title: SW620, H3K4me2, rep1

value: Colon adenocarcinoma


title: Patient R1, BMMCs, HR_MDS, Responder, Pre-AZA

status: Public on Aug 05 2026

type: SRA

city: Patras

first: Argyro

last: Sgourou

address: Parodos Aristotelous 18

country: Greece

institute: Hellenic Open University

description: Library name: PA8066A_S3_L001_R1_001

library_source: transcriptomic

data_processing:
Quality control using FastQC.
Unique Molecular Identifiers using UMI-tools
Adapter trimming using Cutadapt.
Alignment to mirBase using BWA.
Assembly: Hg38
Supplementary files format and content: csv comma-delimited containg raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: BMMCs

extract_protocol:
Total RNA including microRNA species was purified from the HR-MDS patient BMMCs, pre- and post-AZA treatment. RNA quality and integrity was assessed using the QIAxcel RNA QC Kit v2.0 (Qiagen, 929104) on the QIAxcel® Advanced System following the manufacturer’s instructions. All RNA samples showed high Integrity Scores (RIS), ranging from 8.5 to 9.5, except for sample R4 pre-AZA treatment (low RIS<4.5).
Libraries were constructed (QIAseq miRNA library kit, QIAGEN GmbH, Hilden, Germany) and RNA sequencing reactions were performed in Illumina iSeq 100 instrument (Illumina, Inc., US).

tag: tissue

value: BMMCs

tag: treatment

value: Pre-AZA

tag: batch


title: 1525-2 DOX+ MAK rep2

city: Boston

first: Yixiang

last: Li

address: 450 Brookline Ave

country: USA

institute: Dana-Farber Cancer Institute

description: Library name: 1525-2_DOX+MAK_rep2

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: LUAD cell line

growth_protocol: 1525-2, 1533, 1544-2 cell lines were cultured with RPMI-1640 with 10% FBS, 100 U/mL of penicillin, and 100 μg/mL of streptomycin and 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Quick-RNA™ Miniprep kit (Cat # R1055, Zymo Research, CA, USA) including a DNase digestion step according to the manufacturer’s instructions and RNA sequencing was performed.
Poly-A mRNA capture and reverse transcription for cDNA synthesis: oligo-dT primer to capture just the mRNA (contains sample barcode, UMI, and Read 1 sequences). Second strand synthesis and tagmentation: double stranded-cDNA is generated. Tagmentation creates fragments and incorporates Read 2 sequence. Illumina library amplification: adds unique dual indices (UDI = i5, i7) and P5/P7 sequences.

treatment_protocol: In corresponding treatment group, cells were treated with doxycyclin at 1ug/ml and MAK-683 at 2 uM for 6 days.

tag: cell line

value: LUAD cell line

tag: cell type

value: LUAD

tag: genotype

value: DOX+ MAK


title: GeoMx-DSP-1001660010639-D-D09

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: Library name: GeoMx-DSP-1001660010639-D-D09

data_processing:
The samples were sequenced on an Illumina NextSeq 2000 P3 instrument at PE50. Sequencing depth was calculated based on a total area of 9,002,857 μm2 and 900 million read pairs determined from the GeoMx GeoMx-DSP generated Lab Worksheet.
Sequencing-generated FASTQ files were processed using the NanoString GeoMx NGS pipeline to generate DCC files used in downstream data analysis.
Assembly: mm10
Supplementary files format and content: GeoMx_sample_metadata.csv includes the samples metadata
Supplementary files format and content: vwf+_VWF+_DE_analysis.xlsx Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: cd68+_CD68+_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: ela2+_ELA+_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: else_ELSE_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Library strategy: Spatial Transcriptomics

source_name: liver

growth_protocol: human liver FFPE

extract_protocol:
Fresh tissues from surgery were processed for FFPE embedding, 5um section were cut.
Slides were flourensently labeled with  endothelial cell marker Von Willebrand Factor (VWF), macrophage and monocyte marker CD68, and neutrophil marker Elastase (ELA2). Regions of interest (ROIs) were manually draw based on their zonal location within the liver lobule: periportal zone 1, midzonal zone 2, and pericentral zone 3. Each ROI consisted of four segments: segment 4 for VWF+ area, segment 1 for CD68+ area, segment 2 for ELA2+ area, and segment 3 was called ‘else’ to refer to non-stained areas within the ROI. Photo-cleaved oligonucleotide tags were collected from 377 AOI. PCR amplification and liabrary pprepareation were done using GeoMx Human Whole Transcriptome Atlas (WTA) accorrding to manufacture's instruction.

treatment_protocol: 3 patients with normal, 3 patients with steatosis and 4 patients with MASH

value: liver

tag: condition

tag: segment

tag: zone


title: Patient R2, BMMCs, HR_MDS, Responder, Post-AZA

description: Library name: ZB8459C_S5_L001_R1_001

value: Post-AZA


title: GeoMx-DSP-1001660010639-D-D06

description: Library name: GeoMx-DSP-1001660010639-D-D06


title: 1525-2 DOX+ DMSO rep2

description: Library name: 1525-2_DOX+DMSO_rep2

value: DOX+ DMSO


title: HL-60, H3K4me2, rep1

city: Shenzhen

first: Changbin

last: Sun

address: Dapeng

department: Agricultural Genomics Institute at Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: genomic

data_processing:
Sequencing reads from mChIP-seq were demultiplexed to samples by the barcodes in the 5’ end of Read2 using fastq-multx (version 1.4.2) (https://github.com/brwnj/fastq-multx) with a mismatch setting of 0. Then, reads of each sample with adapter contamination and low quality were trimmed and filtered using fastp with parameters as -f 10 -t 5 -F 30 -T 5 --complexity_threshold=30 –n_base_limit=5  --length_required 60 (version 0.23.2) and aligned to the human reference genomes hg38, mouse reference genome mm10, or budding yeast genome sacCer3 using bowtie2 (version 2.2.5) with default parameters. Uniquely mapping reads with mapping quality more than 30 were kept using samtools (version 1.9) and duplicates were removed using picard MarkDuplicates (v2.26.10, http://broadinstitute.github.io/picard).
Assembly: BW25113 genome for E. coli, sacCer3 genome for yeast, GRCh38 genome for humans, mm10 genome for mice
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched by glycine with 0.125 M final concentration. sonicated using Covaris SE220 (75 W, 20% Duty factor, 1,000 cycles per burst) for 5 min at 4°C to obtain fragments with the peak size around 200 bp.
The tailing and ssDNA ligation method used to label sample chromatin, and then multiple barcoded samples were pooled and split for immunoprecipitation with relevant antibodies as standard ChIP-seq. After immunoprecipitation, the purified ChIPed DNA was resuspended in 18 µl of water and extended in an 40 µl reaction containing 1 × KAPA HiFi HotStart ReadyMix and 0.25 µM P7TruSeqHTRev at 98 for 30 sec and 63 °C for 5 min followed by purification with 1.2 × volume of SPRIselect™ beads. Then, the purified DNA was ligated to the second adapter in a 40 µl reaction (1× T4 DNA ligase buffer, 0.5 µM P5TruSeqHT/P5SPlint mixture (1:1), and 10 Weiss units of T4 DNA ligase) at 25 °C for 30 minutes and purified with 1.0 × volume of SPRIselect™ beads. Lastly, library was amplified in 50 μl of PCR reaction Mix containing eluted DNA, 0.5 μM of P5 index primer, 0.5 μM P7 index primers, and 25 μl of KAPA HiFi HotStart ReadyMix (2 ×) (Kapa Biosystems) for 12-16 cycles (each cycle with 20 s at 98°C, 30 s at 58°C, 1 min at 68°C). DNA of 200–700 bp was isolated using a double SPRIselect bead cleanup (0.6 × and 0.85 × volume).

value: Adult acute myeloid leukemia

tag: chip antibody


title: 1525-2 DOX- MAK rep1

description: Library name: 1525-2_DOX-MAK_rep1

value: MAK


title: Patient NR2, BMMCs, HR_MDS, Non-Responder, Post-AZA

description: Library name: PM7551B_S1_L001_R1_001


title: GeoMx-DSP-1001660010639-D-C10

description: Library name: GeoMx-DSP-1001660010639-D-C10


title: NCI-H226, H3K4me2, rep1

value: Pleural epithelioid mesothelioma


title: Patient NR3, BMMCs, HR_MDS, Non-Responder, Post-AZA

description: Library name: DN8485B_S3_L001_R1_001


title: 1525-2 DOX+ MAK rep1

description: Library name: 1525-2_DOX+MAK_rep1


title: GeoMx-DSP-1001660010639-D-C06

description: Library name: GeoMx-DSP-1001660010639-D-C06


title: GeoMx-DSP-1001660010639-D-C02

description: Library name: GeoMx-DSP-1001660010639-D-C02


title: 1525-2 DOX+ DMSO rep1

description: Library name: 1525-2_DOX+DMSO_rep1


title: OVCAR-8, H3K4me2, rep1

value: High grade ovarian serous adenocarcinoma


title: Testis tissue, Sb₂O₃ high-dose group mouse, replicate 3

city: xuzhou

first: zhao

middle: yi

last: wei

state: jiangsu

address: No. 209, Tongshan Road, Xuzhou City, Jiangsu Province

institute: Xuzhou Medical University

description: Library name: con_3

data_processing:
Raw reads were filtered and quality-controlled using fastp to remove adapter sequences, low-quality bases, ambiguous N-containing reads and short reads below 20 bp. Clean reads were mapped to mouse reference genome using HISAT2. Gene expression levels were quantified by RSEM, and differential expression analysis was performed by DESeq2. Genes with |log₂FC| ≥1 and FDR < 0.05 were defined as differentially expressed genes. GO and KEGG enrichment analyses were performed using Goatools and Python scipy package respectively, with corrected P-value < 0.05 as the threshold of significant enrichment.
Assembly: Mouse reference genome assembly GRCm39 (NCBI GCF_000001635.27)
Supplementary files format and content: Processed data contained gene expression matrix with raw counts and TPM values, as well as differentially expressed gene lists annotated with log₂FC, FDR and functional information.

source_name: testis

extract_protocol:
Total RNA was extracted from mouse testis tissues using TRIzol Reagent according to the manufacturer’s instructions. RNA quality and integrity were detected by NanoDrop 2000 and agarose gel electrophoresis, and RNA integrity was evaluated using Agilent 5300 Bioanalyser. Only RNA samples with concentration ≥20 ng/μL, total RNA >1 μg and RQN >4.5 were used for subsequent library construction.
RNA-seq libraries were constructed following Illumina® Stranded mRNA Prep, Ligation protocol at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. Briefly, poly(A) mRNA was enriched by oligo(dT) magnetic beads and fragmented into about 300 bp fragments. First-strand and second-strand cDNA were synthesized sequentially, followed by end repair, A-tailing and adapter ligation. Target fragments were selected and amplified by PCR. Qualified libraries were quantified by Qubit 4.0 and sequenced on NovaSeq X Plus platform with PE150 mode.

