title: X_e

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

institute: Monash University

data_processing:
trim adapters and low-quality basecalls with Trimmomatic parameters: ILLUMINACLIP:TruSeq_palndrm.fa:1:15:10:1:True LEADING:3 TRAILING:3 SLIDINGWINDOW:5:15 MINLEN:40
remove SL-1 and SL-2 spliced-leader sequences (GTTTAATTACCCAAGTTTGAG; GGTTTTAACCCAGTTACTCAAG) with cutadapt
first-pass mapping using STAR and parameters: --outFilterMultimapNmax 10 --alignIntronMax 20000 --alignMatesGapMax 20000 --alignSJoverhangMin 15 --alignSJDBoverhangMin 10
second-pass mapping using STAR and parameters: --outFilterMultimapNmax 10 --alignIntronMax 20000 --alignMatesGapMax 20000 --alignSJoverhangMin 15 --alignSJDBoverhangMin 4 --sjdbFileChrStartEnd [SJDB files from first-pass]
sort using samtools sort
mark duplicates using picard MarkDuplicates
Pipeline A: make a blacklist of read-names where any alignment overlaps with a non-exonic genomic sequence by > 3 nt. Use this to remove all alignments from these reads, to yield pure exonic alignments.
Pipeline A: From the pure exonic alignments, count alignments per-gene using featureCounts
Pipeline A: Analyse counts for gene-level differential expression using limma-voom in DEGust
Pipeline B: make custom annotation of all intronic sequences.
Pipeline B Count alignments overlapping > 3 nt with introns using featureCounts
Pipeline B: Analyse counts for intron-level differential expression using EdgeR QL.
Genome_build: WBCel235.99
Supplementary_files_format_and_content: Pipeline A: Reverse_Strand_counts_cln_wInfo_ProtCod.txt; tab-separated values of pure exonic read-alignment counts per gene.
Supplementary_files_format_and_content: Pipeline B: RI_counts.tsv; tab-separated values of intron-overlapping read-alignment counts per intron.

organism: Caenorhabditis elegans

source_name: synchronised young adult worms_Ethanol control

growth_protocol: C. elegans strain mog-7::degron::gfp; sun-1p::TIR1::mRuby was cultured on Nematode Growth Medium (NGM) plates and fed with OP50 Escherichia coli bacteria at 20 ℃.

extract_protocol:
TRIzol LS Reagent and the RNeasy Micro Kit (QIAGEN) was used for extracting total RNA.
 Illumina TruSeq Stranded mRNA library construction kit employing poly-A selection to capture the mRNA.

treatment_protocol: Auxin induced germline-specific MOG-7 depletion was applied to synchronized young adult hermaphrodites (prior to formation of embryos) for one or two hours. Ethanol treatment for 2 hrs was applied as control.

tag: strain/genotype

value: mog-7::degron::gfp; sun-1p::TIR1::mRuby

tag: developmental stage

value: synchronized young adult hermaphrodites

value: Ethanol control

tag: batch

value: X


title: Sample_217

status: Public on Apr 13 2022

type: SRA

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

country: USA

institute: University of Michigan

description: RNAseq counts from the glomerular compartment from kidney biopsies.

library_source: transcriptomic

data_processing:
fastQC 0.11.5
fastqScreen 0.11.4
cutadapt 1.14 -m 50 -A CTGTCTCTTATA -a CTGTCTCTTATA
STAR 2.5.2.a --bamRemoveDuplicatesType UniqueIdentical --twopassMode Basic --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
htseq-count --stranded=no --order=pos --mode=union
Genome_build: GRCh 38.86

molecule: total RNA

organism: Homo sapiens

source_name: Glomeruli from kidney biopsy

extract_protocol:
Qiagen Allprep DNA/RNA Micro Kit (cat# 80284)
Takara SMART-Seq v4 Ultra Low Input RNA Kit (cat# 634891)
oligo(dT)

tag: tissue

value: Glomeruli from kidney biopsy

tag: disease

value: Minimal Change Disease


title: mcm23A_H3K4me3_eSPAN_S30_rep2

city: New York

first: Zhiguo

last: Zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

library_source: genomic

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis.
For BrdU-IP-ssSeq and eSPAN strand bias calculations, consistent paired-end reads mapped to Watson (W) and Crick (C) strands of the reference genome were separated with the bamtobed function from BEDTools and in-house Perl programs. Genome-wide reads coverage was calculated by deepTools. Strand bias was calculated in 10bp bins from these separated Watson and Crick reads using the formula Bias = (W − C)/(W + C) across the whole genome.
MACS2 was used to perform BrdU peak calling (--broad-cutoff 0.001) in the BrdU-IP-ssSeq samples relative to the corresponding control samples (input).
For spike-in normalization, we first followed the same procedure as above to align FASTQ files to the S. pombe reference genome. S. cerevisiae genome coverage at each base pair was multiplied by scaling factor based on S. pombe reads as described previously (Jeronimo et al., 2019).
Genome_build: S. cerevisiae (UCSC sacCer3) and S. pombe (Downloaded from https://www.pombase.org/ on March 10th 2018)
Supplementary_files_format_and_content: bigwig files were generated for plus strand, minus strand and both strands, scores represent the normalization reads density.

molecule: genomic DNA

organism: Saccharomyces cerevisiae W303

source_name: whole cell

growth_protocol: Yeast cells were grown in rich medium (1% yeast extract, 2% peptone) supplemented with 2% glucose (YPD) or, for galactose-induction experiments, with 2% raffinose (YPRaff). Exponentially growing cells were arrested at G1 phase with 5 ug/ml alpha-factor (EZBiolab) for 3 hours (YPD) or 3.5 hours (YPRaff). Degradation of AID-tagged proteins was achieved with the addition of 1 mM 3-indolacetic acid (IAA, I2886 Sigma) into the media. Induction of proteins under the GAL1 promoter was achieved with the addition of 2% galactose into YPRaff.

extract_protocol:
All ChIP and eSPAN assays were performed as described previously (Yu et al., 2014). For H3K4me3 and H3K56ac ChIP, chromatin was pelleted, washed twice with NP buffer (1.6 M sorbitol, 2 mM CaCl2, 5mM MgCl, 50 mM NaCl, 14 mM b-mercaptoethanol, 10 mM Tris-HCl (pH 7.4), 0.075% NP-40, 5 mM spermidine), resuspended in the same buffer, and digested with MNase (9013-53-0, Worthington Biochemical) for 20 min at 37C yielding a majority of mono- and di-nucleosome fragments. Digestion was stopped with the addition of 5 l 0.5 M EDTA, 1/5 volume of 5xChIP lysis buffer, and incubating 10 min on ice. For RNA Pol II CTD-Ser5p ChIP, chromatin was sheared by sonication using a Bioruptor Pico (15 seconds ON, 30 seconds OFF, 10 cycles)(Diagenode) to yield fragments of an average size of 300 bp.   Sonicated and MNase-digested chromatin was cleared by centrifugation and immunoprecipitated with the appropriate antibody (anti-H3K4me3 (ab8580, Abcam), anti-H3K56ac (38), or anti-RPB1 CTD-Ser5p (04-1572, Millipore)) and protein G Sepharose beads (17-0618-02, GE Healthcare). After washing the beads extensively, DNA from both input and ChIP was recovered with the Chelex-100 protocol (39) and used for BrdU IP/eSPAN or purified with MinElute PCR Purification kit (28004, Qiagen). Single-stranded DNA sequencing libraries were prepared using the Accel-NGS 1S Plus DNA library kit (10096, Swift Biosciences). Input and ChIP DNA was used for BrdU immunoprecipitation to prepare BrdU IP and eSPAN samples, respectively. Recovered DNA from the Chelex-100 extraction was incubated at 100C for 5 min and immediately chilled on ice for 5 min. BrdU immunoprecipitation was performed by diluting DNA 10-fold with BrdU IP buffer (PBS, 0.0625% Triton X-100(v/v), 6.7 g/ml Escherichia coli tRNA, 0.17 g/ml BrdU antibody (555627, BD Bioscience)) and incubated for 2 hours at 4C. Protein G Sepharose beads were added to each sample for 1 additional hour at 4C. Beads were washed extensively and DNA was recovered with TE + 1% SDS at 65C  for 15 min and purified with MinElute PCR Purification kit (28004, Qiagen). Single-stranded DNA sequencing libraries were prepared using the Accel-NGS 1S Plus DNA library kit (10096, Swift Biosciences).
ChIP-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center.

tag: treatment

value: MNase

tag: strains genetic background

tag: genotype

value: mcm2-3A mutant

tag: chip antibody

value: anti-H3K4me3 (ab8580, Abcam)

tag: spike-in

value: whole cell


title: Sample_11

value: Membranous Nephropathy


title: mcm23A_H3K4me3_eSPAN_S90_rep2


title: mcm23A_RNApolII_ChIP_S90_rep1

value: Sonication

value: anti-RPB1 CTD-Ser5p (04-1572, Millipore)


title: X_A2h

country: Australia

molecule: polyA RNA

source_name: synchronised young adult worms_Auxin for 2h

value: Auxin for 2h


title: Sample_176

value: Focal Segmental Glomerulosclerosis


title: mcm23A_Input_G1_rep2


title: Sample_79


title: mcm23A_RNApolII_ChIP_S60_rep1


title: Sample_242


title: VIII_e

value: VIII


title: mcm23A_RNApolII_ChIP_S30_rep1


title: X_A1h

source_name: synchronised young adult worms_Auxin for 1h

value: Auxin for 1h


title: VIII_A2h

value: mog-7::degron::gfp; sun-1p::TIR1::mRuby


title: mcm23A_RNApolII_ChIP_Input_S90_rep1


title: mcm23A_RNApolII_ChIP_G1_rep1


title: Sample_298


title: mcm23A_RNApolII_ChIP_Input_S60_rep1


title: Sample_7


title: mcm23A_H3K56ac_eSPAN_S90_rep1


title: VII_e

value: synchronized young adult hermaphrodites

value: VII


title: Sample_184


title: mcm23A_H3K56ac_ChIP_S90_rep1


title: mcm23A_Input_S90_S_rep1


title: Sample_146


title: mcm23A_H3K4me3_ChIP_G1_rep2


title: VII_A1h


title: mcm23A_BrdU_S60_S_rep1

value: anti-BrdU (555627, BD Bioscience)


title: VIII_A1h


title: Sample_58

value: Glomeruli from kidney biopsy


title: mcm23A_RNApolII_ChIP_Input_G1_rep1


title: mcm23A_BrdU_S90_S_rep1


title: VII_A2h


title: mcm23A_H3K4me3_eSPAN_S90_rep1


title: mcm23A_Input_S30_S_rep1


title: Sample_314


title: mcm23A_BrdU_S90_rep1


title: mcm23A_RNApolII_ChIP_Input_S30_rep1


title: mcm23A_H3K56ac_eSPAN_S60_rep1


title: V_e

value: Ethanol control

value: V


title: Sample_300

value: Other Nephrotic Syndrome


title: II_A2h

value: II


title: mcm23A_H3K56ac_ChIP_S30_rep1

value: mcm2-3A mutant

value: whole cell


title: V_A2h


title: V_A1h


title: mcm23A_Input_S90_rep1

value: MNase


title: Sample_132

value: Membranous Nephropathy


title: mcm23A_BrdU_S30_S_rep1

value: Sonication


title: mcm23A_H3K4me3_ChIP_S90_rep1

value: anti-H3K4me3 (ab8580, Abcam)


title: mcm23A_H3K56ac_ChIP_S60_rep1


title: II_e


title: mcm23A_BrdU_S60_rep1


title: Sample_243

value: Focal Segmental Glomerulosclerosis


title: Sample_292


title: mcm23A_H3K4me3_eSPAN_S60_rep1


title: mcm23A_Input_S60_S_rep1


title: mcm23A_H3K56ac_eSPAN_S30_rep1


title: mcm23A_H3K4me3_ChIP_S60_rep1


title: II_A1h

value: Auxin for 1h


title: Sample_21


title: mcm23A_Input_S60_rep1


title: I_e

value: mog-7::degron::gfp; sun-1p::TIR1::mRuby

value: I


title: mcm23A_H3K4me3_eSPAN_S30_rep1


title: Sample_219


title: Sample_321


title: mcm23A_BrdU_S30_rep1


title: I_A2h

value: synchronized young adult hermaphrodites

value: Auxin for 2h


title: mcm23A_H3K4me3_ChIP_S30_rep1


title: Sample_267

value: Glomeruli from kidney biopsy

value: Minimal Change Disease


title: Sample_128


title: I_A1h


title: mcm23A_H3K4me3_ChIP_G1_rep1


title: WT_H3K4me3_eSPAN_S90

value: WT


title: WT_H3K56ac_eSPAN_S90


title: mcm23A_Input_G1_rep1


title: Sample_263


title: WT_H3K56ac_ChIP_S90


title: WT_RNApolII_ChIP_S90

value: anti-RPB1 CTD-Ser5p (04-1572, Millipore)


title: WT_Input_S90


title: WT_H3K4me3_ChIP_S90


title: Sample_311


title: WT_H3K56ac_eSPAN_S60


title: WT_RNApolII_ChIP_S60


title: WT_H3K4me3_eSPAN_S60


title: WT_BrdU_S60

value: anti-BrdU (555627, BD Bioscience)


title: WT_BrdU_S90


title: Sample_89


title: Sample_273


title: mcm23A_Input_S30_rep1

value: mcm2-3A mutant


title: Sample_10


title: WT_H3K4me3_ChIP_S60

value: whole cell


title: WT_H3K56ac_ChIP_S60

value: MNase


title: WT_Input_S60


title: shSmc1a_B2_Hi-C_2

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
HiC reads were aligned to mm9 genome assembly using BWA with runHiC pipeline using the default settings (https://pypi.org/project/runHiC/)
Assembly: mm9
Supplementary files format and content: The cool file; the matrix of Hi-C for each Sample (generated from all 3 replicates and linked to the corresponding 1st replicate record)

organism: Mus musculus

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured using mouse ES medium prepared in DMEM high glucose (Hyclone) supplemented with 15 percent ES cell FBS (Gibco), 2mM L-glutamine (Gibco), 1X Pen-Strep (Gibco), 100 micromolar MEM non-essential amino acids (Gibco), 100 micromolar 2-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore). The mouse ES line was cultured on plates pre-coated with 0.1 percent gelatine (porcine).

