title: ATRT_VAL_67

status: Public on Jan 31 2020

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description: DNA methylation data from an ATRT tumor sample

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Normalization was performed by applying the function preprocessIllumina available in Bioconductor package minfi

label: biotin/DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary ATRT tumor tissue

label_protocol: standard Illumina protocol

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: molecular subgroup

value: SHH

tag: gender

tag: age (yr)

tag: tumor location


title: ATRT_VAL_69

value: MYC


title: ATRT_VAL_65


title: ATRT_VAL_63


title: ATRT_VAL_62

value: TYR


title: ATRT_VAL_60


title: ATRT_VAL_59


title: ATRT_VAL_68


title: ATRT_VAL_64


title: ATRT_VAL_58


title: ATRT_VAL_56


title: ATRT_VAL_55


title: ATRT_VAL_54


title: ATRT_VAL_52


title: ATRT_VAL_53


title: ATRT_VAL_48


title: ATRT_VAL_50


title: ATRT_VAL_47


title: ATRT_VAL_51


title: ATRT_VAL_49


title: ATRT_VAL_46


title: ATRT_VAL_44

value: male

value: supratentorial


title: ATRT_VAL_39

value: female

value: infratentorial


title: ATRT_VAL_45


title: ATRT_VAL_38


title: ATRT_VAL_36


title: ATRT_VAL_35


title: ATRT_VAL_57


title: ATRT_VAL_33


title: ATRT_VAL_34


title: ATRT_VAL_32


title: ATRT_VAL_30


title: ATRT_VAL_29


title: ATRT_VAL_28


title: ATRT_VAL_37


title: ATRT_VAL_27


title: ATRT_VAL_22


title: ATRT_VAL_24


title: ATRT_VAL_26


title: ATRT_VAL_21


title: ATRT_VAL_23


title: ATRT_VAL_25


title: ATRT_VAL_31


title: ATRT_VAL_15


title: ATRT_VAL_19


title: ATRT_VAL_18


title: ATRT_VAL_16


title: ATRT_VAL_13


title: ATRT_VAL_14


title: ATRT_VAL_17


title: ATRT_VAL_11


title: ATRT_VAL_09


title: ATRT_VAL_06


title: ATRT_VAL_08


title: ATRT_VAL_07


title: ATRT_VAL_05


title: ATRT_VAL_03


title: ATRT_VAL_12


title: ATRT_VAL_02


title: ATRT_VAL_01


title: ATRT_VAL_04


title: ATRT_EURHAB_70


title: ATRT_EURHAB_69


title: ATRT_EURHAB_71


title: ATRT_EURHAB_66


title: ATRT_EURHAB_67


title: ATRT_VAL_10


title: ATRT_EURHAB_65


title: ATRT_EURHAB_64


title: NMB888

description:
9421912051_R04C02
DNA methylation data from an ATRT tumor sample

hyb_protocol: standard Illumina Protocol

scan_protocol: standard Illumina Protocol

data_processing: Data processing of the microarry methylation data included standard quality controls as recommended by Ilumina. Further downstream analysis was performed as detailed in Capper et al., 2018, Nature.

label: cy3, cy5

label_protocol: standard Illumina Protocol

extract_protocol: DNA was extracted using the DNAeasy blood and tissue kit (Qiagen)

tag: tissue

value: Primary ATRT (Atypical Teratoid Rhabdoid Tumor)

value: M

value: INF


title: NMB885

description:
9421912051_R02C02
DNA methylation data from an ATRT tumor sample


title: ATRT_EURHAB_53


title: ATRT_EURHAB_50


title: ATRT_EURHAB_52


title: ATRT_EURHAB_51


title: ATRT_EURHAB_49


title: ATRT_EURHAB_48

value: large, not determinable


title: ATRT_EURHAB_41


title: NMB853

description:
8359018159_R04C01
DNA methylation data from an ATRT tumor sample


title: ATRT_EURHAB_46


title: ATRT_EURHAB_43


title: ATRT_EURHAB_45


title: ATRT_EURHAB_39


title: NMB854

description:
8359018159_R05C01
DNA methylation data from an ATRT tumor sample

value: F

value: SUP


title: ATRT_EURHAB_47


title: ATRT_EURHAB_38


title: ATRT_EURHAB_36


title: ATRT_EURHAB_37


title: NMB842

description:
8359018040_R01C02
DNA methylation data from an ATRT tumor sample


title: NMB856

description:
9421912049_R01C01
DNA methylation data from an ATRT tumor sample


title: ATRT_EURHAB_35


title: ATRT_EURHAB_34


title: ATRT_EURHAB_33


title: ATRT_EURHAB_31


title: ATRT_EURHAB_32


title: ATRT_EURHAB_29


title: ATRT_EURHAB_28


title: ATRT_EURHAB_24


title: ATRT_EURHAB_27


title: ATRT_EURHAB_25

value: spinal


title: ATRT_EURHAB_23


title: ATRT_EURHAB_22


title: ATRT_EURHAB_21


title: ATRT_EURHAB_20


title: NMB776

description:
8359018159_R01C02
DNA methylation data from an ATRT tumor sample


title: ATRT_EURHAB_30


title: ATRT_EURHAB_07


title: ATRT_EURHAB_10


title: ATRT_EURHAB_11


title: ATRT_EURHAB_09


title: ATRT_EURHAB_18


title: ATRT_EURHAB_06


title: ATRT_EURHAB_17


title: ATRT_EURHAB_13


title: ATRT_EURHAB_05


title: ATRT_EURHAB_19


title: ATRT_EURHAB_08


title: NMB834

description:
8359018040_R01C01
DNA methylation data from an ATRT tumor sample


title: WM3211-INV

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation 450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged with standard recommended Illumina scanner settings

data_processing:
Idat files were loaded into R and analyzed with R/Bioconductor packages
Probes were corrected for probe colour bias and intersample quantile normalization, followed by β-mixture quantile normalization (BMIQ). Probes with detection P Values > 0.01 were filtered out.

label: Cy5 and Cy3

source_name: melanoma malingum_selected invasive melanoma cell population

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% FBS at 37°C in an atmosphere containing 5% CO2

extract_protocol: Genomic DNA was isolated using G-spin Genomic DNA exctraction kit according to the manufacturer's protocol

treatment_protocol: To select the invasive subpopulations, the invading cells in the lower layer chamber of Matrigel Invasion Assay were treated with a 0.5% trypsin/0.2% EDTA solution for recovery from the membrane and cultured using standard protocols until the RNA isolation.

