title: DMN-seq of mES DNA site detection

city: Chicago

first: Yang

last: Li

institute: The University of Chicago

description:
Library name: DMN_site
Mouse embryonic stem cell (mESC) genomic DNA supplemented with 0.1% -DNA, was fragmented using dsDNA Fragmentase, spiked with 200bp dsDNA oligos, and end-repaired/dA-tailed. After ligation with a customized DME adaptor, the DNA was digested with exonucleases to remove unligated or incorrectly processed fragments. The cleaned DNA was treated with recombinant DME enzyme under defined buffer conditions to excise 5mC. Resulting 5-phosphorylated fragments were ligated to a customized ssDNA adaptor using the TACS ligation method. Libraries were PCR-amplified, purified, and sequenced on the Illumina NextSeq 2000 platform.

data_processing:
DMN+ : After trimming the TruSeq sequencing adapters from the 3′ ends of read 1 and read 2 via the Cutadapt (v4.9) tool, low-quality, short reads or reads without 3 consecutive A from the beginning were filtered out. The clean reads were then aligned to the spike-in sequences (the 164 bp and 200 bp synthetic dsDNA spike-ins in Supplementary Table 1 and GenBank J02459.1 for λ-DNA) and reference genomes (mouse reference mm10 for mESC samples) via HISAT2 (v2.2.1). The sorted mapped reads in the mESC samples were then processed to remove PCR duplicates via the Picard tool. Finally, the number of signals was calculated by counting the number of starts of reads at each genomic site. DMN-: After trimming the TruSeq sequencing adapters from the 3′ ends of read 1 and read 2 via the Cutadapt (v4.9) tool, low-quality and short reads were filtered out. The clean reads were then aligned to the spike-in sequences (the 164 bp and 200 bp synthetic dsDNA spike-ins in Supplementary Table 1 and GenBank J02459.1 for λ-DNA) and reference genomes (mouse reference mm10 for mESC samples; human hg38 for cfDNA samples and CRC samples) via HISAT2 (v2.2.1). The sorted mapped reads in the mESC, cfDNA and CRC samples were then processed to remove PCR duplicates via the Picard tool. Finally, the reads were summed via the featureCounts (v2.0.8) tool for each TSS upstream 2000 bp region downloaded from the UCSC genome browser.
Assembly: mm10
Supplementary files format and content: TSV of identified sites, or the matrix from deeptools compute matrix.

source_name: Embryonic stem cell

growth_protocol: The mESC cell line ES-E14TG2a was purchased from ATCC and grown on gelatin-coated plates in complete DMEM (Invitrogen Cat. No. 11995) supplemented with 15% vol/vol FBS (Gibco), 1% penicillin/streptomycin (Gibco), 1.25× nucleoside (MilliporeSigma), 62.5 mM 2-mercaptoethanol (Thermo Fisher Scientific), 1.25× nonessential amino acids (Gibco), 104 U/ml leukemia inhibitory factor (LIF) (MilliporeSigma), 0.289 mg per 500 ml of PD0325901 (STEMCELL Technologies), 0.83 mg per 500 ml of CHIR99021 (STEMCELL Technologies), and 5 mg ml−1 Plasmocin Prophylactic (Invitrogen). The cells were cultured at 37 °C with 5.0% CO2 and passaged every 2 days.

extract_protocol:
Cells were harvested via centrifugation for 3 min at 1000 × g, gDNA was extracted with a PureLink Genomic DNA Mini Kit (Invitrogen) following the manufacturer’s protocol.
Library were prepared following DMN+ and DMN- protocol same as the methods part of the paper.

value: Embryonic stem cell


title: DLBCL Patient_6

status: Public on Jan 12 2026

type: RNA

city: Madrid

first: Juana

last: Serrano López

address: Avda Reyes Católicos 2

department: Hematology

country: Spain

institute: IIS-FJD

hyb_protocol: 100 ng of total RNA imput were prepared according to NanoString nCounter guidelines. Each sample imput was adjusted by DV300 value, measured with TapeStation 4200 and RNA ScreenTape Assay (Agilent, Santa Clara, CA, USA). Hybridization of adjusted RNA samples and NanoString IO360 panel probes was performed in a SimpliAmp Thermal Cycler (Thermo Fisher Scientific, Waltham, Massachusetts, USA) during 20 hours at 65ºC.