extract_protocol:
Freshly sorted cells were kept on ice and typically aliquoted to 1M cell pellets and the input levels of chromatin required for Hi-C were determined per million. The cells were immediately crosslinked with 2% formaldehyde for 10 min, quenching with 0.25M glycine for 5 min at room temperature and 5 min on ice, followed by lysis, digestion with a restriction enzyme cocktail, filling the 5′-overhangs while incorporating biotin-14-dATP (a biotinylated nucleotide), followed by ligating the resulting blunt-end fragments, shearing the DNA to a 400–700-bp fragment size using a Covaris ME220 focused ultra-sonicator, capturing the biotinylated ligation junctions with streptavidin beads. The reagents for all reactions were obtained from Arima Hi-C kits.
Libraries were prepared according to Illumina's instructions with optimised rounds of PCR amplification, and finally analyzed the resulting fragments with paired-end sequencing.

treatment_protocol: E14 cells were harvested using trypsinization and were re-seeded into 6-well plates which were pre-coated with gelatine. The seeding density was 300,000 cells per well of the plates. These cells were cultured at 37 degree Celsius for 20-24 hours and the cells were replenished with fresh medium at least 2 hours prior to transfection. The cells were then transfected with 3 microgram of the plasmid constructs (shControl, shSetdb1, shSmc1a) using 4.5 microliters of Lipofectamine 2000 (Thermofisher), as per the manufacturer’s protocol. Puromycin (1 microgram/millliter) containing mESC medium was added to the cells 24 hours after transfection to select for the transfected plasmids. This process of selection was repeated once more 48 hours after transfection. The cells were finally harvested 72 hours after transfection.

tag: cell type

value: E14 mESCs


title: shSmc1a_B2_Hi-C_3


title: Sample_274


title: WT_H3K56ac_eSPAN_S30


title: WT_H3K4me3_eSPAN_S30


title: shSmc1a_B2_Hi-C_1


title: Sample_105


title: Sample_29


title: shSmc1a_B1_Hi-C_3


title: WT_H3K4me3_ChIP_S30


title: WT_BrdU_S30


title: WT_H3K56ac_ChIP_S30


title: Sample_214


title: WT_RNApolII_ChIP_G1


title: Sample_331


title: shSmc1a_B1_Hi-C_1


title: WT_H3K4me3_ChIP_G1


title: Sample_172

value: Membranous Nephropathy


title: WT_Input_G1


title: Sample_240


title: shSetdb1_B2_Hi-C_3


title: shSetdb1_B2_Hi-C_2


title: Sample_60


title: D14

first: Bin

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencing data were aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 3.1.0, 10x Genomics) against the provided GRCh38 reference genome using default parameters, including introns.
Assembly: GRCh38
Supplementary files format and content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: Human postmortem brain sample

extract_protocol:
Nuclei were isolated from frozen tissue, as per 10x Genomics’ recommendations, using chilled, 0.1% Nonident P40 lysis buffer with gentle homogenization and washed.
Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis. Libraries were sequenced using a 2x100PE configuration on a NovaSeq instrument (Illumina, San Diego, CA), targeting a depth of 50,000-100,000 reads per nucleus.

value: Substanstia nigra

tag: disease state

value: Parkinson's Disease Dementia

tag: brain bank donor id

value: HBRI

tag: age

tag: gender

value: Male

tag: race

value: White

tag: ethnicity

value: Not Hispanic

tag: postmortem interval hours

tag: braak stage

value: Stage II


title: shSetdb1_B2_Hi-C_1


title: Sample_5

value: Glomeruli from kidney biopsy


title: shSetdb1_B1_Hi-C_3


title: Sample_143

value: Focal Segmental Glomerulosclerosis


title: A22

value: HBDC

value: Stage IV


title: WT_RNApolII_ChIP_S30

value: WT

value: anti-RPB1 CTD-Ser5p (04-1572, Millipore)


title: shSmc1a_B1_Hi-C_2


title: shSetdb1_B1_Hi-C_2


title: iPSC derived neurons IL-4 rep3

city: Mainz

first: Samantha

last: Schmaul

address: Langenbeckstr 1

department: Neurology

country: Germany

institute: University Medical Centre Mainz

data_processing:
Raw RNAseq data were filtered with the fastp program (Chen et al., 2018) for eliminating low-quality reads. Parameters -g -x -p were set for polyG tail trimming, polyX tail trimming, and overrepresented sequence analysis
The quality of trimmed data was verified with the fastqc program (Babraham Bioinformatics).
Afterwards, data were aligned to the latest reference genome GRCh38.p1 using the long-read STAR aligner (Dobin et al., 2013).
Low-quality alignments were filtered out using SAMtools (Li et al., 2009).
The remaining high-quality alignments were quantified using StringTie (Pertea et al., 2015).
Statistical analysis of the gene counts were carried out with DESeq2 (Love et al., 2014) in R.
Gene ontology (GO) analysis was performed with clusterProfiler and DOSE and visualized with Enrichplot (Yu et al., 2015).
The database org.Hs.eg.db was used in R for annotating purposes; heatmaps were created with pheatmap package in R.
Assembly: GRCh38.p1
Supplementary files format and content: TSV, raw counts of sequencing reads with gene coordinates
Supplementary files format and content: TSV, normalized abundance measurements with gene coordinates

source_name: iPSC

extract_protocol:
RNA was isolated from murine neurons using the RNeasy® Micro Kit (Qiagen) according to the manufacturer’s instructions.
Quantity of total RNA was measured using a Qubit 2.0 Fluorimeter (Invitrogen) and quality was assessed using a RNA 6000 Nano chip on a Bioanalyzer 2100 (Agilent Genomics). Only samples with RNA integrity numbers (RIN) ≥ 7 were included in library preparation. Sequencing libraries were prepared from 10 ng total RNA using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs), according to the manufacturer’s protocol for polyA mRNA workflow. Quality of the cDNA library preparation was checked using the Agilent High Sensitivity DNA assay (Agilent) on a Bioanalyzer 2100 platform.

tag: cell line

value: iPSC

value: neurons


title: Sample_330

tag: tissue

value: Minimal Change Disease


title: WT_Input_S30

value: MNase

value: whole cell


title: iPSC derived neurons IL-4 rep4


title: iPSC derived neurons PBS rep3

value: PBS


title: iPSC derived neurons IL-4 rep2


title: shSetdb1_B1_Hi-C_1

value: E14 mESCs


title: iPSC derived neurons PBS rep2


title: Sample_228

tag: disease


title: iPSC derived neurons PBS rep1

tag: treatment


title: H9_D60

city: Nanjing

first: Yan

last: Liu

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

department: School of Pharmacy

country: China

institute: Nanjing Medical University

data_processing:
Reads were aligned to the hg38 human reference genome, and gene-level unique molecular identifier (UMI) counts were obtained using Cell Ranger (version 3.1.0).
Assembly: hg38
Supplementary files format and content: h5 files include barcodes, gene features and expression matrix for each sample

source_name: Human brain organoids

extract_protocol:
To obtain a single-cell suspension,  5-7 organoids at D30 were randomly selected into a 1.5 ml EP tube with 1 ml of TrypLE (Life Technologies) and incubated in a 37 degrees Celsius incubator for 40 min with gentle agitation every 5-8 min. The organoids were then washed with DPBS (Life Technologies) 3 times and gently dissociated into single cells with a 200 microliter pipette.
The organoids were dissociated by trypLE (Life technology) into single cells. The cell debris and other aggregates were removed by an additional low-speed centrifugation. About 5,000 cells were captured and the released RNA were barcoded through reverse transcription in individual GEMs. Droplet-based single-cell RNA sequencing was performed using the 10X Genomics Chromium Single Cell 3 platform, version 3, according to manufacturers instructions.

tag: culture time

value: 60 days in vitro

value: brain organoids


title: shEV_B2_Hi-C_2

tag: genotype


title: shEV_B2_Hi-C_3


title: Sample_247


title: H9_D30

value: 30 days in vitro


title: shEV_B2_Hi-C_1


title: Sample_322


title: Sample_139

value: Membranous Nephropathy


title: shEV_B1_Hi-C_3


title: Sample_91

value: Glomeruli from kidney biopsy


title: shEV_B1_Hi-C_2


title: Sample_222


title: shEV_B1_Hi-C_1


title: iPSC derived neurons IL-4 rep1


title: Sample_297

value: Other Nephrotic Syndrome


title: BayMSUrep6

city: La Jolla

first: Isidoro

last: Cobo

state: CA

address: Dept. of Cellular & Molecular Medicine, GPL210 9500 Gilman Drive, MC 0651

department: Cellular and Molecular Medicine

institute: University California San Diego

data_processing:
FASTQ sequencing files were mapped to the mm10 or hg38 reference genomes for mouse samples or human samples, respectively using STAR with default parameters. Biological replicates were used in all experiments.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: Raw expression (TPM) files

source_name: BMDM

growth_protocol: Flushed bone marrow from both femurs and tibias of C57BL/6 mice were cultured in DMEM medium supplemented with 10% de-complemented FBS, 100 units/ml penicillin and 100 ug/ml streptomycin, 2mM L-glutamine, and 20% of L929 conditioned media for for six days at 37ºC and 5% CO2. On day six, BMDM were trypsinized and plated in DMEM medium supplemented with 10% de-complemented FBS, 2mM L-glutamine, 100 units/ml penicillin and 100 ug/ml streptomycin, and 10 ng/mL recombinant murine M-CSF (Peprotech, #315-02) for one day prior being stimulated for five hours with 100ng/mL of LPS or 250 μg/mL of MSUc

extract_protocol:
BMDM or mDM were lysed in TRIzol (ThermoFisher, #15596026). RNA isolation and DNase treatment was carried out using Direct-zol RNA MicroPrep kit (Zymoresearch, #11-33MB)
500ng-1 μg total RNA was enriched in poly-A tailed RNA transcripts by double incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and fragmented for 9 min at 94ºC in 2X Superscript III first-strand buffer containing 10mM DTT (Invitrogen, #P2325). The 10 μl of fragmented RNA was added to 0.5 μl of Random primers (Invitrogen, #48190011), 0.5 μl of Oligo d(T) primer (Invitrogen, #18418020), 0.5 μl of SUPERase inhibitor (Ambion, #AM2696), 1 μl of 10mM dNTPs and incubated at 50ºC for three minutes. Then, 5.8 μl of water, 1 μl of 10mM DTT, 0.1 μl of 2 μg/μl Actinomycin D (Sigma, #A1410), 0.2 μl of 1% Tween-20 (Sigma) and 0.5 μl of SuperScript III (Invitrogen, #ThermoFisher 18080044) was added to the mix. Reverse-transcription (RT) reaction was performed at 25ºC for 10 min followed by 50ºC for 50 min. RT product was purified with RNAClean XP (Beckman Coulter, #A63987) and eluted in 10 μl in 0.01% Tween-20. The RNA-cDNA complex was then added to 1.5 μl of 10X Blue Buffer (Enzymatics, #B0110-L), 1.1 μl of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μl of 5U/μl RNAseH (Enzymatics, #Y9220L), 1 μl of 10U/μl DNA polymerase I (Enzymatics, #P7050L), 0.15 μl of 1% Tween-20 and 1.05 μl of nuclease free water; and incubated at 16ºC for 2.5h or overnight. The resulting dsDNA product was purified using 28 μl of SpeedbBead Magnetic Carboxylate (GE Healthcare, #651521050 50250) diluted in 20%PEG8000:2.5M NaCl to a final 13% PEG concentration, washed twice with 80% etOH, air dry and eluted in 40 μl of 0.05% Tween-20. The purified 40 μl of dsDNA was end-repaired by blunting followed by A-tailing and adapter ligation as described elsewhere (69) using BIOO Barcodes (BIOO Scientific, #514104), IDT TruSeq Unique Dual Indexes or Kapa Unique Dual-Indexed Adapters using 15 μl Rapid Ligation Buffer (Enzymatics, #L603-LC-L), 0.33 μl 1% Tween-20 and 0.5 μl T4 DNA ligase HC (Enzymatics, #L6030-HC-L). Libraries were amplified by PCR for 11-15 cycles using Solexa IGA and Solexa IGB primers (AATGATACGGCGACCACCGA and CAAGCAGAAGACGGCATACGA, respectively), purified using 1 μl of SpeedbBead Magnetic Carboxylate in 15.2 μl of 20%PEG8000:2.5M NaCl, washed with 80% etOH and eluted in 0.05% Tween-20. Eluted libraries were quantified using a Qubit dsDNA HS Assay Kit and sequenced on a NextSeq 500 or Hi-Seq 4000 (Illumina, San Diego, California).

