title: ChIPmentation_CMP_TAL1_rep1

value: Bone Marrow

value: CD34+ HSPC


title: CM-PC-4h-1

status: Public on Aug 21 2023

type: SRA

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

library_source: transcriptomic

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of read count for each sample

molecule: polyA RNA

organism: Capsicum annuum

source_name: Leaves

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

tag: tissue

value: Leaves

tag: genotype

value: WT

tag: treatment

tag: timepoint


title: ChIPmentation_CMP_TAL1_rep2

city: Randwick

first: Julie

last: Thoms

state: NSW

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

department: Adult Cancer Program

country: Australia

institute: UNSW Sydney

description:
Coverage_TAL1_CMP_merge_clip.bw
TAL1_CMP_peaks.narrowPeak

library_source: genomic

data_processing:
ChipSeq reads were trimmed using TrimGalore. Adaptors were removed using CutAdapt. The reads were aligned to hg38 using BWA.
ChipSeq reads were sorted, indexed using Samtools. Dupicate reads were removed using Picard. Replicates were merged using Samtools.
ChipSeq peak calling was done using MACS 2.0 with a p value of 1e-5
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak: BED6+4 files containing peaks called from merged replicates with macs2 using p-value of 1 x 10-5 and the IgG track as the control.
Library strategy: ChIPmentation

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, cells were lysed and nuclei frozen. Nuclei were sonicated using a Bioruptor Pico to generate chromatin fragments.
Antibody bound chromatin was collected and crosslinked, before library construction using the KAPA HiFi HotStart Ready Mix and size selection using AMPure XP beads.
ChIPmentation/ Low input ChIP seq using tagmentation

tag: cell type

tag: cell subset

value: CMP

tag: chip antibody

value: TAL1 (SCBT)


title: NC-NFIB-Cuttag

city: Beijing

first: Yongjie

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology

data_processing:
Adapters were removed using Trimmomatic(version 0.36)
Mapping by Bowtie( version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter
PCR duplicates reads were removed using Picard
Peak calling was performed with macs2 2.1.2 using ‘macs2 callpeak -f BAMPE --keep-dup all -g hg’
Peak reads counts were calculated by multicov function from BEDTools
Assembly: hg38/Grhc38
Supplementary files format and content: wig files were generated using bamCoverage; Scores represent reads counts
Library strategy: CUT&Tag

source_name: U2OS cells without NFIB depletion at G1 phase

growth_protocol: U2OS  cells were maintained in DMEM supplemented with 10% FBS in a humidified incubator equilibrated with 5% CO2 at 37°C.

extract_protocol:
Harvest U2OS cells were grown with indicated treatments and count the cells. Cells should be intact and in a homogenous, single-cell suspension.  Immunoprecipitated using indicated antibodies, transposition reaction and purification DNA fragments and amplify transposed DNA fragments by PCR.
DNA libraries were established by NovoNGS CUT&Tag 2.0 High-Sensitivity Kit.

treatment_protocol: NFIB- or ORC1- associated chromatin were immunoprecipitated in G1 phase U2OS cells which were synchronized at G1/S boundary by double-thymidine block and followed by release for 16 h  without or with NFIB depletion.

tag: cell line

tag: cell cycle phase

value: G1 phase

tag: ip

value: NFIB


title: CM-PC-2h-2


title: ATAC_G1_sh_2

data_processing:
Adapters were removed using Trimmomatic(version 0.36)
Mapping by Bowtie( version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter
PCR duplicates reads were removed using Picard
Peak calling was performed with macs2 2.1.2 using ‘macs2 callpeak -f BAMPE --keep-dup all -g hg’
Peak reads counts were calculated by multicov function from BEDTools
Assembly: hg38/Grhc38
Supplementary files format and content: wig files were generated using bamCoverage; Scores represent reads counts

source_name: U2OS cells with NFIB depletion at G1 phase

extract_protocol:
Harvest U2OS cells were grown with indicated treatments and count the cells. Cells should be intact and in a homogenous, single-cell suspension. Transposition reaction and purification DNA fragments and amplify transposed DNA fragments by PCR.
ATAC-Seq libraries were prepared using ATAC protocol and DNA fragments were recovered using Qiagen MinElute PCR Purification Kit Purification DNA

treatment_protocol: U2OS cells without or with NFIB depletion were fractionated into G0, G1, S, and G2/M phases by FACS in the presence of Hoechst 33342 and Pyronin Y. Only G1 phase cells were collected for next library construction.

value: NFIB depletion


title: AMC_LCDM_Case_#17

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

institute: University of Ulsan College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

molecule: total RNA

source_name: Laser capture microdissected (LCMD) tumors from the formalin-fixed paraffin-embedded (FFPE) TURBT specimens

growth_protocol: This retrospective study was approved by the Institutional Review Board of Asan Medical Center (AMC; 2020-0064). It included 105 consecutive MIBC (cT2-4aN0M0) patients who underwent TUR with available formalin-fixed paraffin-embedded (FFPE) tumor tissues and at least 3 cycles of NAC between August 2011 and August 2017 at AMC. Among the 105 patients, 60 patients who underwent curative surgery after NAC were designated as validation cohort since their pathologic response of NAC was assessable using the surgical specimens.

extract_protocol:
Laser capture microdissection (LCMD) was performed on hematoxylin-eosin-stained tissue slides using a Leica LMD6500 laser capture dissection microscope (Leica Microsystems) as described by the manufacturer. The urothelial carcinoma areas were meticulously microdissected as close as possible to the perimeter of tumor cells to avoid contamination of stroma and inflammatory cells while avoiding tumor necrotic area. Total RNA from the LCMD tumor tissues was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA), including treatment with DNase I (QIAGEN)
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: The ASAN cohort was classified into two groups showing marked contrast in NAC response: NAC response (R) patients with the absence of residual invasive tumor and NAC nonresponse (NR) patients with large residual MIBC (4.9 ± 2.5 cm) in the radical/partial cystectomy specimens.

value: Human Bladder cancer

value: NAC response

tag: patholresponse

value: Yes


title: AMC_LCDM_Case_#16

value: Laser capture microdissected (LCMD) tumors from the formalin-fixed paraffin-embedded (FFPE) TURBT specimens


title: AMC_LCDM_Case_#15


title: Microc_G1_NC_1

data_processing:
BWA was used mapping DNA sequences against reference genome
pairtools was used to detect ligation junctions, remove PCR duplicates and generate ValidPairs files
mcool files were converted from ValidPairs by Cooler package
hic file were converted from ValidPairs by Juicer tools
Assembly: hg38/Grhc38
Supplementary files format and content: hic file contains all valid Micro-C pairs with mutiple resolutions
Supplementary files format and content: valid paris file contains 1) read name, 2) chromosome of first locus, 3) read position of first locus,  4) chromosome of second locus, 5) read position of second locus,6) strand of first locus,  7) strand of second locus, 8) pair reads type
Library strategy: MicroC

source_name: U2OS cells without NFIB depletion at G1/S phase

extract_protocol:
Cells were digested into a single-cell suspension and then filtered through a 70-μm cell strainer into 15-ml tubes.
Dovetail Micro-C v1.0

treatment_protocol: U2OS cells without or with NFIB depletion at G1/S phase and S phase were synchronized at G1/S boundary by double-thymidine block and followed by release for 4 h to allow cells entering S phase, respectively.

value: G1/S phase


title: ChIPmentation_CMP_RUNX1_rep2

description:
Coverage_RUNX1_CMP_merge_clip.bw
RUNX1_CMP_peaks.narrowPeak

value: RUNX1 (Abcam)


title: CM-PC-2h-1


title: CM-PC-2h-3


title: ChIPmentation_CMP_RUNX1_rep1


title: CM-PC-1h-3


title: AMC_LCDM_Case_#14


title: ATAC_G1_NC_2


title: ChIPmentation_CMP_LYL1_rep3

description:
Coverage_LYL1_CMP_merge_clip.bw
LYL1_CMP_peaks.narrowPeak

value: LYL1 (SCBT)


title: AMC_LCDM_Case_#13


title: CM-PC-1h-2


title: ATAC_G1_NC_1


title: CM-PC-1h-1


title: AMC_LCDM_Case_#12


title: ChIPmentation_CMP_LYL1_rep2


title: ChIPmentation_CMP_LYL1_rep1


title: ChIPmentation_CMP_RUNX1_rep3


title: Tumor.10x.R2

city: Guangzhou

first: Qing-yun

last: Chen

state: -- None selected --

address: State Key Laboratory of Oncology in South China

institute: Sun-Yat Sen University Cancer Center

data_processing:
The fastq files(10x Genomics) was processed by CellRanger(v.3.0.2) and aligned to the GRCh38(provided by 10x Genomics) with default alignment parameters.
CellRanger aggr pipeline was used to aggregate two libraries and generate a gene-count matrix
Seurat(v.2.3.4) was then applied for further data analysis of clustering and dimensionally reduction. For filtering, cells with more than 4000 or less than 200 detected genes, as well as those with mitochondrial transcripts proportion higher than 10% were excluded
The Monocle3 (v.2.99.3) package was used to construct single-cell developmental trajectories in pseudo-time order.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt and mtx

source_name: Esophageal cell cancer

extract_protocol:
Tumor samples were minced into small pieces and digested with collagenase type IV (0.5 mg/ml) and DNase I (50 μg/ml) in RPMI-1640 (Invitrogen) for 30 min at 37°C. Digested tumor pieces were gently triturated with a 10-ml syringe plunger through a 40-μm Cell-Strainer (BD) in RPMI-1640 medium containing 10% FBS until uniform cell suspensions were obtained.
The mRNA library was prepared following to the Chromium User Guide.

treatment_protocol: Tumor-infiltrating leukocytes were enriched by density-gradient centrifugation (Ficoll, GE Healthcare) and then stained with 7AAD and anti-CD3, anti-CD4, and anti-CD8 antibodies. Single 7AAD-negative CD3+CD4+ and CD3+CD8+ T cells were sorted by FACS.

tag: sample type

value: Tumor-infiltrating T cell


title: AMC_LCDM_Case_#11


title: AMC_LCDM_Case_#10


title: CM-PC-TDW-1D-3


title: ChIPmentation_CMP_LMO2_rep3

description:
Coverage_LMO2_CMP_merge_clip.bw
LMO2_CMP_peaks.narrowPeak

value: Bone Marrow

value: LMO2 (Millipore)


title: CM-PC-TDW-1D-2

value: Leaves


title: H3K9me2_FLA_ddm1_rep2

first: Jincong

last: Zhou

address: Tsinghua Yuan

institute: Tsinghua University

data_processing:
Whole-genome bisulfite-seq: Reads were trimed using trim_galore. Bismark v0.19.0 was used to map the trimmed reads and extract methylation level as described previously. The UCSC application tool wigToBigWig was used to get the bigwig file.
ChIP-seq: Reads were trimed using trim_galore.  Trimmed reads were aligned to the TAIR10 genome with Bowtie 2 version 2.3.0 using the default settings, and samtools 1.3.1 was used to remove reads with more than three mismatches and non-uniquely mapped reads. Then total mapped reads were further divided into forward and reverse reads. MACS2 was used to identify peaks and normalized coverage files (bigWig) with 5 bp bin sizes were obtained using bamCoverage from deeptools v2.26.0 to visualize on the Integrative Genomics Viewer. Furthermore, bamCompare or bigwigCompare from deeptools were used to compare immunoprecipitated and input samples for ChIP-seq analysis.
Assembly: TAIR10
Supplementary files format and content: ChIP-seq: bigwig files were generated using the bamCoverage from deeptools. Whole-genome bisulfite-seq: The UCSC application tool wigToBigWig was used to get the bigwig file.

