title: old rep2 (RNA-seq)

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

description: RNA.cpm.txt

data_processing:
We removed sequencing adaptors from the raw RNA-seq reads using Cutadapt.
Reads were mapped to the hg19 human genome using Tophat v2.1.0
To quantify gene expression, we counted the sequencing reads within each gene and normalized the counts using DESeq2 in R.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, Normalized counts

source_name: HUVEC

growth_protocol: HUVEC cells were maintained at 37 °C in a humidiﬁed incubator with 5% CO2. When HUVECs attained 80% to 90% density, usually in 2 or 3 days with 0.5 × 106 start-up cells, they were passaged in a 10 cm dish coated with 0.25% gelatin and then cultured until they ceased proliferation.

extract_protocol:
Total RNA from different passaged cells were extracted by TRIzol reagent (#15596018, Invitrogen, USA).
RNA library construction and Illumina sequencing with paired-end Hiseq PE150 were performed in Novogene Biotech Co. Ltd., Beijing, China.

value: human umbilical vein endothelial cell (HUVEC)

value: old


title: A375_sh_NT_2

status: Public on Jan 01 2021

type: SRA

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

library_source: transcriptomic

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.7.1, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Homo Sapiens, Ensembl, GRCh38.p10
Supplementary_files_format_and_content: tad-delimited, raw counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: A375 and A549 cells were grown in DMEM supplementet with 10% FBS and 1% Penicillin-Streptomycin at 37°C in a humified atmosphere with 5% of CO2

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (#74104 Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dox-inducible shMCM7 or parental A549 and A375 cells, each arrested in G1 by double thymidine block, were treated for 72 hours with/without 1μg/ml Dox.

tag: cell line

tag: cell type

value: human melanoma cell line

tag: knockdown

tag: transduced with

value: CAG AGG AGG ATT TCT ACG AAA in pRSIT17 MOI=1.4

tag: cell synchronization

value: Double thymidine synchronized

tag: dox treatment

value: No Dox treatment


title: A375_wt_Dox_1

source_name: RNA-Seq_A375_parental cells_withDox

value: 1 microgram/ml Dox 72h


title: Genomic DNA from FF breast tumor tissue_8099

type: genomic

city: Buffalo

first: Yao

last: Song

state: NY

address: Carlton House - A349, Elm and Carlton Streets

country: USA

institute: Roswell Park Comprehensive Cancer Center

description: Tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip (GPL13534) using standard Illumina protocol

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

data_processing:
The raw intensity IDAT files were extracted using GenomeStudio,and processed by the minfi R package. Only loci with a median detection p value <0.05 were retained for analysis, and only samples with detection p values < 1.0E-05 at more than 75% of CpG lici passed the performance criteria for inclusion. Probes containing SNPs and/or those that were ambiguously mapped were excluded from the analysis. The final dataset contained 276,108 CpG loci across 138 samples.
The signal_intensities.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Flash frozen breast tumor tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using a MasterPure DNA purification kit (Epicentre).

tag: gender

value: Female

tag: tissue

value: Flash frozen breast tumor tissue


title: mid-aged rep2 (RNA-seq)

country: China

description: RNA.cpm.txt

tag: age

value: mid-aged


title: A375_sh_NT_1


title: young rep2 (RNA-seq)

description: RNA.cpm.txt

value: young


title: WT golden hamster lung

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description: WT golden hamster

data_processing:
Cell Ranger (v3.0.2) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to MesAur1.0 reference genome
Aligned reads were then read by Seurat (v3.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 500 genes) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control, expression matrices were log normalized and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: MesAur1.0
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for WT hamster organs' single cell data

organism: Mesocricetus auratus

source_name: golden hamster lung

extract_protocol:
After tissue preparation and cell digestion, single-cell suspensions were processed on the 10X chromium system following the manufacturer's protocols.
cDNA libraries were constructed using Chromium Single cell 3' v3 Reagent Kit (10X genomics)

tag: strain

tag: developmental stage

value: Adult

value: lung


title: A375_sh_Dox_3


title: WT golden hamster upper respiaratory tract

description: WT golden hamster

source_name: golden hamster nasal mucosa and trachea

value: nasal mucosa and trachea


title: old rep1 (RNA-seq)

description: RNA.cpm.txt


title: Genomic DNA from FF breast tumor tissue_14535

description: Tumor


title: Genomic DNA from FF breast tumor tissue_10147

description: Tumor


title: Pig_Thyroid_M1

city: Fort Collins

first: Michelle

middle: M

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Basecalling and demultiplexing were performed using ont-guppy-for-minknow (v3.0.5 for cattle data; v3.2.6 for pig and chicken data), and reads with quality score below 7 were discarded to obtain fastq files.
Demultiplexed fastq files were grouped together for each sample, and processed with Pychopper (v2.4.0) to identify and orient full-length reads.
Full-length strand-oriented reads for each sample were mapped to the respective genome assemblies (ARS-UCD1.2 for cattle; Sscrofa11.1 for pig; GRCg6a for chicken) with minimap2 (v2.16r922) with options “-ax splice -uf -k14” and modifying the maximum allowable intron size by species with option "-G 1000000" for pig and cattle, and "-G 400000" for chicken.
Uniquely mapped reads with a minimum quality score of 10 were extracted with Samtools (v1.7).
Uniquely mapped reads were used to obtain raw gene expression counts, based on the Ensembl v101 annotations for each species, using HTSeq (v0.11.2) with options "-i gene_id --type=exon --stranded=yes --mode=intersection-nonempty."
Genome_build: ARS-UCD1.2 (cattle), Sscrofa11.1 (pig), GRCg6a (chicken)
Supplementary_files_format_and_content: Raw gene counts, based on the Ensembl (v101) annotation for each species

molecule: polyA RNA

organism: Sus scrofa

source_name: Thyroid

extract_protocol:
Frozen tissues kept at -80°C were homogenized with a mortar and pestle in liquid nitrogen. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) followed by a column clean-up using the Direct-zol RNA Mini Prep Plus kit (Zymo Research, Irvine, CA) and performing an in-column DNA digestion. Integrity of the DNase-treated RNA was verified on the Experion electrophoresis system (Bio-Rad, Hercules, CA).
For each sample, 50 ng total RNA was transferred to 0.2 ml PCR tubes and adjusted to a final volume of 9µl with nuclease free water.  Reactions were prepared (9 μl total RNA, 1 μl 10 µM VNP primer , 1 μl 10mM dNTPs) and incubated for 5 min at 65°C, then snap cooled on a pre-chilled freezer block. Strand-switching buffer (4 μl 5x RT buffer, 1 μl RNaseOUT, 1 μl nuclease-free water, and 2 μl 10 μM strand-switching primer) was then added to the snap-cooled, annealed mRNA, and incubated at 42°C for 2 min. One μl of Maxima H Minus Reverse Transcriptase was added, and reactions were incubated at 42°C for 90 min, 85°C for 5 min, and held at 4°C. A round of PCR was used to introduce barcodes to the cDNAs using Oxford Nanopore PCR barcoding expansion 1-96 kit (Cat. No.EXP-PBC096). Barcoding PCR reactions were set up for each cDNA (1 μl PCR barcode, 19 μl first-strand cDNA, 20μl LongAmp Taq 2x master mix), and cycled for [3 min at 95°C]x1, [15 sec at 95°C, 15 sec at 62°C, 7 min at 65°C] x13 cycles, [15 min at 65°C]x1, then held at 4°C. Each barcoded cDNA was purified in 1x Ampure XP Beads, eluted in 20µl of nuclease free water and quantified in the Qubit. Barcoded cDNAs were pooled in a final volume of 47µl and the pool was taken to the DNA Technologies Core and Expression Analysis Laboratory at the University of California Davis where they performed the adapter ligation on the cDNA pool using SQK-DCS109 kit following manufacturer's guidelines. 50 fmol of adapter ligated library was loaded onto PromethION flow cell vR9.4.1.
Long-read Nanopore cDNA sequencing

tag: Sex

value: Male

value: Thyroid


title: A375_sh_Dox_1


title: mid-aged rep1 (RNA-seq)

description: RNA.cpm.txt


title: Genomic DNA from FF breast tumor tissue_17454

description: Tumor


title: wt_NT_3

source_name: RNA-Seq_A549_parental cells_withoutDox

value: adenocarcinomic human alveolar basal epithelial cells


title: A375_sh_Dox_2


title: Pig_Spleen_M1

source_name: Spleen

value: Spleen


title: Pig_Spleen_M2


title: Pig_Thymus_M2

source_name: Thymus

value: Thymus


title: senescent rep2 (ATAC-seq)

library_source: genomic

data_processing:
We removed sequencing adaptors from the raw ATAC-seq reads using Cutadapt.
The clean data were mapped to the human reference genome using Bowtie 2 with the following parameters: “-L 25 -X 2000 -t -q -N 1 –no-mixed –no-discordant”.
PCR duplicates were removed using Picard and then MACS, using parameters “-F BAM -g hs -w –nolambda --nomodel”, was used to call significant peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: HUVECs

growth_protocol: HUVEC cells were maintained at 37 °C in a humidiﬁed incubator with 5% CO2. When HUVECs attained 80% to 90% density, usually in 2 or 3 days with 0.5 × 10e6 start-up cells, they were passaged in a 10 cm dish coated with 0.25% gelatin and then cultured until they ceased proliferation.

extract_protocol:
The transposed DNA was purified using the MinElute PCR Purification Kit #28004 (Qiagen, Hilden, Germany) according to the kit instructions.
We split out 7.0 × 10e4 lysed cells to a sterile PCR tube for the subsequent transposition reaction and library construction using the TruePrep DNA Library Prep Kit V2 (Vazyme Biotech Co., Ltd, Nanjing, China).

value: HUVECs

value: senescent


title: wt_NT_1

value: Double thymidine synchronized


title: senescent rep1 (ATAC-seq)


title: wt_NT_2

value: No Dox treatment


title: Pig_Muscle_M2

source_name: Muscle

value: Muscle


title: wt_Dox_3

source_name: RNA-Seq_A549_parental cells_withDox

value: 1 microgram/ml Dox 72h


title: mid-aged rep2 (ATAC-seq)


title: young rep1 (RNA-seq)

description: RNA.cpm.txt

value: human umbilical vein endothelial cell (HUVEC)


title: mid-aged rep1 (ATAC-seq)

value: mid-aged


title: wt_Dox_2


title: Pig_Lymph_M2

source_name: Lymph

value: Lymph


title: Genomic DNA from FF breast tumor tissue_13014

description: Tumor

value: Female

value: Flash frozen breast tumor tissue


title: young rep2 (ATAC-seq)

value: young


title: Genomic DNA from FF breast tumor tissue_14738

description: Tumor


title: wt_Dox_1


title: Pig_Lymph_M1

value: Male


title: sh_NT_3

value: CAG AGG AGG ATT TCT ACG AAA in pRSIT17 MOI=1.4


title: young rep1 (ATAC-seq)


title: Pig_Muscle_M1


title: 15612X1: control

city: Salt Lake City

first: Carl

middle: S

last: Thummel

state: UTAH

address: 15 North 2030 East, Room 5200, University of Utah, Department of Human Genetics

department: Human Genetics

institute: University of Utah

data_processing:
The Drosophila BDGP6 genome and gene feature files were downloaded from Ensembl release 94 and the reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads (Dobin et al 2013). Reads were trimmed of adapters using cutadapt 1.16 and then aligned to the reference database using STAR in two pass mode with alignIntronMax 100000 to output a BAM file sorted by coordinates. Mapped reads were assigned to annotated genes using featureCounts version 1.6.3 and differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.20.0.
Genome_build: dm6
Supplementary_files_format_and_content: excel file, has raw counts, normalized counts, vsd log counts (DESeq2 version 1.22.2), fpkm values, and sample IDs.

