title: MYCNOS1 shRNA knockout Rep 2

city: Bangkok

first: Rossukon

last: Kaewkhaw

address: 270 Rama VI Road Ratchathewi

country: Thailand

institute: Mahidol University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw fastq reads were trimmed using default parameters of Trimmomatic. Only reads with minimum length of 36 base pairs were retained for further downstream analysis.
Transcript level counts using Ensemble version 82 annotation were generated using Kallisto utility.
Gene level counts were computed from transcript level counts using tximport R package
Genome_build: hg38
Supplementary_files_format_and_content: CSV file

source_name: MYCN-amplified retinoblastoma without RB1 mutation

growth_protocol: Tumor tissue was dissociated, and the resulting cells were cultured in the growth medium developed previously in Saengwimol et al. "A three-dimensional organoid model recapitulates tumorigenic aspects and drug responses of advanced human retinoblastoma." Final concentration of a 1% Matrigel matrix solution was added in suspension culture, while that of 65 % Matrigel matrix (growth factor reduced; Corning Inc., Corning, NY, USA) was used to embed cells for organoid culture. RB170 was manually dissociated and passaged at a 1:2 or 1:4 ratio once a week for suspension culture or every 3 weeks for organoids. Cold freezing medium (culture medium containing 10% dimethyl sulfoxide) was used to freeze cells at −80°C for 24 hours before long-term storage in liquid nitrogen. A human retinoblastoma cell line (Y79) was maintained in RPMI-1640 (Hyclone Laboratories Inc., Logan, UT, USA) containing 15% fetal bovine serum (Sigma-Aldrich, St. Louis, MO, USA), 100 U/mL penicillin, 100 µg/mL streptomycin, and 0.25 µg/mL amphotericin B. Medium was changed every 3 days for both RB170 and Y79 cells.

extract_protocol:
RNA was extracted from cultures by using TriPure isolation reagent (Roche Applied Science, Penzberg, Germany). The quality and quantity of RNA were determined by RNA6000 assay (Agilent Technologies, Santa Clara, CA, USA). Specimens with an RNA integrity number (RIN) >8.0 were used in this study.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA Libraries were constructed by using the TruSeq Stranded mRNA LT Sample Prep Kit

tag: genotype/variation

value: shRNA targeting MYCNOS1 transcript


title: MYCNOS1 shRNA knockout Rep 1

status: Public on Dec 15 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: MYCNOS1 shRNA control Rep1

value: shRNA targeting non-targeting control


title: HLO_Differentiation2_Replicate2

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

country: USA

institute: UCSF

description: Sample 5 must be demultiplexed using the provided HTO fastq file with the following barcodes for each sample:   GTCAACTCTTTAGCG

data_processing:
Transcript Quantification: FASTA (fasta.gz) files were quantified using a python wrapper for the kallisto bustools pipeline called kb-python (v0.24.4). The specific command was 'kb count' with default parameters. More information here: https://www.kallistobus.tools/introduction
Preprocessing: Unfiltered count matrices from kb-python were read into R and empty droplets were filtered out using DropletUtils (1.8). The reminaing cells were filtered for Total Genes measured and mitochondrial content using Seurat (v3.2.2)
Demultiplexing: Each sample was multiplexed with TotalSeqB Antibodies. Demultiplexing was performed with an in-house demultiplexing tool (email aidan.winters@ucsf.edu for details)
Analysis: Samples (across both lanes (L003 and L004) were integrated using Seurat's standard worfklow (https://satijalab.org/seurat/v3.2/integration.html)
Genome_build: GRCh38; https://uswest.ensembl.org/info/data/ftp/index.html
Supplementary_files_format_and_content: Processed data is provided as (.csv) files and contain a gene count matrix of cell IDs post filtering.

source_name: Lung Organoid

growth_protocol: Human lung organoids (HLO) were derived from hPSCs as previously described (Carvalho et al., 2019; Jacob et al., 2017; Miller et al., 2019), with minor modifications. Briefly, H9 hPSCs were maintained in mTeSR Plus media and were seeded on Day 0 onto matrigel (Corning) coated surface. On Days 1-4 cells were treated with 100 ng/mL Activin A and increasing concentration of defined FBS (dFBS, HyClone) in RPMI 1640 medium (Thermo), to induce definitive endoderm formation (Day 1: 3 µM CHIR99021 and no dFBS; Day 2: 0.2% dFBS; Days 3-4: 2% dFBS). On Day 4, cells were >95% double positive for CXCR4/CD184 and c-Kit/CD117 as determined by flow cytometry. On Days 5-9 cells were treated with anterior foregut induction medium, containing 10 µM SB431542, 100 nM LDN193189, 2 µM CHIR99021, 1 µM SAG, 500 ng/mL FGF4 in Foregut Basal Medium (Advanced DMEM, 1x B27, 1x N2, 10 mM HEPES, 1x Glutagro (all Thermo), 50 µg/mL ascorbic acid (Sigma), 0.4 µM monothioglycerol (Sigma)). On Day 9, anterior foregut spheroids were harvested by gentle pipetting and transferred into an ultra-low attachment plate, in Lung Organoid Medium I (3 µM CHIR99021, 10 ng/mL BMP4, 10 ng/mL FGF7, 10 ng/mL FGF10, 50 nM all-trans retinoic acid, in Foregut Basal Medium). The medium was changed every two days until Day 15. On Day 15, the medium was changed to Lung Organoid Medium II (3 µM CHIR99021, 10 ng/mL FGF7, 10 ng/mL FGF10, in Foregut Basal Medium). On Day 25 the organoids were embedded in matrigel, in transwell inserts, and grown in Lung Organoid Medium III (3 µM CHIR99021, 10 ng/mL FGF7, 10 ng/mL FGF10, 50 nM dexamethasone (Sigma), 100 µM 8-bromo-cAMP (Sigma), 100 µM IBMX (Sigma), in Foregut Basal Medium). The medium was changed every 3 days. The CHIR99021 was withdrawn on Days 35-42. All media components were from Stem Cell Technologies unless noted otherwise.

extract_protocol:
All tubes and pipet tips used for cell harvesting were pre-treated with 1% BSA in 1X PBS. The HLOs were transferred with a wide end pipet tip from matrigel to 1 mL Organoid Harvesting solution (Cultrex) and incubated 1h at +4C, with end-to-end rotation. Then the cells were dissociated in Accutase (Stem Cell) with DNaseI (200 U/mL, Worthington) and Dispase (100 U/mL, Corning) at 37C, in 10 min increments, with end-to-end rotation, until single cell suspension was obtained. The cells were washed in Cell Staining Buffer (Biolegend) and stained with TotalSeq HTO antibodies for 30 min on ice. The cells were washed twice in Cell Staining Buffer and filtered through a 40 µm pipet tip strainer (BelArt). The cells were counted using Trypan Blue dye and hemocytometer and pooled for sequencing.
scRNA-seq libraries were prepared with Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics), with custom amplification of TotalSeq HTO sequences (Biolegend). The libraries were sequenced on Illumina NovaSeq sequencer in the Center for Advanced Technologies (UCSF).

tag: tissue

value: hPSC-derived Lung Organoid

tag: cell line

tag: plating

value: Matrigel Embedded

tag: differentiation replicate

tag: replicate

tag: totalseq hto#

tag: totalseq hto barcode

value: GTCAACTCTTTAGCG


title: inhibitor-3

city: Bedford Park

first: George

last: Mayne

state: SA

address: Room 3D213, Dept of Surgery, Flinders Medical Center

department: Surgery

country: Australia

institute: Flinders University of South Australia

data_processing:
Raw reads were trimmed and filtered for short sequences using cutadapt v.1.8 [105]. Trimmed FASTQ files, averaging 20 million reads per sample, were quality checked using the FastQC program (v.0.11.8)
Reads were mapped against the human reference genome (Gencode GRCh38) using STAR aligner (version:2.7.0f_0328)
RNA counts were within-lane normalised for differences in GC content and Length using the EDASeq package in R [108], and then between-lane normalized for differences in read depth using the DESeq 2 package in R
Differential expression was assessed via Mann Whitney U test in R.
Genome_build: Gencode GRCh38
Supplementary_files_format_and_content: The mRNA NGS processed data file contains a matrix of normalised data for the samples vs. mRNAs

source_name: OE19 oesophageal adenocarcinoma cell line

growth_protocol: The OE19 cell line (purchased from Sigma ECACC ) was cultured using RPMI 1640 medium (Thermo Fisher Scientific, Scoresby, Australia) supplemented with 10 % foetal bovine serum (FBS) (Thermo Fisher Scientific, #10099141, Scoresby, Australia), 50 U/mL penicillin (Thermo Fisher Scientific, #15070063, Scoresby, Australia), 50 µg/mL streptomycin (Thermo Fisher Scientific, #15070063, Scoresby, Australia), and 100 µg/mL normocin (InvivoGen, #nta-nr-2, San Diego, USA) and cultured using standard techniques and reagents

extract_protocol:
Total RNA isolation, including DNase digestion, was performed using the miRNeasy Mini Kit (Qiagen, #217004, Chadstone, Australia) and RNase-free DNase Set (Qiagen, #79254, Chadstone, Australia) as instructed by the manufacturer. Quantification of the final RNA concentration was performed via UV spectrophotometry (NanoDrop™ 2000 Spectrophotometer, Thermo Fisher Scientific, Wilmington, USA).
Libraries of small RNAs were prepared from 150 ng of RNA using the NEBNext™ kit (New England Biolabs). After reverse transcription, 15 cycles of PCR were performed to enrich for successfully ligated molecules. The libraries were size selected using 3 % agarose gels targeting a 122–182 bp range. Size-selected libraries were run on Bioanalyzer high-sensitivity DNA chips to confirm size, minimal adapter dimers, and to estimate yield.

treatment_protocol: 24 h after seeding, cells at 80 % confluence were irradiated with a dose of 2 Gy, chosen in concordance with previously reported irradiation protocols [6, 9], in an X-Rad 320 irradiation machine (Precision X-Ray, North Branford, CT, USA). Negative controls were mock-irradiated. Samples were irradiated in full scatter conditions with 2 Gy at a SSD of 65 cm with HVL of 2.00 mm Aluminium, at 300 kVp with the tube current at 13 mA at a dose-rate of 2.3 Gy/min. The accuracy of the dose-measurement was ± 5%. The dose calibration of the orthovoltage 300 kVp X-ray beam produced by the X-RAD 320 was performed according to the Institute of Physics and Engineering in Medicine and Biology (IPEMB) protocol.