treatment_protocol: 20 μM of JNK inhibitor SP600125 (Tocris, #1496), 10 μM of BHA (Sigma, B1253), 20nM of BAY-876 (Selleckchem,#S8452), 3 μM of p38 MAPK inhibitor SB203580 (Tocris, #1202) or NLRP3 inflammasome inhibitor MCC950 (1uM, Selleckchem, #S7809) were added to the media one hour prior to stimulation with LPS or MSUc.

tag: agent

value: MSU

tag: time point


title: Sample_122


title: Sample_254


title: BayMSUrep5


title: Sample_7_LivingDonor

value: Healthy living transplant donor


title: Sample_5_LivingDonor


title: BayMSUrep3


title: Sample_6_LivingDonor


title: BayMSUrep4


title: BayMSUrep1


title: BayMSUrep2


title: BayLPSrep6


title: Sample_3_LivingDonor


title: BayLPSrep5

value: LPS


title: Sample_2_LivingDonor


title: Sample_1_LivingDonor


title: BayLPSrep3


title: BayLPSrep4


title: BayLPSrep2


title: BayLPSrep1


title: BayPBSrep5


title: BayPBSrep3


title: BayPBSrep4


title: BayPBSrep2


title: BayPBSrep1


title: RP-1UM-REP2

city: Vancouver

first: Liam

last: Brunham

state: British Columbia

address: 1081 Burrard Street

department: Department of Medicine

country: Canada

institute: University of British Columbia

data_processing:
Basecalls were performed using illumina BaseSpace workflow version 1.1.0.
STAR aligner version STAR-2.5.0b was used for alignment to hg38 genome assembly.
Rawcounts were generated by featureCounts in Subread package version 1.6.3.
Genes with rawcounts more that 5 in at least 2 samples were used for differential expression analysis by DEseq package in R.
Adjusted p-value less that 0.05 was considered significant in differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file includes rawcounts for each sample. Matrix table excel file shows significant differential expressed genes in original (RARG-WT/S427L) and repaired (RARG-WT/WT) iPSC-CM samples comparing drug treatment with 1uM and 0uM doses.

source_name: hiPSC-derived cardiomyocytes

growth_protocol: hiPS cells were differentiated into cardiomyocytes using protocol from Lian et al., 2013. In general, iPSCs were treated with optimized doses of CHIR99021 at day 0 and IWP2 at day 3. Cardiomyocytes purification was performed at day 11-15 using lactate enrichment medium (Burridge et al., 2014; Tohyama et al., 2013). Cardiomyocytes were used for functional assays after day 30.

extract_protocol:
Total RNA of hiPSC-CMs were isolated by illustra™ RNAspin Mini Isolation Kit (GE Healthcare). RNA quality was assessed by measuring the RNA integrity number (RIN) using Bioanalyzer (Agilent Technologies). All 12 samples for library preparation have RIN within 9 to 10.
250ng of total RNA was prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). RNA sequencing was performed on Illumina NextSeq 500 with 2x43 paired_end sequence reads in the depth of 20 millions.

treatment_protocol: hiPSC-derived cardiomyocytes of original (RARG-WT/S427L) and repaired (RARG-WT/WT) cell lines were treated with 1uM doxorubicin in experiment group and vehicle (DMSO) in control group in 12-well plates for 24 hours with 3 replicates in each condition.

value: RARG-WT/WT

value: 1uM doxorubicin

tag: iPSc line


title: Sample_8_LivingDonor


title: RP-1UM-REP3


title: JNKiMSUrep5

value: JNKi


title: RP-1UM-REP1


title: Sample_4_LivingDonor


title: JNKiMSUrep4


title: JNKiMSUrep3


title: JNKiMSUrep2


title: OG-1UM-REP2


title: OG-1UM-REP3


title: JNKiMSUrep1


title: RP-0UM-REP2

value: vehicle (DMSO)


title: RP-0UM-REP3


title: RP-0UM-REP1


title: OG-1UM-REP1


title: BayPBSrep6


title: JNKiLPSrep6


title: JNKiLPSrep5


title: JNKiLPSrep4


title: OG-0UM-REP3


title: OG-0UM-REP2


title: OG-0UM-REP1


title: JNKiLPSrep3


title: JNKiLPSrep1


title: JNKiLPSrep2


title: Trophoblast BMP2-treated 24h rep4

first: Yuyin

last: Yi

address: 4500 Oak St

institute: University of British Columbia, BC Children’s Hospital Research Institute

data_processing:
De-multiplexed sequences were aligned to the Homo sapiens (UCSC hg19) reference sequence using STAR aligner
Fragments per kilobase of exon per million reads (FPKM) estimation of reference genes and transcripts using Cufflinks 2
Assembly of novel transcripts with Cufflinks 2
Differential expression of novel and reference transcripts with Cuffdiff 2
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: *.genes.fpkm_tracking: Tab-delimited text files include FPKM values for each gene.

source_name: First-trimester Placenta Trophoblast

extract_protocol:
Total RNA from human primary trophoblasts was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. Sample quality control was performed using the Agilent 2100 Bioanalyzer.
Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs).

value: Placenta

tag: gestational age

value: 6-10 weeks

tag: cell type

value: Trophoblast

value: 25 ng/ml BMP2 for 24 h


title: Trophoblast BMP2-treated 24h rep5


title: Trophoblast BMP2-treated 24h rep3


title: JNKiPBSrep6

value: PBS


title: JNKiPBSrep5


title: Trophoblast Control rep5

value: vehicle control


title: JNKiPBSrep3


title: JNKiPBSrep4


title: Trophoblast BMP2-treated 24h rep2


title: JNKiPBSrep2


title: Trophoblast Control rep2


title: VehicleMSUrep4

value: Vehicle


title: AML01 patient cell 63 [AML01_H08_181120_scRNAseq_S161]

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

institute: The University of Newcastle

description: processed data file: AML01_scRNAseq_TEtranscripts_counts.txt.gz

data_processing:
scRNA-seq data was trimmed using Trim Galore (v0.6.5), with default setting in paired-end mode.
Hisat2 (v2.1.0) and Samtools (v1.1.0) were used to convert, map and align unique and ambiguous reads to the human reference genome build GRCh38 from raw fastq reads into bam format.
TEtranscripts [Jin, Y., et al., TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics, 2015] was used to obtain raw gene and transposable element counts from the unique and ambiguously aligned reads using the GTF files for 1) TEs (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/) and 2) genes (https://asia.ensembl.org/info/data/index.html; release 101 from the FTP server) in GRCh38 ensembl format. TEtranscripts was run in a Conda (Inc., A., Anaconda Software Distribution. 2020, Anaconda Inc.) environment setup with Python (v3.7.7), Pysam (v0.16.0.1), R-base (v4.0.3) and Bioconductor-Deseq2 (v1.28.0).
Genome_build: GRCh38 ensembl format
Supplementary_files_format_and_content: The read count table are in tab-deliminated format with the first column containing the gene ensembl ID and TE name, followed by each column containing an individual named sample and associated counts.

source_name: patient sample

growth_protocol:
AML01: Enriched mononuclear cells were purified from peripheral blood using Lymphoprep density gradient medium (StemCell, catalog # 7851) and SepMate tubes (StemCell, catalog # 85450), and cryopreserved. Cryopreserved primary human cells were resuspended in thawing media (IMDM, 20% FBS), washed twice and resuspended in thawing media. The cells were then rested for 1h at 37°C before preparation for flow cytometry. Cells (1x106/100ul) were stained with 1.5μg/mL propidium iodide (PI, Sigma-Aldrich), 1:20 CD45-PECy7 (2D1, Invitrogen), 1:20 CD33-FITC (WM-53, Invitrogen) and 1:20 CD19-BV711 (SJ25C1, BD Biosciences). Single blasts (PI-CD45dim) were collected in 2.5μL RLT Plus Lysis Buffer containing 1U/μL SUPERase-In (Invitrogen) in 96 well plates.
KG1a: KG1a cells were resuspended in binding buffer before staining with annexin V and 7-AAD. Live cells (Annexin V - /7-AAD -) were sorted into individual wells of a 96 well plate containing lysis buffer 2.5μL RLT Plus Lysis Buffer (QIAGEN, catalog # 1053393) containing 1U/μL SUPERase-In (ThermoFisher, catalog # AM2696) in 96 well plates. Before sorting, bulk samples of 1000000 cells were collected from both the untreated and treated populations.

extract_protocol:
We utilised the G&T-seq protocol to separate genomic DNA and RNA from the single-cell samples. [Macaulay, I.C., et al., G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nature Methods, 2015]
Matched single cell RNA sequencing (scRNA-seq) libraries were prepared as per the scM&T-seq protocol. [Macaulay, I.C., et al., G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nature Methods, 2015]

treatment_protocol: Cell lines were treated with 100nM decitabine every 24 hours (0, 24 and 48 hours) and harvested at 72 hours

value: untreated

tag: cancer type

value: Acute myeloid leukemia

tag: Sex

value: M

tag: age

tag: sample type

value: patient sample


title: VehicleMSUrep6

value: MSU


title: Trophoblast Control rep4


title: JNKiPBSrep1


title: Trophoblast Control rep3


title: Trophoblast Control rep1


title: VehicleMSUrep3


title: VehicleMSUrep5


title: VehicleMSUrep2


title: VehicleMSUrep1


title: VehicleLPSrep4

value: LPS


title: AML01 patient cell 62 [AML01_H07_181120_scRNAseq_S160]


title: AML01 patient cell 60 [AML01_H05_181120_scRNAseq_S158]


title: AML01 patient cell 59 [AML01_H04_181120_scRNAseq_S157]


title: VehicleLPSrep3


title: AML01 patient cell 57 [AML01_H02_181120_scRNAseq_S155]


title: AML01 patient cell 58 [AML01_H03_181120_scRNAseq_S156]


title: VehicleLPSrep2


title: AML01 patient cell 55 [AML01_G08_181120_scRNAseq_S152]


title: AML01 patient cell 56 [AML01_G09_181120_scRNAseq_S153]


title: VehiclePBSrep5


title: VehiclePBSrep3


title: VehiclePBSrep4


title: AML01 patient cell 61 [AML01_H06_181120_scRNAseq_S159]


title: VehiclePBSrep1


title: VehiclePBSrep2


title: PBS_rep1_mDM

source_name: mDM


title: AML01 patient cell 51 [AML01_G04_181120_scRNAseq_S148]


title: AML01 patient cell 53 [AML01_G06_181120_scRNAseq_S150]


title: AML01 patient cell 49 [AML01_G02_181120_scRNAseq_S146]


title: AML01 patient cell 52 [AML01_G05_181120_scRNAseq_S149]


title: AML01 patient cell 48 [AML01_G01_181120_scRNAseq_S145]


title: AML01 patient cell 50 [AML01_G03_181120_scRNAseq_S147]


title: MSU_rep3


title: AML01 patient cell 46 [AML01_F07_181120_scRNAseq_S143]


title: MSU_rep2


title: AML01 patient cell 47 [AML01_F08_181120_scRNAseq_S144]