organism: Drosophila melanogaster

source_name: whole fly

growth_protocol: Animals were staged as freshly eclosed adults and aged to 8 days of adulthood

extract_protocol:
Zymo Direct-zol RNA miniprep kit (with DNase treatment)
Illumina TruSeq Stranded mRNA Library Prep (RIN 8-10) with UDI. Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Prep kit (20020595) and TruSeq RNA UD Indexes (20022371). Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583). The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis. Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis. Sequencing libraries (1.3 nM) were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP chemistry workflow (20021664).  Following transfer of the flowcell to an Illumina NovaSeq instrument, a 2 x 51 cycle paired end sequence run was performed using a NovaSeq S1 reagent Kit (20027465).

treatment_protocol: All animals were reared on a control diet of 8% Yeast 9% Sugar and transferred every 2-4 days to fresh food.

value: whole fly

tag: genotype/variation

value: control

tag: timepoint


title: Pig_Lung_M2

source_name: Lung

value: Lung


title: Genomic DNA from FF breast tumor tissue_11119

description: Tumor


title: Pig_Lung_M1


title: Genomic DNA from FF breast tumor tissue_17506

description: Tumor


title: Genomic DNA from FF breast tumor tissue_15240

description: Tumor


title: Genomic DNA from FF breast tumor tissue_19000

description: Tumor


title: samples in 3DCS day14 Donor2

city: hanghzou

first: xu

middle: yu

last: lin

state: zhejiang province

address: yuhangtang road 388

department: medicine school

institute: zhejiang university

data_processing:
Each scRNA-seq sample data was separately demultiplexed, aligned to the human genome (version GRCh38), and calculated unique molecular identifier (UMI) were estimated using the Cellranger toolkit (Version 3.0.0, 10X Genomics), with default parameters. Cells with fewer than 200 detected genes, or 20,000 detected transcripts, or total mitochondrial gene expression exceeding 20% were excluded from the analysis. Genes expressed in less than 3 cells were also removed.
Ten UMI matrices from two donors at four time points were designed as replication batches, and data integration were performed into a single Seurat objects with the R package Seurat (v3.0.0). The data was  normalized with the NormalizeData function in Seurat using a scale factor of 10000. Anchors were identified using FindIntegrationAnchors.
Downstream analysis as principal component analysis (PCA), SNN graph building (FindNeighbors), and data feature scaling (ScaleData) were performed.
Genome_build: GRCh38 - 10x reference
Supplementary_files_format_and_content: csv-delimited table of the aggregated UMI count matrix

source_name: normal peripheral blood

growth_protocol: Nonmobilized peripheral blood-derived cells were cultured in 3DCS and collected at day 0, day 5, day 10 and day 14 followed by single cell sequencing analysis.

extract_protocol:
ScRNA-seq RNA were generated from the 10X Chromium Single Cell 3` Reagent Kits v3 according to the manufacturer’s protocol (10x Genomics).
ScRNA-seq libraries were generated from the 10X Chromium Single Cell 3` Reagent Kits v3 according to the manufacturer’s protocol (10x Genomics). Libraries were sequenced on the Illumina Hiseq X10 platform according to the manufacturer’s instructions (Illumina).

treatment_protocol: Nonmobilized peripheral blood-derived cells were culture in 3DCS plus the factors as SCF, FLT3L, TPO, and IL3. Single-cell RNA sequencing samples were collected at four time points: day 0, day 5, day 10 and day 14.

tag: time point

value: day 14

value: PBMCs


title: sh_NT_1

value: adenocarcinomic human alveolar basal epithelial cells

value: Double thymidine synchronized


title: Genomic DNA from FF breast tumor tissue_19072

description: Tumor


title: Pig_Liver_M2

source_name: Liver

value: Liver


title: sh_Dox_3

value: 1 microgram/ml Dox 72h


title: samples in 3DCS day10 Donor2

value: day 10


title: Pig_Liver_M1


title: Genomic DNA from FF breast tumor tissue_18337

description: Tumor


title: sh_Dox_2


title: Genomic DNA from FF breast tumor tissue_18534

description: Tumor


title: Pig_Kidney_M2

source_name: Kidney

value: Kidney


title: Genomic DNA from FF breast tumor tissue_11626

description: Tumor


title: sh_Dox_1


title: Genomic DNA from FF breast tumor tissue_13558

description: Tumor


title: samples in 3DCS day05 Donor2

value: day 05


title: Genomic DNA from FF breast tumor tissue_11691

description: Tumor

value: Female


title: Genomic DNA from FF breast tumor tissue_15564

description: Tumor

value: Flash frozen breast tumor tissue


title: Pig_Kidney_M1


title: samples in 3DCS day0 Donor2

value: day 0


title: Mock-infected lung, 3

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
FastQC (v0.11.8) to check FASTQ quality.
Triim Galore (v0.6.4) for adapter trimming
SortMeRNA (v2.1b) to remove rRNA reads.
STAR (v2.6.1d) to align files
Subread (v1.6.4) featureCounts to quantify gene counts
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene count matrix

source_name: Hesc cells

growth_protocol:
Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). The hESC line-RUES2 was cultured on irradiated mouse embryonic fibroblasts (Global Stem, cat. no. GSC-6001G) at a density of 20,000- 25,000 cells/cm2 in a medium of DMEM/F12, 20% knockout serum replacement (Life Technologies), 0.1 mM β-mercaptoethanol (Sigma Aldrich) and 20 ng/ml bFGF (R&D Systems), and medium was changed daily. hESC cultures were maintained in an undifferentiated state at 37 °C in a 5% CO2/air environment until stem cells reached about 90% confluence.
Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 6-well plates in StemFlex medium (Gibco Thermo Fisher). Cells were maintained at 37℃ with 5% CO2. hESCs were differentiated using a previously reported strategy (Zeng et al., 2016). In brief, on day 0, cells were exposed to basal medium RPMI 1640 supplemented with 1× Glutamax (Thermo Fisher Scientific), 50 μg/mL Normocin, 100 ng/mL Activin A (R&D systems), and 2 μM of CHIR99021 (GSK3β inhibitor 3, Cayman Chemical ) for 24 h. The medium was changed on day 1 to basal RPMI 1640 medium supplemented with 1× Glutamax (Thermo Fisher Scientific), 50 μg/mL Normocin, 0.2% fetal bovine serum (FBS, Corning), 100 ng/mL Activin A (R&D systems) for 2 days. On day 3, the resulting definitive endoderm cells were cultured in MCDB 131 medium (Thermo Fisher Scientific) supplemented with 1.5 g/L sodium bicarbonate, 1× Glutamax, 10 mM glucose (Sigma Aldrich) at final concentration, 2% bovine serum albumin (BSA, Lampire), 0.25 mM L-ascorbic acid (Sigma Aldrich) and 50 ng/ml of fibroblast growth factor 7 (FGF-7, Peprotech) for 2 days to acquire primitive gut tube. On day 5, the cells were induced to differentiate to posterior foregut in MCDB 131 medium supplemented with 2.5 g/L sodium bicarbonate, 1× Glutamax, 10 mM glucose at final concentration, 2% BSA, 0.25 mM L-ascorbic acid, 50 ng/ml of FGF-7, 1 μM Retinoic acid (RA; Sigma Aldrich), 100 nM LDN193189 (LDN, Axon Medchem), 1:200 ITS-X (Thermo Fisher Scientific), 200 nM TPPB (Tocris Bioscience) and 0.25 μM SANT-1 (Sigma Aldrich) for 2 days. On day 7, the cells were induced to differentiate to pancreatic endoderm in MCDB 131 medium supplemented with 2.5 g/L sodium bicarbonate, 1× Glutamax, 10 mM glucose at final concentration, 2% BSA, 0.25 mM L-ascorbic acid, 2 ng/ml of FGF-7, 0.1 μM RA, 200 nM LDN193189, 1:200 ITS-X, 100 nM TPPB and 0.25 μM SANT-1 for 3 days. On day 10, the cells were induced to differentiate to pancreatic endocrine precursors in MCDB 131 medium supplemented with 1.5 g/L sodium bicarbonate, 1× Glutamax, 20 mM glucose at final concentration, 2% BSA, 0.05 μM RA, 100 nM LDN, 1:200 ITS-X, 0.25 μM SANT-1, 1 mM T3 hormone (Sigma Aldrich), 10 μM ALK5 inhibitor II (Cayman Chemical), 10 μM zinc sulfate heptahydrate (Sigma Aldrich) and 10 μg/ml of heparin (Sigma Aldrich) for 3 days. On day 13, cells were exposed to MCDB 131 medium supplemented with 1.5 g/L sodium bicarbonate, 1× Glutamax, 20 mM glucose at final concentration, 2% BSA, 100 nM LDN193189, 1:200 ITS-X, 1 μM T3, 10 μM ALK5 inhibitor II, 10 μM zinc sulfate, 10 μg/ml of heparin, 100 nM gamma secretase inhibitor XX (Millipore) for the first 7 days. On day 27, cells were exposed to MCDB 131 medium supplemented with 1.5 g/L sodium bicarbonate, 1× Glutamax, 20 mM glucose at final concentration, 2% BSA, 1:200 ITS-X, 1 μM T3, 10 μM ALK5 inhibitor II, 10 μM zinc sulfate heptahydrate, 10 μg/ml of heparin, 1 mM N-acetyl cysteine (Sigma Aldrich), 10 μM Trolox (Millipore), 2 μM R428 (MedchemExpress) for 7-15 days. The medium was subsequently refreshed every day.  The protocol details are summarized in Figure S1B.