tag: cell type

value: oesophageal adenocarcinoma derived cell line

tag: treatment

value: miRCURY LNA Power miR-451a microRNA Inhibitor (Qiagen, #EX-4101736-101).


title: HLO_Differentiation1_Replicate1, HLO_Differentiation1_Replicate2, HLO_Differentiation1_Replicate3

description: Sample 1, 2 and 3 came from a multiplexed sequencing run using the Totalseq strategy.   Samples 1-3 must be demultiplexed using the provided HTO fastq file with the following barcodes for each sample:   Sample 1: TTCCGCCTCTCTTTG Sample 2:  AGTAAGTTCAGCGTA Sample 3: CAGTAGTCACGGTCA

value: Matrigel Embedded, Matrigel Embedded, Suspension

value: HTO3, HTO4, HTO9


title: HLO_Differentiation2_Replicate1

description: Sample 4 must be demultiplexed using the provided HTO fastq file with the following barcodes for each sample:   GTCAACTCTTTAGCG


title: inhibitor-2


title: control-3

value: miRCURY LNA Power microRNA Inhibitor Negative Control A (Qiagen, #EX-199006-101)


title: inhibitor-1


title: control-2


title: inhibitor-1 [miRNA-Seq]

data_processing:
Raw reads were trimmed and filtered for short sequences using cutadapt v.1.8 [105]. Trimmed FASTQ files, averaging 20 million reads per sample, were quality checked using the FastQC program (v.0.11.8)
Reads were mapped against the human reference genome (Gencode GRCh38) using STAR aligner (version:2.7.0f_0328)
RNA counts were within-lane normalised for differences in GC content and Length using the EDASeq package in R [108], and then between-lane normalized for differences in read depth using the DESeq 2 package in R
Differential expression was assessed via Mann Whitney U test in R.
Genome_build: Gencode GRCh38
Supplementary_files_format_and_content: Matrix tables with nomalised gene counts for every gene and every sample


title: control-1


title: inhibitor-3 [miRNA-Seq]


title: control-2 [miRNA-Seq]


title: control-3 [miRNA-Seq]


title: siMSI1_2

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 –trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization and FPKM transformation
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample

molecule: polyA RNA

source_name: GBM-derived cell line

growth_protocol: KNS42 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
800ng of total RNA served as input for polyA(+)-RNA enrichment at Novogene (HK). Strand-specific library preperation and sequencing of 150bp long reads was performed by Novogene (HK)
polyA RNA-Seq

treatment_protocol: 72 hours upon transfection cells were harvested for RNA extraction.

tag: sirna

value: siRNA pool against MSI1

tag: passages

value: harvested 72h upon transfection


title: siMSI1_3


title: 6303299045_C: Immune non-Responder (INR)

type: RNA

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

institute: Case Western Reserve University

description: CD4 T cells <350/µL

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

source_name: Immune non-Responder (INR)

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: Whole blood was collected from Immune Responder and Non-Responder HIV-infected ART-treated individuals and gene array analysis was performed

extract_protocol: Whole blood was collected from Immune Responder and Non-Responder HIV-infected ART-treated individuals. Reverse transcription reactions were performed to obtain cDNAs which were hybridized to the Illumina Human HT-12 version 4 Expression BeadChip according to the manufacturer’s instruction, and quantified using an Illumina iScan System. The data were collected with Illumina GenomeStudio software. Analysis of the genome array output data was conducted using the R statistical language and the Limma statistical package from Bioconductor.

treatment_protocol: Individuals were treated for at least 2-3 years with plasma HIV RNA levels below detectable levels using routine clinical assays; typically, less than 50 copies per milliliter. Transient blips in HIV RNA levels did not exclude participation if flanked by levels below limits of detection.

tag: subject

tag: group

value: INR

value: Whole Blood

value: CD4 T cells


title: siC_1

value: Control siRNA


title: siMSI1_1


title: siC_3


title: MYCNOS1 shRNA control Rep2


title: Bulk_HeLa_H3K9me3_rep2

city: New York

first: Zhu

last: Chenxu

email: cxzhu@pku.edu.cn, czhu@nygenome.org

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center

library_source: genomic

data_processing:
Cellular barcodes and the linker sequences are read by Read2. The first base of BC#1, BC#2 and BC#3 should locate within 84-87th, 47-50th and 10-13rd base of Read2. We identify the positions of barcodes by matching the linker sequences adjacent to the cellular barcodes.
Cleaned reads were first mapped to a mouse GRCm38 genome reference genome with STAR (version: 2.6.0a) for RNA or bowtie2 for DNA. Mapped DNA reads of H3K4me1, H3K27ac and H3K27me3 were further filtered by mapping quality (MAPK>10). Duplicates were removed based on the mapped position, cellular barcode, PCR index and UMI.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: tab-delimited text files include cell embeddings for each cell.

molecule: other

source_name: HeLe cell line

growth_protocol: HeLa S3 (human, ATCC CCL-2.2) cells were cultured according to standard procedures in Dulbecco’s Modified Eagles’ Medium (Thermo Fisher Scientific, 10569010) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, 16000044) and 1% penicillin-streptomycin (Thermo Fisher Scientific, 10378016) at 37 °C with 5% CO2.

extract_protocol:
Single-cell suspension were prepared from douncing of the frozen tissues, in Doucing Buffer with Protease/RNase Inhibitor cocktail (DBI: 0.25 M sucrose [Sigma, S7903], 25 mM KCl [Sigma, P9333], 5 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 mM DTT [Sigma, D9779], 1X Protease Inhibitor, 0.5 U/µL RNase OUT and 0.5 U/µL SUPERase Inhibitor) supplemented with 0.1% Triton-X 100 (Sigma T9284). The cell suspension was then filtered by 30 µm Cell-Tric (Sysmex) and spun-down for 10 min, 1,000 g at 4 °C. After washing the cell pellets with DBI and spun-down again, NIB with 0.2% IGEPAL CA-630 were added to resuspend the nuclei pellets and rotate for 10 min at 4 °C. The nuclei were counted by BioRad TC20 cell counter and proceed to Paired-tag experiments immediately.
Libraries were constructed by Paired-tag workflow, briefly: First, permeabilized nuclei were incubated with antibodies targeting chromatin regions of interest to trigger the targeted binding of protein A-fused Tn5. Tagmentation reaction and reverse transcription (RT) were then sequentially performed: specifically, reactions were carried out in 12 different wells, with the same set of barcodes in transposase adaptors and RT primers, to label different samples or replicates (1st round of barcodes). Next, a ligation-based combinatorial barcoding strategy was used to introduce the 2nd and 3rd rounds of barcodes to nuclei, by sequential attaching well-specific DNA barcodes from 96-well plates to the 5’-end of both DNA fragments and cDNA from RT. Lastly, barcoded nuclei were divided into sub-libraries and lysed, the DNA/cDNA was purified and subjected to an optimized “amplify-and-split” strategy based on that we previously developed, to give rise DNA and RNA libraries for sequencing

treatment_protocol: To prepare nuclei, HeLa S3 cells were harvested by centrifugation, washed with PBS (Thermo Fisher Scientific, 10010-23) and counted using BioRad TC20 cell counter. The cells were then resuspended in cold Nuclei Permeabilization Buffer 1 (NPB1: 10 mM Tris-HCl pH 7.4 [Sigma, T4661], 10 mM NaCl [Sigma, S7653], 3 mM MgCl2 [Sigma, 63069], 1X Protease Inhibitor [Roche, 05056489001], 0.5 U/µL RNase OUT [Invitrogen, 10777-019] and 0.5 U/µL SUPERase Inhibitor [Invitrogen, AM2694]) with 0.1% IGEPAL CA-630 (Sigma, I8896) and centrifuged for 10 min at 1,000 g, 4 °C and proceed to Paired-tag experiments.

tag: chip antibody


title: Bulk_HeLa_H3K9me3_rep1


title: Bulk_HeLa_H3K27me3_rep2


title: Bulk_HeLa_H3K27me3_rep1


title: Bulk_HeLa_H3K27ac_rep1


title: Bulk_HeLa_H3K27ac_rep2


title: Bulk_HeLa_H3K4me1_rep1


title: Uchimura organoid

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

description: single cell RNA-seq

data_processing:
Raw reads were demultiplexed using the command “cellranger mkfastq” from the CellRanger toolkit (version 3.0). Read alignment, barcode identification and UMI quantification were completed using the command “cellranger count”.
Genome_build: GRCh38
Supplementary_files_format_and_content: cellranger count

source_name: iPS cells

extract_protocol:
Organoids from Uchimura and Takasato protocols were harvested at day 26 and dissociated into single cells using 0.25% TrypLE. Cells were counted on hemocytometers (InCYTO C-chip) and partitioned into each droplet with a barcoded gel bead using the 10X Chromium instrument (10X Genomics, Pleasanton, CA). Single cell was lysed and RNAs were reverse transcribed into cDNA within each droplet. After breaking the emulsion, cDNAs were amplified and fragmented followed by the addition of Illumina adapters using the Chromium Single Cell 5’ Library & Gel Bead Kit. Samples were indexed and sequenced on the S4 flow cell of NovaSeq 6000 (Illumina).
RNA libraries were prepared for sequencing following the 5' library preparation protocol from 10x Genomics
10x Chromium 5' scRNA-seq library

tag: protocol

value: 10x Genomics 5' library kit

value: Uchimura organoid


title: inhibitor-2 [miRNA-Seq]


title: Takasato organoid

description: single cell RNA-seq

value: Takasato organoid


title: 6303299045_F: Immune non-Responder (INR)

description: CD4 T cells <350/µL


title: control-1 [miRNA-Seq]


title: siC_2


title: ALV-J-susceptible chicken 3

city: Guangzhou

first: Yiming

last: Yan

address: Wushan Road

country: China

institute: South China Agricultural University

data_processing:
paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
 After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC galGal4) with hisat2 software (v2.0.4).
 Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Genome_build: UCSC galGal4
Supplementary_files_format_and_content: counts, FPKM

organism: Gallus gallus

source_name: liver

extract_protocol: library construction protocol

tag: tag

value: ALV-J-susceptible


title: ALV-J-resistant chicken 1

value: ALV-J-resistant


title: ALV-J-susceptible chicken 1


title: ALV-J-resistant chicken 3


title: 118_2_5

type: genomic

city: London

first: Chloe

last: Wong

state: Select a State or Province

address: MRC SGDP Centre, Institute of Psychiatry,

country: United Kingdom

institute: King's College London

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

hyb_protocol: Samples were processed according to the Illumina Infinium Methylation EPIC BeadChip protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

