title: CCD-18CO, TWEAK, Rep3

city: Dublin

first: Mario

last: Manresa

address: UCD Belfield

country: Ireland

institute: School of Biomolecular and Biomedical Sciences

data_processing:
nf-Core RNA-seq pipeline v3.9
Raw FASTQ files were trimmed using Trim Galore.
Trimmed reads were then aligned to the human transcriptome followed by mapping to the genome (GRCh38) and quantified at the transcript level using STAR and SALMON.
Salmon gene-level counts were then passed to DeSeq2 for normalization and downstream analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes normalized gene-level counts for each sample

growth_protocol: Human primary colonic fibroblasts (CCD-18CO, American Type Culture Collection (ATCC), Manassas, VA) were cultured in Eagle’s Minimum Essential Medium (EMEM, ATCC) supplemented with 10% Foetal bovine serum (FBS, BioSciences, Ireland)

extract_protocol: RNA was sent to BGI for library construction and sequencing.

treatment_protocol: Human primary colonic fibroblasts were serum deprived (in serum free EMEM) for a minimum of 6 hours,followed by stimulation with 50 ng/mL of TWEAK (PeproTech, UK) in serum-free medium for 24 hours.

value: colonic fibroblasts

value: WT

value: TWEAK


title: testis A10-2

status: Public on Apr 23 2024

type: SRA

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: testis

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

tag: strain

value: ICR

tag: tissue

value: testis

tag: age

value: 10 weeks

tag: treatment

value: AOS 10mg/kg


title: sample2

city: Chongqing

first: Qijing

last: Lei

address: 30 Gaotanyan Main St, Shapingba District,400038

institute: Third Military Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
barcode processing and single-cell counting was performed using the Cellranger-6.1.2 (10X Genomics).
Assembly: mm10
Supplementary files format and content: Matrix files

source_name: brain

extract_protocol:
Single cell suspensions of freshly mouse brain cells were isolated from P10 mice
scRNA-seq libraries were prepared using the Chromium controller and Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions. The libraries were subsequently sequenced by BGI Genomics Co. on a MGISEQ-2000 platform. Sequencing depth of each sample was 700M raw reads and sample demultiplexing.

value: brain

value: postnatal day 10


title: sample1

description: 10x Genomics


title: ChIP 1 hrp48

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description:
hrp36_peaks_eval.bed
hrp48_peaks_eval.bed

library_source: genomic

data_processing:
NGMerge was used to automatically detect and remove sequencing adapters using options -a -n 18 -v
FastQ files were aligned to the dm3 genome using Bowtie2 v2.2.2 with options -N 1 -k 1.
Duplicated reads for generation of TDF tracks were identified and removed with sambamba 0.8.0. TDF tracks were generated with IGVTools2 and options count -z 5 -w 25 -e 250.
Peak calling between IP and Input samples was performed independently for individual and pooled replicates per group using MACS 1.4.2 with default options (duplicate removal) and genome=dm. Candidate called peaks from pooled replicates were defined as final peaks if they presented overlap with peaks identified in both their respective individual replicates.
Assembly: dm3
Supplementary files format and content: bed

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2 cells

extract_protocol:
Cells were fixed with 1.8% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Twin Sonication System (Diagenode).
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (Illumina)

tag: cell line

value: S2 cells

tag: cell type

value: primary culture of late stage (20-24 hours old)

tag: chip antibody


title: CCD-18CO, TWEAK, Rep2

organism: Homo sapiens

tag: genotype


title: R3_JMC164_csr-1a(tor159)_20C

city: Toronto

first: Julie

last: Claycomb

state: Ontario

address: 661 University Ave.

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: Isolated poly-adenylated RNA using oligo-dT beads

data_processing:
Cutadapt (Matrin 2011) was used to remove adapters using the adapter  “AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC” and discarding any reads not which were not trimmed or not within a 16-30 nucleotide range.
Reads were then mapped to the C. elegans genome (Wormbase release WS262) using STAR alignment tool (Dobin 2013).
A custom script was used for counting the number of reads for each feature from .bam files by STAR-aligner (Dobin, et al. 2013) and outputting counting data as .csv files. These were then converted to tables with an additional custom script [available at www.github.com/ClaycombLab/Charlesworth_2020], and detailing gene, feature, sequence, cigar, position, count, biotype, sample, feature type, total mapped reads, read length, matched read length and RPM for each sequence.
mRNA data quality was initially assessed via FASTQC, and any read that was sequenced into its adapters was trimmed via Cutadapt (adapter sequence “AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC”) All reads without adapters were retained for analysis. Reads were then mapped to the C. elegans genome (Wormbase release WS262) using STAR-aligner (Dobin, et al. 2013). The number of reads mapping to each gene feature was determined using summarizeOverlaps from the GenomicAlignment package (Lawrence, et al. 2013 - v1.22.1). Pre-filtering was used to remove all rows possessing only a single count or less across all samples. Differential expression and statistical analysis was performed using DESeq2 (Love, et al. 2014). mRNA differential gene expression changes were determined using DeSeq2. DE genes were >2-fold change (+/-) and <0.01 Padj.
Assembly: Wormbase release WS262
Supplementary files format and content: sRNA: mapping data, sequences and read counts for features of interest in the C. elegans genome (WS262). mRNA: read count matrix of number of detected reads per gene in N2 or csr-1a mutants at 20C and 25C.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole Worm

growth_protocol: All C. elegans strains were derived from the wild type Bristol N2 strain and cultured according to standard growth conditions <Brenner 1974> on Nematode Growth Medium (NGM) plates inoculated with E. coli OP50 at 20°C, unless otherwise stated.

extract_protocol:
For samples in which only RNA was isolated: Typical total RNA extraction and ethanol precipitation were performed, followed by quantification using a Nanodrop 1800C spectrophotometer. For samples in which Argonaute/sRNA complexes were isolated: Protein lysates were prepared by dounce homogenization of worm samples at 4°C, lysates were cleared by 10min 13,000xg centrifugation. Input (total small RNA) samples were taken first and total RNA was extracted using a typical Tri-Reagent protocol, followed by ethanol precipitation. IPs were performed with anti-GFP (Chromotek) or anti-CSR-1a (rabbit polyclonal). In the final step, beads with Argonaute-sRNA complexes were resuspended in Tri-Reagent, followed by RNA extraction as for other samples.
For sRNA libraries , RNA samples were treated with a 5' polyphosphatase prior to use in library prep with the  NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs) per manufactuer instructions. For mRNA libraries, samples were DNAse treated prior to use with the NEBNext Ultra II Directional RNA Prep Kit for Illumina - with Poly-A selection per manufacterer instructions.

treatment_protocol: Synchronized staged animals were collected in 1X M9 and washed in M9 and MilliQ water. For samples in which only RNA was taken (PolyA RNA): Upon adding 4x volume Tri-Reagent (Molecular Research Center, Inc.), samples were flash frozen in a dry ice/ethanol bath and stored at -80°C for later RNA extraction. For samples in which Argonaute complexes were first isolated before RNA extraction (all other Input and IP samples for sRNA sequencing), all liquid was removed from samples, and samples were flash frozen in a dry ice/ethanol bath and stored at -80°C for later protein extraction.

value: Whole Worm

tag: developmental stage

value: L4 Larval Stage

tag: temperature


title: INPUT 10% ChIP 1


title: Dark_Adapted_T16_B

city: Cambridge

first: Allison

last: Coe

state: MA

address: 15 Vassar St

department: Civil and Environmental Engineering

country: USA

institute: Massachusetts Institute of Technology

data_processing:
Reads were trimmed and adapters were removed with BBDuk (from the BBTools package, V38.16) (parameters: ktrim=r, k=23, mink=11, hdist=1, qtrim=rl, trimq=6)
The trimmed reads were aligned to Prochlorococcus NATL2A (NC_007335.2) and Alteromonas macleodii MIT1002 (NZ_JXRW01000001.1) genomes using bowtie2 (parameters: default)
The number of reads that aligned to each annotated ORF in the “sense” orientation was determined using HTSeq (V0.11.2) (parameters: --nonunique all)
Assembly: NZ_JXRW01000001.1, NC_007335.2
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

organism:
Alteromonas macleodii
Prochlorococcus marinus str. NATL2A

growth_protocol: Prochlorococcus and Alteromonas were maintained on Pro99 amended natural seawater in a 13:11 light:dark incubator at 24C.

extract_protocol:
Total RNA was extracted using the mirVana microRNA (miRNA) extraction kit (Ambion, USA).
Ribosomal RNA was depleted using RiboZero kit (Illumina) and libraries prepared using the KAPA RNA HyperPrep kit (Illumina)

tag: time point


title: Arabidopsis thaliana roots, heat-killed Pseudomonas Root401 in 100mMNaCl, replicate 2

city: Cologne

first: Fantin

last: Mesny

address: Carl-von-Linné-Weg 10

department: Plant-Microbes interaction

country: Germany

institute: Max Planck Institute for Plant Breeding Research

data_processing:
Read trimming with Trimmomatic PE v0.38 (parameters TRAILING:20 AVGQUAL:20 MINLEN:100)
Read mapping against genomic index with Hisat2 v2.2.1 (default parameters)
Per-gene read counting with featureCounts v2.0.0 (parameter -p, default settings)
Assembly: TAIR10.1
Supplementary files format and content: Output files from featureCounts, containing the number of reads mapped on each Arabidopsis thaliana gene as well as information regarding the genes (location in genome and length)

organism: Arabidopsis thaliana

source_name: Roots

extract_protocol:
Qiagen RNeasy Plant Mini Kit
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

value: Roots


title: CCD-18CO, TWEAK, Rep1


title: kidney HFD-2

source_name: kidney

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

value: kidney

value: High fat diet


title: kidney HFD-3


title: Arabidopsis thaliana roots, heat-killed Pseudomonas Root401 in 100mMNaCl, replicate 1


title: R2_JMC164_csr-1a(tor159)_20C


title: BatchA_SW1783_Vehicle(DMSO)_rep3 [A1-3-1]

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: Human astrocytoma cell line, SW1783 (HTB-13) was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). SW1783 cells were maintained in Leibovitz’s L-15 medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, without CO2 incubator. The cells were subcultured every 3 or 4 days, depending on the cell density.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: Dulbecco's Modified Eagle Medium (DMEM), phosphate-buffered saline (PBS), TrypLE Express, penicillin-streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Leibovitz's L-15 medium was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). Cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO), wortmannin, LY294002, Thioridazine were purchased from Sigma-Aldrich (St. Louis, MO, USA) and QIAzol lysis reagents was purchased from Qiagen (Germantown, MD, USA). The Ez-Cytox cell viability assay kit was purchased from Dogen Bio (Seoul, Korea). The dried Poria cocos Wolf (Polyporaceae) were supplied from Kwangmyung-dang Medicinal Herbs Co. (Ulsan, Republic of Korea), and their morphology was carefully validated by Dr. Goya Choi, Herbal Medicine Resources Research Center Korea Institute of Oriental Medicine (KIOM), Republic of Korea. A voucher specimen (2-22-0221) was deposited in the Korean Herbarium of Standard Herbal Resources of KIOM (Naju, Republic of Korea). The crushed material was extracted at 100 ± 3℃ for 3 hours by water refluxed system (MS-DM609, Misung Scientific, Yangu, Republic of Korea) and filtered through 5 um cartridge filter (KOC Biotech, Daejeon, Republic of Korea). The filtrates were concentrated under 40℃ using a rotary evaporator (Ev-1020t, SciLab, Seoul, Republic of Korea), and then freeze dried (LP20, IlShin Biobase, Dongduchen, Republic of Korea). The yield of PC was 24.2 % and final extracts were homogenized and stored at air-tight container in 4℃ cold room. For the in vitro investigation, homogenous PC was vigorously vortexed for 30 min at room temperature in phosphate-buffered saline (PBS; Thermo Fisher Scientific, Rockford, IL, USA) containing 2% DMSO and then sterilized by filtering through a 0.22 um membrane. The stock solution of PC (10mg/mL) was aliquoted in 1.5mL tube and stored at -80°C until use.