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
Whole-genome bisulfite-seq: Nuclear DNA was extracted from 12 days old seedlings as described in DRIP/DRIP-seq section and sonicated to 250bp with COVARIS. After that Bisulfite conversion and DNA recovery was performed with EZ DNA Methylation-Gold Kit (ZYMO Research) by following the manufacturer instructions. Finally, the sequencing library is made using the EpiArt DNA Methylation Library Kit for Illumina V3 (Vazyme, NE103) by following the manufacturer instructions.
ChIP-seq: To gain the nucleosome resolution, native H3K9me2 ChIP without crosslink and sonication was performed as described in (Bernatavichute et al., 2008), with some modifications. In brief, nuclei were extracted from 12 days old seedlings with Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextran T40, 20 mM HEPES–KOH [pH 7.4], 10 mM MgCl2, 0.5% Triton X-100, 5 mM DTT, and protease inhibitors [Roche]). Nuclei were suspended in 1X MNAse buffer (50mM TriHCl pH 7.6, 5mM CaCl2, 0.1mM PMSF) containing 1X proteinase inhibitor cocktail (Roche). After RNase A (Thermo Scientific™) treatment at 37C for 30 minutes, chromatin was digested with MNase enzyme (NEB) for 6 minutes and the reaction was stopped with EDTA (10mM). Then, the nucleosomes were released with the addition of 0.005% SDS while rotating at 4C for 2-3 hours. After that the supernatant was separated and diluted with dilution buffer (0.1% triton, 50mM NaCl, 0.1mM PMSF, 17mM trisHCl, 3.33mM EDTA, 1x Cocktail inhibitor). Chromatin was pre-cleaned with Protein G beads, and immnoprecipitated with anti-H3K9me2 (Abcam, ab1220) antibodies at 4C overnight. The complexes were incubated with protein G beads (Millipore) at 4C for 3 hours with rotation, and washed three times with ChIP wash buffer having different concentration of NaCl in each wash (50mM TrisHCl pH 7.6, 10mM EDTA, 50/100/150 mM NaCl, 0.1mM PMSF, and 1x Cocktail inhibitor). Then DNA was eluted with elution buffer (0.1%SDS and 0.1M NaHCO3) at 65C for 15 minutes. Proteinase K treatment was performed at 55 C for 2 hour. DNA was recovered after phenol:chloroform extraction. Finally, the sequencing library is made using the TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme, TD502) by following the manufacturer instructions.

value: seedlings

tag: ecotype

value: Columbia

tag: antibody

value: H3K9me2 antibody (Abcam, ab1220)


title: AMC_LCDM_Case_#9


title: Tumor.10x.R1

growth_protocol: Tumor samples were minced into small pieces and digested with collagenase type IV (0.5 mg/ml) and DNase I (50 μg/ml) in RPMI-1640 (Invitrogen) for 30 min at 37°C.


title: H3K9me2_FLA_ddm1_rep1


title: CM-PC-TDW-12h-3

value: WT


title: ChIPmentation_CMP_LMO2_rep1

value: CD34+ HSPC

value: CMP


title: H3K9me2_DMSO_wt_rep2


title: ATAC_G1_sh_1

value: NFIB depletion

value: G1 phase


title: ChIPmentation_CMP_IgG

value: IgG


title: AMC_LCDM_Case_#7

value: Human Bladder cancer

value: Laser capture microdissected (LCMD) tumors from the formalin-fixed paraffin-embedded (FFPE) TURBT specimens

value: NAC response

value: Yes


title: H3K9me2_DMSO_wt_rep1


title: CM-PC-TDW-12h-2


title: ChIPmentation_CMP_GATA2_rep3

description:
Coverage_GATA2_CMP_merge_clip.bw
GATA2_CMP_peaks.narrowPeak

value: GATA2 (SCBT)


title: CM-PC-TDW-12h-1


title: CM-PC-TDW-6h-3


title: AMC_LCDM_Case_#5


title: AMC_LCDM_Case_#4


title: ChIPmentation_CMP_LMO2_rep2

value: Bone Marrow


title: AMC_LCDM_Case_#3


title: CM-PC-TDW-1D-1


title: ChIPmentation_CMP_GATA2_rep1


title: CM-PC-TDW-6h-2


title: H3K9me2_DMSO_ddm1_rep1


title: input_FLA_ddm1_rep1

value: no antibody


title: input_DMSO_wt_rep2


title: input_FLA_ddm1_rep2


title: ChIPmentation_CMP_FLI1_rep1

description:
Coverage_FLI1_CMP_merge_clip.bw
FLI1_CMP_peaks.narrowPeak

value: FLI1 (Abcam)


title: ChIPmentation_CMP_FLI1_rep3


title: CM-PC-TDW-6h-1

value: Leaves


title: AMC_LCDM_Case_#2


title: H3K9me2_DMSO_ddm1_rep2

value: seedlings

value: Columbia


title: AMC_LCDM_Case_#8


title: ChIPmentation_CMP_ERG_rep3

description:
Coverage_ERG_CMP_merge_clip.bw
ERG_CMP_peaks.narrowPeak

value: ERG (Abcam)


title: CM-PC-TDW-4h-1

value: WT


title: CM-PC-TDW-4h-3


title: AMC_LCDM_Case_#1


title: ChIPmentation_CMP_FLI1_rep2

value: CD34+ HSPC

value: CMP


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 passage 18 at OD 2 replicate 2

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

department: Molecular Bacteriology

country: Germany

institute: Helmholtz Center for Infection Research

description:
passages 2x per day in LB for 6 days
170522__mgu19__RNAseq__M70564993_passage18__PL__1

data_processing:
cutadapt ( --nextseq-trim=20 -g TTTTT;min_overlap=1 -G GGGGGGG;min_overlap=3 -m 36)
bowtie2 ( --very-sensitive-local -I 100 -X 1200 --fr )
featurecounts (-p -Q 20 10 -t CDS,tRNA,rRNA -g locus --extraAttributes name)
Assembly: NC_008463.1
Supplementary files format and content: reads_per_gene.csv - reads per gene with samples in separate columns

organism: Pseudomonas aeruginosa

source_name: clinical isolate M70564993 passage 18

growth_protocol: Bacterial subcultures were grown in liquid LB, at 37 °C and 180 rpm shaking until OD 2.0

extract_protocol:
RNA extraction was done as previously described (Schinner et al., 2020)
Illumina TruSeq kit

treatment_protocol: Bacterial cell pellets were resuspended in RNAprotect.

tag: strain

value: clinical isolate M70564993 passage 18

value: bacteria

value: passage 18

value: RNAprotect


title: ChIPmentation_CMP_GATA2_rep2


title: AMC_LCDM_Case_#6

value: Human Bladder cancer

value: Laser capture microdissected (LCMD) tumors from the formalin-fixed paraffin-embedded (FFPE) TURBT specimens

value: NAC response


title: input_DMSO_wt_rep1


title: input_DMSO_ddm1_rep2


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 passage 18 at OD 2 replicate 1

description:
passages 2x per day in LB for 6 days
170522__mgu19__RNAseq__M70564993_passage18__PL__2


title: ChIPmentation_CMP_ERG_rep2

value: Bone Marrow

value: ERG (SCBT)


title: CM-PC-TDW-2h-3


title: ChIPmentation_CMP_ERG_rep1


title: input_DMSO_ddm1_rep1

value: no antibody


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 at OD 2 replicate 4

source_name: clinical isolate M70564993 WT

value: clinical isolate M70564993 WT


title: CM-PC-TDW-2h-2

value: Leaves


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 at OD 2 replicate 3


title: CM-PC-TDW-2h-1


title: siKDM4A_3

city: Jinan

first: Lei

address: No.44-1 Wenhua Road West

department: Department of Orthodontics

institute: School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: hg38

source_name: Human tongue squamous cell carcinoma

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: Human tongue squamous cell carcinoma

value: tumor cells


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 at OD 2 replicate 2

value: WT


title: siKDM4A_2


title: CM-PC-TDW-1h-3


title: siKDM4A_1


title: CM-PC-TDW-1h-2


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 at OD 2 replicate 1


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 ΔPA0290 mutant at OD 2 replicate 2

source_name: clinical isolate CH3484

value: clinical isolate CH3484


title: CM-PC-TDW-4h-2


title: siLEF1_2


title: CM-PC-TDW-1h-1


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 ΔPA0290 mutant at OD 2 replicate 1


title: siLEF1_3


title: wt_H3K9me2_IP_rep2

data_processing:
ssDRIP-seq and ChIP-seq: Reads were trimed using trim_galore.  Trimmed reads were aligned to the TAIR10 genome with Bowtie 2 version 2.3.0 using the default settings, and samtools 1.3.1 was used to remove reads with more than three mismatches and non-uniquely mapped reads. Then total mapped reads were further divided into forward and reverse reads. MACS2 was used to identify peaks and normalized coverage files (bigWig) with 5 bp bin sizes were obtained using bamCoverage from deeptools v2.26.0 to visualize on the Integrative Genomics Viewer. Furthermore, bamCompare or bigwigCompare from deeptools were used to compare immunoprecipitated and input samples for ChIP-seq analysis.
pNET-seq : R2 reads were trimmed for Illumina adaptors and then reads <35bp were filtered using the Cutadapt based on the reads distribution density. Filtered reads were aligned to the Arabidopsis reference genome (TAIR10) using Bowtie 2 version 2.3.0 with default settings. Reads were mapped to specific strands (forward or reverse).
Assembly: TAIR10
Supplementary files format and content: ssDRIP-seq, ChIP-seq and pNET-seq: bigwig files were generated using the bamCoverage from deeptools. Whole-genome bisulfite-seq: The UCSC application tool wigToBigWig was used to get the bigwig file.