scan_protocol: After hybridization, samples were processed with NanoString nCounter Prep Station (NanoString Technologies, Seattle, WA, USA) Research mode protocol and scanned with NanoStringnCounter Digital Analyzer (NanoString Technologies, Seattle, WA, USA) according to manufacturer´s guidelines.

data_processing: RCC raw data was processed and analysed with NanoString nSolver version 4.0 + Advanced Analysis Data Package version 2.0. After Quality Control and data normalization, Advanced Analysis was performed with nSolver Software, as well as extracting normalized data (both with housekeeping genes and control probes included in the panel) which has been used in complementary software.

molecule: total RNA

organism: Homo sapiens

source_name: Lymph Node Biopsy

extract_protocol: On average, 5 5 um-thick sections were prepared for the extraction of total RNA from these samples with RNeasy FFPE Kit (Qiagen, Hilden, Germany). 30 uL of eluted RNA were extracted from each sample. Then, measurement of quality and quantity of this RNA was done with NanoDrop 2000c (Thermo Fisher Scientific, Waltham, Massachusetts, USA).

treatment_protocol: Formalin-Fixed Paraffin-Embedded (FFPE) samples from selected tumoral sections were identified by specialized pathologists after diagnose with both routine and additional stainings.

tag: Sex

value: Male

tag: age

tag: survival

value: Alive

tag: subtype

value: GCB


title: DLBCL Patient_8


title: G1m1_1

type: SRA

city: London

first: Hannah

last: Painter

address: Keppel Street

country: United Kingdom

institute: LSHTM

description: Library name: X1

library_source: transcriptomic

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’s BCL Convert Software v3.7.5.
Sequencing data was processed using nf-core/rnaseq (https://doi.org/10.5281/zenodo.7998767). Default parameters were used.
Assembly: GRCm38
Supplementary files format and content: salmon.merged.gene_counts_length_scaled.tsv; matrix of gene-level length-scaled counts for all samples
Supplementary files format and content: salmon.merged.gene_counts_scaled.tsv; matrix of gene-level library size-scaled counts for all samples
Supplementary files format and content: salmon.merged.gene_counts.tsv; matrix of gene-level raw counts for all samples
Supplementary files format and content: salmon.merged.gene_tpm.tsv; matrix of gene-level TPM values for all samples.
Supplementary files format and content: salmon.merged.transcript_counts.tsv; matrix of isoform-level raw counts for all samples.
Supplementary files format and content: salmon.merged.transcript_tpm.tsv; matrix of isoform-level TPM values for all samples