value: Human astrocytoma cell line

value: 2% DMSO

tag: time


title: kidney HFD-1


title: Arabidopsis thaliana roots, Pseudomonas Root401 in 0mMNaCl, replicate 3

value: Pseudomonas Root401 in 0mMNaCl


title: kidney con-3

value: control


title: R2_GR3043_input

description: Total input RNA from lysate used for IPs

value: csr-1(mg661[G120*]) mgIs75[rpn-2::gfp] IV; mgTi14[pbs-5::mcherry]


title: Arabidopsis thaliana roots, Pseudomonas Root401 in 0mMNaCl, replicate 2


title: R1_GR3043_input


title: Arabidopsis thaliana roots, Pseudomonas Root401 in 0mMNaCl, replicate 1


title: kidney con-2

value: ICR


title: kidney con-1

value: 10 weeks


title: HEK293T, ZFX, Rep2 (reanalysis)

city: Los Angeles

first: Peggy

middle: J

last: Farnham

state: CA

address: 1450 Biggy St, NRT6514

department: Biochemistry and Molecular Medicine

institute: University of Southern California

description: reanalysis of GSM4340001

data_processing:
Data was analyzed using the ENCODE pipeline.
Reads were mapped to the genome using BWA
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bigwig with total mapped reads

growth_protocol: LN-229 was grown in DMEM supplemented with 10% FBS and pen/strep

extract_protocol:
Chromatin was prepared using the protocol previously published (PMID: 29429977). Briefly, cells were crosslinked using 1% formedelhyde for 10 mins and lysed. Chromatin was sonicated using a Bioruptor Pico.
Libraries were prepared using Roche KAPA Hyper Prep Kit (Roche# 07962347001) according to provided protocol

value: human embryonic kidney

value: wild type


title: Arabidopsis thaliana roots, heat-killed Pseudomonas Root401 in 0mMNaCl, replicate 3


title: HEK293T, ZFX, Rep1 (reanalysis)

description: reanalysis of GSM4340000


title: R1_JMC164_CSR-1b_input


title: B_WT_M4_r2

city: Washington

first: Mathilde

last: Biot

address: 800 22nd St NW

institute: George Washington University

description: MEI4 ChIP-seq of the B6 mouse, replicate 2

data_processing:
Reads were trimmed to 100bp and then filtered on the Phred score (> 28). Reads were mapped to the mm10 genome using Bowtie 2 with the following parameters: -N 1 -I 100 -X 1000 -no-mixed -no-discordant. Unmapped reads and duplicates were removed in order to obtain our final dataset for post-processing. Bigwig: Read enrichment along the genome with a bin size of 10bp in Count per Million, where the corresponding knockout have been subtracted. Peak detection: To detect regions significantly enriched along the genome and between our replicates, we used the IDR methodology. To do so, we called peaks between true replicate, pooled pseudo-replicates and self-pseudo-replicates with the following relaxed MACS2 parameters: --format BAMPE --p value 0.01, as advised by the authors and a negative control was included (the corresponding knockout, except for CTCF, where input was used). Then, IDR analyses were performed and replicates with an IDR rescue and self-consistency ratio below 4 were considered to be reproducible. Therefore, the final peak datasets were build by taking the N peaks from true replicates below the IDR threshold of 0.05, as recommende by the authors. If replicates do not satisfy those conditions, replicates were considered not reproducible, and thus only one replicate was considered. The one considered contained the highest percentage of peak satisfying IDR conditions. Therefore, the final peak datasets were build by taking the N peaks from pseudo-replicates below the IDR threshold of 0.01, as recommended by authors. For DMC1, reads were processed using the hotSSDS and hotSSDS-extra Nextflow pipelines (Auffret et al., MiMB Germ Cells Development,  2023.), available on github: (https://github.com/jajclement/hotSSDS.git; https://github.com/jajclement/hotSSDS-extra.git).
Assembly: mm10
Supplementary files format and content: bw: read enrichment along the genome where the corresponding knockout has been subtracted; bed: peak coordinates and enrichments

source_name: whole-testis

extract_protocol:
Testes were homogenized and fixed with 4% formaldehyde for 15 minutes. After quenching, cell suspension was washed and lysed to obtain a nuclei suspension. The nuclei suspension was filtered througth a 40µm cell strainer and sonicated. After a high speed of centrifugation, chromatin was collected and incubated with the antibody and then DNA-protein complexes were isolated.
Enriched DNA were prepared using the Next Gen DNA Library kit from Active Motif  following manufacturer's instructions. For DMC1, enriched DNA were prepared using the Illumina Trueseq protocol with an additional step of kinetic enrichment to titrate ssDNA.

treatment_protocol: 1.5dpp male pups were pipette feeding with WIN 18,466, an inhibitor of retinoic acid. Retinoic acid is a key component in the induction of spermatogonia into meiosis. Therefore, after pipette feeding pups for 7 to 10 consecutives days, a single dose of retinoic acid was intraperitonetealy injected to induce accumulated B type spermatogonia into meiosis in the whole testis. 8 days post-injection, testes were collected because enriched at 80-95% of Leptotene-Zygotene spermatocytes.

value: whole-testis

value: L/Z

value: wild-type

value: synchronization of spermatogenesis

value: 8 days post-injection


title: kidney A10-3

value: AOS 10mg/kg


title: Arabidopsis thaliana roots, heat-killed Pseudomonas Root401 in 0mMNaCl, replicate 2

value: Roots


title: Arabidopsis thaliana roots, heat-killed Pseudomonas Root401 in 0mMNaCl, replicate 1


title: R1_JMC248_WAGO-10_input

value: Whole Worm

value: L4 Larval Stage

value: wago-10(tor162[3xflag::wago-10]) V


title: R2_JMC151_CSR-1a_IP

description: Immunoprecipitated RNA using GFP conjugated chromtek GFP Trap MA beads

value: csr-1(tor160[csr-1 exon1::gfp::3xflag IV:7957568]) IV


title: kidney A10-2

value: kidney


title: B_WT_M4_r1

description: MEI4 ChIP-seq of the B6 mouse, replicate 1


title: E12.5 lateral cortex cre negative control #4

status: Public on Apr 22 2024

city: New York

first: Caroline

last: Pearson

state: NY

address: 1300 York Avenue

department: Brain and Mind Research Institute

institute: Weill Cornell Medicine

data_processing:
The quality of the raw fastq files was checked using FastQC (version 0.11.9). The fastq files for each sample from both lanes were then combined using cat Name_L005_R1_001.fastq.gz Name_L006_R1_001.fastq.gz. Multiqc was used to summarize the FastQC results (https://multiqc.info/).
Fastq files were aligned to the mm10 genome using STAR with the parameters   --genomeDir MM10_STAR_Index   --readFilesIn R1_001.fastq.gz R2_001.fastq.gz  --readFilesCommand gunzip  -c  --outSAMtype BAM Unsorted
The quality of alignment was measured using Picard tools (https://broadinstitute.github.io/picard/) function AlignmentSummaryMetrics.
BAM files were sorted by name using samtools and then gene counts were estimated with HTSeq (version 0.9.1) using python (version 3.6.1) with the parameters --format=bam --order=name --stranded=reverse --type=gene --idattr=gene_id --mode=union
Counts were aggregated into a matrix in R (version 4.0.3). Genes with greater than 10 counts across 50% of the samples were used in further analyses. Counts were normalized with the function varianceStabilizingTransformation(as.matrix(count.matrix),blind=FALSE) using the package DESeq2 (version 1.30.1)  in R (version 4.0.3).
Assembly: mm10 (Gencode version M17)
Supplementary files format and content: tab delimited text file with raw counts per sample after gene filtering. Genes with greater than 10 counts across 50% of the samples was used for further analysis (17068 genes passed this filtering threshold)
Supplementary files format and content: tab-delimited text file with normalized counts per sample after gene filtering. The filtered count matrix was normalized with the function varianceStabilizingTransformation(as.matrix(count.matrix),blind=FALSE) using the package DESeq2 (version 1.30.1)  in R (version 4.0.3).

source_name: lateral cortex

extract_protocol:
Qiagen miRNeasy kit
TruSeq Stranded RNA kit

value: lateral cortex

value: Foxp1 fl/+

tag: Sex

value: female

value: embryonic day 12.5


title: E12.5 lateral cortex cre negative control #2


title: E12.5 lateral cortex Foxp1fl/fl;Emx1Cre #1

value: Foxp1 fl/fl;Emx1Cre


title: E12.5 lateral cortex cre negative control #3

value: Foxp1 fl/fl


title: E12.5 lateral cortex Foxp1fl/fl;Emx1Cre #2


title: kidney A10-1

value: ICR

value: 10 weeks


title: E12.5 lateral cortex cre negative control #1


title: NonSPF-G, feces

city: Wanju-gun, Jeollabuk-do

first: Haesun

last: Lee

state: Jeollabuk-Do

institute: National institute of animal science

data_processing:
Metagenome sequencing was performed using an illumine Miseq sequencer platform (Illumina). To ensure data quality, the low-quality reads (Q < 30) were removed from the raw sequencing reads.
Assembly: greengenes
Supplementary files format and content: FASTQ files: This file format includes sequencing reads along with quality scores for each base. Each sequencing read represents a part of the 16S rRNA gene from a specific microorganism. The FASTQ format is the standard for representing raw data.

organism: Sus scrofa

source_name: feces

extract_protocol:
DNA was extracted from the stool samples and 16S amplicon libraries were constructed using Herculase Ⅱ Fusion DNA Polymerase Nextera XT Index Kit V2 (Illumina, San Diego, CA, USA) through the services provided by GnC Bio Co. (Daejeon, Korea).
Sequences of 16S rRNA at V3 and V4 region were targeted to amplify. The quality and quantity of amplicon libraries were assessed using D1000 ScreenTape (Agilent, Palo Alto, CA, USA) and Picogreen (Agilent), respectively.