extract_protocol:
Organoid infections were performed at an MOI of 0.1 and harvested at 24 hpi in DMEM supplemented with 0.3% BSA, 4.5 g/L D-glucose, 4 mM L-glutamine and 1 μg/ml TPCKtrypsin. Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.  cDNA libraries were sequenced using an Illumina NextSeq 500 platform. The resulting single end reads were checked for quality (FastQC v0.11.5) and processed using the Digital Expression Explorer 2 (DEE2) (Ziemann et al., 2019) workflow.  Adapter trimming was performed with Skewer (v0.2.2) (Jiang et al., 2014).  Further quality control done with Minion, part of the Kraken package (Davis et al., 2013).  The resultant filtered reads were mapped to human reference genome GRCh38 using STAR aligner (Dobin et al., 2013) and gene-wise expression counts generated using the “-quantMode GeneCounts” parameter.  BigWig files were generated using the bamCoverage function in deepTools2 (v.3.3.0) (Ramirez et al., 2016).
RNAseq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Mock infected versus SARS-CoV-2 infected

value: lung

tag: agent

value: Mock


title: Genomic DNA from FF breast tumor tissue_17472

description: Tumor

source_name: Flash frozen breast tumor tissue


title: Genomic DNA from FF breast tumor tissue_9020

description: Tumor


title: samples in 3DCS day14 Donor1


title: Pig_Jejunum_M1

source_name: Jejunum

value: Male

value: Jejunum


title: Mock-infected lung, 2


title: samples in 3DCS day10 Donor1


title: samples in 3DCS day05 Donor1


title: Pig_Jejunum_M2


title: Mock-infected lung, 1


title: Pig_Ileum_M2

source_name: Ileum

value: Ileum


title: Pig_Ileum_M1


title: Infected cells from lung for the study of SAR-CoV-2, 3


title: samples in 3DCS day0 Donor1


title: Human nasal mucosa

description: human

data_processing:
Cell Ranger (v3.0.2) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to GRCh38-3.0.0 human reference genome
Aligned reads were then read by Seurat (v3.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 500 genes) and cells with high mitochondiral UMI counts (>10% of total) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control, expression matrices were log normalized and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for human nasal mucosa single cell data

source_name: Dissected human nasal mucosa

value: Adult


title: CT3

city: Nanjing

first: Xiaoyu

last: Wei

state: Jiangsu

address: 101 Longmian Avenue, Nanjing, Jiangsu 211166, P.R. China

institute: Nanjing Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for all samples

source_name: CAL27 cell line

extract_protocol:
Total RNA was extracted from cell  by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The deletion of TCF19 was conducted by using CRISPR/Cas9 system. Briefly, guide RNAs were designed to recognize chr6:31,127,417-31,127,435 (TCF19) (hg19) and inserted into PGL3. Transfection plasmids in CAL27 cell lines were carried out with Lipofectamine 2000 reagent (Invitrogen) and a plasmid encoding Cas9 (1.3 mg of single-guide RNA [sgRNA] and 2.6mg of Cas9) according to the manufacturer’s protocol (Invitrogen). After 24 hours, Puromycin (1.0 mg mL-1, Gibco, Carlsbad, CA) and Blasticidin (10.0 mg mL-1, InvivoGene, San Diego, CA) were added to the medium for a 48 hours treatment and subsequently single clones were selected through serial dilution.

value: oral squamous cell carcinoma cell line

tag: genotype

value: TCF19 KO


title: CT2

tag: cell line


title: Pig_Hypothalamus_M2

source_name: Hypothalamus

value: Hypothalamus


title: Infected cells from lung for the study of SAR-CoV-2, 2


title: Infected cells from lung for the study of SAR-CoV-2, 1


title: Infected cells for the study of SAR-CoV-2, 2

description: hESC.Colon.SARCCoV2.3.indexB9_S6_L001_R1_001

growth_protocol: hESCs were grown and maintained on 1% Matrigel (Corning)-coated six-well plates in StemFlex medium (Gibco) at 37°C with 5% CO2. For definitive endoderm (DE) differentiation, hESCs were cultured to achieve 80-90% confluency, and treated with 3 μM CHIR99021 (CHIR, Stem-RD) and 100 ng/ml Activin A (R&D systems) in basal medium RPMI1640 (Cellgro) supplemented with 1X Pen-Strep (Gibco) for 1 day, and changed to the basal medium containing only 100 ng/ml Activin A the next day. To induce CDX2+ hindgut endoderm, DE were treated with 3 μM CHIR99021 and 500 ng/ml FGF4 (Peprotech) in RPMI1640 supplemented with 1X B27 supplement (Gibco) and 1X Pen-Strep (Gibco) for 4 days with daily changing of fresh media. Organoids began to bud out from the 2D culture during the hindgut differentiation process. The hindgut endoderm was then subjected to colonic lineage induction by treatment with 100 ng/ml BMP2 (Peprotech), 3 μM CHIR99021 and 100 ng/ml hEGF (Peprotech) in Advance DMEM F12 medium supplemented with 1X B27 supplement (Gibco), 1X GlutaMax (Gibco), 10 mM HEPES (Gibco) and 1X Pen-Strep (Gibco) for 3 days with daily changing of fresh medium. After colonic fate induction, the colon progenitor organoids were collected from the initial 2D cultures and embedded in a 100% Matrigel dome in a 24-well plate. Differentiation to mature colonic cell types was achieved by culturing these colon progenitor organoids in differentiation medium containing 600 nM LDN193189 (Axon), 3 μM CHIR99021 and 100 ng/ml hEGF in Advance DMEM F12 medium supplemented with 1X B27 supplement, 1X GlutaMax, 10 mM HEPES and 1X Pen-Strep. The differentiation medium was refreshed every 3 days for at least 40 days to achieve full colonic differentiation. The colon organoids were passaged and expanded every 10 – 14 days at 1:6 density. To passage the organoids, the Matrigel domes containing the organoids were scrapped off the plate and resuspended in cold splitting media (Advance DMEM F12 medium supplemented with 1X GlutaMax, 10 mM HEPES and 1X Pen-Strep). The organoids were mechanically dislodged from the Matrigel dome and fragmented by pipetting in cold splitting media. The old Matrigel and splitting media were removed after pelleting cells and the organoids were resuspended in 100% Matrigel. 50 µL Matrigel containing fragmentized colon organoids were plated in one well of a pre-warmed 24-well plate.

value: Colon


title: CT1

tag: cell type


title: Pig_Hypothalamus_M1


title: CN3

value: WT


title: Pig_Duodenum_M1

source_name: Duodenum

value: Duodenum


title: Infected cells for the study of SAR-CoV-2, 1

description: hESC.Colon.SARCCoV2.1.indexB7_S4_L001_R1_001


title: CN2


title: Mock infected colon cells, 2

value: mock infected


title: Pig_BrainCortex_M1

source_name: BrainCortex

value: BrainCortex


title: Genomic DNA from FF breast tumor tissue_11326

description: Tumor

value: Female


title: Genomic DNA from FF breast tumor tissue_11086

description: Tumor

value: Flash frozen breast tumor tissue


title: CN1


title: Mock infected colon cells, 1


title: Pig_Colon_M1

source_name: Colon


title: SETDB1.KO2-MOCK-rep2

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

institute: Wuhan university

description: processed data file: SETDB1.KO2_MOCK_FPKM.txt

data_processing:
RNASeq raw data quality control by FastQC.
RNASeq raw data clean performed by cutadapt.
RNASeq data mapping to hg19/mm10 reference genomes by tophat2 with at most 2 mismatch for each reads. Cufflinks was used for differential expression gene analysis. Gene expression value with more than 2 fold change was defined differential expression genes.
Genome_build: Human hg19 (GRCh37); Mouse mm10 (GRCm38)
Supplementary_files_format_and_content: *_FPKM.txt: Tab-delimited text format file for RNASeq gene expression level in each sample.

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 10% FBS, 1% penicillin and streptomycin. All the other cells were cultured in DMEM supplemented with 10% FBS, 1% penicillin and streptomycin.

extract_protocol:
For RNASeq 10ug total RNA was used, and mRNA purification was performed using oligo-dT magnetic beads (NEBNext PolyA mRNA magnetic isolation module). mRNA was fragmented and reverse transcript into 200-400bp dscDNA for library construction.
RNA-seq library was performed by using Illumina TruSeq library construction kit. Using 5 μg total RNA as initiation, and then prepared according to the manufacturer's instruction. mRNA-seq libraries were sequenced using Illumina HiSeq X Ten for 100 bp paired-end sequencing.

treatment_protocol: All the cells were treated with 10 μM BIX-01294 for 12 hr.

value: SETDB1 KO

tag: treatment

value: MOCK


title: Pig_Heart_M1

source_name: Heart

value: Heart


title: Pig_Cerebellum_M2

source_name: Cerebellum

value: Male

value: Cerebellum


title: HSkM_day4 3

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

description: differentiated for 4 days HSkM

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2). The first four and the last four nucleotides are derived from the NEXTflex Adapter. Those nucleotides have been trimmed with cutadapt (version 1.12).
Quality filtering: fastq_quality_filter from FASTX-Toolkit (0.0.13.2) was used with -Q33, -p 95 and -q 20 parameters
Conversion to fasta:  fastq_to_fasta from FASTX-Toolkit (0.0.13.2) was used
Read collapsing: read redundance was removed and reads were counted with fastx_collapser from FASTX-Toolkit (0.0.13.2)
Calculating raw counts using an in-house Python script
Genome_build: NA
Supplementary_files_format_and_content: sequence and raw read count in the header

source_name: Human Skeletal Myoblats

growth_protocol: Primary skeletal myoblasts and HSkM cells were grown in HAM F-10 medium (Lonza) supplemented with 20% FBS (BioWest), 2 mM l-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin (Invitrogen) at 37°C, 5% CO2. Upon shifting to a 2% horse serum-containing medium, HSkM myoblasts were induced to differentiate and fuse.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) from cells according to the manufacturer's protocol.
Small RNA libraries were generated using a NEXTflex Small RNA-Seq Kit (Bioo Scientific) according to the manufacturer’s instructions. Number of biological replicas per group: 3.

tag: differentiation

value: day 4

value: HSkM


title: SETDB1.KO2-MOCK-rep1


title: Genomic DNA from FF breast tumor tissue_19082

description: Tumor


title: HSkM_day4 2

description: differentiated for 4 days HSkM cells


title: SETDB1.KO1-MOCK-rep2

description: processed data file: SETDB1.KO1_MOCK_FPKM.txt


title: HSkM_day4 1

description: differentiated for 4 days HSkM cells


title: Genomic DNA from FF breast tumor tissue_10603

description: Tumor


title: Pig_Adipose_M2

source_name: Adipose

value: Adipose


title: sh_NT_2

value: adenocarcinomic human alveolar basal epithelial cells

tag: knockdown

tag: transduced with

value: CAG AGG AGG ATT TCT ACG AAA in pRSIT17 MOI=1.4

tag: cell synchronization

value: Double thymidine synchronized

value: No Dox treatment


title: SETDB1.KO1-MOCK-rep1


title: Genomic DNA from FF breast tumor tissue_17074

description: Tumor

tag: gender

tag: tissue


title: Genomic DNA from FF breast tumor tissue_10280

description: Tumor


title: Genomic DNA from FF breast tumor tissue_14462

description: Tumor


title: Pig_Adipose_M1


title: Genomic DNA from FF breast tumor tissue_18313

description: Tumor


title: Genomic DNA from FF breast tumor tissue_13958

description: Tumor


title: WT-MOCK-rep2

description: processed data file: WT_MOCK_FPKM.txt

value: WT


title: WT-MOCK-rep1

description: processed data file: WT_MOCK_FPKM.txt


title: HSkM_day0 1

description: proliferating cells

value: day 0


title: HSkM_day0 2

description: proliferating cells


title: HSkM siMEF2C_2 2

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) from cells according to the manufacturer's protocol.
Small RNA libraries were generated using a NEXTflex Small RNA-Seq Kit (Bioo Scientific) according to the manufacturer’s instructions. Number of biological replicas per group: 2.

treatment_protocol: To knock down MEF2C (MEF2C KD), the HSkM cells were transfected using Lipofectamine 2000 (Invitrogen) according to the manufacturer's protocols; 50 nM siRNA was used.

value: MEF2C knock-down


title: Vector-BIX

description: This Sample represents two replicates.