value: testis

value: testicular tissue


title: GeoMx-DSP-1001660010639-D-B07

description: Library name: GeoMx-DSP-1001660010639-D-B07


title: NCI-H23, H3K4me2, rep1

value: Lung adenocarcinoma


title: Patient NR4, BMMCs, HR_MDS, Non-Responder, Post-AZA

description: Library name: NA8599B_S4_L001_R1_001


title: Testis tissue, Sb₂O₃ high-dose group mouse, replicate 2

description: Library name: con_2


title: GeoMx-DSP-1001660010639-D-B04

description: Library name: GeoMx-DSP-1001660010639-D-B04


title: Testis tissue, Sb₂O₃ high-dose group mouse, replicate 1

description: Library name: con_1


title: Patient NR4, BMMCs, HR_MDS, Non-Responder, Pre-AZA

description: Library name: NA8599A_S3_L001_R1_001


title: WT P1 sample 1

city: Houston

first: Riham

middle: Raafat Elgharib

last: Abouleisa

state: Texas

address: 6519 Fannin Street

department: surgery

institute: Baylor College of Medicine

description:
Library name: A1
column  B in gene_fpkm.xlsx: A1

data_processing:
Following end-repair and adapter ligation, libraries were PCR-amplified for nine cycles. Library quality was assessed using a Bioanalyzer High-Sensitivity DNA chip (Agilent), and concentrations were determined by qPCR (KAPA). Sequencing was performed on an Illumina NovaSeq platform using a 50-cycle single-read format. RNA-seq data processing followed a previously described pipeline. Briefly, adapter sequences and low-quality bases were removed using Fastq-mcf (http://code.google.com/p/ea-utils), and read quality was evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the GRCh38 (human) or mm10 (mouse) reference genomes using TopHat v2.0.13. Gene expression levels were quantified using Subread featureCounts based on Ensembl annotations. Differential gene expression was analyzed using edgeR. Genes were filtered to include only those with at least two samples having counts per million (CPM) between 0.5 and 5000; genes with CPM < 0.5 were considered undetectable, and genes with CPM > 5000 (typically mitochondrial) were excluded to prevent skewed normalization. Remaining genes were normalized using the calcNormFactor function in edgeR, and P-values for differential expression were computed based on the negative binomial distribution model.
Assembly: GRCm39
Supplementary files format and content: gene_fpkm.xlsx

source_name: heart

extract_protocol:
RNA was extracted following the miRNeasy micro kit protocol (Qiagen Cat# 217084).
the Ovation Ultralow V2 Kit (NuGEN)

value: heart

value: wt


title: K562, H3K4me2, rep1

value: Chronic myeloid leukemia


title: GeoMx-DSP-1001660010639-D-B03

description: Library name: GeoMx-DSP-1001660010639-D-B03


title: DU145, H3K4me2, rep1

value: Prostate carcinoma


title: Patient R3, BMMCs, HR_MDS, Responder, Post-AZA

description: Library name: LP8606B_S2_L001_R1_001

value: BMMCs


title: Testis tissue, control mouse, replicate 3

description: Library name: n3_6


title: GeoMx-DSP-1001660010639-D-A11

description: Library name: GeoMx-DSP-1001660010639-D-A11


title: HCT116, H3K4me2, rep1

value: Colon carcinoma


title: U251, H3K4me2, rep1

value: Astrocytoma


title: Patient R2, BMMCs, HR_MDS, Responder, Pre-AZA

description: Library name: ZB8459A_S4_L001_R1_001

value: Pre-AZA


title: Patient R3, BMMCs, HR_MDS, Responder, Pre-AZA

description: Library name: LP8606A_S1_L001_R1_001


title: Testis tissue, control mouse, replicate 2

description: Library name: n3_3


title: GeoMx-DSP-1001660010639-D-A07

description: Library name: GeoMx-DSP-1001660010639-D-A07

value: liver


title: Inoculated, shoot, biol rep 3

city: Pozuelo de Alarcón

first: Stephan

last: Pollmann

state: Madrid

address: Campus de Montegancedo, Autovia M-40 (km 38)

country: Spain

institute: CBGP (UPM-INIA/CSIC)

description:
Library name: Sample 24
Column name in gene_fpkm_D7.txt: FS3

data_processing:
Novogene GmbH, Munich Omics Center, Germany
Original image data files from the Illumina platform were transformed to sequenced reads by CASAVA base recognition.
Sequence reads were trimmed for the adaptor sequence/low-quality reads were deleted using a Novogene in-house script (quality parameter limit: 0.05)
Trimmed sequence reads were mapped against the TAIR10 Arabidopsis genome using hisat2 v2.0.5.
Read count extraction and normalization was performed using HTSeq v0.6.1 with ‐m union parameter.
Assembly: TAIR10 Arabidopsis genome
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Shoots

growth_protocol: Seedlings were grown vertically for seven days on 0.5x MS medium. Then, they were transferred to solidified Plant Nutrition Medium. Root and shoot tissue was harvested after seven days of co-cultivation.

extract_protocol:
DNA-free total RNA was extracted by employing the phenol/chloroform method described by Oñate-Sánchez & Vicente-Carbajosa, 2008, BMC Res. Notes.
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations.

treatment_protocol: Each seedling was either mock-infected (50 µl water) or inoculated with 50 µl of a solution containing 1 x 105 spores ml-1.

value: Shoots

tag: ecotype

value: Penicillium sp. D7 inoculated


title: A549, H3K4me2, rep1


title: Testis tissue, control mouse, replicate 1

description: Library name: n1_4


title: GeoMx-DSP-1001660010639-D-A03

description: Library name: GeoMx-DSP-1001660010639-D-A03


title: Patient NR3, BMMCs, HR_MDS, Non-Responder, Pre-AZA

description: Library name: DN8485A_S2_L001_R1_001


title: NCI-H522, H3K4me2, rep1


title: 786-O, H3K4me2, rep1

value: Renal cell carcinoma


title: Inoculated, shoot, biol rep 2

description:
Library name: Sample 23
Column name in gene_fpkm_D7.txt: FS2


title: GD2836_40_days_EAE_Rep5

city: Morgantown

first: Lei

last: Wang

state: West Virginia

address: 64 Medical Center Drive

department: Department of Microbiology, Immunology and Cell Biology

institute: west virginia university

description: Library name: Sample 30

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: mm10
Supplementary files format and content: Txt file, from left to right represent entrz ID, gene symbol, and gene expression values in log2(RPKM+1) for each samples.

source_name: EDL muscle

extract_protocol:
Muscle was first homogonized using TissueRuptor Disposable Probes (Qiagen #990890) and RNA was then purified using the RNeasy Fibrous Tissue Mini Kit (Qiagen #74704) according to the manufacture protocol.
Extracted RNA samples were sent to Admera Health (South Plainfield, NJ) for library construction and sequencing. All samples were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc., Massachussetts, USA). Final library size was ~435bp with an insert size of ~305bp and sequenced with read length configuration of 150 PE for 40M PE reads per sample.

treatment_protocol: EDL muscles were dissected from SJL mice 14 and 40 days following EAE induction. Mice that were not immunized or immunized with OVA emulsified in CFA served as controls.

value: EDL muscle

value: WT SJL mice

value: 40 days, EAE


title: NCI-H460, H3K4me2, rep1

value: Lung large cell carcinoma


title: GD2835_40_days_EAE_Rep4

description: Library name: Sample 29


title: Patient NR2, BMMCs, HR_MDS, Non-Responder, Pre-AZA

description: Library name: PM7551A_S5_L001_R1_001


title: Inoculated, shoot, biol rep 1

description:
Library name: Sample 22
Column name in gene_fpkm_D7.txt: FS1


title: Inoculated, root, biol rep 3

description:
Library name: Sample 21
Column name in gene_fpkm_D7.txt: FR3

source_name: Roots

value: Roots


title: SNB19, H3K4me2, rep1


title: GD2834_40_days_EAE_Rep3

description: Library name: Sample 28


title: WT_no_N_3h_rep2

type: RNA

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

description: Gene expression after cultivation for 3 h in BG11-N medium without any source of nitrogen

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Microarray Scanner C, Model G2505C, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays.

data_processing: Here, the raw data are submitted. For further analysis, raw data were normexp background corrected (Ritchie et al., 2014) and quantile normalized using the limma R package version 3.52.4 (Ritchie et al., 2015). The transcriptome differences were calculated between WT and ∆ssr3189 deletion mutant under strandard growth conditions and for cultures after 3 h  and 24 h without nitrogen.

organism: Synechocystis sp. PCC 6803

source_name: liquid culture

label_protocol: 5 µg total RNA was DNase-treated. Then, DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. For hybridization to microarrays, 600 ng of the labeled RNA was used. Further details of the labeling and hybridization protocol were published in:  Voß, B. and Hess, W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: The Synechocystis 6803 substrain M (Trautmann et al., 2012) was used throughout. The ∆ssr3189 mutant was obtained by homologous recombination (gene deletion replacment by an a streptomycin resistance cassette). The wild-type (WT) and ∆ssr3189 mutant strains were grown in glass Erlenmeyer flasks (250 mL) filled with 100 mL of BG11 buffered medium (pH 8.0) (Rippka et al., 1979), with 0.38 mM sodium carbonate under the following conditions: 30 ± 2°C, continuous light of 30-50 μmol photons m-2 s-1 with continuous shaking at 130 rpm (standard growth conditions). Gene expression analysese were performed for 3 h and 24 h under continuous light of 50 μmol photons m-2 s-1 in BG11 medium without nitrogen. The ∆ssr3189 mutant was grown in the presence of 20 µg mL-1 a streptomycin during pre-culture and without antibiotics during the experiments for accurate comparison with the WT.

extract_protocol: Aliquots corresponding to 20xOD were collected by filtration through hydrophilic polyethersulfone filters (Pall Supor®−800, 0.8 μm), transferred into PGTX buffer, and instantly frozen in liquid N2. Total RNA was prepared from the frozen filter membranes using the PGTX method (Pinto et al., 2009), with modifications as  previously described (Kraus et al., 2024).

treatment_protocol: Gene expression analyses were performed with WT and ∆ssr3189 mutant at standard growth conditions, or after 3 h and 24 h in BG11 medium without any source of nitrogen (BG11-N medium). The cultures were precultivated under continuous light of 50 μmol photons m-2 s-1 (standard growth conditions).

tag: strain

value: strain PCC-M

value: wild type


title: SK-MEL-28, H3K4me1, rep1

value: Cutaneous melanoma


title: WT_no_N_24h_rep2

description: Gene expression after cultivation for 24 h in BG11-N medium without any source of nitrogen


title: WT_no_N_3h_rep1


title: GD2833_40_days_EAE_Rep2

description: Library name: Sample 27


title: Inoculated, root, biol rep 2

description:
Library name: Sample 20
Column name in gene_fpkm_D7.txt: FR2


title: Inoculated, root, biol rep 1

description:
Library name: Sample 19
Column name in gene_fpkm_D7.txt: FR1


title: GD2832_40_days_EAE_Rep1

description: Library name: Sample 26


title: MDA-MB-468, H3K4me1, rep1

value: Breast adenocarcinoma


title: A498, H3K4me2, rep1


title: RPMI-8226, H3K4me1, rep1

value: Multiple myeloma


title: Inoculated, arsenite, shoot, biol rep 3

description:
Library name: Sample 18
Column name in gene_fpkm_D7.txt: FAS3

value: Penicillium sp. D7 inoculated, Arsenite


title: WT_no_N_24h_rep1


title: GD2831_40_days_OVA_Rep5

description: Library name: Sample 25

value: 40 days, OVA


title: SK-MEL-2, H3K4me1, rep1

value: Melanoma


title: GD2830_40_days_OVA_Rep4

description: Library name: Sample 24


title: dssr3189_no_N_3h_rep2

value: ∆ssr3189 mutant


title: Inoculated, arsenite, shoot, biol rep 2

description:
Library name: Sample 17
Column name in gene_fpkm_D7.txt: FAS2

value: Shoots


title: dssr3189_no_N_3h_rep1


title: CCRF-CEM, H3K4me1, rep1

source_name: CCRF-CEM

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: Inoculated, arsenite, shoot, biol rep 1

description:
Library name: Sample 16
Column name in gene_fpkm_D7.txt: FAS1


title: GD2829_40_days_OVA_Rep3

description: Library name: Sample 23

value: EDL muscle


title: dssr3189_no_N_24h_rep2


title: T47D, H3K4me1, rep1

value: Invasive breast carcinoma


title: Inoculated, arsenite, root, biol rep 3

description:
Library name: Sample 15
Column name in gene_fpkm_D7.txt: FAR3


title: GD2828_40_days_OVA_Rep2

description: Library name: Sample 22

value: WT SJL mice


title: PC-3, H3K4me1, rep1

value: Prostate carcinoma


title: Inoculated, arsenite, root, biol rep 2

description:
Library name: Sample 14
Column name in gene_fpkm_D7.txt: FAR2

value: Roots


title: dssr3189_no_N_24h_rep1

value: strain PCC-M


title: K562, H3K4me1, rep1

value: Chronic myeloid leukemia


title: GD2827_40_days_OVA_Rep1

description: Library name: Sample 21


title: Inoculated, arsenite, root, biol rep 1

description:
Library name: Sample 13
Column name in gene_fpkm_D7.txt: FAR1


title: GD2826_40_days_Control_Rep5

description: Library name: Sample 20

value: 40 days, Unimmunized


title: WT_with_N_LL_rep2

description: Gene expression in BG11 medium with nitrogen under standard growth conditions

