL, Germany) and re-suspended in elution buffer.

extract_protocol: UHRR was bought from Agilent,HBRR was bought from Ambion.tumor samples and normal tissues were collected from the Oncology Department of the Second Affiliated Hospital of Zhen Zhou University by related surgeons. Plasma samples were isolated by EDTA and centrifuged at 820 ×g for 10 min. The postoperative samples were collected 2 to 34 days after surgery.

value: cervical tumor

source_name: adjacent normal

value: adjacent normal


title: High-fat diet_No Bacteria_mouse 3


title: genomic DNA from blood 9969489009_R03C02

description: stroke blood sample

value: Male


title: Patient 9 9N_9T


title: BM CD34+ cells from Healthy Donor 9 (miEP)_reanalyzed

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

hyb_protocol: Regarding miEP, tagged RNA was hybridized to the Affymetrix Genechip miRNA array 2.0 using manufacturer's recommendations (FlashTag™ Biotin HSR RNA Labeling Kit, P/N 703095 Rev. 1). The miRNA arrays were washed and stained by GeneChip Hybridization, Wash and Stain Kit (Affymetrix) with Fluidic Station 450 using fluidic script FS450_003.

scan_protocol: Affymetrix Genechip miRNA arrays 2.0 were scanned using the Affymetrix GCS3000 7G Scanner.

data_processing: Gene and miRNA expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

source_name: Bone marrow CD34+ Cells

label_protocol: Gene expression profiling (GEP) and miRNA expression profiling (miEP) were performed on the same RNA preparation. As regards miEP, total RNA (100ng for samples) were labeled using the FlashTag® Biotin HSR kit (Affymetrix).

growth_protocol: Bone marrow (BM) CD34+ cells were obtained from PV (n=26), and ET (n=24) patients. CD34+ cells were collected from 5 ml of BM aspirates, all obtained in preservative free heparin. Mononuclear cells were separated over a Ficoll-Paque gradient (Lympholyte; Cederlane Labs) and processed through two sequential steps of immunomagnetic CD34  selection (Miltenyi Biotec, Bergisch Gladbach,Germany,http://www.miltenyibiotec.com). Purity of the isolated CD34+ cell population was evaluated by flow cytometry after labeling with PE-HPCA2 anti-CD34 monoclonal antibody (BD Biosciences) and was always > 95%.

extract_protocol: CD34+ cells were purified from BM aspirates and immediately  lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA). Total RNA from CD34+ cells was extracted using miRNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations for Purification of Total RNA, Including Small RNAs, from Animal Cells. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

tag: supplier

value: Vannucchi

tag: Sex

value: not provided

tag: condition

value: Control (CTR)

tag: disease

value: healthy control

value: neg

value: Bone marrow

tag: cell marker


title: retina_cavtratin_rep1

city: GuangZhou

first: Zhongshu

last: Tang

state: Guangdong

address: 54 South Xianlie Road

institute: Sun Yat-sen University

description: cavtratin injected

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)

data_processing: Data command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: mouse retina isolated 2 hr after injection of cavtratin

label_protocol: Total RNA were amplified, labeled and purified by using Ambion  WT Expression Kit(Cat#411973， Ambion, US) and GeneChip  WT Terminal Labeling Kit(Cat#90067biotin labeled cDNA.1, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Animals were housed in a 12-h light-dark cycle and maintained in the Animal Laboratory of ZOC.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies,Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Cav1-shRNA or cavtratin was injected into the mouse eye vitrous and kept for 2 days or 2 hours, respectively. AP was used as the control at the same time as cavtratin. 5-6 Retinae were collected and pooled in one group for the array.

value: retina


title: Control diet_No Bacteria_mouse 1

value: Skin

tag: diet

tag: bacteria

value: No bacteria


title: Control diet_No Bacteria_mouse 2

tag: tissue

value: Control diet


title: retina_Cav1-shRNA_rep1

description: Cav1-shRNA injected

source_name: mouse retina isolated 2 days after injection of Cav1-shRNA


title: XL_wtGC.B

city: Montreal

first: Hua

last: Gu

state: QC

address: 110 avenue des pins ouest

country: Canada

institute: IRCM

data_processing:
Reads were aligned to the GRCm38 genome with TopHat v2.0.10
Raw alignment counts were calculated with featureCounts
Differential expression measurements were performed with DESeq2 v1.4.5
Genome_build: GRCm38
Supplementary_files_format_and_content: Diff files with DESeq2

source_name: Germinal Center B cells

growth_protocol: WT and Cbl-/-Cblb-/- mice were immunized with 1000million sheep red blood cells through IV injection

extract_protocol:
Spleens were harvested 10 day after immunization. GC B cells were sorted based on surface marker B220+Fas+GL7+CD138-. RNA was purified by using Rneasy Mini kit.
Illumina TruSeq RNA system; sequencing using PE50 on a HiSeq 2000 sequencer (Illumina technologies)

value: Germinal Center B cells

tag: immunization time

value: day 10

tag: genotype

value: wild type


title: genomic DNA from blood 9969489007_R06C01

description: stroke blood sample

source_name: stroke blood sample

tag: age

tag: stroke subtype

value: small-vessel disease

tag: sample type

value: blood

tag: disease state

value: stroke


title: Patient 16 16N_16T

value: cervical tumor

value: adjacent normal


title: XL_GammaGC.B

tag: strain

value: Cbl-/-Cblb-/-


title: Patient 10 10N_10T


title: genomic DNA from blood 9969489007_R05C02

description: stroke blood sample

tag: gender

value: Female


title: genomic DNA from blood 9969489007_R04C02

description: stroke blood sample

value: Male

value: cardioembolic


title: retina_AP-ctl_rep1

description: AP injected

source_name: mouse retina isolated 2 hr after injection of AP


title: Patient 5 5N_5T


title: BM CD34+ cells from Healthy Donor 6 (miEP)_reanalyzed

value: Vannucchi

value: not provided

value: Control (CTR)