tag: group

value: NonSPF


title: NonSPF-F, feces


title: RNH-_LacZ_2

description:
C12
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx

data_processing:
NGMerge was used to automatically detect and remove sequencing adapters using options -a -n 18 -v
FastQ files were aligned to the dm3 genome using Bowtie2 v2.2.2 with options -N 1 -k 1.
Duplicated reads for generation of TDF tracks were identified and removed with sambamba 0.8.0. TDF tracks were generated with IGVTools2 and options count -z 5 -w 25 -e 250.
Peak calling between IP and Input samples was performed independently for individual and pooled replicates per group using MACS 1.4.2 with default options (duplicate removal) and genome=dm. Candidate called peaks from pooled replicates were defined as final peaks if they presented overlap with peaks identified in both their respective individual replicates.
Definition of final Rloops was performed using DESeq2 with lfcShrinkage fold change estimation (type=’normal’) to assess level of RNH+ depletion. Final Rloops were defined as those RNH- candidate Rloops with a DESeq2 lfcShrinkage FC RNH+/RNH- (RNH depletion) of -1.25 or less
Assembly: dm3
Supplementary files format and content: xlsx with DESeq2estimated intensities for candidate Rloops and lfcShrink RNH+ vs RNH- fold estimation
Library strategy: DRIP-Seq

extract_protocol:
Cells were lyzed and genomic DNA purified, using phenol-chloroform extractions followed by DNA precipitation. DNA was sonicated using a Bioruptor Twin Sonication System (Diagenode).
DRIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (Illumina)

value: S2 cells

value: primary culture of late stage (20-24 hours old)


title: SPF-D, feces

value: SPF


title: Parental_T13_B

source_name: Parental

value: Parental


title: NonSPF-E, feces


title: SPF-A, feces


title: SPF-B, feces


title: SPF-C, feces


title: 5'-uncapped mRNA transcript in somatic embryos

city: Bari

first: Vitantonio

last: Pantaleo

address: Via Amendola 165/a

country: Italy

institute: Institute for Sustainable Plant Protection

description: 5'-uncapped mRNAs

data_processing:
FastX tool kit (http://hannonlab.cshl.edu/fastx_toolkit/) was used for elaboration of row data
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.Then converted to FASTA
Fasta files form sRNA datasets mock-inoculated and virus-infected were filtered for 16-26nt long sequences
Fasta files from PARE datasets mock-inoculated and virus-infected were filtered for 20-21nt long sequences
sRNAs were used as imput for miRPROOF and miRCAT, whereas PARE dataset and sRNA dataset we used as input of PAREsnp (
Supplementary_files_format_and_content: tab-delimited textl files  for each Sample

organism: Vitis vinifera

source_name: Somatic embryos

growth_protocol: Somatic embryos of Vitis vinifera, variety Brachetto were obtained from in vitro culture of immature anthers collected during spring following the protocol of Gambino et al. (2007, DOI: 10.1007/s11240-007-9256-x).

extract_protocol:
Total RNA was extracted from somatic embryos using the rapid CTAB method (Gambino et al., 2008;DOI: 10.1002/pca.1078)
short RNA libraries were generated usingTrueSeq Small RNA kit, Illumina. PARE libraries were generated following the protocol by German et al., 2008, Nature protocols).    Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

tag: cultivar

value: Brachetto

tag: tissues

value: in vitro culture of immature antherS


title: Short RNAs in somatic embryos

description: small RNAs


title: mutant-2 - 9 months, periT

city: Vienna

first: Latifa

last: Bakiri

address: Lazarettgasse 14, BT25/2, 6th floor Lab 2

department: Laboratory Medicine

country: Austria

institute: Medical University of Vienna

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
Reads were converted from .bam to .fastq format using bedtools v2.27.1 (1) and compressed using gzip
Reads in fastq format were aligned to the mouse reference genome version GRCm38 with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode. Raw reads per gene were counted by STAR. Differential gene expression was calculated using DESeq2 version 1.22.2. TPM were generated by RSEM
Assembly: mm10 murine reference genome downloaded from Ensembl (2018-09-28, link last accessed 2023-02-10):
Supplementary files format and content: includes raw counts for each sample

source_name: liver

extract_protocol:
RNA was extracted using Trizol -Sample RNA Integrity Numbers were in the range 7.5-8.2 (average 7.9) for the 2 months samples and   in the range 7.2 to 9.1 (median 8.5) for the 9 months samples, when assayed on an Agilent 2100 Bioanalyzer.
PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

value: liver

value: not applicable :primary material

value: mostly transformed hepatocyte

value: mutant

value: Male

value: Dox OFF at 3 weeks during 9 months


title: control-3 - 9 months

value: mostly hepatocyte

value: control


title: mutant-1 - 9 months, Tumor-2


title: mutant-1 - 9 months, Tumor-1


title: mutant-3 - 9 months, periT


title: mutant-3 - 9 months, Tumor


title: mutant-1 - 9 months, periT


title: NonSPF-H, feces


title: control-1 - 9 months


title: control-2 - 9 months


title: control-5 - 2 months

value: Dox OFF at 3 weeks during 2 months


title: control-6 - 2 months


title: Arabidopsis thaliana roots, heat-killed Pseudomonas Root401 in 100mMNaCl, replicate 3

value: Roots


title: control-2 - 2 months


title: control-3 - 2 months


title: Parental_T20_A


title: control-4 - 2 months


title: mutant-2 - 9 months, Tumor


title: mutant-1 - 2 months


title: mutant-3 - 2 months


title: control-1 - 2 months


title: mutant-2 - 2 months


title: mouse kidney, spatial, IMQ, MM04030

city: Oxford

first: Rui

last: Qi

state: Oxford

address: Old Road Campus

country: United Kingdom

institute: University of Oxford

description:
MM04030_DP8400019635TR_L01_read_1
processed_data: 4030_1.txt
processed_data: 4030_2.txt

library_source: other

data_processing:
BGI's SAW pipeline was used to process fastq files into resulting gene expression matrices
Assembly: mm10
Supplementary files format and content: GEM formatted counts file including X/Y coordinates
Library strategy: spatial transcriptomics

molecule: other

source_name: Kidney

extract_protocol:
10 µm kidney tissue sections were cryosectioned from OCT embedded frozen blocks and adhered to the Stereo-seq chip surface, fixed in methanol and stained with nucleic acid dye for imaging. Then we performed permeabilization, reverse transcription, cDNA amplification and library preparation following Stereo-seq protocol.
After cDNA interruption, amplification and double-selection, libraries were subjected to Agilent 2100 quality inspection. Finally, the double-selection libraries were constructed into libraries suitable for the MGI DNBSEQ-Tx sequencing platform through circularization steps and were sequenced to collect data (50 bp for read 1 and 100 bp for read 2).

value: Kidney

value: imq


title: testis HA10-2

value: ICR

value: testis

value: 10 weeks

value: High fat diet +AOS10mg/kg


title: BatchA_SW1783_Vehicle(DMSO)_rep1 [A1-1-1]

value: Human astrocytoma cell line

value: 2% DMSO


title: BatchA_Wortmannin_rep1 [1-1-2]

description:
sample 1-1-2
RCM_poria_cocos_HT29.txt

growth_protocol: Human colorectal adenocarcinoma cell line, HT29 (HTB-38) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). HT29 cells were maintained in DMEM medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 5% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.

value: wortmannin 10 uM


title: testis HA10-3


title: R2_JMC207_ALG-4_IP

value: Whole Worm

value: L4 Larval Stage

value: alg-4(tor143[gfp::3xflag::alg-4]) III


title: Arabidopsis thaliana roots, Pseudomonas Root401 in 100mMNaCl, replicate 2

value: Pseudomonas Root401 in 100mMNaCl


title: genomic DNA from FFPE material of MB patient biopsy 24

type: genomic

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

address: Martinistrasse 52

department: ZMNH

institute: University Hospital Hamburg Eppendorf

description: GR4 sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850K/EPIC Beadchip using standard Illumina protocol

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

data_processing: Raw idats files were processed further in Rstudio (version 4.3.0) using minfi package

label: Cy5 and Cy3

source_name: FFPE material of MB patient biopsy 24

label_protocol: Standard Illumina Protocol

extract_protocol: 100 - 250 ng DNAgenomic DNA was extracted and purified using Illumina FFPE Restore Kit

tag: gender

value: Female

tag: proteome subtype

tag: main molecular subgroup


title: genomic DNA from FFPE material of MB patient biopsy 22

description: GR4 sample

source_name: FFPE material of MB patient biopsy 22

value: Male


title: genomic DNA from FFPE material of MB patient biopsy 28

description: WNT sample

source_name: FFPE material of MB patient biopsy 28

value: WNT


title: genomic DNA from FFPE material of MB patient biopsy 13

description: SHH sample

source_name: FFPE material of MB patient biopsy 13

value: SHHt

value: SHH


title: genomic DNA from FFPE material of MB patient biopsy 21

description: SHH sample

source_name: FFPE material of MB patient biopsy 21


title: genomic DNA from FFPE material of MB patient biopsy 19

description: WNT sample

source_name: FFPE material of MB patient biopsy 19


title: genomic DNA from FFPE material of MB patient biopsy 29

description: GR4 sample

source_name: FFPE material of MB patient biopsy 29


title: genomic DNA from FFPE material of MB patient biopsy 27

description: SHH sample

source_name: FFPE material of MB patient biopsy 27

value: SHHs


title: genomic DNA from FFPE material of MB patient biopsy 20

description: SHH sample

source_name: FFPE material of MB patient biopsy 20


title: genomic DNA from FFPE material of MB patient biopsy 18

description: GR3 sample

source_name: FFPE material of MB patient biopsy 18


title: genomic DNA from FFPE material of MB patient biopsy 25

description: GR3 sample

source_name: FFPE material of MB patient biopsy 25


title: genomic DNA from FFPE material of MB patient biopsy 14

description: GR4 sample

source_name: FFPE material of MB patient biopsy 14


title: genomic DNA from FFPE material of MB patient biopsy 17

description: SHH sample

source_name: FFPE material of MB patient biopsy 17


title: genomic DNA from FFPE material of MB patient biopsy 11

description: GR4 sample

source_name: FFPE material of MB patient biopsy 11


title: genomic DNA from FFPE material of MB patient biopsy 16

description: GR4 sample

source_name: FFPE material of MB patient biopsy 16


title: genomic DNA from FFPE material of MB patient biopsy 7

description: GR4 sample

source_name: FFPE material of MB patient biopsy 7


title: genomic DNA from FFPE material of MB patient biopsy 4

description: GR3 sample

source_name: FFPE material of MB patient biopsy 4


title: genomic DNA from FFPE material of MB patient biopsy 12

description: GR3 sample

source_name: FFPE material of MB patient biopsy 12


title: genomic DNA from FFPE material of MB patient biopsy 23

description: GR3 sample

source_name: FFPE material of MB patient biopsy 23


title: genomic DNA from FFPE material of MB patient biopsy 26

description: GR4 sample

source_name: FFPE material of MB patient biopsy 26


title: genomic DNA from FFPE material of MB patient biopsy 9

description: SHH sample

source_name: FFPE material of MB patient biopsy 9


title: genomic DNA from FFPE material of MB patient biopsy 6

description: SHH sample

source_name: FFPE material of MB patient biopsy 6


title: genomic DNA from FFPE material of MB patient biopsie 32

description: GR4 sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

data_processing: raw .idat files were processed in Rstudio (Version 4.0.5). (minfi package, Version 1.36.0). Briefly, samples were read from EPIC and 450k arrays separately and combined using combinedarrays(). The samples were normalized using single sample noob normalization since we combined intensities from two different arrays and casted as a 450k array.