value: wild type


title: WT_with_N_LL_rep1


title: Csrp3 KO P1 sample 1

description:
Library name: A7
column  E in gene_fpkm.xlsx: A7

value: heart

value: Csrp3 ko


title: SK-OV-3, H3K4me1, rep1

value: Ovarian serous cystadenocarcinoma


title: GD2825_40_days_Control_Rep4

description: Library name: Sample 19


title: Mock, shoot, biol rep 3

description:
Library name: Sample 12
Column name in gene_fpkm_D7.txt: CS3

value: Control


title: SW620, H3K4me1, rep1

value: Colon adenocarcinoma


title: Mock, shoot, biol rep 2

description:
Library name: Sample 11
Column name in gene_fpkm_D7.txt: CS2

value: Shoots


title: dssr3189_with_N_LL_rep2

value: ∆ssr3189 mutant


title: IgG

city: Nanjing

first: xiaohong

last: dong

address: Qixia District, Hongshan Road, Shizi Street 100

department: technical support

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine

description:
Library name: sample5
IgG

data_processing:
Raw reads filtered by Fastp, mapped to GRCh38 via Bowtie2, peaks called by MACS2.
Peak annotation, motif prediction and differential peak analysis performed with ChIPseeker & HOMER.
DeepTools generated bigwig files; IDR filtered reproducible peaks for replicates.
GO/KEGG/DO enrichment on target genes of total and differential peaks.
PCA, correlation heatmap and TSS signal profile plotted for sample QC.
Assembly: Homo sapiens GRCh38 (Ensembl v112) reference genome.
Supplementary files format and content: Clean fastq, sorted bam, bw, narrowPeak, diff peak xlsx and motif html outputs.
Supplementary files format and content: GO/KEGG enrichment tables, peak annotation spreadsheets and QC statistic files.
Library strategy: CUT&Tag

source_name: peripheral blood

growth_protocol: RPMI-1640, 10% fetal bovine serum, 2 mM L-glutamine, 1% penicillin-streptomycin. Cells were cultured at 37℃ at 5% co2.

extract_protocol:
DNA captured by Vazyme DNA Extract Beads Pro after Tn5 fragmentation.
CUT&Tag library built with TD904 kit, amplified then purified for Illumina PE150 sequencing.

treatment_protocol: Cells were differentiated into macrophages by treatment with phorbol 12-myristate 13-acetate (PMA) prior to experiments.

value: peripheral blood

value: macrophage

value: PMA-differentiated, none


title: HCT116, H3K4me1, rep1

value: Colon carcinoma


title: GD2824_40_days_Control_Rep3

description: Library name: Sample 18

value: EDL muscle

value: WT SJL mice


title: dssr3189_with_N_LL_rep1

value: strain PCC-M


title: Mock, shoot, biol rep 1

description:
Library name: Sample 10
Column name in gene_fpkm_D7.txt: CS1


title: GD2823_40_days_Control_Rep2

description: Library name: Sample 17


title: Lactate+TA2

description:
Library name: sample4
Lactate+TA2

value: PMA-differentiated, Lactate+TA


title: GD2822_40_days_Control_Rep1

description: Library name: Sample 16

value: 40 days, Unimmunized


title: HL-60, H3K4me1, rep1

value: Adult acute myeloid leukemia


title: Mock, root, biol rep 3

description:
Library name: Sample 9
Column name in gene_fpkm_D7.txt: CR3

value: Roots


title: Lactate+TA1

description:
Library name: sample3
Lactate+TA1

value: wild type


title: Mock, root, biol rep 2

description:
Library name: Sample 8
Column name in gene_fpkm_D7.txt: CR2


title: GD2821_14_days_EAE_Rep5

description: Library name: Sample 15

value: 14 days, EAE


title: MOLT-4, H3K4me1, rep1

value: Adult T acute lymphoblastic leukemia


title: Lactate2

description:
Library name: sample2
Lactate2

value: PMA-differentiated, Lactate


title: Mock, root, biol rep 1

description:
Library name: Sample 7
Column name in gene_fpkm_D7.txt: CR1

value: Control


title: NCI-H226, H3K4me1, rep1

value: Pleural epithelioid mesothelioma


title: GD2820_14_days_EAE_Rep4

description: Library name: Sample 14


title: 1525-2 DOX- DMSO rep1

description: Library name: 1525-2_DOX-DMSO_rep1

value: LUAD cell line

value: LUAD

value: DMSO


title: Lactate1

description:
Library name: sample1
Lactate1

value: peripheral blood

value: macrophage


title: Mock, arsenite, shoot, biol rep 3

description:
Library name: Sample 6
Column name in gene_fpkm_D7.txt: AS3

value: Shoots

value: Arsenite


title: GD2819_14_days_EAE_Rep3

description: Library name: Sample 13

value: EDL muscle

value: WT SJL mice


title: OVCAR-8, H3K4me1, rep1

value: High grade ovarian serous adenocarcinoma


title: Activated CD4 T cell, 5 nM AZD4573 + 5 μM SMAP-2, 24h, rep3

city: San Francisco

first: Zichong

state: CA

address: 1650 Owens Street

department: Gladstone Infectious Disease Institute

institute: The J. David Gladstone Institutes

description: Library name: Don3_activated_AZD_SMAP

data_processing:
Base-call files were converted to FASTQ format and demultiplexed using BCL Convert v4.3.6 and fqtk v0.3.1. Reads were filtered using fastp v0.24.0, including poly-X-tail trimming, 3′ quality-based tail trimming, a minimum Phred quality score of 15, and a minimum retained read length of 50 bp. Filtered reads were aligned to the human reference genome using STAR v2.7, with removal of alignments containing noncanonical splice junctions. BAM files were coordinate-sorted using SAMtools v1.21. PCR and optical duplicates were removed on the basis of UMI sequences using UMICollapse v1.1.0. Alignment quality, strand specificity, and read distribution across genomic features were assessed using RustQC v0.2.1, and aggregate quality-control reports were generated using MultiQC v1.33.
Gene-level expression counts were generated using featureCounts in the Subread package v2.1.1 with strand-specific counting. Multimapping reads were assigned fractionally, and reads assigned to exons and 3′ untranslated regions were grouped by gene_id. Gene counts were annotated with gene biotype and other metadata obtained from the reference GTF annotation. TMM-normalized counts were used to calculate Pearson sample-to-sample correlations and principal-component analyses. Differential gene-expression analysis was performed using edgePython v0.2.5 through the Plasmidsaurus analysis platform. Within the resting and anti-CD3/CD28-activated groups, cells treated with AZD4573 plus SMAP-2 were compared with the corresponding DMSO-treated controls. Volcano plots were generated from the differential-expression results, and genes showing concordant differential expression across the three donors were identified.
Assembly: GRCh38 (Genome Reference Consortium Human Build 38; hg38)
Supplementary files format and content: Processed data are provided as a Microsoft Excel workbook (.xlsx) containing gene-level raw counts and counts per million (CPM) for each sample. Each row represents an annotated gene and includes the gene identifier (gene_id), gene name, chromosome, genomic start and end coordinates, and  gene length. Sample-specific columns report the corresponding raw count and CPM values.

source_name: Blood

growth_protocol: Peripheral blood collected in leukoreduction system chambers from healthy donors was obtained from Vitalant. Peripheral blood mononuclear cells were isolated using Lymphoprep density-gradient medium, and CD4+ T cells were purified by negative selection using the EasySep Human CD4+ T Cell Isolation Kit according to the manufacturer’s instructions. Primary CD4+ T cells were cultured at 1 × 10^7 cells/mL in RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37°C in a humidified incubator containing 5% CO2. For the RNA-seq experiment, CD4+ T cells from three independent HIV-negative donors were divided into resting and activated groups. Resting cells were maintained without stimulation for 48 h, whereas activated cells were cultured for 48 h with plate-bound anti-CD3 and anti-CD28 antibodies.

extract_protocol:
Primary CD4+ T cells were lysed and preserved in DNA/RNA Shield (Zymo Research, catalog no. R1100-250) and submitted to Plasmidsaurus for RNA extraction and sequencing. Each submitted condition contained approximately 100,000 cells in 50 μL DNA/RNA Shield. Total RNA was extracted by Plasmidsaurus using a bead-based extraction method. Following extraction, RNA concentration was measured using a fluorescence-based plate-reader assay, and sample concentrations were normalized before library preparation.
Polyadenylated RNA was captured and reverse-transcribed using a poly(dT)VN/oligo-dT primer containing a sample barcode, a unique molecular identifier (UMI), and the Read 1 sequence. Second-strand synthesis was performed to generate double-stranded cDNA. The cDNA was fragmented by tagmentation, which also incorporated the second sequencing-adapter sequence. Libraries were then amplified to add unique dual i5/i7 indices and P5/P7 flow-cell sequences. Libraries were sequenced by Plasmidsaurus on an Illumina NovaSeq X Plus using a stranded, single-end, 3′-end-counting configuration. Sequencing reads were approximately 90 bp long and were strongly enriched within the terminal approximately 400 nucleotides of polyadenylated transcripts. UMIs incorporated during reverse transcription were used to distinguish independently captured RNA molecules from PCR-derived duplicates.

treatment_protocol: Following the 48-h resting or anti-CD3/CD28 activation period, cells in each group were treated for 24 h with either vehicle control consisting of 0.1% DMSO or a combination of 5 nM AZD4573 and 5 μM SMAP-2. This generated four donor-matched experimental conditions: resting cells treated with DMSO, resting cells treated with AZD4573 plus SMAP-2, activated cells treated with DMSO, and activated cells treated with AZD4573 plus SMAP-2. At the end of the 24-h treatment, 100,000 cells from each sample were collected in 50 μL DNA/RNA Shield and submitted for RNA extraction and RNA-seq.

value: Blood

value: Primary cells

value: Activated CD4+ T cells

value: WT

value: 5 nM AZD4573 + 5 μM SMAP-2 for 24 hours


title: NCI-H522, H3K4me1, rep1

value: Lung adenocarcinoma


title: Mock, arsenite, shoot, biol rep 2

description:
Library name: Sample 5
Column name in gene_fpkm_D7.txt: AS2


title: GD2818_14_days_EAE_Rep2

description: Library name: Sample 12

value: 14 days, EAE


title: Activated CD4 T cell, DMSO, 24h, rep3

description: Library name: Don3_activated_DMSO

value: 0.1% DMSO for 24 hours


title: NCI-H23, H3K4me1, rep1


title: Mock, arsenite, shoot, biol rep 1

description:
Library name: Sample 4
Column name in gene_fpkm_D7.txt: AS1


title: Resting CD4 T cell, 5 nM AZD4573 + 5 μM SMAP-2, 24h, rep3

description: Library name: Don3_resting_AZD_SMAP

value: Resting CD4+ T cells


title: A498, H3K4me1, rep1

value: Renal cell carcinoma


title: GeoMx-DSP-1001660010639-D-D02

description: Library name: GeoMx-DSP-1001660010639-D-D02

value: liver


title: GD2816_14_days_OVA_Rep5

description: Library name: Sample 10

value: 14 days, OVA


title: Resting CD4 T cell, DMSO, 24h, rep3

description: Library name: Don3_resting_DMSO


title: Mock, arsenite, root, biol rep 3

description:
Library name: Sample 3
Column name in gene_fpkm_D7.txt: AR3

value: Roots


title: DU145, H3K4me1, rep1

value: Prostate carcinoma


title: Activated CD4 T cell, 5 nM AZD4573 + 5 μM SMAP-2, 24h, rep2

description: Library name: Don2_activated_AZD_SMAP


title: Mock, arsenite, root, biol rep 2

description:
Library name: Sample 2
Column name in gene_fpkm_D7.txt: AR2

value: Arsenite


title: U251, H3K4me1, rep1

value: Astrocytoma


title: GD2815_14_days_OVA_Rep4

description: Library name: Sample 9

value: EDL muscle

value: WT SJL mice


title: Mock, arsenite, root, biol rep 1

description:
Library name: Sample 1
Column name in gene_fpkm_D7.txt: AR1


title: Activated CD4 T cell, DMSO, 24h, rep2

description: Library name: Don2_activated_DMSO

value: Blood

value: Primary cells


title: A549, H3K4me1, rep1


title: GD2814_14_days_OVA_Rep3

description: Library name: Sample 8


title: WRKY21-4

city: New York

first: Will

middle: E

last: Hinckley

state: New York

address: 12 Waverly Pl

department: Biology

institute: New York University

description:
Library name: W-4
S1 1x100 Cycle v1.5

data_processing:
The reads were basecalled using Picard IlluminaBasecallsToFastq version 2.23.81, with APPLY_EAMSS_FILTER set to false. Following basecalling, the reads were demultiplexed using Pheniqs version 2.1.02. The entire process was executed using a custom nextflow pipeline, GENEFLOW3.
Reads were trimmed using CutAdapt to remove the standard illumina universal adapters. Trimmed reads were aligned to the Tair10 genome using STAR. FeatureCounts from SubRead  was used to generate a count matrix that was used in DESEq2 for downstream analysis.
Assembly: TAIR10
Supplementary files format and content: matrix of raw counts from FeatureCounts

source_name: 10 day old root

growth_protocol: Col-0 plants were grown upright for 10 days under long day conditions on 1/2 MS plate media. Roots were harvested for protoplast isolation the morning of the 10th day of growth, following Bargmann et al 2013.

