title: JEK14275

value: PFOA 1mg/kg 14d


title: P1052615H02 [saliva EV small RNA-seq]

status: Public on Jan 31 2020

type: SRA

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

country: USA

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
P1052615H02_sX_3__P1_052615_H02_CGATGT_L007

library_source: transcriptomic

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.

molecule: total RNA

organism: Homo sapiens

source_name: saliva EV_pre-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)

tag: tissue

value: saliva extra cellular vesicle (EV)

tag: molecule subtype

value: small RNA


title: SLX.14720.A014

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 Scrapie, 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

tag: treatment

value: Scrapie


title: JEK14274

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

molecule: polyA RNA

organism: Rattus norvegicus

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.

tag: strain

value: Sprague-Dawley

value: Liver

tag: age

value: 8-9 weeks

tag: Sex

value: male


title: P1052515H24 [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
P1052515H24_sX_2__P1_052515_H24_GCCAAT_L006


title: P1052515H23 [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
P1052515H23_sX_2__P1_052515_H23_ACAGTG_L006


title: P1052615H06 [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
P1052615H06_sX_3__P1_052615_H06_GCCAAT_L007


title: P1052515H22 [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
P1052515H22_sX_2__P1_052515_H22_TGACCA_L006


title: JEK14273


title: SLX.14720.A012

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

value: Elav x 51D


title: P1052515H21 [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
P1052515H21_sX_2__P1_052515_H21_TTAGGC_L006


title: P1052515H20 [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
P1052515H20_sX_2__P1_052515_H20_CGATGT_L006


title: SLX.14720.A011

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

value: Normal Brain Homogenate


title: P1052515H18 [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
P1052515H18_sX_2__P1_052515_H18_GGTAGC_L006


title: P1052515H19 [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
P1052515H19_sX_2__P1_052515_H19_ATCACG_L006


title: SLX.14720.A010

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


title: P1052515H16 [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
P1052515H16_sX_2__P1_052515_H16_CGTACG_L006


title: JEK14270

value: Control 14d


title: P1052515H17 [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
P1052515H17_sX_2__P1_052515_H17_GAGTGG_L006


title: P1052515H15 [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
P1052515H15_sX_2__P1_052515_H15_GTTTCG_L006


title: P1052515H14 [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
P1052515H14_sX_2__P1_052515_H14_GTGGCC_L006


title: SLX.14720.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: JEK14269


title: SLX.14720.A008

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


title: JEK14268


title: P1052615H01 [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
P1052615H01_sX_3__P1_052615_H01_ATCACG_L007


title: P1052515H13 [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
P1052515H13_sX_2__P1_052515_H13_GTGAAA_L006


title: P1052515H12 [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
P1052515H12_sX_2__P1_052515_H12_GTCCGC_L006


title: SLX.14720.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: JEK14267


title: P1052515H11 [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
P1052515H11_sX_2__P1_052515_H11_GTAGAG_L006


title: P1052515H10 [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
P1052515H10_sX_2__P1_052515_H10_CCGTCC_L006


title: JEK14272


title: JEK14271


title: P1052515H09 [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
P1052515H09_sX_1_P1_052515_H09_ATGTCA_L006


title: P1052515H08 [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
P1052515H08_sX_1_P1_052515_H08_AGTTCC_L006


title: JEK14266


title: P1052515H07 [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
P1052515H07_sX_1_P1_052515_H07_AGTCAA_L006


title: JEK14265

value: 7-8 weeks

value: PFOA 15mg/kg 7d


title: JEK14264


title: P1051815H08 [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
P1051815H08_sX_1_P1_051815_H08_CTTGTA_L006


title: P1050415H08 [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
P1050415H08_sX_1_P1_050415_H08_TAGCTT_L006


title: P1042715H08 [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
P1042715H08_sX_1_P1_042715_H08_GATCAG_L006


title: P1051115H08 [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
P1051115H08_sX_1_P1_051115_H08_GGCTAC_L006


title: JEK14263


title: SLX.14720.A007

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


title: P1042015H08 [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
P1042015H08_sX_1_P1_042015_H08_ACTTGA_L006


title: P1040615H08 [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
P1040615H08_sX_1_P1_040615_H08_GCCAAT_L006


title: P1041315H08 [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
P1041315H08_sX_1_P1_041315_H08_CAGATC_L006


title: P1033015H08 [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
P1033015H08_sX_1_P1_033015_H08_ACAGTG_L006


title: JEK14262


title: P1032315H08 [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
P1032315H08_sX_1_P1_032315_H08_TGACCA_L006


title: P1031416H08 [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
P1031416H08_sX_7__P1_031416_H08_GTTTCG_L006


title: JEK14260

value: PFOA 5mg/kg 7d


title: P1031715H08 [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
P1031715H08_sX_1_P1_031715_H08_TTAGGC_L006


title: JEK14259


title: P1031015H08 [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
P1031015H08_sX_1_P1_031015_H08_CGATGT_L006


title: P1030315H08 [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
P1030315H08_sX_1_P1_030315_H08_ATCACG_L006


title: JEK14258


title: P1011116H08 [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
P1011116H08_sX_7__P1__011116_H08_GTGAAA_L006


title: JEK14257


title: P1062915H08 [PBMCs_RNA-seq]

description: P1062915H08_P1_P1062915H08_PBMCs_TAGCTT_L001

data_processing:
Data QC using FastQC, and reads trimmed 13 from the left and 13 from the right
Trimmed paired reads mapped using Tophat 2.0.13 (using --no-coverage-search --library-type fr-firststrand)
Mapped files quantitated using Cufflinks (--no-effective-length-correction, using hg38 annotation)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample corresponding to Cufflinks output.

source_name: PBMCs_post-vaccination respons for pneumococcal vaccine (PPSV23)

growth_protocol: RNA Peripheral Blood Mononuclear Cells was used to prepare RNA-Sequencing libraries. Briefly, PBMCs (~10 Million) were extracted using centrifugation of peripheral blood with lymphocyte separation medium (LSM) from peripheral blood (~10ml collected in EDTA tubes) within 30 min. of donation. Extracted PBMC cell pellets were immediately flash frozen and stored at -80C.

extract_protocol:
RNA extraction was done using Qiagen RNAeasy kit. RNA from ~2 million cells was extracted, with concentration measured on a Qubit (Life Technologies). Additionally, RNA integrity was checked on a Bioanalyzer (Agilent, Santa Clara CA) and only RNA with an RNA integrity number (RIN) of > 7 was used for subsequent library construction.
Two sets of sequencing were carried out. Initially, libraries were constructed using Illumina's TruSeq kits with Ribo-Zero following the manufacturer's protocol. These libraries were sequenced at 125bp paired end reads on an Illumina HiSeq 2500. In the next round of sequencing libraries were constructed by Novogene, with poly-A selection using a Eukaryotic directional  mRNA  library (NEB) and sequenced on a HiSeq4000 at 150bp paired end reads. cDNA was quantitated on a Qubit (Life Technologies) and additionally the library quality was evaluated on a Bioanalyzer (Agilent)

value: blood

tag: cell type

value: Peripheral Blood Mononuclear Cell (PBMC)


title: P1062215H08 [PBMCs_RNA-seq]

description: P1062215H08_P1_P1062215H08_PBMCs_GATCAG_L001


title: P1060815H08 [PBMCs_RNA-seq]

description: P1060815H08_P1_P1060815H08_PBMCs_TTAGGC_L001


title: JEK14256


title: P1061515H08 [PBMCs_RNA-seq]

description: P1061515H08_P1_P1061515H08_PBMCs_ACTTGA_L001


title: JEK14255

value: PFOA 1mg/kg 7d


title: P1060215H08 [PBMCs_RNA-seq]

description: P1060215H08_P1_P1060215H08_PBMCs_ATCACG_L001

source_name: PBMCs_pre-vaccination respons for pneumococcal vaccine (PPSV23)


title: JEK14261


title: P1051115H08 [PBMCs_RNA-seq]

description: P1051115H08_P1_P1051115H08_PBMCs_GGCTAC_L008


title: P1042715H08 [PBMCs_RNA-seq]

description: P1042715H08_P1_P1042715H08_PBMCs_GATCAG_L008


title: P1050415H08 [PBMCs_RNA-seq]

description: P1050415H08_P1_P1050415H08_PBMCs_TAGCTT_L008


title: P1021516H08 [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
P1021516H08_sX_7__P1_021516_H08_GTGGCC_L006

value: saliva extra cellular vesicle (EV)

value: small RNA


title: P1042015H08 [PBMCs_RNA-seq]

description: P1042015H08_P1_P1042015H08_PBMCs_ACTTGA_L008


title: JEK14253


title: Patient 53, sample B93, Left colon

type: genomic

city: Salamanca

first: Juan Luis

last: Garcia

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer IBMCC-CIC

hyb_protocol: The digested DNA target was hybridized onto the OncoScan array and incubated at 49ºC in a GeneChip Hybridization oven 640 (Affymetrix) for 17h at 60rpm. OncoScan arrays were then washed and stained in a GeneChips Fluidics Station 450 (Affymetrix) using OncoScan stain and wash reagents according to the manufacturer’s instructions.