value: healthy control

value: neg

value: Bone marrow


title: genomic DNA from blood 9969489007_R04C01

description: stroke blood sample


title: BM CD34+ cells from Healthy Donor 7 (miEP)_reanalyzed


title: Patient 4 4N_4T


title: Patient 3 3N_3T


title: BM CD34+ cells from Healthy Donor 5 (miEP)_reanalyzed


title: BM CD34+ cells from Healthy Donor 8 (miEP)_reanalyzed


title: BM CD34+ cells from Healthy Donor 4 (miEP)_reanalyzed


title: Patient 2 2N_2T


title: genomic DNA from blood 9969489007_R03C01

description: stroke blood sample


title: genomic DNA from blood 9969489007_R03C02

description: stroke blood sample


title: Patient 8 8N_8T


title: BM CD34+ cells from Healthy Donor 3 (miEP)_reanalyzed


title: genomic DNA from blood 9969489007_R02C01

description: stroke blood sample


title: genomic DNA from blood 9969489007_R02C02

description: stroke blood sample


title: genomic DNA from blood 9969489006_R06C02

description: stroke blood sample


title: BM CD34+ cells from Healthy Donor 15 (miEP)_reanalyzed


title: BM CD34+ cells from Healthy Donor 13 (miEP)_reanalyzed


title: BM CD34+ cells from Healthy Donor 12 (miEP)_reanalyzed


title: genomic DNA from blood 9969489006_R06C01

description: stroke blood sample


title: genomic DNA from blood 9969489006_R05C02

description: stroke blood sample


title: BM CD34+ cells from Healthy Donor 14 (miEP)_reanalyzed


title: genomic DNA from blood 9969489006_R05C01

description: stroke blood sample


title: genomic DNA from blood 9969489006_R04C01

description: stroke blood sample


title: genomic DNA from blood 9969489006_R04C02

description: stroke blood sample


title: BM CD34+ cells from Healthy Donor 1 (miEP)_reanalyzed


title: BM CD34+ cells from Healthy Donor 11 (miEP)_reanalyzed


title: BM CD34+ cells from patient 5764 (miEP)

value: M

value: myeloproliferative neoplasm (MPN)

value: PV

value: pos

tag: mpl-mutated

tag: calr-mutated

tag: gene mutation


title: genomic DNA from blood 9969489006_R03C02

description: stroke blood sample

value: blood

value: stroke


title: Patient 1 1N_1T

value: cervical tumor

value: adjacent normal


title: BM CD34+ cells from Healthy Donor 2 (miEP)_reanalyzed

tag: supplier

tag: Sex

tag: condition


title: genomic DNA from blood 9969489006_R02C01

description: stroke blood sample


title: genomic DNA from blood 9969489005_R06C02

description: stroke blood sample

value: Female


title: BM CD34+ cells from Healthy Donor 10 (miEP)_reanalyzed

tag: disease

tag: cell marker


title: genomic DNA from blood 9969489005_R06C01

description: stroke blood sample

value: Male


title: BM CD34+ cells from patient 11_122 (miEP)

value: Cazzola

value: F

value: ND

tag: tissue


title: BM CD34+ cells from patient 11_202 (miEP)


title: genomic DNA from blood 9969489005_R05C02

description: stroke blood sample

value: small-vessel disease


title: BM CD34+ cells from patient 11_46 (miEP)


title: genomic DNA from blood 9969489005_R05C01

description: stroke blood sample

value: cardioembolic


title: BM CD34+ cells from patient 10_591 (miEP)

value: neg


title: genomic DNA from blood 9969489005_R04C02

description: stroke blood sample

value: atherotrombotic


title: BM CD34+ cells from patient 7164 (miEP)

value: Vannucchi

value: Bone marrow


title: genomic DNA from blood 9969489005_R04C01

description: stroke blood sample


title: BM CD34+ cells from patient 7201 (miEP)

value: M

value: myeloproliferative neoplasm (MPN)

value: PV


title: BM CD34+ cells from patient 7153 (miEP)

value: pos


title: genomic DNA from blood 9969489005_R03C02

description: stroke blood sample

value: blood

value: stroke


title: BM CD34+ cells from patient 7144 (miEP)


title: genomic DNA from blood 9969489005_R03C01

description: stroke blood sample


title: BM CD34+ cells from patient 7124 (miEP)


title: BM CD34+ cells from patient 7083 (miEP)


title: genomic DNA from blood 9969489005_R02C02

description: stroke blood sample

value: Female


title: genomic DNA from blood 9969489005_R02C01

description: stroke blood sample

value: Male


title: genomic DNA from blood 9969489002_R05C01

description: stroke blood sample


title: genomic DNA from blood 9969489002_R06C01

description: stroke blood sample


title: BM CD34+ cells from patient 7028 (miEP)


title: genomic DNA from blood 9969489002_R04C02

description: stroke blood sample


title: genomic DNA from blood 9969489002_R03C02

description: stroke blood sample


title: genomic DNA from blood 9969489002_R01C02

description: stroke blood sample


title: genomic DNA from blood 9969489002_R03C01

description: stroke blood sample


title: Normal_thyroid_from_patient_I10

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol with Agilent SureScan microarray scanner (G2505C).

data_processing: Scanned images were processed with Agilent Feature Extraction v10.7 with default parameters to obtain raw data. Raw data were imported in R and processed using the AgiMicroRna package. microRNA-level processed signals were obtained using the RMA algorithm with quantile normalization.