extract_protocol:
Cells were collected and frozen in RLT lysis buffer for later processing with the Qiagen RNeasy RNA micro prep kit with on-column DNAse digestion, and quality checked using Agilent Tapestation HSRNA Kit.
mRNA was isolated using the NEB mRNA purification module. RNA was processed for sequencing using the NEB Ultra II library prep kit. Libraries were pooled and sequenced using an Illumina Novaseq 6000 S1 1x100 run.

treatment_protocol: 35 µM cycloheximide for 20 minutes, then 10 µM dexamethasone for 2 hours, nefore FACS sorting on a BD FacsDiscoverS8.

value: 10 day old root

value: protoplast


title: GD2813_14_days_OVA_Rep2

description: Library name: Sample 7


title: Resting CD4 T cell, 5 nM AZD4573 + 5 μM SMAP-2, 24h, rep2

description: Library name: Don2_resting_AZD_SMAP

value: WT

value: 5 nM AZD4573 + 5 μM SMAP-2 for 24 hours


title: 786-O, H3K4me1, rep1


title: WRKY21-3

description:
Library name: W-3
S1 1x100 Cycle v1.5

value: 35 µM cycloheximide for 20 minutes, then 10 µM dexamethasone for 2 hours


title: GD2812_14_days_OVA_Rep1

description: Library name: Sample 6


title: Resting CD4 T cell, DMSO, 24h, rep2

description: Library name: Don2_resting_DMSO

value: Resting CD4+ T cells

value: 0.1% DMSO for 24 hours


title: NCI-H460, H3K4me1, rep1

value: Lung large cell carcinoma


title: WRKY21-2

description:
Library name: W-2
S1 1x100 Cycle v1.5


title: GD2811_14_days_Control_Rep5

description: Library name: Sample 5

value: 14 days, Unimmunized


title: GD2810_14_days_Control_Rep4

description: Library name: Sample 4


title: SNB19, H3K4me1, rep1


title: WRKY21-1

description:
Library name: W-1
S1 1x100 Cycle v1.5


title: Activated CD4 T cell, 5 nM AZD4573 + 5 μM SMAP-2, 24h, rep1

description: Library name: Don1_activated_AZD_SMAP

value: Activated CD4+ T cells


title: Activated CD4 T cell, DMSO, 24h, rep1

description: Library name: Don1_activated_DMSO


title: SK-MEL-28, H3K36me3, rep1

value: Cutaneous melanoma


title: GD2809_14_days_Control_Rep3

description: Library name: Sample 3


title: Resting CD4 T cell, 5 nM AZD4573 + 5 μM SMAP-2, 24h, rep1

description: Library name: Don1_resting_AZD_SMAP


title: MDA-MB-468, H3K36me3, rep1

value: Breast adenocarcinoma


title: Tregs, IL-2 only, Day 16, GEX

city: San Francsico

first: Qizhi

last: Tang

address: 513 Parnassus Ave

department: Diabetes Center

institute: University of California, San Francsico

description: 10X Genomics Multiome (ATAC + GEX)

library_source: transcriptomic single cell

data_processing:
The demulitplexing, barcode processing, fragment (ATAC) or gene (GEX) counting were done via the Cell Ranger ARC v2.0.0 using default settings.
Assembly: hg38
Supplementary files format and content: File formats: filtered feature barcode matrix (filtered_feature_bc_matrix.h5) includes gene and peak features in rows and barcodes from CellRanger-identified cells in columns; ATAC fragments (atac_fragments.tsv.gz) includes count and barcode data for each ATAC fragment; GEX molecule info (gex_molecule_info.h5) in hdf5 file format includes count and barcode details for each GEX molecule observed; GEX files (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz) also provided in tab-separated value (TSV)  and matrix file format.

molecule: nuclear RNA

growth_protocol: Freshly isolated primary human regulatory T cells (CD4+CD25+CD127dim/low) were stimulated or re-stimulated with CD3/CD28 Dynabeads at 1:1 cell:bead ratio on Days 0, 9, and 16. Cultures were maintained in RPMI-1640 plus recombinant human IL-2 (300 units/mL until Day 9, then reduced to 100 units/mL from Day 9 onward).

extract_protocol:
Nuclei were isolated according to 10X Genomics instructions for scMultiome (ATAC + Gene Expression) nuclei isolation. Briefly, cells were pelleted and washed with PBS + 0.04% BSA prior to cell lysis with Lysis Buffer (10 mM Tric-HCl, pH7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20; 0.1% NP-40 Substitute; 0.01% Digitonin; 1% BSA; 1 mM DTT; 1 U/uL RNase inhibitor) for 5 min on ice. The resulting nuclei were washed 3 times with pre-chilled Wash Buffer (10 mM Tric-HCl, pH7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20; 1% BSA; 1 mM DTT; 1 U/uL RNase inhibitor) and resuspended in Diluted Nuclei Buffer (10X Genomics Nuclei Buffer; 1 mM DTT; 1 U/uL RNase inhibitor).
Library was constructed according to manufacturer instructions for scMultiome (ATAC + Gene Expression). Briefly, the nuclei suspensions were incubated with Transposition Mix to fragment and append accesible chromatin regions with adapter sequences. The transposed nuclei are then combined with the master mix and loaded with barcoded Gel Beads and Partition Oil into a Chromium Next GEM Chip J to generate the gel bead-in-emulsion (GEM). Following retrotranscription of poly-A mRNA to cDNA, each GEM produces transposed DNA (for ATAC) and full-length cDNA (for gene expression), each with Illumina R1 primer sequences, 10X barcodes, and unique molecular identifiers (UMIs). Pooled fractions are recovered from each GEM with silane magnetic beads, and the barcoded transposed DNA and full-length cDNA are PCR-amplified to generate the input for library construction. For ATAC library construction, Illumina P7 and sample indexes are added via PCR to generate paired-end libraries with P5 and P7 sequences. For gene expression (GEX) libraries, cDNA amplicons are enzymatically fragmented and selected for appropriate size prior to addition of P5, P7, sample indexes, and TruSeq Read 2 primer sequences via end repair, A-tailing, adaptor ligation, and PCR.
snATAC-seq plus snRNA-seq

treatment_protocol: For the inflammatory cytokine-exposed samples, the culture media was supplemented with 25 ng/mL recombinant human IL-6, 20 ng/mL recombinant human IL-1beta, 20 ng/mL recombinant human IL-23 every 2-3 days.

value: peripheral blood

value: primary

value: Treg

value: IL-2 only


title: Tregs, IL-2 only, Day 16, ATAC

description: 10X Genomics Multiome (ATAC + GEX)

library_source: genomic single cell


title: ULT1-2

description:
Library name: U-2
S1 1x100 Cycle v1.5


title: Resting CD4 T cell, DMSO, 24h, rep1

description: Library name: Don1_resting_DMSO

value: Blood

value: Primary cells


title: GD2808_14_days_Control_Rep2

description: Library name: Sample 2

value: EDL muscle

value: WT SJL mice


title: RPMI-8226, H3K36me3, rep1

value: Multiple myeloma


title: GD2807_14_days_Control_Rep1

description: Library name: Sample 1


title: SK-MEL-2, H3K36me3, rep1

value: Melanoma


title: ULT1-1

description:
Library name: U-1
S1 1x100 Cycle v1.5

value: 10 day old root

value: protoplast

value: 35 µM cycloheximide for 20 minutes, then 10 µM dexamethasone for 2 hours


title: EV-4

description:
Library name: N-4
S1 1x100 Cycle v1.5


title: KO_8384

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA95160

data_processing:
Sequencing was performed on an Illumina Illumina NovaSeq X Plus platform in single-read mode and 101 base reads were obtained.
Illumina RTA v4 software was used for base calling.
Generated reads were mapped to the mouse (GRCm38.p4) reference genome using HISAT2 v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: GRCm38.p4
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted from the liver and adipose tissue using the RNeasy tissue kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: liver

value: ZFP90 knockout


title: M2-polarized THP-1 macrophages, WTAP overexpression, biological replicate 3

city: Shenyang

first: Ming

last: Zhang

state: China

address: Department of Pharmacology, School of Pharmacy

institute: China Medical University

description: Library name: OE3

data_processing:
Base calling and conversion of raw sequencing images to FASTQ files were performed with the sequencing platform’s standard pipeline (CASAVA base calling).
Raw reads were quality-trimmed and filtered with fastp v0.19.5 to obtain clean reads (adapter removal, low-quality base trimming); Q30 was above 96% for all libraries.
Clean reads were aligned to the human reference genome with HISAT2 v2.1.0 (orientation mode: paired-end); the overall mapping rate ranged from 97.59% to 98.07%.
Transcripts were assembled with StringTie v2.1.2 and gene/transcript expression was quantified with RSEM v1.3.3 (read counts and TPM).
Assembly: GRCh38
Supplementary files format and content: xls files include reads counts for each Sample
Supplementary files format and content: xls files include TPM values for each Sample

growth_protocol: The human monocytic cell line THP-1 was obtained from the Cell Resource Center, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, and maintained in suspension culture in RPMI-1640 medium (Gibco) supplemented with 10% fetal bovine serum (TransGen Biotech) and 1x penicillin-streptomycin (Solarbio) at 37 C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted with EZol reagent (GenePharma) according to the manufacturer’s instructions. RNA concentration and purity were measured on a NanoDrop 2000 (Thermo Fisher Scientific), integrity was checked by agarose gel electrophoresis and the RQN value was determined on an Agilent 5300 Fragment Analyzer. Libraries were built from samples with >= 1 ug total RNA, concentration >= 30 ng/uL, RQN > 6.5 and OD260/280 between 1.8 and 2.2.
Libraries were prepared by Majorbio (Shanghai, China). mRNA was enriched from total RNA with oligo(dT) magnetic beads and randomly fragmented to approximately 300 bp in fragmentation buffer. First-strand cDNA was synthesized with random primers and reverse transcriptase, followed by second-strand synthesis. Double-stranded cDNA was end-repaired, A-tailed and ligated to sequencing adapters; the ligation products were purified and size-selected, then enriched by PCR to generate the final library. Libraries were quantified (Qubit 4.0), pooled and sequenced as 150 bp paired-end reads.

treatment_protocol: THP-1 cells were seeded at 1 x 10^6 cells per well in 6-well plates and differentiated into macrophages with 100 ng/mL PMA (G-clone) for 24 h. M2 polarization was induced with 20 ng/mL IL-4 (KeyGen BioTech) for 48 h. Cells were then transfected with 4 ug pcDNA3.1 (NC) or pcDNA3.1-WTAP (OE, Addgene #53741) using Lipofiter (Hanhen Biologicals) in Opti-MEM I (Gibco) for 6 h, after which the medium was replaced with RPMI-1640 containing 10% FBS and cells were cultured for a further 48 h before RNA extraction.