tag: origin

value: selected from WM3211 cell line


title: WM1366-INV

value: selected from WM1366 cell line


title: WM3211

source_name: melanoma malingum_original cell line

value: primary melanoma tumor

tag: growth phase

value: RGP/VGP

tag: histologic type

value: SSM

tag: braf mutation status

value: wt


title: WM793B-INV

value: selected from 7WM793B cell line


title: ATRT_EURHAB_04

value: SHH

value: male


title: NT sample 6

type: SRA

city: Bethesda

first: Iago

last: Pinal-Fernandez

state: MARYLAND

address: 50 South Drive, Room 1142, Building 50, MSC 8024

department: NIAMS

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
Demultiplexing with bcl2fastq/2.20.0
Raw sequencing data was cleaned using trimmomatic/0.36
Samples were aligned using star/2.5
Gene abundance was quantified using stringtie/1.3.3
Genome_build: hg19
Supplementary_files_format_and_content: csv text files include FPKM values for each sample

molecule: total RNA

source_name: Muscle

extract_protocol:
Trizol
NeoPrepTM system according to the TruSeqM Stranded mRNA Library Prep protocol (Illumina)

value: Muscle

tag: patient diagnosis

value: normal


title: NT sample 8


title: NT sample 9


title: WM983A-INV

value: selected from WM983A cell line


title: NT sample 7


title: NT sample 5


title: WM1366

value: VGP


title: WM793B


title: WM983A


title: NT sample 4


title: NT sample 13


title: NT sample 2


title: NT sample 3


title: NT sample 11


title: DM sample 8

value: dermatomyositis


title: NT sample 19


title: DM sample 7


title: NT sample 16


title: NT sample 14


title: NT sample 12


title: NT sample 18


title: A_M_14d_N2: aged MCAO 2

city: Pittsburgh

first: Xiaoming

last: Hu

state: PA

address: 200 lothrop street

department: Neurology

institute: University of Pittsburgh

data_processing:
Tophat2 (http://tophat.cbcb.umd.edu) to align the trimmed reads to mouse reference genome sequences (mm10) and to annotate the reads.
Cufflinks (2.2.1) was then applied to estimate gene and isoform abundance. The abundance of mapped reads is expressed as Fragment Per Kilobase of transcript per Million mapped reads (FPKM) format.
In addition, we applied HTSeq (version: 0.11.2) to quantify the gene expression by number of read counts.
We used R software (version: 3.6.0) with several packages for the bioinformatics analysis.
Genome_build: mm10

organism: Mus musculus

source_name: microglia

extract_protocol:
Brain homogenates was prepared with the Neural Tissue Dissociation Kit (T) (Miltenyi Biotec 130-093-231). Cell sorting was performed using FACS ARIA , and RNA was harvested using RNeasy Plus micro/mini kits (Qiagen). Sequencing was performed on Illumina Hiseq3000.
Libraries were prepared with the Clonetech SMARTer Stranded Total RNA-Seq (Pico) Kit

tag: strain

tag: age

value: 18-month old

tag: genotype

value: wild type

value: microglia


title: Y_M_14d_N3: young MCAO 2

value: 10-week old


title: A_M_14d_N1: aged MCAO 1


title: A_S_N3: aged sham 2


title: NT sample 17


title: NT sample 1


title: A_S_N1: aged sham 1


title: Y_S_N2: young sham 2


title: NT sample 15


title: NT sample 20


title: DM sample 9


title: Y_S_N1: young sham 1


title: NT sample 10


title: Control 8

type: RNA

city: CAGLIARI

first: AMEDEO

last: COLUMBANO

state: CA

address: VIA PORVELL 4

department: DIPARTIMENTO DI SCIENZE BIOMEDICHE

country: Italy

institute: UNIVERSITA' DEGLI STUDI DI CAGLIARI

description:
replicate 5
SAMPLE 48

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina BeadStudio 3.0.19.0 software (Illumina Inc) and BRB Array Tools (Version 4.6.0)

label: biotin

organism: Rattus norvegicus

source_name: Rat Liver

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

extract_protocol: RNA was extracted with Trizol reagent  and Mirvana Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Male Fischer rats


title: DM sample 6


title: DM sample 4


title: DM sample 38


title: Control 7

description:
replicate 5
SAMPLE 47


title: DM sample 39


title: DM sample 5


title: DM sample 35


title: DM sample 36


title: DM sample 32


title: DM sample 33


title: Control 6

description:
replicate 5
SAMPLE 46


title: DM sample 34


title: DM sample 30


title: DM sample 31


title: Control 4

description:
replicate 5
SAMPLE 44


title: Control 3

description:
replicate 5
SAMPLE 43


title: DM sample 37


title: KRT-19-positive preneoplastic nodules+T3 4 d 8

description:
replicate 4
SAMPLE 38


title: DM sample 29


title: KRT-19-positive preneoplastic nodules+T3 4 d 9

description:
replicate 4
SAMPLE 39


title: Control 5

description:
replicate 5
SAMPLE 45


title: DM sample 28


title: Control 1

description:
replicate 5
SAMPLE 41


title: DM sample 26


title: KRT-19-positive preneoplastic nodules+T3 4 d 7

description:
replicate 4
SAMPLE 37


title: DM sample 25


title: Control 2

description:
replicate 5
SAMPLE 42


title: KRT-19-positive preneoplastic nodules+T3 4 d 10

description:
replicate 4
SAMPLE 40


title: KRT-19-positive preneoplastic nodules+T3 4 d 5

description:
replicate 4
SAMPLE 35


title: DM sample 24


title: DM sample 3


title: DM sample 22


title: DM sample 23


title: KRT-19-positive preneoplastic nodules+T3 4 d 3

description:
replicate 4
SAMPLE 33


title: DM sample 21


title: DM sample 27


title: KRT-19-positive preneoplastic nodules+T3 4 d 2

description:
replicate 4
SAMPLE 32


title: DM sample 2


title: DM sample 19


title: DM sample 17


title: KRT-19-positive preneoplastic nodules+T3 2 d 8

description:
replicate 3
SAMPLE 28


title: KRT-19-positive preneoplastic nodules+T3 4 d 4

description:
replicate 4
SAMPLE 34


title: DM sample 16


title: KRT-19-positive preneoplastic nodules+T3 4 d 1

description:
replicate 4
SAMPLE 31


title: KRT-19-positive preneoplastic nodules+T3 2 d 9

description:
replicate 3
SAMPLE 29


title: DM sample 15


title: DM sample 20


title: DM sample 14


title: KRT-19-positive preneoplastic nodules+T3 2 d 10

description:
replicate 3
SAMPLE 30


title: KRT-19-positive preneoplastic nodules+T3 2 d 1

description:
replicate 3
SAMPLE 21


title: KRT-19-positive preneoplastic nodules+T3 2 d 6

description:
replicate 3
SAMPLE 26


title: KRT-19-positive preneoplastic nodules+T3 2 d 7

description:
replicate 3
SAMPLE 27


title: KRT-19-positive preneoplastic nodules+T3 2 d 2

description:
replicate 3
SAMPLE 22


title: KRT-19-positive preneoplastic nodules+T3 4 d 6

description:
replicate 4
SAMPLE 36


title: KRT-19-positive preneoplastic nodules+T3 2 d 4

description:
replicate 3
SAMPLE 24


title: DM sample 13


title: KRT-19-negative preneoplastic nodules 7

description:
replicate 2
SAMPLE 17


title: KRT-19-positive preneoplastic nodules+T3 2 d 5

description:
replicate 3
SAMPLE 25


title: DM sample 18


title: KRT-19-positive preneoplastic nodules+T3 2 d 3

description:
replicate 3
SAMPLE 23


title: KRT-19-negative preneoplastic nodules 8

description:
replicate 2
SAMPLE 18


title: DM sample 11


title: DM sample 12


title: DM sample 10


title: DM sample 1


title: M4M5_P4_336

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

data_processing:
Raw reads in FASTQ files were aligned to the human hg38 genome build and transcript (Ensembl 92) quantities calculated using the kallisto (v0.44.0) per instructions.
Differential gene expression analysis was performed using the Sleuth (v0.30.0) R package. Differential expression was tested using a negative binomial test, and corrected for multiple testing using the Benjamini-Hochberg correction.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a tab delimeted txt file with Ensembl 92 gene symbol ID in the first column. Sample names are given on the first row with TPM values for each gene running down the column.