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

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions. Normalized betas using dasen function

label: Cy5 and Cy3

molecule: genomic DNA

source_name: buccal swab at age 5

label_protocol: 500 ng DNA was sodium bisulphite treatedas amplified using the EZ-96 DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s standard protocol

extract_protocol: genomic DNA was extracted and purified from buccal and blood samples using standardised protocols.

tag: familyid

tag: twinid

tag: gender

value: Male

value: Buccal

tag: age

value: Age 5

tag: disease state

value: Notexposed

tag: smokingpackyears

tag: category


title: 118_2_18B

description:
comments: This sample matched with  118_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

source_name: whole blood at age 18

tag: tissue

value: Blood

value: Age 18


title: 118_2_10

source_name: buccal swab at age 10

value: Age 10


title: ALV-J-susceptible chicken 2


title: 118_2_18C

source_name: buccal swab at age 18


title: 118_1_5


title: 118_1_18B

description:
comments: This sample matched with  118_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 117_2_5

value: Female

value: Exposed


title: ALV-J-resistant chicken 2


title: 118_1_10


title: 117_2_18C


title: 117_2_18B

description:
comments: This sample matched with  117_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 118_1_18C


title: 117_1_5


title: 117_2_10


title: Bulk_HeLa_H3K4me1_rep2


title: 117_1_18C


title: 116_2_5


title: 117_1_10


title: 116_2_18C


title: 116_2_18B

description:
comments: This sample matched with  116_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 116_2_10


title: 116_1_5


title: 116_1_18C


title: 116_1_18B

description:
comments: This sample matched with  116_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 115_2_18C


title: 116_1_10


title: 115_1_5


title: 115_2_5


title: 115_1_18B

description:
comments: This sample matched with  115_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 115_1_18C


title: 114_2_18C


title: 115_2_10


title: 114_2_5


title: 114_1_18C


title: 114_2_10


title: 114_1_10


title: 113_2_18B

description:
comments: This sample matched with  113_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 114_1_18B

description:
comments: NA
genomic DNA from blood sample
betas_normalised.csv


title: 113_2_18C


title: 117_1_18B

description:
comments: This sample matched with  117_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 113_1_5


title: 113_2_10


title: 113_1_18B

description:
comments: This sample matched with  113_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 113_2_5


title: 113_1_18C


title: 113_1_10


title: 112_2_5


title: 112_2_18C


title: 115_2_18B

description:
comments: This sample matched with  115_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 112_2_18B

description:
comments: This sample matched with  112_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 115_1_10


title: 114_2_18B

description:
comments: This sample matched with  114_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 112_1_5


title: 112_1_18B

description:
comments: This sample matched with  112_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 112_1_18C


title: 112_2_10


title: 111_2_18C


title: 112_1_10


title: 114_1_5


title: 111_2_18B

description:
comments: This sample matched with  111_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 111_1_5


title: 111_1_18B

description:
comments: This sample matched with  111_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 111_1_18C

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv


title: 110_2_18C


title: 111_1_10


title: 110_2_10


title: 111_2_10


title: 110_1_5


title: 110_1_18B

description:
comments: This sample matched with  110_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 110_1_10


title: 110_2_5


title: 109_2_18B

description:
comments: This sample matched with  109_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 110_2_18B

description:
comments: This sample matched with  110_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 109_2_5


title: 109_2_18C


title: 109_1_5


title: 109_1_18C


title: 109_1_18B

description:
comments: This sample matched with  109_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 111_2_5


title: 108_2_5


title: 108_2_18C


title: 108_2_10


title: 108_2_18B

description:
comments: This sample matched with  108_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 109_1_10


title: 108_1_18C


title: 108_1_18B

description:
comments: This sample matched with  108_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 108_1_5


title: 107_2_5


title: 107_2_18B

description:
comments: This sample matched with  107_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 107_1_18C


title: 107_2_18C


title: 107_1_5


title: 107_2_10


title: 107_1_10


title: 106_2_18C


title: 106_2_18B

description:
comments: This sample matched with  106_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 109_2_10


title: 106_1_5


title: 106_2_5


title: 106_2_10


title: 106_1_18B

description:
comments: This sample matched with  106_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 106_1_18C


title: 105_2_5


title: 106_1_10


title: 105_2_18B

description:
comments: This sample matched with  105_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 105_1_5


title: 105_2_10


title: 105_1_18C


title: 105_2_18C


title: 105_1_18B

description:
comments: This sample matched with  105_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 108_1_10


title: 105_1_10


title: 104_2_5


title: 104_2_18C


title: 104_2_18B

description:
comments: This sample matched with  104_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 104_2_10


title: 104_1_5


title: 104_1_18C


title: 107_1_18B

description:
comments: This sample matched with  107_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 103_2_5


title: 103_2_18B

description:
comments: This sample matched with  103_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 103_2_18C


title: 104_1_10


title: 103_2_10


title: 103_1_5


title: 103_1_18B

description:
comments: This sample matched with  103_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 103_1_10


title: 102_2_5


title: 102_2_18B

description:
comments: This sample matched with  102_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 102_2_10

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv


title: 103_1_18C


title: 102_1_5


title: 102_1_10


title: 101_2_18C


title: 101_2_18B

description:
comments: This sample matched with  101_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 101_1_5


title: 101_1_18C


title: 101_1_10


title: 101_2_10


title: 102_1_18C


title: 100_2_5


title: 100_2_18C


title: 101_1_18B

description:
comments: This sample matched with  101_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 100_2_18B

description:
comments: This sample matched with  100_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 104_1_18B

description:
comments: This sample matched with  104_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 100_1_5


title: 100_1_18C


title: 100_2_10


title: 102_2_18C


title: 99_2_5


title: 99_2_18C


title: 100_1_10


title: 99_2_10


title: 102_1_18B

description:
comments: This sample matched with  102_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 99_1_18C


title: 99_1_18B

description:
comments: This sample matched with  99_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 99_1_5


title: 99_1_10


title: 98_2_5


title: 98_2_18B

description:
comments: This sample matched with  98_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 98_2_10


title: 98_1_18C


title: 98_1_5


title: 98_1_18B

description:
comments: This sample matched with  98_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 97_2_18C


title: 97_2_5


title: 97_2_10


title: 97_2_18B

description:
comments: This sample matched with  97_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 97_1_5


title: 100_1_18B

description:
comments: This sample matched with  100_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 99_2_18B

description:
comments: This sample matched with  99_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 101_2_5


title: 97_1_18B

description:
comments: This sample matched with  97_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 96_2_5


title: 96_2_18B

description:
comments: This sample matched with  96_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 96_2_18C


title: 97_1_10


title: 96_2_10


title: 98_2_18C


title: 96_1_5


title: 96_1_18C


title: 98_1_10


title: 96_1_10


title: 95_2_18C


title: 97_1_18C


title: 95_2_5


title: 95_2_18B

description:
comments: This sample matched with  95_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 95_2_10


title: 95_1_18C


title: 95_1_18B

description:
comments: This sample matched with  95_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 95_1_5


title: 95_1_10


title: 94_2_5


title: 94_2_18C


title: 6_Kidney_smallRNA

city: Ames

first: Joe

last: Webb

state: IA

address: 2302 Osborn drive, 220 Mackay Hall

institute: Iowa State University

description: Table 2

data_processing:
Fastqc was used to examine individual fastq files and determine the number of reads per sample
BBDUK was used to trim the adapters off of small RNA and total RNA samples
Fastqc was used to examine trimmed fastq files and determine the number of reads per sample following adapter removal with quality control
small RNA samples were processed using smallrnaseq (https://github.com/dmnfarrell/smallrnaseq)
total RNA files were processed according to the quantseq pipeline described here: https://www.lexogen.com/wp-content/uploads/2015/11/015UG009V0211_QuantSeq-Illumina.pdf
Genome_build: RNO_6
Supplementary_files_format_and_content: Quantseq Gene Expression Deseq Results
Supplementary_files_format_and_content: Quantseq Gene Expression Raw Counts
Supplementary_files_format_and_content: microRNA data Deseq results
Supplementary_files_format_and_content: microRNA Raw Counts

organism: Rattus norvegicus

source_name: Kidney

growth_protocol: Animals were randomly assigned and placed on their respective diets for two weeks with ad libitum food/water.

extract_protocol:
Total RNA and microRNA samples were extracted from tissue or blood using the Lexogen SPLIT Kit ( https://www.lexogen.com/split-rna-extraction/) according to the manufacturers instructions. Briefly, samples undergo a phenol/chlorophorm phase seperation to purify the RNA on a column, followed by size exclusion to seperate any small RNA samples from large RNA.
Libraries were prepared according to Lexogen's instructions accompanying the smallRNA & Quantseq library preparation kits. Briefly, RNA was diluted following a Lexogen SPLIT KIT RNA extraction and  samples were loaded with equal concentrations of either total or small RNA. Total RNA libraries were generated according to the manufacturers instructions here: https://www.lexogen.com/wp-content/uploads/2015/11/015UG009V0211_QuantSeq-Illumina.pdf --- small RNA libraries  were prepared following the manufacturers instructions here: https://www.lexogen.com/wp-content/uploads/2020/02/052UG128V0110_Small-RNA-Seq-Library-Preparation-Kit_2020-01-22.pdf. The purified DNA libraries were processed on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 3000 following the manufacturer's protocols.

treatment_protocol: Immediately prior to the 2 week feeding protocol, animals were fed/fast trained to consume their diet within a 1 hour window for three days. Animals were given a 4 gram diet pellet and following consumption, blood was serially collected for microRNA sequencing across a time curve analysis. Tissue samples were collected at the end of the study and gene expression analysis was conducted on the kidney, liver, adipose and prefrontal cortex tissues.