extract_protocol:
ssDRIP-seq: Nuclei were isolated from Arabidopsis plants with Honda buffer, followed by SDS/proteinase K treatment at 37°C overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases (MboI, MseI, NlaIII, DdeI); the negative control was treated with RNase H (New England Biolabs) overnight. DRIP was performed as described in Xu et al., 2017 and Sun et al., 2013. Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 ul Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55˚C. DNA was purified and sonoicated to 150 bp fragments.
pNET-seq was performed as described (Zhu et al., 2019). In brief, nuclei were extracted from 12 days old seedlings using percoll-gradient (30%-80%) and washed with 1X transcription buffer (2 M Hexylene glycol. 20mM PIPES-KOH [PH 7], 10mM MgCl2, 5mM β-mercaptoethanol) and 1x nuclei storage buffer (50mM Tris-HCL [PH7.2], 5mM mgCl2, 5mM KCl, 1mM MnCl2, 5mM DTT, 50% glycerol), respectively. After that nuclei were resuspended in 1x reaction buffer (1mM ATP, 1mM GTP, 1mM CTP, 1mM Br-UTP, 4U RNasin, 1% sarcosyl) and incubated at 30C for 5 minutes. The reaction was stopped with TRIzol and nuclear RNA was precipitated with 1/10 vol 5M NH4AC, 3 vol Ethanol and 1μl GlycoBlue. RNA was then treated with 5μl 1M NaOH for 40min on ice, and the reaction was stopped with 25μl 1M Tris-HCl pH7.0. After RNA purification with Bio-spin 30 Column (Cat. #732-6250/6251) and DNase treatment with RQ1 RNase-free DNase (Promega), RNA de-phosphorylation was performed with antarctic phosphatase (NEB, B0289S), and incubated with pre-blocked Anti-BrdU argarose beads (Santa Cruz Biotech) and the reaction mixture was rotated for 1 hr at 4C. Beads were then was with Low salt (0.2x SSPE, 1mM EDTA, 0.05% tween-20), high salt (0.5x SSPE, 1mM EDTA, 0.05% tween-20, 150mM NaCl) and TET buffers (10mM Tris-HCL [PH 8], 0.1mM EDTA, 0.05% Tween-20), respectively. RNA was then eluted from beads with elution buffer (20mM DTT, 300mM NaCl, 5mM Tris [PH 7.5], 1mM EDTA, 0.10% SDS), and precipitated with 1/10 vol 5M NH4AC, 3 vol Ethanol and 1μl GlycoBlue. RNA was then end-repaired with T4 PNK (NEB, M0201L) and RNAsin Plus (Promega, N2611) and precipitated with 1/10 vol 5M NH4AC, 3 vol Ethanol and 1μl GlycoBlue. Ploy A tail was added to end-repaired DNA with poly-A polymerase (NEB, B0276S), and reverse transcription was performed with SSIII reverse transcriptase (Invitrogen). After that extra RT-primers and RNA were cleaned, cDNA was size selected (more than 120 bp) with page gel. Size selected cDNA was circularized with CircLigase (Epicentre) and relinearized with 4× relinearization supplement (100mM KCl, 2mM DTT) and Ape I (NEB, M0282S). Then relinearized DNA was run on page gel, and precipitated with 1/10 vol 5M NH4AC, 3 vol Ethanol and 1μl GlycoBlue. Size selected cDNA was finally amplified with 2x Kapa HiFi mixture (KK2602), using universal forward primer F and reverse index primer R. The amplified libraries were size selected, purified and precipitated with page gel.
ChIP-seq: To gain the nucleosome resolution, native native H3K9me2, H3K27me1, H2A.W-FLAG, H2A.Z ChIP without crosslink and sonication was performed as described in (Bernatavichute et al., 2008), with some modifications. In brief, nuclei were extracted from 12 days old seedlings with Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextran T40, 20 mM HEPES–KOH [pH 7.4], 10 mM MgCl2, 0.5% Triton X-100, 5 mM DTT, and protease inhibitors [Roche]). Nuclei were suspended in 1X MNAse buffer (50mM TriHCl pH 7.6, 5mM CaCl2, 0.1mM PMSF) containing 1X proteinase inhibitor cocktail (Roche). After RNase A (Thermo Scientific™) treatment at 37C for 30 minutes, chromatin was digested with MNase enzyme (NEB) for 6 minutes and the reaction was stopped with EDTA (10mM). Then, the nucleosomes were released with the addition of 0.005% SDS while rotating at 4C for 2-3 hours. After that the supernatant was separated and diluted with dilution buffer (0.1% triton, 50mM NaCl, 0.1mM PMSF, 17mM trisHCl, 3.33mM EDTA, 1x Cocktail inhibitor). Chromatin was pre-cleaned with Protein G beads, and immnoprecipitated with anti-H3K9me2 (Millipore),anti-H3K27me1 (Millipore), anti-FLAG (Sigma) and anti-H2A.Z antibodies at 4C overnight. The complexes were incubated with protein G beads (Millipore) at 4C for 3 hours with rotation, and washed three times with ChIP wash buffer having different concentration of NaCl in each wash (50mM TrisHCl pH 7.6, 10mM EDTA, 50/100/150 mM NaCl, 0.1mM PMSF, and 1x Cocktail inhibitor). Then DNA was eluted with elution buffer (0.1%SDS and 0.1M NaHCO3) at 65C for 15 minutes. Proteinase K treatment was performed at 55 C for 2 hour. DNA was recovered after phenol:chloroform extraction.
ssDRIP-seq: DRIPed DNA was conducted to library construction using the VAHTS ssDNA Library Prep Kit (Vazyme, ND620). Bisulphite-seq: to use EpiArt DNA Methylation Library Kit for Illumina V3 (Vazyme, NE103) for library construction. ChIP-seq: ChIPed DNA was conducted to library construction using the TruePrep DNA Library Prep Kit V2 (Vazyme, TD502). pNET-seq:  NEXTflex TM small RNA-Seq Kit V3 was used to construct the libraries.

value: seedlings

value: Columbia

value: H3K9me2 antibody (Abcam, ab1220)


title: wt_H3K27me1_IP_rep1

value: H3K27me1 antibody (Millipore, 07-448)


title: siLEF1_1


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 ΔPA3177 mutant at OD 2 replicate 2

value: bacteria

value: RNAprotect


title: wt_H3_IP_rep1

value: H3 antibody (ABclonal, A2348)


title: CM-0h-2


title: wt_H3_IP_rep2


title: wt_H3K27me1_IP_rep2


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 ΔPA3177 mutant at OD 2 replicate 1


title: CM-0h-1


title: Control_3

value: Control


title: wt_FLAG_ChIP_rep2

value: FLAG antibody (Sigma, M8823)


title: wt_FLAG_ChIP_rep1


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 at OD 2 replicate 2

source_name: clinical isolate CH3484 WT

value: clinical isolate CH3484 WT


title: Control_2


title: wt_H3K9me2_IP_rep1


title: RB383_siSFRP2_48h

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

country: USA

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Retinoblastoma

growth_protocol: RB383 cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% fetal bovine serum. 10 microgram/ml insulin, and 55 microM beta-mercaptoethanol. Cells were maintained in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total cellular RNA was isolated using TRIzol reagent (Invitrogen).
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

treatment_protocol: RB383 cells were transfected with either scrambled-siRNA or SFRP2-siRNAs (Dharmacon) for 24 or 48 hours. Transfection was carried out  using Lipofectamine™ RNAiMAX Transfection Reagent (Thermo Fisher) according to the manufacturer’s protocol.

value: Retinoblastoma

value: SFRP2 knockdown

tag: harvest time

value: 48 hours


title: Control_1

value: Human tongue squamous cell carcinoma


title: RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate CH3484 at OD 2 replicate 1


title: CM-0h-3

value: Leaves


title: Preop97H116

city: Minneapolis

first: Charles

middle: Scott

last: Cameron

state: Minnesota

address: 420 Delaware St SE

department: Pediatrics

institute: University of Minnesota-Twin Cities,

description:
Extracellular vesicle  total RNA
novaseq_counts

data_processing:
Reads from the 128 samples that underwent total RNA sequencing were processed using the CHURP pipeline. Briefly, read quality was assessed with fastqc, and reads were trimmed using trimmomatic (v.33) to remove the first 3 base pairs of R2 (as these are from the SMART-seq Stranded adapter), adapters and low quality bases. Reads were aligned to hg38 using hisat2 and assigned to genes in Ensembl GrCh38 release 100 using Rsubread.
Assembly: HG38
Supplementary files format and content: text file containing count table

source_name: Serum Sample

extract_protocol:
RNA was harvested using ExoRNeasy Serum/Plasma Midi Kit (QIAGEN, Cat. No. 77144). 2.5 ng of total RNA was used for the construction of sequencing libraries.
SMART-Seq Stranded Kit (Cat. No. 634444) was used to generate cDNA libraries.

value: Serum Sample

tag: disease

value: Glioblastoma


title: RB383_Control_RNAi_48h

value: scrambled-siRNA control


title: Preop95H114

tag: tissue


title: ddm1_H3K9me2_IP_rep2

value: seedlings

value: Columbia


title: ddm1_H3K27me1_IP_rep1

value: H3K27me1 antibody (Millipore, 07-448)


title: ddm1_H3K27me1_IP_rep2


title: Preop96H115


title: RB383_siSFRP2_24h

value: 24 hours


title: Preop94H113


title: ddm1_H3_IP_rep2


title: Preop93H112


title: RB383_Control_RNAi_24h


title: Preop91H110


title: ddm1_H3K9me2_IP_rep1

value: H3K9me2 antibody (Abcam, ab1220)


title: ddm1_H3_IP_rep1

value: H3 antibody (ABclonal, A2348)


title: L1_1

city: 镇江市

first: 文信

last: 笪

state: 江苏省

address: 镇江市京口区学府路301号江苏大学

institute: 江苏大学医学院

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Mus musculus

source_name: spleen

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: spleen

value: MDSCs

value: lactic acid


title: c1_1

address: 镇江市京口区学府路301号江苏大学

value: control


title: c2_1

address: 镇江市京口区学府路301号江苏大学


title: DDM1_FLAG_ChIP_rep1

value: FLAG antibody (Sigma, M8823)


title: DDM1_FLAG_ChIP_rep2


title: Preop89H108


title: Preop90H109


title: wt_NETseq_rep2

data_processing:
ssDRIP-seq and ChIP-seq: Reads were trimed using trim_galore.  Trimmed reads were aligned to the TAIR10 genome with Bowtie 2 version 2.3.0 using the default settings, and samtools 1.3.1 was used to remove reads with more than three mismatches and non-uniquely mapped reads. Then total mapped reads were further divided into forward and reverse reads. MACS2 was used to identify peaks and normalized coverage files (bigWig) with 5 bp bin sizes were obtained using bamCoverage from deeptools v2.26.0 to visualize on the Integrative Genomics Viewer. Furthermore, bamCompare or bigwigCompare from deeptools were used to compare immunoprecipitated and input samples for ChIP-seq analysis.
pNET-seq : R2 reads were trimmed for Illumina adaptors and then reads <35bp were filtered using the Cutadapt based on the reads distribution density. Filtered reads were aligned to the Arabidopsis reference genome (TAIR10) using Bowtie 2 version 2.3.0 with default settings. Reads were mapped to specific strands (forward or reverse).
Assembly: TAIR10
Supplementary files format and content: ssDRIP-seq, ChIP-seq and pNET-seq: bigwig files were generated using the bamCoverage from deeptools. Whole-genome bisulfite-seq: The UCSC application tool wigToBigWig was used to get the bigwig file.
Library strategy: pNET

value: Pol II-CTD antibody (Abcam, ab817)


title: Preop88H107


title: wt_NETseq_rep1


title: ddm1_NETseq_rep2


title: L2_1

address: 镇江市京口区学府路301号江苏大学


title: Preop86H105


title: HAP1 SETDB1 KO cells, small-RNA-seq

city: Daejeon

first: Kyuheum

last: Jeon

address: 125 Gwahak-ro

institute: KRIBB

description: small RNA

data_processing:
TrimGalore v0.4.4 was used to remove adapters from the sequencing reads.
The trimmed reads were uniquely mapped to the human reference genome (hg38) using Bowtie v2.3.5.1.
The number of read counts mature miRNAs from miRBase was calculated using HTSeq-Count v0.11.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include count values for each sample

growth_protocol: HAP1 cells were cultured in IMDM supplemented with 100 U/ml penicillin/streptomycin and 10% FBS at 37 °C in 5% CO2.

extract_protocol:
Total RNA was resolved on a 15% denaturing polyacrylamide gel and a part of the gel containing 17-50 nt RNA was excised using a clean razor blade. Small RNAs were eluted from the gel piece by incubating in 250 μl of 1 M NaCl overnight at 4 °C and purified by ethanol precipitation method.
The eluted RNAs were proceeded for Illumina sequencing library construction using NEBNext Small RNA Library Prep Kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos (New England Biolabs) according to the manufacturer’s protocol.