scan_protocol: The microarrays were ﬁnally scanned with a GeneChip scanner 3000 (Affymetrix).

data_processing: CEL files were processed using the Affymetrix OncoScan console (version 1.3) and the Affymetrix ChAS software (version 3.2.0.1252).

label: Biotin

molecule: genomic DNA

source_name: Left colon

label_protocol: MIP probe annealing and hybridization were performed according to manufacturer's protocols.

growth_protocol: Not applicable.

extract_protocol: Genomic DNAs were extracted according to manufacturer's protocols.

treatment_protocol: Not applicable.

tag: disease status

value: Synchronous colorectal cancer (SCRC)

tag: patient pair number

value: Male

tag: age at diagnosis

value: Left colon


title: Patient 50, sample B92, Sigmoid colon

source_name: Sigmoid colon

value: Sigmoid colon


title: Patient 51, sample B81, Right colon

source_name: Right colon

value: Right colon


title: JEK14252

value: Sprague-Dawley

value: Liver

value: male


title: JEK14251


title: SLX.7179.A019

description: RNA from Drosophila Melanogaster Elav x PrP (GPI) whole head homogenate treated with Scrapie, harvested at 40 days of age

value: Whole head homogenate

value: Elav x PrP (GPI)

value: Scrapie


title: P1041315H08 [PBMCs_RNA-seq]

description: P1041315H08_P1_P1041315H08_PBMCs_TTAGGC_L008


title: Patient 48, sample B90, Sigmoid colon


title: Patient 49, sample B78, Right colon


title: P1040615H08 [PBMCs_RNA-seq]

description: P1040615H08_P1_P1040615H08_PBMCs_ATCACG_L008


title: Patient 52, sample B94, Left colon


title: Patient 47, sample B89, Right colon

value: Female


title: JEK14250

value: 7-8 weeks

value: Control 7d


title: Patient 49, sample B77, Right colon


title: SLX.7179.A018

source_name: Drosophila Melanogaster Elav x PrP (GPI) whole head homogenate treated with Scrapie, harvested at 40 days of age


title: Patient 53, sample B97, Left colon


title: DBL-treated vs. control_rep2

type: RNA

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) containing fragmented Cy-dye-labeled cRNA were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially by Wash Buffer 1 (6x SSPE, 0.005% N-lauroylsarcosine) and Wash Buffer 2 (0.06x SSPE, 0.005% N-lauroylsarcosine) for 1 min at room temperature.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: control SH-SY5Y cells

label_protocol: Total RNA samples (200 ng) from untreated and treated cells were used to prepare Cy3- or Cy5-labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer's instructions.

growth_protocol: SH-SY5Y cells were maintained in DMEM with 15% FBS.

extract_protocol: Total RNA extracted using RNeasy following manufacturer's instructions. The quality of total RNA was checked by Agilent tapestation 2200.

treatment_protocol: SH-SY5Y cells were treated with DBL, CAPE, or cultured in the medium alone for 6h.

tag: cell line

value: cell line derived from neuroblastoma

tag: time after plating

value: 4 days

value: addition of medium only

tag: time after treatment

source_name: DBL-treated SH-SY5Y cells

value: addition of medium including DBL


title: Patient 50, sample B95, Sigmoid colon

value: Synchronous colorectal cancer (SCRC)

value: Male


title: SLX.7179.A016


title: Patient 51, sample B82, Left colon

value: Left colon


title: Patient 52, sample B96, Left colon


title: Patient 47, sample B102, Sigmoid colon

value: Sigmoid colon


title: Patient 48, sample B105, Rectum

source_name: Rectum

value: Rectum


title: CAPE-treated vs. control_rep1

source_name: CAPE-treated SH-SY5Y cells

value: addition of medium including CAPE


title: DBL-treated vs. control_rep1


title: JEK14248

value: Sprague-Dawley

value: Liver

value: male


title: JEK14249


title: SLX.7179.A014

description: RNA from Drosophila Melanogaster Elav x PrP (GPI) whole head homogenate treated with Normal Brain Homogenate, harvested at 40 days of age

value: Whole head homogenate

value: Elav x PrP (GPI)

value: Normal Brain Homogenate


title: SLX.7179.A015

source_name: Drosophila Melanogaster Elav x PrP (GPI) whole head homogenate treated with Normal Brain Homogenate, harvested at 40 days of age


title: JEK14247

value: 7-8 weeks

value: Control 7d


title: SLX.7179.A013


title: Patient 46, sample B104, Rectum


title: SLX.7179.A012

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

value: Scrapie


title: JEK14246


title: SLX.7179.A007

source_name: Drosophila Melanogaster Elav x PrP (GPI) whole head homogenate treated with Scrapie, harvested at 5 days of age


title: CAPE-treated vs. control_rep2

value: cell line derived from neuroblastoma

value: 4 days

value: addition of medium only


title: Patient 46, sample B88, Sigmoid colon

value: Synchronous colorectal cancer (SCRC)

value: Male


title: SLX.7179.A004

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


title: SLX.7179.A005

source_name: Drosophila Melanogaster Elav x PrP (GPI) whole head homogenate treated with Normal Brain Homogenate, harvested at 5 days of age


title: Patient 45, sample B87, Sigmoid colon

value: Sigmoid colon


title: SLX.7179.A002


title: KO+treatment 3

city: Düsseldorf

first: Silvia

last: Maglioni

state: NRW

address: Auf' m hennekamp 50

country: Germany

institute: IUF-Leibniz Institute

description: extracted total RNA

hyb_protocol: Samples were prepared and hybridized to C. elegans Gene 2.0 ST Microarray according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
RMA normalization; normalized also per gene to the median
RMA value, normalized to median

label: Affymetrix labeling

organism: Caenorhabditis elegans

source_name: nematodes pellet, RNA extracted

growth_protocol: C. elegans strains were grown and mantained at 20°C. Worms at the desired larval stage (L3) were wash off three big agar plates spotted with the RNAi bacteria under study (nuo-5 and pL4440 for control). The strong RNAi was achieved in the filial generation.

extract_protocol: Individual C. elegans were collected into nuclease-free water and frozen at −80 °C until needed. Frozen worm pellets were re-suspended in lysis buffer and the same volume of Stainless steel beads (6.0 mm RNase free) was added. A TissueLyser II (Qiagen) was used with 2 shakes for 2 minutes at 30 Hz. Total RNA was prepared from each sample using the RNeasy Mini Kit and QIAshredder according to the manufacturer’s instructions (Qiagen-74104 and 79654). Total RNA from 5 different biological replicas was extracted, on column purified to remove small RNA fractions, and treated with DNAse (RNeasy kit, Quiagen). The RNA was be then processed, cDNA synthesis and quality control, hybridization and Affymetrix C. elegans Gene 2.0 ST Microarrays scanning were performed.

treatment_protocol: The plates were supplemented either with 1 µM Lutein or 0.25 % DMSO for control.

tag: genotype

value: nuo-5 RNAi strong

tag: development stage

value: N2, L3 larval stage


title: KO+treatment 2

description: extracted total RNA

label_protocol: Samples were prepared and hybridized to C. elegans Gene 2.0 ST Microarray according to Affymetrix specifications.


title: KO+treatment 4

description: extracted total RNA


title: JEK14254

value: Sprague-Dawley

tag: tissue

value: PFOA 1mg/kg 7d


title: KO+treatment 1

description: extracted total RNA


title: SLX.7179.A006


title: Patient 44, sample B99, Rectum

value: Rectum


title: Patient 44, sample B85, Rectum


title: KO-4

description: extracted total RNA


title: Patient 43, sample B84, Recto-sigmoid junction

source_name: Recto-sigmoid junction

value: Recto-sigmoid junction


title: KO-3

description: extracted total RNA


title: KO-1

description: extracted total RNA


title: HCC515_plusdoxLUCsh_suspension_rep2

city: South San Francisco

first: Anneleen

last: Daemen

state: CA

address: 1 DNA Way

institute: GENENTECH, INC.