value: Kidney

tag: timepoint

value: End of study

tag: animal number

value: Animal 6

tag: data type

value: miRNA-Seq


title: 7_Kidney_smallRNA

description: Table 2

value: Animal 7


title: 10_Kidney_smallRNA

description: Table 2

value: Animal 10


title: 11_Kidney_smallRNA

description: Table 2

value: Animal 11


title: 9_Kidney_smallRNA

description: Table 2

value: Animal 9


title: 8_Kidney_smallRNA

description: Table 2

value: Animal 8


title: 3_Kidney_smallRNA

description: Table 2

value: Animal 3


title: 4_Kidney_smallRNA

description: Table 2

value: Animal 4


title: 12_Kidney_smallRNA

description: Table 2

value: Animal 12


title: 94_2_18B

description:
comments: This sample matched with  94_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Male

value: Blood


title: 94_2_10

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

value: Buccal

value: Age 10


title: 96_1_18B

description:
comments: This sample matched with  96_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Age 18

value: Notexposed


title: 94_1_5

value: Age 5


title: AD P004

city: Shenyang

first: Ke

last: Zhang

address: No.77 Puhe Road

institute: China Medical University

description: Gene expression

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Differentially expressed circRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively.

source_name: AD Plasma replicate 1

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: The total RNA from fresh blood plasma supernatant was isolated using TRizol reagent (Thermo Fisher Scientific). The total RNA was digested with Ribonuclease R (Epicentre, Inc.) to remove linear RNAs and enrich the circRNAs.

treatment_protocol: Approximately 10 mL of peripheral whole blood was sampled from each subject by venipuncture and collected into test tubes containing dipotassium ethylenediaminetetraacetic acid. The plasma and whole blood cells were separated by centrifugation

tag: sample type

value: plasma


title: AD P005

description: Gene expression

source_name: AD Plasma replicate 2


title: 1_Kidney_smallRNA

description: Table 2

value: Kidney

value: End of study

value: Animal 1

value: miRNA-Seq


title: 5_Kidney_smallRNA

description: Table 2

value: Animal 5


title: 94_1_18C


title: AD P006

description: Gene expression

source_name: AD Plasma replicate 3


title: 11_Liver_smallRNA

description: Table 2

source_name: Liver

value: Liver

value: Animal 11


title: 10_Liver_smallRNA

description: Table 2

value: Animal 10


title: 110_1_18C

value: Female

value: Exposed


title: 94_1_18B

description:
comments: This sample matched with  94_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Male

value: Blood


title: Control EP

description: Gene expression

source_name: Control Plasma replicate 1


title: Control XP

description: Gene expression

source_name: Control Plasma replicate 3


title: Control FP

description: Gene expression

source_name: Control Plasma replicate 2


title: 9_Liver_smallRNA

description: Table 2

value: Animal 9


title: 93_2_18B

description:
comments: This sample matched with  93_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Age 18


title: 94_1_10

value: Buccal

value: Age 10

value: Notexposed


title: 8_Liver_smallRNA

description: Table 2

value: Animal 8


title: 12_Liver_smallRNA

description: Table 2

value: End of study

value: Animal 12


title: 2_Kidney_smallRNA

description: Table 2

value: Kidney

value: Animal 2

value: miRNA-Seq


title: 6_Liver_smallRNA

description: Table 2

value: Liver

value: Animal 6


title: 5_Liver_smallRNA

description: Table 2

value: Animal 5


title: 7_Liver_smallRNA

description: Table 2

value: Animal 7


title: 93_2_18C

value: Female


title: 93_1_5

value: Age 5


title: 4_Liver_smallRNA

description: Table 2

value: Animal 4


title: 93_1_18C

value: Age 18


title: 93_1_18B

description:
comments: This sample matched with  93_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: 1_Liver_smallRNA

description: Table 2

value: Animal 1


title: 93_2_10

value: Buccal

value: Age 10

value: Notexposed


title: 12_Brain_smallRNA

description: Table 2

value: Brain

value: End of study

value: Animal 12


title: 92_2_5

value: Male

value: Exposed


title: 3_Liver_smallRNA

description: Table 2

value: Liver

value: Animal 3

value: miRNA-Seq


title: 2_Liver_smallRNA

description: Table 2

value: Animal 2


title: 92_2_18C


title: 93_1_10

value: Female


title: 11_Brain_smallRNA

description: Table 2

value: Animal 11


title: 92_2_10


title: 93_2_5

value: Age 5


title: 10_Brain_smallRNA

description: Table 2

value: Animal 10


title: 9_Brain_smallRNA

description: Table 2

value: Animal 9


title: 92_1_18C

value: Buccal

value: Age 18


title: 92_1_18B

description:
comments: This sample matched with  92_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: 92_1_10

value: Age 10


title: 6_Brain_smallRNA

description: Table 2

value: Brain

value: End of study

value: Animal 6


title: 5_Brain_smallRNA

description: Table 2

value: Animal 5


title: 3_Brain_smallRNA

description: Table 2


title: 91_2_18B

description:
comments: This sample matched with  91_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Male

value: Exposed


title: 4_Brain_smallRNA

description: Table 2

value: Animal 4

value: miRNA-Seq


title: 92_2_18B

description:
comments: This sample matched with  92_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 91_2_18C


title: 91_1_5


title: 92_1_5


title: 1_Brain_smallRNA

description: Table 2

value: Animal 1


title: 91_1_18B

description:
comments: This sample matched with  91_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 7_Brain_smallRNA

description: Table 2

value: Animal 7


title: 11_Adipose_smallRNA

description: Table 2

source_name: Adipose

value: Adipose

value: Animal 11


title: 12_Adipose_smallRNA

description: Table 2

value: Animal 12


title: 10_Adipose_smallRNA

description: Table 2

value: Animal 10


title: 91_1_10

value: Buccal


title: 8_Brain_smallRNA

description: Table 2

value: Animal 8


title: 9_Adipose_smallRNA

description: Table 2

value: Animal 9


title: 91_1_18C

value: Age 18


title: 7_Adipose_smallRNA

description: Table 2

value: End of study


title: 90_2_5

value: Female

value: Age 5

value: Notexposed


title: 6_Adipose_smallRNA

description: Table 2

value: Animal 6


title: 8_Adipose_smallRNA

description: Table 2


title: 90_2_18C


title: 91_2_5

value: Male

value: Exposed


title: 90_2_18B

description:
comments: This sample matched with  90_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: 2_Brain_smallRNA

description: Table 2

value: Brain

value: Animal 2

value: miRNA-Seq


title: 91_2_10

value: Age 10


title: 90_2_10


title: 90_1_5


title: 90_1_18C


title: 5_Adipose_smallRNA

description: Table 2

value: Adipose

value: Animal 5


title: 3_Adipose_smallRNA

description: Table 2

value: Animal 3


title: 2_Adipose_smallRNA

description: Table 2


title: 89_2_5

value: Buccal


title: 90_1_10


title: 89_2_18C

value: Age 18


title: 1_Adipose_smallRNA

description: Table 2

value: End of study

value: Animal 1


title: 90_1_18B

description:
comments: This sample matched with  90_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Female


title: 11_Kidney_Quantseq

description: Table 1

value: Kidney

value: Animal 11

value: Quantseq


title: 12_Kidney_Quantseq

description: Table 1

value: Animal 12


title: 89_2_18B

description:
comments: This sample matched with  89_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood

value: Exposed


title: 89_2_10


title: 89_1_5

value: Age 5


title: 9_Kidney_Quantseq

description: Table 1

value: Animal 9


title: 10_Kidney_Quantseq

description: Table 1

value: Animal 10


title: 89_1_18B

description:
comments: This sample matched with  89_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 89_1_18C


title: 8_Kidney_Quantseq

description: Table 1

value: Animal 8


title: 6_Kidney_Quantseq

description: Table 1

value: Animal 6


title: 7_Kidney_Quantseq

description: Table 1

value: Animal 7


title: 5_Kidney_Quantseq

description: Table 1

value: Animal 5


title: 89_1_10

value: Buccal

value: Age 10


title: 88_2_5

value: Male


title: 88_2_18C

value: Age 18


title: 4_Kidney_Quantseq

description: Table 1

value: Kidney

value: End of study

value: Animal 4


title: 3_Kidney_Quantseq

description: Table 1

value: Animal 3

value: Quantseq


title: 1_Kidney_Quantseq

description: Table 1

value: Animal 1


title: 2_Kidney_Quantseq

description: Table 1

value: Animal 2


title: 88_1_5

value: Age 5

value: Exposed


title: 12_Liver_Quantseq

description: Table 1

value: Liver

value: Animal 12


title: 88_1_18C


title: 9_Liver_Quantseq

description: Table 1

value: Animal 9


title: 11_Liver_Quantseq

description: Table 1

value: Animal 11


title: 10_Liver_Quantseq

description: Table 1

value: Animal 10


title: 8_Liver_Quantseq

description: Table 1

value: Animal 8


title: 88_1_10

value: Male

value: Buccal

value: Age 10


title: 88_1_18B

description:
comments: This sample matched with  88_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood

value: Age 18


title: 87_2_18C

value: Female

value: Notexposed


title: 7_Liver_Quantseq

description: Table 1

value: End of study

value: Animal 7

value: Quantseq


title: 87_2_18B

description:
comments: This sample matched with  87_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 87_2_10


title: 4_Adipose_smallRNA

description: Table 2

value: Adipose

value: Animal 4

value: miRNA-Seq


title: 87_1_5

value: Age 5

value: Exposed


title: 5_Liver_Quantseq

description: Table 1

value: Liver

value: Animal 5


title: 4_Liver_Quantseq

description: Table 1


title: 6_Liver_Quantseq

description: Table 1

value: Animal 6


title: 3_Liver_Quantseq

description: Table 1

value: Animal 3


title: 2_Liver_Quantseq

description: Table 1

value: Animal 2


title: 87_1_18B

description:
comments: This sample matched with  87_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: 88_2_18B

description:
comments: This sample matched with  88_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Male

value: Age 18


title: 1_Liver_Quantseq

description: Table 1

value: Animal 1


title: 88_2_10

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

value: Buccal

value: Age 10


title: 12_Brain_Quantseq

description: Table 1

value: Brain

value: End of study

value: Animal 12

value: Quantseq


title: 11_Brain_Quantseq

description: Table 1

value: Animal 11


title: 87_2_5

value: Female

value: Age 5

value: Notexposed


title: 87_1_10

value: Exposed


title: 86_2_18B

description:
comments: This sample matched with  86_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 86_2_18C