value: chronic myelogenous leukemia

tag: genotype

value: SETDB1 knockout


title: Preop85H104

value: Serum Sample


title: HAP1 wild-type cells, small-RNA-seq

description: small RNA

value: WT


title: Preop83H96

value: Glioblastoma


title: HAP1 SETDB1 KO cells, Directional RNA-seq, biol rep 3

data_processing:
TrimGalore v0.4.4 was used to remove adapters from the sequencing reads.
The trimmed reads were uniquely mapped to the human reference genome (hg38) using STAR aligner v2.6.0a with ‘–outFilterMultimapNmax 1, –outFilterMultimapScoreRange 1 and –outFilterMismatchNoverLmax 0.03’ and the resulting SAM files were converted to sorted BAM files using Samtools v1.9.
Duplicated reads were removed using the MarkDuplicates tool of Picard v2.23.8.
The number of read counts per gene from RefSeq was calculated using HTSeq-Count v0.11.1 and normalized using DESeq2 v3.14.
For quantification of retroelement expression, Bedtools intersect with ‘-c’ option was used to count reads aligned to the L1 copies.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include count values for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using either the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) or the NEBNext Ultra II Directional RNA Library Prep Kit according to the manufacturer’s instructions.


title: HAP1 SETDB1 KO cells, Directional RNA-seq, biol rep 2


title: ddm1_NETseq_rep1

value: seedlings


title: wt_ATAC_rep1

value: Columbia

value: no antibody


title: wt_ATAC_rep2


title: ph6.7_1_1

address: 镇江市京口区学府路301号江苏大学

tag: treatment

value: acid at ph 6.7


title: Preop82H95


title: Preop81H94


title: ddm1_ATAC_rep1


title: S8

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

country: United Kingdom

institute: King's College London

library_source: transcriptomic single cell

data_processing:
kallisto
Assembly: Mus Musculus Ensembl v96, built with kallisto version 0.45.1
Supplementary files format and content: gene-level kallisto output files (matrix.cells, genes.txt, matrix.abundance.gene.mtx)
Supplementary files format and content: Seurat object with meta-data (FinalObject.Robj)

molecule: nuclear RNA

source_name: Spinal Cord

extract_protocol:
Frozen spinal cord tissue was defrosted, chopped into small pieces and placed into 5 ml of hypotonic lysis buffer in a 15 ml centrifuge tube on ice. The hypotonic lysis buffer contained Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl 3 mM, and Nonidet P40 0.01% in nuclease free water. Tissue was left to stand on ice for 15 minutes and then 5ml of Neurobasal medium (2% B27 supplement, 1% N2 supplement, 1% Glutamax, (Thermo Fisher Scientific)) was added. The tissue was triturated using a series of 4 progressively smaller diameter fire polished pipettes. Each trituration involved passing the tissue in and out of the pipette ten times until it flowed easily. After each round, 2ml of supernatant was removed and passed through a 70 µm strainer into another 15ml centrifuge tube. Following the fourth round of trituration, after which tissue was no longer visible, the remaining liquid was passed through the filter into the second tube. The solution of dissociated nuclei was then centrifuged at 1,000 x g for 10 minutes at 4 °C. The resulting pellet was resuspended in 2.5 ml of low sucrose buffer (Sucrose 0.32 M, HEPES (pH = 8.0) 10 mM, CaCl 5 mM, MgAc 3 mM, DTT 1mM, EDTA-free Protease Inhibitor Cocktail (Roche) 1 tablet per 10ml, RNAsin RNAase inhibitor (Promega) 40 U/ml, all in nuclease free water). A 2.5 ml sucrose cushion (Sucrose 1 M, HEPES (pH = 8.0) 10 mM, MgAc 3 mM, DTT 1 mM, all in nuclease free water) was then layered underneath using a serological pipette and the tube centrifuged at 3,200 x g for 20 minutes at 4 °C. Following centrifugation, the supernatant was discarded, and the pellet resuspended in 0.5 ml of 1x PBS containing 2% BSA, EDTA-free Protease Inhibitor Cocktail (Roche) (1 tablet per 10ml) and RNAsin 40 U/ml. The solution was transferred to a 6ml FACS tube and kept on ice prior to FACS sorting. FACS sorting was conducted on a BD FACS Aria IIU equipped with a 100-micron nozzle, and BD FACSDiva software version 9.01. Prior to sorting, nuclei were stained with DRAQ7 (1:500, Invitrogen) to enable the sorting of nuclei from debris. Phox2a-lineage nuclei were identified based on GFP fluorescence and sorted into 96-well LoBind plates (Eppendorf) using single-cell purity settings such that each well contained a single nucleus. Prior to sorting, each well of the plate was filled with 2 µl of nuclease free water containing Triton X-100 0.2% and RNAsin 1 U/µl.
Smart-Seq2 - Reverse transcription conditions were: 42°C for 90 minutes, 10 cycles 50°C for 2 min, 42°C for 2 min, hold at 4°C; PCR amplification conditions were: 98°C for 3 min, 21 cycles: 98°C for 20 sec, 67°C for 15 sec, 72°C for 6 min, final extension 72°C for 5 min, hold at 4°C. Amplified cDNA underwent bead clean-up in a 1:0.8X volumetric ratio of AMPure XP Beads (Beckman Coulter) and eluted into 25 μl of Nuclease Free Water. Sequencing libraries were generated using an automated, reduced-volume version of the Nextera XT protocol (Illumina) using the SPT Labtech Mosquito LV. Libraries were cleaned up using a 1:0.7x volumetric ratio of AMPure XP Beads (Beckman Coulter)

value: Spinal Cord

value: Spinal Cord Nuclei

tag: Sex

value: Female

value: SNI


title: S7

tag: cell type

value: Male


title: S6


title: N8

value: Niave


title: Controls


title: Preop87H106


title: ph6.7_2_1

address: 镇江市京口区学府路301号江苏大学

value: spleen

value: MDSCs


title: wt_H2AZ_IP_rep2

value: H2A.Z antibody (Luo et al., 2020)


title: N7


title: Preop80H93


title: N6


title: HAP1 wild-type cells, Directional RNA-seq, biol rep 3

value: chronic myelogenous leukemia


title: wt_H2AZ_IP_rep1


title: S5


title: Preop79H92

value: Serum Sample


title: Preop78H91


title: N5


title: HAP1 wild-type cells, Directional RNA-seq, biol rep 2

value: WT


title: ddm1_ATAC_rep2


title: wt_H2AZ_input_rep2


title: HAP1 wild-type cells, Directional RNA-seq, biol rep 1


title: wt_H2AZ_input_rep1


title: S4


title: Preop76H89

value: Glioblastoma


title: Preop77H90


title: N4

value: Naïve


title: HAP1 SETDB1 KO cells, Directional RNA-seq, biol rep 1

value: SETDB1 knockout


title: Preop74H84


title: wt_H2AW_FLAG_IP_rep2

value: seedlings

value: Columbia

value: FLAG antibody (Sigma, M8823)


title: S3

value: Spinal Cord

value: Spinal Cord Nuclei


title: HAP1 SETDB1 KO cells, RNA-seq, biol rep 2


title: Preop73H83


title: wt_H2AW_FLAG_input_rep2

value: no antibody


title: N3

value: Male


title: HAP1 wild-type cells, RNA-seq, biol rep 3


title: N2

value: Female


title: Preop72H82


title: HAP1 SETDB1 KO cells, RNA-seq, biol rep 3


title: HAP1 SETDB1 KO cells, RNA-seq, biol rep 1


title: S2

value: SNI


title: wt_H2AW_FLAG_input_rep1


title: HAP1 wild-type cells, RNA-seq, biol rep 2


title: hta6712_H2AZ_IP_rep2


title: HAP1 wild-type cells, RNA-seq, biol rep 1


title: hta6712_H2AZ_IP_rep1


title: wt_H2AW_FLAG_IP_rep1


title: Preop17H24


title: HAP1 SETDB1 KO cells, MBD-seq

data_processing:
Raw sequencing data were preprocessed to remove low quality reads using ‘Trim Galore v0.65’.
The trimmed reads were aligned on the reference genome (hg38) using a short read mapper, ‘bwa v0.7.17'.
Duplicated reads were removed using ‘MarkDuplicates’ in the GATK v4.1.9.0 suit.
For quantification of MBD-seq enrichments, reads overlapped with genomic bins of 300 bases in each sample were counted using ‘Bedtools intersect v2.0.0 with the option ‘-c’.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Genomic DNAs (gDNAs) were extracted from the wild-type and SETDB1 KO HAP1 cells using DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer's instruction, and sonicated using Bioruptor Pico (Diagenode) and purified using with AMPure XP beads (Beckman).
Illumina sequencing libraries were generated using the enriched methylated DNA fragments. All the captured DNAs were end-repaired by reacting with T4 DNA polymerase, Klenow, and T4 polynucleotide kinase in the presence of dNTP at 20°C for 2 h, and then 3′-end adenylated using Klenow fragment at 30°C for 2 h. Finally, the end-repaired DNA fragments were ligated with NEBNext adapters (New England Biolabs) and were enriched by 18 cycles of PCR.


title: S1


title: hta6712_H2AZ_input_rep2


title: control_C32

value: Healthy Control


title: HAP1 wild-type cells, MBD-seq


title: control_C31


title: N2a cells, shk6161

city: Shanghai

first: Yifan

last: Wang

address: 130 Dong An Road

institute: Fudan University

data_processing:
We aligned ChIP-seq reads to mm10 using bowtie2 with default parameters.
PCR duplicates were discarded then the uniquely mapped reads were acquired by picard.jar.
After indexing the bam files using SAMtools, BAM files were converted to bigwig files and normalized to RPGC using bamCoverage in deepTooLs v2.5.5.
then, the bigwig files of the biological replicates were merged by bigwigCompare in deepTooLs v2.5.5.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: N2a cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: CUT & Tag library generation was performed by Hyperactive Universal CUT & Tag Assay Kit for Illumina kit (Vazyme Biotech, TD903).

value: mouse neuroblasts

value: KDM7A (Abclonal, custom)


title: HAP1_WT_ChIP-seq_KAP1

data_processing:
TrimGalore v0.4.4 was used to remove adapters from the sequencing reads.
The trimmed reads were mapped to the human reference genome (hg38) using Bowtie2 v2.3.5.1.
Duplicate reads were removed using the MarkDuplicates tool of Picard v2.23.8.
Peak calling was performed using the findPeaks of HOMER v4.11.
The aligned reads were further converted to bigwig format using bamCoverage (deepTools).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, the cross-linked chromatin was sheared to the size ranging from 200 to 500 bp using a Sonic dismembrator (Thermo Fisher Scientific).
The purified DNA fragments were subjected to Illumina sequencing library construction using NEBNext DNA Library Prep modules (New England Biolabs) and NEBNext Multiplex Oligos (New England Biolabs) according to the manufacturer’s protocol.