source_name: FFPE material of MB patient biopsie 32

extract_protocol: Illumina FFPE Restore Kit for  was used to extract DNA from FFPE samples,100 - 250 ng DNA was hybridized. Concentrations of DNA was measured with Qubit High Sensitivity DNA Kit


title: genomic DNA from FFPE material of MB patient biopsy 10

description: GR4 sample

source_name: FFPE material of MB patient biopsy 10


title: genomic DNA from FFPE material of MB patient biopsy 3

description: WNT sample

source_name: FFPE material of MB patient biopsy 3


title: genomic DNA from FFPE material of MB patient biopsy 5

description: GR3 sample

source_name: FFPE material of MB patient biopsy 5


title: genomic DNA from FFPE material of MB patient biopsie 31

description: WNT sample

source_name: FFPE material of MB patient biopsie 31

value: pWNT


title: genomic DNA from FFPE material of MB patient biopsy 15

description: GR4 sample

source_name: FFPE material of MB patient biopsy 15


title: genomic DNA from FFPE material of MB patient biopsie 33

description: WNT sample

source_name: FFPE material of MB patient biopsie 33


title: ECIS36T_chip1

city: Houston

first: Nicholas

last: Navin

state: Texas

address: 6565 MD Anderson Blvd

department: Systems Biology

institute: MD anderson Cancer Center

data_processing:
The scRNA-seq FASTQ files were trimmed with Trimmomatic to remove sequencing and library adaptors
The trimmed reads were alignment to the reference genomes of human (hg19 reference) with STARsolo
The processed rds (count matrix) files were generated with Seurat 4.1.0
Assembly: hg19
Supplementary files format and content: Gene count

source_name: Breast

extract_protocol:
The genomic DNA and RNA was extract from isolated single nuclei
The in house nanowell based DNA-RNA sequencing (wellDA-seq) protocol

tag: tissue

value: Breast

tag: biomaterial provider

value: MD Anderson

tag: histology

value: DCIS


title: BCIS13T_chip2

value: Baylor College of Medicine

value: IDC with DCIS


title: genomic DNA from FFPE material of MB patient biopsie 34

description: SHH sample

source_name: FFPE material of MB patient biopsie 34

value: pSHHs


title: ECIS36T_chip2


title: genomic DNA from FFPE material of MB patient biopsy 2

description: SHH sample

source_name: FFPE material of MB patient biopsy 2


title: BCIS13T_chip1


title: genomic DNA from FFPE material of MB patient biopsy 1

description: SHH sample

source_name: FFPE material of MB patient biopsy 1


title: genomic DNA from FFPE material of MB patient biopsie 27

description: WNT sample

source_name: FFPE material of MB patient biopsie 27


title: genomic DNA from FFPE material of MB patient biopsie 24

description: GR3 sample

source_name: FFPE material of MB patient biopsie 24


title: genomic DNA from FFPE material of MB patient biopsie 29

description: WNT sample

source_name: FFPE material of MB patient biopsie 29


title: genomic DNA from FFPE material of MB patient biopsie 23

description: GR4 sample

source_name: FFPE material of MB patient biopsie 23


title: ECIS44T_chip3


title: genomic DNA from FFPE material of MB patient biopsie 30

description: SHH sample

source_name: FFPE material of MB patient biopsie 30

value: pSHHt


title: genomic DNA from FFPE material of MB patient biopsie 19

description: GR4 sample

source_name: FFPE material of MB patient biopsie 19


title: genomic DNA from FFPE material of MB patient biopsie 20

description: GR4 sample

source_name: FFPE material of MB patient biopsie 20

value: uncertain


title: genomic DNA from FFPE material of MB patient biopsie 17

description: GR3 sample

source_name: FFPE material of MB patient biopsie 17


title: genomic DNA from FFPE material of MB patient biopsie 28

description: WNT sample

source_name: FFPE material of MB patient biopsie 28


title: genomic DNA from FFPE material of MB patient biopsie 16

description: SHH sample

source_name: FFPE material of MB patient biopsie 16


title: genomic DNA from FFPE material of MB patient biopsie 22

description: GR4 sample

source_name: FFPE material of MB patient biopsie 22


title: genomic DNA from FFPE material of MB patient biopsie 26

description: GR4 sample

source_name: FFPE material of MB patient biopsie 26


title: genomic DNA from FFPE material of MB patient biopsie 18

description: WNT sample

source_name: FFPE material of MB patient biopsie 18


title: genomic DNA from FFPE material of MB patient biopsie 25

description: GR3 sample

source_name: FFPE material of MB patient biopsie 25


title: ECIS44T_chip5

source_name: Breast


title: genomic DNA from FFPE material of MB patient biopsy 8

description: GR4 sample

source_name: FFPE material of MB patient biopsy 8


title: ECIS44T_chip1


title: ECIS48T_chip2


title: ECIS48T_chip1


title: genomic DNA from FFPE material of MB patient biopsie 21

description: GR4 sample

source_name: FFPE material of MB patient biopsie 21


title: genomic DNA from FFPE material of MB patient biopsie 11

description: SHH p53 sample

source_name: FFPE material of MB patient biopsie 11


title: BCIS28T_chip2


title: BCIS28T_chip1


title: genomic DNA from FFPE material of MB patient biopsie 12

description: SHH p53 sample

source_name: FFPE material of MB patient biopsie 12


title: ECIS25T_chip3


title: ECIS25T_chip2


title: ECIS44T_chip2


title: Boscalid, infected biol rep 3

city: Winnipeg

first: Mark

last: Belmonte

state: MB

address: 50 Sifton Road

institute: University of Manitoba

description:
BoscIN3
B.napus_RawCounts.txt
S.sclerotiorum_RawCounts.txt

data_processing:
Read quality was determined using FastQC
Reads were aligned using HISAT2 and raw counts were generated using featureCounts
DESeq2 was used to conduct differencial gene expression analysis
Assembly: B.napus genome v5.0 - GenBank assembly accession: GCA_000751015.1 (Chalhoub et al. 2014)
Assembly: S. sclerotiorum genome - RefSeq assembly accession: GCF_000146945.2 (Amselem et al., 2011)
Supplementary files format and content: B.napus_RawCounts.txt - tab delimited txt file including raw counts for each sample aligned to B. napus
Supplementary files format and content: S.sclerotiorum_RawCounts.txt - tab delimited txt file including raw counts for each sample aligned to S. sclerotiorum

organism:
Brassica napus
Sclerotinia sclerotiorum

source_name: Leaf

growth_protocol: Canola (B. napus) cultivar Westar was grown to the 30% flowering stage in Sungrow mix #4 supplemented with Osmocote fertilizer (1.5-2g/pot) in pots sized 8.5cm x 8.5cm x 9cm. Plants were grown in greenhouse, long day conditions.

extract_protocol:
RNA was extracted using the Qiagen RNEasy Plant Mini Kit with the addition of Qiagen's on-column DNAse treatment. 1µg of RNA was sent to Genome Québec for library construction.
Genome Québec constructed cDNA libraries according to their mRNA stranded library preparation protocol. Paired-end 100bp reads were sequenced (Illumina NovaSeq 6000)

treatment_protocol: Plants were treated with 4.5mL of foliar spray treatment per plant. Treatments consisted of distilled water, 40mM boric acid (as a boron source), and 10 ppm boscalid. Treatment remained on the plants for 24 hours prior to incoulation. As inoculant, 4.0mL of S. sclerotiorum ascospore suspension was sprayed onto plants (1x10^6 spores/mL in potato dextrose broth). Plants then went into a humidty chamber to maintain 90-100% humidity for four day sto allow for infection to progress. At this point, leaves were collected and flash frozen in liquid N  as samples for RNA extraction.

value: Leaf

tag: cell line

value: Cultivar - Westar

tag: treatment

value: Boscalid, infected


title: genomic DNA from FFPE material of MB patient biopsie 13

description: WNT sample

source_name: FFPE material of MB patient biopsie 13

value: Female


title: ECIS25T_chip1


title: Boscalid, infected biol rep 2

description:
BoscIN2
B.napus_RawCounts.txt
S.sclerotiorum_RawCounts.txt


title: Boscalid, infected biol rep1

description:
BoscIN1
B.napus_RawCounts.txt
S.sclerotiorum_RawCounts.txt


title: genomic DNA from FFPE material of MB patient biopsie 15

description: WNT sample

source_name: FFPE material of MB patient biopsie 15


title: genomic DNA from FFPE material of MB patient biopsie 9

description: GR3 sample

source_name: FFPE material of MB patient biopsie 9

value: Male


title: PC3 cells, siNTC, repeat 1 set2

city: Boston

first: Zifeng

last: Wang

state: Massachusetts

address: 100 Morrissey Blvd, ISC/4610

department: CPCT

institute: UMASS Boston

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) /GRCm38 using STAR (version 2.7.2) followed by counting with featureCounts (v2.0.1) from GRCh37 Ensembl reference.
Gene level read counts was produced by setting the parameter 'quantMode' as 'GeneCounts' in STAR
Assembly: GRCh37/GRCm38
Supplementary files format and content: tab-deliminated text files include raw gene counts

growth_protocol: PC3,LNCaP cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. NCI-H660 cells were cultured in RPMI-1640 base medium supplemented with 5% FBS, 10nM β-estradiol, 10nM hydrocortisone, and 1% Insulin-Transferrin-Selenium. DKO cells were cultured in DMEM base medium supplemented with 10% FBS