organism: Mus musculus

source_name: Lung

extract_protocol:
Lung accessory lobes were collected in RNAprotect tissue reagent (Qiagen) overnight before removal from the reagent and storage at -80oC until RNA extraction. RNA was extracted from the acessory lobe by homogenising the tissue in RLT buffer (+1% BME) using a Precellys 24 Tissue Homogenizer. The homogenate was centrifuged at full speed and RNA was extracted from the supernatant using the RNeasy Mini kit (Qiagen), including an on-column RNase-free DNase digestion step (Qiagen).
Total RNA quantification and integrity was confirmed using Agilent’s 4200 Tapestation (Standard Total RNA assay). For each sample, 500ng of total RNA were processed using the KAPA mRNA HyperPrep Kit (Roche p/n KK8580) according to manufacturer’s instructions. Briefly, mRNA was isolated from 500ng total RNA by use of paramagnetic Oligo dT beads to pull down poly-adenylated transcripts. The purified mRNA was fragmented using chemical hydrolysis (heat and divalent metal cation) and primed with random hexamers. Strand-specific first-strand cDNA was generated using reverse transcriptase in the presence of actinomycin D. The second cDNA strand was synthesised using dUTP in place of dTTP, to mark the second strand. The resultant cDNA was then “A-tailed” at the 3’ end to prevent self-ligation and adapter dimerisation. Full-length xGen adaptors (IDT), containing two unique 8-bp sample specific indexes, a unique molecular identifier (N8) and a T overhang are ligated to the A-tailed cDNA. Successfully ligated cDNA molecules were then enriched with limited cycle PCR (11 PCR cycles). The high fidelity polymerase employed in the PCR is unable to extend through uracil. This means only the first strand cDNA is amplified for sequencing, making the library strand specific (first-strand). High yield, adaptor-dimer free libraries were confirmed on the Agilent TapeStation 4200 (High Sensitivity Agilent DNA 1000 assay) and a library quantification was estimated using the Qubit dsDNA HS assay (Life Technolgies). Libraries were normalised to 4nM and then an equal volume of each were pooled together. The library pool was denatured and sequenced on the NextSeq 2000 instrument (Illumina, San Diego, US) at 750pM, using a 56bp paired-read run with corresponding 8bp unique dual sample indexes and 8bp unique molecular index.

tag: strain

value: Female

tag: mcmv status

value: negative

tag: mtb status

tag: tissue

value: Lung

tag: sample time_point_post_mtb_infection

tag: lung log10_cfu

value: uninfected

tag: spleen log10_cfu

tag: lymph node_log10_cfu


title: UBS-seq of mES DNA, batch 1

country: USA

description:
Library name: UBS_1
200 ng of mESC gDNA supplemented with 0.1% (w:w) -DNA were fragmented and purified with a DNA Clean & Concentrate Kit (Zymo Research). The fragmented mESC gDNA/-DNA mixture was supplemented with 0.01% (w:w) 200 bp dsDNA oligo and 0.01% (w:w) 164 bp dsDNA oligo as spike-ins. The DNA mixture was then added to reagents from the NEBNext Ultra II End Repair/dA-Tailing Module (NEB) and incubated sequentially at 20 C for 30 mins and 65 C for 30 mins. Using the NEBNext Ultra II Ligation Module (NEB), 1/4 of the DNA mixture, which serves as the UBS-seq control samples, was ligated with 15 M methylated NEBNext adaptor (NEB), while the rest was ligated with 15 M customized DME dsDNA adaptor with phosphorothioate modifications (IDT, Table S1) at 20 C for 15 mins. The ligated DNA samples were purified with 1.0 AMPure XP beads and eluted in H2O. The UBS-seq sample was subjected to UBS-1 conditions and desulphonated via DNA Methylation-Gold Kit (Zymo Research) following the UBS-seq procedure [28].

library_source: genomic

molecule: genomic DNA


title: DN1

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

country: China

institute: Nanjing Medical University

description: Library name: DN1

data_processing:
Raw paired-end sequenced reads were first cut for adapter sequences and trimmed using trim_galore (v.0.6.6).
Cleaned fastq data were mapped to the mm10 reference genome for sample from mouse using STAR (v.2.7.10a).
Reads from specific chromosome regions with annotation were counted using htseq-count (0.13.5).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

source_name: spleen

extract_protocol:
Briefly, single-cell suspensions were obatined by mincing and filtering mouse spleens and bone marrows through 70-μm cell strainers.  Cells were incubated in phosphate-buffered saline (PBS) containing 2% (w/v) FCS with indicated antibodies for 25min at 4°C. Cell sorting were performed with BD Aria II or Aria Fusion.
2 ug total RNAs were used for stranded RNA sequencing library preparation using KC-Digital(TM) Stranded mRNA Library Prep Kit for Illumina(R) (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer's instruction.

treatment_protocol: To obatin enough GC center B cells, mice were immunized with 2×107 SRBCs (i.p.) and challenged with 2×108 SRBCs (i.p.) 5days later. At day 12, mice were euthanized for analysis.