title: VehicleLPSrep1


title: Trophoblast BMP2-treated 24h rep1


title: MSU_rep1


title: VehiclePBSrep6


title: LPS_rep3


title: AML01 patient cell 45 [AML01_F06_181120_scRNAseq_S142]


title: LPS_rep1


title: LPS_rep2


title: AML01 patient cell 54 [AML01_G07_181120_scRNAseq_S151]


title: AML01 patient cell 44 [AML01_F05_181120_scRNAseq_S141]


title: PBS_rep3


title: AML01 patient cell 43 [AML01_F04_181120_scRNAseq_S140]


title: AML01 patient cell 41 [AML01_F02_181120_scRNAseq_S138]


title: AML01 patient cell 42 [AML01_F03_181120_scRNAseq_S139]


title: PBS_rep2


title: AML01 patient cell 36 [AML01_E05_181120_scRNAseq_S133]


title: AML01 patient cell 40 [AML01_F01_181120_scRNAseq_S137]


title: AML01 patient cell 37 [AML01_E06_181120_scRNAseq_S134]


title: AML01 patient cell 39 [AML01_E08_181120_scRNAseq_S136]


title: PBS_rep1


title: RS10_784 (Distal Colon)

city: Beltsville

first: Celine

last: Chen

state: Maryland

address: 10300 Baltimore Ave, B307C, RM211E

institute: USDA

description:
distal colon tissue
RS10_784
d_10%

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus musculus GRCm39.104 whole genome using CLC Genomics Workbench 12 (Qiagen, CA)
Raw counts were calculated form unique exon reads in each gene.
Genes with zero expression values across treatment groups were excluded from downstream analyses.
Genome_build: Mus musculus GRCm39.104
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: distal colon

extract_protocol:
RNA was extracted from tissues using Tri-Reagent and ThermoFisher PureLink RNA isolation kits followed by further purification using Zymo RNA Clean and Concentrate kits. RNA was quantified using ThermoFisher Quant-It RNA Kits.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Prep kit with IDT for Illumina TruSeq RNA UD Indexes following manufacturer's recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. The libraries from each project were pooled with equimolar proportions of each library. Pools were quantified using the Invitrogen Collibri Quantification qPCR kit.

treatment_protocol: Mice were fed the Total Western Diet for 6 weeks followed by subgroups receiveing diet with raw potato starch added to 2, 5, or 10% for an additional 3 weeks before collecting tissues for RNASeq analysis.

tag: stain

value: 10% raw potato starch


title: AML01 patient cell 35 [AML01_E04_181120_scRNAseq_S132]


title: RS10_724 (Distal Colon)

description:
distal colon tissue
RS10_724
c_5%

value: 5% raw potato starch


title: RS10_731 (Distal Colon)

description:
distal colon tissue
RS10_731
d_10%


title: RS10_725 (Distal Colon)

description:
distal colon tissue
RS10_725
d_10%


title: RS10_727 (Distal Colon)

description:
distal colon tissue
RS10_727
d_10%


title: AML01 patient cell 34 [AML01_E03_181120_scRNAseq_S131]


title: AML01 patient cell 32 [AML01_E01_181120_scRNAseq_S129]


title: AML01 patient cell 33 [AML01_E02_181120_scRNAseq_S130]


title: RS10_718 (Distal Colon)

description:
distal colon tissue
RS10_718
c_5%


title: AML01 patient cell 31 [AML01_D08_181120_scRNAseq_S128]


title: AML01 patient cell 38 [AML01_E07_181120_scRNAseq_S135]


title: AML01 patient cell 29 [AML01_D06_181120_scRNAseq_S126]


title: RS10_715 (Distal Colon)

description:
distal colon tissue
RS10_715
b_2%

value: 2% raw potato starch


title: AML01 patient cell 28 [AML01_D05_181120_scRNAseq_S125]


title: RS10_717 (Distal Colon)

description:
distal colon tissue
RS10_717
c_5%


title: AML01 patient cell 27 [AML01_D04_181120_scRNAseq_S124]


title: RS10_712 (Distal Colon)

description:
distal colon tissue
RS10_712
b_2%


title: RS10_729 (Distal Colon)

description:
distal colon tissue
RS10_729
d_10%


title: AML01 patient cell 30 [AML01_D07_181120_scRNAseq_S127]


title: RS10_748 (Distal Colon)

description:
distal colon tissue
RS10_748
b_2%


title: RS10_709 (Distal Colon)

description:
distal colon tissue
RS10_709
b_2%


title: AML01 patient cell 24 [AML01_D01_181120_scRNAseq_S121]


title: AML01 patient cell 26 [AML01_D03_181120_scRNAseq_S123]


title: RS10_708 (Distal Colon)

description:
distal colon tissue
RS10_708
a_0%

value: 0% raw potato starch


title: RS10_716 (Distal Colon)

description:
distal colon tissue
RS10_716
b_2%


title: AML01 patient cell 25 [AML01_D02_181120_scRNAseq_S122]


title: RS10_719 (Distal Colon)

description:
distal colon tissue
RS10_719
c_5%


title: RS10_721 (Distal Colon)

description:
distal colon tissue
RS10_721
c_5%


title: AML01 patient cell 22 [AML01_C07_181120_scRNAseq_S119]


title: RS10_704 (Distal Colon)

description:
distal colon tissue
RS10_704
a_0%


title: AML01 patient cell 23 [AML01_C08_181120_scRNAseq_S120]


title: RS10_703 (Distal Colon)

description:
distal colon tissue
RS10_703
a_0%


title: RS10_701 (Distal Colon)

description:
distal colon tissue
RS10_701
a_0%


title: AML01 patient cell 21 [AML01_C06_181120_scRNAseq_S118]


title: AML01 patient cell 20 [AML01_C05_181120_scRNAseq_S117]


title: AML01 patient cell 18 [AML01_C03_181120_scRNAseq_S115]


title: AML01 patient cell 16 [AML01_C01_181120_scRNAseq_S113]


title: AML01 patient cell 14 [AML01_B07_181120_scRNAseq_S111]


title: AML01 patient cell 15 [AML01_B08_181120_scRNAseq_S112]


title: RS10_732 (Cecum)

description:
Cecum tissue
RS10_732

source_name: cecum


title: RS10_725 (Cecum)

description:
Cecum tissue
RS10_725


title: RS10_731 (Cecum)

description:
Cecum tissue
RS10_731


title: RS10_720 (Cecum)

description:
Cecum tissue
RS10_720


title: RS10_748 (Cecum)

description:
Cecum tissue
RS10_748


title: RS10_729 (Cecum)

description:
Cecum tissue
RS10_729


title: AML01 patient cell 17 [AML01_C02_181120_scRNAseq_S114]


title: RS10_719 (Cecum)

description:
Cecum tissue
RS10_719


title: AML01 patient cell 10 [AML01_B03_181120_scRNAseq_S107]


title: RS10_726 (Cecum)

description:
Cecum tissue
RS10_726


title: AML01 patient cell 12 [AML01_B05_181120_scRNAseq_S109]


title: AML01 patient cell 11 [AML01_B04_181120_scRNAseq_S108]


title: RS10_752 (Cecum)

description:
Cecum tissue
RS10_752


title: RS10_707 (Distal Colon)

description:
distal colon tissue
RS10_707
a_0%


title: RS10_714 (Cecum)

description:
Cecum tissue
RS10_714


title: Spp1AID_mcm23A_+IAA_S30_Input_rep1

value: MNase

tag: strains genetic background

value: mcm2-3A mutant and Spp1 KO

tag: chip antibody

tag: spike-in

value: whole cell


title: AML01 patient cell 7 [AML01_A08_181120_scRNAseq_S104]


title: RS10_717 (Cecum)

description:
Cecum tissue
RS10_717


title: AML01 patient cell 6 [AML01_A07_181120_scRNAseq_S103]


title: RS10_711 (Cecum)

description:
Cecum tissue
RS10_711


title: AML01 patient cell 19 [AML01_C04_181120_scRNAseq_S116]


title: AML01 patient cell 13 [AML01_B06_181120_scRNAseq_S110]


title: RS10_718 (Cecum)

description:
Cecum tissue
RS10_718


title: RS10_712 (Cecum)

description:
Cecum tissue
RS10_712


title: RS10_705 (Cecum)

description:
Cecum tissue
RS10_705


title: AML01 patient cell 2 [AML01_A03_181120_scRNAseq_S99]


title: AML01 patient cell 3 [AML01_A04_181120_scRNAseq_S100]


title: AML01 patient cell 9 [AML01_B02_181120_scRNAseq_S106]


title: RS10_707 (Cecum)

description:
Cecum tissue
RS10_707


title: RS10_709 (Cecum)

description:
Cecum tissue
RS10_709


title: AML01 patient cell 5 [AML01_A06_181120_scRNAseq_S102]


title: RS10_702 (Cecum)

description:
Cecum tissue
RS10_702


title: RS10_706 (Cecum)

description:
Cecum tissue
RS10_706


title: RS10_708 (Cecum)

description:
Cecum tissue
RS10_708


title: KG1a untreated cell 41 [KG1a_unt_H07_180808_scRNAseq_S91]

description: processed data file: KG1a_scRNAseq_TEtranscripts_counts.txt.gz

source_name: KG-1a cell line

tag: cell line


title: KG1a untreated cell 44 [KG1a_unt_H10_180808_scRNAseq_S94]

tag: treatment


title: AML01 patient cell 8 [AML01_B01_181120_scRNAseq_S105]


title: KG1a untreated cell 46 [KG1a_unt_H12_180808_scRNAseq_S96]


title: AML01 patient cell 1 [AML01_A02_181120_scRNAseq_S98]


title: KG1a untreated cell 43 [KG1a_unt_H09_180808_scRNAseq_S93]


title: KG1a untreated cell 45 [KG1a_unt_H11_180808_scRNAseq_S95]


title: RS10_727 (Proximal Colon)

source_name: proximal colon

tag: strain


title: RS10_784 (Proximal Colon)


title: RS10_729 (Proximal Colon)


title: RS10_725 (Proximal Colon)


title: RS10_724 (Proximal Colon)


title: KG1a untreated cell 42 [KG1a_unt_H08_180808_scRNAseq_S92]


title: KG1a decitabine treated cell 43 [KG1a_dac_H03_180808_scRNAseq_S87]

value: decitabine treated:at 0, 24 and 48 hours, harvested at 72 hours


title: RS10_719 (Proximal Colon)


title: KG1a decitabine treated cell 46 [KG1a_dac_H06_180808_scRNAseq_S90]


title: RS10_748 (Proximal Colon)


title: RS10_718 (Proximal Colon)


title: AML01 patient cell 4 [AML01_A05_181120_scRNAseq_S101]


title: RS10_717 (Proximal Colon)


title: RS10_715 (Proximal Colon)


title: KG1a decitabine treated cell 42 [KG1a_dac_H02_180808_scRNAseq_S86]


title: KG1a untreated cell 39 [KG1a_unt_G11_180808_scRNAseq_S83]


title: RS10_712 (Proximal Colon)


title: KG1a untreated cell 37 [KG1a_unt_G09_180808_scRNAseq_S81]


title: KG1a untreated cell 40 [KG1a_unt_G12_180808_scRNAseq_S84]


title: RS10_711 (Proximal Colon)


title: RS10_716 (Proximal Colon)


title: RS10_753 (Proximal Colon)


title: RS10_721 (Proximal Colon)


title: KG1a untreated cell 38 [KG1a_unt_G10_180808_scRNAseq_S82]


title: RS10_708 (Proximal Colon)


title: KG1a decitabine treated cell 41 [KG1a_dac_H01_180808_scRNAseq_S85]


title: KG1a decitabine treated cell 45 [KG1a_dac_H05_180808_scRNAseq_S89]


title: RS10_706 (Proximal Colon)


title: RS10_707 (Proximal Colon)


title: KG1a untreated cell 35 [KG1a_unt_G07_180808_scRNAseq_S79]


title: KG1a decitabine treated cell 44 [KG1a_dac_H04_180808_scRNAseq_S88]


title: KG1a untreated cell 36 [KG1a_unt_G08_180808_scRNAseq_S80]


title: KG1a decitabine treated cell 40 [KG1a_dac_G06_180808_scRNAseq_S78]


title: KG1a decitabine treated cell 39 [KG1a_dac_G05_180808_scRNAseq_S77]


title: RS10_701 (Proximal Colon)


title: KG1a decitabine treated cell 38 [KG1a_dac_G04_180808_scRNAseq_S76]


title: KG1a decitabine treated cell 37 [KG1a_dac_G03_180808_scRNAseq_S75]


title: RS10_703 (Proximal Colon)