value: Vector

value: 10 uM BIX-01294 for 12 hr


title: H37Rv_T0d_SG11474142_256407810014_S001_GE1_1105_Oct12_1_1_rep2

type: RNA

city: Borstel

first: Christian

last: Utpatel

address: Parkallee 1

country: Germany

institute: Forschungszentrum Borstel

description: Gene expression after 10 days of oxygen depletion

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to custom Agilent 8x15K microarrays (OakLabs), eArray design ID 064078 for 17 hours at 65 °C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent). Remaining liquids at the bottom edge of the slide were removed by dabing it on a cleaning tissue.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan settings for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using the protocol GE1_1105_Oct1 and  grid 064078_D_F_20140130. Data was further analyzed by Agilent GeneSpring 13.1.1 software, with percentile shift normalization to the 75th percentile. Expression was analyzed in the biological significance workflow in gene-level experiments and differential expressed genes were selected using the moderated t-test, a corrected p-value of ≥0.05 (FDR, Benjamini-Hochberg) and a fold change ≥2.

organism: Mycobacterium tuberculosis

label_protocol: 50 ng of total RNA were labeled by the “Low Input Quick AMP WT Labeling Kit, one color“ (Agilent Technologies, Santa Clara, USA) according to the manufacturer`s instructions. Briefly, mRNA was amplified by reverse transcription. cDNA was transcribed by T7 RNA Polymerase integrating Cyanine 3 dye (Cy3)-labeled Cytidintriphosphate (CTP).

extract_protocol: Bacteria were inactivated with 1:1 (v/v) guanidine thiocyanate buffer (300 g guanidin thiocyanate, 2.5g N´laurylsarcosine, 3.7 g sodium citrate in 500 ml Diethylpyrocarbonate (DEPC)-H2O, 3.5 mL ß-Mercaptoethanol), centrifuged at 3k x g for 30 minutes, resuspended in lysis binding buffer from MirVana kit (Thermo Fisher Scientific) and disrupted in lysing matrix B beads (MP Biomedicals) in a FastPrep shaker (FastPrep-24, MP Biomedicals). RNA isolation was performed according to MirVana kit manufacturer’s instructions.

tag: strain


title: pericolonic; stromal pellet; F44

city: Stanford

first: Heather

last: Clemons

state: CA

address: Beckman Center

department: Dept of Biochemistry

institute: Stanford School of Medicine

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78526.gif

hyb_protocol: not provided

scan_protocol: Model: GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene Human Universal Reference

source_name: pericolonic; stromal pellet; F44, 10 ug labeled aRNA

extract_protocol:
Adipose Tissue Samples; Specimen Collection Adipose tissue specimens were collected either from the Stanford Tissue Bank, Stanford Dermatology Clinic, Stanford Surgical Pathology or directly from the surgeon at the time of surgery. All surgeries were performed at Stanford Hospital and Clinics. When necessary a trained pathologist dissected the desired adipose specimen from the organ/limb/skin to which it was attached. Samples acquired by Stanford Tissue Bank or Surgical Pathology may have been stored at 4C for up to several hours but were always processed on the same day as the surgery was performed. All samples are considered normal human tissues and were originally collected under the IRB Study of Messenger RNA Expression in Normal Human Tissues ID: 76363, which did not require patient consent as very little patient information (age, gender, procedure) was provided. Subsequently it was determined that our sample collection does not meet the definitions of human subject research under Stanfords Human Research Protection Program and therefore an IRB protocol was no longer required.
Tissue Fractionation - Clemons; Tissue Fractionation Adipose tissue samples were thoroughly rinsed with 70% ethanol to minimize risk of microbial contamination of cell cultures. Tissues were then rinsed with Hanks Balanced Salt Solution (HBSS) and transferred to a clean dish. At this time 1-4 g of tissue were removed and stored at -80C. Additionally a thin slice of each tissue was placed in 10% formalin for paraffin embedding. The remainder of each tissue sample was minced using surgical scissors. Tissue pieces were transferred to 50 ml conical tubes (up to 25 ml tissue per tube), and an equivalent volume of collagenase solution* was added to the tube. Tissue was again minced with scissors until no large pieces remained. Tubes were shaken to mix and incubated at 37C for 30 min to 4 hours, until pieces of tissue were no longer visible. Shin/calf adipose tissue in general took the longest and abdominal and thigh lipoaspirate the shortest time to digest. Digested tissues were then passed through a 180-micron nylon net filter and centrifuged at 100g for 5 minutes to pellet stromal-vascular cells. A 16-gauge needle attached to a 20 ml syringe was passed through the top visible lipid/adipocyte layer and the entire bottom layer containing buffer, cell pellet and blood cells was aspirated from the bottom and transferred to a new conical, tube. This cell suspension (stromal-vascular fraction) was thoroughly mixed by pipetting and divided equally into 2 conical tubes. One of these was set aside for cell culture (see Cell Culture) and the other was centrifuged at 400g for 7 minutes. Buffer was carefully aspirated with a pipette to avoid losing pelleted cells and 15 ml Trizol was added. The remaining lipid/adipocyte layer was washed 1-2 times depending on the amount of visible blood cells: 25 ml HBSS was added to the adipocytes, and gently inverted to mix. Adipocytes were centrifuged at 100g and excess buffer along with contaminating cells was aspirated from the bottom using a needle and syringe as described above. An equal volume of Trizol was added to the washed adipocytes. The stromal-vascular pellet sample and the adipocyte sample were stored in Trizol at -80C.  Collagenase Solution: For stock solution 1000 U/ml Sigma Type II Collagenase (Cat# C6885) was dissolved in HBSS and centrifuged at 1000g for 20 minutes. Resulting liquid fraction was filtered (.22 micron) and stored at -20C and pelleted crystals were discarded. For working solution 1000 U/ml collagenase stock solution was diluted 3x in HBSS containing 5mM CaCl2
Amplification 1 ug of each total RNA sample was amplified using Ambion Amino Allyl MessageAmp II-96 Kit (Cat# 1821) according to manufacturers protocol

tag: age

value: 44 years

tag: organism part

value: pericolonic

tag: sample fraction

value: stromal pellet

value: female


title: HSkM_day0 3

description: proliferating cells


title: HSkM siMEF2C_2 1

value: day 4


title: ATG5.KD-MOCK

description: This Sample represents two replicates.

tag: genotype/variation

value: ATG5 KD

value: MOCK


title: H37Rv_T0d_D_anaerobic_20-01-2016_25-04-2016_1_rep1


title: H37Rv_T0d_D_anaerobic_14-10-2013_20-01-2016_1_rep3


title: HSkM siMEF2C_1 2

value: HSkM


title: knee (popliteal); tissue; M77

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79633.gif

scan_protocol: Model: GenePix 4000B

source_name: knee (popliteal); tissue; M77, 10 ug labeled aRNA

value: 77 years

value: knee (popliteal)

value: tissue

tag: Sex

value: Male


title: Beijing_T10d_D_anaerobic_02-06-2014_22-03-2016_rep3


title: Genomic DNA from FF breast tumor tissue_14309

description: Tumor

value: Female

value: Flash frozen breast tumor tissue


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79589.gif

source_name: perirenal (retroperitoneal); stromal pellet; F41, 10 ug labeled aRNA

value: 41 years

value: perirenal (retroperitoneal)


title: Beijing_T10d_D_anaerobic_13-01-2014_22-03-2016_rep1


title: HSkM siMEF2C_1 1

tag: genotype

value: MEF2C knock-down


title: breast L; tissue; F23

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79603.gif

value: Stratagene Human Universal Reference

source_name: breast L; tissue; F23, 10 ug labeled aRNA

value: 23 years

value: breast (left)


title: SETDB1.KO2-INPUT

data_processing:
FastQC for ChIP-seq raw sequence data quality control.
Cutadapt was used to remove low quality reads and adaptor contamination.
ChIP-seq clean data mapped to hg19 reference genome by bowtie2 with at most 2 mismatch and only unique mapped reads were allowed for next step analysis.
MACS2 was used for ChIP-seq peaks calling.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file for ChIP-seq mapped results.

growth_protocol: U2OS cells were cultured in RPMI 1640 supplemented with 10% FBS, 1% penicillin and streptomycin. All the other cells were cultured in DMEM supplemented with 10% FBS, 1% penicillin and streptomycin

extract_protocol:
DNA and histone were cross-link and digested into single nucleosome by using micrococcal nuclease,  and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND604). Briefly, 50 μL purified ChIP DNA (8-10 ng) was end-reparied for dA tailing, followed by adaptor ligation. Each adaptor marked with a barcode of 6 bp which can be recognized after mixing different sample together. Adaptor-ligated ChIP DNA was purified by AMPure XP beads (1:1) and then amplifying by PCR of 11-13 cycles with the primer matching with adaptor universal part. Amplified ChIP DNA was purified again using AMPure XP beads (1:1) in 35 μL EB elution buffer. For multiplexing, libraries with different barcode were mixed together with equal molar quantities by considering appropriate sequencing depth (30-40 million reads per library). Libraries were sequenced by Illumina Hiseq X Ten platform with pair-end reads of 150 bp.

treatment_protocol: cells were treated with 10 μM BIX-01294 for 12 hr.

tag: cell line


title: pericolonic; tissue; F23a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79598.gif

source_name: pericolonic; tissue; F23a, 10 ug labeled aRNA

value: pericolonic

value: female


title: HSkM siCTRL 2

value: day 4

value: siCTRL


title: ATG5.KD-BIX

description: This Sample represents two replicates.

value: ATG5 KD

value: 10 uM BIX-01294 for 12 hr


title: SETDB1.KO2-H3K9me3

tag: chip antibody


title: HSkM siCTRL 1

value: HSkM


title: SETDB1.KO1-INPUT


title: thigh; tissue; M24a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78553.gif

source_name: thigh; tissue; M24a, 10 ug labeled aRNA

value: 24 years

value: thigh

value: tissue


title: H37Rv_T10d_D_anaerobic_23-01-2014_22-03-2016_rep2


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79616.gif

source_name: perirenal (retroperitoneal); tissue; M67, 10 ug labeled aRNA

value: 67 years

value: Male


title: Chicken_Thymus_M4

organism: Gallus gallus

source_name: Thymus

value: Thymus


title: Pig_Cerebellum_M1

value: Cerebellum


title: Chicken_Thymus_M3


title: SETDB1.KO1-H3K9me3


title: CON_Ad.lib_7

city: Dallas

first: Li

last: Li

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

data_processing:
We obtained averaged 2.5 million mapped reads per sample with 90% unique mapped efficiency.
The paired-end clean reads were aligned to the mouse reference genome GRCm38_mm10 (release99) using STAR and each gene reads numbers were count by FeatureCounts.
Differential expression gene (DEG) analysis was performed by DEseq2 package in which gene length and dispersion bias was corrected.
The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR).
Genes with an adjusted P value < 0.05 and logFold > 0.3 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts

organism: Mus musculus

source_name: Hypothalamus slice

extract_protocol:
Total RNA was extracted by the Direct-zol RNA Kits (ZYMO) according to manufacturer’s recommendations and validated by the Agilent 2100 Bioanalyzer.
150 bp paired-end reads were sequenced on DNBseq platform in BGI Americas Corporation.