value: chronic myelogenous leukemia

value: KAP1 (ab109287, Abcam)


title: control_C30

value: Serum Sample


title: HAP1_WT_ChIP-seq_AGO2

value: WT

value: AGO2 (ab57113, Abcam)


title: hta6712_H2AZ_input_rep1

value: seedlings


title: ddm1_H2AZ_IP_rep2

value: Columbia

value: H2A.Z antibody (Luo et al., 2020)


title: N2a cells, shk6162


title: N2a cells, shCtrl6161

value: shCtrl


title: HAP1_WT_ChIP-seq_SETDB1

value: SETDB1 (11231-1-AP, Proteintech)


title: control_C28


title: Preop71H81

value: Glioblastoma


title: N9

value: Spinal Cord

value: Spinal Cord Nuclei

value: Male

value: Naïve


title: HAP1 SETDB1 KO cells, ChIP-seq, biol rep 3

value: SETDB1 knockout

value: H3K9me3 (ab8898, Abcam)


title: ddm1_H2AZ_input_rep2

value: no antibody


title: N2a cells, shk6142

value: mouse neuroblasts

value: KDM7A (Abclonal A14692)


title: N2a cells, shk6141


title: HAP1 SETDB1 KO cells, ChIP-seq, biol rep 2

value: chronic myelogenous leukemia


title: ddm1_H2AW_FLAG_IP_rep2

value: FLAG antibody (Sigma, M8823)


title: control_C26

value: Serum Sample

value: Healthy Control


title: HAP1 SETDB1 KO cells, ChIP-seq, biol rep 1


title: control_C25


title: ddm1_H2AW_FLAG_IP_rep1

value: seedlings

value: Columbia


title: N2a cells, shCtrl6142

value: shCtrl


title: ddm1_H2AZ_IP_rep1

value: H2A.Z antibody (Luo et al., 2020)


title: N2a cells, shCtrl6141


title: HAP1 wild-type cells, ChIP-seq, biol rep 2

value: WT


title: control_C29


title: control_C24


title: ddm1_H2AW_FLAG_input_rep2


title: control_C23


title: HAP1 wild-type cells, ChIP-seq, biol rep 1


title: N2a cells, shCtrl6162

value: KDM7A (Abclonal, custom)


title: control_C22


title: ddm1_H2AW_FLAG_input_rep1


title: wt_DMSO_DRIP_rep2

data_processing:
ssDRIP-seq and ChIP-seq: Reads were trimed using trim_galore.  Trimmed reads were aligned to the TAIR10 genome with Bowtie 2 version 2.3.0 using the default settings, and samtools 1.3.1 was used to remove reads with more than three mismatches and non-uniquely mapped reads. Then total mapped reads were further divided into forward and reverse reads. MACS2 was used to identify peaks and normalized coverage files (bigWig) with 5 bp bin sizes were obtained using bamCoverage from deeptools v2.26.0 to visualize on the Integrative Genomics Viewer. Furthermore, bamCompare or bigwigCompare from deeptools were used to compare immunoprecipitated and input samples for ChIP-seq analysis.
pNET-seq : R2 reads were trimmed for Illumina adaptors and then reads <35bp were filtered using the Cutadapt based on the reads distribution density. Filtered reads were aligned to the Arabidopsis reference genome (TAIR10) using Bowtie 2 version 2.3.0 with default settings. Reads were mapped to specific strands (forward or reverse).
Assembly: TAIR10
Supplementary files format and content: ssDRIP-seq, ChIP-seq and pNET-seq: bigwig files were generated using the bamCoverage from deeptools. Whole-genome bisulfite-seq: The UCSC application tool wigToBigWig was used to get the bigwig file.
Library strategy: ssDRIP


title: control_C27


title: ddm1_H2AZ_input_rep1


title: wt_DMSO_DRIP_rep1


title: The DNA was digested with 10 U of P1, replicate 3

city: Xiamen

first: Dongyang

last: Xu

state: Fujian

address: 668 Jimei Road

institute: Huaqiao University

data_processing:
Raw reads were filtered to get clean reads by removing read pairs with the following features: (1) paired-end reads containing adaptor sequence, (2) the fraction of N bases in either read exceeds 10%, (3) the fraction of low-quality bases (Q ≤ 5) exceeds 50%.
Only paired-end clean reads, where read 1 started with 9-11 Gs, read 2 started with 11-13 Ts and each base of each read had Phred quality score >20 were selected.
The polyG and polyT sequences at the beginning of reads 1 and 2 respectively were trimmed.
For the analysis of essDNAs in the mitochondrial genome, trimmed reads were aligned to the human mitochondrial genome (GRCh37/hg19) using BWA-MEM (v0.7.12) with the default settings.
For the analysis of essDNAs in the nuclear genome, trimmed reads were aligned to the human genome (GRCh37/hg19) (including nuclear and mitochondrial genome) using BWA-MEM (v0.7.12) with the default settings.
Only pairs of reads where both reads 1 and 2 uniquely mapped to the genome with appropriate configuration and spacing were kept.
The 3'-OH termini were defined as the first bases after the stretches of the 11-13 Ts in the reads 2.
For the analysis of essDNAs in the mitochondrial genome, read count of each nucleotide was obtained and then normalized to the total number of reads aligned to the mitochondrial genome in that sample.
For the analysis of essDNAs in the nuclear genome, to avoid alignments likely arising from internal priming to A-rich sequences in the genome, 3'-OH termini where fraction of Ts in the 20-base 5′ upstream sequence in the read 2 alignment was >40% were removed from the downstream analysis.
For the analysis of essDNAs in the nuclear genome, SICER (v1.1) software was used to obtain essDNA regions using the coordinates of the 3'-OH termini in the P1-treated samples versus those untreated samples with the following parameters: redundancy threshold = 1, window size = 10 bp, fragment size = 1 bp, effective genome fraction = 0.8, gap size = 30 bp, and E-value = 0.01.
Assembly: GRCh37/hg19
Supplementary files format and content: Processed data1 are in BED files containing coordinates of unique 3'-OH sites in the mitochondrial genome. The 4th and 5th columns show the raw and normalized count of each site.
Supplementary files format and content: Processed data2 are in BED files containing coordinates of unique 3'-OH sites in the nuclear genome. The sites likely arising from internal priming to A-rich sequences have been removed. The 4th column shows the count of each site.
Supplementary files format and content: Processed data3 are in BED files containing coordinates of clustered P1 cut sites. The 4th column shows the count of each site.
Supplementary files format and content: Processed data4 are in BED files containing coordinates of essDNA regions obtained from SICER analysis.

growth_protocol: Human chronic myeloid leukemia cell line K562 was maintained in RPMI 1640 (Gibco, Billings, MT, USA) supplemented with 10% heat-inactivated fetal bovine serum (ExCell Bio, Montevideo, Uruguay) and 1% penicillin-streptomycin (Gibco) and cultured at 37℃ in 5% CO2.

extract_protocol:
First, one million K562 cells were crosslinked with 1% formaldehyde, and lysed to isolate nuclei as described previously (PMID: 31862872). Second, digestion of essDNA regions in the nuclei was performed as follows: nuclei were centrifuge at 4000 rpm for 10 min at room temperature. After removal of supernatant, the pellet was incubated in 320 µl 0.2% SDS buffer for 10 min at 62℃ and quenched with 50 µl of 10% Triton X-100. The nuclei were collected by centrifugation at 4000 rpm at 27℃ for 10 min and washed twice with 500 µl 1x NEBuffer 1.1 (NEB, Ipswich, MA, USA). After aspiration of the supernatant, the nuclei were resuspended in 50 µl 1x NEBuffer 1.1 (NEB) containing different amount of the Nuclease P1 (NEB) (0.01 U, 0.1 U, 1 U, and 10 U) at 37℃ for 10 min, followed by inactivation at 75℃ for 10 min. Third, DNA was isolated from the P1 digested samples as described previously (PMID: 31862872) and purified with 2x volumes of VAHTS DNA Clean Beads (Vazyme, Nanjing, China) to a final volume of 20 µl.
The NGS sequencing libraries were constructed with the SSiNGLe-ILM method developed by us previously (PMID: 31862872), using 100 ng of DNA as input.

value: human chronic myeloid leukemia cell line


title: control_C21


title: satedM

city: Princeton

first: Adelaide

last: Minerva

state: New Jersey

address: Washington Road

department: Princeton Neuroscience Institute

institute: Princeton University

description: 10X Genomics

data_processing:
Demultiplexing, barcode processing, and gene counting were done using CellRanger software v6.1.1 or v7.1.0 (10X Genomics) using the --include-introns flag
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files

source_name: Brain section (ventral tegmental area)

extract_protocol:
Bilateral VTA punches from two animals of the same sex and condition were pooled together and Dounce homogenized. Pairs were selected randomly from within each sex and condition. Pooling ensured a high enough concentration of nuclei per sample for quality sequencing. The sample was filtered through a 40um strainer and nuclei were isolated via iodixanol gradient centrifugation. Nuclei were hand-counted using a hemocytometer on an EVOS M5000 microscope and final concentrations were 850-1,450 nuclei per ul. The volume of suspension used for library preparation was adjusted in order to load a target of 20,000 nuclei and capture 10,000 nuclei per sample.
Library construction was performed according to the manufacturer's instructions (10X Genomics Chromium v3). Briefly, nuclei were resuspended in the master mix and loaded together with partioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the lysate contained in every single GEM was retrotranscripted to cDNA, which contains an illumina R1 primer sequence, unique molecular identifier (UMI), and the 10X barcode. The pooled and barcoded cDNA was then cleaned up with Silance DynaBeads, amplified by PCR, and the appropriate sized fragments were selected qith SPRIselect reagent for subsequent library construction. During library construction the Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added.

value: Brain section (ventral tegmental area)

value: All nuclei

value: Wild type

value: Pre-fed with sweetened condensed milk

value: male


title: hungryM

description: 10X Genomics

value: 16 hour fast


title: control_C20


title: The DNA was digested with 10 U of P1, replicate 2


title: wt_4h_FLA_DRIP_rep2


title: HAP1 wild-type cells, ChIP-seq, biol rep 3

value: chronic myelogenous leukemia

value: H3K9me3 (ab8898, Abcam)


title: controlF3

description: 10X Genomics

value: female


title: The DNA was digested with 10 U of P1, replicate 1


title: wt_4h_FLA_DRIP_rep1


title: The DNA was digested with 1 U of P1, replicate 3


title: controlF2

description: 10X Genomics


title: control_C19

value: Serum Sample

value: Healthy Control


title: control_C18


title: hungryF

description: 10X Genomics


title: The DNA was digested with 1 U of P1, replicate 2


title: wt_2_DRIP_setD

value: seedlings

value: Columbia


title: control_C17


title: controlM3

description: 10X Genomics


title: controlF1

description: 10X Genomics


title: control_C16


title: wt_2_DRIP_setC


title: control_C15


title: wt_2_DRIP_setB


title: The DNA was digested with 1 U of P1, replicate 1


title: The DNA was digested with 0.1 U of P1, replicate 3


title: wt_2_DRIP_setA


title: controlM2

description: 10X Genomics


title: controlM1

description: 10X Genomics


title: The DNA was digested with 0.1 U of P1, replicate 2


title: wt_1_DRIP_setD


title: The DNA was digested with 0.1 U of P1, replicate 1


title: control_C14


title: wt_1_DRIP_setC


title: N2a cells, KDM7A-1

data_processing:
We aligned ChIP-seq reads to mm10 using bowtie2 with default parameters.
PCR duplicates were discarded then the uniquely mapped reads were acquired by picard.jar.
After indexing the bam files using SAMtools, BAM files were converted to bigwig files and normalized to RPGC using bamCoverage in deepTooLs v2.5.5.
for Kdm7a, MACS2 with board mode was applied on each replicate to call peaks with q-value < 0.1.
Then peaks of replicates were handled by the Irreproducibility Discovery Rate (IDR) with scaled IDR >290.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
DNA library generation was performed by a VAHTS Universal DNA Library Prep Kit for IlluminaV3 (Vazyme Biotech, ND607).