value: M2-polarized macrophage (PMA- and IL-4-treated THP-1)


title: M2-polarized THP-1 macrophages, WTAP overexpression, biological replicate 2

description: Library name: OE2


title: GD2817_14_days_EAE_Rep1

description: Library name: Sample 11

value: 14 days, EAE


title: EV-3

description:
Library name: N-3
S1 1x100 Cycle v1.5


title: CCRF-CEM, H3K36me3, rep1

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: KO_8382

description: Library name: GA95159


title: M2-polarized THP-1 macrophages, WTAP overexpression, biological replicate 1

description: Library name: OE1


title: EV-2

description:
Library name: N-2
S1 1x100 Cycle v1.5


title: T47D, H3K36me3, rep1

value: Invasive breast carcinoma


title: M2-polarized THP-1 macrophages, empty vector control, biological replicate 3

description: Library name: NC7


title: KO_8379

description: Library name: GA95158


title: EV-1

description:
Library name: N-1
S1 1x100 Cycle v1.5


title: PC-3, H3K36me3, rep1

value: Prostate carcinoma


title: M2-polarized THP-1 macrophages, empty vector control, biological replicate 2

description: Library name: NC6


title: HRS1-3

description:
Library name: HR-3
S1 1x100 Cycle v1.5


title: WT_8357

description: Library name: GA95157

value: WT


title: K562, H3K36me3, rep1

value: Chronic myeloid leukemia


title: WT_8356

description: Library name: GA95156


title: WT_8353

description: Library name: GA95155


title: HRS1-2

description:
Library name: HR-2
S1 1x100 Cycle v1.5


title: M2-polarized THP-1 macrophages, empty vector control, biological replicate 1

description: Library name: NC5


title: SW620, H3K36me3, rep1

value: Colon adenocarcinoma


title: SK-OV-3, H3K36me3, rep1

value: Ovarian serous cystadenocarcinoma


title: HeLa_rep2

city: Chicago

first: Daniel

last: Arango

state: IL

address: 303 E Superior St, Office 7-119

institute: Northwestern University

description: Library name: S10

data_processing:
Raw reads were pre-processed to remove low quality bases, adapter sequences, and a stretch of at least 10 consecutive guanine nucleotides at the 3’ end using cutadapt/4.2.
Reads were aligned to the human genome using STAR/2.7.9a in local alignment mode. Alignments were converted to bigwig.
Assembly: GRCh38
Supplementary files format and content: Bigwig

source_name: Cervix

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% Bovine Calf Serum (FBS) and 1% Penicillin/Streptomycin. All cells were grown in an incubator condition of 37oC and 5% CO2 and passaged every 3 days.

extract_protocol:
Total RNA isolation was performed using Trizol Reagent (ThermoFisher Scientific) according to the manufacturer's protocol. Total RNA was then DNase treated with DNase I (NEB) and reconstituted in nuclease-free water.
Total RNA was ribodepleted, fargmented, and dephosphorylated followed by a 3' adapter ligation. The 3' adapter contains a spacer that impedes the self-ligation of RNA. Reverse transcription was performed using the Maxima H minus enzyme with a tempalte switch primer containing an (UMI) of ten randomized nucleotides.Final libraries were PCR amplified using Q5® High-Fidelity 2X Master Mix (NEB) and NEBNext® Multiplex Oligos for Illumina®. Each sample was assigned a different indexed primer.

value: Cervix

value: HeLa

value: Cervical Cancer

value: Wildtype


title: HRS1-1

description:
Library name: HR-1
S1 1x100 Cycle v1.5

value: 10 day old root

value: protoplast

value: 35 µM cycloheximide for 20 minutes, then 10 µM dexamethasone for 2 hours


title: HCT116, H3K36me3, rep1

value: Colon carcinoma


title: CUT&RUN Experiment 2, proximal small intestine villus epithelium, SMAD4, rep 2

city: Piscataway

last: Logerfo

state: New Jersey

address: 145 Bevier Road

institute: Rutgers University

description: Library name: CnR_SMAD4_Rep2

data_processing:
For samples with two lanes worth of sequencing (IgG_1 and SMAD1_Rep2), R1 and R2 reads from each lane (_L1.fq.gz and _L2.fq.gz) were merged prior to additional processing and analysis (resulting in _LM.fq.gz files). Raw reads were aligned to the reference genome (mm10) using Bowtie2 v2.4.1 using the respective parameters (--local --very-sensitive --no-mixed -I 10 -X 700 –dovetail). Samtools v1.3.1 was used to convert aligned SAM files to BED files. Peaks were called using MACS2 v2.2.7.1 callpeak for different statistical stringencies.
bigwig files were generated using Bedtools (v2.26.0) bamcoverage with ---normalizeUsing RPKM and --binSize 10 parameters
Assembly: mm10
Supplementary files format and content: IgG_1.bw: IgG Experiment 1 bigwig file for read coverage visualization
Supplementary files format and content: SMAD1_Rep1.bw: SMAD1 Rep1 bigwig file for read coverage visualization
Supplementary files format and content: SMAD1_Rep2.bw: SMAD1 Rep2 bigwig file for read coverage visualization
Supplementary files format and content: IgG_2.bw: IgG Experiment 2 bigwig file for read coverage visualization
Supplementary files format and content: SMAD4_Rep1.bw: SMAD4 Rep1 bigwig file for read coverage visualization
Supplementary files format and content: SMAD4_Rep2.bw: SMAD4 Rep2 bigwig file for read coverage visualization
Library strategy: CUT&Run

source_name: Proximal half of small intestine, villus epithelium

extract_protocol:
Villi from the proximal intestinal epithelium, estimated at 500,000 cells per sample, were isolated from C57BL6 mice using EDTA isolation methods described above. Whole villi underwent gentle crosslinking in 1mM disuccinimidyl glutarate for 30min. The crosslinking reaction was quenched in 2.5M glycine for 15min and the villi were washed with and resuspended in PBS prior to CUT&RUN. CUT&RUN was conducted per Epicypher’s CUT&RUN protocol using crosslinking (XL) buffers. Bead bound villi were mixed with antibody buffer and antibodies were added to respective samples for overnight incubation, shaking at 4C (IgG, SMAD4, and SMAD1). Reverse crosslinking reactions using 10% SDS and 20ug/uL Proteinase K were incubated overnight at 55C. DNA was purified using the CUTANA DNA Purification Kit and provided instructions.
10uL of purified DNA from each reaction was used for library preparation. Takara ThruPLEX® DNA-Seq Kit and Takara Unique Dual Index kit were used for library preparation per manufacturer’s protocol with slight modifications to enrich for smaller fragment sizes from CUT&RUN.

tag: cut&run antibody

value: SMAD4 (Cell Signaling, D3R4N, Rabbit Monoclonal Antibody #46535)


title: HHO5_WRKY21-4

description:
Library name: HHW-4
S1 1x100 Cycle v1.5


title: CUT&RUN Experiment 2, proximal small intestine villus epithelium, SMAD4, rep 1

description: Library name: CnR_SMAD4_Rep1

value: Proximal half of small intestine, villus epithelium


title: NCI-H226, H3K4me2, rep2

value: Pleural epithelioid mesothelioma


title: HeLa_rep1

description: Library name: S7


title: HHO5_WRKY21-3

description:
Library name: HHW-3
S1 1x100 Cycle v1.5


title: HL-60, H3K36me3, rep1

value: Adult acute myeloid leukemia


title: CUT&RUN Experiment 2, proximal small intestine villus epithelium, IgG (Control)

description: Library name: CnR_IgG_2

value: IgG (Epicypher)


title: Micro-C mAID_SMC1_Aux+HU R1

city: Madrid

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

institute: CNIO

description:
Library name: Micro-C_mAID_SMC1_Aux_HU_R1
Micro-C_SMC1_HU_Auxin.mcool

data_processing:
Micro-C data were processed using a standardized Hi-C analysis pipeline. Raw paired-end sequencing reads were quality-trimmed using Trim Galore (quality threshold = 20, minimum length = 30 bp) and aligned to the hg38 human reference genome using BWA-MEM (10) ) with Hi-C-specific parameters (-5SP -T0). Aligned reads were processed with the pairtools suite: contacts were parsed with a minimum mapping quality of 40 (--min-mapq 40), allowing walks of up to 5 unique alignments (--walks-policy 5unique) with a maximum inter-alignment gap of 30 bp. Parsed pairs were sorted, and PCR duplicates were removed while retaining duplicate marking statistics. Valid contact pairs were converted to “.hic” format using Juicer Tools (v1.22.01) and to multi-resolution cool format (.mcool) using HiCExplorer with Knight-Ruiz (KR) matrix balancing normalization. For comparative analyses between conditions, biological replicates were merged using pairtools merge, and datasets were downsampled to equalize sequencing depth across conditions using pairtools sample. Downsampling fractions were calculated to match the condition with the lowest sequencing depth, ensuring unbiased comparisons
Assembly: hg38
Supplementary files format and content: .hic , .mcool

extract_protocol:
The Micro-C library was prepared using the Dovetail® Micro-C Kit according to the manufacturer’s protocol. Briefly, cells were treated with 1 µg/mL dox for 48 h, 2 µM auxin for 5 h where indicated. The chromatin was fixed with disuccinimidyl glutarate (DSG) and formaldehyde in the nucleus. The cross-linked chromatin was then digested in situ with micrococcal nuclease (MNase). Following digestion, the cells were lysed with SDS to extract the chromatin fragments and the chromatin fragments were bound to Chromatin Capture Beads. Next, the chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter-containing ends.
After proximity ligation, the crosslinks were reversed, the associated proteins were degraded, and the DNA was purified and then converted into a sequencing library using Illumina-compatible adaptors. Biotin-containing fragments were isolated using streptavidin beads prior to PCR amplification. The library was sequenced on an Illumina Novaseq X

value: OsTIR (F74G)

value: Auxin +HU


title: Micro-C mAID_SMC1_Aux+HU R2

description:
Library name: Micro-C_mAID_SMC1_Aux_HU_R2
Micro-C_SMC1_HU_Auxin_merged-down.hic


title: MDA-MB-468-Input, rep1

value: Breast adenocarcinoma


title: HHO5_WRKY21-2

description:
Library name: HHW-2
S1 1x100 Cycle v1.5


title: MOLT-4, H3K36me3, rep1

value: Adult T acute lymphoblastic leukemia


title: Micro-C mAID_SMC1+HU R2

description:
Library name: Micro-C_mAID_SMC1_HU_R2
Micro-C_SMC1_HU_merged-down.hic

value: +HU


title: CUT&RUN Experiment 1, proximal small intestine villus epithelium, SMAD1, rep 2

description: Library name: CnR_SMAD1_Rep2

value: SMAD1 (Cell Signaling, D59D7, Rabbit Monoclonal Antibody #6944)


title: NCI-H226, H3K36me3, rep1


title: CUT&RUN Experiment 1, proximal small intestine villus epithelium, SMAD1, rep 2, merged lanes

description: Library name: CnR_SMAD1_Rep2_LM


title: NCI-H522, H3K36me3, rep1

value: Lung adenocarcinoma


title: HHO5_ULT1-3

description:
Library name: HHU-3
S1 1x100 Cycle v1.5


title: CUT&RUN Experiment 1, proximal small intestine villus epithelium, SMAD1, rep 1

description: Library name: CnR_SMAD1_Rep1


title: HHO5_WRKY21-1

description:
Library name: HHW-1
S1 1x100 Cycle v1.5


title: Micro-C mAID_SMC1+HU R1

description:
Library name: Micro-C_mAID_SMC1_HU_R1
Micro-C_SMC1_HU.mcool


title: Micro-C mAID_CTCF+Aux R1

description: Library name: Micro-C_mAID_CTCF_Aux_R1

value: MAID-mClover-Sororin

value: Auxin


title: OVCAR-8, H3K36me3, rep1

value: High grade ovarian serous adenocarcinoma


title: HHO5_ULT1-2

description:
Library name: HHU-2
S1 1x100 Cycle v1.5

value: 10 day old root

value: protoplast

value: 35 µM cycloheximide for 20 minutes, then 10 µM dexamethasone for 2 hours


title: CUT&RUN Experiment 1, proximal small intestine villus epithelium, IgG (Control), merged lanes