treatment_protocol: Hypothalamus slice were collected from 4-week risperidone diet fed mice at at ad litem or pair feed condition where their body weight were not different from control diet fed mice.

value: wild type

value: Hypothalamus

tag: treatment


title: Genomic DNA from FF breast tumor tissue_18197

description: Tumor

source_name: Flash frozen breast tumor tissue

value: Female

value: Flash frozen breast tumor tissue


title: DMSO-INPUT

value: DMSO for 12hr


title: Chicken_Thymus_F2


title: RISP_PF_6


title: RISP_Ad.lib_7


title: DMSO-H3K9me3


title: Chicken_Thymus_F1


title: BIX01294-INPUT

value: 10 μM BIX-01294 for 12 hr


title: Chicken_Testis_M4

source_name: Testis

value: Testis


title: BIX01294-H3K9me3


title: CON_Ad.lib_6


title: CON_Ad.lib_5


title: breast L; adipocyte; F52b

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79595.gif

value: Stratagene Human Universal Reference

source_name: breast L; adipocyte; F52b, 10 ug labeled aRNA

value: 52 years

value: breast (left)

value: adipocyte

value: female


title: Chicken_Spleen_M4

source_name: Spleen

value: Spleen


title: thigh; tissue; F73a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79607.gif

source_name: thigh; tissue; F73a, 10 ug labeled aRNA

value: 73 years

value: thigh

value: tissue


title: Beijing_T10d_D_anaerobic_02-06-2014_22-03-2016_rep2


title: Chicken_Testis_M3

value: Male


title: RISP_PF_5

value: wild type


title: Chicken_Spleen_M2


title: RISP_Ad.lib_6

value: Hypothalamus


title: thigh; tissue; UUc

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78554.gif

source_name: thigh; tissue; UUc, 10 ug labeled aRNA

value: unknown


title: Chicken_Spleen_F2

value: Female


title: pericolonic; tissue; M46

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79599.gif

source_name: pericolonic; tissue; M46, 10 ug labeled aRNA

value: 46 years

value: pericolonic


title: NK anti-PBX1_rep1.

city: Hefei

first: Zhou

last: Yonggang

state: Anhui

address: 443 HuangShan Road

department: School of Life Science and Medical Center

institute: University of Science and Technology of China

description: NK anti-PBX1_rep1.

data_processing:
Raw reads in fastq format were first processed using cutadapt (v1.12). Clean reads were obtained by trimming adapters, removing sequences containing unknown bases more than 5% or low quality bases. All the downstream analyses were based on the clean reads.
The reference genome and gene model annotation files were downloaded directly from the genome website. The reference genome index was built using BWA (v0.7.13), and paired-end clean reads were aligned to the reference genome using BWA (v0.7.13).
Peak calling was performed using MACS (v2.1.0) with default parameters. The p-value could be adjusted based on the total clean reads. The location and length of peaks could be obtained, which would be used in the downstream analyses.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include the peak information of NK cell transcription factor PBX1 binding to DNA.

source_name: Decidua NK cells

extract_protocol:
Lysates were clarified from sonicated nuclei and transcription factor PBX1-DNA complexes were isolated with antibody.
A total amount of 10ng qualified ChIP-ed DNA per sample was used as input material for the library preparation. The sequencing libraries were generated using the VAHTS Universal DNA Library Prep Kit for Illumina® (Vazyme, ND604) following manufacturer’s recommendations. Firstly, the end repair of DNA fragments was performed and an "A" base was added at the 3'-end of each strand. Adapters (Vazyme, N801) were then ligated to both ends of the end repaired/dA tailed DNA fragments for amplification and sequencing. The DNA fragments were purified and selected with VAHTSTM DNA Clean Beads (Vazyme, N411) in order to get appropriate size for sequencing. PCR was performed and aimed products were purified finally.

treatment_protocol: NK cells from normal decidua have been isolated by Human NK cell Isolation Kit (Miltenyi Biotec, Cat# 130-092-657).

value: decidua tissue

tag: cell type

value: CD56+CD3- NK cells

tag: antibody

value: Rabbit anti-human PBX1 (CST, Cat# 4342S, RRID:AB_2160295)


title: NK IgG control

description: NK IgG control

value: Rabbit IgG (CST,Cat# 2729S, RRID:AB_1031062)


title: NK anti-PBX1_rep2.

description: NK anti-PBX1_rep2.


title: breast L; stromal pellet; F52b

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79594.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

value: Stratagene Human Universal Reference

source_name: breast L; stromal pellet; F52b, 10 ug labeled aRNA

value: 52 years

value: breast (left)

value: stromal pellet


title: Vector-MOCK

description: This Sample represents two replicates.

value: Vector

value: MOCK


title: RISP_PF_4


title: H37Rv_T10d_D_anaerobic_24-10-2013_22-03-2016_rep1


title: 1000ng HCT116 DNA rep2

city: Tampa

first: Jinyong

last: Huang

state: Florida

address: 12902 USF Magnolia Drive

department: Tumor biology

institute: Moffitt Cancer Center

description:
RaMWAS summary.xlsx
cfMBD_CpG_annotation_coverage_TPM.txt
cfMBD_CpG_annotation_coverage_TPM_sum.txt
HCT1000.wig

data_processing:
The sequenced reads were then aligned to the human genome (hg19) using Bowtie-2 (Version 2.4.2) with the default settings.
After the alignment, the generated sam files were converted to bam files, followed by sorting and indexing duplicate read removal, and  read count extractions on chr1 - chr22 using SAMtools (Version 1.11) ‘view’, ‘sort’, ‘index’, and ‘markdup’ command lines.
R (Version 4.0.3 or greater) package RaMWAS (Version 1.12.0) was used for quality control of the overall mapping quality and calculation of average non-CpG/ CpG coverage and coverage by CpG density.
R package MEDIPS (Version 1.40.0) was then applied for saturation analysis and calculation of correlations of genome wide short read coverage profiles between samples.
Normalized data were exported as wiggle file for visualization on the Integrative Genomics Viewer. BEDtools (Version 2.28.0) ‘coverage’ command line was used to call the coverage according to CpG annotations, using hg19 CpG annotations table as a template. TPM (Transcripts Per Kilobase Million) normalization was performed before comparing the CpG annotations coverage between different samples.
Genome_build: hg19
Supplementary_files_format_and_content: RaMWAS summary.xlsx (Output of RaMWAS summary qc)
Supplementary_files_format_and_content: cfMBD_CpG_annotation_coverage_TPM.txt (TPM normalized reads of each CpG annotation feature (cfMBD-seq))
Supplementary_files_format_and_content: cfMBD_CpG_annotation_coverage_TPM_sum.txt (Sum of mapped reads for each CpG annotation feature (cfMBD-seq))
Supplementary_files_format_and_content: MBD_CpG_annotation_coverage_TPM_sum.txt (Sum of mapped reads for each CpG annotation feature (low input MBD-seq))
Supplementary_files_format_and_content: cfMeDIP_CpG_annotation_coverage_TPM_sum.txt (Sum of mapped reads for each CpG annotation feature (cfMeDIP-seq))

source_name: HCT116 cell line

extract_protocol:
QIAamp Circulating Nucleic Acid Kit and QIAamp DNA Blood Mini Kit
KAPA Hyper Prep Kit

tag: input (ng)

tag: filler dna methylation ratio

tag: filler dna amount (ng)

tag: mbd protein (ug)

tag: mbd-specific beads (ul)

tag: wash

value: Standard

tag: elution fraction

value: Single

tag: elution salt level

value: High


title: thigh lipo; tissue; UUb

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78551.gif

tag: reference

source_name: thigh lipo; tissue; UUb, 10 ug labeled aRNA

tag: age

value: unknown

tag: organism part

value: thigh lipo

tag: sample fraction

value: tissue


title: H37Rv_T10d_D_anaerobic_19-02-2015_22-03-2016_rep3

tag: strain


title: CON_Ad.lib_4

tag: genotype

value: wild type

tag: tissue

value: Hypothalamus


title: breast R; tissue; F57a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79585.gif

source_name: breast R; tissue; F57a, 10 ug labeled aRNA

value: 57 years

value: breast (right)

tag: Sex

value: female


title: Chicken_Spleen_F1

value: Female

value: Spleen


title: 1000ng HCT116 DNA rep1


title: Chicken_Ovary_F2

source_name: Ovary

value: Ovary


title: CON_Ad.lib_3

tag: treatment


title: RISP_Ad.lib_5


title: 100ng HCT116 DNA rep2

description:
RaMWAS summary.xlsx
cfMBD_CpG_annotation_coverage_TPM.txt
cfMBD_CpG_annotation_coverage_TPM_sum.txt
HCT100.wig

tag: input (ng)


title: Chicken_Ovary_F1


title: 100ng HCT116 DNA rep1

tag: filler dna methylation ratio


title: Chicken_Muscle_M2

source_name: Muscle

value: Male

value: Muscle


title: pericolonic; adipocyte; F44

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78525.gif

value: Stratagene Human Universal Reference

source_name: pericolonic; adipocyte; F44, 10 ug labeled aRNA

value: 44 years

value: pericolonic

value: adipocyte


title: RISP_Ad.lib_3

source_name: Hypothalamus slice


title: 10ng HCT116 DNA rep2

description:
RaMWAS summary.xlsx
cfMBD_CpG_annotation_coverage_TPM.txt
cfMBD_CpG_annotation_coverage_TPM_sum.txt
HCT10.wig

tag: filler dna amount (ng)

value: Standard

value: Single

value: High


title: 10ng HCT116 DNA rep1

tag: mbd protein (ug)


title: Chicken_Muscle_F2


title: RISP_Ad.lib_4

value: wild type


title: arm (upper); tissue; UUd

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79619.gif

source_name: arm (upper); tissue; UUd, 10 ug labeled aRNA

value: unknown

value: arm (upper)

value: tissue


title: 1ng HCT116 DNA rep2

description:
RaMWAS summary.xlsx
cfMBD_CpG_annotation_coverage_TPM.txt
cfMBD_CpG_annotation_coverage_TPM_sum.txt
HCT1.wig

tag: mbd-specific beads (ul)


title: RISP_Ad.lib_2

value: Hypothalamus


title: RISP_PF_3


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79617.gif

source_name: perirenal (retroperitoneal); adipocyte; M58, 10 ug labeled aRNA

value: 58 years

value: perirenal (retroperitoneal)


title: Chicken_Muscle_F1

value: Female


title: Chicken_Lung_M4

source_name: Lung

value: Male

value: Lung


title: 1000ng filler rep2

description:
RaMWAS summary.xlsx
cfMBD_CpG_annotation_coverage_TPM.txt
cfMBD_CpG_annotation_coverage_TPM_sum.txt

source_name: Pooled healthy plasma

tag: wash


title: Chicken_Lung_M3


title: CON_Ad.lib_1


title: CON_Ad.lib_2


title: heel; tissue; F31

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79612.gif

value: Stratagene Human Universal Reference

source_name: heel; tissue; F31, 10 ug labeled aRNA

value: 31 years

value: heel

value: female


title: heel; tissue; M24a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79614.gif

source_name: heel; tissue; M24a, 10 ug labeled aRNA

value: 24 years


title: bladder (retroperitoneal); tissue; F57

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79597.gif

source_name: bladder (retroperitoneal); tissue; F57, 10 ug labeled aRNA

value: 57 years

value: bladder (retroperitoneal)