title: mcm2-3A_spp1W45A_Swd1-HA_HAChIP_G1_rep2

organism: Saccharomyces cerevisiae

value: Sonication

tag: genotype

value: mcm2-3A mutant and spp1W45A and Swd1-HA

value: anti-HA


title: KG1a decitabine treated cell 36 [KG1a_dac_G02_180808_scRNAseq_S74]


title: mcm2-3A_spp1W45A_Swd1-HA_Input_G1_rep2


title: KG1a decitabine treated cell 35 [KG1a_dac_G01_180808_scRNAseq_S73]


title: KG1a untreated cell 34 [KG1a_unt_F12_180808_scRNAseq_S72]

value: untreated


title: KG1a untreated cell 33 [KG1a_unt_F11_180808_scRNAseq_S71]

value: Acute myeloid leukemia


title: mcm2-3A_spp1W45A_Swd1-HA_HAChIP_G1_rep1


title: KG1a untreated cell 32 [KG1a_unt_F10_180808_scRNAseq_S70]

value: M


title: KG1a untreated cell 31 [KG1a_unt_F09_180808_scRNAseq_S69]


title: mcm2-3A_Swd1-HA_HAChIP_G1_rep1

value: mcm2-3A mutant and Swd1-HA


title: mcm2-3A_HAChIP_G1

value: mcm2-3A mutant


title: KG1a untreated cell 30 [KG1a_unt_F08_180808_scRNAseq_S68]


title: mcm2-3A_spp1W45A_Swd1-HA_Input_G1_rep1


title: KG1a untreated cell 29 [KG1a_unt_F07_180808_scRNAseq_S67]


title: mcm2-3A_Swd1-HA_HAChIP_G1_rep2


title: Spp1-FLAG_H3K4R_FLAGChIP_asynch_rep2

value: H3K4R mutant and Spp1-FLAG

value: anti-FLAG


title: KG1a decitabine treated cell 33 [KG1a_dac_F05_180808_scRNAseq_S65]


title: KG1a decitabine treated cell 32 [KG1a_dac_F04_180808_scRNAseq_S64]


title: mcm2-3A_Swd1-HA_Input_G1_rep1


title: Spp1-FLAG_Input_asynch_rep2


title: KG1a decitabine treated cell 31 [KG1a_dac_F03_180808_scRNAseq_S63]


title: mcm2-3A_Input_G1


title: Spp1-FLAG_H3K4R_Input_asynch_rep2


title: KG1a decitabine treated cell 34 [KG1a_dac_F06_180808_scRNAseq_S66]


title: Spp1-FLAG_FLAGChIP_asynch_rep2


title: KG1a decitabine treated cell 30 [KG1a_dac_F02_180808_scRNAseq_S62]


title: KG1a decitabine treated cell 29 [KG1a_dac_F01_180808_scRNAseq_S61]


title: Spp1-FLAG_H3K4R_FLAGChIP_asynch_rep1


title: mcm2-3A_Swd1-HA_Input_G1_rep2


title: KG1a untreated cell 27 [KG1a_unt_E11_180808_scRNAseq_S59]


title: Spp1-FLAG_H3K4R_Input_asynch_rep1


title: KG1a untreated cell 28 [KG1a_unt_E12_180808_scRNAseq_S60]


title: WT_FLAGChIP_asynch

value: WT


title: Spp1-FLAG_Input_asynch_rep1


title: KG1a untreated cell 25 [KG1a_unt_E09_180808_scRNAseq_S57]


title: KG1a untreated cell 26 [KG1a_unt_E10_180808_scRNAseq_S58]


title: KG1a untreated cell 24 [KG1a_unt_E08_180808_scRNAseq_S56]


title: KG1a decitabine treated cell 28 [KG1a_dac_E05_180808_scRNAseq_S53]


title: Swd1AIDdpb3D+IAA_H3K4me3_ChIP_S90_rep2

value: dpb3 KO and Swd1 KO

value: anti-H3K4me3 (ab8580, Abcam)


title: Swd1AIDdpb3D+IAA_Input_S90_rep2

value: MNase


title: KG1a decitabine treated cell 25 [KG1a_dac_E02_180808_scRNAseq_S50]


title: KG1a decitabine treated cell 24 [KG1a_dac_E01_180808_scRNAseq_S49]


title: Swd1AIDdpb3D+IAA_BrdU_S90_rep2

value: anti-BrdU (555627, BD Bioscience)


title: KG1a decitabine treated cell 23 [KG1a_dac_D12_180808_scRNAseq_S48]


title: Swd1AIDdpb3D+IAA_H3K4me3_eSPAN_S90_rep2


title: KG1a decitabine treated cell 22 [KG1a_dac_D11_180808_scRNAseq_S47]


title: Swd1AIDdpb3D+IAA_BrdU_S30_rep2


title: KG1a decitabine treated cell 21 [KG1a_dac_D10_180808_scRNAseq_S46]


title: Swd1AIDdpb3D+IAA_H3K4me3_ChIP_G1_rep2


title: Swd1AIDdpb3D+IAA_H3K4me3_ChIP_S30_rep2


title: WT_Input_asynch


title: Swd1AIDdpb3D+IAA_Input_S30_rep2


title: Spp1-FLAG_FLAGChIP_asynch_rep1


title: KG1a decitabine treated cell 19 [KG1a_dac_D08_180808_scRNAseq_S44]


title: Swd1AIDdpb3D+IAA_H3K4me3_eSPAN_S30_rep2


title: Swd1AIDdpb3D+IAA_Input_G1_rep2


title: KG1a untreated cell 23 [KG1a_unt_D05_180808_scRNAseq_S41]


title: KG1a decitabine treated cell 26 [KG1a_dac_E03_180808_scRNAseq_S51]


title: KG1a untreated cell 22 [KG1a_unt_D04_180808_scRNAseq_S40]


title: Swd1AIDdpb3D-IAA_BrdU_S90_rep2

value: dpb3 KO


title: Swd1AIDdpb3D-IAA_Input_S90_rep2


title: Swd1AIDdpb3D-IAA_H3K4me3_ChIP_S90_rep2


title: KG1a untreated cell 21 [KG1a_unt_D03_180808_scRNAseq_S39]


title: KG1a untreated cell 20 [KG1a_unt_D02_180808_scRNAseq_S38]


title: Swd1AIDdpb3D-IAA_H3K4me3_eSPAN_S30_rep2


title: KG1a decitabine treated cell 18 [KG1a_dac_C12_180808_scRNAseq_S36]

value: decitabine treated:at 0, 24 and 48 hours, harvested at 72 hours


title: Swd1AIDdpb3D-IAA_BrdU_S30_rep2


title: KG1a decitabine treated cell 17 [KG1a_dac_C11_180808_scRNAseq_S35]


title: Swd1AIDdpb3D-IAA_Input_S30_rep2


title: KG1a decitabine treated cell 16 [KG1a_dac_C10_180808_scRNAseq_S34]


title: KG1a decitabine treated cell 20 [KG1a_dac_D09_180808_scRNAseq_S45]


title: Swd1AIDdpb3D-IAA_Input_G1_rep2


title: Swd1AIDdpb3D+IAA_H3K4me3_eSPAN_S90_rep1


title: Swd1AIDdpb3D-IAA_H3K4me3_eSPAN_S90_rep2


title: Swd1AIDdpb3D-IAA_H3K4me3_ChIP_S30_rep2


title: KG1a decitabine treated cell 15 [KG1a_dac_C09_180808_scRNAseq_S33]


title: KG1a decitabine treated cell 27 [KG1a_dac_E04_180808_scRNAseq_S52]


title: KG1a untreated cell 18 [KG1a_unt_C06_180808_scRNAseq_S30]


title: Swd1AIDdpb3D-IAA_H3K4me3_ChIP_G1_rep2


title: KG1a decitabine treated cell 14 [KG1a_dac_C08_180808_scRNAseq_S32]


title: Sample 10_shLATS+IFN

city: Suzhou

first: Yibo

last: Zuo

address: Renai road 199

institute: Soochow university

data_processing:
Total RNA in human fibroblast cells were extracted followed protocol of Trizol (Invitrogen, USA) and then made to cDNA librares for sequencing with Universal Plus mRNA-Seq with NuQuant (TECAN GENOMICS, 0520B-A01). Then the libraries were sequenced on NovaSeq 6000 platform (Illumina). The pair-end sequencing data was treated by fastp software to filter reads with bad quality, and then mapped to Ensembl hg19 reference genome by CLC genomic worbench 12.0 (Qiagen).
The pair-end sequencing data was treated by fastp software to filter reads with bad quality.
RPKMs and differential expression fold changes were mapped and calculated by CLC genomic worbench 12.0 (Qiagen).
Genome_build: Genome build. hg19
Supplementary_files_format_and_content: Select ISGs for analysis ( shLATS-IFN vs. shCON-IFN comparison )

source_name: shLATS+IFN

extract_protocol:
2fTGH cells were transfected with shRNAs and then treated with IFNα (1,000 IU/ml) for 8 hrs. Total RNAs were isolated from 2fTGH cells using TRIzol reagent (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 2fTGH cells

tag: knockdown

value: LATS

value: IFN


title: KG1a untreated cell 15 [KG1a_unt_C03_180808_scRNAseq_S27]

value: untreated


title: Sample 11_shLATS+IFN


title: Swd1AIDdpb3D+IAA_H3K4me3_ChIP_S90_rep1


title: Swd1AIDdpb3D+IAA_BrdU_S90_rep1


title: Swd1AIDdpb3D+IAA_Input_S90_rep1


title: KG1a untreated cell 17 [KG1a_unt_C05_180808_scRNAseq_S29]

value: Acute myeloid leukemia


title: KG1a decitabine treated cell 13 [KG1a_dac_C07_180808_scRNAseq_S31]

value: M


title: KG1a untreated cell 16 [KG1a_unt_C04_180808_scRNAseq_S28]


title: Sample 12_shLATS+IFN


title: KG1a untreated cell 19 [KG1a_unt_D01_180808_scRNAseq_S37]


title: Sample 8_shLATS+Mock

source_name: shLATS+Mock

value: mock


title: Swd1AIDdpb3D+IAA_H3K4me3_eSPAN_S30_rep1

source_name: whole cell


title: Swd1AIDdpb3D+IAA_BrdU_S30_rep1


title: KG1a untreated cell 14 [KG1a_unt_C02_180808_scRNAseq_S26]


title: KG1a untreated cell 13 [KG1a_unt_C01_180808_scRNAseq_S25]


title: Swd1AIDdpb3D+IAA_H3K4me3_ChIP_S30_rep1


title: Swd1AIDdpb3D+IAA_H3K4me3_ChIP_G1_rep1


title: Swd1AIDdpb3D+IAA_Input_S30_rep1


title: Sample 6_shCON+IFN

source_name: shCON+IFN

value: control


title: Sample 7_shLATS+Mock


title: KG1a decitabine treated cell 11 [KG1a_dac_B11_180808_scRNAseq_S23]


title: Sample 5_shCON+IFN


title: liver HCF-2

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: includ gene expression

source_name: Liver

extract_protocol:
Liver were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used tp abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

tag: tissue

value: liver

value: 10 weeks

value: High fat diet +control-FMT


title: KG1a decitabine treated cell 12 [KG1a_dac_B12_180808_scRNAseq_S24]


title: liver HCF-3


title: Sample 9_shLATS+Mock


title: Sample 4_shCON+IFN


title: KG1a decitabine treated cell 9 [KG1a_dac_B09_180808_scRNAseq_S21]


title: Sample 3_shCON+Mock

source_name: shCON+Mock


title: KG1a decitabine treated cell 10 [KG1a_dac_B10_180808_scRNAseq_S22]


title: Swd1AIDdpb3D+IAA_Input_G1_rep1

value: dpb3 KO and Swd1 KO


title: liver HCF-1


title: liver HAF-3

value: High fat diet +AOS10mg/kg-FMT


title: Swd1AIDdpb3D-IAA_BrdU_S90_rep1

value: MNase

value: anti-BrdU (555627, BD Bioscience)


title: liver HAF-2


title: Sample 2_shCON+Mock


title: KG1a decitabine treated cell 8 [KG1a_dac_B08_180808_scRNAseq_S20]

value: decitabine treated:at 0, 24 and 48 hours, harvested at 72 hours


title: Swd1AIDdpb3D-IAA_H3K4me3_ChIP_S90_rep1

value: dpb3 KO

value: anti-H3K4me3 (ab8580, Abcam)


title: KG1a decitabine treated cell 7 [KG1a_dac_B07_180808_scRNAseq_S19]


title: liver HAF-1


title: Sample 1_shCON+Mock

value: 2fTGH cells


title: KG1a untreated cell 12 [KG1a_unt_B06_180808_scRNAseq_S18]

value: untreated


title: Swd1AIDdpb3D-IAA_Input_S90_rep1


title: liver HA10-3

value: High fat diet +AOS10mg/kg


title: Swd1AIDdpb3D-IAA_H3K4me3_eSPAN_S30_rep1


title: liver HA10-2


title: KG1a untreated cell 11 [KG1a_unt_B05_180808_scRNAseq_S17]

value: Acute myeloid leukemia

value: M


title: Non-tumor thyroid tissue from patient 4

city: Jinan

first: Lei

last: Sheng

state: Shandong Province

address: 107, Wenhuaxi Road

department: Department of General Surgery

institute: Qilu Hospital, Shandong University

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

source_name: Thyroid

extract_protocol:
All freshly resected thyroid specimens were immediately washed twice  with phosphate-buffered saline (PBS) and digested with digestive enzyme mixture containing 10 ml pre-warmed RPMI 1640 (ThermoFisher Scientific), 1 mg/ml type IV collagenase (Sigma), 2 mg/ml dispase (Roche), and 10 U/µl DNase (Roche) for an hour at 37°C. The reaction was deactivated by adding 10% FBS (ThermoFisher Scientific). Cell suspensions were filtered using a 70 μm filter and then centrifuged at 500 rpm for 6 min at 4°C to pellet dead cells and red blood cells. The cells were washed twice and suspended in PBS with 0.5% bovine serum albumin (BSA, Sigma). Cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion using single cell 3 'Library and Gel Bead Kit V3.1(10x Genomics, 1000121) and Chromium Single Cell G Chip Kit (10x Genomics, 1000120) according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA.   About 6,000 cells were added to each channel, and the target cell that will be recovered was estimated to be about 3,000 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing).
According to the manufacture’s introduction, Single-cell RNA-seq libraries were   constructed using Single Cell 3’ Library and Gel Bead Kit V3.1. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp strategy (performed by CapitalBio Technology, Beijing).