title: 86_2_5


title: 9_Brain_Quantseq

description: Table 1

value: Animal 9


title: 8_Brain_Quantseq

description: Table 1

value: Animal 8


title: 10_Brain_Quantseq

description: Table 1

value: Animal 10


title: 7_Brain_Quantseq

description: Table 1

value: Animal 7


title: 86_1_18B

description:
comments: This sample matched with  86_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood

value: Age 18


title: 86_2_10

value: Buccal


title: 86_1_5


title: 6_Brain_Quantseq

description: Table 1

value: Animal 6


title: 5_Brain_Quantseq

description: Table 1

value: Brain

value: Animal 5


title: 85_2_5

value: Male


title: 86_1_10

value: Age 10


title: 87_1_18C


title: 85_2_18C


title: 4_Brain_Quantseq

description: Table 1

value: End of study

value: Animal 4

value: Quantseq


title: 85_2_18B

description:
comments: This sample matched with  85_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Notexposed


title: 12_Adipose_Quantseq

description: Table 1

value: Adipose

value: Animal 12


title: 3_Brain_Quantseq

description: Table 1

value: Animal 3


title: 85_1_5

value: Age 5

value: Exposed


title: 1_Brain_Quantseq

description: Table 1

value: Animal 1


title: 85_2_10


title: 85_1_18C

value: Age 18


title: 10_Adipose_Quantseq

description: Table 1

value: Animal 10


title: 11_Adipose_Quantseq

description: Table 1

value: Animal 11


title: 85_1_10

value: Buccal


title: 86_1_18C

value: Female


title: 9_Adipose_Quantseq

description: Table 1

value: Animal 9


title: 85_1_18B

description:
comments: This sample matched with  85_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Male

value: Blood


title: 8_Adipose_Quantseq

description: Table 1

value: End of study

value: Animal 8


title: 84_2_18C


title: 7_Adipose_Quantseq

description: Table 1

value: Animal 7

value: Quantseq


title: 6_Adipose_Quantseq

description: Table 1

value: Adipose

value: Animal 6


title: 84_2_18B

description:
comments: This sample matched with  84_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 4_Adipose_Quantseq

description: Table 1

value: Animal 4


title: 5_Adipose_Quantseq

description: Table 1

value: Animal 5


title: 2_Brain_Quantseq

description: Table 1

value: Brain

value: Animal 2


title: 84_2_10

value: Age 10

value: Exposed


title: 3_Adipose_Quantseq

description: Table 1

value: Animal 3


title: 2_Adipose_Quantseq

description: Table 1


title: 84_1_5

value: Buccal

value: Age 5


title: 84_1_18B

description:
comments: This sample matched with  84_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Male

value: Age 18


title: 1_Adipose_Quantseq

description: Table 1

value: End of study

value: Animal 1


title: 83_2_18C

value: Female


title: 83_2_5


title: 84_1_10


title: S71ABIC Replicate3

city: Los Angeles

first: Kelsey

last: Martin

address: 615 Charles E Young Drive South

department: Biological Chemistry

institute: UCLA

data_processing:
Reads were aligned to Rattus_norvegicus reference genome version Rnor_6.0 (rn6), and reads per gene was quantified by STAR 2.27a (Dobin 2013) using Rnor_6.0 gtf file.
DESeq2 (Love 2014) was used to obtain normalized read counts and perform differential expression analysis, including batch correction for replicate number
Genome_build: rn6
Supplementary_files_format_and_content: Table including normalized read counts for each sample for all genes, as well as differential expression analysis results for each gene

source_name: Forebrain

growth_protocol: Forebrain from postnatal day 0 Sprague-Dawley rats was dissected in cold Hanks’ Balanced Salt Solution (HBSS, Thermo Fisher) supplemented with 10 mM HEPES buffer and 1 mM sodium pyruvate. Sex was not determined and tissue from male and female pups were pooled. The tissue was chopped finely and digested in 1x trypsin solution (Thermo Fisher) in HBSS (supplemented with 120 µg/mL DNase and 1.2 mM CaCl2) for 15 minutes at 37°C. The tissue was washed and triturated in Dulbecco's Modified Eagle Medium (Thermo Fisher) + 10% Fetal Bovine Serum (Omega Scientific) before plating on poly-DL-lysine (PDLL)-coated (0.1 mg/mL, Sigma) 10 cm dishes or 24-well plates containing acid-etched PDLL-coated coverslips (Carolina Biologicals). Neurons were plated at a density of 1 forebrain per 10 cm dish. Neurons were cultured in Neurobasal-A (Thermo Fisher) supplemented with 1x B-27 (Thermo Fisher), 1x glutaMAX (Thermo Fisher), 25 µM monosodium glutamate (Sigma), and 25 µM β-mercaptoethanol (Sigma) and incubated at 37°C, 5% CO2.

extract_protocol:
RNA was extracted from neuronal cultures using the RNeasy Micro Kit (Qiagen) according to manufacturer’s instructions.
Libraries were prepared with Nugen Universal plus mRNA-Seq Kit (Nugen) to generate strand-specific RNA-seq libraries. Samples were multiplexed, and sequencing was performed on Illumina HiSeq 3000 to a depth of 25 million reads/sample with single-end 65  bp reads.

treatment_protocol: Cultures were transduced with AAV expressing either WT or S71A PDCD4 at DIV 13. At DIV 20, neurons were pre-incubated with either vehicle or cycloheximide (CHX, 60 µM, Sigma) for 15 min, To silence the neurons, 1 µM tetrodotoxin (TTX, Tocris) was applied to the neurons for 1 hr. To stimulate the neurons, 40 µM (-)-bicuculline methiodide (Bic, Tocris) was applied to the neurons for 1 hr.

tag: strain

value: Charles River Sprague Dawley

tag: pdcd4 transduced

tag: treatment 1

value: BIC

tag: treatment 2

value: vehicle


title: 83_2_18B

description:
comments: This sample matched with  83_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: 83_2_10


title: 84_2_5


title: WTBIC Replicate3

value: WT


title: 83_1_5


title: 83_1_18C


title: S71ABICchx Replicate3

value: cycloheximide


title: 83_1_18B

description:
comments: This sample matched with  83_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: WTTTXchx Replicate3

value: TTX


title: 84_1_18C


title: 83_1_10

value: Age 10


title: 82_2_5

value: Notexposed


title: S71ATTX Replicate2


title: WTBICchx Replicate3


title: S71ABIC Replicate2


title: 82_2_18B

description:
comments: This sample matched with  82_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: S71ATTX Replicate3


title: 82_2_18C


title: 82_2_10


title: WTBIC Replicate2


title: WTTTX Replicate2


title: 82_1_5


title: WTTTX Replicate3


title: 82_1_18C


title: S71ATTXchx Replicate2


title: WTTTXchx Replicate2


title: S71ABICchx Replicate2


title: 82_1_18B

description:
comments: This sample matched with  82_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 82_1_10


title: 81_2_5


title: S71ATTX Replicate1


title: WTBICchx Replicate2


title: S71ABIC Replicate1


title: WTTTX Replicate1


title: WTBIC Replicate1


title: S71ABICchx Replicate1


title: S71ATTXchx Replicate1


title: 81_2_10


title: 81_2_18C


title: 81_2_18B

description:
comments: This sample matched with  81_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 81_1_5


title: 81_1_10


title: 80_2_18C

value: Exposed


title: WTTTXchx Replicate1


title: 80_2_5

value: Buccal


title: 81_1_18B

description:
comments: This sample matched with  81_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 80_1_5

value: Age 5


title: S71ATTXchx Replicate3


title: 80_2_18B

description:
comments: This sample matched with  80_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 80_1_18B

description:
comments: This sample matched with  80_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 80_1_10


title: 80_1_18C


title: 81_1_18C


title: Myocardium NS-DADm rep3

city: Houston

first: Sichong

last: Qian

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC
We filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%)to get the clean reads. Then we map those clean reads onto reference genome, followed with novel gene prediction, SNP &INDEL calling and gene splicing detection
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step. For HISAT which is much faster, sensitive and high accuracy analysis software.
Genome_build: HISAT
Supplementary_files_format_and_content: FPKM values for each Sample

organism: Mus musculus

source_name: Myocardium NS-DADm

extract_protocol:
myocardium were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Qiagen RNA Sample Prep Kit (Cat#74104) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGI protocols

tag: strain background

tag: genotype/variation

value: whole-body knock-in mutations in DADs of both NCOR and SMRT (NS-DADm)

value: Myocardium


title: 79_2_18C

tag: familyid

tag: twinid

value: Male

value: Age 18


title: Myocardium NS-DADm rep1

tag: age


title: 80_2_10

tag: gender

value: Female

tag: disease state


title: Myocardium WT rep3

source_name: Myocardium WT

value: wild type


title: 79_2_10

tag: smokingpackyears

tag: category


title: 79_2_18B

description:
comments: This sample matched with  79_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

tag: tissue


title: WTBICchx Replicate1

value: Charles River Sprague Dawley

value: BIC


title: Myocardium WT rep2


title: 79_1_18C


title: Myocardium WT rep1


title: 79_1_18B

description:
comments: This sample matched with  79_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: 79_1_5

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv


title: u6bsD haploid MATa TES seq YPDlog replicate 2

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

description: TES seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin 2011) with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length=20”.
STAR (version 2.5.2) (Dobin et al. 2013) with parameters “--alignIntronMin 2 --alignIntronMax 1” (i.e. not allowing introns) was used to align TES-seq reads to the SK1 genome assembly (plus three spike-in sequences). The alignments with mapping quality of >=10 were kept for further analysis.
For the TES-seq data, the reads kept were those with soft-clipping at the 3’ end (size of soft-clipping part <=10) and with at least two consecutive non-templated As in the soft-clipping part. Insertions/deletions were also not allowed.
Alignments from forward strand and reverse strand were separated by using  "samtools view -b -f 0x10" and "samtools view -b -F 0x10".  The 3’-most nucleotide of aligned reads were extracted to generate the genome-wide tracks of TSSs.
The tool “bedtools genomecov” (Quinlan and Hall 2010) was used to generate the TES BedGraph tracks across the genome, for both forward and reverse strands. The BedGraph tracks were normalized by the number of usable reads in each library.
BedGraph files were converted to bigWig using the tool bedGraphToBigWig from UCSC (Kent et al., 2010).
Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary_files_format_and_content: Genome-wide bigWig files for both sense and antisense coverage. See data processing step for more details.