description: plusdoxLUCsh suspension

hyb_protocol: 12.5 micrograms of cRNA was fragmented and hybridized to Human Genome U133 Plus 2.0 arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm.

scan_protocol: Arrays were washed and stained using Affymetrix HWS kit using their Fluidics station and then scanned on GeneChip scanner 3000.

data_processing: Microarray data were normalized using the R package RMA from Bioconductor. The annotate R package was used for probe-to-gene mapping, and the most variable probeset per gene was selected using the rowIQR function.

label: biotin

source_name: HCC515 KEAP1-wt LKB1-mut suspension

label_protocol: Preparation of cRNA was done using Affymetrix 3'IVT Express kit and protocol provided by Affymetrix. Briefly, 0.5 ug of total RNA was converted into double-stranded cDNA and used to generate biotin labeled cRNA which was then purified.

growth_protocol: All NSCLC cell lines were maintained in DMEM (Hyclone) supplemented with 10% FBS (Invitrogen) and 1% Penicillin-Streptomycin, 1% HEPES at 37°C in a humidified atmosphere containing 5% CO2. For suspension culture, cells were seeded in poly-HEMA (Sigma–Aldrich, St. Louis, USA) coated plates.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Kit with DNase digestion. RNA was eluted from RNeasy columns using DNase/RNase free water.

treatment_protocol: For lentivirus infection and selection, 106 cells were incubated lentivirus solution containing polybrene (EMD Millipore). The infected cells were selected with 1ug/ml puromycin, or 20ug/ml blasticidin for 1~2 weeks.

value: Lung


title: KO-2

description: extracted total RNA


title: HCC515_plusdoxLKB1plusLUCsh_suspension_rep2

description: plusdoxLKB1plusLUCsh suspension

source_name: HCC515 KEAP1-wt LKB1-wt suspension


title: WT-4

description: extracted total RNA

value: WT


title: HCC515_plusdoxLKB1plusKEAP1shminus1_suspension_rep1

description: plusdoxLKB1plusKEAP1shminus1 suspension

source_name: HCC515 KEAP1-mut LKB1-wt suspension


title: HCC515_plusdoxLUCsh_suspension_rep1

description: plusdoxLUCsh suspension


title: HCC515_minusdoxKEAP1shminus1_suspension_rep1

description: minusdoxKEAP1shminus1 suspension


title: HCC515_plusdoxLKB1plusLUCsh_suspension_rep1

description: plusdoxLKB1plusLUCsh suspension


title: HCC515_plusdoxLKB1plusKEAP1shminus1_suspension_rep2

description: plusdoxLKB1plusKEAP1shminus1 suspension


title: HCC515_minusdoxLUCsh_suspension_rep2

description: minusdoxLUCsh suspension


title: HCC515_plusdoxLKB1plusKEAP1shminus1_baseline_rep2

description: plusdoxLKB1plusKEAP1shminus1 baseline

source_name: HCC515 KEAP1-mut LKB1-wt baseline


title: HCC515_minusdoxKEAP1shminus1_suspension_rep2

description: minusdoxKEAP1shminus1 suspension


title: HCC515_plusdoxKEAP1shminus1_suspension_rep1

description: plusdoxKEAP1shminus1 suspension

source_name: HCC515 KEAP1-mut LKB1-mut suspension


title: Patient 41, sample B75, Left colon

source_name: Left colon

value: Female

value: Left colon


title: HCC515_minusdoxLUCsh_suspension_rep1

description: minusdoxLUCsh suspension


title: Patient 42, sample B83, Cecum

source_name: Cecum

value: Cecum


title: HCC515_plusdoxLKB1plusLUCsh_baseline_rep1

description: plusdoxLKB1plusLUCsh baseline

source_name: HCC515 KEAP1-wt LKB1-wt baseline


title: Patient 42, sample B100, Sigmoid colon

source_name: Sigmoid colon


title: HCC515_plusdoxLKB1plusKEAP1shminus1_baseline_rep1

description: plusdoxLKB1plusKEAP1shminus1 baseline


title: HCC515_plusdoxLKB1plusLUCsh_baseline_rep2

description: plusdoxLKB1plusLUCsh baseline


title: WT-3

description: extracted total RNA


title: WT-2

description: extracted total RNA


title: Patient 43, sample B101, Rectum


title: HCC515_plusdoxKEAP1shminus1_baseline_rep2

description: plusdoxKEAP1shminus1 baseline

source_name: HCC515 KEAP1-mut LKB1-mut baseline


title: WT-1

description: extracted total RNA


title: Patient 40, sample B79, Right colon

source_name: Right colon

value: Right colon


title: Patient 39, sample B73, Left colon


title: Patient 41, sample B76, Right colon


title: Patient 39, sample B74, Rectum

source_name: Rectum


title: Patient 40, sample B80, Right colon


title: HCC515_plusdoxLUCsh_baseline_rep2

description: plusdoxLUCsh baseline

source_name: HCC515 KEAP1-wt LKB1-mut baseline


title: HCC515_plusdoxKEAP1shminus1_suspension_rep2

description: plusdoxKEAP1shminus1 suspension


title: Patient 38, sample B72, Cecum


title: HCC515_plusdoxLUCsh_baseline_rep1

description: plusdoxLUCsh baseline


title: HCC515_minusdoxKEAP1shminus1_baseline_rep1

description: minusdoxKEAP1shminus1 baseline


title: Patient 38, sample B71, Cecum


title: HCC515_minusdoxKEAP1shminus1_baseline_rep2

description: minusdoxKEAP1shminus1 baseline


title: Patient 37, sample B8, Right colon


title: HCC515_plusdoxKEAP1shminus1_baseline_rep1

description: plusdoxKEAP1shminus1 baseline


title: HCC515_minusdoxLUCsh_baseline_rep2

description: minusdoxLUCsh baseline


title: C_3_V

description: extracted total RNA

data_processing: RMA normalization; normalized also per gene to the median

growth_protocol: C. elegans strains were grown and mantained at 20°C. Worms at the desired larval stage (L3) were wash off three big agar plates spotted with the RNAi bacteria under study (nuo-5 and pL4440 for control). The mild RNAi was achieved in the parental generation while the strong effect in the filial generation.

tag: developmental stage


title: C_2_I

description: extracted total RNA

value: nuo-5 RNAi mild


title: C_3_I

description: extracted total RNA


title: C_3_III

description: extracted total RNA


title: Patient 45, sample B86, Sigmoid colon


title: HCC515_minusdoxLUCsh_baseline_rep1

description: minusdoxLUCsh baseline


title: C_2_IV

description: extracted total RNA


title: Patient 37, sample B7, Appendix

source_name: Appendix

value: Appendix


title: C_2_III

description: extracted total RNA


title: Patient 35, sample B66, Sigmoid colon

value: Synchronous colorectal cancer (SCRC)


title: HS_HeLa

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

data_processing:
Quality of the sequenced reads was estimated using FASTQC from the Babraham Institute (Sept.2016).
Adapter trimming using cutadapt and mapping using bwa (aln option – default parameters) was done as described previously [Zovoilis et al, Cell 2016]. The genome assembly used for the alignment was hg19 (Sept. 2016).
Conversion of bam files to genomic coordinates was done using bedtools and subsequently coordinates of the 5’ end were extracted with in house scripts. Repeat annotation files were constructed using the filter utility of UCSC table browser tools against the repeatmasker track of Sept. 2016.
Metagene profiles of the read distribution across the Alu sequences was done using the SeqMonk (Babraham Institute) trend probe plots for mapped reads with the same strand with the Alus. Normalization was done using the relative distribution option.
Genome_build: hg19
Supplementary_files_format_and_content: Read count per position across the Alu RNA consensus sequence and the AluY RNA consensus sequence. Txt files inlcude two columns whith column one representing the position and column 2 the relative distribution counts of the 5 end of each read mapping to these Alu RNAs as produced by SeqMonk. In detail: 5' end genomic co-ordinates of the short-RNA-sequencing reads were extracted using in home text parsing scripts from the bed files created as described in the previous step. The resulting 5 end read files consisting of three columns (1st: Chr name, 2nd: position, 3rd: strand orientation of the reads' 5'end) were mapped and plotted against the Alu repeat start gemonic co-ordinates as defined by Repeat Masker for hg19 using Seqmonk relative distribution probe trend plot.