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations.

extract_protocol: Total RNA, including the miRNA fraction, was extracted from the FFPE sections by using the miRNeasy FFPE kit (Qiagen, Valencia, CA, USA) according to the protocol provided by the manufacturer; RNA quality was assessed  by the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: sampleID

value: Thyroid


title: genomic DNA from blood 9969477167_R06C02

description: stroke blood sample

hyb_protocol: The bisulfite converted DNA was processed and hybridized to the HumanMethylation450 BeadChip (Illumina, Inc.), according to the manufacturer's instructions.

data_processing:
GenomeStudio 2011.1 software and R version 3.1.2. Processed data: raw Average Beta obtained from GenomeStudio, quality controls were done by MINFI Bioconductor package and probe type correction by SWAN bioconductor package.
Average Beta, normalized provided in
betas_normalized_meneas_185.txt
pval_detection_meneas_185.txt
Raw unmethylated and methylated signal intensities data is provided in
meth_raw_meneas_185.txt
unmeth_raw_meneas_185.txt


title: genomic DNA from blood 9969477167_R06C01

description: stroke blood sample


title: genomic DNA from blood 9969477167_R05C02

description: stroke blood sample


title: genomic DNA from blood 9969477167_R05C01

description: stroke blood sample


title: genomic DNA from blood 9969489002_R04C01

description: stroke blood sample


title: genomic DNA from blood 9969477167_R04C01

description: stroke blood sample


title: BM CD34+ cells from patient 5903 (miEP)


title: PPARg Hom2 lung Mph_10002897002_B.mean

description:
replicate 2
SAMPLE 2

tag: genotype/variation

value: female

value: lung

tag: cell type

value: wild type alveloar macrophages


title: BM CD34+ cells from patient 5933 (miEP)

value: F

value: ND


title: BM CD34+ cells from patient 5883 (miEP)


title: BM CD34+ cells from patient 5983 (miEP)


title: genomic DNA from blood 9969477167_R03C01

description: stroke blood sample

tag: age

tag: stroke subtype

value: small-vessel disease


title: BM CD34+ cells from patient 5827 (miEP)

value: Vannucchi

value: neg


title: BM CD34+ cells from patient 7025 (miEP)

value: M

value: Bone marrow


title: BM CD34+ cells from patient 5772 (miEP)

value: myeloproliferative neoplasm (MPN)

value: PV


title: BM CD34+ cells from patient 5811 (miEP)

value: pos


title: BM CD34+ cells from patient 5907 (miEP)


title: BM CD34+ cells from patient 5884 (miEP)


title: BM CD34+ cells from patient 4765 (miEP)


title: genomic DNA from blood 9969477167_R02C01

description: stroke blood sample

value: cardioembolic

tag: sample type

value: blood

tag: disease state

value: stroke


title: BM CD34+ cells from patient 5995 (miEP)


title: BM CD34+ cells from patient 4764 (miEP)


title: BM CD34+ cells from patient 7169 (miEP)

value: ET


title: genomic DNA from blood 9969477167_R04C02

description: stroke blood sample

tag: gender

value: Female


title: somite_E11.5

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the mm10 mouse transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: mm10
Supplementary_files_format_and_content: txt files which include theTPM values of RefSeq genes.

source_name: Mouse Fetal Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, after MACS and FACS purification, a single cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the cells were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform (sequenced by Novogene).

tag: strain

tag: developmental stage

value: male

value: somite

value: Mouse Fetal Cells


title: lung_E11.5

value: lung


title: BM CD34+ cells from patient 7015 (miEP)

value: F

tag: mpl-mutated

tag: calr-mutated

tag: gene mutation


title: genomic DNA from blood 9969477167_R02C02

city: Barcelona

first: Carolina

last: Soriano-Tarraga

address: Calle Doctor Aiguader 88

institute: Institut Hospital del Mar d’Investigacions Mèdiques (IMIM).Hospital del Mar

description: stroke blood sample

extract_protocol: DNA samples were extracted from whole peripheral blood collected in 10 mL EDTA tubes. The Chemagic Magnetic Separation Module I system (Chemagen)


title: genomic DNA from blood 9969477167_R03C02

description: stroke blood sample

value: Male

value: small-vessel disease


title: BM CD34+ cells from patient 7200 (miEP)

tag: supplier

value: Vannucchi

tag: Sex

value: M

tag: condition

value: neg


title: skin_E11.5

tag: tissue

value: skin


title: liver_E11.5

value: liver


title: serum-severe-rep2

city: Kerman

first: Sedigheh

last: Gharbi

address: Mostafa Khomeyni St.

department: Department of Biology

country: Iran

institute: Shahid Bahonar University of Kerman

description:
sulfur mustard exposure, no lung diseases, no smoking, no cancer
e2

data_processing:
The given normalized data is IPC/delta Ct normalized on the R statistical platform according to the recommendations by the Exiqon company. The R HTqPCR package was utilized for quality control. R code can be requested from the corresponding authors.
Fold Change worksheet reports mild/normal, severe/normal and severe/mild ratios of the matrix normalized worksheet.

label: SYBR Green

source_name: serum

label_protocol: 1.5 microliters of each RNA samples were reverse transcribed in a volume of 10 microliters. This amount of RNA input has the least inhibitory effect based on our previous experiments on serum samples assessing the inhibitory effect of RNA input on microRNA expression [14]. cDNA synthesis was performed in a two-step protocol of RNA polyadenylation followed by universal cDNA synthesis (Exiqon, Denmark). Thereafter, the quantitative PCR panel was run using SYBR green master mix (Exiqon, Denmark) by the Light Cycler 480 (Roche, Germany)

extract_protocol: The patients from the mild, moderate and severe groups were randomly pooled into two, disjunct biological replicates. Equal volumes of sera were mixed together and the pooled samples were subjected to RNA extraction. Total RNA was extracted from 250 microliters of each pooled serum samples using miRNeasy mini kit (Qiagen, Germany) based on manufacture`s protocol. To increase the yield of microRNA extraction, MS2 RNA (Roche Applied Science, Germany) was added to each sample before adding QIAzole.