value: wild type

tag: lymph node stage

value: Not applicable


title: Swd1AIDdpb3D-IAA_BrdU_S30_rep1


title: Swd1AIDdpb3D-IAA_H3K4me3_eSPAN_S90_rep1


title: Papillary thyroid cancer from right lobe in patient 3

value: BRAF V600E mutation


title: liver HA10-1

value: ICR

value: liver

value: 10 weeks


title: Swd1AIDdpb3D-IAA_H3K4me3_ChIP_S30_rep1


title: KG1a untreated cell 9 [KG1a_unt_B03_180808_scRNAseq_S15]


title: liver HFD-3

value: High fat diet


title: Papillary thyroid cancer from right lobe in patient 2


title: Papillary thyroid cancer from left lobe in patient 2


title: KG1a untreated cell 8 [KG1a_unt_B02_180808_scRNAseq_S14]


title: Papillary thyroid cancer from left lobe in patient 3


title: Swd1AIDdpb3D-IAA_Input_S30_rep1

value: MNase


title: liver HFD-2


title: liver HFD-1


title: KG1a untreated cell 7 [KG1a_unt_B01_180808_scRNAseq_S13]


title: Swd1AIDdpb3D-IAA_H3K4me3_ChIP_G1_rep1


title: Papillary thyroid cancer from left lobe in patient 1

value: RET/FARP1 fusion


title: KG1a decitabine treated cell 6 [KG1a_dac_A12_180808_scRNAseq_S12]

value: decitabine treated:at 0, 24 and 48 hours, harvested at 72 hours


title: liver con-3

value: control


title: Swd1AIDdpb3D-IAA_Input_G1_rep1

value: dpb3 KO


title: LN18_EGCG+HC3

city: Sungai Buloh

first: Amirah

last: Abdul Rahman

state: SELANGOR

address: Sungai Buloh Campus, UiTM Cawangan Selangor

department: Dept. of Biochemistry & Molecular Medicine

country: Malaysia

institute: Universiti Teknologi MARA

data_processing:
base call performed by HiSeq® 2500 Sequencing System
For quality control, RNA-seq raw data was trimmed at a PHRED score of <Q25, with a read length of at least 33 bp, and read quality was evaluated for each sample using FastQC.
A total of 28-47 million paired end reads were aligned and mapped against the Human Genome version 37, GRCh37/hg19.
Significant differences in gene/transcript expression were determined for pairwise comparisons between two sets of samples using the Empirical analysis of DGE [19] by Negative Binomial distribution followed by Bonferroni multiple testing correction (MTC) and Benjamini-Hochberg false discovery rate (FDR) using the CLC Genomics Workbench (7.0.6 version)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with normalized abundance measurements for every gene and every sample (EDGE analysis)

source_name: glioma cell lines

growth_protocol: Cells were seeded at a density of 5×105 per well in 6-well plates. After a 24-h incubation period, the media was withdrawn and DMEM medium were added, which contains combined treatments EGCG+HC or EGCG/HC singly.

extract_protocol:
After 24 hours of glioma cells treatment, total RNA was using TRI Reagent® (Molecular Research Center, USA). RNase-free DNase treatment was used to remove contaminating DNA (QIAGEN), and RNA was purified using the RNeasy Mini Kit (QIAGEN).
The cDNA libraries were prepared according to the protocol outlined in the TruSeq RNA sample Preparation Kit v-2 (Illumina, San Diego, USA). A total of 10-12 samples per lane were multiplexed and sequenced on an Illumina HiSeq 2500 using the paired-end cluster generation kit (Illumina).

treatment_protocol: Three independent tests were carried out for each treatments

value: brain

tag: disease state

value: glioma

tag: tumor stage

value: grade IV

tag: treatment (24 hours)


title: ME-3

city: Shanghai

first: Feikai

last: Lin

address: No. 1665, Kong Jiang Road

institute: Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
FeatureCounts was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: peritoneal metastasis tissues

extract_protocol:
total RNA (1 ug) was isolated from ovarian cancer tissues and peritoneal metastasis tissues and incubated with VAHTS mRNA Capture Beads (Vazyme, Nanjing, China) to enrich polyA + RNA before construction of RNA libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peritoneal metastasis tissues

value: ovarian cancer stage III


title: KG1a decitabine treated cell 5 [KG1a_dac_A11_180808_scRNAseq_S11]

tag: cancer type

value: Acute myeloid leukemia

tag: Sex

value: M


title: liver con-2

tag: age


title: KG1a untreated cell 10 [KG1a_unt_B04_180808_scRNAseq_S16]

value: untreated


title: LN18_EGCG+HC2


title: ME-2

value: ovarian cancer stage IV


title: KG1a decitabine treated cell 4 [KG1a_dac_A10_180808_scRNAseq_S10]


title: liver A10-3

value: ICR

value: liver

value: AOS 10mg/kg


title: KG1a decitabine treated cell 3 [KG1a_dac_A09_180808_scRNAseq_S9]


title: liver con-1

value: 10 weeks


title: ME-1


title: LN18_HC3

value: hydroxychavicol


title: liver A10-2


title: KG1a decitabine treated cell 2 [KG1a_dac_A08_180808_scRNAseq_S8]

value: decitabine treated:at 0, 24 and 48 hours, harvested at 72 hours


title: Papillary thyroid cancer from right lobe in patient 1

value: BRAF V600E mutation


title: OC-2

source_name: ovarian cancer tissues

value: ovarian cancer tissues


title: liver A10-1


title: LN18_HC2

value: brain


title: KG1a decitabine treated cell 1 [KG1a_dac_A07_180808_scRNAseq_S7]


title: LN18_HC1

value: glioma


title: OC-1


title: KG1a untreated cell 6 [KG1a_unt_A06_180808_scRNAseq_S6]


title: LN18_EGCG3

value: grade IV


title: HEY-NC-3

source_name: HEY cells

extract_protocol:
total RNA (1 ug) was isolated from HEY cells and incubated with VAHTS mRNA Capture Beads (Vazyme, Nanjing, China) to enrich polyA + RNA before construction of RNA libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HEY cells

value: treated with lentiviruses harboring control shRNA (negative control, NC)


title: KG1a untreated cell 5 [KG1a_unt_A05_180808_scRNAseq_S5]

value: Acute myeloid leukemia


title: LN18_EGCG+HC1


title: LN18_EGCG2


title: WGBS TKO_PP

city: Houston

first: Jianfang

last: Li

address: 2121 W. Holcombe Boulevard

institute: Texas A&M University

data_processing:
Library strategy: WGBS
For the 150 bp paired-end raw data of RNA-seq, low quality bases and adaptor were trimmed using TrimGalore v.0.5.0. Clean reads were aligned to hg38 reference genome using STAR v.2.5.354 with default parameters and only uniquely mapped reads were used for downstream analysis. Count matrix for each gene were generated using htseq-count (HTSeq package55). DESeq2 was used to identify significantly differentially expressed genes (DEGs) between groups (WT and TKO ; WT and TET1KO) at the ES, DE and PP stages (fold change ≥ 2; FDR < 0.05). Hierarchical cluster analysis of the union DEGs was used to determine the signature genes and groups. The ‘ClusterProfilter’ package in R was performed for the functional enrichment analysis of DEGs in KEGG pathways.
Adaptor trimming of raw reads were performed by TrimGalore v0.5.0, and high-quality reads were uniquely aligned to hg38 reference genome using Bowtie2 with ‘--very-sensitive’ option. Reads mapped to Mitochondrial DNA and PCR duplicate reads were removed and those uniquely mapped reads were finally extracted for downstream analysis. Genrich v.0.5 with ATAC-seq mode (option: -j, -q 0.01) was applied for each sample (with two biological replicates) to call ATAC peaks. Bedtools intersect was used to count the reads fall into peak regions, and the significantly differential accessible regions (DARs) were detected using DESeq2. Volcano plots were plotted using R package ggplot2. Motif annotation of DARs was performed using HOMER software.
The analysis of CMS-IP data was performed by in house software ‘CMSIP’ v0.1.1. Briefly, raw reads were mapped to hg38 and mm10 genome references using bsmap v.2.89 (options: -n 1 -q 3 -r 0). After removing the PCR duplicates and reads mapped to both human and spike-in mouse genome, species specific reads were used to do the normalization for each sample according to the spike-in size factors. The mean wigsum for every 200 bp windows of the whole human genome was used to call the hydroxymethylation enriched peak regions for each group agaist to input, respectively. Differentially hydroxymethylation regions (DHMRs) in between WT_PP and TKO_PP were identified (g-test; FDR < 0.05). GREAT analysis with single-nearest genes option was used to perform the functional annotation of hypo-DHMRs.
For WGBS data analysis, paired-end 100 bp reads were mapped against hg38 using bsmap v.2.89 with paired mode (options: -n 1 -q 3 -r 0), and only uniquely mapped reads were retained. More than 26.6 million CpG sites with coverage ≥ 5 reads were detected in both WT_PP and TKO_PP samples, which were used for downstream analyses. BSeQC and mcall module in MOABS30 was applied to do the quality control and calculate the methylation ratio for each CpG site (options: --trimWGBSEndRepairPE2Seq 40). Bisulfite conversion efficiencies were estimated using spike-in unmethylated lambda phage DNA. Mcomp module was used to call significantly differentially methylation CpG sites (DMCs) and differentially methylation regions (DMRs) (absolute credible difference of DNA methylation ratio of at least 20% and adjust p value of less than 0.05). The output bedGraph files from mcall include single base resolution DNA methylation ratios, which were transformed to a bigwig file format. The bigwig files were uploaded to the UCSC genome browser for visualization. Motif enrichment analysis of DMRs was performed using HOMER software and the functional annotation was performed by using GREAT with default settings.
The quality control and alignment for raw reads of ChIP-seq data were similar to ATAC-seq data analysis above, TrimGalore (options: --quality 20 and --length 50) was used to remove adaptor and only uniquely mapped reads were retained. Bam2wig.py was used to transform the bam file to normalized bigWig files (option: -t 2000000000). For the WT_PP TET1 ChIP-seq, Macs262 was used to call ChIP-seq enriched peak regions with default parameters.
Genome_build: hg38