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol
RNA libraries for RNA-seq were prepared using TruSeq Strnd Total,RNA LT (Illumina)  mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: PC3,NCI-H660 cells were treated with vehicle versus  ORY-1001, or C12 for 4hrs

tag: cell type

value: Prostate cancer cell line

value: Negative control knockdown


title: Boron, infected biol rep 3

description:
BoronIN3
B.napus_RawCounts.txt
S.sclerotiorum_RawCounts.txt

value: Boron, infected


title: PC3 cells, siNTC, repeat 3 set2


title: genomic DNA from FFPE material of MB patient biopsie 10

description: SHH p53 sample

source_name: FFPE material of MB patient biopsie 10


title: PC3 cells, siLSD1, repeat 3

value: LSD1 knockdown


title: genomic DNA from FFPE material of MB patient biopsie 8

description: SHH sample

source_name: FFPE material of MB patient biopsie 8


title: Boron, infected biol rep 2

description:
BoronIN2
B.napus_RawCounts.txt
S.sclerotiorum_RawCounts.txt


title: PC3 cells, siNTC, repeat 2 set2


title: ECIS44T_chip4

value: Breast


title: genomic DNA from FFPE material of MB patient biopsie 6

description: SHH sample

source_name: FFPE material of MB patient biopsie 6


title: genomic DNA from FFPE material of MB patient biopsie 14

description: WNT sample

source_name: FFPE material of MB patient biopsie 14

value: pWNT


title: Boron, infected biol rep 1

description:
BoronIN1
B.napus_RawCounts.txt
S.sclerotiorum_RawCounts.txt


title: LNCaP_FOXA2OE, siNC, repeat 2

value: prostate cancer cell line (generated from LNCaP)


title: Untreated control, infected biol rep 3

description:
UTCIN3
B.napus_RawCounts.txt
S.sclerotiorum_RawCounts.txt

value: Control, infected


title: LNCaP_FOXA2OE, siNC, repeat 1


title: Parascaris univalens, testes - region 3, H3K9me3, cut-and-run, rep1

city: Knoxville

first: Jianbin

state: TN

address: 1311 Cumberland Avenue, Ken and Blaire Mossman Building Rm 309

institute: The University of Tennessee

data_processing:
CUT&RUN reads were mapped to the Parascaris genome using bowtie2 and processed using SAMtools and BEDTools.
Assembly: Pu_v2
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

organism: Parascaris univalens

source_name: testes

extract_protocol:
Parascaris tissues were frozen at -80°C and ground to a fine powder using a mortar and pestle with liquid nitrogen.
CUT&RUN was done using the EpiCypher CUTANA ChIC-CUT&RUN kit (#14-1048). For each reaction, 0.5 μg of antibody against H3K9me3 (CMA318), H3K4me3 (CMA304), or CENP-A (#345) was used.
Sequencing library preparation was done using a 2S Plus DNA Library Kit from Swift/IDT (# 21024).

value: testes

tag: developmental stage

value: adult male

tag: antibody


title: LNCaP_FOXA2OE, siJUN, repeat 3

value: JUN knockdown


title: PC3 cells, siLSD1, repeat 1


title: LNCaP_FOXA2OE, siNC, repeat 3


title: Untreated control, infected biol rep 2

description:
UTCIN2
B.napus_RawCounts.txt
S.sclerotiorum_RawCounts.txt


title: Parascaris univalens, L1 larvae, H3K4me3, cut-and-run, rep1

source_name: L1 larvae

value: L1 larvae


title: LNCaP_FOXA2OE, siJUN, repeat 2


title: Untreated control, infected, biol rep 1

description:
UTCIN1
B.napus_RawCounts.txt
S.sclerotiorum_RawCounts.txt

value: Leaf


title: Parascaris univalens, testes - region 3, CENP-A (345), cut-and-run, rep1

source_name: testes (region 3)

value: testes (region 3)


title: LNCaP_FOXA2K265R, siNC, repeat 3


title: LNCaP_FOXA2OE, siJUN, repeat 1


title: LNCaP_FOXA2K265R, siNC, repeat 1


title: NT_TGF_4

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

data_processing:
Sequence reads underwent quality and adapter trimming using skewer
Trimmed reads were mapped to human genome build GRCh38 (Ensembl) using STAR aligner
Tags aligning to genes were counted using FeatureCounts with Ensembl annotations
Assembly: GRCh38
Supplementary files format and content: GEC_SETD7_RNA.tsv is a tab separated counts matrix of RNA-seq gene counts for all cultured human GEN samples

growth_protocol: Immortalized human GEN cells were cultured and differentiated as previously described (Satchell SC, Tasman CH, Singh A, et al. Conditionally immortalized human glomerular endothelial cells expressing fenestrations in response to VEGF. Kidney Int. 2006;69(9):1633–1640. doi:10.1038/sj.ki.5000277).

extract_protocol:
Samples were homogenized or lysed in TRIzol® (Life Technologies, Waltham, MA) and RNA was isolated using the Direct-zol™ RNA Mini prep kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions.
Barcoded RNA-seq libraries were generated from ribosomal RNA depleted total RNA using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (New England Biolabs, Ipswich, MA) in conjunction with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) using 1μg of input total RNA and following the manufacturer’s instructions for depletion and library construction.

treatment_protocol: For target validation experiment using the Set7 inhibitor, human immortalized cells were cultured with or without 15 mM (R)-PFI-2 (PFI-2; Cayman Chemicals) dissolved in DMSO for 24 hours before exposing them to 5.5 or 25 mM D-glucose in the presence or absence of 5 ng/ml TGF-b1 (R&D Systems) for 48 hours at 37°C. Knockdown of Set7 was performed in GEN cells by MISSION shRNA expressing lentivirus vector (Sigma). Cells transduced with MISSION Non-target shRNA control vector (Sigma) was used as a control.

value: 25 mM D-glucose + MISSION Non-target shRNA + 5 ng/ml TGF-b1


title: LNCaP_FOXA2K265R, siNC, repeat 2


title: Parascaris univalens, testes - region 2, CENP-A (345), cut-and-run, rep1

source_name: testes (region 2)

value: testes (region 2)


title: GR3 MB21

data_processing:
usegalaxy and rstudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic (reads with quality < 20 were trimmed)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR aligner (length of genome sequence around annotated junction = 100, using basic 2 pass-mapping,excluding alignements with indels or soft clippings, MAPQ value for unique mapper filter = 60, number of genome bins for coordinate-sorting = 50 and maximum number of loci anchor allowed to map to = 50)
Read count extraction and normalization using featureCount and VST normalized files from DESeq2 were used for downstream analysis
Batch effect correction was performed with the HarmonizR algorithm using combat mode in order to combine data with a previously published dataset (obtained from the European Genome-phenome Archive: EGAS00001001953)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include featureCount files for each sample, and a VST-file from DESeq2

source_name: brain

extract_protocol:
Maxwell RSC RNA FFPE Kit
400 ng total per sample, rRNA depletion (Lexogen RiboCop rRNA Depletion with prob mix HMR V2, according to manufacture protocol), followed by the Lexogen CORALL total RNA-Seq V2 Library Prep Kit with UDIs (according to manufacture protocol, short insert size version).
Illumina NextSeq2000 machine using the P3 Reagents / 100 cycle kit as paired-end sequencing  2x 57 bp (+ 2x index read 12bp)

treatment_protocol:
NA
NA

tag: disease

value: Medulloblastomas

value: brain

tag: main molecular_subgroup

tag: proteome subtype_voss


title: NT_TGF_3

source_name: immortalized human glomerular endothelial cells


title: genomic DNA from FFPE material of MB patient biopsie 4

description: GR4 sample

source_name: FFPE material of MB patient biopsie 4

value: Female


title: Parascaris univalens, testes - region 1, CENP-A (345), cut-and-run, rep1

source_name: testes (region 1)

value: testes (region 1)


title: GR4 MB20


title: genomic DNA from FFPE material of MB patient biopsie 3

description: SHH sample

source_name: FFPE material of MB patient biopsie 3

value: pSHHt


title: NT_TGF_2

value: immortalized human glomerular endothelial cells


title: genomic DNA from FFPE material of MB patient biopsie 2

description: GR3 sample

source_name: FFPE material of MB patient biopsie 2

value: Male


title: GR4 MB19


title: GR4 MB18


title: NT_TGF_1


title: SHH MB17

value: SHH

value: tSHH


title: SHH MB16


title: KD_TGF_4

value: 25 mM D-glucose + Set7 shRNA + 5 ng/ml TGF-b1


title: Parascaris univalens, embryo (4 Hr), CENP-A (345), cut-and-run, rep2

source_name: embryo (4 Hr)

value: embryo (4 Hr)

value: embryo


title: Parascaris univalens, L1 larvae, CENP-A (345), cut-and-run, rep1

value: L1 larvae


title: SHH MB15


title: Parascaris univalens, oocytes, CENP-A, cut-and-run (325), rep1

source_name: ovaries

extract_protocol:
Parascaris tissues were frozen at -80°C and ground to a fine powder using a mortar and pestle with liquid nitrogen.
CUT&RUN was done using the EpiCypher CUTANA ChIC-CUT&RUN kit (#14-1048). For each reaction, 0.5 μg of antibody against H3K9me3 (CMA318), H3K4me3 (CMA304), or CENP-A (#325 and #345) was used.
Sequencing library preparation was done using a 2S Plus DNA Library Kit from Swift/IDT (# 21024).

value: ovaries

value: adult

tag: Sex

value: female

tag: chip antibody


title: SHH MB13

value: sSHH


title: SHH MB12

value: Medulloblastomas


title: KD_TGF_3


title: genomic DNA from FFPE material of MB patient biopsie 5

description: GR4 sample

source_name: FFPE material of MB patient biopsie 5


title: SHH MB11

value: brain


title: genomic DNA from FFPE material of MB patient biopsie 7

description: GR4 sample

source_name: FFPE material of MB patient biopsie 7


title: Parascaris univalens, middle region, CENP-A (325), cut-and-run, rep1


title: genomic DNA from FFPE material of MB patient biopsie 1

description: GR4 sample

source_name: FFPE material of MB patient biopsie 1

value: Female


title: KD_TGF_2


title: SHH MB14


title: Parascaris univalens, germinal region, CENP-A (325), cut-and-run, rep1


title: GR3 MB9


title: KD_TGF_1


title: GR3  MB8


title: Parascaris univalens, ovaries, CENP-A (325), cut-and-run, rep2


title: GR4 MB7


title: Parascaris univalens, ovaries, CENP-A (345), cut-and-run, rep2


title: WNT MB6

value: WNT


title: GEC_TGF_4

value: 25 mM D-glucose + 5 ng/ml TGF-b1


title: WNT MB5


title: WNT MB3


title: GEC_TGF_2

value: immortalized human glomerular endothelial cells


title: Parascaris univalens, ovaries, CENP-A (325), cut-and-run, rep1


title: Parascaris univalens, ovaries, CENP-A (345), cut-and-run, rep1


title: WNT MB1


title: PC3 cells, siNTC, repeat 3

description:
PC3_5CSS_siNTC_3_S9
PC3_siFOXA2_rawCount.txt

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (v2.0.1) from GRCh37 Ensembl reference.
Gene level read counts was produced by setting the parameter 'quantMode' as 'GeneCounts' in STAR
Assembly: GRCh37
Supplementary files format and content: tab-deliminated text files include raw gene counts

growth_protocol: PC3,LNCaP cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. NCI-H660 cells were cultured in RPMI-1640 base medium supplemented with 5% FBS, 10nM β-estradiol, 10nM hydrocortisone, and 1% Insulin-Transferrin-Selenium.