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in regular YPD  (2.0% (wt/vol) glucose) and grown to saturation (OD600 ~ 10) at 30°C and 300 rpm. About 0.4 OD of saturated yeast culture were inoculated into new flasks containing pre-sporualtion media which contains no glucose. After 16-18 hours, cells were then pelleted, washed with sterile miliQ water, and re-suspended in sporulation (SPO) media at an OD600 of 1.8.

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using hot acid phenol and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in RNAse-free sterile water.
To obtain libraries representing the 3’ ends of polyadenylated transcripts, at least 1 μg was used for 3’ end sequencing. RNA fragments were mixed with 2.5 μM GsuI20TVN primer (/5BiotinTEG/ GAGCTAGTTCTGGAGTTTTTTTTTTTTTTTTTTTTVN), 0.5 mM 5-Methylcytosine-dNTPs (D1030, Zymo Research) and 0.5 μl RNasin Plus. Reaction mixtures were denatured at 65°C for 5 minutes and held at 50°C without allowing to cool. SuperScript IV, reaction buffer and 0.4 μg of Actinomycin D were added to the hot reaction mixtures and reverse transcription was performed at 50°C for 10 minutes, 80°C for 10 minutes and held at 4°C. Samples were cleaned with 1.8x volume HighPrep beads and biotinylated RNA:DNA hybrids were captured on MyOne Streptavidin C1 Dynabeads. After capture, streptavidin beads were washed once with 1x NEbuffer 2 (B7002S, NEB), re-suspended in water and subjected to second strand synthesis. The 50 μl second strand synthesis reaction consisted of 20 μl re-suspended streptavidin beads, 1X NEbuffer 2, 250 μM dNTPs, 26 μM NAD+ (B9007S), 2.5 units RNase H, 10 units E.coli DNA ligase (M0205S), and 15 units DNA polymerase I (M0209S). Second strand synthesis reactions were conducted at 16°C for 2.5 hours on a thermomixer (1400 rpm for 15 seconds, rest for 2 minutes). After reaction, beads were washed once with 1x binding and washing buffer (5.0 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1.0 M NaCl) and once with buffer B (10 mM Tris-HCl pH 7.5, 10 mM MgCl2, 0.1 mg/ml BSA). Washed beads were re-suspended in 18 μl buffer B and digested with 10 units of GsuI (ER0461, ThermoFisher Scientific) at 30°C for 1 hour on a thermomixer (1400 rpm for 15 seconds, rest for 2 minutes). After digestion, the DNA fragments in the supernatant were extracted with Phenol/chloroform and precipitated at -20°C overnight in ethanol with 0.3 M sodium acetate and 1 μl linear acrylamide. Double-stranded cDNA was quantified by Qubit (Life Technologies) and used as input for library preparation using a KAPA Hyper Prep kit (KAPA Biosystems) and KAPA Single-indexed adapters (KAPA Biosystems). Gel purified libraries were quantified by Qubit and were sequenced on the Illumina HiSeq 4000 platform with 75-base single-end reads.
TES-seq

tag: strain/background

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1, u6bsD

tag: treatment

value: no treatment


title: u6bsD haploid MATa TES seq YPDlog replicate 1

description: TES seq


title: PC3_TGF_A

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

hyb_protocol: After fragmentation,  cRNA were hybridized on Clariom D human  Array. Microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scan protocol was performed according to the manufacturer's instruction

data_processing: The signal intensities of the Clariom D array were background corrected by RMA and normalized by quantile algorithm with oligo  package of Bioconductor. Genes were annotated with biomartR  and duplicate probes for the same gene were collapsed by selecting the probe with the highest interquartile range. Differentially expressed profiles on protein coding genes were computing with the limma package by a moderate t-test and adjusted p-value by FDR method. Genes with a log fold change ± 0.5 and p value < 0.05 were considered statistically significant.

label: biotin

source_name: PC3 cells treated during 24 hrs with TGF-β1 (5 ng/mL)

label_protocol: Two  independent experiments per condition were evaluated for a total N=8. Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Cells were seeded in RPMI-1640 medium supplemented with 5 % fetal bovine serum, 2 mM L-glutamine, 100 units/mL penicillin G sodium, 100 μg/mL streptomycin sulfate and 0.25 μg/mL amphotericin B.

extract_protocol: RNA was extracted for gene expression studies. Total RNA from treated cells was isolated using Trizol reagent. In all cases, the amount RNA were estimated spectrophotometrically at 260/280 nm using a Synergy HT (Biotek, USA).

treatment_protocol: Cells were plated at a density of 150, 000 cells in six well plates with supplemented medium and incubated with calcitriol (10 nM), TGF-β1 (5 ng/mL) or their combination during 24 h

tag: cell line

tag: cell type

value: human prostate cell line


title: 79_1_10

value: Age 10


title: PC3_Calcitriol_A

source_name: PC3 cells treated during 24 hrs with calcitriol (10 nM)


title: 78_2_5

source_name: buccal swab at age 5

value: Notexposed


title: PC3_Cal_TGF_B

source_name: PC3 cells treated during 24 hrs with calcitriol (10 nM) and TGF-β1 (5 ng/mL) in combination


title: 79_2_5


title: Wild-type haploid MATa TES seq YPDlog replicate 2

description: TES seq

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG


title: 78_2_18C

source_name: buccal swab at age 18

value: Buccal


title: Myocardium NS-DADm rep2


title: 78_2_18B

description:
comments: This sample matched with  78_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

source_name: whole blood at age 18


title: PC3_Control_B

source_name: PC3 cells non-treated, control condition


title: Wild-type diploid MATa/alpha TES seq SPO 6h replicate 2

description: TES seq

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG


title: 78_2_10

source_name: buccal swab at age 10


title: Wild-type haploid MATa TES seq SPO 4h replicate 2

description: TES seq


title: Wild-type diploid MATa/alpha TES seq SPO 6h replicate 1

description: TES seq


title: 78_1_18C


title: PC3_Calcitriol_B


title: 78_1_5

value: Age 5


title: 78_1_18B

description:
comments: This sample matched with  78_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: PC3_TGF_B


title: 78_1_10


title: u6bsD haploid MATa TSS seq YPDlog replicate 2

description: TSS seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin 2011) with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length=20”.
The custom 5’ adapter sequence specific to the protocol was removed by re-running cutadapt with the parameters “-g CACTCTGAGCAATACC -O 16 --minimum-length=20”, and only the reads containing the adapter sequence were used for further analysis.
STAR (version 2.5.2) (Dobin et al. 2013) with parameters “--alignIntronMin 2 --alignIntronMax 1” (i.e. not allowing introns) was used to align TSS-seq reads to the SK1 genome assembly (plus three spike-in sequences). The alignments with mapping quality of >=10 were kept for further analysis.
Alignments from forward strand and reverse strand were separated by using  "samtools view -b -f 0x10" and "samtools view -b -F 0x10".  The 5’-most nucleotide of aligned reads were extracted to generate the genome-wide tracks of TSSs.
The tool “bedtools genomecov” (Quinlan and Hall 2010) was used to generate the TSS BedGraph tracks across the genome, for both forward and reverse strands. The BedGraph tracks were normalized by the number of usable reads in each library.
BedGraph files were converted to bigWig using the tool bedGraphToBigWig from UCSC (Kent et al., 2010).
Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary_files_format_and_content: Genome-wide bigWig files for both sense and antisense coverage. See data processing step for more details.

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using hot acid phenol and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in RNAse-free sterile water.
To obtain libraries representing the 5’ ends of polyadenylated and capped transcripts, approximately 5 µg of poly(A)+-RNA together with in-vitro spike ins were first subjected to zinc-mediated fragmentation (Ambion) at 70 °C. The reaction was cleaned up using Qiagen min-elute columns to isolate RNA fragments with mode length of ~200 nt. These fragments were then incubated with shrimp alkaline phosphatase at 37 °C to remove the 5’ phosphate groups of non-capped fragments followed by acid-phenol/chloroform extraction and ethanol precipitation. With the exception of a non-decapping control sample, dephosphorylated fragments were next treated with Cap-Clip™ acid pyrophosphatase (CellScript) to remove the 5’-terminal caps from fragments representing the bona fide 5’ ends of transcripts. After another round of acid-phenol/chloroform extraction and ethanol precipitation, all samples were treated with T4 RNA ligase 1, high concentration (NEB) to introduce a custom adapter sequence to the 5’ un-capped ends of fragments. Excess adapters were removed via a column clean up step. First strand cDNA synthesis was performed using Superscript IV (ThermoFisher) and second strand synthesis was performed using a KAPA HiFi HotStart ReadyMix (KAPA Biosystems). Double-stranded cDNA was quantified by Qubit (Life Technologies) and used as input for library preparation using a KAPA Hyper Prep kit (KAPA Biosystems) and KAPA Single-indexed adapters (KAPA Biosystems). Amplified libraries were cleaned and purified by gel extraction. Libraries quantified by Qubit and were sequenced on the Illumina HiSeq 4000 platform with 75-base single-end reads.
TSS-seq


title: u6bsD haploid MATa TSS seq YPDlog replicate 1

description: TSS seq


title: Wild-type haploid MATa TES seq YPDlog replicate 1

description: TES seq


title: 77_2_5

value: Exposed


title: PC3_Cal_TGF_A


title: Wild-type haploid MATa TSS seq YPDlog replicate 2

description: TSS seq


title: Wild-type haploid MATa TSS seq YPDlog replicate 1

description: TSS seq


title: Wild-type haploid MATa TES seq SPO 4h replicate 1

description: TES seq


title: 77_2_18C

value: Male


title: 77_2_18B

description:
comments: This sample matched with  77_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Age 18


title: 77_2_10


title: Wild-type diploid MATa/alpha TSS seq SPO 6h replicate 2

description: TSS seq


title: 77_1_5


title: 77_1_18C


title: 77_1_18B

description:
comments: This sample matched with  77_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Rpb3-FLAG rtt109D haploid MATa mRNA seq SPO 4h replicate 2

description: PolII associated RNA seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin 2011) with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length=20”.
STAR (version 2.5.2) (Dobin et al. 2013) with parameters “--alignIntronMin 3 --alignIntronMax 5000” was used to perform the read mapping to the S. cerevisiae SK1 genome assembly from Keeney lab. Alignments with mapping quality of <10 or soft/hard-clipping were filtered.
Alignments from forward strand and reverse strand were separated by using  "samtools view -b -f 0x10" and "samtools view -b -F 0x10" to split the alignments.
The tool “bedtools genomecov” (Quinlan and Hall 2010) was used to generate the RNA-seq BedGraph tracks across the genome, for both forward and reverse strands. The BedGraph tracks were normalized by the number of usable reads in each library.
BedGraph files were converted to bigWig using the tool bedGraphToBigWig from UCSC (Kent et al., 2010).
Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary_files_format_and_content: Genome-wide bigWig files for both forward and reverse strands. See data processing step for more details.