value: spleen

tag: cell type

value: Spleen germinal center B cells

tag: genotype

value: WT

tag: treatment

value: SRBC (i.p.)

tag: batch


title: Huh7-DENV2

city: Stanford

first: Alina

last: Isakova

state: CA

address: 290 Jane Stanford Way

institute: Stanford University

description:
Library name: SSTX-DENV2
TotalX

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed using Cell Ranger mkfastq (v8.0.1) and Read2 was trimmed using Cutadapt with the following parameters: -u 6 -a "AAAAAAAAAA;min_overlap=10" -m 18. Trimmed reads were then processed using cellranger count with a dual-pass alignment strategy to enable quantification of both long and short RNA species. Two custom reference transcriptomes were constructed from the GRCh38 primary assembly (Ensembl release 109; GRCh38.p13). Gene annotations were sourced from GENCODE v44 and manually curated to include an expanded set of biotypes. The primary (long RNA) reference included the following biotypes: protein_coding, lncRNA, miRNA, snRNA, snoRNA, scaRNA, tRNA, Mt_tRNA, vault_RNA, misc_RNA, antisense, scRNA, and immunoglobulin and T-cell receptor genes (e.g., IG_*, TR_*). tRNA annotations were appended using curated entries from high confidence set in GtRNAdb62. For viral infection studies, the dengue virus serotype 2 (DENV2) genome (GenBank NC_001474; GCF_000871845.1) and its corresponding annotation (modified_dengue.gtf) were appended.
Assembly: Ensembl release 109; GRCh38.p13
Supplementary files format and content: h5ad objects with processsed counts and annotations

growth_protocol: HEK293T cells were cultured in complete DMEM high glucose medium (Thermo Fisher Scientific, 11965092) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, 16000044), 1mM sodium pyruvate (Thermo Fisher Scientific, 11360070) and 100 μg/mL Penicillin/Streptomycin (Thermo Fisher Scientific, 15070063). Cells were dissociated using 0.25% Trypsin-EDTA (Thermo Fisher Scientific, 25200056) for 2-4 min at 37°C and collected for analysis.