value: mouse neuroblasts

value: KDM7A（Abclonal A14692）


title: wt_1_DRIP_setB


title: control_C12


title: N2a cells, KDM7A Input


title: control_C11


title: The DNA was digested with 0.01 U of P1, replicate 2

value: WT


title: satedF

description: 10X Genomics


title: The DNA was digested with 0.01 U of P1, replicate 3

value: human chronic myeloid leukemia cell line


title: wt_1_DRIP_setA


title: N2a cells, H3K9me2_ChIP_Input

value: control


title: Hep3B KD, RIP-seq, YTHDF1 IP

city: xi'an

first: mengyun

last: ke

address: No 277 west yanta road

institute: the first affiliated hospital of xi'an jiaotong university

data_processing:
we used fastp (v0.20.0) to remove the adaptors，low quality bases and undetermined bases. FastQC (v0.20.0) was used to quality control checks on sequence data. We used hisat2 (2.2.0) to map reads to the reference genome with default parameters.
Peak calling results with IP and input libraries were generated by R package RIPSeeker(v1.26.0). We used HOMER (v4.11) to find motifs of the data distribution in peak regions. Called peaks were annotated by intersection with gene and transcript architecture using ChIPpeakAnno (v3.20.1).
StringTie (v2.1.1) was used to try to perform expression level for all RNAs from IP libraries by calculating FPKM ( FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)] ).
The peak quantitative differential analysis between groups was performed by DESeq (v1.38.0) and some scripts in house.
Assembly: GRCh38（hg38）
Supplementary files format and content: Excel file includes FPKM values and annotation for each Sample

extract_protocol:
Cells were washed twice with ice cold PBS, cells were homogenized in adequate volumes of polysome lysis buffer (10 mM HEPES-KOH [pH 7.0], 100 mM KCl, 5 mM MgCl2, 25 mM EDTA, 0.5% IGEPAL, 2 mM  dithiothreitol [DTT], 50 U/ml RNase OUT [Life Technologies, NY, USA], 1× complete protease inhibitor tablet [Roche]). The suspension was centrifuged at 14,000 g at 4°C for 10 min to remove debris. and then immunoprecipitated with Protein A+G Magnetic beads coupled with YTHDF1 antibody, then washed five times with NT2 buffer (50mM Tris-HCl pH 7.4，150 mM NaCl，1mM MgCl2，0.5% IGEPAL, 2 mM dithiothreitol [DTT], 50 U/ml RNase OUT [Life Technologies, NY, USA], 1× complete protease inhibitor tablet [Roche]), and treated with proteinase K. RNA was extracted using Trizol (thermo).
RNA immunoprecipitated RNA and input RNA use KAPA RNA HyperPrep Kit with RiboErase (HMR)

value: human  liver cancer cell line

value: YTHDF1 knockdown

value: Hep3B cells infected by YTHDF1 knockdown lentivirus

tag: rip antibody

value: YTHDF1-specific antibody (Abcam, ab220162)


title: The DNA was digested with 0.01 U of P1, replicate 1


title: N2a cells, H3K9me2_ChIP_shctrl-2

tag: chip antibody

value: H3K9me2（abcam ab1220）


title: The DNA was not digested with P1, replicate 3

tag: cell line


title: Hep3B KD, RIP-seq, input


title: wt_1h_FLA_DRIP_rep2


title: wt_1h_FLA_DRIP_rep1


title: N2a cells, H3K9me2_ChIP_shctrl-1


title: The DNA was not digested with P1, replicate 2


title: N2a cells, H3K9me2_ChIP_Sh12-2

value: KDM7A knockdown


title: The DNA was not digested with P1, replicate 1


title: N2a cells, KDM7A-2


title: wt_12h_FLA_DRIP_rep2


title: control_C13


title: Hep3B NC, RIP-seq, input

value: Hep3B cells infected by control lentivirus


title: wt_12h_FLA_DRIP_rep1


title: Hep3B NC, RIP-seq, YTHDF1 IP


title: Treat_N2

city: Taipei

first: Chen-Si

last: Lin

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Veterinary Medicine

country: Taiwan

institute: Nationwide Taiwan University

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1).
Genome_build: CanFam3.1

organism: Canis lupus familiaris

source_name: PBMC

growth_protocol: Canine DLBCL cell line CLBL-1 was cultured in RPMI-1640 medium (Cat. SH30027.02, HyClone™, Logan, Utah) containing 10% fetal bovine serum (Cat. 10437028 Gibco™ Thermo Fisher Scientific) and supplemented with 1% penicillin, streptomycin, and amphotericin B (Cat. CC501-0100, GeneDireX®, Taiwan) at 37°C, 5% CO2.

extract_protocol:
PBMCs were stimulated at 1 × 106 cells/ mL in 12 well-plate (PC312-0100) 37 °C and 5% CO2 in RPMI-1640 growth medium supplemented with 2500 IU/mL IL-2 (PROLEUKIN® huIL-2 (aldesleukin)) and 50 uM 2-Mercaptoethanol (Cat. M3148-25ML, Sigma-Aldrich) respectively, cultured for 14 to 20 days.
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

treatment_protocol: Seeding appropriate (according to different experimental requirements) CD8+ T cells amount after purifying in 24 well plates (in 500 uL RPMI-1640 growth medium supplemented with 2500 IU/mL IL-2 and 50 uM 2-Mercaptoethanol). Immediately, added 50/100/200 µg/mL exosomes of CLBL1 and cells were incubated for 48 hours at 37 °C with 5% CO2, and the corresponding vehicle control groups were added an equal amount of PBS.

tag: breed

value: Mix (breed)

value: 50/100/200 µg/mL exosomes of CLBL1

value: male


title: N2a cells, H3K9me2_ChIP_Sh12-1


title: Hep3B_shYTHDF1 m6A-Seq, rep2

data_processing:
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 of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: GRCh38（hg38）
Supplementary files format and content: Excel file contains peak information and FPKM.

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 50μg 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 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was 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 withE. coliDNA 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  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.


title: ddm1_2_DRIP_setC

value: seedlings


title: Control_N2

value: PBS


title: ddm1_1_DRIP_setC

value: Columbia


title: N2a cells, Shk-H3K27tri-2

data_processing:
We aligned ChIP-seq reads to mm10 using bowtie2 with default parameters.
PCR duplicates were discarded then the uniquely mapped reads were acquired by picard.jar.
After indexing the bam files using SAMtools, BAM files were converted to bigwig files and normalized to RPGC using bamCoverage in deepTooLs v2.5.5.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
CUT & Tag library generation was performed by Hyperactive Universal CUT & Tag Assay Kit for Illumina kit (Vazyme Biotech, TD903).
CUT & Tag library generation was performed by Hyperactive Universal CUT & Tag Assay Kit for Illumina kit (Vazyme Biotech, TD903).

value: mouse neuroblasts

value: H3K27me3(Active Motif 39155)


title: Treat_N1

value: female


title: N2a cells, Shk-H3K27tri-1


title: Control_N1


title: N2a cells, Shk-H3K27di-2

value: H3K27me2 (Abcam ab24684)


title: Hep3B_shYTHDF1 m6A-Seq, rep1

value: human  liver cancer cell line

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)


title: Hep3B_shcontrol m6A-Seq, rep2

value: control


title: suvh456_2_DRIP_setA

extract_protocol:
ssDRIP-seq: Nuclei were isolated from Arabidopsis plants with Honda buffer, followed by SDS/proteinase K treatment at 37°C overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases (MboI, MseI, NlaIII, DdeI); the negative control was treated with RNase H (New England Biolabs) overnight. DRIP was performed as described in Xu et al., 2017 and Sun et al., 2013. Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 ul Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55˚C. DNA was purified and sonoicated to 150 bp fragments.
pNET-seq was performed as described (Zhu et al., 2019). In brief, nuclei were extracted from 12 days old seedlings using percoll-gradient (30%-80%) and washed with 1X transcription buffer (2 M Hexylene glycol. 20mM PIPES-KOH [PH 7], 10mM MgCl2, 5mM β-mercaptoethanol) and 1x nuclei storage buffer (50mM Tris-HCL [PH7.2], 5mM mgCl2, 5mM KCl, 1mM MnCl2, 5mM DTT, 50% glycerol), respectively. After that nuclei were resuspended in 1x reaction buffer (1mM ATP, 1mM GTP, 1mM CTP, 1mM Br-UTP, 4U RNasin, 1% sarcosyl) and incubated at 30C for 5 minutes. The reaction was stopped with TRIzol and nuclear RNA was precipitated with 1/10 vol 5M NH4AC, 3 vol Ethanol and 1μl GlycoBlue. RNA was then treated with 5μl 1M NaOH for 40min on ice, and the reaction was stopped with 25μl 1M Tris-HCl pH7.0. After RNA purification with Bio-spin 30 Column (Cat. #732-6250/6251) and DNase treatment with RQ1 RNase-free DNase (Promega), RNA de-phosphorylation was performed with antarctic phosphatase (NEB, B0289S), and incubated with pre-blocked Anti-BrdU argarose beads (Santa Cruz Biotech) and the reaction mixture was rotated for 1 hr at 4C. Beads were then was with Low salt (0.2x SSPE, 1mM EDTA, 0.05% tween-20), high salt (0.5x SSPE, 1mM EDTA, 0.05% tween-20, 150mM NaCl) and TET buffers (10mM Tris-HCL [PH 8], 0.1mM EDTA, 0.05% Tween-20), respectively. RNA was then eluted from beads with elution buffer (20mM DTT, 300mM NaCl, 5mM Tris [PH 7.5], 1mM EDTA, 0.10% SDS), and precipitated with 1/10 vol 5M NH4AC, 3 vol Ethanol and 1μl GlycoBlue. RNA was then end-repaired with T4 PNK (NEB, M0201L) and RNAsin Plus (Promega, N2611) and precipitated with 1/10 vol 5M NH4AC, 3 vol Ethanol and 1μl GlycoBlue. Ploy A tail was added to end-repaired DNA with poly-A polymerase (NEB, B0276S), and reverse transcription was performed with SSIII reverse transcriptase (Invitrogen). After that extra RT-primers and RNA were cleaned, cDNA was size selected (more than 120 bp) with page gel. Size selected cDNA was circularized with CircLigase (Epicentre) and relinearized with 4× relinearization supplement (100mM KCl, 2mM DTT) and Ape I (NEB, M0282S). Then relinearized DNA was run on page gel, and precipitated with 1/10 vol 5M NH4AC, 3 vol Ethanol and 1μl GlycoBlue. Size selected cDNA was finally amplified with 2x Kapa HiFi mixture (KK2602), using universal forward primer F and reverse index primer R. The amplified libraries were size selected, purified and precipitated with page gel.
ChIP-seq: To gain the nucleosome resolution, native native H3K9me2, H3K27me1, H2A.W-FLAG, H2A.Z ChIP without crosslink and sonication was performed as described in (Bernatavichute et al., 2008), with some modifications. In brief, nuclei were extracted from 12 days old seedlings with Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextran T40, 20 mM HEPES–KOH [pH 7.4], 10 mM MgCl2, 0.5% Triton X-100, 5 mM DTT, and protease inhibitors [Roche]). Nuclei were suspended in 1X MNAse buffer (50mM TriHCl pH 7.6, 5mM CaCl2, 0.1mM PMSF) containing 1X proteinase inhibitor cocktail (Roche). After RNase A (Thermo Scientific™) treatment at 37C for 30 minutes, chromatin was digested with MNase enzyme (NEB) for 6 minutes and the reaction was stopped with EDTA (10mM). Then, the nucleosomes were released with the addition of 0.005% SDS while rotating at 4C for 2-3 hours. After that the supernatant was separated and diluted with dilution buffer (0.1% triton, 50mM NaCl, 0.1mM PMSF, 17mM trisHCl, 3.33mM EDTA, 1x Cocktail inhibitor). Chromatin was pre-cleaned with Protein G beads, and immnoprecipitated with anti-H3K9me2 (Millipore),anti-H3K27me1 (Millipore), anti-FLAG (Sigma) and anti-H2A.Z antibodies at 4C overnight. The complexes were incubated with protein G beads (Millipore) at 4C for 3 hours with rotation, and washed three times with ChIP wash buffer having different concentration of NaCl in each wash (50mM TrisHCl pH 7.6, 10mM EDTA, 50/100/150 mM NaCl, 0.1mM PMSF, and 1x Cocktail inhibitor). Then DNA was eluted with elution buffer (0.1%SDS and 0.1M NaHCO3) at 65C for 15 minutes. Proteinase K treatment was performed at 55 C for 2 hour. DNA was recovered after phenol:chloroform extraction.
ssDRIP-seq: DRIPed DNA was conducted to library construction using the VAHTS ssDNA Library Prep Kit (Vazyme, ND620). Bisulphite-seq: to use EpiArt DNA Methylation Library Kit for Illumina V3 (Vazyme, NE103) for library construction. ChIP-seq: ChIPed DNA was conducted to library construction using the TruePrep DNA Library Prep Kit V2 (Vazyme, TD502). pNET-seq:  NEXTflex TM small RNA-Seq Kit V3 was used to construct the libraries.