value: Prostate cancer cell line

value: Negative control knockdown


title: GEC_TGF_1


title: GEC_PFI_4

value: 25 mM D-glucose + 15 mM (R)-PFI-2


title: Parascaris univalens, oocytes, H3K9me3, cut-and-run, rep1


title: PC3 cells, siNTC, repeat 1

description:
PC3_5CSS_siNTC_1_S7
PC3_siFOXA2_rawCount.txt


title: GR3 MB10


title: PC3 cells, siNTC, repeat 2

description:
PC3_5CSS_siNTC_2_S8
PC3_siFOXA2_rawCount.txt


title: Parascaris univalens, ovaries, H3K9me3, cut-and-run, rep2


title: PC3 cells, siFOXA2, repeat 3

description:
PC3_5CSS_siFOXA2_3_S12
PC3_siFOXA2_rawCount.txt

value: FOXA2 knockdown


title: GEC_PFI_3


title: PC3 cells, siLSD1, repeat 2

value: LSD1 knockdown


title: PC3 cells, siFOXA2, repeat 2

description:
PC3_5CSS_siFOXA2_2_S11
PC3_siFOXA2_rawCount.txt


title: Parascaris univalens, ovaries, H3K9me3, cut-and-run, rep1


title: GEC_PFI_2


title: PC3 cells, siNC, repeat 2

description:
PC3_siNC_2_S26
PC3_siJUN_rawCount.txt


title: WNT MB4


title: GEC_TGF_3


title: LNCaP_FOXA2K265R cells, vehicle, ChIP-JUN

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.17-r1188) with aln and samse or sampe sub-commands.
Samtools (version 1.9) was used to convert sam files to bam format.
MACS2 (version 2.1.4) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 357).
Assembly: hg19
Supplementary files format and content: bigWig, bed

growth_protocol: PC3,LNCaP cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were crosslinked with 1% formaldehyde and then sonicated. DNA were immunoprecipitatted with antibody and protein A/G beads. After reverse crosslinking, DNA were purifed with Qiagen PCR purification kit.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA) or Qiagen Qiaseq UltraLow Input Library Kit


title: GEC_PFI_1


title: PC3 cells, siJUN, repeat 2

description:
PC3_siJUN_2_S28
PC3_siJUN_rawCount.txt

value: JUN knockdown


title: PC3 cells, siNC, repeat 1

description:
PC3_siNC_1_S25
PC3_siJUN_rawCount.txt


title: WNT MB2


title: Parascaris univalens, ovaries, H3K4me3, cut-and-run, rep1


title: PC3 cells, vehicle, repeat 3

description:
PC3_Veh_3_S20
PC3_LSD1i_rawCount.txt


title: GEC_NG_4

value: 5.5 mM D-glucose


title: Parascaris univalens, testes, CENP-A (345), cut-and-run, rep2

value: testes

value: male


title: PC3 cells, vehicle, repeat 2

description:
PC3_Veh_2_S19
PC3_LSD1i_rawCount.txt


title: PC3 cells, siJUN, repeat 1

description:
PC3_siJUN_1_S27
PC3_siJUN_rawCount.txt


title: GEC_NG_3


title: PC3 cells, vehicle, repeat 1

description:
PC3_Veh_1_S18
PC3_LSD1i_rawCount.txt


title: PC3 cells, ORY-1001, repeat 2

description:
PC3_ORY_2_S22
PC3_LSD1i_rawCount.txt

value: 10μm ORY-1001 for 24hours


title: Parascaris univalens, testes, CENP-A (345), cut-and-run, rep1

value: adult


title: GEC_NG_2


title: GEC_NG_1


title: PC3 cells, ORY-1001, repeat 3

description:
PC3_ORY_3_S23
PC3_LSD1i_rawCount.txt


title: PC3 cells, C12, repeat 3

description:
PC3_C12_3_S26
PC3_LSD1i_rawCount.txt

value: 0.5μm C12 for 24hours


title: PC3 cells, siFOXA2, repeat 1

description:
PC3_5CSS_siFOXA2_1_S10
PC3_siFOXA2_rawCount.txt


title: Parascaris univalens, testes, H3K9me3, cut-and-run, rep2


title: PC3 cells, C12, repeat 2

description:
PC3_C12_2_S25
PC3_LSD1i_rawCount.txt


title: Parascaris univalens, ovaries, H3K4me3, cut-and-run, rep2

value: ovaries

value: female


title: PC3 cells, C12, repeat 1

description:
PC3_C12_1_S24
PC3_LSD1i_rawCount.txt


title: Parascaris univalens, testes, H3K9me3, cut-and-run, rep1


title: CAVIN1KD rep2

city: Hangzhou

first: Panyang

last: Shen

address: Qingchun road

department: Medical College

institute: Zhejiang University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCh38.p13 human genome
Read count extraction and normalization were performed using RSEM software
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: articular cartilage

extract_protocol:
RNA was harvested using Rneasy mini plus kit (VZ6). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: articular cartilage

tag: group

value: CAVIN1 knockout group

tag: collection date

tag: location


title: NCI-H660 cells, siJUN, repeat 3

description:
NCI_siJUN_3_S17
NCIH660_siFOXA2_siJUN_rawCount.txt


title: Parascaris univalens, testes, H3K4me3, cut-and-run, rep2


title: NCI-H660 cells, siNC, repeat 2

description:
NCI_siNC_2_S10
NCIH660_siFOXA2_siJUN_rawCount.txt


title: NCI-H660 cells, siNC, repeat 3

description:
NCI_siNC_3_S11
NCIH660_siFOXA2_siJUN_rawCount.txt


title: Parascaris univalens, testes, CENP-A (325), cut-and-run, rep1


title: CAVIN1KD rep3


title: CAVIN1KD rep1


title: Parascaris univalens, testes, H3K4me3, cut-and-run, rep1


title: NCI-H660 cells, siJUN, repeat 2

description:
NCI_siJUN_2_S16
NCIH660_siFOXA2_siJUN_rawCount.txt


title: NCI-H660 cells, siNC, repeat 1

description:
NCI_siNC_1_S9
NCIH660_siFOXA2_siJUN_rawCount.txt


title: control rep2

value: control


title: Parascaris univalens, testes M8, RNA-seq, rep3

data_processing:
bowtie2, STAR
Assembly: Pu_v2
Supplementary files format and content: bigwig

source_name: Testes

extract_protocol:
Total RNA was prepared using the TRIzol protocol.  The ribosomal RNAs were removed using the RiboCop rRNA Depletion Kit.
RNA-seq libraries were constructed using the CORALL Total RNASeq Library Prep Kit.

value: Testes

tag: tissue region

value: testes M8


title: NCI-H660 cells, siFOXA2, repeat 3

description:
NCI_siFOXA2_3_S14
NCIH660_siFOXA2_siJUN_rawCount.txt

value: Prostate cancer cell line


title: NCI-H660 cells, siJUN, repeat 1

description:
NCI_siJUN_1_S15
NCIH660_siFOXA2_siJUN_rawCount.txt


title: Parascaris univalens, testes M7, RNA-seq, rep3

tag: tissue

value: testes M7


title: control rep3


title: PC3 cells, ORY-1001, repeat 1

description:
PC3_ORY_1_S21
PC3_LSD1i_rawCount.txt


title: NCI-H660 cells, siFOXA2, repeat 2

description:
NCI_siFOXA2_2_S13
NCIH660_siFOXA2_siJUN_rawCount.txt

value: FOXA2 knockdown


title: LNCaP_FOXA2OE_cells, DHT 10nM repeat 3

description:
LN_FOXA2OE_DHT_3_S24
LN_FOXA2OE_DHT_rawCount.txt

value: prostate cancer cell line (generated from LNCaP)

value: 10 nM DHT


title: control rep1


title: LNCaP_FOXA2OE_cells, DHT 10nM repeat 2

description:
LN_FOXA2OE_DHT_2_S23
LN_FOXA2OE_DHT_rawCount.txt


title: Parascaris univalens, testes M6, RNA-seq, rep3

value: testes M6


title: KYSE180 cells, shEZH2#3_3

city: 蚌埠市

first: 嘉昊

last: 管

state: 安徽省

address: 安徽省蚌埠市龙子湖区凤阳东路536号4幢1单元1002

institute: 安徽医科大学第一附属医院

data_processing:
We performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts.
StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: KYSE180 cell

growth_protocol: All cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) at 37˚C in a 5% CO2 atmosphere

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacture's

treatment_protocol: All cells were exposed 6 Gy IR

value: KYSE180 cell

value: esophageal squamous cell carcinoma

tag: genotype

value: EZH2 knockout

value: 6 Gy IR


title: NCI-H660 cells, siFOXA2, repeat 1

description:
NCI_siFOXA2_1_S12
NCIH660_siFOXA2_siJUN_rawCount.txt


title: LNCaP_FOXA2OE_cells, DHT 10nM repeat 1

description:
LN_FOXA2OE_DHT_1_S22
LN_FOXA2OE_DHT_rawCount.txt


title: Parascaris univalens, testes M5, RNA-seq, rep3

value: testes M5


title: LNCaP_CTL_cells, DHT 10nM repeat 3

description:
LN_CTL_DHT_3_S21
LN_FOXA2OE_DHT_rawCount.txt


title: KYSE180 cells, shEZH2#3_2

address: 安徽省蚌埠市龙子湖区凤阳东路536号4幢1单元1002

institute: 安徽医科大学第一附属医院


title: Parascaris univalens, testes M4, RNA-seq, rep3

value: testes M4


title: LNCaP_FOXA2OE, vehicle, repeat 3

description:
LN_FOXA2OE_CSS_3_S18
LN_FOXA2OE_rawCount.txt

value: vehicle


title: KYSE180 cells, shEZH2#3_1

address: 安徽省蚌埠市龙子湖区凤阳东路536号4幢1单元1002

institute: 安徽医科大学第一附属医院


title: LNCaP_CTL_cells, DHT 10nM repeat 1

description:
LN_CTL_DHT_1_S19
LN_FOXA2OE_DHT_rawCount.txt


title: Parascaris univalens, testes M3, RNA-seq, rep3

value: testes M3


title: Parascaris univalens, testes M2, RNA-seq, rep3

value: testes M2


title: KYSE180 cells, shEZH2#1_3

address: 安徽省蚌埠市龙子湖区凤阳东路536号4幢1单元1002

institute: 安徽医科大学第一附属医院


title: LNCaP_FOXA2OE, vehicle, repeat 2

description:
LN_FOXA2OE_CSS_2_S17
LN_FOXA2OE_rawCount.txt


title: LNCaP_FOXA2OE, vehicle, repeat 1

description:
LN_FOXA2OE_CSS_1_S16
LN_FOXA2OE_rawCount.txt


title: KYSE180 cells, shEZH2#1_1

address: 安徽省蚌埠市龙子湖区凤阳东路536号4幢1单元1002

institute: 安徽医科大学第一附属医院


title: LNCaP_CTL_cells,vehicle, repeat 1

description:
LN_CTL_CSS_1_S13
LN_FOXA2OE_rawCount.txt


title: LNCaP_CTL_cells,vehicle, repeat 3

description:
LN_CTL_CSS_3_S15
LN_FOXA2OE_rawCount.txt


title: PC3 cells, vehicle, ChIP-H3K27AC

description: PC3, H3K27AC, Millipore

extract_protocol:
Cells were crosslinked with 1% formaldehyde and then sonicated. DNA were immunoprecipitatted with antibody and protein A/G beads. After reverse crosslinking, DNA were purifed with Qiagen PCR purification kit.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).