source_name: HeLa Cells

growth_protocol: HeLa cells were cultured in DMEM supplemented with Glutamax (Life Technologies) supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin.

extract_protocol:
Cell pellets were directly resuspended into Trizol (Thermofischer) for the RNA-seq analysis following the extraction protocol recommended by the manufacturer.
We used a modified version of small RNA-seq called short-RNAseq described in detail in Zovoilis et al, Cell 2016. In brief, after enrichment for shorter fragments , samples were treated with T4 ploynucloetide kinase  and subsequently libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible) from NEB.

treatment_protocol: Before heat shock stimulus cells were trypsinized and resuspended in 5ml complete medium in a 15ml falcon tube. Subsequently, cells were placed in 45ºC  for 15 min. After the end of this 15 minutes period, cells were centrifuged shortly (2min)

value: HeLa

value: heat shock


title: Patient 35, sample B65, Sigmoid colon

value: Male

value: Sigmoid colon


title: Patient 36, sample B69, Right colon


title: C_1_V

description: extracted total RNA

source_name: nematodes pellet, RNA extracted

value: N2, L3 larval stage


title: Patient 36, sample B70, Rectum


title: ME-180_X-ray_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:
MEX
ME180.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: cervical carcinoma

tag: race

value: Caucasian


title: Patient 34, sample B67, Rectum

value: Rectum


title: ME-180_control

description:
MEN
ME180.fpkm_tracking


title: Patient 33, sample B62, Right colon


title: Patient 34, sample B68, Right colon


title: C_3_IV

description: extracted total RNA

value: nuo-5 RNAi strong


title: pUbi-OsNAR2.1 transgenic line MeDIP-seq

city: Nanjing, Jiangshu Province

first: Xiaorong

last: Fan

state: Jiangshu

address: Tongwei Road 1

country: China

institute: Nanjing Agricultural University

description:
MeDIP_Peak Annotation.xlsx
pUbi-OsNAR2.1

library_source: genomic

data_processing:
Whole-genome bisulfite sequencing
After downloading raw data from sequencing machine, in order to avoid alignment error, the raw reads will be filtered and trimmed to obtain clean reads. First, remove polluted adapter reads (remove the reads with the number of contaminants in the base more than 5bp) . Second, remove the reads with base calling quality Qemo), and third, remove reads with the percentage of N >5% (For pair-end sequencing, if one end is removed, both ends will be removed). After filtering, the available data were compared with the reference genome Oryza_sativa.IRGSP-1.0.32 to obtain the alignment results using Bismark (v0.9.0) (K Felix, et al. 2011).  The uniquely mapped reads will be used to call the methylated cytosines(C) in highly enriched regions.Valid coverage of methylated cytosine, i.e. the percentage of methylated C among all C on genome, is associated with methylation level. C sites with read depths less than 5 are eliminated firstly. Then for each C site, valid coverage is calculated by for all C or C within each pattern (CpG, CGH, and CHH). Coverage is the count of C sites with more than 5 depth divided by total number of C site by its pattern. For each C site, the methylation level (%) is calculated by: 100* (reads supportted methylation)/ (total reads depth of this site). For methylated region, methylation level (%) is calculated by: 100*methylation level of all C sites in this region/Total number of C sites in this region. The conversion ratio of  Lambda DNA is around 99.5% to 99.6% in all samples.
MeDIP sequecing
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). After passing Solexa CHASTITY quality filter, the clean reads were aligned to rice genome (Ensembl Plants Oryza sativa Japonica, IRGSP-1.0) using BOWTIE software (V2.1.0, B Langmead, et al. 2012). MeDIP peaks were identified by MACS2(Zhang et al 2008), and statistically significant MeDIP-enriched regions (peaks) were identified by comparison to a Poisson background model (Cut-off q-value=10-2). Differentially Methylated Regions (DMRs) in MeDIP dataset was identified by diffReps(Shen et al 2013) (p < 0.0001), and promoter-associated DMRs were annotated with IRGSP-1.0 database.
Genome_build: IRGSP1
Supplementary_files_format_and_content: Processed data were stored in excel files, which included differentially methylated regions from WGBS and enriched peaks from MeDIP.

organism: Oryza sativa

source_name: DNA methylation of pUbi-OsNAR2.1

growth_protocol: We grew plants water for 10 days after germination. The Nipponbare WT (NP), OsNAR2.1 RNAi and  pUbi-OsNAR2.1 lines for MEDIP-seq were  grown in plots at Nanjing Agricultural University in Nanjing, Jiangsu, 2014. Nanjing, Jiangsu is in a subtropical monsoon climate zone. Chemical properties of the soils in the plots included organic matter, 11.56 g/kg; total N content, 0.91 g/kg; available P content, 18.91 mg/kg; exchangeable K, 185.67 mg/kg; and pH 6.5. Basal applications of 30 kg P/ha (Ca(H2PO4)2) and 60 kg K/ha (KCl) were made to all plots 3 days before transplanting. N fertilizer as urea accounted for 40%, 30% and 40% of the total N fertilizer was applied prior to transplanting, at tillering, just before the heading stage, respectively.

extract_protocol:
Genomic DNA were extracted from 10-day-old seedlings, and shipped to the Anoroad Genome company(Beijing) for whole-genome bisulfite sequencing(WGBS). WGBS librarie preparation, sequencing and data analysis was described as before. WGBS libraries are prepared for subsequent cluster generation starting from sample DNA through adaptor ligation, library purification, and quantification. Input gDNA (5 μg) is fragmented by sonication. The fragments are blunt-ended and phosphorylated, and a single ʹAʹ nucleotide is added to the 3ʹ ends of the fragments in preparation for ligation to a methylated adapter that has a single-base ʹTʹ overhang. The ligation products are purified and size-selected by agarose gel electrophoresis. Size-selected DNA is bisulfite-treated and purified. The treated DNA is PCR-amplified to enrich the fragment that have adapters on both ends. The final purified product is then quantitated prior to cluster generation. The WGBS libraries will be sequenced using Illumina HiSeq2500 /4000 Analyzer according to the manufacturer’s instructions.
MeDIP sequecing in this study done by KangChen Bio-tech, Shanghai, China. Sequencing library preparation and data analysis was described as before (Ding et al 2015 ). Genomic DNA was sonicated to ~200 - 600bp with a Bioruptor sonicator (Diagenode). 800 ng of sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina genomic DNA protocol. After agarose size-selection to remove unligated adapters, the adaptor-ligated DNA was used for immunoprecipitation using a Rat monoclonal anti-5-methylcytosine antibody (Diagenode). For this, DNA was heat-denatured at 94°C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μL primary antibody overnight at 4°C with rocking agitation in 400 μL immunoprecipitation buffer (0.5% BSA in PBS). To recover the immunoprecipitated DNA fragments, 100 μL of protein G magnetic beads (Life Technologies) were added and incubated for an additional 2 hours at 4°C with agitation. After immunoprecipitation, a total of five immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. A nonspecific Rat IgG immunoprecipitation was performed in parallel to methyl DNA immunoprecipitation as a negative control. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg/mL proteinase K for 2 hours at 65°C and then allowed to cool down to room temperature. MeDIP and supernatant DNA were purified using Qiagen MinElute columns and eluted in 16 μL EB (Qiagen). 14 cycles of PCR were performed on 5 μL of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (300-700 bp) was performed by electrophoresis in 2% agarose. Libraries were quality controlled by Agilent 2100 Bioanalyzer. An aliquot of each library was diluted in EB to 5 ng/μL and 1 μL was used in real-time PCR reactions to confirm the enrichment for methylated region.