title: suvh456_1_DRIP_setA


title: N2a cells, Shk-H3K27di-1


title: Hep3B_shcontrol m6A-Seq, rep1


title: Hep3B_shYTHDF1 m6A-Seq input, rep2

value: YTHDF1 knockdown

value: Hep3B cells infected by YTHDF1 knockdown lentivirus


title: smc4_2_DRIP_setB


title: N2a cells, Shk-H3K27ac-2

value: H3K27ac (Active Motif 39133)


title: N2a cells, Shk-H3K27ac-1


title: N2a cells, Shk-H3K9tri-2

value: H3K9me3(Abcam ab8898)


title: Colonic epithelial cells, Organoid culture, replica 1

city: Lausanne

last: Lutolf

address: Route Cantonale

country: Switzerland

institute: EPFL

data_processing:
Alignment with STAR version 2.7.0e
Default parameters except peOverlapNbasesMin=12, peOverlapMMp=0.1, quantMode=geneCounts
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts

source_name: Colonic epithelium

extract_protocol:
Rneasy Micro Kit (Qiagen)
QuantSeq 3' mRNA-Seq Library Prep Kit FWD

value: Colonic epithelium


title: Colonic epithelial cells, Organoid culture, replica 2


title: Colonic epithelial cells, Transgel culture, replica 3


title: rdr2_2_DRIP_setC


title: Hep3B_shYTHDF1 m6A-Seq input, rep1


title: Hep3B_shcontrol m6A-Seq input, rep2

value: Hep3B cells infected by control lentivirus


title: rdr2_1_DRIP_setC


title: Hep3B_shcontrol m6A-Seq input, rep1


title: N2a cells, Shk-H3K9tri-1


title: Colonic epithelial cells, Organoid culture, replica 3


title: N2a cells, Shk-H3K4tri-2

value: H3K4me3(Abclonal A2357)


title: Hep3B_shYTHDF1 rna seq, rep2

data_processing:
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 of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of RNA libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: GRCh38（hg38）
Supplementary files format and content: Excel file includes FPKM values and annotation for each Sample


title: nrpe1_1_DRIP_setA

value: seedlings


title: N2a cells, Shk-H3K4tri-1


title: Colonic epithelial cells, Transgel culture, replica 1


title: smc4_1_DRIP_setB


title: nrpd1_2_DRIP_setC


title: Hep3B_shcontrol rna seq, rep2


title: Colonic epithelial cells, freshly extracted, replica 2


title: Hep3B_shcontrol rna seq, rep1


title: N2a cells, Shc-H3K27tri-2


title: nrpd1_1_DRIP_setC


title: nrpb2_2_DRIP_setA


title: N2a cells, Shc-H3K27tri-1


title: COH2.CFZ3

city: Duarte

middle: David

last: Warden

state: CA

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

institute: City of Hope

description: RNA-Seq data, COH2 Cell Line, Carfilzomib Treatment, replicate 3

data_processing:
Real Time Analysis (RTA, v1.18.64) was used for base calling, and bcl2fastq v2.18 was used to generate FASTQ files
Reads aligned using STAR (version 2.5), with --twopassMode Basic --outSAMstrandField intronMotif
Unique reads quantified using htseq-count (version 0.9.1), with database generated from TxDb.Hsapiens.UCSC.hg38.knownGene (Bioconductor annotations, downloaded 8/30/2018).
Assembly: hg38
Supplementary files format and content: FPKM normalized expression (using aligned reads and TxDb annotations in R) and read counts (calculated using htseq-count)

growth_protocol: Primary cells were cultured in a specialized medium without serum at 37oC, 5% CO2 and hypoxic condition (5% oxygen).

extract_protocol:
The RNA was extracted from 1 million cells using the RNeasy micro kit from Qiagen.
KAPA Stranded RNA-Seq Kit

treatment_protocol: The cells were IC50 concentration of drugs for 6h and harvested for RNA extraction sequencing and analysis

value: Carfilzomib

tag: processing batch


title: N2a cells, Shc-H3K27di-2


title: COH2.CFZ2

description: RNA-Seq data, COH2 Cell Line, Carfilzomib Treatment, replicate 2


title: Caecal epithelial cells, Organoid culture, replica 3

source_name: Caecal epithelium

value: Caecal epithelium


title: nrpb2_1_DRIP_setA

city: Beijing

value: Columbia


title: Colonic epithelial cells, Transgel culture, replica 2


title: Caecal epithelial cells, Organoid culture, replica 2


title: nrpe1_2_DRIP_setA


title: morc6_2_DRIP_setB


title: COH2.CFZ1

description: RNA-Seq data, COH2 Cell Line, Carfilzomib Treatment, replicate 1


title: N2a cells, Shc-H3K27di-1

value: mouse neuroblasts


title: Hep3B_shYTHDF1 rna seq, rep1


title: Caecal epithelial cells, Organoid culture, replica 1


title: Colonic epithelial cells, freshly extracted, replica 3


title: COH2.Act3

description: RNA-Seq data, COH2 Cell Line, Actinomycin D Treatment, replicate 3

value: Actinomycin D


title: morc6_1_DRIP_setB


title: COH2.Act2

description: RNA-Seq data, COH2 Cell Line, Actinomycin D Treatment, replicate 2


title: mom1_2_DRIP_setB


title: COH2.Act1

description: RNA-Seq data, COH2 Cell Line, Actinomycin D Treatment, replicate 1


title: Colonic epithelial cells, freshly extracted, replica 1


title: mom1_1_DRIP_setB


title: Caecal epithelial cells, Transgel culture, replica 3


title: Caecal epithelial cells, Transgel culture, replica 1


title: N2a cells, Shc-H3K9tri-2


title: N2a cells, Shc-H3K27ac-1


title: CM_pi_1D-3

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

institute: Gyeongsang National University

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of read count for each sample

source_name: Leaves

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

value: Leaves

value: WT

tag: timepoint


title: COH2.Cntrl3

description: RNA-Seq data, COH2 Cell Line, Control Treatment, replicate 3

value: Control


title: COH2.Cntrl2

description: RNA-Seq data, COH2 Cell Line, Control Treatment, replicate 2


title: hta6712_2_DRIP_setD


title: Caecal epithelial cells, freshly extracted, replica 3


title: N2a cells, Shc-H3K4tri-2


title: hta6712_1_DRIP_setD


title: Caecal epithelial cells, Transgel culture, replica 2


title: Caecal epithelial cells, freshly extracted, replica 2


title: N2a cells, Shc-H3K27ac-2


title: drm12_2_DRIP_setC


title: N2a cells, Shc-H3K4tri-1


title: COH2.Cntrl1

description: RNA-Seq data, COH2 Cell Line, Control Treatment, replicate 1


title: N2a cells, Shc-H3K9tri-1


title: Caecal epithelial cells, freshly extracted, replica 1


title: N2a cells, R-negative


title: drm12_1_DRIP_setC


title: Small intestinal epithelial cells, Organoid culture, replica 3

source_name: Small intestinal epithelium

value: Small intestinal epithelium


title: SBC5.CFZ2

description: RNA-Seq data, SBC5 Cell Line, Carfilzomib Treatment, replicate 2


title: drd1_2_DRIP_setC


title: SBC5.CFZ3

description: RNA-Seq data, SBC5 Cell Line, Carfilzomib Treatment, replicate 3


title: SBC5.CFZ1

description: RNA-Seq data, SBC5 Cell Line, Carfilzomib Treatment, replicate 1


title: SBC5.Act3

description: RNA-Seq data, SBC5 Cell Line, Actinomycin D Treatment, replicate 3


title: Small intestinal epithelial cells, Organoid culture, replica 2


title: Small intestinal epithelial cells, Organoid culture, replica 1


title: ddm1_DMSO_DRIP_rep2


title: Mouse, Heart, input, 17_3500,  vl0142

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

institute: Queen Mary University of London

data_processing:
ChIP-seq peak files were generated my MACS2 callPeak function (default parameters).
4C data was processed with pipe4C (Krijger et al. 2020)
Supplementary files format and content: MACS2 peak files for each ChIP and input combination (.narrowPeak extension)
Supplementary files format and content: 4C wig files for each 4C experiment

source_name: Heart

extract_protocol:
Tissues were prepared by direct perfusion of the liver with PBS, followed by dicing the whole organs (liver and heart) in small pieces around 1cm3. Blood clots within the heart ventricles were removed. Cross-linking of the diced tissue was performed in 1% formaldehyde solution for 20 min, addition of 250 mM glycine and incubation for a further 10 min to neutralize the formaldehyde. After homogenization of cross-linked tissues in a dounce tissue grinder, samples were washed twice with PBS and lysed according to published protocols (SCHMIDT et al. 2009 for ChIP and Krijger et al. 2020 for 4C) to solubilize DNA-protein complexes. For ChIP, chromatin was fragmented to 300 bp average size by sonication on a Misonix sonicator 3000 with a 418 tip (1/16 inch diameter). Chromatin from 50-200 mg of dounced tissue was used for each ChIP experiment using antibodies against H3K4me3 (millipore 05-1339), H3K27ac (abcam ab4729), H3K4me1 (abcam ab8895), TBX5 (Insight bio sc-515536), RXRA (sc-553), FOXA1 (ab70382), HNF4A (ARP31946), CEBPA (sc-9314) and HNF6 (sc-13050). For 4C, locus-specific 4C templates were made using two rounds of enzyme digestion (primary and secondary) and ligation. Purified 4C templates were amplified by inverse PCR with bait-specific primers.
Illumina sequencing libraries were prepared from ChIP-enriched or 4C-enriched DNA using ThruPLEX DNA-seq library preparation kit (Takara Bio) or NEBNext Ultra II DNA Library Prep Kit for Illumina with up to 10ng of input DNA and 8-15 PCR cycles. After PCR, libraries were pooled in equimolar concentrations and sequenced on Illumina HiSeq 4000, NextSeq 500 or NovaSeq 6000 instruments.
ChIP-Seq, 4C-Seq

treatment_protocol: We performed chromatin immunoprecipitation experiments followed by high throughput sequencing (ChIP-seq) or 4C-seq using liver and heart tissue samples isolated from naked mole-rat, Damaraland mole-rat, guinea pig and mouse. At least two independent biological replicates from different animals were performed for each species and antibody. Wherever possible, tissues from young adult males were used. Tissues were prepared immediately post-mortem (typically within an hour) to maximize experimental quality. Post-mortem tissues were kept on ice until processed to minimize potential loss of protein-DNA interactions during post-mortem time. Sample allocations to experimental batches were randomised to ensure unbiased distributions of species, tissue, individual and sex, using the R/Bioconductor package OSAT (YAN et al. 2012).