value: serum

value: severe disease state


title: serum-severe-rep1

description:
sulfur mustard exposure, no lung diseases, no smoking, no cancer
e1


title: serum-mild-rep2

description:
sulfur mustard exposure, no lung diseases, no smoking, no cancer
i2

value: mild disease state


title: hindbrain_E11.5

value: hindbrain


title: intestine_E11.5

value: intestine


title: [48_Control/Cyclic_Cy3]-[reference]

city: Urbana

first: Mario

middle: Pietro Emilio

last: Vailati Riboni

state: IL

address: 1207 W Gregory Dr

department: Animal Science

institute: University of Illinois at Urbana-Champaign

description: Sample were total RNA extracted from sheep uterus biopsy tissue, and a reference obtain by equal combination of all sample collected

hyb_protocol: The labeled cRNA was fragmented and then hybridized to the microarray slide according to manufacturer’s protocol. Briefly, 825 ng of Cy3 and Cy5 labeled cRNA sample were combined, mixed with 11 μL of 10× Blocking Agent (Agilent Technologies Inc.), 2.2 μL of 25× Fragmentation Buffer (Agilent Technologies Inc.), and nuclease-free water (to a final volume of 55 μL); and then fragmented at 60°C for 30 s. The reaction was then stopped by adding 55 μL of 2× GEx Hybridization Buffer (Agilent Technologies Inc.), and the samples were loaded onto the slide. These were hybridized in a rotating hybridization oven (Agilent Technologies Inc.) at 65°C for 17 h.

scan_protocol: The slides were washed according to the manufacturer’s recommended procedures and scanned using a GenePix 4000B scanner (Axon Instruments Inc., Sunnyvale, CA) and GenePix Pro v.6.1 software. Resulting spots where features were substandard were flagged as bad and excluded from subsequent analysis.

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 30 microarrays were normalized for dye and array effects (i.e., Loess normalization and array centering and scaling) before statistical analysis.

organism: Ovis aries

source_name: Uterus Biopsy

label_protocol: The Agilent platform was chosen to conduct the microarray experiment, using the 8x15K Ovine gene expression microarray chip (Agilent Technologies Inc.), following the manufacturer’s protocols. Briefly, a total of 200 ng of RNA per sample were used to generate first-strand cDNA, which was reverse transcribed to cRNA using the low-input quick amp labeling kit (Agilent Technologies Inc). The resulting cRNA was labeled with either Cy3 or Cy5 fluorescent dye, purified using RNeasy mini spin columns (Qiagen), and subsequently eluted in 30 μL of DNase-RNase-free water. The NanoDrop ND-1000 (Thermo Fisher Scientific Inc., Waltham, MA) was used to confirm the manufacturer’s recommended criteria for yield and specific activity of at least 0.825 μg and ≥6.

growth_protocol: 46 adult multiparous Rasa Aragonesa ewes were housed in individual pens and offered a diet (once daily) that provided 1 x live weight maintenance requirements for 1 month prior to the beginning of the experimental procedures. The estrus cycles were synchronized using intravaginal sponges, which were inserted for 14 days. At the time of sponge insertion, ewes were allocated to one of two planes of nutrition: a control (n= 21; 7.8 MJ of metabolisable energy per ewe), which continued to receive the same diet for 28 days, and a low plane of nutrition (n = 25; 3.9 MJ of metabolisable energy per ewe), which was offered at 50% of estimated daily requirements (pellet and straw) until the end of the experiment. At the time of sponge withdrawal, ewes were injected with 300 IU, i.v., equine chorionic gonadotropin (Intervet, Salamanca, Spain), and the occurrence of estrus (Day 0) was monitored every 8 h. Thirteen control ewes and 18 ewes in the low plane of nutrition were mated to vasectomized or intact rams to establish a cyclic and pregnant group, respectively, within each plane of nutrition. On day 14 of the estrus cycle or pregnancy, uterine horns were flushed with 10 mL saline solution (0.9% w/v NaCl) and pregnancy was defined as the presence of an apparently normal conceptus. After embryo recovery, animals were euthanized by injection of T-61 (Intervet, Salamanca, Spain), and one-third of the intercaruncular uterine horn ipsilateral to the corpus luteum was dissected. The intercaruncualr tissue was selected due to the relevance of the secretion of glandular endometrium and due to its role in the process of maternal recognition of pregnancy [13]. Tissues collected were snap frozen in liquid nitrogen and stored at −80ºC until RNA extraction and microarray analysis. The final treatment groups consisted of 5 cyclic and 6 pregnant control ewes, and 6 cyclic and 7 pregnant ewes in the low group.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA, USA), followed by precipitation with lithium chloride to remove inhibitors of cDNA synthesis and DNase treatment with a DNA-Free kit (Ambion, Austin, TX, USA) to remove contaminating DNA. The concentration of the RNA was determined by measuring absorbance at 260 nm, the purity of all RNA isolates was assessed as the ratio of absorbance at 260/280 nm (A260/280) and the integrity of the RNA was determined by electrophoresis (on a 1% agarose gel) and the Agilent Bioanalyzer (Agilent technologies). All samples had an average of A260/280 ratios of 1.95 ± 0.21 and an RNA Integrity Number of 8 ± 1.4.

treatment_protocol: See growth protocol

value: Uterus

tag: plane of nutrition

value: Control

tag: pregnancy

value: Cyclic


title: heart_E11.5

value: male

value: heart

tag: cell type

value: Mouse Fetal Cells


title: serum-mild-rep1

description:
sulfur mustard exposure, no lung diseases, no smoking, no cancer
i1


title: BM CD34+ cells from patient 7018 (miEP)

value: F

value: myeloproliferative neoplasm (MPN)

tag: disease

value: ET

value: pos

value: Bone marrow

tag: cell marker


title: BM CD34+ cells from patient 7009 (miEP)

value: Vannucchi

value: neg


title: BM CD34+ cells from patient 4763 (miEP)

value: PV

value: ND


title: BM CD34+ cells from patient 7092 (miEP)


title: BM CD34+ cells from patient 5946 (miEP)


title: forebrain_E11.5

value: forebrain


title: [44_Underfed/Cyclic_Cy3]-[reference]