source_name: Triple-knockout pancreatic progenitors

extract_protocol:
Total RNA was isolated using the Trizol reagent following the manufacturer’s instructions. RNA integrity was determined using Agilent 2100 Bioanalyzer (Agilent Technologies). Subsequently, polyA tailed RNA were selected using the Dynabeads oligo(dT) (Thermo Fisher Scientific). Total gnomic DNA was isolated using the DNeasy Blood & Tissue kit (Qiagen).
RNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep kit for Illumina (New England Biolabs). ATAC-seq libraries were prepared as previously described60. In brief, cells were enzymatically dissociated and lysed in lysis buffer (10 mM Tris-HCl, PH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Immediately after centrifugation, transposition reactions were carried out by adding Tn5 Transposes from the Illumina Nextera DNA library preparation kit to the isolated nuclei and incubated at 37 oC for 30 min. DNA fragments were purified using the MinElute PCR Purification kit (Qiagen) and amplified using the KAPA real-time library amplification kit. Libraries were purified using the PCRClean DXTM beads (Aline Biosciences).  CMS-IP-seq libraries were performed as previously described with small modifications (Huang et al., 2012). Purified genomic DNA (with 5% of mouse DNA and 0.5% lambda DNA spike-in) was sheared to 200–500 bp fragments using the M220 Focused-ultrasonicator (Covaris). Bisulfite converted DNA libraries with methylated adapters were enriched using an in-house anti-CMS antibody bound to protein A/G dynabeads. Amplified libraries were purified by AmpuXP beads (Beckman Coulter) and then sequenced using the Illumina NextSeq (75 and 40 cycle, single-end) systems. Genomic DNA was isolated using the DNeasy Blood & Tissue kit (Qiagen). WGBS library preparation and sequencing were conducted by BGI (Shengzhen, China). In brief, purified genomic DNA (with 1% of unmethylated lambda DNA spike-in, Promega) was sheared to a fragment size of 100–700 bp (main size 250bp) using Covaris focused ultrasonicator according to the manufacturer’s instructions. DNA fragments were subjected to bisulfited conversion using the EZ DNA Methylation-gold kit (Zymo Research). Bisulfite converted DNA was amplified and finally subjected to sequence on a MGISEQ-2000 system (100-cycle, paired-end) at BGI (Shengzhen, China).  ChIP-seq was performed for TET1 (WT_PP cells), H3K4me1 (WT_PP and TKO_PP cells), and H3K27ac (WT_PP and TKO_PP cells). For TET1 ChIP-seq, approximately 5 x 107 cells were crosslinked, washed and snap frozen following the Cell Fixation protocol from Active Motif. TET1 ChIP-seq library preparation and sequencing were conducted by Active Motif. Chromatin immunoprecipitation of H3K4me1 and H3K27ac were performed as previously described28. WT_PP and TKO_PP cells were fixed, washed, and lysed in nuclear lysis buffer (50 mM Trish HCl, pH 8.0, 5mM EDTA, 1% SDS, and 1 protease inhibitor cocktail). Chromatin was sheared to 200-500 bp fragments using Bioruptor® (Diagenode), and the DNA fragments were precipitated with appropriate antibodies. ChIP-seq libraries were prepared using the NEBNext® Ultra IITM DNA Library Prep kit (New England Biolabs) following the manufacture’s instruction and subjected to high throughput sequencing on a Illumina HiSeq 2500 system (150 bp, paired-end) at Novogene (Tianjin, China).

tag: cell type

value: Triple-knockout pancreatic progenitors


title: HEY-NC-2


title: KG1a untreated cell 4 [KG1a_unt_A04_180808_scRNAseq_S4]

value: untreated

value: M


title: WGBS WT_PP

source_name: Normal pancreatic progenitor

value: Normal pancreatic progenitor


title: OC-3

value: ovarian cancer stage III


title: LN18_EGCG1


title: HEY-NC-1


title: KG1a untreated cell 1 [KG1a_unt_A01_180808_scRNAseq_S1]


title: KG1a untreated cell 3 [KG1a_unt_A03_180808_scRNAseq_S3]


title: LN18_C1

value: control


title: HEY-KD-3

value: treated with lentiviruses harboring specific shRNAs against STC1 (STC1-sh1)


title: HEY-KD-2


title: LN18_C2


title: LN18_C3


title: TP53-KO_NCS_IN_rep4

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

institute: Heidelberg University

data_processing:
Adapters were removed with the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), retaining only sequences that are at least 28 nt long. The four random nucleotides at the beginning and the end of the reads were trimmed with an in-house developed perl script.
Alignment was performed with bowtie v1.2.2 (Langmead et al., Genome Biology 2009) allowing a maximum of two mismatches and reporting all alignments in the best stratum (settings: -a –best –stratum –v 2). Reads that did not map to tRNA or rRNA sequences (as downloaded from the UCSC Genome Browser) were aligned to a human transcriptome (Gencode V27 as downloaded from the UCSC Genome Browser wgEncodeGencodeBasicV27 table).
Reads were filtered with in-house developed perl scripts to retain only reads that are between 25 and 35 nt long and map to ORFs of isoforms arising from one specific gene (as defined by a common gene symbol). An offset of 12 nt upstream of the start codon and 15 nt upstream of the stop codon with respect to the 5’end of the read was assumed.
Normalization was performed using size factors obtained with the median ratio method of the DeSeq2 package, v1.18.1 (Love et al., Genome Biology 2014).
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts

molecule: cytoplasmic RNA

growth_protocol: HCT116 cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS, Biochrome), 2 mM L-Glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin (all PAN Biotech) at 37°C in a humidified atmosphere with 5% CO2. Every two to three days, cells were trypsinized and diluted 1:10. Two days before experiments, HCT116 cells were seeded at a density of 2 x 106 cells per 10 cm dish (Sarstedt, 83.3902).

extract_protocol:
Cells grown in 10-cm dishes were washed once with ice-cold PBS containing 100 µg/ml cycloheximide (CHX) and directly lysed using 290 µl of Ribo-Seq lysis buffer (20 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 200 mM KCl, 2 mM DTT, 100 µg/ml CHX, 1% NP-40, 40 U/ml RNasin (Promega), EDTA-free complete protease inhibitors (Roche)). The total RNA concentrations between samples were adjusted by measuring absorbance at 260 nm. From the adjusted cellular lysates, 50 µl was taken and diluted with in 250 µl of Ribo-Seq lysis buffer for preparing input samples to be analyzed by RNA-Seq. The remaining lysate (approximate volume of 250 µl) was treated with 240 U/1 A260 of RNase I (Ambion) for 5 min at 4°C on a rotator, and then loaded on top of 3.95 ml 17.5–50% sucrose density gradients  for which sucrose was dissolved in a buffer containing 20 mM Tris-HCl, pH 7.5, 5 mM MgCl2, and 150 mM NaCl. Centrifugation and profile recording were carried out as in the above section, and fractions of 300 µl each were collected with the fraction collector as part of the Teledyne ISCO Foxy RI system. Fractions corresponding to monosomes and disomes were used for preparation of ribosome protected fragments (RPF). Input samples and the monsome/disome fractions were first mixed with 300 µl of urea buffer (10 mM Tris-pH 7.5, 350 mM NaCl, 10 mM EDTA, 1% SDS, 7% urea), incubated with 300 µl phenol:chloroform:isamylalcohol (25:24:1) for 10 min at 65°C, and the RNA was extracted upon centrifugation by recovery of the aqueous phase followed by precipitation using 600 µl isopropanol and 1 µl of GlycoBlue (Invitrogen) at -20°C over night. After washing with 70% ethanol, the RNA was dissolved in 10 µl H2O. To prepare monosome footpints, cell lysates were first separated on 17.5-50% sucrose gradients and monosome fractions were collected manually. Monosome containing fraction was treated with 24 U/1 A260 (according to input sample) of RNase I as indicated above and RNA was purified with the same method with total foot prints.
From both input and ribosome protected fragments, ribosomal RNA was depleted from the RFP samples using the Ribo-Zero Gold Kit (Illumina).  Input RNA was randomly fragmented by alkaline hydrolysis at pH 10.0 for 12 min at 95°C. Fragmented RNA and RPFs were then size-selected (25–35 nt) on a 15% polyacrylamide Tris-borate-EDTA-urea gel. The gel pieces were crashed and RNAs were extracted by incubating overnight in 300 µl buffer containing (0.3 M NaCl and 80 u RNase OUT (invitrogen)) at 4oC. Gels were removed by centrifugation at 14.000 x g for 5 min at 4oC with a 0.45 µm NanoSep MF tubes (PALL) and RNAs were precipitated with 300 µl isopropanol and 1 µl GlycoBlue (Ambion). After washing with 70% Ethanol, RNA were dissolved in 14 µl H2O and subjected to end-repair with T4 polynucleotide kinase (NEB) for 1 h at 37°C. Following an additional round of purification and precipitation using isopropanol, upto 20 ng RNA were used for library preparation using the NEXTflex Small RNA-Seq Kit v3 (PerkinElmer) according to the manufacturer’s manual. Libraries were multiplexed and sequenced with a NextSeq500 sequencer (Illumina).

treatment_protocol: HCT116 cells were treated with PBS or neocarizinostatin (0.2 µg/ml, Sigma-Aldrich, N0162) for 4 h.

tag: material

value: Input

value: neocarzinostatin (4 h)


title: HEY-KD-1


title: 1321N1_EGCG+HC3

value: grade II


title: TP53-KO_NCS_RPF_rep4

value: ribosome-protected fragments


title: TP53-KO_Ctrl_IN_rep4

value: PBS


title: HSPCs, RUNX3_4

city: Cardiff

first: Alex

last: Tonks

address: Heath Park Way

department: Department of Haematology

country: United Kingdom

institute: Cardiff University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were filtered to discard the reads with low quality, adapter contamination or uncertain nucleotides. HISAT2 was used to map the reads to the human reference genome (hg19).
Quantification of gene expression was determined by transcript abundance and estimated by counting the reads that align to genes or exons. Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was used as normalised estimation method of gene expression. HTSeq package was used to determine gene expression levels using the union mode.
Differential expression analysis was performed in three steps: normalisation of read counts using DESeq2, p-value estimation following a negative binomial distribution model, and false discovery rate (FDR) estimation based on Benjamini-Hochberg method.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with read counts for each gene and in each sample
Supplementary_files_format_and_content: Matrix table with normalized FPKM values for each gene and in each sample

source_name: Cord blood

growth_protocol: HSPC were maintained in IMDM supplemented with IL-3, IL-6, SCF, Flt3, G-CSF and GM-CSF at 5 ng/mL

extract_protocol:
Total RNA was extracted from cells using the RNeasy® Plus Mini Kit, following manufacturer’s instructions. RNA concentration and purity were assessed using NanoDrop™.
RNA-sequencing was performed by Novogene (Cambridge, UK), and RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cord blood-derived HSPC were transduced with either a GFP control or RUNX3 GFP recombinant retrovirus.

value: HSPC

value: Cord blood

value: RUNX3 overexpression


title: HSPCs, RUNX3_2


title: 1321N1_EGCG+HC1

value: brain

value: glioma


title: HSPCs, RUNX3_5


title: D2M24: Monocytes_Donor2_HD_24hr

type: RNA

city: Southampton

first: Rosanna

middle: C G

last: Smith

state: Hampshire

address: Centre for Cancer Immunology, University Hospital Southampton (MP 127), Tremona Road

department: Cancer Sciences Unit, Faculty of Medicine

institute: University of Southampton

hyb_protocol: Standard Illumina Whole-Genome DASL HT hybridisation protocol.

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: Data was processed using the limma package (version 3.24.15) in R (version 3.3.3). Non-normalised, probe and control-probe matrices were inputed using the read.ilmn function. Data was then background-corrected and quantile normalised using the neqc function and quality checked by only including probes that were expressed in at least 3 arrays according to detection p-values of 5%. This is the data provided in the normalised matrix.

label: biotin

source_name: Monocytes, Donor 2, high density culture, 24hr.

label_protocol: Standard Illumina Whole-Genome DASL HT labeling protocol

growth_protocol: After isolation from PBMCs, cells were cultured at an initial density of 1 x 10^7 cell/mL in CTL-Test Medium ((Europe GmbH, Bonn, Germany), supplemented with glutamine (2 mM), pyruvate (1 mM), penicillin (100 IU/mL), and streptomycin (100 IU/mL)), at 37°C in 5% CO2. Cells were cultured for 0 (no culture), 2, 10 or 24 hours before RNA extraction.

extract_protocol: Total RNA extraction using RNAeasy Mini Kit (Qiagen).

tag: donor

value: Monocyte

tag: timepoint

tag: initial culture density

value: 1x10^7 cells/mL

tag: isolation from pbmcs

value: Pan Monocyte Isolation Kit, human, Miltenyi Biotech


title: WT_NCS_IN_rep4

tag: treatment

value: wild type


title: KG1a untreated cell 2 [KG1a_unt_A02_180808_scRNAseq_S2]

source_name: KG-1a cell line

tag: cell line

value: untreated

value: Acute myeloid leukemia

value: M


title: D2M10: Monocytes_Donor2_HD_10hr.

source_name: Monocytes, Donor 2, high density culture, 10hr.


title: 1321N1_HC3

value: hydroxychavicol


title: 1321N1_HC2


title: D2M0: Monocytes_Donor2_0hr

source_name: Monocytes, Donor 2, not cultured.


title: HSPCs, RUNX3_3

tag: genotype


title: HSPCs, RUNX3_1

tag: tissue


title: D2B24: Bcell_Donor2_HD_24hr

source_name: B cells, Donor 2, high density culture, 24hr.