value: Heart

value: wild-type

tag: developmental stage

value: adult

tag: age (months)

value: male

tag: individual

value: input


title: Mouse, Heart, input, 17_3499,  vl0159

tag: strain

tag: antibody


title: SBC5.Act2

description: RNA-Seq data, SBC5 Cell Line, Actinomycin D Treatment, replicate 2


title: drd1_1_DRIP_setC

institute: Tsinghua University

source_name: seedlings

tag: ecotype


title: Mouse, Heart, input, 17_3498,  vl0141

tag: tissue


title: SBC5.Act1

description: RNA-Seq data, SBC5 Cell Line, Actinomycin D Treatment, replicate 1


title: Mouse, Heart, H3K4me1, 17_3501,  vl0162

tag: genotype


title: ddm1_4h_FLA_DRIP_rep2


title: ddm1_DMSO_DRIP_rep1


title: Mouse, Heart, H3K4me1, 17_3498,  vl0081


title: SBC5.Cntrl3

description: RNA-Seq data, SBC5 Cell Line, Control Treatment, replicate 3

tag: treatment


title: Small intestinal epithelial cells, Transgel culture, replica 3


title: ddm1_4h_FLA_DRIP_rep1


title: Mouse, Heart, H3K4me1, 17_3500,  vl0203

tag: Sex


title: Small intestinal epithelial cells, Transgel culture, replica 2


title: Small intestinal epithelial cells, Transgel culture, replica 1


title: Small intestinal epithelial cells, freshly extracted, replica 3


title: aHepGHRkd_STAT5bCA _replicate6_D23

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

data_processing:
RNA-seq data was processed using a custom pipeline, as described in Connerney et al., 2017 (PMID: 28323953)
Sequence reads were mapped to the mouse genome (mm9) using STAR aligner.
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for a total of 75,798 genes, including RefSeq genes and lncRNA genes defined in: Goldfarb CN et al, Endocrinology (2022) PMID: 35512247. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene.
Differential expression analysis was performed with edgeR as described in Robinson et al., 2010 (PMID: 19910308)
Assembly: mm9
Supplementary files format and content: Microsoft Excel file containing normalized read counts and differential expression results for a set of 75,798 mouse mm9 genes comprised of the following: n = 20,884 RefSeq protein coding genes, n=48,360 mouse liver-expressed lncRNAs genes, n=2,061 RefSeq non-coding genes (NR accession numbers) that do not overlap with the set of 48,360 lncRNAs, n =4,490 Ensembl non-coding lncRNAs that do not overlap either the RefSeq NR gene set or the 48,360 lncRNA gene set, and n=3 other lncRNAs with interesting liver functions (lnc-LFAR1, LeXis, Lnclgr). Further details about these genes are provided in the annotation fields of the processed data file and in Goldfarb CN et al, Endocrinology (2022) PMID: 35512247.

source_name: liver

growth_protocol: All Ghrfl/fl mice were housed in a specific pathogen-free barrier facility maintained at 22-24C with a 12h light/12h dark cycle and were fed standard chow diet.

extract_protocol:
Livers were weighed and snap-frozen in liquid nitrogen and stored at -80C.  Total RNA from livers (6 mice/group), from GHR-intact controls, aHepGHRkd, aHepGHRkd+rIGF1 and aHepGHRkd+STAT5bCA mice were extracted using Rneasy Plus Mini Kit (Cat# 74134; Qiagen). Total RNA was quality checked (RIN>7) using the Agilent Bioanalyser 2100 system.
polyA-seelcted RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: aHepGHRkd were generated by treating 10-12 week-old male and female Ghrfl/fl littermates with a single lateral tail vein injection of 1.5*E11 genome copies (GC) of an adeno-associated virus serotype 8 (AAV8) vector bearing a hepatocyte-specific thyroxine-binding globulin promoter (TBGp) driving a Cre recombinase transgene [AAV8-TBGp-Cre; AAV.TBG.PI.Cre.rBG (AAV8), Addgene, Watertown, MA, diluted in 100ul sterile PBS)]. To maintain hepatocyte IGF1 expression in aHepGHRkd, a subset of mice were co-injected with AAV8-TBGp-Cre (1.5*E11 GC) + AAV8-TBGp-rIGF1 (2.0*E11 GC; AAV8.TBG.PI.ratIGF1.WPRE.bGH). In a subset of mice, a constitutively active STAT5b (STAT5bCA) was used to sustain STAT5b activity in aHepGHRkd, by co-injecting with AAV8-TBGp-Cre (1.5*E11 GC) + AAV8-TBGp-STAT5bCA (0.75*E11 GC; AV8.TBG.PI.N-FLAG-mSTAT5bCA.WPRE.bGH). Injection of an AAV8-TBGp-Null (pAAV8.TBG.PI.Null.bGH, Addgene) was used to generate control mice and to equalize the total amount of AAV8 injected in each mouse across groups (3.5*E11 GC).

tag: group

tag: replicate

value: liver

tag: cell type

value: Hepatocyte

value: Male

value: GHRfl/fl

tag: age

value: 10-12 weeks-old

tag: time point

value: 7 days after AAV-injection

tag: diet

value: Chow diet


title: SBC5.Cntrl2

description: RNA-Seq data, SBC5 Cell Line, Control Treatment, replicate 2

tag: cell line

tag: processing batch


title: ddm1_2_DRIP_setA

address: Tsinghua Yuan

value: seedlings

value: Columbia


title: Small intestinal epithelial cells, freshly extracted, replica 2


title: aHepGHRkd_STAT5bCA _replicate5_D20


title: ddm1_1_DRIP_setA


title: SBC5.Cntrl1

description: RNA-Seq data, SBC5 Cell Line, Control Treatment, replicate 1


title: aHepGHRkd_STAT5bCA _replicate4_D14


title: Small intestinal epithelial cells, freshly extracted, replica 1


title: H520.CFZ3

description: RNA-Seq data, H520 Cell Line, Carfilzomib Treatment, replicate 3

value: Carfilzomib


title: ddm1_1h_FLA_DRIP_rep2


title: H520.CFZ2

description: RNA-Seq data, H520 Cell Line, Carfilzomib Treatment, replicate 2


title: Antral epithelial cells, Organoid culture, replica 3

source_name: Antral epithelium

value: Antral epithelium


title: H520.CFZ1

description: RNA-Seq data, H520 Cell Line, Carfilzomib Treatment, replicate 1


title: Antral epithelial cells, Organoid culture, replica 2


title: aHepGHRkd_STAT5bCA _replicate3_D12


title: aHepGHRkd_STAT5bCA _replicate2_D7


title: H520.Act3

description: RNA-Seq data, H520 Cell Line, Actinomycin D Treatment, replicate 3

value: Actinomycin D


title: Antral epithelial cells, Transgel culture, Air-Liquid Interface, replica 5


title: Antral epithelial cells, Transgel culture, Air-Liquid Interface, replica 4


title: ddm1_12h_FLA_DRIP_rep2


title: ddm1_12h_FLA_DRIP_rep1


title: aHepGHRkd_rIGF1 _replicate6_D22


title: H520.Act2

description: RNA-Seq data, H520 Cell Line, Actinomycin D Treatment, replicate 2


title: aHepGHRkd_STAT5bCA _replicate1_D3


title: aHepGHRkd_rIGF1 _replicate5_D17


title: Antral epithelial cells, Transgel culture, Air-Liquid Interface, replica 3


title: H520.Act1

description: RNA-Seq data, H520 Cell Line, Actinomycin D Treatment, replicate 1


title: ddm1-1-H


title: dcl234_2_DRIP_setC


title: H520.Cntrl3

description: RNA-Seq data, H520 Cell Line, Control Treatment, replicate 3

value: Control


title: ddm1_1h_FLA_DRIP_rep1


title: dcl234_1_DRIP_setC


title: Antral epithelial cells, Transgel culture, Air-Liquid Interface, replica 2


title: H520.Cntrl2

description: RNA-Seq data, H520 Cell Line, Control Treatment, replicate 2


title: aHepGHRkd_rIGF1 _replicate2_D6


title: Antral epithelial cells, Transgel culture, Air-Liquid Interface, replica 1


title: aHepGHRkd_rIGF1 _replicate3_D8


title: Antral epithelial cells, Organoid culture, replica 1


title: atxr56_1_DRIP_setA


title: atxr56_2_DRIP_setA


title: ago4_2_DRIP_setA


title: Antral epithelial cells, Transgel culture, replica 5


title: S26 cell line, siSRSR3-2

city: Guangzhou

first: Jin-Xin

last: Bei

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District, Guanzhou, P.R. China

institute: Sun Yat-sen University Cancer Center

data_processing:
Paired-end sequencing reads were subjected to quality trimming using the software tool TrimGalore (version 0.6.1) with the following parameters: -q 20 --phred33 --stringency 3 --length 50 -e 0.1. Reads mapping to ribosomal RNA (rRNA) are removed. The remaining reads was aligned to the hg38 human reference genome and the EBV genome using STAR (version 2.7.5b) followed by quantification of gene expression levels using RSEM (version 1.3.3) to generate the gene expression matrix.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each sample

source_name: nasopharyngeal carcinoma

extract_protocol:
RNA was harvested using trizol (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq RNA Library Preparation Kits following manufacturer's protocols.

treatment_protocol: Total RNA were extracted with S26 cells, which were transfected with siRNAs against SRSF3 or control siRNA.

value: nasopharyngeal carcinoma

value: tumor cell

value: SRSR3 knockdown 1


title: Antral epithelial cells, Transgel culture, replica 4


title: aHepGHRkd_rIGF1 _replicate1_D5


title: ago4_1_DRIP_setA

first: Jincong

last: Zhou


title: S26 cell line, siSRSR3-1


title: Antral epithelial cells, Transgel culture, replica 3

first: Matthias


title: adcp1_2_DRIP_setD


title: aHepGHRkd _replicate5_D16

value: aHepGHRkd


title: S26 cell line, siNC

value: negative control


title: aHepGHRkd_rIGF1 _replicate4_D11

value: liver

value: Hepatocyte


title: Antral epithelial cells, Transgel culture, replica 2


title: Antral epithelial cells, Transgel culture, replica 1


title: aHepGHRkd _replicate3_D13

value: Male

value: GHRfl/fl


title: miR-34abc-KO_5FU_3

city: Munich

first: Markus

last: Kaller

address: Thalkirchner Str. 36

institute: LMU Munich

data_processing:
alignment : RNA-Seq FASTQ files were processed using the RNA-Seq module implemented in the CLC Genomics Workbench v20.0.2 software (Qiagen Bioinformatics) and mapped to the GRCh38/hg38 human reference genome and its associated gene and transcript annotation (ENSEMBL) using the settings mismatch cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8
expression : RNA-Seq FASTQ files were processed using the RNA-Seq module implemented in the CLC Genomics Workbench v20.0.2 software (Qiagen Bioinformatics) and mapped to the GRCh38/hg38 human reference genome and its associated gene and transcript annotation (ENSEMBL) using the settings mismatch cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for each sample

growth_protocol: The human colorectal cancer cell line HCT116 and its derivatives generated here were grown in McCoy’ 5A medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Invitrogen), 100 units/ml penicillin and 0.1 mg/ml streptomycin

extract_protocol:
Total RNA from HCT116 cells was isolated using the High Pure RNA Isolation Kit (Roche) with an on-column DNase digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon


title: adcp1_1_DRIP_setD


title: miR-34abc-KO_5FU_2


title: aHepGHRkd _replicate4_D15

value: 10-12 weeks-old

value: 7 days after AAV-injection

value: Chow diet