description: Library name: CnR_IgG_1_LM

value: Proximal half of small intestine, villus epithelium


title: Micro-C mAID_CTCF R1

description: Library name: Micro-C_mAID_CTCF_R1


title: CUT&RUN Experiment 1, proximal small intestine villus epithelium, IgG (Control)

description: Library name: CnR_IgG_1


title: NCI-H23, H3K36me3, rep1


title: HHO5_ULT1-1

description:
Library name: HHU-1
S1 1x100 Cycle v1.5


title: A498, H3K36me3, rep1

value: Renal cell carcinoma


title: Micro-C mAID_WAPAL +Aux R1

description: Library name: Micro-C_mAID_WAPAL_Aux_R1

value: MAID-mClover-WAPAL


title: HHO5_HRS1-3

description:
Library name: HHHR-3
S1 1x100 Cycle v1.5


title: Micro-C mAID_WAPAL R1

description: Library name: Micro-C_mAID_WAPAL_R1


title: DU145, H3K36me3, rep1

value: Prostate carcinoma


title: Jejunum, control and iDKO, 7 days

description: Library name: GM_S1_L001

data_processing:
Space Ranger (v3.1.3 and v4.0) was used to process and quantify Visium HD libraries, outputting FASTQ files with data binned at 8μm resolution
Gene expression was quantified using Space Ranger (v3.1.3 and v4.0) with default parameters and a RefSeq based transcriptome.
Initial analysis with all samples and the full sequencing library from the spatial transcriptomic slide resulted in the raw_barcodes.tsv.gz, raw_features.tsv.gz, and raw_matrix.mtx.gz files. The selection of barcodes and reanalysis for only samples relevant to this study (control and SMAD1/5 iDKO) was done using the Loupe Browser > Visium Image Alignment > Visium HD Manual Alignment > identify tissue. The analysis using only those tissues resulted in the filtered_barcodes.tsv.gz, filtered_features.tsv.gz, and filtered_matrix.mtx.gz files. The iDKOvControl.cloupe file provides transcriptomic clustering and visualization and analysis capabilities specifically for the control and SMAD1/5 iDKO tissues relevant for this study. The READ_ME_iDKOvControl_spatial.jpg file provides details for visualization and further analysis.
Assembly: mm10
Supplementary files format and content: raw_barcodes.tsv.gz: list of spatial barcodes from all tissues/sequencing data in capture window
Supplementary files format and content: raw_features.tsv.gz: list of gene IDs from all tissues/sequencing data in capture window
Supplementary files format and content: raw_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format from all tissues/sequencing data in capture window
Supplementary files format and content: filtered_barcodes.tsv.gz: list of spatial barcodes from only selected tissues within the capture window (control and SMAD1/5 iDKO)
Supplementary files format and content: filtered_features.tsv.gz: list of gene IDs from only selected tissues within the capture window (control and SMAD1/5 iDKO)
Supplementary files format and content: filtered_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format from only selected tissues within the capture window (control and SMAD1/5 iDKO)
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: iDKOvControl.cloupe: Space Ranger output file designed to be opened using Loupe Browser
Library strategy: Spatial Transcriptomics

source_name: Jejunum of small intestine

extract_protocol:
Freshly harvested tissues were formalin-fixed paraffin-embedded (FFPE) into tissue blocks. 5μm sections were cut for spatial transcriptomics assay using Visium HD 10x Genomics, and as per manufacturor's protcol
Spatial transcriptomic sequencing library was prepared using 10x Genomics Visium HD FFPE Spatial Gene Expression Slides & Reagents Kit. Sequencing was performed using Illumina NovaSeq X Plus platform

treatment_protocol: Littermate, sex-matched Control and SMAD1/5 iDKO mice were treated with tamoxifen for 4 consecutive days for induction of tissue-specific knockout and intesetinal tissues were collected 7 days after first injection. Jejunum harvest took place on the same day for all mice, and processed together for spatial transcriptomics

value: Jejunum of small intestine

value: Control and SMAD1/5 iDKO

value: tamoxifen


title: PC9_miR206

city: Kaghosima City

first: Takuya

last: Tokunaga

address: 8-35-1 Sakuragaoka

institute: Kagoshima University

description: Library name: D004-P-206

data_processing:
Quality control of raw FASTQ files was performed using FastQC version 0.12.1 and MultiQC version 1.18.
Adapter trimming was performed using Trimmomatic version 0.39.
Reads were aligned to the human reference genome hg38 using STAR version 2.7.10b.
Gene expression levels were quantified and normalized as TPM values using StrandNGS version 4.0 with Ensembl Genes annotation release 2016.12.01.
Differential expression analysis was performed between miR-206-transfected cells and mock-transfected controls.
Assembly: hg38
Supplementary files format and content: Processed data files include TPM-normalized gene expression matrices and differential expression analysis results generated from RNA sequencing data.

source_name: lung

growth_protocol: PC9 and A549 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted using ISOGEN II reagent according to the manufacturer's instructions.
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

value: lung


title: U251, H3K36me3, rep1

data_processing:
Sequencing reads from mChIP-seq were demultiplexed to samples by the barcodes in the 5’ end of Read2 using fastq-multx (version 1.4.2) (https://github.com/brwnj/fastq-multx) with a mismatch setting of 0. Then, reads of each sample with adapter contamination and low quality were trimmed and filtered using fastp with parameters as -f 10 -t 5 -F 30 -T 5 --complexity_threshold=30 –n_base_limit=5  --length_required 60 (version 0.23.2) and aligned to the human reference genomes hg38, mouse reference genome mm10, or budding yeast genome sacCer3 using bowtie2 (version 2.2.5) with default parameters. Uniquely mapping reads with mapping quality more than 30 were kept using samtools (version 1.9) and duplicates were removed using picard MarkDuplicates (v2.26.10, http://broadinstitute.github.io/picard).
Assembly: BW25113 genome for E. coli, sacCer3 genome for yeast, GRCh38 genome for humans, mm10 genome for mice
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched by glycine with 0.125 M final concentration. sonicated using Covaris SE220 (75 W, 20% Duty factor, 1,000 cycles per burst) for 5 min at 4°C to obtain fragments with the peak size around 200 bp.
The tailing and ssDNA ligation method used to label sample chromatin, and then multiple barcoded samples were pooled and split for immunoprecipitation with relevant antibodies as standard ChIP-seq. After immunoprecipitation, the purified ChIPed DNA was resuspended in 18 µl of water and extended in an 40 µl reaction containing 1 × KAPA HiFi HotStart ReadyMix and 0.25 µM P7TruSeqHTRev at 98 for 30 sec and 63 °C for 5 min followed by purification with 1.2 × volume of SPRIselect™ beads. Then, the purified DNA was ligated to the second adapter in a 40 µl reaction (1× T4 DNA ligase buffer, 0.5 µM P5TruSeqHT/P5SPlint mixture (1:1), and 10 Weiss units of T4 DNA ligase) at 25 °C for 30 minutes and purified with 1.0 × volume of SPRIselect™ beads. Lastly, library was amplified in 50 μl of PCR reaction Mix containing eluted DNA, 0.5 μM of P5 index primer, 0.5 μM P7 index primers, and 25 μl of KAPA HiFi HotStart ReadyMix (2 ×) (Kapa Biosystems) for 12-16 cycles (each cycle with 20 s at 98°C, 30 s at 58°C, 1 min at 68°C). DNA of 200–700 bp was isolated using a double SPRIselect bead cleanup (0.6 × and 0.85 × volume).

value: Astrocytoma


title: HHO5_HRS1-2

description:
Library name: HHHR-2
S1 1x100 Cycle v1.5


title: Proximal intestinal organoids, +48H BMP in ER media

description: Library name: ATAC_48H_BMP

data_processing:
Adapter removal: The ATAC-seq FASTQ files were adapter-trimmed using CutAdapt v1.9.1.
The adapter-trimmed FASTQ files were aligned to the mouse (mm10) genome using Bowtie2 v2.4.1. The SAM files were converted into BAM files using SAMtools v1.3.1 samtobam. The BAM files sorted using SAMtools v1.3.1 sortbam. Picard suite v2.18.27 CollectInsertSizeMetrics and MarkDuplicates were used to 5’ shift inserts by one-half the median insert length by median insert size and remove duplicates in BAM file.
BigWig coverage: A BigWig file was generated for each sorted BAM file using deeptools v3.5.4 bamcoverage (duplicate reads ignored, RPKM normalized and extended reads)
Peak calling: ATAC-seq Picard-modified BAM files were used for peak calling. MACS2 v2.2.7.1 callpeak was used on BAM files to identify enriched genomic regions ("peaks") of varying statistical significance (p<1e-5, p<1e-10). Each peak was re-centered on its summit and extended by 300bp on either side of the summit. Provided BED files have 601bp peak sites which were used for further processing and intersection.
Intersections: Bedtools (v2.26.0) intersect -v was used for intersection/subtraction of BED files for identification of enriched sites found in 0H vs 72H of BMP treatment conditions.
Assembly: mm10
Supplementary files format and content: atac_0h_bmp_macs2_summits_pval_ext_1e-5.bed: MACS2 called  summit centered and extended peaks for 0H BMP condition at p<1e-5 significance.
Supplementary files format and content: atac_0h_bmp_macs2_summits_pval_ext_1e-10.bed: MACS2 called summit centered and extended peaks for 0H BMP condition at p<1e-10 significance.
Supplementary files format and content: atac_0h_bmp_enriched.bed: MACS2 called summit centered and extended peaks for 0H BMP condition at p<1e-10 significance with subtraction of 72H BMP condition peaks at p<1e-5 significance
Supplementary files format and content: ATAC_0H_BMP.bw: RPKM normalized bigwig generated for 0H BMP condition
Supplementary files format and content: ATAC_24H_BMP.bw: RPKM normalized bigwig generated for 24H BMP condition
Supplementary files format and content: ATAC_48H_BMP.bw: RPKM normalized bigwig generated for 48H BMP condition
Supplementary files format and content: atac_72h_bmp_macs2_summits_ext_pval_1-e5.bed: MACS2 called  summit centered and extended peaks for 72H BMP condition at p<1e-5 significance.
Supplementary files format and content: atac_72h_bmp_macs2_summits_ext_pval_1-e10.bed: MACS2 called summit centered and extended peaks for 72H BMP condition at p<1e-10 significance.
Supplementary files format and content: atac_72h_bmp_enriched.bed: MACS2 called summit centered and extended peaks for 72H BMP condition at p<1e-10 significance with subtraction of 0H BMP condition peaks at p<1e-5 significance
Supplementary files format and content: ATAC_72H_BMP.bw: RPKM normalized bigwig generated for 72H BMP condition

source_name: Intestinal organoids from mouse jejunum epithelium

growth_protocol: Mouse small intestine jejunum derived organoids were cultured and treated as mentioned above. Primary crypt-derived organoids were isolated from the proximal half of mouse small intestine and cultured in Cultrex® reduced growth factor basement membrane matrix, Type R1 (BMER1; R&D, 3433-010-R1) according to established methods (Sato et al, 2009). ~500 crypts were plated per 20uL of BMER1 in a 12-well plate with 4-5 “drops” per well.

extract_protocol:
Primary cultured organoids were collected by removing BMER1 using cold PBS. Organoids were pelleted by centrifugation at 300 g for 3 minutes at 4 °C and washed with cold PBS. After removing the PBS and BMER1, organoids were resuspended in 1 mL pre-warmed (37 °C) TrypLE and rotated at 37 °C for 15 to 30 minutes until organoids were dissociated into single cells (confirmed via microscope). Cells were pelleted at 300 g for 3 minutes at 4 °C and washed with cold PBS. Cells were passed through SP Bel-Art Flowmi a 40-μm cell strainer and collected into a new protein LoBind tube. 30,000 cells per condition were centrifuged at 500 g for 5 minutes at 4°C and resuspended in ice-cold lysis buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40). Cells were then centrifuged at 500 g for 10 minutes at 4°C. The isolated nuclear pellets were incubated with a 50 μL reaction of Tn5 Transposase (Illumina Tagment DNA Enzyme and Buffer Large Kit 20034198) for 30 minutes at 37°C.
The transposed chromatin was purified with MinElute PCR purification kit (QIAGEN REF 28004), and PCR was amplified with high-fidelity 2x PCR Master Mix (New England Biolabs M0541). One third of the maximum fluorescent intensity during a qPCR trial run was used to determine the additional cycles for library prep. The PCR amplified libraries were purified and sent to Novogene America for sequencing.