value: first blade, culm and panicles in anthesis stage


title: Patient 33, sample B61, Right colon


title: mTAIL-seq DKO2

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

description: mTAIL-seq for DKO2

data_processing:
The base calls and signal intensities were processed by RTA 1.17.28 for MiSeq. The read 1 corresponds to R5 (5' read, 51 bp) and read 2 to R3 (3' read, 251 bp), respectively. The read 1 sequences were reanalyzed for more sensitive basecalling using AYB 2. The read 1 sequences were aligned to the common contaminants set, which is composed of rDNA repeat units (GenBank accession U13369.1), PhiX genome (GenBank accession J02482.1), Illumina TruSeq primer sequences, and all sequences for 5S and 5.8S rRNAs of respective species (retrieved from Rfam 11.0 of the Wellcome Trust Sanger Institute) using GSNAP 2013-03-31 with maximum 5% mismatches allowed. Clusters with any match to the contaminants were removed from the subsequent analyses. The sequences having completely identical nucleotides in the 21st to 35th cycle in read 1 (representative region of the insert) and the 1st to 15th cycle in read 2 (degenerate bases in 3′ adapter) are deduplicated by leaving only a cluster with the maximum PHRED quality sum of read 1. The degenerate and fixed delimiter sequence in 3′ adapter was clipped out from read 2 by searching perfect match of delimiter sequence (‘GTCAG’ as in the direction of read 2) between the 14th and 16th cycles in read 2. The clusters missing a delimiter sequence or having low diversity in degenerate region (at least two occurrences for all of A, C, G and T) were removed from further analyses.
The fluorescence signal intensities were processed into “Relative T signal” as described in our previous paper (Chang et al, 2014). The signals from a spike-in sample were purified with an outlier filter based on robust Mahalanobis distance (mvoutlier package 1.9.9; quan=0.5, alpha=0.025). Random 500 clusters per each spike-in were chosen for parameter calculation of a Gaussian mixture hidden Markov model (GMHMM). We trained the model using Baum-Welch algorithm implemented in the GHMM library (http://ghmm.org) with topology and initial parameters shown in fig. S1A and table S7 and S8 (1,000 iterations). The procedure was iterated to maximize likelihood, not using any property (eg. designed length of poly(A) tail) of spike-ins. Relative T signals outside the range of [-5, 5] were clipped into the range for both training and later calculations.
The remaining reads after contaminant filter and the first duplication filters were then aligned to the genome sequences (UCSC mm10, positions of splicing junctions were processed from the UCSC Genome Browser database for version of Jan 24, 2013) using GSNAP 2013-03-31. Three different versions of alignments to genome were used in this study. (1) Read 1 (R5) alignment: using only the full read 1 sequences which are 51 nt long. This was used for identification of a cluster. (2) Read 2 (R3) short alignment: using only 40 nt right next to the 3′ adapter of read 2. This was used in searching for the poly(A)-free 3′ hydroxyl ends. (3) paired alignment: using the full read 1 sequences and part of read 2 sequences trimmed of degenerate bases and delimiter. We filtered out poly(A) stretches encoded from genome using this alignment set. All the alignments were performed with maximum mismatches of 5%, minimum mapping quality of 3. All multi-mapped reads were removed. The remaining PCR artifacts with few mismatches were removed again using the R1 alignment with 15 degenerate bases inside the 3′ adapter region. To detect that kind of artifacts, we clustered the R1 alignments with maximum distance between mapped positions of 10 bp, they were then clustered again within the first cluster using degenerate bases from read 2 of respective reads with CD-HIT-EST 4.5.4 (word size=6, sequence identity=0.85). For a set of detected duplicates, we chose a read with maximum sum of PHRED quality in read 1 to leave.
For classification and transcript-level analyses, we compiled reference annotations for human and mouse using NCBI RefSeq, RepeatMasker, gtRNAdb, Rfam and miRBase databases (the first three were downloaded from the UCSC Genome Browser on Apr 25, 2013; Rfam version 11; miRBase version 19). The R1 alignments were annotated with intersection with the compiled annotations using BEDTools. When multiple annotations were overlapped to an alignment, we chose a class for the statistics requiring exclusive assignment of a genomic source type by the following priority: miRNA, rRNA, tRNA, Mt-tRNA, snoRNA, scRNA, srpRNA, snRNA, lncRNA, RNA, ncRNA, misc_RNA, Cis-reg, ribozyme, RC, IRES, frameshift_element, LINE, SINE, Simple_repeat, Low_complexity, Satellite, DNA, LTR, CDS, 3′ UTR, 5′ UTR, intron, Other, Unknown (higher priority first). The transcript-level analyses were performed using our custom non-redundant RefSeq (nrRefSeq) transcript set, which is a reduced set retaining only the longest isoform or transcript when regions overlap with each other. The positions of read 1 in nrRefSeq transcripts were positioned with BEDTools intersection between alignments to genome sequences and nrRefSeq annotation set, and then translated to the transcript-level coordination with in-house software.
As poly(A) tails were initially detected with a constraint that it must begin within the first 30 cycles, so the maximum detectable 3′ end modification of poly(A) tails was limited to the last 30 nucleotides of insert. To exclude A stretches obviously encoded from genomic sequence (with or without 3′ end modifications), we masked detected poly(A) tail ranges with read 2 alignments so that the 3′-most position of alignable (not clipped) is eliminated from poly(A) tail or its 3′ end modifications. All statistics regarding transcript-level modification rates were calculated for transcripts having more than 200 tags with poly(A) tails longer than 8 nt.
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: The all.txt, mapped.txt and association.txt file are output files of tailseeker3 with the untemplated tail informtion of the RNA fragment. The first two columns represent the tile and cluster id of the RNA fragment. The third column of the association.txt file is the ensembl gene id. The sixth column of the all.txt and mapped.txt file is the estimated poly(A) tail length and the last column is the untemplated tail sequence. The mapped.txt file only contains RNA fragments from all.txt that are mapped to the genome. The stats.csv files contain genelevel stats of poly(A) tail length and 3' end modification frequencies.

organism: Mus musculus

source_name: Naïve T cells

growth_protocol: Naive CD4 T cells (TCRb+CD4+CD25-CD62LhiCD44low) from two pairs of WT and DKO mice were isolated by FACS sorting.

extract_protocol:
Total RNAs were extracted by RNA Bee (Amsbio, CS-501B) according to manufacturer’s instruction..
mTAIL-seq was performed as previously described. Briefly, ~500 ng of total RNA was ligated to the 3′ hairpin adaptor and partially fragmented by RNase T1 (Ambion, AM2283). The fragmented RNAs were pulled-down with C1 streptavidin beads (Invitrogen, 65001), 5′ phosphorylated by PNK (NEB, M0201L), cleaved by APE1 (NEB, M0282S), and purified by RNAClean XP beads (Beckman Coulter, A63987). The purified RNAs were ligated to the 5′ adaptor, reverse transcribed, and amplified by PCR.

value: naive T cells

tag: surface marker

value: BTG1/2 double KO, Btg1f/f Btg2f/f-CD4-Cre


title: mTAIL-seq DKO3

description: mTAIL-seq for DKO3


title: OsNAR2.1RNAi MeDIP-seq

description:
MeDIP_Peak Annotation.xlsx
RNAi

source_name: DNA methylation of OsNAR2.1RNAi


title: C_1_III

description: extracted total RNA

value: WT


title: C_2_V

description: extracted total RNA


title: Nipponbare MeDIP-seq

description:
MeDIP_Peak Annotation.xlsx
NP

source_name: DNA methylation of NP


title: mTAIL-seq DKO1

description: mTAIL-seq for DKO1


title: mTAIL-seq WT3

description: mTAIL-seq for WT3

value: Wildtype (littermate control), Btg1f/f Btg2f/f


title: C_1_IV

description: extracted total RNA


title: C_1_I

description: extracted total RNA


title: Patient 32, sample B63, Cecum

value: Female

value: Cecum


title: mTAIL-seq WT2

description: mTAIL-seq for WT2


title: mTAIL-seq WT1

description: mTAIL-seq for WT1


title: Patient 31, sample B56, Terminal ileon

source_name: Terminal ileon

value: Synchronous colorectal cancer (SCRC)

value: Terminal ileon


title: Patient 31, sample B55, Sigmoid colon


title: Patient 28, sample B51, Cecum


title: Patient 30, sample B60, Right colon

value: Right colon


title: Patient 29, sample B57, Right colon


title: Subject 24 120 min after GH administration

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

description: Gene expression data

hyb_protocol: Affymetrix hybridization kit, hybridize 16 hours at 45° at 60rpm to the GeneChip® Human Gene 2.0 ST Array

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX 13. RMA16 algorithm was used for normalization

source_name: Adipose tissue biopsy

label_protocol: 100 ng total RNA was labeled using the Ambion® WT Expression Kit (Ambion)

extract_protocol: TRIzol extraction

treatment_protocol: Subjects were studied in random order on two occasions after an overnight fast for 12 hours receiving an intravenous bolus of either GH (0.5 mg (Genotropin miniquick, Pfizer) or saline.