extract_protocol:
Cell pellets were grinded in fine powder using a cryo-mill instrument. Powder was re-suspended in lysis buffer and lysate subected to DNAse I treatment for 20min. Lysate was then clarifed through two rounds of centrifugation. Anti-Flag immunoprecipitation was performed using anti-FLAG M2 agarose beads for 2.5h at 4C on a rotating wheel. Beads were then washed 5 times using cold wash buffer for 5min at 4C. Beads were then cleaned using a Pierce column and elution performed using FLAG peptide (450ul 10mg/ml Sigma FLAG peptide) for 30min at 4C. Elution was then subjected to a phenol:Chloroform extraction and RNA precipitated in ethanol containing 0.3M Na acetate. RNAs were then resuspended in Nuclease free water, quantified by Qubit and analysed by Bioanalyser.
At least 500 ng of purified RNA was treated with DNAse and purified on column (Macherey-Nagel). At least 100 ng of purified total RNA was used as the inputs for the KAPA RNA hyperPrep kit (KK8540, Roche). Libraries were prepared according to manufacturer’s instructions. After bead based clean up, libraries were sequenced on an Illumina HiSeq 4000 to an equivalent of 75 bases single-end reads, at a depth of approximately 20 million reads per library.

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, Rpb3-FLAG::KanMX, rtt109D::HygMX


title: Wild-type diploid MATa/alpha TSS seq SPO 6h replicate 1

description: TSS seq


title: Wild-type haploid MATa TSS seq SPO 4h replicate 1

description: TSS seq


title: PC3_Control_A


title: Wild-type haploid MATa TSS seq SPO 4h replicate 2

description: TSS seq


title: 77_1_10


title: 76_2_5

value: Female


title: Rpb3-FLAG rtt109D haploid MATa mRNA seq SPO 4h replicate 1

description: PolII associated RNA seq


title: Rpb3-FLAG haploid MATa mRNA seq YPDlog replicate 1

description: PolII associated RNA seq

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, Rpb3-FLAG::KanMX


title: 76_2_18C


title: 76_2_10


title: 76_1_5


title: Rpb3-FLAG haploid MATa mRNA seq SPO 4h replicate 2

description: PolII associated RNA seq


title: Wild-type haploid MATa mRNA seq YPDlog replicate 1

description: RNA seq

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using hot acid phenol and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in RNAse-free sterile water.
At least 5 μg of total RNA was treated with DNAse and purified on column (Macherey-Nagel). At least 500 ng of purified total RNA was used as the inputs for the KAPA mRNA Hyper Prep kit (KK8580, Roche). Libraries were prepared according to manufacturer’s instructions. After bead based clean up, libraries were sequenced on an Illumina HiSeq 4000 to an equivalent of 75 bases single-end reads, at a depth of approximately 20 million reads per library.


title: Wild-type haploid MATa mRNA seq YPDlog replicate 2

description: RNA seq


title: 76_1_18C


title: 76_2_18B

description:
comments: This sample matched with  76_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type haploid MATa mRNA seq SPO 4h replicate 2

description: RNA seq


title: Rpb3-FLAG haploid MATa mRNA seq YPDlog replicate 2

description: PolII associated RNA seq


title: 76_1_18B

description:
comments: This sample matched with  76_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type haploid MATa mRNA seq SPO 4h replicate 1

description: RNA seq


title: Rpb3-FLAG haploid MATa mRNA seq SPO 4h replicate 1

description: PolII associated RNA seq


title: Wild-type TES seq 9h replicate 3

description:
TES seq
CHI114A65_S65_L008

data_processing:
library strategy: TES-Seq
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin 2011) with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length=20”.
STAR (version 2.5.2) (Dobin et al. 2013) with parameters “--alignIntronMin 2 --alignIntronMax 1” (i.e. not allowing introns) was used to align TES-seq reads to the SK1 genome assembly (plus three spike-in sequences). The alignments with mapping quality of >=10 were kept for further analysis.
For the TES-seq data, the reads kept were those with soft-clipping at the 3’ end (size of soft-clipping part <=10) and with at least two consecutive non-templated As in the soft-clipping part. Insertions/deletions were also not allowed.
Alignments from forward strand and reverse strand were separated by using  "samtools view -b -f 0x10" and "samtools view -b -F 0x10".  The 3’-most nucleotide of aligned reads were extracted to generate the genome-wide tracks of TSSs.
The tool “bedtools genomecov” (Quinlan and Hall 2010) was used to generate the TES BedGraph tracks across the genome, for both forward and reverse strands.
BedGraph files were converted to bigWig using the tool bedGraphToBigWig from UCSC (Kent et al., 2010).
Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary_files_format_and_content: Genome-wide bigWig files for both sense and antisense coverage. See data processing step for more details.

source_name: Wild-type TES seq 9h

growth_protocol: Cells were grown in regular YPD  (2.0% (wt/vol) glucose) and grown to exponential phase (OD600 < 2.0) at 30°C and 300 rpm. Approximately 0.05 OD of exponentially growing yeast were inoculated into new flasks containing reduced glucose YPD (1.0% (wt/vol) glucose). After 16-18 hours, cells were then pelleted, washed with sterile miliQ water, and re-suspended in supplemented sporulation (SPO) media at an OD600 of 2.5.

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using hot acid phenol:chloroform:isoamyl alcohol (25:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in RNAse-free sterile water.
To obtain libraries representing the 3’ ends of polyadenylated transcripts, at least 1 μg was used for 3’ end sequencing. RNA fragments were mixed with 2.5 μM GsuI20TVN primer (/5BiotinTEG/ GAGCTAGTTCTGGAGTTTTTTTTTTTTTTTTTTTTVN), 0.5 mM 5-Methylcytosine-dNTPs (D1030, Zymo Research) and 0.5 μl RNasin Plus. Reaction mixtures were denatured at 65°C for 5 minutes and held at 50°C without allowing to cool. SuperScript IV, reaction buffer and 0.4 μg of Actinomycin D were added to the hot reaction mixtures and reverse transcription was performed at 50°C for 10 minutes, 80°C for 10 minutes and held at 4°C. Samples were cleaned with 1.8x volume HighPrep beads and biotinylated RNA:DNA hybrids were captured on MyOne Streptavidin C1 Dynabeads. After capture, streptavidin beads were washed once with 1x NEbuffer 2 (B7002S, NEB), re-suspended in water and subjected to second strand synthesis. The 50 μl second strand synthesis reaction consisted of 20 μl re-suspended streptavidin beads, 1X NEbuffer 2, 250 μM dNTPs, 26 μM NAD+ (B9007S), 2.5 units RNase H, 10 units E.coli DNA ligase (M0205S), and 15 units DNA polymerase I (M0209S). Second strand synthesis reactions were conducted at 16°C for 2.5 hours on a thermomixer (1400 rpm for 15 seconds, rest for 2 minutes). After reaction, beads were washed once with 1x binding and washing buffer (5.0 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1.0 M NaCl) and once with buffer B (10 mM Tris-HCl pH 7.5, 10 mM MgCl2, 0.1 mg/ml BSA). Washed beads were re-suspended in 18 μl buffer B and digested with 10 units of GsuI (ER0461, ThermoFisher Scientific) at 30°C for 1 hour on a thermomixer (1400 rpm for 15 seconds, rest for 2 minutes). After digestion, the DNA fragments in the supernatant were extracted with Phenol/chloroform and precipitated at -20°C overnight in ethanol with 0.3 M sodium acetate and 1 μl linear acrylamide. Double-stranded cDNA was quantified by Qubit (Life Technologies) and used as input for library preparation using a KAPA Hyper Prep kit (KAPA Biosystems) and KAPA Single-indexed adapters (KAPA Biosystems). Gel purified libraries were quantified by Qubit and were sequenced on the Illumina HiSeq 4000 platform with 75-base single-end reads.

treatment_protocol: For the regular WT time course, 50 μM CuSO4 was added after 2h in SPO and 1 μM β-estradiol was added after 6h in SPO for synchronous sporulation. For the mutant samples and their controls,  50 μM CuSO4 was added after 2h in SPO. Additionally after 2h in SPO, all cells with the SPT16-AID allele were treated with 3-indole-acetic acid (3-IAA, Sigma-Aldrich I3750) to a final concentration of 500 μM from a 1 M stock dissolved in DMSO.