molecule: polyA RNA

source_name: corneal endothelium

growth_protocol: Cells were grown using two published protocols (Tryp-LN-F99 and ColA-ColIV-M4M5), and in a humidified incubation chamber at 37C with 5% CO2.

extract_protocol:
TriReagent extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNeasy Clean-Up Kit.
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep Kit using an automated liquid handler (Janus G3 – PerkinElmer) according to manufacturer’s instruction at the UCLA Institute for Quantitative and Computational Biology

value: corneal endothelium

tag: media

tag: passage

tag: protocol


title: M4M5_P4_316


title: M4M5_P4_326


title: M4M5_P4_306


title: KRT-19-negative preneoplastic nodules 3

description:
replicate 2
SAMPLE 13


title: KRT-19-negative preneoplastic nodules 4

description:
replicate 2
SAMPLE 14


title: KRT-19-negative preneoplastic nodules 6

description:
replicate 2
SAMPLE 16


title: M4M5_P4_219


title: M4M5_P4_296


title: KRT-19-negative preneoplastic nodules 5

description:
replicate 2
SAMPLE 15


title: KRT-19-positive preneoplastic nodules 10

description:
replicate 1
SAMPLE 10


title: M4M5_P3_335


title: KRT-19-negative preneoplastic nodules 10

description:
replicate 2
SAMPLE 20


title: KRT-19-negative preneoplastic nodules 1

description:
replicate 2
SAMPLE 11


title: KRT-19-negative preneoplastic nodules 2

description:
replicate 2
SAMPLE 12


title: M4M5_P3_325


title: M4M5_P4_286


title: KRT-19-positive preneoplastic nodules 7

description:
replicate 1
SAMPLE 7


title: Y_M_14d_N2: young MCAO 1


title: KRT-19-positive preneoplastic nodules 8

description:
replicate 1
SAMPLE 8


title: M4M5_P3_305


title: KRT-19-positive preneoplastic nodules 3

description:
replicate 1
SAMPLE 3


title: KRT-19-positive preneoplastic nodules 1

description:
replicate 1
SAMPLE 1


title: M4M5_P3_217


title: M4M5_P3_285


title: KRT-19-positive preneoplastic nodules 5

description:
replicate 1
SAMPLE 5


title: KRT-19-positive preneoplastic nodules 9

description:
replicate 1
SAMPLE 9


title: M4M5_P2_324


title: M4M5_P3_315


title: KRT-19-positive preneoplastic nodules 6

description:
replicate 1
SAMPLE 6


title: M4M5_P2_314


title: KRT-19-positive preneoplastic nodules 4

description:
replicate 1
SAMPLE 4


title: M4M5_P2_334


title: KRT-19-positive preneoplastic nodules 2

description:
replicate 1
SAMPLE 2


title: M4M5_P2_304


title: M4M5_P2_294


title: 3908-ACP-0017_TAC

city: Nashville

first: Alvin

middle: C

last: Powers

state: TN

address: 7465 MRBIV 2215 Garland Avenue

institute: Vanderbilt University

data_processing:
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha's unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Raw reads were mapped to the reference hg19 using TopHat v2.0. The alignment metrics of the mapped reads were estimated using SAMtools. Aligned reads were imported to the commercial data analysis platform AvadisNGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered on the basis of read quality metrics; reads with a base quality score of less than 30, alignment score of less than 95, and mapping quality of less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics; missing mates, translocated, unaligned, and flipped reads were removed. The reads list was then filtered to remove duplicates. Samples were grouped and transcript abundance was quantified for this final read list using Trimmed Means of M-values (TMM) as the normalization method. Output data utilized for all subsequent comparisons were summarized as normalized expression values generated by AvadisNGS. Differential expression of genes was calculated based on fold changes observed in comparisons between defined conditions, and the p-value of the differentially expressed gene list was estimated by z-test using Benjamini Hochberg corrections of 0.05 for false-discovery rate. DAVID v6.8 analysis was performed on the differentially expressed gene list.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: Human islet graft

extract_protocol:
Total RNA was extracted from human islet grafts using RNAqueous RNA isolation kit (Ambion, Austin, TX)
The concentration and integrity of the extracted total RNA were estimated using the Qubit® 2.0 Fluorometer (Invitrogen) and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA, USA), respectively. Five hundred nanograms of total RNA was required for downstream RNA-seq applications. Polyadenylated RNAs were isolated using NEBNext Magnetic Oligo d(T)25 Beads. The NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs Inc., Ipswich, MA, USA) was then used to prepare individually bar-coded next-generation sequencing expression libraries as per manufacturer's recommended protocol. Library concentration was assessed using the Qubit 2.0 Fluorometer, and the library quality was estimated by utilizing a DNA 1000 Chip on an Agilent 2100 Bioanalyzer. Accurate quantification for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Paired-end sequencing (100 million, 100-bp, paired-end reads) was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc., San Diego, CA, USA).

treatment_protocol: SIR (0.2mg/kg, every 72 hours) or PBS were given by intraperitoneal injection; TAC (0.25mg/kg/day) was delivered by micro-osmotic pumps. Treatment was given for 4 weeks before harvesting grafts for analysis.

value: Human islet graft

value: 44 years old

tag: treatment

value: TAC for 4 weeks


title: 3908-ACP-0018_SIR

value: SIR for 4 weeks


title: 3908-ACP-0015_SIR

value: 55 years old


title: M4M5_P2_284


title: M14N9 replicate 3

city: Gothenburg

first: Mattias

last: Andersson

address: Medicinaregatan 1F

department: Sahlgrenska Cancer Center

country: Sweden

institute: University of Gothenburg

hyb_protocol: Hybridization to Affymetrix Human Gene 1.0 ST arrays was performed using standard Affymetrix protocols.

scan_protocol: Arrays were scanned using a GeneChip scanner 3000 and image analysis was performed using the GeneChip Operating Software.

data_processing: Probe summarization and data normalization were performed using Robust Multi-array Analysis (RMA) with the Expression Console Software v1.1.2.

label: Biotin

source_name: breast

label_protocol: Biotin labled cRNA was syntesized from 200 ng total RNA according to standard Affymetrix protocols.

growth_protocol: DMEM/F12 medium supplemented with human epidermal growth factor (20 ng/ml), hydrocortisone (0.5μg/ml ), cholera toxin (100 ng/ml), insulin (10 μg/ml 9, (Sigma Aldrich), horse serum (5%), penicillin-streptomycin (100 U/mL), G418 (800 μg/ml)

extract_protocol: Total RNA was isolated using the Trizol reagent (Life Technologies) followed by the RNeasy Mini kit (Qiagen).