value: Underfed


title: serum-healthy-rep2

description:
no sulfur mustard exposure, no lung diseases, no smoking, no cancer
n2

value: serum

value: healthy normal


title: serum-healthy-rep1

description:
no sulfur mustard exposure, no lung diseases, no smoking, no cancer
n1


title: [41_Control/Cyclic_Cy3]-[reference]

value: Uterus

value: Control

value: Cyclic


title: somite_E10.5

value: male

value: somite

value: Mouse Fetal Cells


title: [25_Underfed/Pregnant_Cy3]-[reference]

value: Pregnant


title: BM CD34+ cells from patient 5927 (miEP)

value: M

value: myeloproliferative neoplasm (MPN)

value: ET

value: pos


title: BM CD34+ cells from patient 5909 (miEP)

value: Vannucchi

value: neg

value: Bone marrow


title: [46_Underfed/Cyclic_Cy3]-[reference]

value: Underfed


title: lung_E10.5

value: lung


title: BM CD34+ cells from patient 5908 (miEP)

value: F

value: ND


title: [16_Underfed/Pregnant_Cy3]-[reference]

value: Uterus


title: [19_Control/Pregnant_Cy3]-[reference]

value: Control


title: [23_Control/Pregnant_Cy3]-[reference]


title: intestine_E10.5

value: male

value: intestine


title: BM CD34+ cells from patient 5882 (miEP)


title: liver_E10.5

value: liver

value: Mouse Fetal Cells


title: genomic DNA from blood 9969489007_R05C01

description: stroke blood sample

tag: age

value: Female

tag: stroke subtype

value: small-vessel disease

tag: sample type

value: blood

value: stroke


title: BM CD34+ cells from patient 5864 (miEP)

value: Vannucchi

value: myeloproliferative neoplasm (MPN)

value: ET

value: pos


title: BM CD34+ cells from patient 5890 (miEP)

value: M

value: neg

value: Bone marrow


title: skin_E10.5

tag: strain

tag: gender

value: skin


title: [39_Underfed/Cyclic_Cy3]-[reference]

value: Uterus

value: Underfed

value: Cyclic


title: BM CD34+ cells from patient 5886 (miEP)

value: F

tag: mpl-mutated

value: ND


title: BM CD34+ cells from patient 5862 (miEP)

tag: calr-mutated


title: SmNPC_CHIR_C

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression of NPC

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Agilent's human GXP_8X60k Array designed by Genotypic Technology Private Limited. (AMADID: 039494). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift normalization method .

source_name: Human ES derived NPC

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Cells were in NPC maintenance medium containing 1:1 DMEM/F12 Neurobasal medium supplemented with specified growth factors

extract_protocol: RNA extraction was perforemd by using RNeasy Mini & Micro Kit with DNase Treatment

treatment_protocol: Cells were exposed to 100mM OH for 48 hours

value: ES derived NPC

tag: treatment

value: control


title: heart_E10.5

tag: developmental stage

value: male

value: heart

value: Mouse Fetal Cells


title: [38_Control/Cyclic_Cy3]-[reference]

value: Control


title: R_H9_T_100_OH_48H

description: Gene expression of 100mM OH treated EB

source_name: Human ES derived EB treated with 100mM OH 48 hr

value: ES derived EB

value: OH


title: BM CD34+ cells from patient 5838 (miEP)

tag: supplier

value: Vannucchi

tag: Sex

value: myeloproliferative neoplasm (MPN)

value: ET

value: pos

tag: gene mutation


title: [35_Underfed/Cyclic_Cy3]-[reference]

tag: tissue

value: Uterus

tag: plane of nutrition


title: hindbrain_E10.5

value: hindbrain

tag: cell type


title: forebrain_E10.5

value: forebrain


title: skin_intestine_somite_E9.5_embryo3


title: BM CD34+ cells from patient 5815 (miEP)

value: F

tag: condition

tag: disease

value: neg

value: Bone marrow


title: R_H9_EB_C

description: Gene expression of EB

source_name: Human ES derived EB

value: control


title: BM CD34+ cells from patient 5947 (miEP)

value: M

tag: calr mutation

value: L367FS52 (tipo I)

value: CALR

tag: cell marker


title: SmNPC_CHIR_T_100_OH_48H

description: Gene expression of 100mM OH treated NPC

source_name: Human ES derived NPC treated with 100mM OH 48 hr

value: ES derived NPC


title: BM CD34+ cells from patient 9198 (miEP)

value: del52 (tipo I)


title: lung_liver_E9.5_embryo3

value: male

value: Mouse Fetal Cells


title: [34_Control/Cyclic_Cy3]-[reference]

value: Control

tag: pregnancy

value: Cyclic


title: abacavir-exposed keratinocyte drived from HLA-B*57:01 transgenic mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

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

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

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

source_name: primary keratinocyte

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

growth_protocol: Keratinocytes were isolated from 1 or 2-day-old HLA-B*57:01 or HLA-B*57:03 transgenic mice, then cultured in keratinocyte growth medium for 4 days. Culture medium was replaced 1 day after the start of the culture.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

treatment_protocol: Keratinocytes were exposed to 500 μM abacavir for 12 hr in keratinocyte differentiation medium.

tag: strain

value: derived from HLA-B*57:01 transgenic mice


title: [13_Underfed/Pregnant_Cy3]-[reference]

value: Uterus

value: Underfed

value: Pregnant


title: Chd7 KD rep3

source_name: Chd7 knockdown virus-infected mouse E15.5 OPCs, cultured in the presence of FGF2 and PDGF-AA

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

growth_protocol: OPCs derived from E15.5 mouse forebrains were maintained in the presence of FGF2 and PDGF-AA.

extract_protocol: Total RNA was isolated using an RNeasy Kit (Qiagen) according to the manufacturer's instructions.