extract_protocol:
Single-cell total RNA sequencing was performed using TotalX, a modified 10x Genomics Chromium 3′ v3.1 workflow incorporating enzymatic strategies adapted from Smart-seq-total. The protocol enables the simultaneous capture of polyadenylated and non-polyadenylated transcripts through a co-incubation approach integrating 3′ polyadenylation, 5′ capping, and reverse transcription (RT) in a single reaction. RT master mix was prepared by supplementing the standard 10x RT reagents with the addition of following components: E. coli poly(A) polymerase (New England Biolabs, M0276S; final 1 U/µl), ATP (10 mM), Vaccinia capping enzyme (NEB, M2080S; 0.1 U/µl), S-adenosylmethionine (SAM, 2 mM; NEB, M2080S), guanosine triphosphate (GTP, 10 mM; NEB, M2080S), and a custom biotinylated template-switching oligonucleotide (5′ Biotin-ATGGCUCGGAGAUGUGUAUAAGAGACAGUCUrGrG+G; Integrated DNA Technologies). Reagents were mixed immediately prior loading and kept on ice until droplet generation. Cells or nuclei were loaded into the 10x Genomics Chromium controller following the manufacturer’s protocol for 3′ v3.1 chemistry.
Following reverse transcription, emulsion droplets were broken according to 10x recovery steps. cDNA was then treated with uracil-DNA glycosylase (UDG; NEB, M0280S) to remove dUTSO fragments at 37°C for 50-60 min. This was followed by 5 cycles of amplification using 10x proprietary primers and a custom spike in primer (according to TotalX protocol). pre-amped cDNA (for 5 cycles) was cleaned up using 1.8X SPRI Select (Beckman Coulter, B23317) and cDNA corresponding to ribosomal RNA was depleted by Cas9-mediated cleavage using guide RNAs targeting mitochondrial and cytoplasmic ribosomal sequences (DASH). CRISPR ribonucleoprotein complexes were assembled from Alt-R S.p. Cas9 Nuclease V3 (NEB, 1081059), tracrRNA (IDT, 1072532), and a custom pool of 57 crRNAs (IDT) designed based on Smart-seq-total DASH oligos (Supplementary Table 1). The reaction was incubated at 37°C for 60 min, followed by treatment with proteinase K (Thermo Fisher Scientific, EO0491) for 10 min at 56°C. cDNA was then cleaned up using SPRI Select and amplified for additional 7-10 cycles using 10x proprietary primers and a custom spike in primer. Amplified cDNA was separated into long- and short-fragment pools using SPRIselect magnetic beads (Beckman Coulter, Cat# B23318). To obtain the long-fragment pool, SPRIselect beads were added to amplified cDNA at a 0.6X bead-to-sample ratio, and bound fragments were retained according to the manufacturer’s instructions. Unbound fragments in the supernatant were further purified at a 1.2X bead ratio (1.8X final) to isolate the short-fragment pool. The long-fragment pool was processed according to the Chromium Single Cell 3′ v3.1 protocol (10x Genomics), using the Single Index Kit T Set A (PN-1000213/PN-2000240). Short fragments were indexed using custom primers through PCR amplification containing 10x Genomics 3′ v3.1 library amplification mix, SI primer and custom index primers (see Supplementary Table 1) For each 40 μl reaction, the following components were combined: 20 μl Amp Mix, 4 μl SI primer, 1 μl custom index primer (10 μM), 1 μl amplified cDNA (1 ng/μl), and 14 μl nuclease-free water. PCR conditions were as follows: 98°C for 3 min; 12 cycles of 98°C for 15 sec, 62°C for 20 sec, and 72°C for 2 min; and a final extension at 72°C for 1 min. PCR products were purified with a 1.2X SPRIselect bead clean-up and eluted in 30 μl nuclease-free water. The resulting libraries were either split for further purification to remove very short fragments (below 200-250bp) and obtain the small RNA fraction or used for optional miRNA enrichment. The miRNA(+) fragments were further size-selected from the short-fragment pool by enrichment of fragments corresponding to small RNAs (18–30 bp) using the Pippin Prep gel system (Sage Science, 3% agarose), following the manufacturer’s protocol. Short and long pools were recombined in desired ratios prior to final library quality control and sequencing. Resulting libraries were sequenced on a NovaSeq X instrument (Illumina) with the following configuration: Read 1, 28 bp; Index 1, 8 bp; Index 2, 0 bp; Read 2, 91 bp.

treatment_protocol: Huh7 human hepatoma cells (Apath LLC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Thermo Fisher Scientific, 11965092) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific, 16000044), 1 mM sodium pyruvate (Thermo Fisher Scientific, 11360070), and 100 U/ml penicillin-streptomycin (Thermo Fisher Scientific, 15140122) at 37°C in a 5% CO2 humidified incubator. Cells were seeded in 6-well plates and infected at ~70% confluence with dengue virus serotype 2 (DENV2; strain 16681) at a multiplicity of infection (MOI) of 1.For infection, virus-containing media was diluted in serum-free DMEM and added to cells for 1 h at 37°C with gentle rocking every 15 min. After incubation, the inoculum was removed, and cells were washed once with phosphate-buffered saline (PBS; Thermo Fisher Scientific, 10010023) before replacing with fresh complete medium. Cells were incubated for 48h post-infection to allow for robust viral replication. Mock-infected controls were treated identically with virus-free media. At the endpoint, cells from two replicate wells (approximately 1 × 106 cells per well) were harvested by trypsinization (0.25% Trypsin-EDTA; Thermo Fisher Scientific, 25200056), pelleted by centrifugation (300 × g, 5 min), and resuspended in PBS for downstream processing. Cell viability was assessed using the Luna automated cell counter (Logos Biosystems), and cells were diluted to 750–1,000 cells/µl prior to encapsulation for single-cell TotalX.