treatment_protocol: Organoids were grown in CVENR (CHIR99021, valproic acid, mEGF, Noggin, and R-spondin as described in Yin et al, 2014) medium and medium was changed every 1-2 days. Recombinant BMP2 (Peprotech) was prepared according to the supplier’s instructions. 100ng/mL BMP2 was added on Day 3, 4, and/or 5 after seeding for ATAC-seq zonation simulation experiment. 0H BMP condition remained in CVENR media, 24H BMP condition removed CVN for 24H and added 100ng/mL of BMP2, 48H BMP condition removed CVN for 48H and added 100ng/mL of BMP2, and 72H BMP condition removed CVN for 72H and added 100ng/mL of BMP2


title: Proximal intestinal organoids, +72H BMP in ER media

description: Library name: ATAC_72H_BMP

value: Intestinal organoids from mouse jejunum epithelium


title: HHO5-4

description:
Library name: HH-4
S1 1x100 Cycle v1.5


title: HHO5_HRS1-1

description:
Library name: HHHR-1
S1 1x100 Cycle v1.5


title: A549, H3K36me3, rep1

value: Lung adenocarcinoma


title: A549_miR206

description: Library name: D002-A-206


title: Proximal intestinal organoids, +24H BMP in ER media

description: Library name: ATAC_24H_BMP


title: PC9_mock

description: Library name: D003-P-mock


title: 786-O, H3K36me3, rep1


title: HHO5-3

description:
Library name: HH-3
S1 1x100 Cycle v1.5


title: A549_mock

description: Library name: D001-A-mock


title: Proximal SI Epithelium, iTBX3KO, 30 days, rep3

description: Library name: RNAseq_Tbx3_iTBX3KO_rep3

data_processing:
fastq files were aligned to Ensembl GRCm39 version 109 using HISAT2 (v 2.2.1)
reads were quantified with Subread featureCounts (v2.0.1)
genes with zero counts in all replicates across all conditions were removed from subsequent analyses
FPKM from counts for each dataset were calculated using GenomicFeatures (v1.58.0) and makeTxDbFromGFF with the gencode.vM10.annotation.gtf annotation file to calculate gene length for all transcripts.
Assembly: mm10
Supplementary files format and content: FPKMs_iDKOvCtrl.txt: FPKMs calculated for SMAD1;SMAD5 iDKO vs control RNA-seq experiment
Supplementary files format and content: FPKMs_iDKO-iTKO.txt: FPKMs calculated for SMAD1;SMAD4;SMAD5 iTKO vs SMAD1;SMAD5 iDKO vs control RNA-seq experiment
Supplementary files format and content: FPKMs_iSMAD4KO.txt: FPKMs calculated for SMAD4 iKO vs control RNA-seq experiment
Supplementary files format and content: FPKMs_iTBX3KO.txt: FPKMs calculated for TBX3 iKO vs control RNA-seq experiment

source_name: Intestinal epithelium

extract_protocol:
Whole epithelium preparations were used for bulk RNA-seq. For primary mouse intestinal epithelium, ~50 μl of epithelial cell pellet was resuspended in 1 ml of TRIzol, and RNA was isolated according to the manufacturer’s instructions.
mRNA libraries were prepared by Novogene with polyA enrichment for NovaSeq X Plus Series (PE150) paired-end sequencing

treatment_protocol: Mice were injected i.p. with tamoxifen or oil (vehicle for tamoxifen) for 4 consecutive days and were sacrificed 6 or 30 days after first injection per experimental design. Tamoxifen-inducible intestinal epithelium specific knockouts (Villin-CreERT2) were used for all studies with controls being Villin-CreERT2 negative, tamoxifen injected or Villin-CreERT2 positive, corn oil injected to maintain littermate and sex-matched controls

value: Intestinal epithelium

value: TBX3 iKO


title: HHO5-2

description:
Library name: HH-2
S1 1x100 Cycle v1.5


title: CD56 low, CD16 positive NK cells from peripheral blood

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Advanced Biomedical Computational Science

institute: Frederick National Labroatory for Cancer Research

description: Library name: CD56-Dim NK

data_processing:
Sequencing reads were processed using Biomodal duet v1.5.0 software (Biomodal) to generate aligned BAM files and genome-wide methylation profiles.
Differential methylation analysis using Modality XPLR v1.0.0 software (Biomodal) was performed across developmental stages to identify regions with changes in cytosine modification.
Assembly: hg38
Supplementary files format and content: Processed epigenetic quantification plain text reports include three quantification files per sample: one containing mC calls; one containing hmC calls; and one containing modC calls. From Biomodall evoC reports, modC calls are the union of the mC calls, the hmC calls, and any undifferentiated modC calls (where a modification was detected but it was not possible to determine whether the modification was an mC or a hmC).
Supplementary files format and content: Processed epigenetic quantification reports in BED format from BedMethyl, which include three quantification files per sample: one containing mC calls; one containing hmC calls; and one containing modC calls.

growth_protocol: Cells were obtained from healthy donor apheresis cones through negative selection of non-NK lineage markers followed by FACS sorting for cells representing the four stages of development studied

extract_protocol:
DNA was extracted using the QIAamp DNA Mini Kit Qiagen).
Genomic DNA libraries were prepared using the duet evoC assay kit (Biomodal), which enables simultaneous detection of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Libraries were constructed according to the manufacturer’s protocol and subjected to whole genome sequencing.

treatment_protocol: Fresh ex vivo cells obtained by FACS sorting

value: Blood

tag: developmental stage

value: CD56 low, CD16 positive NK cells


title: SNB19, H3K36me3, rep1

city: Shenzhen

address: Dapeng

institute: Chinese Academy of Agricultural Sciences


title: HHO5-1

description:
Library name: HH-1
S1 1x100 Cycle v1.5

value: 10 day old root

value: protoplast


title: CD56 high, CD94, KLRF1-positive, CD16-, KIR-negative NK cells from peripheral blood

description: Library name: CD56-Bright NK


title: Proximal SI Epithelium, iTBX3KO, 30 days, rep1

description: Library name: RNAseq_Tbx3_iTBX3KO_rep1


title: OERHON1-atrnh1c_R2

city: Hefei

first: Wenjie

state: Anhui

address: No. 130, Changjiang West Road

institute: Anhui Agricultrual University

description: Library name: Sample6

data_processing:
The duplicated reads with both the same forward and reverse reads were removed according to scripts (https://github.com/PEHGP/DEtail-seq/blob/master/RemoveSamReads.py)
The rest reads were aligned to the reference genome with Bowtie2 using --local settings.
For visualization and splitting strands, the aligned reads files (BAM) including the second read in pairs were converted to the first single base bigWig file with 1bp bins using bamCoverage from deepTools with --binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse. The option --filterRNAstrand forward means Crick strand and -- filterRNAstrand reverse means Watson strand.
Normalization was performed by deepTools based on RPGC with correction by the count of reads mapped to I-CeuI sites from each sample, and the signals around I-CeuI sites (± 8 bp) were deleted in the final normalized bigWig files.
Assembly: Tair10
Supplementary files format and content: bw

source_name: true leaf

extract_protocol:
The chloroplasts were embedded in 0.5% low-melting-point agarose (Promega) and lysed in 1% sarkosyl, 0.45 M EDTA (pH 8.0), 10 mM Tris-HCl (pH 8.0), and 2 mg/mL proteinase K at 48°C for 16 h with shaking. The agarose plugs were washed in TE buffer six times at 37°C, with the first two washes containing 1 mM PMSF. Cut agarose plug into 12 pieces and incubated in 1 ml TE with 10 μg/ml RNase A at 37°C overnight. The agarose pieces were washed five times with 1 ml TE buffer at 37°C for 6 min, then stored in plug storage solution (0.05 M EDTA pH 8.0, 60% glycerol) at -20°C until all samples were ready for the next step.
The DNA library was constructed with Scale ssDNA-seq Lib Prep Kit for Illumina V2 (ABclonal, RK20228). Five agarose pieces (~30 mg) were washed three times with 200 μl 1× CutSmart buffer (NEB) at 37°C for 6 min. The spike-in was performed by incubating the agarose pieces with 15 U I-CeuI (NEB) in 150 μl 1× CutSmart buffer at 37°C for 12 h. After digestion, the agarose pieces were washed three times with 500 μl TE buffer at 37°C for 6 min, followed by twice washes with 200 μl Low EDTA TE (ABclonal) at 37°C for 6 min. The agarose pieces were incubated in 80 μl T7 Tailing & Ligation buffer (ABclonal) at 37°C for 12 h. Then, heated the agarose pieces at 98°C for 2 min. The DNA in the agarose was recovered using a DNA purification kit (Magen, Catalog No D2111-02) and eluted with Low EDTA TE. The DNA was then sonicated to ~250 bp using Focused-ultrasonicator (Covaris S220). To finish the library preparation, the subsequent steps were performed according to the manufacturer's protocol exactly.

value: true leaf

value: Normal light


title: MDA-MB-468, H3K36me2, rep1

value: Breast adenocarcinoma


title: OERHON1-atrnh1c_R1

description: Library name: Sample5


title: Proximal SI Epithelium, control (TBX3), 30 days, rep3

first: Alexandra

description: Library name: RNAseq_Tbx3_Ctrl_rep3

value: Control

value: oil


title: CD34 positive hematopoietic progenitor cells from peripheral blood

description: Library name: CD34+


title: atrnh1c-R2

description: Library name: Sample4


title: RPMI-8226, H3K36me2, rep1

first: Changbin

value: Multiple myeloma


title: Proximal SI Epithelium, control (TBX3), 30 days, rep2

description: Library name: RNAseq_Tbx3_Ctrl_rep2


title: Donor C, SCR0, IL-10

city: Stanford

first: Judith

last: Lunger

address: 240 Pasteur Drive

department: Genetics

institute: Stanford University

description: Library name: Sample C6

data_processing:
Transcript abundances were quantified using Salmon (v1.10.3)
Assembly: Gencode GRCh38.p14
Supplementary files format and content: quant.sf files contain gene counts outputted from Salmon data processing step

growth_protocol: Monocytes from three different donors were isolated from peripheral blood using negative selection. Cells were immediately thawed and differentiated using 50ng/mL of M-CSF in Immunocult SF Macrophage Media (STEMCELL Technologies)

extract_protocol:
Total RNA was extracted from each well using the RNeasy Mini Kit (QIAGEN, #74104).
cDNA library construction using mRNA library preparation (poly A enrichment) by Novogene (Sacramento, CA)

treatment_protocol: Cells were transduced with either SCR(-), pHR-PGK-SCR(S2-S2)-T2A-GFP, pHR-PGK-SCR(S3-S3)-T2A-GFP, or pHR-PGK-SCR(S1-S1)-T2A-GFP, and the media was changed the following day. Cells were then incubated for 3 days, after which, the treatment-indicated cells were treated with either IL-10 (50 ng/mL) or IFN-γ (50 ng/mL). 48 hours after cytokine treatment, cells were imaged on the Cellcyte (Echo, CellCyte 1) to verify high (>80%) and even transduction efficiency across samples.