value: brain

value: oligodendrocyte precursor cells

tag: infection

value: Chd7 knockdown retrovirus


title: QS+3

city: Perth

first: Timothy

last: Haskett

state: WA

address: 50 South Street Murdoch

department: Biological Sciences

country: Australia

institute: Murdoch University

description:
processed data file:
DEseq2-NF
HTSeq-NF
DEseq2-F
HTSeq-F

data_processing:
Read sets from technical repetitions were combined and adapter sequences were removed using nesoni clip (http://www.vicbioinformatics.com/software.nesoni.shtml). To reduce any potential rRNA/total-RNA abundance biases introduced during rRNA depletion, reads mapping to rRNA genes were removed using FastQ Screen (https://www.bioinformatics.babraham.ac.uk).
For differential gene expression analysis, read sets were filtered to remove sequences matching plasmids pPR3-traI1 and pSDz-traR1 prior to mapping with Bowtie2.  An average (per biological replicate) of 14 million (standard deviation (SD) = 3.3 million) QS+ and 8.5 million (SD = 1.5 million) QS- post-filter reads were mapped to WSM1271 with 96.7-98.6% alignment rate. Differential gene expression analysis of the traI1 and traI2 untranslated mRNA promoter regions, PtraI1 and PtraI2, was carried out prior to filtering – as these reads were able to be distinguished from plasmid-borne mRNAs.
Read counts for gene features were performed using HTSeq with default settings then imported into DESeq2 for identification of differentially expressed genes using default parameters
Genome_build: NC_014923.1
Supplementary_files_format_and_content: HTSeq output (Microsoft excel worksheets) contains the raw HTSeq read counts for the RNASeq libraries QS-1a/b, QS-2a/b, QS-3a/b and QS+1a/b, QS+2a/b, QS+3a/b where reads corresponding to the plasmids pSDz-traR and pSDz-traI1 were filtered (HTSeq-F) or not filtered (HTSeq-NF) prior to mapping to the WSM1271 chromosome using Bowtie 2. DESeq2 files (Microsoft excel worksheets) contain DESeq2 output for differential gene expression analysis for each read count file (F or NF)

organism: Mesorhizobium ciceri biovar biserrulae WSM1271

source_name: Bacterial cells_QS+

growth_protocol: Cultures were initially grown by streaking single colonies onto TY agar slopes and incubating for 5 days at 28°C. Two technical replicates of each slope culture was washed off into 50 mL TY broths and incubated for 24 h to achieve OD600 ~ 0.8. 12 mL of culturewas added to 24 mL RNA later solution (Qiagen) prior to RNA extraction.

extract_protocol:
Cell pellet was resuspended in 250 μL of 10 mM Tris-Cl (pH 8.0). This cell suspension was added to 2 mL lysis tubes filled with: 300 mg silica beads (0.1mm), 100 mg glass beads (0.1mm), 350 μL RLT buffer (Qiagen), and 3.5 μL β-mercaptoethanol and mechanically lysed in a FastPrep®-24 instrument (MP biomedicals) at speed 6.5 for 30 s. Total RNA was extracted from the lysate using a RNease Mini Kit (Qiagen) as per the manufacturers recommendations.
DNA was removed from approximately 3 μg of total RNA using the TURBO DNA-free™ kit (Invitrogen) and confirmed using a Qubit fluorometer dsDNA BR assay. rRNA was depleted from total RNA using a Ribo-Zero rRNA magnetic kit (Illumina) and resulting RNA was purified using a RNA Clean & Concentrator™ (Zymo Research). Barcoded cDNA libraries were prepared from rRNA depleted RNA samples using Ion Total RNA-Seq kit v2 (Thermo Fisher).

tag: plasmids

value: Late log phase


title: [10_Control/Pregnant_Cy3]-[reference]


title: QS+2


title: QS+1


title: abacavir-exposed keratinocyte drived from HLA-B*57:03 transgenic mice against abacavir

value: derived from HLA-B*57:03 transgenic mice


title: Chd7 KD rep2


title: [4_Control/Pregnant_Cy3]-[reference]


title: QS-3

source_name: Bacterial cells_QS-


title: Chd7 KD rep1


title: BM CD34+ cells from patient 2766 (miEP)

source_name: Bone marrow CD34+ Cells

value: Vannucchi

value: F

value: myeloproliferative neoplasm (MPN)

value: ET

value: neg

tag: mpl-mutated

tag: calr-mutated

value: pos

value: 385insTTGTC (tipo II)

value: Bone marrow


title: BM CD34+ cells from patient 3057 (miEP)

value: M

value: CALR


title: BM CD34+ cells from patient 5928 (miEP)

value: K391fs51 (tipo II)


title: BM CD34+ cells from patient 2485 (miEP)

value: L367FS52 (tipo I)


title: BM CD34+ cells from patient 3840 (miEP)

value: E386del AGGA


title: Control rep3

source_name: Control virus-infected mouse E15.5 OPCs, cultured in the presence of FGF2 and PDGF-AA

tag: developmental stage

value: brain

value: oligodendrocyte precursor cells

value: control retrovirus


title: QS-1

value: Late log phase


title: QS-2


title: Control rep2


title: UHRR rep2

description: in the raw data file, gProcessedSignal represented signal of this sample

data_processing: Microarray data was extracted using Agilent Feature Extraction software. Data summarization, quantile normalization, quality control and most of the subsequent data processing were executed using GeneSpring software V12.0 (Agilent, Santa Clara, CA) or R software package.