title: RISP_PF_2

value: wild type


title: 1000ng filler rep1

value: Standard

tag: elution fraction

value: Single

value: High


title: Chicken_Lung_F1


title: 1ng HCT116 DNA rep1

tag: elution salt level


title: Chicken_Lung_F2


title: breast L; tissue; F52b

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79600.gif

tag: reference

source_name: breast L; tissue; F52b, 10 ug labeled aRNA

value: 52 years

value: breast (left)

value: tissue


title: breast L; stromal pellet; F58

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79602.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

source_name: breast L; stromal pellet; F58, 10 ug labeled aRNA

tag: age

value: 58 years

value: stromal pellet


title: thigh; tissue; F61

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78552.gif

source_name: thigh; tissue; F61, 10 ug labeled aRNA

value: 61 years

tag: organism part

value: thigh


title: RISP_Ad.lib_1

value: Hypothalamus


title: perispleenic; tissue; M59

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79761.gif

value: Stratagene Human Universal Reference

source_name: perispleenic; tissue; M59, 10 ug labeled aRNA

value: 59 years

value: perispleenic

tag: sample fraction

value: Male


title: Chicken_Liver_M4

source_name: Liver

value: Liver


title: thigh; stromal pellet; F58a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78529.gif

source_name: thigh; stromal pellet; F58a, 10 ug labeled aRNA

value: female


title: breast L; adipocyte; F23

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79604.gif

source_name: breast L; adipocyte; F23, 10 ug labeled aRNA

value: 23 years

value: adipocyte


title: breast L; stromal pellet; F23

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79632.gif

source_name: breast L; stromal pellet; F23, 10 ug labeled aRNA


title: 500ng filler rep1

value: Standard

value: Single

value: High


title: RISP_PF_1

source_name: Hypothalamus slice

tag: strain

value: wild type


title: pericolonic; adipocyte; F51c

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79605.gif

source_name: pericolonic; adipocyte; F51c, 10 ug labeled aRNA

value: 51 years

value: pericolonic


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79618.gif

source_name: perirenal (retroperitoneal); adipocyte; F41, 10 ug labeled aRNA

value: 41 years

value: perirenal (retroperitoneal)


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79634.gif

source_name: perirenal (retroperitoneal); tissue; F56, 10 ug labeled aRNA

value: 56 years

value: tissue


title: Double wash Multiple medium+high elution

source_name: Pooled healthy plasma

value: Double

value: Multiple

value: Medium+High


title: Chicken_Liver_M2

value: Male

value: Liver


title: breast R; tissue; F52b

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79596.gif

value: Stratagene Human Universal Reference

source_name: breast R; tissue; F52b, 10 ug labeled aRNA

value: 52 years

value: breast (right)

value: female


title: arm lipo; tissue; UU

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79586.gif

source_name: arm lipo; tissue; UU, 10 ug labeled aRNA

value: unknown

value: arm lipo


title: Double wash Multiple high elution

value: High


title: Double wash Multiple low elution

value: Low


title: J_770_H3K27me3_input

city: Bandar Baru Bangi

first: Norashikin

last: Sarpan

state: Selangor

address: 6 Persiaran Institusi

department: Advanced Biotechnology and Breeding Centre

country: Malaysia

institute: Malaysian Palm Oil Board

data_processing:
Raw reads were checked using FastQC v0.11.3 software.
Raw reads were trimmed using Flexbar v3.4.0 (Dodt et al., 2012).
Trimmed reads were aligned to Elaeis guineensis P5 gene models (Sanusi et al., 2018) ±1 kb flanking regions using Bowtie2 v2.2.5 (Langmead and Salzberg, 2012).
Removal of duplicate reads was performed using SAMtools v1.9 (Li et al., 2009).
Histone-bound regions were identified using MACS2 v2.1.1.20160309 (Zhang et al., 2008) with options -q 0.05 specified for H3K4me3, while --broad --broad-cutoff 0.05 was conducted for H3K27me3.
Genome_build: Elaeis guineensis P5-build reference genome (NCBI BioProject accessions PRJNA192219, accessions ASJS00000000) (Singh et al., 2013).
Supplementary_files_format_and_content: Called peaks files (.xls) of histone-associated regions based on P5 gene models (Sanusi et al., 2018).

organism: Elaeis guineensis

source_name: leaf

extract_protocol:
Chromatin was isolated, sheared, and immunoprecipitated (Sarpan et al., 2018). ChIP-grade antibodies, anti-H3K4me3 (ab12209) and anti-H3K27me3 (ab6002) (Abcam, UK), were used for the ChIP assay.
Sequencing libraries were prepared from non-immunoprecipitated and ChIP DNA using the TruSeq® ChIP library preparation kit (Illumina, USA).

tag: plant type

value: clonal plant

tag: leaf number

value: frond 0

tag: fruit phenotype

value: mantled

tag: palm tree id

tag: chip antibody


title: Chicken_Liver_F2

extract_protocol:
Frozen tissues kept at -80°C were homogenized with a mortar and pestle in liquid nitrogen. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) followed by a column clean-up using the Direct-zol RNA Mini Prep Plus kit (Zymo Research, Irvine, CA) and performing an in-column DNA digestion. Integrity of the DNase-treated RNA was verified on the Experion electrophoresis system (Bio-Rad, Hercules, CA).
For each sample, 50 ng total RNA was transferred to 0.2 ml PCR tubes and adjusted to a final volume of 9µl with nuclease free water.  Reactions were prepared (9 μl total RNA, 1 μl 10 µM VNP primer , 1 μl 10mM dNTPs) and incubated for 5 min at 65°C, then snap cooled on a pre-chilled freezer block. Strand-switching buffer (4 μl 5x RT buffer, 1 μl RNaseOUT, 1 μl nuclease-free water, and 2 μl 10 μM strand-switching primer) was then added to the snap-cooled, annealed mRNA, and incubated at 42°C for 2 min. One μl of Maxima H Minus Reverse Transcriptase was added, and reactions were incubated at 42°C for 90 min, 85°C for 5 min, and held at 4°C. A round of PCR was used to introduce barcodes to the cDNAs using Oxford Nanopore PCR barcoding expansion 1-96 kit (Cat. No.EXP-PBC096). Barcoding PCR reactions were set up for each cDNA (1 μl PCR barcode, 19 μl first-strand cDNA, 20μl LongAmp Taq 2x master mix), and cycled for [3 min at 95°C]x1, [15 sec at 95°C, 15 sec at 62°C, 7 min at 65°C] x13 cycles, [15 min at 65°C]x1, then held at 4°C. Each barcoded cDNA was purified in 1x Ampure XP Beads, eluted in 20µl of nuclease free water and quantified in the Qubit. Barcoded cDNAs were pooled in a final volume of 47µl and the pool was taken to the DNA Technologies Core and Expression Analysis Laboratory at the University of California Davis where they performed the adapter ligation on the cDNA pool using SQK-DCS109 kit following manufacturer's guidelines. 50 fmol of adapter ligated library was loaded onto PromethION flow cell vR9.4.1.
Long-read Nanopore cDNA sequencing

tag: Sex

value: Female

tag: tissue


title: Double wash Multiple low+medium+high elution

tag: input (ng)

tag: filler dna methylation ratio

tag: filler dna amount (ng)

tag: mbd protein (ug)

value: Double

value: Low+Medium+High


title: Double wash Multiple medium elution

tag: mbd-specific beads (ul)

tag: wash

tag: elution fraction

value: Multiple

tag: elution salt level

value: Medium


title: J_770_H3K27me3_ChIP


title: J_770_H3K4me3_input


title: Chicken_Kidney_M4

source_name: Kidney

value: Male

value: Kidney


title: Double wash Single low elution

value: Single


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79615.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

tag: reference

value: Stratagene Human Universal Reference

source_name: perirenal (retroperitoneal); tissue; M49, 10 ug labeled aRNA

tag: age

value: 49 years

tag: organism part

value: perirenal (retroperitoneal)

tag: sample fraction

value: tissue


title: Double wash Single medium elution

description:
RaMWAS summary.xlsx
cfMBD_CpG_annotation_coverage_TPM.txt
cfMBD_CpG_annotation_coverage_TPM_sum.txt


title: Chicken_Liver_F1

value: Liver


title: 190031C_E116_ovary

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: fetal ovary

data_processing:
The Cell Ranger software (version 3.0.2) was used to perform sample demultiplexing, reads mapping and barcode processing to generate a matrix of gene counts versus cells. Briefly, the raw BCL files generated by Illumina NovaSeq 6000 sequencing were demultiplexed into fastq files through the Cell Ranger mkfastq pipeline. Next, the fastq files were processed using the Cell Ranger count pipeline to map high-quality reads to the monkey reference genome (Macaca_fascicularis_5.0). Aligned reads were further filtered for valid cell barcodes and unique molecular identifiers (UMIs) to produce a count matrix.
Then, count matrix was imported into the R package Seurat and quality control was performed to remove outlier cells and genes. Cells with 200-3000 detected genes were retained. Genes were retained in the data if they were expressed in ≥ 3 cells. After applying these quality control criteria, 11742 cells and 19204 genes remained for downstream analyses. Additional normalization was performed in Seurat on the filtered matrix to obtain the normalized count. Highly variable genes across single cells were identified and principal component analysis (PCA) was performed to reduce the dimensionality on the top 18 principal components. Then, cells were clustered at a resolution of 0.6 and visualized in 2-dimension using Uniform Manifold Approximation and Projection (UMAP).
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: scRNA-Seq: UMI counts matrix with gene and barcode annotations

organism: Macaca fascicularis

source_name: fetal ovary cells

extract_protocol:
RNAs were prepared for sequencing
Cell instrument to generate a single cell Gel bead in Emulsion(GEM). Single cell RNA libraries were prepared  for sequencing according to standard Illumina protocols accompanying the Single Cell 3’ Reagent Kits v3 (10X Genomics)

treatment_protocol: The ovaries samples for scRNA-seq were from two fetal female Macaca fascicularis (embryonic day 84 and 116). For each single cell sequencing experiment, two ovaries were washed twice in 1× PBS, and subjected to a standard digestion procedure through Tumor Dissociation Kit, human (Miltenyi Biotec # 130-095-929). First, the ovaries were cut into small pieces of 2–4 mm, and transferred into the gentleMACS C Tube containing the enzyme mix (4.7 mL DMEM, 200 µL Enzyme H, 100 µL Enzyme R, and 25 µL Enzyme A). Then, the C Tube was attached onto the sleeve of the gentleMACS dissociator. After termination of the program, C Tube was detached from the gentleMACS Dissociator. The sample was incubated for 30 minutes at 37 °C under continuous rotation using the MACSmix Tube Rotator. Next, C Tube was attached onto the sleeve of the gentleMACS dissociator and then perform a short centrifugation step to collect the sample material at the bottom of the tube. Resuspend sample and apply the cell suspension to a MACS SmartStrainer (70 µm) placed on a 50 mL tube and wash cell MACS SmartStrainer (70 µm) with 20 mL DMEM. Finally, centrifuge cell suspension at 300×g for 7 minutes, aspirate supernatant completely and resuspend cells as required for further applications.