value: H3K27AC, Millipore


title: Parascaris univalens, embryos - over 64 cell, RNA-seq, rep1

source_name: Embryos

value: Embryos

value: embryos - over 64 cell


title: Parascaris univalens, testes M1, RNA-seq, rep3

value: Testes

value: testes M1


title: LNCaP_CTL_cells,vehicle, repeat 2

description:
LN_CTL_CSS_2_S14
LN_FOXA2OE_rawCount.txt

value: prostate cancer cell line (generated from LNCaP)


title: PC3 cells, siNC, ChIP-JUN

description: PC3, JUN, CST

value: Prostate cancer cell line

value: anti-JUN

value: Negative control knockdown


title: Parascaris univalens, embryos - 32-64 cell, RNA-seq, rep1

value: embryos - 32-64 cell


title: PC3 cells, siNC, ChIP-FOSL1

description: PC3, FOSL1, CST


title: KYSE180 cells, shluc_3

address: 安徽省蚌埠市龙子湖区凤阳东路536号4幢1单元1002

institute: 安徽医科大学第一附属医院

value: KYSE180 cell

value: esophageal squamous cell carcinoma

value: WT


title: PC3 cells, vehicle, ATAC

description: PC3, ATAC, CST


title: KYSE180 cells, shluc_2

address: 安徽省蚌埠市龙子湖区凤阳东路536号4幢1单元1002

institute: 安徽医科大学第一附属医院

value: 6 Gy IR


title: PC3 cells, siFOXA2, ChIP-JUN

description: PC3, JUN, CST

value: FOXA2 knockdown


title: LNCaP_CTL_cells, DHT 10nM repeat 2

description:
LN_CTL_DHT_2_S20
LN_FOXA2OE_DHT_rawCount.txt

value: 10 nM DHT


title: PC3 cells, vehicle, ChIP-FOXA2

description: PC3, FOXA2, Millipore

value: anti-FOXA2, Millipore

value: vehicle


title: LNCaP cells, siNC, ChIP-JUN

description: LNCaP, JUN, CST

source_name: LNCaP

value: LNCaP


title: PC3 cells, C12, ChIP-FOXA2

description: PC3, FOXA2, Millipore

value: 0.5μm C12 for 4hours


title: SNU719, H3K27ac, Acitve Motif, siCtrl, rep 1

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg38 reference human genome, using bowtie2(v2.3.3.1)
Duplication reads were removed from aligned file by using picard-tools-2.18.21.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&TAG

growth_protocol: For GES1 and SNU719, RPMI1640, 10% fetal bovine serum, 1×penicillin/streptomycin. Cells were cultured at 37C at 5% CO2; For YCC10, EMEM, 10% fetal bovine serum, 1×penicillin/streptomycin. Cells were cultured at 37C at 5% CO2

extract_protocol:
ChIP: Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Picorupter (Diagenode); ATAC and CUT&Tag: Cell nuclei were transposed by Tn5 Transpose
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol; ATAC-seq libraries were amplified from the transposed DNA fragments. CUT&Tag libraries were amplified by KAPA HiFi HotStart Ready Mix.

value: Human gastric cancer

value: H3K27ac (Active Motif, #91193)

value: siCtrl


title: PC3 cells, ORY-1001, ChIP-FOXA2

description: PC3, FOXA2, Millipore

value: Prostate cancer cell line

value: 10μm ORY-1001 for 4hours


title: Parascaris univalens, female intestine, Hi-C, rep1

data_processing:
Paired-end Hi-C reads are mapped and analyzed with HiC-Pro.  A shell script was used to convert the allValidPairs file to a .hic file.
Assembly: Pu_v2
Supplementary files format and content: .hic

source_name: intestine

extract_protocol:
Parascaris tissues were frozen at -80°C and ground to a fine powder using a mortar and pestle with liquid nitrogen.
Hi-C was performed using the Arima-HiC 2.0 kit according to the manufacturer’s protocol (Arima, #A410110).
Libraries were constructed for Illumina sequencing using the Swift Biosciences Accel-NGS 2S Plus DNA Library kit (Swift, #21024) and the KAPA Library Amplification kit (Roche, #KK2620)

value: intestine

value: adult

value: female


title: SNU719, H3K27ac, Acitve Motif, siTCF7, rep 1


title: KYSE180 cells, shEZH2#1_2

address: 安徽省蚌埠市龙子湖区凤阳东路536号4幢1单元1002

institute: 安徽医科大学第一附属医院

value: KYSE180 cell

value: esophageal squamous cell carcinoma

value: EZH2 knockout


title: LNCaP cells, siFOXA1, ChIP-JUN

description: LNCaP, JUN, CST

value: anti-JUN

value: FOXA1 knockdown


title: LNCaP_FOXA2OE cells, vehicle, ChIP-FOXA2

description: LNCaP_FOXA2OE, FOXA2, Millipore

value: anti-FOXA2, Millipore


title: Parascaris univalens, ovaries, Hi-C, rep1

value: ovaries


title: NCI-H660 cells, vehicle, ATAC

description: NCI-H660, ATAC, CST

value: vehicle


title: Parascaris univalens, male intestine, Hi-C, rep1

value: male


title: Parascaris univalens, testes, Hi-C, rep1

source_name: testes

value: testes


title: Parascaris univalens, embryos - 4-16 cell, RNA-seq, rep1

value: Embryos

value: embryos - 4-16 cell


title: LNCaP_FOXA2OE cells, vehicle, ChIP-JUN

description: LNCaP_FOXA2OE, JUN, CST

value: Prostate cancer cell line


title: PC3 cells, siFOXA2, ChIP-FOSL1

description: PC3, FOSL1, CST

value: FOXA2 knockdown


title: h- snf22-(D996A-E997A)::kanMX, biol_rep_3

first: Ana

middle: M

last: Sanchez

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description:
SNF22-(D996A-E997A)-3
count_matrix_snf22.xlsx
snf22_D996A_E997A_DESeq2.xlsx

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
Resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts

organism: Schizosaccharomyces pombe

source_name: fission yeast

growth_protocol: Log phase cultures grown at 30˚C in YES medium

extract_protocol:
Hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA seq

tag: lab strain number

tag: growth conditions

value: log phase culture, YES medium

value: Vegetative growth

value: fission yeast


title: KYSE180 cells, shluc_1

address: 安徽省蚌埠市龙子湖区凤阳东路536号4幢1单元1002

institute: 安徽医科大学第一附属医院

tag: cell line

value: KYSE180 cell

value: WT

tag: treatment

value: 6 Gy IR


title: PESTEM [RNA-seq]

city: Seoul

first: Hyuk-Jin

last: Cha

address: 215-20 Gwan-ak ro Gwan-ak gu

institute: Seoul National University

data_processing:
Raw sequence reads produced by the sequencer were cleaned using Trim Galore version 0.6.5. The cleaned reads were aligned on human reference genome (GRCh38.p13) and quantified using Rsubread version 2.10.5.
Assembly: GRCh38.p13
Supplementary files format and content: comma-separated values(.csv) for each sample

growth_protocol: H9 cells were maintained in stemMACS(Milteni Biotec.) media with 0.1% gentamicin.

extract_protocol:
RNAs were harvested by using easy-BLUE™ Total RNA Extraction Kit(iNtRON). Total
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA wassynthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library.Then it was followed by end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: PESTEM


title: NCI-H660 cells, siNC, ChIP-JUN

description: NCI-H660, JUN, CST

tag: cell type

value: anti-JUN

value: Negative control knockdown


title: BE4 [RNA-seq]


title: BESTEM [RNA-seq]

value: BESTEM


title: PE4 [RNA-seq]


title: NCI-H660 cells, vehicle, ChIP-FOXA2

description: NCI-H660, FOXA2, Millipore

value: anti-FOXA2, Millipore

value: vehicle


title: Parascaris univalens, embryos - 1 cell, RNA-seq, rep1

tag: developmental stage

value: embryos - 1 cell


title: NCI-H660 cells, siFOXA2, ChIP-JUN

description: NCI-H660, JUN, CST


title: h- snf22-(D996A-E997A)::kanMX, biol_rep_2

description:
SNF22-(D996A-E997A)-2
count_matrix_snf22.xlsx
snf22_D996A_E997A_DESeq2.xlsx


title: NCI-H660 cells, ORY-1001, ChIP-FOXA2

description: NCI-H660, FOXA2, Millipore

value: 10μm ORY-1001 for 4hours


title: C.elegans L4_Cd 20_rep3

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

description: Cultured on NGM for 47 hours (L1 to L4 stage) in the presence of 20 μM cadmium chloride

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Caenorhabditis elegans WBcel235 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
The gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Genome_build: WBcel235
Supplementary_files_format_and_content: Text file containing unique gene hit counts for each sample
Supplementary_files_format_and_content: MS Excel files containing gene expression for each comparison.
Supplementary_files_format_and_content: MS Excel files containing variation analysis results within each group.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: P_L4_Cd 0_rep3

growth_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach preparation and grown to L3 and  L4 stage in the presence or absence of cadmium chloride.

extract_protocol:
The RNA isolation followed the standard procedures using the Quick-RNA Kit (Zymo Research), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage.
Libraries were prepared according to Illumina's instructions. Briefly, mRNAs were purified using Poly(A) selection from total RNA and then fragmented. First strand of cDNA was synthesized using random priming, followed by the synthesis of the second strand of cDNA. The resulting double-strand cDNA was end repaired, phosphorylated and A-tailed. Adapter ligation and PCR amplification were performed, rendering the library ready for Illumina flow cell clustering and sequencing on an Illumina HiSeq following the manufacturer's protocols.

treatment_protocol: L1 stage animals were exposed for 27 and 47 hours at 20 ºC to cadmium chloride which was  added to the  food source (E. coli OP50).

tag: Stage

value: staged L4 hermaphrodite

value: Cadmium chloride exposed (20uM)


title: EP [RNA-seq]

value: EP


title: NCI-H660 cells, vehicle, ChIP-H3K4me2

description: NCI-H660, H3K4me2, Millipore

value: Prostate cancer cell line

value: anti-H3K4me2, Millipore


title: YCC10, CRISPRi, sgMYB-E3, rep 1

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: For GES1 and SNU719, RPMI1640, 10% fetal bovine serum, 1×penicillin/streptomycin. Cells were cultureed at 37C at 5% CO2; For YCC10, EMEM, 10% fetal bovine serum, 1×penicillin/streptomycin. Cells were cultureed at 37C at 5% CO2

extract_protocol:
RNA was harvested using Direct-zol RNA mini-prep (ZYMO Research), 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)  following manufacture's protocols.