source_name: Universal Human Reference RNA replicated sample 2

value: total RNA from 10 human cell lines


title: UHRR rep1

source_name: Universal Human Reference RNA replicated sample 1


title: HBRR rep2

source_name: Human Brain Reference total RNA replicated sample 2

value: the mixture of dozens of human brain tissues


title: HBRR rep1

source_name: Human Brain Reference total RNA replicated sample 1


title: Patient 17 17_4

description: in the raw data file, gProcessedSignal represented raw signal of this sample

source_name: plasma postoperative

value: plasma


title: Patient 17 17_2


title: Control rep1


title: [3_Underfed/Pregnant_Cy3]-[reference]

value: Uterus

value: Underfed

value: Pregnant


title: Patient 17 17_3


title: Patient 9 9_2


title: Patient 8 8_6


title: PatientF_2008_2N

city: Basel

first: Joël

middle: Roman

last: Federer-Gsponer

address: Tangentenweg 34

department: Department of Pathology

country: Switzerland

institute: University Hospital Basel

hyb_protocol: Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 20 rpm for 40 hours then washed according to array supplier's (Agilent)protocol

scan_protocol: All microarray slides were scanned using an Agilent G2505C DNA scanner and default settings for CGH.

data_processing: Data was extracted from the TIFF files using Agilent FE 10.5. The data quality was assessed using the QC Report output in F.E. 10.5. All arrays that passed the experimental Q.C. were then analysed using the Limma package in the R environment. With minimum background correction and printtiploess normalization.

source_name: Prostate

label_protocol: A 1 microgram aliquot of each sample and reference DNA was digested with DNAse 1 then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.

growth_protocol: Tumor samples from patients with prostate carcinoma were flash-frozen and maintaned at -80 degrees C until processed for flow sorting

extract_protocol: 25-100 mg of tumor was thawed then minced in the presence of NST and DAPI. Each sample was then mechanically sheared then filtered through a 30 micron mesh filter prior to sorting. All sorting was done with an Influx Flow Cytometer equiped with a UV laser. DNA was extracted from each sorted fraction using Qiagen DNA micro kits. All phi29 amplifications were done with a 100ng aliquot of either sample or reference genomic DNA using the GenomiPhi kit (G.E Health Care)

tag: amplification

tag: year

tag: ploidy

source_name: pooled 46, XX DNA (Promega, Madison, WI)

tag: sample type

value: reference


title: Patient 8 8_4

tag: tissue


title: Placenta_ preeclampsia_rep2

first: Zhenyu

last: Zhang

address: Gongtinanlu 8hao

institute: Beijing Chao-Yang Hospital,Capital Medical University

description: Different gene expression of basal plate of the placenta between normal and preeclampsia pregnancy

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: basal plate of the placenta, preeclampsia patient

label_protocol: rRNA was removed from Total RNA use Ribo-Zero rRNA Removal Kit , then the RNA(-rRNA) was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany)

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) 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: All specimens were obtained at the time of cesarean section for obstetrical indications. Placental bed biopsy specimens were collected around the umbilical cord, about 1×1×1cm3 size, and preserved in 600μl RNA Stabilization Solution (Cat#AM7020, Ambion, Austin, TX, US)under -20℃.

tag: gender

value: female

tag: age

value: 26 years old


title: Placenta_normal_rep4

source_name: basal plate of the placenta, normal pregnancy

value: 33 years old


title: Placenta_normal_rep1

value: 29 years old


title: Placenta_ preeclampsia_rep3

value: 30 years old


title: Patient 8 8_2


title: Patient 16 16_2


title: Patient 8 8_3


title: Placenta_normal_rep2

value: 31 years old


title: Patient 5 5_2


title: PatientC_2011_Liver2N

value: Liver 2N


title: PatientF_2008_AN

value: AN


title: Patient 4 4_2


title: PatientC_2011_LiverAneuploid

value: Liver aneuploid


title: PatientF_2012_2N


title: Patient 8 8_5


title: PatientC_2011_2N


title: PatientB_2011_2N


title: PatientA_2008_2N


title: PatientB_2011_3.7N


title: PatientF_2012_AN


title: Placenta_normal_rep3

value: 28 years old


title: PatientA_2000_2N


title: PatientA_2000_3.7N


title: Patient 1 1_2


title: Patient 17 17_1

source_name: plasma preoperative


title: Patient 5 5_1


title: PatientB_2012_2N


title: Patient 16 16_1


title: Patient 9 9_1


title: Patient 4 4_1


title: Patient 3 3_2


title: BC5

city: Tartu

first: Kaarel

last: Krjutskov

state: Tartumaa

address: Teaduspargi tänav 13

country: Estonia

institute: The Competence Centre on Health Technologies

description: umi1.csv, umi2.csv, umi3.csv, umi4.csv, umi5.csv, umi6.csv, umi7.csv, umi8.csv, umi9.csv, umi10.csv

data_processing:
Library strategy: TAC-seq
Sequences were trimmed to 88 bp and de-multiplexed.
Converted FASTQ files to FASTA format, sequences were trimmed to 62 bp, shorter sequences were discarded.
Reorded bases to 4 + 54 + 4 to 4 + 4 + 54.
Discarded sequences with unknown (N) nucleotides.
De-multiplex (allow 5 mismatch).
Calculated total read count and total molecule count with different threshold of UMI effect.
Genome_build: Homo sapiens GRCh38 reference assembly
Supplementary_files_format_and_content: Semicolon delimited text files (for each UMI separate file) containing molecule counts for each sample.