tag: cell type

value: epithelial

tag: cell line

tag: genotype/variation


title: MYB replicate 3

value: MYB


title: M4M5_P3_295


title: control replicate 3

value: control


title: M4M5_P2_215


title: 3908-ACP-0011_SIR


title: M14N9 replicate 2


title: MYB replicate 1


title: control replicate 2


title: control replicate 1


title: MYB replicate 2


title: M14N9 replicate 1


title: 3908-ACP-0010_TAC


title: M4M5_P1_333


title: 3908-ACP-0009_TAC


title: 3908-ACP-0006_TAC


title: 3908-ACP-0005_PBS

value: PBS for 4 weeks


title: pen2 bak1-5 Ab 24 hpi_rep4

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description: Gene expression of leaves of pen2 bak1-5 mutant at 24 h post inoculation of Alternaria brassicicola

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarray 4x44K (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The images were analyzed using Feature Extraction Software (Ver. 10.7.3.1; Agilent Technologies). These data were analyzed further with GeneSpring GX12.1 software (Agilent Technologies). Normalization was performed as follows: 1, intensity-dependent Lowess normalization; 2, data transformation, with measurements less than 0.01 set to 0.01; 3, per-chip normalization, in which the 75th percentile method was used to normalize each array

organism: Arabidopsis thaliana

source_name: pen2 bak1-5 vs Ab 24 hpi_replication4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low RNA Input Quick Amp kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Arabidopsis seeds were sown on rockwool (Grodan, http://www.grodan.com) and kept at 4˚C in the dark for 2 days, later grown at 25˚C with a 16h/8h (light/dark) in Hoagland medium.

extract_protocol: After sampling at 24 hours post-inoculation (hpi), total RNA was extracted by using Plant RNA Isolation Mini Kit (Agilent Technologies., CA, USA). 200 ng of total RNAs were used to prepare Cy3-labeled cRNA, using a Low Input Quick Amp Labeling Kit (Agilent Technologies).

treatment_protocol: Alternaria brassicicola conidia suspension (5x10^5 conidia/ml) were spray inoculated onto 4-5 weeks old pen2 and pen2 bak1-5 mutant plants, and kept at 100% of relative humididy for 24 hours.

value: mature rosette leaves

value: pen2 bak1-5

tag: time post inoculation

value: inoculated leaves with Alternaria brassicicola


title: M4M5_P1_323

tag: tissue


title: pen2 bak1-5 Ab 24 hpi_rep3

source_name: pen2 bak1-5 vs Ab 24 hpi_replication3


title: 3908-ACP-0003_PBS


title: 3908-ACP-0014 _SIR


title: 3908-ACP-0001_PBS


title: 3908-ACP-0002_PBS


title: M4M5_P1_313


title: M4M5_P1_303


title: M4M5_P1_293


title: M4M5_P1_283


title: M4M5_P1_213


title: pen2 bak1-5 Ab 24 hpi_rep2

source_name: pen2 bak1-5 vs Ab 24 hpi_replication2


title: 3908-ACP-0004_PBS


title: NR-S1_C-ion_resistant

city: Suita-shi, Osaka

first: Masayasu

last: Toratani

address: (D10), 2-2, Yamadaoka

department: Radiation Oncology

institute: Osaka University Graduate School of Medicine

description:
NRC
NRS1.fpkm_tracking

data_processing:
Illumina Casava1.8.2 software used for basecalling.
We removed adapter sequence "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" with FASTX-toolkit.
We trimmed low quality reads which has less than 20 quality score using FASTX-toolkit.
We performed mapping using Tophat2, and calculate FPKM using cufflinks.
Genome_build: mm10 (mouse) or hg38 (human)
Supplementary_files_format_and_content: text file with FPKM, cufflinks output

source_name: cancer cell line

extract_protocol:
total RNA was extracted using ISOGEN (NIPPON GENE).
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA with Ribo-Zero Kit (Illumina)

value: squamous cell carcinoma

tag: mouse strain


title: NR-S1_X-ray_resistant

description:
NRX
NRS1.fpkm_tracking


title: RNA_seq_UCLA1_iMeLCs_d1_hPGCLCs_d4_EChPGCLCs_D4C10_rep1

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

data_processing:
RNA-seq data were analyzed as described before (Chen et al., 2017). In general, raw paired end sequencing reads were first mapped to hg19 genome with TopHat (Trapnell et al., 2009)allowing up to two mismatches and one maximal multi-hit (-g 1).  Then the read count for each individual gene were calculated by HTseq (Anders et al., 2015) with default parameters. Expression level of individual gene were then calculated as RPKM (reads per kilobase of exons per million aligned reads) in R. For published datasets (GSE76970 and GSE93126) (Chen et al., 2017; Pastor et al., 2016), processed data of the raw read count for each genes were utilized, while the downstream analysis were processed in the same way as RNA-seq data generated from this study.
Raw reads of WGBS data were first aligned to hg19 genome using BSMAP (Xi and Li, 2009) by allowing up to 2 mismatches (-v2), maximal one equal best hit to count (-w 1) and mapping to both strand (-n 1). When calculating methylation level over each cytosine, only reads uniquely mapped were kept and PCR duplicates were removed. Methylation level at CG sites were then calculated by #C/(#C+#T).
Genome_build: hg19
Supplementary_files_format_and_content: readsCount.txt files for RNA-Seq samples; methratio_reduced.txt files for WGBS samples

source_name: UCLA1 hESCs

extract_protocol:
Ovation RNASeq System V2
Sorted cells or cell pellets were lysed in 350uL of RLT buffer (QIAGEN) and total RNA was extracted with RNeasy micro kit (QIAGEN, 74004). Total RNA was reverse transcribed and cDNA was amplified using Ovation RNA-Seq System V2 (Nugen, 7102-32) according to manufacturer’s instructions. Amplified cDNA was fragmented into ~200bp by Covaris S220 Focused-ultrasonicators.
RNA-seq libraries were generated using Ovation® Rapid Library Systems (Nugen, 0319-32 for index 1-8 and 0320-32 for index 9-16) and quantified by KAPA library quantification kit (Illumina, KK4824).  WGBS libraries were generated using NuGen, Ovation Ultralow Methyl-Seq Library Sytem 1-6, 0535-32.

value: hESCs

tag: passage number

value: passage 16


title: RNA_seq_UCLA2_iMeLCs_d1_hPGCLCs_d4_EChPGCLCs_D4C10_rep1

source_name: UCLA2 hESCs

value: passage 17


title: RNA_seq_UCLA2_iMeLCs_d1_hPGCLCs_d4_EChPGCLCs_D4C10_rep3

value: passage 20


title: RNA_seq_UCLA1_iMeLCs_d1_hPGCLCs_d4_EChPGCLCs_D4C10_rep2

value: passage 18


title: RNA_seq_UCLA1_iMeLCs_d1_hPGCLCs_d4_EChPGCLCs_D4C10_rep3

value: passage 19


title: pen2 bak1-5 Ab 24 hpi_rep1

source_name: pen2 bak1-5 vs Ab 24 hpi_replication1


title: M4M5_P0_332

value: corneal endothelium


title: NR-S1_control

description:
NRN
NRS1.fpkm_tracking


title: pen2 Ab 24 hpi_rep3

description: Gene expression of leaves of pen2 mutant at 24 h post inoculation of Alternaria brassicicola

source_name: pen2 vs Ab 24 hpi_replication3


title: Sample 17

city: Shanghai

first: Yanqing

last: Wang

address: NO. 160 Pujian Road

department: Urology

country: China

institute: Shanghai Renji Hospital

description: serum  extracellular vesicle delivered miRNAs of patients with non-bone -metastatic prostate cancer