value: peripheral blood

value: monocytes, differentiated with M-CSF

value: Transduced with SCR0 and IFNg (50ngs/mL) for 48 hrs


title: atrnh1c-R1

description: Library name: Sample3


title: Proximal SI Epithelium, control (TBX3), 30 days, rep1

description: Library name: RNAseq_Tbx3_Ctrl_rep1


title: Donor C, SCR0, IFNg

description: Library name: Sample C5

value: Transduced with SCR0 and IL-10 (50ngs/mL) for 48 hrs


title: Col-0-R2

description: Library name: Sample2


title: Proximal SI Epithelium, iSMAD4KO, 6 days, rep2

description: Library name: RNAseq_S4_iKO_rep2

value: SMAD4 iKO

value: tamoxifen


title: T47D, H3K36me2, rep1

last: Sun

value: Invasive breast carcinoma


title: Donor C, SCR(S1-S1)

description: Library name: Sample C4

value: Transduced with SCR(S1-S1)


title: Col-0-R1_1

description: Library name: Sample1


title: Proximal SI Epithelium, iSMAD4KO, 6 days, rep1

description: Library name: RNAseq_S4_iKO_rep1

value: Intestinal epithelium


title: Donor C, SCR(S2-S2)

description: Library name: Sample C3

value: Transduced with SCR(S3-S3)


title: PC-3, H3K36me2, rep1

value: Prostate carcinoma


title: why1/3/polIb-NL2-AsA

description: Library name: Sample9

data_processing:
The duplicated reads with both the same forward and reverse reads were removed according to scripts (https://github.com/PEHGP/DEtail-seq/blob/master/RemoveSamReads.py)
The rest reads were aligned to the reference genome with Bowtie2 using --local settings.
For visualization and splitting strands, the aligned reads files (BAM) including the second read in pairs were converted to the first single base bigWig file with 1bp bins using bamCoverage from deepTools with --binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse. The option --filterRNAstrand forward means Crick strand and -- filterRNAstrand reverse means Watson strand.
Normalization was performed by deepTools based on RPGC with correction by the count of reads mapped to I-CeuI sites from each sample, and the signals around I-CeuI sites (± 2 bp) were deleted in the final normalized bigWig files.
Assembly: Tair10
Supplementary files format and content: bw

value: true leaf

value: Normal light and 0.5 mM ascorbic acid


title: K562, H3K36me2, rep1

value: Chronic myeloid leukemia


title: why1/3/polIb-NL2

description: Library name: Sample8

value: Normal light


title: Proximal SI Epithelium, control (SMAD4), 6 days, rep1

description: Library name: RNAseq_S4_Ctrl_rep1

value: Control

value: oil


title: Donor C, SCR0

description: Library name: Sample C1

value: peripheral blood

value: Transduced with SCR0


title: SK-OV-3, H3K36me2, rep1

value: Ovarian serous cystadenocarcinoma


title: Col0-NL2-H2O2

description: Library name: Sample7

value: Normal light and 2 mM H2O2


title: Proximal SI Epithelium, SMAD1/4/5 iTKO, 30 days, rep3

description: Library name: RNAseq_Smad_iTKO_rep3

value: SMAD1/4/5 iTKO


title: Donor B, SCR0, IL-10

description: Library name: Sample B6

value: monocytes, differentiated with M-CSF

value: Transduced with SCR0 and IFNg (50ngs/mL) for 48 hrs


title: SW620, H3K36me2, rep1

value: Colon adenocarcinoma


title: Proximal SI Epithelium, SMAD1/4/5 iTKO, 30 days, rep2

description: Library name: RNAseq_Smad_iTKO_rep2

value: Intestinal epithelium

value: tamoxifen


title: Donor B, SCR0, IFNg

description: Library name: Sample B5

value: Transduced with SCR0 and IL-10 (50ngs/mL) for 48 hrs


title: HCT116, H3K36me2, rep1

value: Colon carcinoma


title: Col0-HL2-AsA

description: Library name: Sample5

value: true leaf

value: High light and 0.5 mM ascorbic acid


title: Proximal SI Epithelium, SMAD1/4/5 iTKO, 30 days, rep1

description: Library name: RNAseq_Smad_iTKO_rep1


title: HL-60, H3K36me2, rep1

value: Adult acute myeloid leukemia


title: Col0-NL2

description: Library name: Sample4

value: Normal light


title: Donor B, SCR(S1-S1)

description: Library name: Sample B4

value: Transduced with SCR(S1-S1)


title: Proximal SI Epithelium, SMAD1/5 iDKO, 30 days, rep2

description: Library name: RNAseq_Smad_iDKO_rep2

value: SMAD1/5 iDKO


title: Donor B, SCR(S2-S2)

description: Library name: Sample B3

value: peripheral blood

value: Transduced with SCR(S3-S3)


title: MOLT-4, H3K36me2, rep1

value: Adult T acute lymphoblastic leukemia


title: Col0-HL2

description: Library name: Sample3

value: High light


title: Proximal SI Epithelium, SMAD1/5 iDKO, 30 days, rep1

description: Library name: RNAseq_Smad_iDKO_rep1


title: Proximal intestinal organoids, +0H BMP in CVENR media

description: Library name: ATAC_0H_BMP

value: Intestinal organoids from mouse jejunum epithelium


title: Col0-BL2-AsA

description: Library name: Sample2

value: Blue light and 0.5 mM ascorbic acid


title: Donor B, SCR(S3-S3)

description: Library name: Sample B2

value: monocytes, differentiated with M-CSF

value: Transduced with SCR(S2-S2)


title: Proximal SI Epithelium, control (SMAD1/4/5), 30 days, rep5

description: Library name: RNAseq_Smad_Ctrl_rep5

value: Intestinal epithelium

value: Control

value: oil


title: NCI-H460, H3K36me3, rep1

value: Lung large cell carcinoma


title: Donor B, SCR0

description: Library name: Sample B1

value: Transduced with SCR0


title: NCI-H226, H3K36me2, rep1

value: Pleural epithelioid mesothelioma


title: SK-MEL-28, H3K36me2, rep1

value: Cutaneous melanoma


title: Proximal SI Epithelium, iTBX3KO, 30 days, rep2

description: Library name: RNAseq_Tbx3_iTBX3KO_rep2

value: TBX3 iKO

value: tamoxifen


title: NCI-H522, H3K36me2, rep1

value: Lung adenocarcinoma


title: Col0-BL2

description: Library name: Sample1

value: true leaf

value: Blue light


title: Proximal SI Epithelium, control (SMAD1/4/5), 30 days, rep4

description: Library name: RNAseq_Smad_Ctrl_rep4


title: Donor A, SCR0, IL-10

description: Library name: Sample A6

value: peripheral blood

value: Transduced with SCR0 and IFNg (50ngs/mL) for 48 hrs


title: OVCAR-8, H3K36me2, rep1

value: High grade ovarian serous adenocarcinoma


title: LL-sigma6

description: Library name: Sample40

value: Low light


title: Proximal SI Epithelium, control (SMAD1/4/5), 30 days, rep3

description: Library name: RNAseq_Smad_Ctrl_rep3


title: Donor A, SCR0, IFNg

description: Library name: Sample A5

value: monocytes, differentiated with M-CSF

value: Transduced with SCR0 and IL-10 (50ngs/mL) for 48 hrs


title: NCI-H23, H3K36me2, rep1


title: LL-why1/3/polIb

description: Library name: Sample39


title: Proximal SI Epithelium, control (SMAD1/5), 30 days, rep2

description: Library name: RNAseq_Smad_Ctrl_rep2

value: Intestinal epithelium

value: Control


title: Donor A, SCR(S1-S1)

description: Library name: Sample A4

value: Transduced with SCR(S1-S1)


title: A498, H3K36me2, rep1

value: Renal cell carcinoma


title: SK-MEL-2, H3K36me2, rep1

value: Melanoma


title: CCRF-CEM, H3K36me2, rep1

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: Proximal SI Epithelium, control (SMAD1/5), 30 days, rep1

description: Library name: RNAseq_Smad_Ctrl_rep1

value: tamoxifen


title: LL-why1/3/reca1

description: Library name: Sample38


title: DU145, H3K36me2, rep1

value: Prostate carcinoma


title: Donor A, SCR(S2-S2)

description: Library name: Sample A3

value: Transduced with SCR(S3-S3)


title: LL-polIb

description: Library name: Sample37

value: true leaf

value: polIb


title: Proximal SI Epithelium, SMAD1/5 iDKO, 6 days, rep3

description: Library name: RNAseq_S15_iDKO_rep3

value: SMAD1/5 iDKO


title: Donor A, SCR(S3-S3)

description: Library name: Sample A2

value: peripheral blood

value: Transduced with SCR(S2-S2)


title: U251, H3K36me2, rep1

value: Astrocytoma


title: LL-polIa

description: Library name: Sample36

value: polIa

value: Low light


title: Proximal SI Epithelium, SMAD1/5 iDKO, 6 days, rep2

description: Library name: RNAseq_S15_iDKO_rep2

value: Intestinal epithelium


title: Donor A, SCR0

description: Library name: Sample A1

value: monocytes, differentiated with M-CSF

value: Transduced with SCR0


title: Proximal SI Epithelium, SMAD1/5 iDKO, 6 days, rep1

description: Library name: RNAseq_S15_iDKO_rep1


title: LL-why1/3

description: Library name: Sample35


title: A549, H3K36me2, rep1

value: Lung adenocarcinoma


title: Donor C, SCR(S3-S3)

description: Library name: Sample C2


title: Proximal SI Epithelium, control (SMAD4), 6 days, rep2

description: Library name: RNAseq_S4_Ctrl_rep2

value: Control

value: oil


title: RES_3

first: Chen

last: Yang

address: 1068 Xueyuan Avenue, Nanshan District, Shenzhen,China

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

description: Library name: con_18

data_processing:
Raw sequencing reads (FASTQ files) were quality-checked using Fastp
The cleaned reads were aligned to the GRCh38/hg38 reference genome using STAR
Gene-level counts were generated using featureCounts
Differential expression analysis was performed using the DESeq2 R package with default parameters.
Functional enrichment analysis of KEGG pathways was performed on the DEGs using the clusterProfilerR package with the enrich KEGG function.
Assembly: GRCh38/hg38
Supplementary files format and content: FFA_gene.csv is a comma-separated values (CSV) text file containing the processed raw gene expression count matrix for all samples. The first column provides gene annotation identifiers, and each subsequent column represents the expression data for a single sample.

source_name: liver

extract_protocol:
RNA was extracted from tissues or cells using standard extraction methods, followed by stringent quality control of the RNA samples, primarily through quantification with Nanodrop and assessment of RNA integrity using the Agilent 4200 TapeStation.
A total of 1 µg total RNA per sample was used as input material for the mRNA library reparation. Most of Eukaryote 'mRNA have polyA tails, which are enriched by Oligo (dT) agnetic beads. Then, the obtained mRNA was randomly interrupted by bivalent cations, and the irst strand of cDNA was synthesized in the 1st Strand Enzymes Reverse transcriptase system sing the segmented mRNA as the template and the random oligonucleotide as the primer, and the econd strand of cDNA was synthesized using the 2nd Strand Enzymes and dNTPs. Purified ouble-stranded cDNA undergoes end repair, A-tailing, and ligation with sequencing adapters. DNA with an insert size of approximately 200-300 bp is screened. PCR amplification is erformed and the PCR product is purified again, ultimately obtaining a library.And then, library uality was assessed on the Agilent 4200 TapeStation.

value: liver

value: liver cancer cells


title: 786-O, H3K36me2, rep1

value: Renal cell carcinoma


title: LL-reca1

description: Library name: Sample34

value: true leaf


title: RES_2

description: Library name: con_17


title: LL-Col0

description: Library name: Sample33

value: wildtype


title: Proximal SI Epithelium, control (SMAD1/5), 6 days, rep2

description: Library name: RNAseq_S15_Ctrl_rep2

value: tamoxifen


title: SNB19, H3K36me2, rep1


title: NCI-H460, H3K36me2, rep1

value: Lung large cell carcinoma


title: Proximal SI Epithelium, control (SMAD1/5), 6 days, rep3

description: Library name: RNAseq_S15_Ctrl_rep3


title: RES_1

description: Library name: con_16


title: HL-sigma6

description: Library name: Sample32

value: High light


title: Proximal SI Epithelium, control (SMAD1/5), 6 days, rep1

description: Library name: RNAseq_S15_Ctrl_rep1


title: FUCO-2_3

description: Library name: con_15


title: SK-MEL-28, H3K36me1, rep1

value: Cutaneous melanoma


title: HL-why1/3/polIb

description: Library name: Sample31


title: Col0-NL2-AsA

description: Library name: Sample6

value: Normal light and 0.5 mM ascorbic acid