tag: gender

value: Male


title: Subject 24 120 min after saline administration

description: Gene expression data


title: Patient 29, sample B58, Sigmoid colon

value: Sigmoid colon


title: Patient 27, sample B54, Recto-sigmoid junction

source_name: Recto-sigmoid junction

value: Recto-sigmoid junction


title: Patient 27, sample B53, Sigmoid colon


title: Patient 30, sample B59, Right colon


title: Subject 22 120 min after GH administration

description: Gene expression data


title: Patient 28, sample B52, Right colon


title: Patient 26, sample B5, Right colon


title: Patient 26, sample B6, Right colon


title: Subject 21 120 min after GH administration

description: Gene expression data


title: Subject 22 120 min after saline administration

description: Gene expression data


title: Subject 18 120 min after GH administration

description: Gene expression data


title: Subject 18 120 min after saline administration

description: Gene expression data


title: Patient 25, sample B49, Left colon

source_name: Left colon

value: Left colon


title: Subject 21 120 min after saline administration

description: Gene expression data


title: Subject 8 120 min after GH administration

description: Gene expression data


title: Subject 8 120 min after saline administration

description: Gene expression data


title: Patient 24, sample B47, Rectum


title: Patient 23, sample B46, Sigmoid colon

source_name: Sigmoid colon


title: Patient 22, sample B44, Right colon


title: Patient 24, sample B48, Sigmoid colon


title: etoposide resistant K562 cells (K/VP.5)-3

city: Columbus

first: Hatice Gulcin

last: Ozer

state: OH

address: 1800 Cannon Dr

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
3′ adaptor sequences and low quality bases were trimmed from 75 base pair paired-end sequence reads using Cutadapt v2.4 (Martin, 2011).
Trimmed reads with a sequence length between 15 and 50 base pairs were aligned to potential contaminant sequences of human genome (ribosomal RNAs and tRNAs) using Bowtie v1.1.2 (Langmead et al., 2009) with a seed length of 18 and allowing zero mismatches in the seed.
Remaining reads were aligned to miRbase (Griffiths-Jones, 2004) v21 mature sequences using Bowtie v1.1.2 with a seed length of 18, allowing 1 mismatch in seed and reporting maximum 5 alignments per read.
Remaining reads were aligned to human reference genome, GRCh38, using Bowtie v1.1.2 with a seed length of 18, allowing 1 mismatch in seed and reporting only unique alignments for each read.
Using Samtools (Li et al., 2009) and in-house R scripts, total number of reads for each mature miRNA was counted.
Genome_build: miRbase v21
Genome_build: GRCh38
Supplementary_files_format_and_content: Microsoft Excel file with raw read counts for each mature miRNA sequence and human reference gene

source_name: myelogenous leukemia cell line

growth_protocol: Human K562 leukemia cells were maintained in DMEM supplemented with 10% fetal bovine serum. Cloned etoposide resistant K562 cells (K/VP.5) were generated by continuous incubation in 0.5 µM etoposide followed by isolation via limiting dilution, as previously described (Ritke and Yalowich, 1993). K/VP.5 cells were maintained in DMEM/10% FBS with 0.5 µM etoposide added every other week. All experiments described below were performed utilizing K562 and K/VP.5 cells growing in log phase.

extract_protocol:
A mirVana miRNA Isolation Kit with phenol was used to isolate total RNA from K562 and K/VP.5 cells. The total RNA was subsequently DNase I treated and concentrated on a spin-column.
NEB Next Small RNA libraries were prepared form the purified K562 and K/VP.5 total RNA samples and the libraries were size selected using Sage Pippin (130-200 bp range, adapters are ~128 bp) with an average final library size of 180 bp and sequenced on MiniSeq as 2 x 75 bp reads.  3′ adaptor sequences and low quality bases were trimmed from 75 base pair paired-end sequence reads using Cutadapt v2.4 (Martin, 2011). Trimmed reads with a sequence length between 15 and 50 base pairs were aligned to potential contaminant sequences of human genome (ribosomal RNAs and tRNAs) using Bowtie v1.1.2 (Langmead et al., 2009) with a seed length of 18 and allowing zero mismatches in the seed. Then, remaining reads were aligned to miRbase (Griffiths-Jones, 2004) v21 mature sequences using Bowtie v1.1.2 with a seed length of 18, allowing 1 mismatch in seed and reporting maximum 5 alignments per read. Finally, remaining reads were aligned to human reference genome, GRCh38, using Bowtie v1.1.2 with a seed length of 18, allowing 1 mismatch in seed and reporting only unique alignments for each read. Using Samtools (Li et al., 2009) and in-house R scripts, total number of reads for each mature miRNA was counted.

value: etoposide resistant K562 cells (K/VP.5)


title: Subject 6 120 min after saline administration

description: Gene expression data


title: etoposide resistant K562 cells (K/VP.5)-4


title: etoposide resistant K562 cells (K/VP.5)-2


title: etoposide resistant K562 cells (K/VP.5)-1


title: Patient 32, sample B64, Sigmoid colon


title: Subject 6 120 min after GH administration

description: Gene expression data


title: K562 cells-4

value: K562 cells


title: Patient 25, sample B50, Left colon


title: Subject 2 120 min after saline administration

description: Gene expression data


title: Patient 22, sample B43, Left colon


title: Subject 1 120 min after saline  administration

description: Gene expression data


title: Subject 2 120 min after GH administration

description: Gene expression data


title: Patient 21, sample B42, Rectum

value: Rectum


title: Patient 21, sample B41, Rectum


title: K562 cells-2


title: ScxKO14D-3

city: New York

first: Christopher

middle: L

last: Mendias

state: NY

address: 535 E 70th St

institute: Hospital for Special Surgery

data_processing:
Quality assessment and fold change calculations were performed in DESeq2
Sequencing data was quality checked using FastQC, aligned to the reference genome (mm10, UCSC, Santa Cruz, CA, USA) with the STAR software package
Differential expression based on FKPM was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2

source_name: Plantaris tendon

extract_protocol:
RNA was purified with a miRNeasy Micro Kit (Qiagen) supplemented with DNase I (Qiagen). RNA concentration was determined using a NanoDrop 2000 (Thermo Fisher). For each sample, 250ng of RNA was delivered to the University of Michigan Sequencing Core for RNA sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Scx-

tag: tamoxifen treatment

value: Yes


title: K562 cells-1


title: K562 cells-3


title: ScxKO14D-2


title: ScxKO14D-1


title: Joanna_Gell_UCLA2_iMeLC_d1_hPGCLC_d4_EChPGCLC_D4C10_rep2_2019

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

description: UCLA2_D4C10_exPGCLC WGBS replicate 2

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: UCLA2 hESCs

extract_protocol:
NuGen, Ovation Ultralow Methyl-Seq Library Sytem 1-6, 0535-32
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 21


title: Patient 20, sample B39, Left colon

tag: Sex


title: Patient 19, sample B38, Sigmoid colon


title: Subject 1 120 min after GH  administration

description: Gene expression data


title: Joanna_Gell_UCLA2_iMeLC_d1_hPGCLC_d4_EChPGCLC_D4C10_rep1_2019

description: UCLA2_D4C10_exPGCLC WGBS replicate 1

tag: cell type

value: passage 20


title: ScxWT14D-4

value: Scx+


title: ScxKO14D-4


title: ScxWT14D-3


title: ScxWT14D-2


title: Joanna_Gell_UCLA2_iMeLC_d1_hPGCLC_d4_rep1_2019

description: UCLA2_D4_PGCLC WGBS replicate 1

value: passage 17


title: Patient 20, sample B40, Rectum

source_name: Rectum

tag: disease status

value: Synchronous colorectal cancer (SCRC)

value: Female


title: Joanna_Gell_UCLA2_iMeLC_d1_hPGCLC_d4_rep2_2019

description: UCLA2_D4_PGCLC WGBS replicate 2

value: passage 18


title: Patient 17, sample B29, Left colon

tag: patient pair number

value: Male


title: Patient 18, sample B3, Rectum

tag: age at diagnosis


title: Patient 18, sample B4, Right colon

source_name: Right colon

value: Right colon


title: ScxWT14D-1


title: ScxKO7D-4


title: Joanna_Gell_UCLA2_hESC_rep1_2019

description: UCLA2 hESC WGBS replicate 1

tag: cell line


title: ScxKO7D-3


title: ScxKO7D-2


title: Patient 17, sample B28, Left colon


title: ScxKO7D-1


title: ASC_NTAPP_9h

first: Kiwon

last: Song

address: Yonsei-ro 50

institute: Yonsei University

data_processing:
Preprocessed reads were matched to reference genome sequence using HISAT2 program and then aligned reads were generated.
After overall read mapping, StringTie program was used for the transcript assambly.
Expression profile was exported by normalized FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Differentially expressed genes included in two or more groups were selected through statistical verification.
Fusion genes were predicted using the defuse program.
Genome_build: USCS hg 19