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 16 nt.
The clean reads were compared to the miRbase21 and Rfam database  to identify known miRNA and other non-coding RNAs.
The raw count for known miRNAs  were summarized and then normalized using reads per million mapped reads (RPM).
Total clean reads were  also mapped to the Human reference genome using the bwa aligner.The mapped reads were further annotated to the repeats and exon regions based on the genome annotation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample ...

source_name: serum extracellular vesicle

extract_protocol:
Venous blood samples (5ml) were collected in non-anticoagulant acquisition tubes one day before prostate biopsy for serum harvest (1ml) after coagulation.The blood was centrifuged at 2000 g for 10 min at 4 °C to extract the serum. The serum was stored at -80°C till processed.. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.One milliliter serum was used to isolate EV for each sample. After unfrozen in a 25 °C water bath, the serum was centrifuged at 2000 g for 30 min at room temperature to eliminate residual cell fragments. The serum EV was extracted using Total Exosome Isolation Kit (from serum, Thermo fisher scientific) according to the manufacturer's protocol. After extraction, Exosome Purification and RNA Isolation Kit (Norgen Biotek) was employed to purify EV and extract total RNA in EV consequentially.Small RNA libraries were set up with 200 ng EV-delivered total RNAs for each sample. Illumina HiSeqTM 2500 platform was used for deep sequencing assay.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: serum extracellular vesicle

tag: disease state

value: non-bone -metastatic prostate cancer


title: Sample 18


title: RNA_seq_UCLA2_iMeLCs_d1_hPGCLCs_d4_EChPGCLCs_D4C10_rep2


title: M4M5_P0_322


title: pen2 Ab 24 hpi_rep2

source_name: pen2 vs Ab 24 hpi_replication2


title: Sample 15


title: M4M5_P0_312


title: Sample 19

description: serum  extracellular vesicle delivered miRNAs of patients with bone -metastatic prostate cancer

value: bone -metastatic prostate cancer


title: Sample 14


title: pen2 Ab 24 hpi_rep4

source_name: pen2 vs Ab 24 hpi_replication4


title: pen2 Ab 24 hpi_rep1

source_name: pen2 vs Ab 24 hpi_replication1


title: M4M5_P0_302


title: Sample 9


title: Sample 10


title: Sample 11


title: Sample 8


title: M4M5_P0_292


title: Sample 7


title: M4M5_P0_282


title: Sample 12


title: M4M5_P0_211


title: Sample 6

description: serum  extracellular vesicle delivered miRNAs of patients with benign prostatic hyperplasia

value: benign prostatic hyperplasia


title: Sample 5


title: F99_P4_331


title: Sample 4


title: mtf4 in planta, rep3

description:
Gene expression of the mtf4Δ mutant at 4 hpi on cucumber leaf surfaces.
Replicate 3

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-060762 Colletotrichum orbiculare Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) and GeneSpring GX12.1 using default parameters.

organism: Colletotrichum orbiculare

source_name: mtf4 in planta, 4 hpi

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low RNA Input Fluorescent Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Strains were cultured on potato dextrose agar at 24°C in the dark. Conidia were harvested from 6-day-old mycelia.

extract_protocol: RNA was prepared using the Agilent Plant RNA Isolation Mini kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For sampling of immature appressoria in planta, 10 µL of a conidial suspension (5 × 10^5 conidia/mL distilled water) was spotted onto the abaxial surface of cucumber cotyledons and incubated in a humid box at 24 °C in the dark. After 4 h, the lower epidermises of the cotyledons were peeled off and grinded in liquid nitrogen.

value: germinating conidia on cucumber leaf surfaces

tag: time

value: 4 hpi

tag: Stage

value: appressorium formation


title: Sample 13


title: mtf4 in planta, rep4

description:
Gene expression of the mtf4Δ mutant at 4 hpi on cucumber leaf surfaces.
Replicate 4


title: Sample 3


title: Sample 2


title: Sample 16


title: Sample 1


title: mtf4 in planta, rep2

description:
Gene expression of the mtf4Δ mutant at 4 hpi on cucumber leaf surfaces.
Replicate 2


title: MTF4-OX in planta, rep4

description:
Gene expression of the MTF4-OX strain at 4 hpi on cucumber leaf surfaces.
Replicate 4

source_name: MTF4-OX in planta, 4 hpi


title: ASC_NONOateP_9h

city: Seoul

first: Kiwon

last: Song

address: Yonsei-ro 50

country: South Korea

institute: Yonsei University

data_processing:
Following cluster amplification of denaturated templates, sequencing was progressed as paired-end using Illumina HiSeq2500.
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases, reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20. The whole filtering
Filtered reads were mapped to the reference genome related to the species using the aligner TopHat.
Gene expression level was measured with Cufflingks v2.1.1 using the gene annotation database of the species. To improve the accuracy of the measurement, multi-read-correction and frag-bias-correct options were applied.
Differential expression analysis was performed by Cuffdiff. DEGs were identified based on the q-value threshold less than 0.05 for correcting errors caused by multiple-testing.
Genome_build: ENSEMBL 72 (GRCh37.p11)

source_name: Human adipose tissue-derived stem cells

growth_protocol: ASCs were cultured in DMEM/F12 supplemented with 10 % FBS and 10 ml/L penicillin-streptomycin. ASCs were incubated at 37℃ in humidified atmosphere containing 5 % CO2.

extract_protocol:
Cells were collected and their total RNA was extracted using the Rneasy Mini kit.
The libraries were prepared for 100 bp paired-end sequencing using TruSeq Stranded mRNA Sample Prep Kit (Illumina, CA, USA)

treatment_protocol: 3 × 10^4 ASCs were seeded in 35-mm culture dishes and incubated for 16 h for ASCs. Cells were pretreated with the culture medium alone, CP or NONOate prior to NTAPP exposure. ASCs pretreated with CP and culture medium alone were exposed to the indicated dose (5 standard liter/min [slm], 20 voltage [V]) of NTAPP for 50 s per h for 10 times. NTAPP-exposed cells and -unexposed cells were further incubated for 72 h at 37℃ in a 5% CO2 incubator. The distance between the device and cells was fixed to 1 cm, and 1.5 mL of medium was used.