organism: synthetic construct

source_name: ERCC spike-in

extract_protocol:
Non-skirted low profile PCR Strip Tube Plate (Thermo Fisher) was used with domed cap strips (Thermo Fisher). ERCC Spike-In Mix 1 (Life Technologies) was first 10 and next additional 100 diluted with water. Aliquots, each containing 1.3 ul of 1,000 dilution, were stored at -70°C until use. Next, 199 ul of water was added to 1.3 ul aliquot and pipetted through. 1 ul of diluted ERCC spike-in content (Supplementary Table 1), as a template for each individual library was added to 2 ul denaturation buffer, containing 5 mM Tris-HCl (pH 7.0) (Sigma-Aldrich), 1 mM dNTP mixture (Thermo Fisher), 400 nM Oligo-T30 primer and 0.05% Triton X-100 (Sigma-Aldrich). Reaction was mixed by pipetting and centrifuged briefly. RNA was denatured by 1 min at 80°C and placed on ice. After that, reverse transcriptase (RT) master mix containing 100 mM Tris-HCl (pH 8.5) (Sigma-Aldrich), 2.5 M betaine (Sigma-Aldrich), 150 mM KCl (Sigma-Aldrich), 10 mM DTT (Sigma-Aldrich), 15 mM MgCl (Sigma-Aldrich), 4 U RiboLock RNase inhibitor (Thermo Fisher) and 20 U Maxima H Minus Reverse Transcriptase (Thermo Fisher) was prepared. The content was mixed on vortex and centrifuged briefly. 2 ul of RT master mix was added to previously denatured RNA (3 ul). All RT pipetting steps were performed on ice. cDNA synthesis was performed by 30 min at 42°C, following 5 min at 85°C for RT inactivation. 22 TAC-seq detector pairs targeting ERCC spike-in molecules were previously mixed together from 100 uM stock solutions, creating a 100 u oligo pool. The mixture was diluted to 5 uM by water and stored at -20°C. Once cDNA synthesis was completed, 1 ul of 5 uM TAC-seq detector mixture was added to RT mixture. The content was mixed on vortex and centrifuged briefly. Strip tubes were placed on thermocycler, denatured 1 min at 98°C and following 1 h at 60°C to enable specific cDNA and TAC-seq probe hybridization. After hybridization, thermostable ligase reaction mixture was added on thermocycler, keeping a constant (60°C) hybridization temperature. The cycler lid was opened and strip caps were removed. 5 ul of Taq DNA ligase master mix, containing 2 Taq DNA ligation buffer (New England Biolabs, NEB) and 1 U Taq DNA ligase (NEB, cat no M0208) were added to each individual reaction tube and mixed by pipetting. The strip tubes were not removed from 60°C thermocycler to avoid self- and mispairing of TAC-seq probes. Ligation reaction was stopped after 20 min incubation by placing reaction plate on ice. 15 ul of previously combined Dynabeads MyOne Carboxylic Acid beads (2 ul) (Thermo Fisher) and 13 ul of capture buffer (30% PEG-6000 (Sigma-Aldrich), 2 M NaCl (Sigma-Aldrich), 5 mM Tris-HCl (pH 7.5) (Sigma-Aldrich), 10 mM EDTA (Sigma-Aldrich) and 0.02% Tween-20 (Sigma-Aldrich)) was added to ice-cooled ligated sample. The content was mixed by vortex. The capture was carried out for 10 min at RT, and after that the samples were placed on DynaMag-96 Side Magnet (Thermo Fisher) holding 8-well strip tubes on VersiPlate Frame (Thermo Fisher). The clean supernatant was removed. The beads on magnet were washed once with 50 ul fresh 80% ethanol. Ethanol was removed by pipetting, and the clean pellet, without ethanol drops, was dried for 2 min. Once beads were dry, strip tubes were removed from the magnet and 18 ul of PCR master mix was added directly to beads. (We have successfully performed magnetic bead capture prior PCR without ethanol washing to avoid the risk of bead over drying. In that option the supernatant should be removed completely.) The master mix contained 1 proofreading HOT FIREPol Blend Master Mix (SolisBiodyne, Tartu, Estonia) and 250 nM TAC-seq Left primer. In addition to universal TAC-seq Left, 16 different TAC-seq barcode oligonucleotides were used to introduce a six-nucleotide barcode to each studied sample (Supplementary Table 2). For that, 2 ul of 5 uM TAC-seq Barcoded 1â€“16 primers were added individually to each PCR reaction. Strip tubes were closed with clean domed caps, mixed on vortex until all beads were suspended. The ERCC spike-in reaction was incubated at 95°C for 12 min, followed by two cycles of 95°C for 20 s, 57°C for 60 s and 72°C for 20 s. In addition, 16 cycles of 95°C for 20 s, 65°C for 20 s and 72°C for 20 s with a final extension at 72°C for 1 min using the default ramp speed of the T100 cycler (Bio-Rad) were performed. PCR products were pooled together into 1.5 ml tube. The pooled tube was placed on magnet to remove carboxylated beads before the following column purification. Clear supernatant was purified with DNA Clean & Concentrator-5 column (Zymo Research) and eluted with 50 ul EB. The library was size-selected using AMPure XP beads (Beckman Coulter) in a single-step selection to reduce 81 bp linear PCR double-stranded by-product. 50 ul beads were added to 50 ul of the purified PCR product, incubated for 5 min at room temperature and captured by a magnet for 3 min. After incubation on magnet, the supernatant was discarded and the remaining beads were centrifuged at 500g for 10 s. After centrifugation, the beads were placed again on the magnet and all remaining supernatant was removed. The beads were eluted directly without ethanol washing in 25 ul of EB and incubated for 1 min at RT. (It is not shown here but AMPure XP bead elution has almost 100% efficiency even without previous ethanol wash.) Finally, the eluted library was transferred to a clean tube after 1 min incubation on the magnet. The library (single 180 bp product) was visualized on a TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies) and quantified using KAPA Library Quantification Kit (Roche).
Illumina NextSeq 500 high output 75 cycles kit using 2 pM library concentration. The library was sequenced using 90 bp single-read protocol that was primed by Illumina Read1 (HP10) primer.

value: ERCC spike-in


title: Placenta_ preeclampsia_rep1

value: 32 years old


title: BC7


title: BC2


title: BC3


title: BC4


title: Patient 17 17T_17N

description:
in the raw data file, rProcessedSignal represented Normal
in the raw data file, gProcessedSignal represented Tumor

source_name: adjacent normal

value: adjacent normal

value: cervical tumor


title: Patient 3 3_1

value: plasma


title: BC6


title: BC1


title: Patient 16 16T_16N


title: Patient 8 8T_8N


title: Patient 10 10T_10N


title: Patient 5 5T_5N


title: Patient 3 3T_3N


title: Patient 4 4T_4N


title: Patient 1 1_1


title: Patient 9 9T_9N


title: Patient 2 2T_2N