value: Ovary

value: Embryonic day 116 (E116)


title: Double wash Single high elution

value: High


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79711.gif

source_name: perirenal (retroperitoneal); adipocyte; M55a, 10 ug labeled aRNA

value: 55 years

value: adipocyte


title: I_765_H3K27me3_ChIP

tag: plant type

value: clonal plant

tag: leaf number

value: frond 0

tag: fruit phenotype

value: mantled


title: J_770_H3K4me3_ChIP

tag: palm tree id

tag: chip antibody


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79723.gif

source_name: perirenal (retroperitoneal); stromal pellet; M55a, 10 ug labeled aRNA

value: stromal pellet

tag: Sex


title: thigh; adipocyte; F58a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79606.gif

source_name: thigh; adipocyte; F58a, 10 ug labeled aRNA

value: 58 years

value: thigh

value: female


title: Chicken_Kidney_M3

data_processing:
Basecalling and demultiplexing were performed using ont-guppy-for-minknow (v3.0.5 for cattle data; v3.2.6 for pig and chicken data), and reads with quality score below 7 were discarded to obtain fastq files.
Demultiplexed fastq files were grouped together for each sample, and processed with Pychopper (v2.4.0) to identify and orient full-length reads.
Full-length strand-oriented reads for each sample were mapped to the respective genome assemblies (ARS-UCD1.2 for cattle; Sscrofa11.1 for pig; GRCg6a for chicken) with minimap2 (v2.16r922) with options “-ax splice -uf -k14” and modifying the maximum allowable intron size by species with option "-G 1000000" for pig and cattle, and "-G 400000" for chicken.
Uniquely mapped reads with a minimum quality score of 10 were extracted with Samtools (v1.7).
Uniquely mapped reads were used to obtain raw gene expression counts, based on the Ensembl v101 annotations for each species, using HTSeq (v0.11.2) with options "-i gene_id --type=exon --stranded=yes --mode=intersection-nonempty."
Genome_build: ARS-UCD1.2 (cattle), Sscrofa11.1 (pig), GRCg6a (chicken)
Supplementary_files_format_and_content: Raw gene counts, based on the Ensembl (v101) annotation for each species

value: Male

tag: tissue

value: Kidney


title: I_765_H3K4me3_input


title: Chicken_Jejunum_M3

source_name: Jejunum

value: Jejunum


title: Chicken_Kidney_F2

value: Female


title: pericolonic; stromal pellet; F50b

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79707.gif

value: Stratagene Human Universal Reference

source_name: pericolonic; stromal pellet; F50b, 10 ug labeled aRNA

value: 50 years

value: pericolonic


title: pericolonic; tissue; F50b

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79705.gif

source_name: pericolonic; tissue; F50b, 10 ug labeled aRNA

value: tissue


title: Chicken_Jejunum_M4


title: Chicken_Jejunum_F1


title: Standard wash Multiple low+medium+high elution

tag: input (ng)

tag: filler dna methylation ratio

tag: filler dna amount (ng)

value: Standard

value: Multiple

value: Low+Medium+High


title: pericolonic; adipocyte; M65

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79736.gif

source_name: pericolonic; adipocyte; M65, 10 ug labeled aRNA

value: 65 years

value: adipocyte


title: Standard wash Multiple medium+high elution

tag: mbd protein (ug)

tag: mbd-specific beads (ul)

tag: wash

value: Medium+High


title: Chicken_Jejunum_F2


title: I_765_H3K27me3_input

value: clonal plant

value: frond 0

value: mantled


title: retroperitoneal; tissue; M57

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78530.gif

tag: reference

source_name: retroperitoneal; tissue; M57, 10 ug labeled aRNA

value: 57 years

value: retroperitoneal

value: Male


title: I_765_H3K4me3_ChIP


title: Chicken_Kidney_F1

value: Female

value: Kidney


title: Chicken_Muscle_M1

source_name: Muscle

value: Muscle


title: H_754_H3K27me3_input


title: Standard wash Multiple high elution

source_name: Pooled healthy plasma

tag: elution fraction

tag: elution salt level

value: High


title: Standard wash Multiple medium elution

value: Medium


title: 190031A_E84_monkey_ovary

description: fetal ovary

value: Ovary

tag: age

value: Embryonic day 84 (E84)


title: 500ng filler rep2

value: Standard

value: Single


title: Chicken_Ileum_M4

source_name: Ileum

value: Ileum


title: Standard wash Single low elution

value: Low


title: H_754_H3K27me3_ChIP

tag: plant type

value: clonal plant


title: pericolonic; adipocyte; F50b

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79706.gif

value: Stratagene Human Universal Reference

source_name: pericolonic; adipocyte; F50b, 10 ug labeled aRNA

value: 50 years

tag: organism part

value: pericolonic

tag: sample fraction

value: adipocyte

value: female


title: perirenal (retroperitoneal); tissue; UU

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79763.gif

source_name: perirenal (retroperitoneal); tissue; UU, 10 ug labeled aRNA

value: unknown

value: perirenal (retroperitoneal)

value: tissue


title: Chicken_Ileum_F1

value: Female


title: G_687_H3K27me3_input

source_name: leaf

tag: leaf number

value: frond 0

tag: fruit phenotype

value: mantled

tag: palm tree id


title: Standard wash Multiple low elution

value: Multiple


title: Chicken_Ileum_F2

tag: Sex

tag: tissue


title: pericolonic; stromal pellet; M52

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79704.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

source_name: pericolonic; stromal pellet; M52, 10 ug labeled aRNA

value: 52 years

value: stromal pellet

value: Male


title: Chicken_Hypothalamus_M2

source_name: Hypothalamus

value: Hypothalamus


title: H_754_H3K4me3_ChIP

value: clonal plant

tag: chip antibody


title: H_754_H3K4me3_input


title: Chicken_Ileum_M3

value: Ileum


title: G_687_H3K27me3_ChIP


title: Standard wash Single medium elution

tag: input (ng)

tag: filler dna methylation ratio

tag: filler dna amount (ng)

value: Standard

value: Single

value: Medium


title: G_687_H3K4me3_input


title: Standard wash Single high elution

tag: mbd protein (ug)

tag: mbd-specific beads (ul)

tag: wash

value: High


title: Chicken_Hypothalamus_M1


title: 0.2ug MBD 30ul beads rep2

tag: elution fraction

tag: elution salt level


title: Chicken_Hypothalamus_F2


title: G_687_H3K4me3_ChIP

tag: plant type


title: thigh; tissue; F52b

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79737.gif

tag: reference

value: Stratagene Human Universal Reference

source_name: thigh; tissue; F52b, 10 ug labeled aRNA

tag: age

tag: organism part

value: thigh

value: female


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80304.gif

source_name: flank/back lipo; stromal pellet; UUa_redo, 10 ug labeled aRNA

value: unknown

value: flank/back lipo

tag: sample fraction


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79708.gif

source_name: perirenal (retroperitoneal); tissue; F67, 10 ug labeled aRNA

value: 67 years

value: perirenal (retroperitoneal)

value: tissue


title: 0.2ug MBD 30ul beads rep1


title: 0.2ug MBD 30ul beads rep3


title: Chicken_Heart_M4

source_name: Heart

value: Heart


title: 50% methylated filler rep3


title: F_673_H3K27me3_ChIP

tag: leaf number

value: frond 0

tag: fruit phenotype

value: mantled

tag: palm tree id


title: Chicken_Heart_F1

tag: Sex

value: Female

tag: tissue


title: 50% methylated filler rep2

tag: input (ng)

tag: filler dna methylation ratio


title: E_768_H3K27me3_ChIP

value: clonal plant

value: normal

tag: chip antibody


title: E_768_H3K27me3_input


title: Unmethylated filler rep3

value: 100% UNME

tag: filler dna amount (ng)

tag: mbd protein (ug)

tag: mbd-specific beads (ul)

value: Standard

value: Single


title: Chicken_Hypothalamus_F1

value: Hypothalamus


title: omentum (colon); adipocyte; F59_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80286.gif

value: Stratagene Human Universal Reference

source_name: omentum (colon); adipocyte; F59_redo, 10 ug labeled aRNA

value: 59 years

value: omentum (colon)

value: adipocyte


title: Unmethylated filler rep2

tag: wash

tag: elution fraction

tag: elution salt level

value: High


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79710.gif

tag: reference

source_name: perirenal (retroperitoneal); tissue; M55a, 10 ug labeled aRNA

tag: age

value: 55 years

value: perirenal (retroperitoneal)

value: Male


title: 50% methylated filler rep1


title: Chicken_Gizzard_M4

source_name: Gizzard

value: Gizzard


title: Chicken_Gizzard_M3


title: Chicken_Gizzard_F2


title: thigh; adipocyte; F73a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79696.gif

source_name: thigh; adipocyte; F73a, 10 ug labeled aRNA

value: 73 years

tag: organism part

value: thigh

tag: sample fraction

value: female


title: omentum (colon); tissue; M17

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79657.gif

source_name: omentum (colon); tissue; M17, 10 ug labeled aRNA

value: 17 years

value: tissue


title: pericolonic; adipocyte; F59

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79630.gif

source_name: pericolonic; adipocyte; F59, 10 ug labeled aRNA

value: pericolonic


title: D_767_H3K27me3_input

tag: plant type

value: clonal plant

tag: leaf number

value: frond 0

tag: fruit phenotype

value: normal


title: 2ug MBD 3ul beads rep3

description:
RaMWAS summary.xlsx
cfMBD_CpG_annotation_coverage_TPM.txt
cfMBD_CpG_annotation_coverage_TPM_sum.txt

source_name: Pooled healthy plasma

value: Standard

value: Single


title: thigh; tissue; M94

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79644.gif

value: Stratagene Human Universal Reference

source_name: thigh; tissue; M94, 10 ug labeled aRNA

value: 94 years

tag: Sex


title: Chicken_Duodenum_M4

source_name: Duodenum

tag: tissue

value: Duodenum


title: Unmethylated filler rep1

tag: input (ng)

tag: filler dna methylation ratio

value: 100% UNME

value: High


title: E_768_H3K4me3_ChIP

source_name: leaf

tag: palm tree id

tag: chip antibody


title: D_767_H3K27me3_ChIP


title: Chicken_Duodenum_F2

value: Female


title: D_767_H3K4me3_input


title: 2ug MBD 3ul beads rep1

tag: filler dna amount (ng)

tag: mbd protein (ug)

tag: mbd-specific beads (ul)


title: pericolonic; stromal pellet; F44_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80300.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

source_name: pericolonic; stromal pellet; F44_redo, 10 ug labeled aRNA

value: 44 years

value: stromal pellet


title: D_767_H3K4me3_ChIP


title: Chicken_BrainCortex_M2

source_name: BrainCortex

value: Male

value: BrainCortex


title: omentum (colon); tissue; F69

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79659.gif

source_name: omentum (colon); tissue; F69, 10 ug labeled aRNA

value: 69 years

value: omentum (colon)

value: tissue

value: female


title: abdominal; adipocyte; F33_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80295.gif