value: Human gastric cancer

value: MYB knockdown

value: CRISPRi editing


title: h- snf22∆::kanMX, biol_rep_3

description:
SNF22-3
count_matrix_snf22.xlsx
snf22_DESeq2.xlsx

value: log phase culture, YES medium

value: Vegetative growth

value: snf22 knockout

value: fission yeast


title: h- snf22-(D996A-E997A)::kanMX, biol_rep_1

description:
SNF22-(D996A-E997A)-1
count_matrix_snf22.xlsx
snf22_D996A_E997A_DESeq2.xlsx


title: C.elegans L4_Cd 20_rep2

source_name: P_L4_Cd 0_rep2


title: SNU719, CRISPRi, sgMYB-E3, rep 1


title: C.elegans L4_Cd 20_rep1

source_name: P_L4_Cd 0_rep1


title: h- snf22∆::kanMX, biol_rep_1

description:
SNF22-1
count_matrix_snf22.xlsx
snf22_DESeq2.xlsx


title: C.elegans L3_Cd 20_rep3

description: Cultured on NGM for 27 hours (L1 to L3 stage) in the presence of 20 μM cadmium chloride

source_name: P_L3_Cd 0_rep3

value: staged L3 hermaphrodite


title: SNU719, CRISPRi, sgCtrl, rep 1

value: WT


title: YCC10, CRISPRi, sgCtrl, rep 1


title: h-, biol_rep_3

description:
WT-3
count_matrix_snf22.xlsx


title: C.elegans L4_Cd 0_rep3

description: Cultured on NGM for 47 hours (L1 to L4 stage)

source_name: C_L4_Cd 0_rep3


title: h- snf22∆::kanMX, biol_rep_2

description:
SNF22-2
count_matrix_snf22.xlsx
snf22_DESeq2.xlsx


title: C.elegans L3_Cd 20_rep1

source_name: P_L3_Cd 0_rep1


title: C.elegans L3_Cd 20_rep2

source_name: P_L3_Cd 0_rep2


title: NC1_Ribo

city: Nanning

first: Jingsu

last: Yu

state: Guangxi

address: Daxuedong Road, Xixiangtang District

department: College of Animal Science and Technology

institute: Guangxi University

data_processing:
Raw reads containing more than 50% low quality bases, or more than 10% N bases were discarded. The FANSe2 algorithm was used to retain, and map reads between the lengths of 15 and 35 to the reference genome, while the edgeR package’s RPKM (Reads Per Kilobase of Transcript per Million mapped Reads) function was used to normalize the relative abundance between two groups.
Assembly: Sus_scrofa.11.1
Supplementary files format and content: bigWig
Library strategy: Ribo-seq

source_name: the longissimus dorsi muscles

extract_protocol:
Ribo-seq:In a nutshell, ribosome protected mRNA is obtained through MNase digestion and RNA purification. Briefly, the longissimus dorsi muscle samples were ground in liquid nitrogen and extracted with 800 μL of polysome lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 5 mM MgCl2, 24 U/mL TurboDNase, 100 μg/mL cycloheximide, 1 mM dithiothreitol (DTT), 1% Triton X-100, and protease inhibitor mixture) for 30 min.
Ribo-seq libraries were prepared according to reference with a minor modification. In total, 5 μg of ribosome-protected mRNA was used to prepare a library with the NEBNext Multiple Small RNA Library Prep Set for Illumina HiSeqX Ten. Briefly, adapters were added to both ends of Ribosome footprints (RFPs), followed by reverse transcription and PCR amplification.

treatment_protocol: At the end of the experiment, the pigs were euthanized through bloodletting. Samples were taken from the selected pigs’ blood, backfat, and longissimus dorsi muscle.

value: the longissimus dorsi muscles

value: normal calcium


title: HC2_Ribo

value: calcium supplement


title: HC1_Ribo


title: NC2_Ribo


title: NC3_Ribo


title: HC3_RNA

data_processing:
For mRNA sequencing data sets, high quality reads were mapped to a RefSeq mRNA reference sequence (Sus_scrofa.11.1) using the FANSe2 algorithm. Reads that corresponded to different splice variants of the same gene were combined. The mRNA in each sample was normalized using RPKM (reads per kilobase per million reads), whereas the relative abundance between two groups was standardized using the edgeR program.
Assembly: Sus_scrofa.11.1
Supplementary files format and content: bigWig

extract_protocol:
RNA_seq:The total RNA of a longissimus dorsi muscle sample was extracted by TRIzol reagent (Ambion, Inc., Austin, TX, USA) according to the manufacturer’s protocol.
RNA libraries were prepared according to the VAHTS mRNA-seq v.3 Library Prep Kit for Illumina protocol, and the raw sequencing reads were generated on an Illumina HiSeqX Ten sequencer.


title: YCC10, TCF7, KD, siTCF7, rep 1

value: TCF7 knockdown


title: HC3_Ribo


title: h-, biol_rep_1

city: New York

description:
WT-1
count_matrix_snf22.xlsx


title: C.elegans L4_Cd 0_rep2

source_name: C_L4_Cd 0_rep2

value: staged L4 hermaphrodite


title: SNU719, TCF7, KD, siTCF7, rep 1


title: YCC10, TCF7, KD, siCtrl, rep 1


title: HC2_RNA


title: C.elegans L4_Cd 0_rep1

source_name: C_L4_Cd 0_rep1


title: SNU719, TCF7, KD, siCtrl, rep 1


title: C.elegans L3_Cd 0_rep3

description: Cultured on NGM for 27 hours (L1 to L3 stage)

source_name: C_L3_Cd 0_rep3


title: h-, biol_rep_2

description:
WT-2
count_matrix_snf22.xlsx


title: YCC10, MYB, KD, siMYB, rep 2


title: HC1_RNA


title: NC2_RNA


title: HaCaT shIQGAP3 cells with cytokine stimulation, biol. rep 2

city: Moscow

first: Alena

middle: D

last: Zolotarenko

address: Gubkina street 3

country: Russia

institute: Vavilov Institute of General Genetics Russian Academy of Sciences

data_processing: none provided

source_name: keratinocytes

extract_protocol: none provided

value: keratinocytes

value: HaCaT

value: Human immortalized keratinocytes

value: IL-17 100 ng/ml, TNFa 25 ng/ml, IFNg 20 ng/ma


title: YCC10, MYB, KD, siCtrl, rep 2

value: Human gastric cancer


title: HaCaT shIQGAP3 cells with cytokine stimulation, biol. rep 3


title: NC1_RNA


title: YCC10, H3K27ac, Active Motif, CRISPRi, MYB, enhancer, rep 1

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg38 reference human genome, using bowtie2(v2.3.3.1)
Duplication reads were removed from aligned file by using picard-tools-2.18.21.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
ChIP: Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Picorupter (Diagenode); ATAC and CUT&TAG: Cell nuclei were transposed by Tn5 Transpose
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol; ATAC-seq libraries were amplified from the transposed DNA fragments. CUT&Tag libraries were amplified by KAPA HiFi HotStart Ready Mix.

value: H3K27ac (Active Motif, #91193)

value: CRISPRi editing, sgMYB_E3


title: SNU719, H3K27ac, Active Motif, CRISPRi, MYB, enhancer, rep 2


title: HaCaT shIQGAP3 cells with cytokine stimulation, biol. rep 1


title: HaCaT control cells with cytokine stimulation, biol rep 1


title: SNU719, MYB, KD, siCtrl, rep 2


title: HaCaT control cells with cytokine stimulation, biol rep 2


title: YCC10, H3K27ac, Active Motif, CRISPRi, MYB, enhancer, rep 2


title: SNU719, H3K27ac, Active Motif, CRISPRi, MYB, enhancer, rep 1


title: YCC10, H3K27ac, Active Motif, CRISPRi, Ctrl, rep 1

value: CRISPRi editing, sgCtrl


title: HaCaT shIQGAP3 cells without stimulation, biol. rep 2

value: no treatment


title: HaCaT shIQGAP3 cells without stimulation, biol. rep 3


title: HaCaT control cells with cytokine stimulation, biol rep 3


title: SNU719, H3K27ac, Active Motif, CRISPRi, Ctrl, rep 2


title: HaCaT control cells without stimulation, biol rep 3


title: NC3_RNA


title: SNU719, H3K27ac, Active Motif, CRISPRi, Ctrl, rep 1


title: SNU719, MYB, KD, siMYB, rep 2

value: MYB knockdown


title: C.elegans L3_Cd 0_rep2

source_name: C_L3_Cd 0_rep2

value: staged L3 hermaphrodite


title: C.elegans L3_Cd 0_rep1

source_name: C_L3_Cd 0_rep1


title: YCC10, TCF7, CST, rep 2


title: DKO cells, ORY-1001, ChIP-FOXA2

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.17-r1188) with aln and samse or sampe sub-commands.
Samtools (version 1.9) was used to convert sam files to bam format.
MACS2 (version 2.1.4) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 357).
Assembly: mm10
Supplementary files format and content: bigWig, bed

source_name: DKO (Pten-/-/Rb-/-) murine PCa cells

growth_protocol: DKO cells were cultured in DMEM base with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

treatment_protocol: DKO cells were treated with vehicle versus  ORY-1001,for 4hrs

value: DKO (Pten-/-/Rb-/-) murine PCa cells

value: Prostate cancer cell line

value: 10um ORY-1001 for 4hours


title: HaCaT control cells without stimulation, biol rep 2


title: YCC10, TCF7, CST, rep 1


title: HaCaT control cells without stimulation, biol rep 1


title: DKO cells, siNC, repeat 3

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) /GRCm38 using STAR (version 2.7.2) followed by counting with featureCounts (v2.0.1) from GRCh37 Ensembl reference.
Gene level read counts was produced by setting the parameter 'quantMode' as 'GeneCounts' in STAR
Assembly: GRCh37/GRCm38
Supplementary files format and content: tab-deliminated text files include raw gene counts

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol
RNA libraries for RNA-seq were prepared using TruSeq Strnd Total,RNA LT (Illumina)  mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Negative control knockdown


title: YCC10, H3K27ac, Active Motif, CRISPRi, Ctrl, rep 2


title: SNU719, TCF7, CST, rep 1


title: S. pombe, Set1_del, rep3

city: 南京

first: 冯

last: 刚

address: 江苏省南京市仙林街道南京师范大学

institute: 南京师范大学

description:
WT-vs-set1_del.all.annot.txt
WT-vs-set1_del.filter.annot.txt

data_processing:
First, the descending raw reads was quality-controlled using the fastp
clean reads were aligned to the ribosome database of this species using the short reads alignment tool bowtie2[2], the reads on the upper ribosomes were removed without mismatch allowed, and the retained unmapped reads was used for subsequent transcriptome analysis.
Using the HISAT2 software, a reference genome-based alignment analysis was performed.
Based on the alignment results of the HISAT2, we reconstructed the transcripts using the Stringtie and calculated the expression levels of all the genes in each sample using the RSEM
Input data for gene differential expression analysis are the reads count data obtained from gene expression level analysis and were analyzed using DESeq2[6] software
Using the STRING protein interaction database (http://string-db.org).
Assembly: Ensembl_release45
Supplementary files format and content: Each txt file corresponds to the information of one sample, with a total of two tables, namely all gene expression and significant gene expression.

source_name: Schizosaccharomyces strains

extract_protocol:
Total RNA was extracted using Trizol reagent kit.The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT), reverse transcribed to cDNA, after PCR amplification, and then sequenced.
The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT), following manufacturer's protocols.

value: Set1 knockdown


title: DKO cells, siNC, repeat 1


title: GES1, TCF7, CST, rep 2

value: Human gastric epithelial cell


title: S. pombe, Set1_del, rep2

address: 江苏省南京市仙林街道南京师范大学