value: B-cell

value: B cell Isolation Kit II, human, Miltenyi Biotech


title: WT_Ctrl_IN_rep4

value: Input


title: D2M2: Monocytes_Donor2_HD_2hr

source_name: Monocytes, Donor 2, high density culture, 2hr.


title: 1321N1_EGCG+HC2

value: grade II


title: WT_NCS_RPF_rep4

value: ribosome-protected fragments

value: neocarzinostatin (4 h)


title: D1M10: Monocytes_Donor1_HD_10hr.

source_name: Monocytes, Donor 1, high density culture, 10hr.


title: HSPCs, Ctrl_5

value: HSPC

value: Cord blood

value: Control


title: TP53-KO_Ctrl_RPF_rep4

value: PBS


title: D1M24: Monocytes_Donor1_HD_24hr

source_name: Monocytes, Donor 1, high density culture, 24hr.

value: Monocyte

value: 1x10^7 cells/mL


title: 1321N1_EGCG3

value: brain

value: glioma


title: HSPCs, Ctrl_4


title: WT_Ctrl_RPF_rep4

value: wild type


title: 1321N1_EGCG2


title: D1M2: Monocytes_Donor1_HD_2hr

source_name: Monocytes, Donor 1, high density culture, 2hr.

value: Pan Monocyte Isolation Kit, human, Miltenyi Biotech


title: HSPCs, Ctrl_3


title: 1321N1_EGCG1


title: TP53-KO_NCS_IN_rep3


title: HSPCs, Ctrl_2


title: D1M0: Monocytes_Donor1_0hr

source_name: Monocytes, Donor 1, not cultured.


title: TP53-KO_NCS_RPF_rep3


title: 1321N1_HC1

source_name: glioma cell lines

value: hydroxychavicol


title: D1B0: Bcell_Donor1_0hr

source_name: B cells, Donor 1, not cultured.

value: B-cell


title: D2B0: Bcell_Donor2_0hr

source_name: B cells, Donor 2, not cultured.

value: B cell Isolation Kit II, human, Miltenyi Biotech


title: D1B24: Bcell_Donor1_HD_24hr

source_name: B cells, Donor 1, high density culture, 24hr.


title: HSPCs, Ctrl_1


title: TP53-KO_Ctrl_IN_rep3

value: Input


title: TP53-KO_Ctrl_RPF_rep3


title: 1321N1_C2

value: grade II

value: control


title: KO_Bicarb_1

city: Moscow

first: Daniil

middle: M.

last: Bobrovskiy

address: Leninskiye Gory, MSU, 1-73, Faculty of Bioengineering and Bioinformatics, office 433

country: Russia

institute: Lomonosov Moscow State University

data_processing:
The RNA-seq reads were quality controlled and quantified using salmon v1.5.2 selective alignment with unstranded library type and parameters --validateMappings and --seqBias, using the entire Mus musculus reference genome (GRCm39, GENCODE M27) as the decoy sequence.
The resulting abundances were processed using edgeR package v3.34.0, the offsets being calculated with tximport v1.20.0.
Only protein-coding genes, according to BioMart (Ensembl release 104), were considered for analysis.
The transcripts expressed in less than 25% of samples or having less than 10 counts in each sample or total count less than 100 were filtered out. After all these filtration steps, our dataset contained 13430 genes.
The RPKM values were exported using edgeR.
Assembly: mm10
Supplementary files format and content: CSV file with the RPKM values, genes in rows. First row – Ensembl gene IDs, first column – sample names.

source_name: Kidney

growth_protocol: Female mice C57Bl/6 strain, age 2-3 month, were obtained with a status of specific free-pathogens.

extract_protocol:
The kidney was removed from the abdominal cavity, washed in sterile PBS solution, and then, depending on the purpose of the experiment, was processed in two ways. For RNA sequencing, a segment of the kidney with a thickness of 3 mm was cut from the middle section along the horizontal plane; this part of the kidney was placed in RNAlater buffer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two genotypes were taken - wild type and IRR-/- knockout. Under normal conditions, the mice were given water as a drink, and under conditions of bicabonate loading, sodium bicarbonate NaHCO3 at a concentration of 250 mM (pH = 8.5) was added to the drinking water. Then four groups of animals were formed, n = 4, in total 16 animals. Bicarbonate loading was provided for 7 days.  Before experiment mice were fasting for 12 hours with free access of water or bicarbonate treated water.

tag: strain

value: female

value: Bicarb


title: T24T-vector

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Trimmomatic
duplicated reads were removed by UID tags
clean reads were mapped to hg38 whole genome using hisat2 with default parameters
The differentially expressed genes were screened from the difference multiples and the significant levels. Here, we use the absolute value of logFC >1 and pvalue<0.05 as the standard to indicate that the gene is a differentially expressed gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Samples
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: bladder cancer cell

extract_protocol:
Total RNA was isolated from has_circ_0008399-overexpressed EJ and T24T cells using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EJ and T24T cells transfected with has_circ_0008399 and compaired vector

value: bladder cancer

tag: transfected with

value: vector


title: KO_Bicarb_2

department: Faculty of Bioengineering and Bioinformatics


title: 1321N1_C1

tag: disease state

tag: tumor stage


title: KO_Bicarb_3


title: KO_Water_4

value: Water


title: KO_Bicarb_4


title: EJ-circ0008399

value: EJ


title: KO_Water_3


title: EJ-vector


title: RNA TKO2_GT 1

data_processing:
For the 150 bp paired-end raw data of RNA-seq, low quality bases and adaptor were trimmed using TrimGalore v.0.5.0. Clean reads were aligned to hg38 reference genome using STAR v.2.5.354 with default parameters and only uniquely mapped reads were used for downstream analysis. Count matrix for each gene were generated using htseq-count (HTSeq package55). DESeq2 was used to identify significantly differentially expressed genes (DEGs) between groups (WT and TKO ; WT and TET1KO) at the ES, DE and PP stages (fold change ≥ 2; FDR < 0.05). Hierarchical cluster analysis of the union DEGs was used to determine the signature genes and groups. The ‘ClusterProfilter’ package in R was performed for the functional enrichment analysis of DEGs in KEGG pathways.
Adaptor trimming of raw reads were performed by TrimGalore v0.5.0, and high-quality reads were uniquely aligned to hg38 reference genome using Bowtie2 with ‘--very-sensitive’ option. Reads mapped to Mitochondrial DNA and PCR duplicate reads were removed and those uniquely mapped reads were finally extracted for downstream analysis. Genrich v.0.5 with ATAC-seq mode (option: -j, -q 0.01) was applied for each sample (with two biological replicates) to call ATAC peaks. Bedtools intersect was used to count the reads fall into peak regions, and the significantly differential accessible regions (DARs) were detected using DESeq2. Volcano plots were plotted using R package ggplot2. Motif annotation of DARs was performed using HOMER software.
The analysis of CMS-IP data was performed by in house software ‘CMSIP’ v0.1.1. Briefly, raw reads were mapped to hg38 and mm10 genome references using bsmap v.2.89 (options: -n 1 -q 3 -r 0). After removing the PCR duplicates and reads mapped to both human and spike-in mouse genome, species specific reads were used to do the normalization for each sample according to the spike-in size factors. The mean wigsum for every 200 bp windows of the whole human genome was used to call the hydroxymethylation enriched peak regions for each group agaist to input, respectively. Differentially hydroxymethylation regions (DHMRs) in between WT_PP and TKO_PP were identified (g-test; FDR < 0.05). GREAT analysis with single-nearest genes option was used to perform the functional annotation of hypo-DHMRs.
For WGBS data analysis, paired-end 100 bp reads were mapped against hg38 using bsmap v.2.89 with paired mode (options: -n 1 -q 3 -r 0), and only uniquely mapped reads were retained. More than 26.6 million CpG sites with coverage ≥ 5 reads were detected in both WT_PP and TKO_PP samples, which were used for downstream analyses. BSeQC and mcall module in MOABS30 was applied to do the quality control and calculate the methylation ratio for each CpG site (options: --trimWGBSEndRepairPE2Seq 40). Bisulfite conversion efficiencies were estimated using spike-in unmethylated lambda phage DNA. Mcomp module was used to call significantly differentially methylation CpG sites (DMCs) and differentially methylation regions (DMRs) (absolute credible difference of DNA methylation ratio of at least 20% and adjust p value of less than 0.05). The output bedGraph files from mcall include single base resolution DNA methylation ratios, which were transformed to a bigwig file format. The bigwig files were uploaded to the UCSC genome browser for visualization. Motif enrichment analysis of DMRs was performed using HOMER software and the functional annotation was performed by using GREAT with default settings.
The quality control and alignment for raw reads of ChIP-seq data were similar to ATAC-seq data analysis above, TrimGalore (options: --quality 20 and --length 50) was used to remove adaptor and only uniquely mapped reads were retained. Bam2wig.py was used to transform the bam file to normalized bigWig files (option: -t 2000000000). For the WT_PP TET1 ChIP-seq, Macs262 was used to call ChIP-seq enriched peak regions with default parameters.
Genome_build: hg38

source_name: Triple-knockout hESCs clone2

value: Triple-knockout hESCs clone2


title: WT_NCS_RPF_rep3

value: ribosome-protected fragments

value: neocarzinostatin (4 h)


title: RNA TKO2_GT 2


title: KO_Water_2


title: WT_Ctrl_IN_rep3

value: PBS

value: wild type


title: WT_Ctrl_RPF_rep3


title: KO_Water_1


title: H24RNAU

data_processing:
Illumina bcl2fastq v2.20.0 was used for converting bcl files to fastq.
Alignment: Sequenced reads from each sample and run were aligned to the human genome (primary assembly, GRCh38.p12, GCA_000001405.27) using the STAR alignment algorithm (version 2.5.2b, default parameters) and filtered for uniquely-mapped alignments using samtools (version 1.6, parameters: -q 255). Alignments were merged for sequencing runs from the same sample.
Counts: Uniquely-mapped alignments overlapping gene exons were counted using feature Counts from the Rsubread package (version 1.32.4). Counting was performed relative to Ensembl 97 (Jul 2019) gene annotation and counts summarized at the gene level. Rsubread parameters: countMultiMappingRead=FALSE, strandSpecific=2, isPairedEnd=TRUE, minFragLength=50, maxFragLength=700.
Gene expression: Gene expression filtering and normalization was carried out in R, using the edgeR package (version 3.24.2). Genes with below-threshold counts were filtered out (filterByExpr parameters: min.count=30, min.count.total=45) and between-sample normalization was performed using the trimmed mean of M-values method. Gene expression is reported as counts-per-million (CPM).
Genome_build: GRCh38.p12, GCA_000001405.27
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Matrix table with between-sample normalised CPM expression values for every sample and those genes passing minimum counts threshold filter.

source_name: Primary human monocytes - Donor H, 24hr, untreated

growth_protocol: Anonymized leukocyte cones were sourced from healthy adult donors attending blood donation clinics at the National Blood Service (Southampton, UK). Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation (Lymphoprep, Axis-Shield). Primary human monocytes were isolated from PBMCs using the Pan Monocyte Isolation Kit, human, (Miltenyi Biotech) from 1x108 PBMCs per isolation, according to the manufacturer’s protocol and cultured at low density (1 x 106/mL in a 24-well plate) in complete CTL medium at 37°C and 5% CO2.

extract_protocol:
Monocytes were lysed immediately (0hr) using QIAzol lysis reagent (Qiagen) or after culturing for 2, 10 or 24 hours. Total RNA was isolated using miRNeasy mini kit (Qiagen) as per manufacturer’s protocol.
Total RNA samples were enriched for mature, poly-A mRNA transcripts and prepared for sequencing using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. Two runs of 150 base pair paired-end sequencing were carried out per sample on the NovaSeq 6000 (Illumina) platform with v1.0 chemistry.

treatment_protocol: Samples were either cultured in the absence (untreated (U)) or presence (treated (T)) of 20μM Dimethyloxalylglycine (DMOG, EMD Millipore).

value: H

value: Untreated

value: Primary human monocytes


title: RNA WT_GT 2

source_name: Normal hESC

value: Normal hESC


title: RNA WT_GT 1


title: 1321N1_C3

value: brain

value: glioma

value: grade II

tag: treatment (24 hours)


title: T24T-circ0008399


title: H24RNAT

source_name: Primary human monocytes - Donor H, 24hr, DMOG treated

value: DMOG


title: WT_NCS_IN_rep3

value: Input


title: H10RNAU

source_name: Primary human monocytes - Donor H, 10hr, untreated


title: TP53-KO_NCS_RPF_rep2


title: TP53-KO_NCS_IN_rep2