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:
NTAPP-exposed and unexposed ASCs were collected and their total RNA was extracted using the Rneasy Mini kit.
RNA libraries were prepared with TruSeq Stranded mRNA sample preparation guide (Part # 15031047 Rev.E)

treatment_protocol: 3 × 10^4 ASCs were seeded in 35-mm culture dishes and incubated for 16 h for ASCs. Cells 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.

tag: passage

value: Human adipose tissue-derived stem cells


title: Joanna_Gell_UCLA2_hESC_rep2_2019

description: UCLA2 hESC WGBS replicate 2


title: Patient 16, sample B31, Rectum


title: Patient 23, sample B45, Left colon

value: Left colon


title: Patient 15, sample B27, Right colon


title: Patient 16, sample B30, Sigmoid colon

value: Sigmoid colon


title: ASC_unexposed_9h


title: ScxWT7D-3


title: ScxWT7D-2


title: P1120715H08 [PBMCs_RNA-seq]

description: P1120715H08_P1_120715_H08_HNGVFCCXX_L6_1

source_name: PBMCs_post-vaccination respons for pneumococcal vaccine (PPSV23)

tag: time point (mmddyy_hhh)

value: blood

value: Peripheral Blood Mononuclear Cell (PBMC)


title: Patient 14, sample B23, Transverse colon

source_name: Transverse colon

value: Transverse colon


title: ScxWT7D-4

tag: genotype

value: Yes


title: Patient 19, sample B37, Sigmoid colon


title: ASC_unexposed_24h


title: Patient 14, sample B24, Sigmoid colon


title: P1110915H08 [PBMCs_RNA-seq]

description: P1110915H08_P1_110915_H08_HNH7KCCXX_L1_1


title: Patient 15, sample B26, Right colon


title: ScxWT7D-1


title: P1101215H08 [PBMCs_RNA-seq]

description: P1101215H08_P1_101215_H08_HW5LCCCXX_L7_1


title: NOC3

value: No


title: P1091415H08 [PBMCs_RNA-seq]

description: P1091415H08_P1_091415_H08_HW5LCCCXX_L7_1


title: ASC_NTAPP_24h


title: NOC2


title: Patient 13, sample B21, Distal transverse colon

source_name: Distal transverse colon

value: Distal transverse colon


title: Patient 12, sample B19, Transverse colon


title: Patient 12, sample B20, Left colon


title: Patient 13, sample B22, Left colon


title: P1081015H08 [PBMCs_RNA-seq]

description: P1081015H08_P1_081015_H08_HVNVKCCXX_L4_1


title: NOC1


title: P1070615H08 [PBMCs_RNA-seq]

description: P1070615H08_P1_070615_H08_HNHC7CCXX_L6_1


title: Patient 11, sample B18, Right colon


title: P1052615H08 [PBMCs_RNA-seq]

description: P1052615H08_P1_052615_H08_HNHC7CCXX_L6_1

source_name: PBMCs_pre-vaccination respons for pneumococcal vaccine (PPSV23)


title: Patient 10, sample B16, Sigmoid colon


title: Patient 11, sample B17, Sigmoid colon


title: P1031416H08 [PBMCs_RNA-seq]

description: P1031416H08_P1_031416_H08_HW5LCCCXX_L1_1


title: Patient 9, sample B14, Left colon


title: Patient 10, sample B15, Sigmoid colon


title: P1072015H08 [PBMCs_RNA-seq]

description: P1072015H08_P1_072015_H08_HVNVKCCXX_L3_1


title: 20180810_7423: mES_GFP-bcatenin_GFP

first: Alicia

middle: Viridiana

last: Zamudio

state: MA

address: 455 Main St

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
Reads were aligned to the mm9 mouse reference genome using Bowtie  version 1.2.2 with parameters  -p 4 --best -k 1 -m 1 --sam -l 40.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Embryonic stem cell

growth_protocol: V6.5 mouse embryonic stem (ES) cells were cultured in serum-free 2i media (1:1 of DMEM/F-12 and Neurobasal media, supplemented with 1x N-2 supplement, 1x B-27 supplement, 100 U/ml PenStrep, 3 μg/ml AlbuMAX II, 1x MEM NEAA, 1mM Sodium pyruvate, 1mM L-glutamine (all from Thermo Fisher Scientific), 0.1 μM 2-Mercaptoethanol (Sigma- Aldrich), 1mM MEK inhibitor (PD0325910, Stemgent), 3mM GSK3β inhibitor (CHIR99021, Stemgent) and 100 U/ml LIF (Leukemia Inhibitory Factor, EMD Millipore) without feeder cells). Prior to cell culturing, all the flasks or petri dishes were incubated in 37°C for more than 5 hours with 5 μg/ml poly-L-ornithine (PLO, Sigma) in 1x PBS buffer, followed by 5 μg/ml Laminin (VWR) in 1x PBS buffer with >5 hours incubation in 37°C. The cells were grown in 37°C incubator maintaining 5% CO2 in a water-saturated atmosphere. Cell culture media were exchanged every 24 hours.

extract_protocol:
Cells were crosslinked on plates with 1% formaldehyde in media for 15 minutes at room temperature. 50 million cells were used per ChIP reaction. Whole cell extracts were sonicated on a QSonica Q700 tip sonicator to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Library construction was performed by the Whitehead Institute Genome Technology Core using the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit according to manufacturer's protocol.

treatment_protocol: Cells were treated with 1 ug/mL doxycicline to induce expression of piggy bac proteins.

value: V6.5 mouse embryonic stem (ES) cells

tag: chip antibody

value: GFP (Abcam ab290)


title: 20180810_7425: mES_GFP-bcatenin_MED1

value: MED1 (Abcam ab64965)


title: 20190523_8100: mES_GFP-chimera_GFP

value: Piggy Bac GFP-chimera


title: P1030315H08 [PBMCs_RNA-seq]

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

institute: Michigan State University

description: P1030315H08_P1_033015_H08_HNHC7CCXX_L6_1

tag: tissue


title: P1071315H08 [PBMCs_RNA-seq]

description: P1071315H08_P1_071315_H08_HVMT7CCXX_L6_1


title: P1011116H08 [PBMCs_RNA-seq]

description: P1011116H08_P1_011116_H08_HVVFLCCXX_L3_1


title: 20190523_8101: mES_GFP-armadillo_GFP

value: Piggy Bac GFP-armadillo


title: 20190523_8102: mES_GFP-bcatenin_GFP


title: Patient 9, sample B13, Right colon

value: Synchronous colorectal cancer (SCRC)


title: P1120715H08 [saliva RNA-seq]

description: P1120715H08_S1_120715_H08_HVLV5CCXX_L6_1

data_processing:
Data QC using FastQC, and reads trimmed 15 from the left and 15 from the right
Trimmed paired reads mapped using Tophat 2.0.13 (using --no-coverage-search --library-type fr-firststrand)
Mapped files quantitated using Cufflinks (--no-effective-length-correction, using hg38 annotation)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample corresponding to Cufflinks output.

source_name: saliva_post-vaccination respons for pneumococcal vaccine (PPSV23)

growth_protocol: Saliva RNA sequencing: Saliva was collected from the subject in an Oragene RNA sample tube (DNAGenotek). Approximately 2ml were selected and stabilized with the Oragene kit solution. Samples were inclubated in the lab at 60 degrees, aliquoted in 2ml tubes and stored at -80C until processing.

extract_protocol:
For RNA-Seq, total RNA was extracted using the Qiagen RNeasy kit (Qiagen) and treated with RNAse-free DNase (Qiagen). RNA integrity was checked on a Bioanalyzer 2100 (Agilent, Santa Clara CA)
Libraries were constructed by Novogene, using a Eukaryotic directional  mRNA  library (NEB).  cDNA preliminary concentration was quantitated on a Qubit (Life Technologies), an Agilent Bioanalyzer 2100 was used to test the insert size, and Q-PCR was used to quantify the library effective concentration precisely.