source_name: abdominal; adipocyte; F33_redo, 10 ug labeled aRNA

value: 33 years

value: abdominal

value: adipocyte


title: 2ug MBD 30ul beads rep3

tag: wash

value: Standard

tag: elution fraction

value: Single

tag: elution salt level


title: C_764_H3K27me3_input

value: clonal plant

value: frond 0

value: normal


title: Chicken_BrainCortex_F2

value: Female


title: C_764_H3K27me3_ChIP


title: omentum (colon); stromal pellet; M17

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79656.gif

tag: reference

value: Stratagene Human Universal Reference

source_name: omentum (colon); stromal pellet; M17, 10 ug labeled aRNA

tag: age

value: 17 years

tag: organism part


title: pericolonic; adipocyte; F85

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79621.gif

source_name: pericolonic; adipocyte; F85, 10 ug labeled aRNA

value: 85 years

value: pericolonic

tag: sample fraction


title: C_764_H3K4me3_input

tag: plant type

tag: leaf number

tag: fruit phenotype


title: shin/calf; stromal pellet; F83

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79647.gif

source_name: shin/calf; stromal pellet; F83, 10 ug labeled aRNA

value: 83 years

value: shin/calf

value: stromal pellet

tag: Sex


title: Chicken_Colon_M4

source_name: Colon

value: Male

tag: tissue

value: Colon


title: bumS-Butyrate3

city: Athens

first: Matthew

last: Powers

state: GA

address: 501 DW Brooks Dr

institute: University of Georgia

description: Grown in absence of butyrate

data_processing:
Reads were trimmed at the 5' and 3' ends to remove ambiguous nucleotides using CLC Genomics Software
Reads were then mapped to Campylobacter jejuni 81-176 using CLC Genomics Software
RPKM values were calculated using CLC Genomics Software
Comparisons were made between relevant genotypes and considered significant if different by a log2 value > |2| with an FDR p-value < 0.05
Genome_build: Campylobacter jejuni 81-176

organism: Campylobacter jejuni

source_name: Bacterial

growth_protocol: Cultures were grown in Campylobacter defined medium as outlined in the manuscript.

extract_protocol:
PureLink Mini RNA (Invitrogen)
Strand-Specific RNAseq

treatment_protocol: Treatment included growth in the presence or absence of 12.5 mM butyrate

tag: strain

tag: genotype/variation

value: bumS

tag: treatment

tag: molecule

value: rRNA-depleted RNA


title: breast R; stromal pellet; F60a_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80283.gif

source_name: breast R; stromal pellet; F60a_redo, 10 ug labeled aRNA

value: 60 years

value: breast (right)

value: female


title: C_764_H3K4me3_ChIP

value: clonal plant

value: frond 0

tag: palm tree id

tag: chip antibody


title: pericolonic; stromal pellet; F75

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79628.gif

source_name: pericolonic; stromal pellet; F75, 10 ug labeled aRNA

value: 75 years


title: 2ug MBD 3ul beads rep2

tag: input (ng)

tag: filler dna methylation ratio

tag: filler dna amount (ng)

tag: mbd protein (ug)

tag: mbd-specific beads (ul)

tag: wash

value: Standard

tag: elution fraction

value: Single

value: High


title: E_768_H3K4me3_input

tag: plant type

tag: leaf number

value: normal


title: thigh; adipocyte; MU

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79645.gif

tag: reference

value: Stratagene Human Universal Reference

source_name: thigh; adipocyte; MU, 10 ug labeled aRNA

tag: age

value: unknown

tag: organism part

value: thigh

tag: sample fraction

value: adipocyte

tag: Sex


title: bumS+Butyrate3

description: Grown in presence of 12.5 mM butyrate

tag: strain

tag: genotype/variation

tag: treatment

value: 12.5 mM butyrate

tag: molecule


title: F_673_H3K27me3_input

tag: fruit phenotype

value: mantled

tag: palm tree id

tag: chip antibody


title: B_758_H3K27me3_input


title: Chicken_Colon_M3

value: Male

tag: tissue

value: Colon


title: thigh; adipocyte; F52b_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80292.gif

source_name: thigh; adipocyte; F52b_redo, 10 ug labeled aRNA

value: 52 years


title: Chicken_BrainCortex_M1

value: BrainCortex


title: bumS-Butyrate2

description: Grown in absence of butyrate

value: bumS

value: rRNA-depleted RNA


title: B_758_H3K27me3_ChIP

value: clonal plant

value: frond 0


title: Chicken_Colon_F2

value: Female


title: abdominal; adipocyte; M60_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80296.gif

source_name: abdominal; adipocyte; M60_redo, 10 ug labeled aRNA

value: 60 years

value: abdominal


title: breast; adipocyte; F31a_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80284.gif

value: Stratagene Human Universal Reference

source_name: breast; adipocyte; F31a_redo, 10 ug labeled aRNA

value: 31 years

value: breast

value: female


title: bumS+Butyrate2

description: Grown in presence of 12.5 mM butyrate

value: 12.5 mM butyrate


title: Chicken_Colon_F1


title: bumS-Butyrate1

description: Grown in absence of butyrate


title: B_758_H3K4me3_input

source_name: leaf

value: normal


title: Chicken_Cerebellum_M2

source_name: Cerebellum

value: Male

value: Cerebellum


title: B_758_H3K4me3_ChIP


title: bumS+Butyrate1

description: Grown in presence of 12.5 mM butyrate


title: A_753_H3K27me3_input


title: Chicken_Cerebellum_M1


title: bumR-butyrate3

description: Grown in absence of butyrate

value: bumR


title: breast R; tissue; F39

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79625.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

source_name: breast R; tissue; F39, 10 ug labeled aRNA

value: 39 years

value: breast (right)

value: tissue


title: A_753_H3K27me3_ChIP

value: clonal plant


title: Chicken_Cerebellum_F2


title: thigh; stromal pellet; MU

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79690.gif

source_name: thigh; stromal pellet; MU, 10 ug labeled aRNA

value: unknown

value: thigh

value: stromal pellet


title: bumR+Butyrate3

description: Grown in presence of 12.5 mM butyrate

value: rRNA-depleted RNA


title: Chicken_Cerebellum_F1

value: Female


title: knee; tissue; M25

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78546.gif

value: Stratagene Human Universal Reference

source_name: knee; tissue; M25, 10 ug labeled aRNA

value: 25 years

value: knee


title: breast R; adipocyte; F62b_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80299.gif

source_name: breast R; adipocyte; F62b_redo, 10 ug labeled aRNA

value: 62 years

value: adipocyte

value: female


title: retroperitoneal; adipocyte; M57_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80301.gif

source_name: retroperitoneal; adipocyte; M57_redo, 10 ug labeled aRNA

value: 57 years

value: retroperitoneal

value: Male


title: bumR-Butyrate2

description: Grown in absence of butyrate

value: bumR


title: Chicken_Cecum_M4

source_name: Cecum

value: Cecum


title: A_753_H3K4me3_ChIP

value: clonal plant

value: frond 0

value: normal


title: Chicken_Cecum_M3


title: bumR-Butyrate1

description: Grown in absence of butyrate


title: bumR+Butyrate1

description: Grown in presence of 12.5 mM butyrate

value: 12.5 mM butyrate


title: Chicken_BrainCortex_F1

source_name: BrainCortex

value: BrainCortex


title: Chicken_Cecum_F1

value: Female


title: tRNAseq, A.thaliana seedling leaf

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

institute: Tianjin Normal University

description:
pretreated RNA
tRNAseq_tRNA.xlsx

data_processing:
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by a self-designed pipeline for quantifications of tRFs and tRNAs.
YAMAT-seq data were first processed to trim the 5’ and 3’ adaptor sequences using Cutadapt, and the 5’ nucleotide complementary to the discriminator base was also trimmed. Then, the adaptor-free sequences that have perfect match to annotated mature tRNAs were counted and normalized against total tRNA reads to measure mature tRNA expression levels.
Genome_build: TAIR10, Phytozome
Supplementary_files_format_and_content: The file tRNAseq_tRNA.xlsx summarizes tRNA expressions in various plants. The YAMATseq files are tRNA count data.

organism: Arabidopsis thaliana

source_name: A.thaliana seedling leaf

growth_protocol: Arabidopsis thaliana, Glycine max, Hordeum vulgare, Setaria italica, Sorghum bicolor, Triticum aestivum, Zea mays plants were germinated in the soil and grown at 23 ºC under the standard long-day condition (16 hours of light followed by 8 hours of darkness). The 10-day old seedlings were collected for tRNA-seq or YAMAT-seq analysis.

extract_protocol:
RNA extraction was conducted using TRIzol reagent (Invitrogen). Ethanol precipitation was performed overnight at -20ºC to maximize sRNA yield.
RNA pretreatment was conducted using rtStar tRF&tiRNA pretreatment kit (Arraystar). Pretreated RNAs were purified by Phenol:Chloroform extraction and ethanol precipitation. tRNA-seq library was constructed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). Purification of PCR amplified cDNAs were conducted using VAHTS DNA Clean Beads (Vazyme). YAMAT-seq was performed as previously described (Shigematsu et al Nucleic Acids Res. 2017) with some modifications. The design of Y-shaped adapters followed previous study. 2 µl of 3’ adaptor (10 µM) and 2 µl of 5’ adaptor mix (10 µM) were incubated at 70ºC for 2 min and cooled at room temperature to allow 5’ and 3’ adaptors to fully anneal. Then, the Y-shaped adaptor was mixed with 2 µg pretreated RNA, 4 unit T4 Rnl2 (New England Biolabs) and 2 µl ligation buffer with total reaction of 20 µl, and incubated at 37 ºC for 2 h. Next, 1 µl RNA RT Primer (RTP, Illumina) was added to the reaction and incubated at 70 ºC for 3 min, and then immediately chilled on ice. Subsequently, reverse transcription and cDNA amplification reactions were performed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). A Universal Primer and RNA PCR Index Primers (Illumina) were used for amplifying cDNAs with 12 PCR cycles. The PCR products were purified using VAHTS DNA Clean Beads (Vazyme).

value: seedling leaf


title: bumR+Butyrate2

description: Grown in presence of 12.5 mM butyrate

source_name: Bacterial

value: rRNA-depleted RNA


title: hip lipo; tissue; F62_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80288.gif

value: Stratagene Human Universal Reference

source_name: hip lipo; tissue; F62_redo, 10 ug labeled aRNA

value: hip lipo

value: tissue


title: tRNAseq, A.thaliana seedling root

description:
pretreated RNA
tRNAseq_tRNA.xlsx

source_name: A.thaliana seedling root

value: seedling root


title: pericolonic; stromal pellet; F59

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79629.gif

source_name: pericolonic; stromal pellet; F59, 10 ug labeled aRNA

value: 59 years

value: pericolonic

value: stromal pellet

value: female


title: Chicken_Adipose_M2

source_name: Adipose

value: Male

value: Adipose


title: A_753_H3K4me3_input

value: clonal plant

value: frond 0


title: 2ug MBD 30ul beads rep1

description:
RaMWAS summary.xlsx
cfMBD_CpG_annotation_coverage_TPM.txt
cfMBD_CpG_annotation_coverage_TPM_sum.txt

source_name: Pooled healthy plasma

tag: input (ng)

tag: filler dna methylation ratio

tag: filler dna amount (ng)

tag: mbd protein (ug)

tag: mbd-specific beads (ul)

tag: wash

value: Standard

value: Single

tag: elution salt level

value: High