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) SK1 derivative

value: 50 μM CuSO4 (2h), 1 μM β-estradiol (6h)


title: 75_2_18C


title: 75_2_18B

description:
comments: This sample matched with  75_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: 76_1_10


title: Wild-type TES seq 9h replicate 2

description:
TES seq
CHI114A54_S60_L007


title: 75_1_5


title: 75_1_18C


title: 75_1_10


title: 75_1_18B

description:
comments: This sample matched with  75_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 75_2_5


title: Wild-type TES seq 9h replicate 1

description:
TES seq
CHI114A43_S55_L007


title: 75_2_10


title: Wild-type TES seq 8h replicate 1

description:
TES seq
CHI114A42_S54_L007

source_name: Wild-type TES seq 8h


title: Wild-type TES seq 8h replicate 3

description:
TES seq
CHI114A64_S64_L008


title: Wild-type TES seq 7h NDT80 uninduced replicate 3

description:
TES seq
CHI114A67_S67_L008

source_name: Wild-type TES seq 7h NDT80 uninduced

value: 50 μM CuSO4 (2h)


title: Wild-type TES seq 8h replicate 2

description:
TES seq
CHI114A53_S59_L007


title: 74_1_10


title: 73_2_18C


title: 74_1_18C


title: 74_2_10


title: 74_2_5


title: 74_1_18B

description:
comments: This sample matched with  74_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 73_2_18B

description:
comments: This sample matched with  73_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 73_2_5


title: 74_1_5


title: 74_2_18B

description:
comments: This sample matched with  74_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 74_2_18C


title: Wild-type TES seq 7h replicate 2

description:
TES seq
CHI114A52_S58_L007

source_name: Wild-type TES seq 7h


title: Wild-type TES seq 7h NDT80 uninduced replicate 1

description:
TES seq
CHI114A45_S57_L007


title: SPT16-AID control TES seq 6h replicate 2

description:
TES seq
CHI114A162_S67_L008

source_name: SPT16-AID control TES seq 6h

value: FW6109 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6) SK1 derivative

value: 50 μM CuSO4 (2h), 500 μM indole-3-acetic acid (2h)


title: 73_1_18C


title: 73_1_5


title: SPT16-AID control TES seq 6h replicate 1

description:
TES seq
CHI114A161_S66_L008


title: 73_2_10

value: Age 10

value: Notexposed


title: Wild-type TES seq 7h NDT80 uninduced replicate 2

description:
TES seq
CHI114A56_S62_L008


title: SPT16-AID control TES seq 6h replicate 3

description:
TES seq
CHI114A163_S68_L008


title: Wild-type TES seq 7h replicate 1

description:
TES seq
CHI114A41_S53_L007


title: SPT16-AID, OsTIR TES seq 6h replicate 2

description:
TES seq
CHI114A156_S47_L006

source_name: SPT16-AID, OsTIR TES seq 6h

value: FW6083 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX) SK1 derivative


title: SPT16-AID, OsTIR TES seq 6h replicate 1

description:
TES seq
CHI114A155_S46_L006


title: Wild-type TES seq 7h replicate 3

description:
TES seq
CHI114A63_S63_L008


title: set2 TES seq 6h replicate 3

description:
TES seq
CHI114A112_S21_L002

source_name: set2 TES seq 6h

value: FW5767 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set2::His3MX) SK1 derivative


title: set2 TES seq 6h replicate 2

description:
TES seq
CHI114A99_S30_L003


title: SPT16-AID, OsTIR TES seq 6h replicate 3

description:
TES seq
CHI114A157_S48_L006


title: set3 TES seq 6h replicate 1

description:
TES seq
CHI114A113_S22_L002

source_name: set3 TES seq 6h

value: FW5770 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set3::His3MX) SK1 derivative


title: set3 TES seq 6h replicate 3

description:
TES seq
CHI114A115_S3_L001


title: 73_1_18B

description:
comments: This sample matched with  73_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Exposed


title: set3 TES seq 6h replicate 2

description:
TES seq
CHI114A114_S23_L002


title: 72_2_18B

description:
comments: This sample matched with  72_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 72_2_18C

value: Buccal


title: Wild-type control TES seq 6h replicate 3

description:
TES seq
CHI114A106_S52_L005

source_name: Wild-type control TES seq 6h


title: set2 set3 TES seq 6h replicate 1

description:
TES seq
CHI114A107_S53_L005

source_name: set2 set3 TES seq 6h

value: FW2912 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3, set3::His3MX, set2::His3MX) SK1 derivative


title: set2 set3 TES seq 6h replicate 2

description:
TES seq
CHI114A108_S54_L005


title: set2 TES seq 6h replicate 1

description:
TES seq
CHI114A110_S19_L002


title: set2 set3 TES seq 6h replicate 3

description:
TES seq
CHI114A109_S44_L004


title: 73_1_10

value: Male


title: 72_1_5

value: Female

value: Age 5


title: 72_1_10


title: 72_1_18C

value: Age 18


title: 72_1_18B

description:
comments: This sample matched with  72_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 71_2_18C


title: Wild-type control TES seq 6h replicate 2

description:
TES seq
CHI114A105_S1_L001

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) SK1 derivative


title: 71_2_18B

description:
comments: This sample matched with  71_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: Wild-type control TES seq 6h replicate 1

description:
TES seq
CHI114A104_S43_L004

value: 50 μM CuSO4 (2h)


title: Wild-type TES seq 60 min RTG replicate 3

description:
TES seq
CHI114A136_S10_L001

source_name: Wild-type TES seq 60 min RTG

value: 50 μM CuSO4 (2h), shift from SPO to YPD (6h)


title: 72_2_5

source_name: buccal swab at age 5


title: Wild-type TES seq 6h replicate 2

description:
TES seq
CHI114A51_S30_L004

source_name: Wild-type TES seq 6h


title: Wild-type TES seq 6h replicate 1

description:
TES seq
CHI114A40_S23_L003


title: 71_1_5


title: 71_2_10


title: Wild-type TES seq 5h replicate 3

description:
TES seq
CHI114A61_S35_L004

source_name: Wild-type TES seq 5h


title: Wild-type TES seq 6h replicate 3

description:
TES seq
CHI114A62_S36_L004


title: 71_1_18C

source_name: buccal swab at age 18


title: 71_2_5


title: 72_2_10


title: 70_2_18C


title: Wild-type TES seq 5h replicate 1

description:
TES seq
CHI114A39_S22_L003


title: Wild-type TES seq 5h replicate 2

description:
TES seq
CHI114A50_S29_L004


title: 71_1_18B

description:
comments: This sample matched with  71_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

source_name: whole blood at age 18


title: Wild-type TES seq 60 min RTG replicate 1

description:
TES seq
CHI114A134_S8_L001


title: 71_1_10

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

source_name: buccal swab at age 10


title: Wild-type TES seq 60 min RTG replicate 2

description:
TES seq
CHI114A135_S9_L001


title: 70_2_5


title: Wild-type TES seq 4h replicate 2

description:
TES seq
CHI114A49_S28_L004

source_name: Wild-type TES seq 4h


title: Wild-type TES seq 4h replicate 3

description:
TES seq
CHI114A60_S34_L004


title: 70_2_10


title: Wild-type TES seq 4h replicate 1

description:
TES seq
CHI114A38_S21_L003


title: Wild-type TES seq 3h IME1 uninduced replicate 2

description:
TES seq
CHI114A55_S61_L008

source_name: Wild-type TES seq 3h IME1 uninduced

value: no treatment


title: 70_1_5


title: Wild-type TES seq 3h IME1 uninduced replicate 1

description:
TES seq
CHI114A44_S56_L007


title: Wild-type TES seq 3h replicate 3

description:
TES seq
CHI114A59_S33_L004

source_name: Wild-type TES seq 3h


title: 70_1_10

value: Age 10


title: Wild-type TES seq 3h replicate 2

description:
TES seq
CHI114A48_S26_L003


title: Wild-type TES seq 3h replicate 1

description:
TES seq
CHI114A37_S20_L003


title: 70_1_18C

value: Notexposed


title: 70_1_18B

description:
comments: This sample matched with  70_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 69_2_5


title: 69_2_18C


title: Wild-type TES seq 30 min RTG replicate 3

description:
TES seq
CHI114A133_S60_L005

source_name: Wild-type TES seq 30 min RTG


title: Wild-type TES seq 3h IME1 uninduced replicate 3

description:
TES seq
CHI114A66_S66_L008


title: 69_1_5

description:
comments: The idat files for the Red and Green channel for this sample are the same when generated bu the service laboratory due to some untraceable reason, thus were excluded from dwonstream analysis.
genomic DNA from buccal samples
betas_normalised.csv


title: 69_2_10


title: 69_1_18C


title: 69_2_18B

description:
comments: This sample matched with  69_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 69_1_18B

description:
comments: This sample matched with  69_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type TES seq 2h replicate 3

description:
TES seq
CHI114A58_S32_L004

source_name: Wild-type TES seq 2h


title: Wild-type TES seq 30 min RTG replicate 1

description:
TES seq
CHI114A131_S47_L004


title: Wild-type TES seq 2h replicate 2

description:
TES seq
CHI114A47_S25_L003


title: Wild-type TES seq 30 min RTG replicate 2

description:
TES seq
CHI114A132_S48_L004


title: 68_2_5


title: 69_1_10


title: Wild-type TES seq 120 min RTG replicate 3

description:
TES seq
CHI114A139_S24_L002

source_name: Wild-type TES seq 120 min RTG


title: Wild-type TES seq 15 min RTG replicate 1

description:
TES seq
CHI114A128_S1_L008

source_name: Wild-type TES seq 15 min RTG


title: Wild-type TES seq 15 min RTG replicate 2

description:
TES seq
CHI114A129_S45_L004


title: 68_2_18B

description:
comments: This sample matched with  68_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type TES seq 15 min RTG replicate 3

description:
TES seq
CHI114A130_S46_L004


title: 68_2_10


title: 70_2_18B

description:
comments: This sample matched with  70_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 68_1_5


title: 68_1_18C


title: Wild-type TES seq 120 min RTG replicate 1

description:
TES seq
CHI114A137_S11_L001


title: 68_2_18C


title: SPT16-AID control TES seq 0h replicate 1

description:
TES seq
CHI114A158_S63_L008

source_name: SPT16-AID control TES seq 0h

value: FW6109 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6) SK1 derivative


title: SPT16-AID control TES seq 0h replicate 3

description:
TES seq
CHI114A160_S65_L008


title: Wild-type TES seq 2h replicate 1

description:
TES seq
CHI114A36_S19_L003


title: Wild-type TES seq 120 min RTG replicate 2

description:
TES seq
CHI114A138_S12_L001


title: 68_1_10


title: 67_2_18C


title: SPT16-AID, OsTIR TES seq 0h replicate 3

description:
TES seq
CHI114A154_S45_L006

source_name: SPT16-AID, OsTIR TES seq 0h

value: FW6083 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX) SK1 derivative


title: 67_2_5


title: SPT16-AID, OsTIR TES seq 0h replicate 2

description:
TES seq
CHI114A153_S44_L006


title: 67_1_5


title: set3 TES seq 0h replicate 3

description:
TES seq
CHI114A91_S18_L002

source_name: set3 TES seq 0h

value: FW5770 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set3::His3MX) SK1 derivative


title: SPT16-AID, OsTIR TES seq 0h replicate 1

description:
TES seq
CHI114A152_S43_L006


title: set3 TES seq 0h replicate 2

description:
TES seq
CHI114A90_S2_L001


title: 67_2_18B

description:
comments: This sample matched with  67_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: SPT16-AID control TES seq 0h replicate 2

description:
TES seq
CHI114A159_S64_L008


title: 67_1_18B

description:
comments: This sample matched with  67_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Exposed


title: 67_2_10

value: Buccal