value: Saliva


title: P1021516H08 [PBMCs_RNA-seq]

description: P1021516H08_P1_021516_H08_HNJGJCCXX_L8_1

data_processing:
Data QC using FastQC, and reads trimmed 13 from the left and 13 from the right
Trimmed paired reads mapped using Tophat 2.0.13 (using --no-coverage-search --library-type fr-firststrand)
Mapped files quantitated using Cufflinks (--no-effective-length-correction, using hg38 annotation)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample corresponding to Cufflinks output.


title: Patient 8, sample B98, Right colon

data_processing: CEL files were processed using the Affymetrix OncoScan console (version 1.3) and the Affymetrix ChAS software (version 3.2.0.1252).

value: Female

value: Right colon


title: P1110915H08 [saliva RNA-seq]

description: P1110915H08_S1_110915_H08_HVMY3CCXX_L3_1


title: Patient 6, sample B12, Left colon

value: Male

value: Left colon


title: P1101215H08 [saliva RNA-seq]

description: P1101215H08_S1_101215_H08_HVMKYCCXX_L3_1


title: J23_J20_WT_06m

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital, Barrack Rd

institute: University of Exeter Medical School

data_processing:
Raw files were demultiplexed into FASTQ files (Phred (Q) ≥ 35) and checked for potential contamination
The randomized FASTQ files underwent quality control (QC) assessments using FastQC
Trimming (ribosomal sequences removal, quality threshold 20, minimum sequence length 35) was performed with FastqMcf
Trimmed samples were aligned to the mm10 (GRCm38.p4) reference mouse genome using STAR
Gene expression quantification was achieved using featureCounts
Read counts were analysed for differential expression in R (version 3.4.3) using the R package DESeq2 (version 1.16.1)
Data sets were filtered for non-expressed and lowly expressed genes (minimum of 6 counts across all samples)
Genome_build: mm10 (GRCm38.p4)
Supplementary_files_format_and_content: Format: .csv; Content: output from featureCounts (i.e., DESeq2 input) containing gene expression levels for each gene (rows) in each sample (columns)

source_name: Entorhinal cortex

growth_protocol: rTg4510 mice, licensed from the Mayo Clinic (Jacksonville, FL, USA), were bred on a mixed 129S6/SvEvTac + FVB/NCrl background (heterozygous tau responder x heterozygous tTA effector). Bi-transgenic (here referred as TG) female mice and littermate controls (here identified as WT), 2, 4, 6 and 8 months-old (n = 9-10 animals per group), were used for this study. J20 mice, licensed from Gladstone Institute (San Francisco, California, United States), with founder mice purchased from MMRRC at The Jackson Laboratory (Bar Harbor, Maine, United States), were bred on a C57BL/6JOlaHsd background (parental generation: hemizygous male x wild type female). Hemizygous (here identified as TG) females and littermate controls (WT), 6, 8, 10 and 12 months of age (n = 9-10 animals per group), were used for this study. Animals were housed under standard conditions (constant temperature and humidity) with a 12h light/dark cycle in individually ventilated cages, with free access to food (Teklad irradiated global rodent diet (Envigo, United Kingdom)) and water.

extract_protocol:
Total RNA from all samples was isolated from the entorhinal cortex using the AllPrep DNA/RNA Mini Kit (Qiagen)
Stranded-specific mRNA sequencing libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) using the Bravo Automated Liquid Handling Platform (Agilent). cDNA libraries were prepared from ~450ng of total RNA plus ERCC spike-in synthetic RNA controls (Ambion, dilution 1:100). Final library pools were sequenced on a HiSeq2500 (Illumina) using 125bp paired-end reads at a mean untrimmed read depth of ~20 million reads/sample

treatment_protocol: Mice were terminally anaesthetized with pentobarbital (intraperitoneal injection) and transcardially perfused with phosphate-buffered saline (PBS). The entorhinal cortex was dissected from the left brain hemisphere on wet ice and snap-frozen on dry ice for subsequent RNA-seq analysis

value: Entorhinal cortex

tag: genotype/variation

value: Wild Type


title: P1091415H08 [saliva RNA-seq]

description: P1091415H08_S1_091415_H08_HNJT7CCXX_L7_1


title: Patient 7, sample B118, Rectum

value: Rectum


title: Patient 7, sample B36, Anus

source_name: Anus

value: Anus


title: J21_J20_WT_12m


title: Patient 8, sample B122, Right colon


title: P1081015H08 [saliva RNA-seq]

description: P1081015H08_S1_081015_H08_HVMY3CCXX_L2_1


title: P1072015H08 [saliva RNA-seq]

description: P1072015H08_S1_072015_H08_HVVG5CCXX_L7_1


title: J20_J20_TG_10m


title: J24_J20_TG_06m


title: J22_J20_TG_12m


title: Patient 4, sample B107, Left colon


title: J19_J20_WT_10m


title: P1071315H08 [saliva RNA-seq]

description: P1071315H08_S1_071315_H08_HWCHMCCXX_L4_1


title: J17_J20_WT_08m


title: Patient 6, sample B11, Left colon


title: Patient 5, sample B109, Sigmoid colon

value: Sigmoid colon


title: Patient 4, sample B108, Left colon


title: Patient 5, sample B110, Sigmoid colon


title: Patient 3, sample B106, Rectum


title: I20_J20_TG_08m


title: Patient 2, sample B9, Right colon


title: H24_J20_TG_10m


title: Patient 3, sample B103, Rectum


title: H23_J20_WT_10m


title: P1070315H08 [saliva RNA-seq]

description: P1070315H08_S1_070315_H08_HW5J7CCXX_L4_1


title: H21_J20_WT_08m


title: H22_J20_TG_08m


title: Patient 2, sample B10, Transverse colon

value: Transverse colon


title: P1070215H08 [saliva RNA-seq]

description: P1070215H08_S1_070215_H08_HWFKYCCXX_L6_1


title: Patient 1, sample B1, Anal channel

source_name: Anal channel

value: Anal channel


title: P1070115H08 [saliva RNA-seq]

description: P1070115H08_S1_070115_H08_HVLV5CCXX_L8_1


title: P1070515H08 [saliva RNA-seq]

description: P1070515H08_S1_070515_H08_HW5LCCCXX_L5_1


title: P1070415H08 [saliva RNA-seq]

description: P1070415H08_S1_070415_H08_HVLV5CCXX_L2_1


title: A23_KEAP: KRAS_4

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

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

source_name: Tumor from BL/6 mouse with mutant Kras allele and knockout of Keap1

label_protocol: For whole-genome gene expression profiling, 200ng of total RNA was processed and Biotin labeled using the GeneChip WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol. Labeled cRNA was hybridized to Affymetrix Mouse Gene 2.0 ST array.

growth_protocol: All the mice were fed the 2018SX diet (Harlan Teklad) and had access to water ad libitum; they were housed under controlled conditions (23±2°C; 14-h light/ 10-h dark cycles). All experimental protocols conducted on the mice were performed in accordance with National Institutes of Health guidelines and were approved by the Johns Hopkins University Animal Care and Use Committee. Ten-eleven million adenovirus cre-recombinase particles diluted in 50 μl of minimal essential medium were administered by oropharyngeal aspiration (50 μl, twice at an interval of 5 min) according to the standard protocol (DuPage et al., 2009).

extract_protocol: Total RNA was isolated using TRIzol method. RNA was further cleaned up using RNeasy kit. RNA integrity was assessed with an Agilent 2100 Bioanalyzer and the RNA 6000 nano Chip kit.

treatment_protocol: Kras LSL (G12D) (strain number 01XJ6) (Johnson et al., 2001) and Stk11fl/fl (strain number 01XN2) (Bardeesy et al., 2002) were obtained from a mouse repository (NCI, Frederick) and were bred with Keap1fl/fl mice (Blake et al., 2010) to generate compound mutant mice in our facility. All experimental mice were maintained on a mixed genetic background.

tag: strain


title: P1070615H08 [saliva RNA-seq]

description: P1070615H08_S1_070615_H08_HVMKYCCXX_L3_1


title: H18_J20_TG_12m


title: H17_J20_WT_12m


title: Patient 1, sample B2, Left colon

source_name: Left colon

extract_protocol: Genomic DNAs were extracted according to manufacturer's protocols.


title: G24_J20_TG_08m


title: A22_KEAP: KRAS_3


title: P1062915H08 [saliva RNA-seq]


title: P1063015H08 [saliva RNA-seq]


title: G23_J20_WT_08m


title: A21_KEAP: KRAS_2


title: P1062815H08 [saliva RNA-seq]

description: P1062815H08_S1_062815_H08_HVVG5CCXX_L7_1