value: Human adipose tissue-derived stem cells


title: F99_P4_321

source_name: corneal endothelium


title: mtf4 in planta, rep1

description:
Gene expression of the mtf4Δ mutant at 4 hpi on cucumber leaf surfaces.
Replicate 1


title: ASC_NTAPP_9h


title: MTF4-OX in planta, rep3

description:
Gene expression of the MTF4-OX strain at 4 hpi on cucumber leaf surfaces.
Replicate 3


title: F99_P4_301


title: F99_P4_311


title: HCRASFB2

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

data_processing:
Illumina Casava1.8.2 software was used for basecalling
Reads were processed using fastx toolkit to trim for adapter and low quality bases and filter for low quality reads.
Processed reads were mapped to the Human  genome using hisat2 version 2.0.4
Reads mapping to genes were counted using htseq-count
Gene normalization and differential expression analysis were performed using Deseq2
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: tab delimited text file containing deseq2 normalized values in a single matrix format.
Supplementary_files_format_and_content: Deseq2 Normalized Counts Matrix

source_name: PBMC

extract_protocol:
RNA was extracted using Qiagen AllPrep DNA/RNA kit with an additional on-column Dnase I treatment
Total RNA libraries were prepared using theClontech SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian (Takara Bio)

tag: group

value: HIV- Healthy Controls


title: MTF4-OX in planta, rep2

description:
Gene expression of the MTF4-OX strain at 4 hpi on cucumber leaf surfaces.
Replicate 2


title: ICL5

value: Idiopathic CD4 Cell Lymphopenia


title: ASC_NTAPP+CP_9h


title: F99_P4_281


title: IRIS3D0

value: HIV1 Viremia not on ARV


title: KRT-19-negative preneoplastic nodules 9

description:
replicate 2
SAMPLE 19

source_name: Rat Liver

tag: strain

value: Male Fischer rats


title: WTF2

value: Paradoxical CD4 Responders


title: F99_P4_209


title: MTF4-OX in planta, rep1

description:
Gene expression of the MTF4-OX strain at 4 hpi on cucumber leaf surfaces.
Replicate 1


title: IRIS4W96

value: 2 years ARV, Normal Response


title: F99_P3_330


title: IRIS4D0


title: ICL4


title: WTF3


title: F99_P3_320


title: F99_P3_310


title: IRIS3W96


title: HCRASFB1


title: ICL2


title: IRIS5W96


title: WT_Abaxial_ZT6_rep2

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL19764 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 at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting.

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Data was thresholded to 1, log2 transformed and normalized to the 75th percentile in Genespring GX (Agilent)

organism: Nicotiana attenuata

source_name: Abaxial sides of peduncles collected at ZT6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Wild type plants for peduncle collection were grown in glasshouse conditions under a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from floral peduncles using the Plant RNeasy kit (Qiagen) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Ambion). RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Adaxial and abaxial sides were separated with a longitudinal cut across the midline of the flower peduncle at the indicated times and inmediatly placed in liquid nitrogen.

value: wild type

tag: peduncle side

value: Abaxial

tag: zeitgeiber time


title: WT_Abaxial_ZT14_rep2

source_name: Abaxial sides of peduncles collected at ZT14


title: IRIS1D0


title: HCRASFB3


title: WT_Abaxial_ZT14_rep3


title: WT_Abaxial_ZT6_rep3


title: WT_Abaxial_ZT14_rep1


title: F99_P4_291

value: corneal endothelium

tag: media

tag: passage


title: WTF4


title: F99_P3_290

tag: protocol


title: HCRASFB5


title: ICL1


title: F99_P3_280


title: IRIS5D0


title: IRIS2W96


title: F99_P2_329


title: ICL3


title: HCRASFB4


title: WTF1


title: F99_P3_300


title: F99_P3_207


title: IRIS1W96


title: WT_Abaxial_ZT0_rep3

source_name: Abaxial sides of peduncles collected at ZT0


title: F99_P2_319


title: IRIS2D0


title: WT_Abaxial_ZT0_rep2


title: WT_Abaxial_ZT0_rep1


title: WT_Adaxial_ZT14_rep2

source_name: Adaxial sides of peduncles collected at ZT14

value: Adaxial


title: WT_Adaxial_ZT14_rep3


title: WT_Abaxial_ZT6_rep1


title: F99_P2_309


title: WT_Adaxial_ZT6_rep3

source_name: Adaxial sides of peduncles collected at ZT6


title: WT_Adaxial_ZT14_rep1


title: WTF5


title: P1120715H08 [saliva EV small RNA-seq]

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

institute: Michigan State University

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1120715H08_sX_6__P1_120715_H08_AGTTCC_L005

data_processing:
Data was processed through the Genboree exceRpt small RNA-seq Pipeline, Version 4.6.2. Specific settings for the pipeline include: minBaseCallQuality: 20; minReadLength:12; exogenous Mismatch:0; endogenousMismatch:1; exogenousClaves:Bacteria,FPV,Metazoa,Plants,Vertebrates; endogenousLibraryOrder: miRNA,tRNA,piRNA,gencode,circRNA; trimBases3p:0, fractionForMinBaseCallQuality:80, minAdapterBases3p:7.
Within the exceRpt 4.6.2 database search the sources for small RNA library mapping are:   rRNAs: 45S, 5S, and mt_rRNA sequences for human and mouse  miRNAs from miRBase version 21  tRNAs from gtRNAdb  piRNAs from piRNABank (removed duplicate sequences)  Annotations from Gencode version 24 (hg38)  CircularRNAs from circBase
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Read Count or Read Count Per Million for all Samples corresponding to Genboree exceRpt small RNA-seq Pipeline (4.6.2) output.

source_name: saliva EV_post-vaccination respons for pneumococcal vaccine (PPSV23)

growth_protocol: Saliva for RNA EV sequencing: Saliva was collected from the subject in a 15ml conical tube. Samples were stored at -80C until processing.

extract_protocol:
Extracellular vesicles (EVs) were extracted from 500ul of saliva, and centrifuged at 3000g for 20 min, at 4C, to remove cells and ebris. ExoQuick-TC Exosome Precipitation Solution (SBI), was added to the sample supernatant in 2:1 ratio and refrigerated overnight at 4C. Following overnight incubation, precipitated EVs were processed per manufacturer's kit instructions. EVpellets were stored at -80C for further use. For RNA extraction, the SeraMir RNA Amplification Kit (SBI) was used per manufacturer's instructions.
Small RNA library preparation was carried out using NEBNext Multiplex Small RNA library prep kit (New England Biolabs) following manufacturer’s instructions. After PCR amplification, quality of libraries was assessed using a high sensitivity DNA kit on a Bioanalyzer (Agilent) according to manufacturer’s instructions. Size selection was performed using 3% agarose dye-free marker H cassettes on a Pippin Prep (Sage Science) following manufacturer’s instructions with a specified collection size range of 125–153 bp. Libraries were further purified and concentrated by ethanol precipitation, resuspended in 10 μl of 10 mM tris-HCl (pH = 8.5) and quantified using Qubit and Bioanalyzer. Based on the quantification, equimolar library pools were prepared, quality was assessed as described above and the library was further diluted to 4 nM using 10 mM tris-HCl (pH = 8.5). Pooled libraries were sequenced at a final concentration of 1.2 pM on an Illumina HiSeq 2500.

treatment_protocol: The subject received vaccination for pneumococcal pneumonia (PPSV23) on  060715, ~10.30 am.

tag: time point (mmddyy_hhh)

value: saliva extra cellular vesicle (EV)

tag: molecule subtype

value: small RNA


title: P1110915H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1110915H08_sX_7__P1_110915_H08_GTAGAG_L006


title: P1091415H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1091415H08_sX_7__P1_091415_H08_ATGTCA_L006


title: P1101215H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1101215H08_sX_7__P1_101215_H08_CCGTCC_L006


title: F99_P2_289


title: P1081015H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1081015H08_sX_7__P1_081015_H08_AGTTCC_L006


title: F99_P2_279


title: WT_Adaxial_ZT6_rep1

tag: genotype/variation


title: P1070715H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1070715H08_sX_7__P1_070715_H08_GGCTAC_L006


title: P1071315H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1071315H08_sX_7__P1_071315_H08_CTTGTA_L006


title: F99_P2_299


title: F99_P2_205


title: WT_Adaxial_ZT6_rep2


title: JEK14325

city: Bloomington

first: Xilin

last: Li

state: Indiana

address: 2719 E 10th street Rm230

institute: Indiana University

data_processing:
Data included 60 single-read fastq libraries (raw read length 75 nt). Base-calling was done bcl2fastq v2.20.0.422.
Reads were quality filtered using Trimmomatic ver. 0.33 (http://www.usadellab.org/cms/?page=trimmomatic), with the cutoff threshold for average base quality score set at 20 over a window of 3 bases.
Reads shorter than 20 bases post-trimming were excluded. About 97.5% of the reads passed quality filters
Rattus_norvegicus genome reference - Rnor_6.0 using STAR version STAR_2.5.2b. Approximately 98.7% of the total cleaned reads mapped to the reference
Number of reads aligned to the exon regions of each of the annotated genes (ENSEMBL - Rnor_6.0.93) were generated using featureCounts tool of subread package version 1.6.0
Read alignments were considered stranded. Multiple mapped reads and reads overlapping with multiple features were excluded.
Genome_build: Rnor_6.0.93
Supplementary_files_format_and_content: Excel spread sheet including the raw counts of each gene for each sample

source_name: Liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was isolated using Qiagen Rneasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA HT Library kit following the standard proctocol.

value: Sprague-Dawley

value: Liver

tag: age

value: 10-11 weeks

tag: treatment

value: PFOA 15mg/kg 28d

tag: Sex

value: male


title: P1070615H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1070615H08_sX_7__P1_070615_H08_TAGCTT_L006

tag: tissue


title: F99_P1_328


title: P1070515H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1070515H08_sX_7__P1_070515_H08_GATCAG_L006


title: WT_Adaxial_ZT0_rep2

source_name: Adaxial sides of peduncles collected at ZT0


title: WT_Adaxial_ZT0_rep1


title: WT_Adaxial_ZT0_rep3


title: JEK14324


title: P1070315H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1070315H08_sX_7__P1_070315_H08_CAGATC_L006


title: F99_P1_318


title: P1072015H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1072015H08_sX_7__P1_072015_H08_AGTCAA_L006


title: P1070415H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1070415H08_sX_7__P1_070415_H08_ACTTGA_L006


title: P1070215H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1070215H08_sX_7__P1_070215_H08_GCCAAT_L006


title: P1063015H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1063015H08_sX_6__P1_063015_H08_TGACCA_L005


title: JEK14323


title: P1070115H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1070115H08_sX_6__P1_070115_H08_ACAGTG_L005


title: P1062915H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1062915H08_sX_6__P1_062915_H08_TTAGGC_L005


title: F99_P1_308


title: JEK14322


title: F99_P1_288


title: P1062715H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1062715H08_sX_6__P1_062715_H08_ATCACG_L005


title: P1062815H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1062815H08_sX_6__P1_062815_H08_CGATGT_L005


title: F99_P1_298


title: P1062415H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1062415H08_sX_6__P1_062415_H08_CGTACG_L005


title: P1062615H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1062615H08_sX_6__P1_062615_H08_GGTAGC_L005


title: F99_P1_278


title: JEK14320

value: PFOA 5mg/kg 28d


title: ASC_unexposed_9h

value: Human adipose tissue-derived stem cells


title: P1062215H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1062215H08_sX_6__P1_062215_H08_GTGGCC_L005


title: F99_P1_203


title: P1062115H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1062115H08_sX_6__P1_062115_H08_GTGAAA_L005


title: F99_P0_327


title: JEK14318


title: JEK14319


title: P1061915H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1061915H08_sX_6__P1_061915_H08_GTAGAG_L005


title: P1062315H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1062315H08_sX_6__P1_062315_H08_GTTTCG_L005


title: P1062015H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1062015H08_sX_6__P1_062015_H08_GTCCGC_L005


title: JEK14317


title: P1061715H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1061715H08_sX_5__P1_061715_H08_ATGTCA_L004


title: P1061815H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1061815H08_sX_6__P1_061815_H08_CCGTCC_L005


title: JEK14321


title: F99_P0_317


title: P1061615H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1061615H08_sX_5__P1_061615_H08_AGTTCC_L004


title: P1061515H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1061515H08_sX_5__P1_061515_H08_AGTCAA_L004


title: JEK14316


title: F99_P0_307


title: JEK14314

value: PFOA 1mg/kg 28d


title: P1061215H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1061215H08_sX_5__P1_061215_H08_TAGCTT_L004


title: JEK14315


title: P1061415H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1061415H08_sX_5__P1_061415_H08_CTTGTA_L004


title: F99_P0_287


title: F99_P0_297


title: P1061315H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1061315H08_sX_5__P1_061315_H08_GGCTAC_L004


title: P1061115H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1061115H08_sX_5__P1_061115_H08_GATCAG_L004


title: JEK14313


title: P1061015H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1061015H08_sX_5__P1_061015_H08_ACTTGA_L004


title: JEK14312


title: P1060815H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060815H08_sX_5__P1_060815_H08_GCCAAT_L004


title: P1060915H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060915H08_sX_5__P1_060915_H08_CAGATC_L004


title: F99_P0_277


title: F99_P0_201


title: P1060815H06 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060815H06_sX_5__P1_060815_H06_ACAGTG_L004


title: P1060815H05 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060815H05_sX_5__P1_060815_H05_TGACCA_L004


title: P1060815H04 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060815H04_sX_5__P1_060815_H04_TTAGGC_L004


title: JEK14311


title: JEK14310

value: Control 28d


title: P1060815H03 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060815H03_sX_5__P1_060815_H03_CGATGT_L004


title: P1060815H02 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060815H02_sX_5__P1_060815_H02_ATCACG_L004


title: P1060815H01 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060815H01_sX_4__P1_060815_H01_GCCAAT_L008


title: JEK14308


title: JEK14309


title: P1060715H24 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H24_sX_4__P1_060715_H24_ACAGTG_L008


title: P1060715H23 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H23_sX_4__P1_060715_H23_TGACCA_L008


title: SLX.14774.A013

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: RNA from Drosophila Melanogaster Elav x PrP (Cyt) whole head homogenate treated with Normal Brain Homogenate, harvested at 30 days of age

data_processing:
Fastq reads were mapped to Drosophila Genome (built BDGP6) using Tophat V2.0.11
htseq-count 0.6.1p1 was used to generate gene level counts based on Ensembl V77 GTF
Differential gene expression was performed using edgeR
Genome_build: BDGP6
Supplementary_files_format_and_content: tab-delimited text containing raw gene-level count for each sample

organism: Drosophila melanogaster

extract_protocol:
15 fly heads was homogenised by manual grinding in an eppendorf tube with 50μl Trizol (Cat No. 15596-018; Invitrogen). A further 50μl of Trizol were mixed with the homogenate, which was then microfuged at 16,160 x g for 10 minutes and the supernatant transferred to RNAse-free tubes before adding a further 50μl Trizol and incubated for 5 minutes. RNA was isolated by conventional chloroform:isoamylalcohol:isopropanol extraction followed by ethanol precipitation. Air-dried RNA pellets were treated with DNAse 1 (Cat No. EN0521; Thermo Scientific) at 37 ̊C for 60 minutes, with the reaction halted by the addition of EDTA and incubation at 65 ̊C for 10 minutes. RNA samples were then subjected to the Qiagen RNeasy RNA Cleanup protocol according to the manufacturers’ instructions. The RNA samples were eventually eluted from RNeasy mini-spin columns, ethanol precipitated, re-suspended in RNAse-free water and stored at -80 ̊C.
A library of mRNA was prepared from 200 ng of total RNA, extracted as described above and that had been originally pooled from 15 fly heads from each experimental condition, using the Illumina TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: Drosophila at were Drosophila at the larval stage of development were exposed to brain homogenates of cerebral cortex tissue from confirmed scrapie-positive or known scrapie-negative sheep. After hatching, Drosophila were transferred to inoculum-free tubes and allowed to develop normally. At 5 days and 30/40 days post hatching, the flies were euthanized and then decapitated for RNA extraction

value: Whole head homogenate

tag: fly line

value: Elav x PrP (Cyt)

tag: age in days

value: Normal Brain Homogenate


title: SLX.14774.A014

description: RNA from Drosophila Melanogaster Elav x PrP (Cyt) whole head homogenate treated with Scrapie, harvested at 30 days of age

value: Scrapie


title: JEK14307


title: SLX.14774.A011

description: RNA from Drosophila Melanogaster Elav x 51D whole head homogenate treated with Normal Brain Homogenate, harvested at 30 days of age

value: Elav x 51D


title: SLX.14774.A012

description: RNA from Drosophila Melanogaster Elav x 51D whole head homogenate treated with Scrapie, harvested at 30 days of age


title: SLX.14774.A010

description: RNA from Drosophila Melanogaster Elav x PrP (Cyt) whole head homogenate treated with Scrapie, harvested at 5 days of age


title: P1060715H21 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H21_sX_4__P1_060715_H21_CGATGT_L008


title: P1060715H19 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H19_sX_4__P1_060715_H19_GGTAGC_L008


title: P1060715H20 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H20_sX_4__P1_060715_H20_ATCACG_L008


title: P1060715H22 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H22_sX_4__P1_060715_H22_TTAGGC_L008


title: SLX.14774.A009

description: RNA from Drosophila Melanogaster Elav x PrP (Cyt) whole head homogenate treated with Normal Brain Homogenate, harvested at 5 days of age


title: JEK14306


title: JEK14285

value: 8-9 weeks

value: PFOA 15mg/kg 14d


title: P1060715H17 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H17_sX_4__P1_060715_H17_CGTACG_L008

value: saliva extra cellular vesicle (EV)

value: small RNA


title: P1060715H16 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H16_sX_4__P1_060715_H16_GTTTCG_L008


title: SLX.14774.A008

description: RNA from Drosophila Melanogaster Elav x 51D whole head homogenate treated with Scrapie, harvested at 5 days of age


title: JEK14284

value: Sprague-Dawley

value: Liver


title: SLX.14774.A007

description: RNA from Drosophila Melanogaster Elav x 51D whole head homogenate treated with Normal Brain Homogenate, harvested at 5 days of age


title: P1060715H14 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H14_sX_4__P1_060715_H14_GTGAAA_L008


title: P1060715H15 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H15_sX_4__P1_060715_H15_GTGGCC_L008


title: P1060715H13 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H13_sX_4__P1_060715_H13_GTCCGC_L008


title: P1060715H12 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H12_sX_4__P1_060715_H12_GTAGAG_L008


title: JEK14282


title: P1060715H09 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H09_sX_3__P1_060715_H09_AGTTCC_L007

source_name: saliva EV_pre-vaccination respons for pneumococcal vaccine (PPSV23)


title: P1060715H11 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H11_sX_4__P1_060715_H11_CCGTCC_L008


title: JEK14280

value: PFOA 5mg/kg 14d


title: P1060715H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H08_sX_3__P1_060715_H08_AGTCAA_L007


title: SLX.14773.A013

description: RNA from Drosophila Melanogaster Elav x PrP (Cyt) whole head homogenate treated with Normal Brain Homogenate, harvested at 30 days of age


title: P1060715H18 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H18_sX_4__P1_060715_H18_GAGTGG_L008


title: SLX.14773.A012

description: RNA from Drosophila Melanogaster Elav x 51D whole head homogenate treated with Scrapie, harvested at 30 days of age


title: SLX.14773.A011

description: RNA from Drosophila Melanogaster Elav x 51D whole head homogenate treated with Normal Brain Homogenate, harvested at 30 days of age


title: SLX.14773.A010

description: RNA from Drosophila Melanogaster Elav x PrP (Cyt) whole head homogenate treated with Scrapie, harvested at 5 days of age


title: JEK14279

value: male


title: P1060515H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060515H08_sX_3__P1_060515_H08_TAGCTT_L007


title: P1060615H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060615H08_sX_3__P1_060615_H08_GGCTAC_L007


title: JEK14278


title: P1052615H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1052615H08_sX_3__P1_052615_H08_ACTTGA_L007


title: SLX.14773.A009

description: RNA from Drosophila Melanogaster Elav x PrP (Cyt) whole head homogenate treated with Normal Brain Homogenate, harvested at 5 days of age


title: JEK14283


title: P1052615H07 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1052615H07_sX_3__P1_052615_H07_CAGATC_L007


title: SLX.14773.A014

description: RNA from Drosophila Melanogaster Elav x PrP (Cyt) whole head homogenate treated with Scrapie, harvested at 30 days of age


title: P1052615H04 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1052615H04_sX_3__P1_052615_H04_TGACCA_L007


title: SLX.14773.A008

description: RNA from Drosophila Melanogaster Elav x 51D whole head homogenate treated with Scrapie, harvested at 5 days of age


title: P1052615H05 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1052615H05_sX_3__P1_052615_H05_ACAGTG_L007


title: JEK14276


title: P1060215H08 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060215H08_sX_3__P1_060215_H08_GATCAG_L007


title: SLX.14773.A007

description: RNA from Drosophila Melanogaster Elav x 51D whole head homogenate treated with Normal Brain Homogenate, harvested at 5 days of age


title: P1060715H10 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H10_sX_3__P1_060715_H10_ATGTCA_L007


title: JEK14281


title: P1052615H03 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1052615H03_sX_3__P1_052615_H03_TTAGGC_L007


title: JEK14277


title: P1060715H07 [saliva EV small RNA-seq]

description:
processed data file:
circularRNA_ReadCounts.txt
circularRNA_ReadsPerMillion.txt
exogenousGenomes_taxonomySpecific_ReadCounts.txt
exogenousGenomes_taxonomySpecific_ReadsPerMillion.txt
exogenous_miRNA_ReadCounts.txt
exogenous_miRNA_ReadsPerMillion.txt
exogenousRibosomal_taxonomySpecific_ReadCounts.txt
exogenousRibosomal_taxonomySpecific_ReadsPerMillion.txt
gencode_ReadCounts.txt
gencode_ReadsPerMillion.txt
miRNA_ReadCounts.txt
miRNA_ReadsPerMillion.txt
piRNA_ReadCounts.txt
piRNA_ReadsPerMillion.txt
tRNA_ReadCounts.txt
tRNA_ReadsPerMillion.txt
P1060715H07_sX_3__P1_060715_H07_CTTGTA_L007