tag: cell line

value: Human hepatoma cells

value: infected with DENV2


title: spleen, Wt3

description: Library name: Wt3

data_processing:
Raw paired-end sequenced reads were first cut for adapter sequences and trimmed using trim_galore (v.0.6.6).
Cleaned fastq data were mapped to the mm10 reference genome for sample from mouse using Bowtie 2 (v.2.4.2).
SAMtools (v.1.11) was used to convert and sort the SAM files into BAM format.
DeepTools was used to normalize signals from sorted BAM files via bamCoverage.
SEACR（1.3）was used for peak calling with default model.
Assembly: mm10
Supplementary files format and content: bigWig,bed
Library strategy: CUT&Tag

extract_protocol:
Briefly, single-cell suspensions were obatined by mincing and filtering mouse spleens and bone marrows through 70-μm cell strainers.  Cells were incubated in phosphate-buffered saline (PBS) containing 2% (w/v) FCS with indicated antibodies for 25min at 4°C. Cell sorting were performed with BD Aria II or Aria Fusion.
CUT&Tag assay was conducted using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme TD904). 1-5×103 GCB cells were collected and bound to ConA beads for 10 min at 25 °C. Cells were washed then incubated with 1 μg indicated antibodies at 4 °C overnight. Secondary antibodies were added for 1 hr at 25 °C followed by 0.04 μM pA/G–Tnp for 1 hr at 25 °C. For fragmentation, cells were incubated at 37 °C for 1hr. After stopping fragment， DNA was collected with DNA magnetic beads (Vazyme) for library construction using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) and TruePrep Index Kit V2 for Illumina (Vazyme).

tag: chip antibody

value: CD83+ly75+GCB cells


title: DMN-seq input of mES DNA site detection

description:
Library name: input_site
Mouse embryonic stem cell (mESC) genomic DNA supplemented with 0.1% -DNA, was fragmented using dsDNA Fragmentase, spiked with 200bp dsDNA oligos, and end-repaired/dA-tailed. After ligation with a customized DME adaptor, the DNA was digested with exonucleases to remove unligated or incorrectly processed fragments. The cleaned DNA was treated with recombinant DME enzyme under defined buffer conditions to excise 5mC. Resulting 5-phosphorylated fragments were ligated to a customized ssDNA adaptor using the TACS ligation method. Libraries were PCR-amplified, purified, and sequenced on the Illumina NextSeq 2000 platform.


title: HEK293T, TotalX miRNA(+)/DASH(-)

description:
Library name: SSTX-HEK293T-noDASH
TotalX

value: Human embryonic kidney cells


title: DLBCL Patient_4

tag: Sex

tag: age


title: DLBCL Patient_5

tag: survival

tag: subtype


title: HEK293T, TotalX miRNA(+)/DASH(++)

description:
Library name: SSTX-HEK293T-2XDASH
TotalX


title: spleen, Wt4

description: Library name: Wt4

tag: strain


title: DLBCL Patient_3


title: DLBCL Patient_2


title: spleen, OE4

description: Library name: OE4

value: OE


title: spleen, OE1

description: Library name: OE1


title: LWHR84

first: Gilles

last: Laverny

address: 1 rue Laurent fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 108 and “union” mode. Only non-ambiguously assigned reads were retained for further analyses. Read counts were normalized across libraries as described (Anders & Huber, 2010).
Assembly: mm10
Supplementary files format and content: Raw_GEO.txt

source_name: prostate

extract_protocol:
P2869
TRIZOL
P2869 : Full length cDNA were generated from --- pg of total RNA (or directly from --- cells/tissues frozen in PBS buffer containing RNAses inhibitor) using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with --- cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

value: prostate

value: luminal cells

value: PTEN/VDR(i)pe-/-

value: 3 months after gene inactivation


title: M+NSPCC1_M04

city: Guangzhou

first: Zhaoyun

last: Xue

address: Second of the Zhongshan Road

institute: Sun Yat-sen University

description: Library name: M+NSPCC1_M04

data_processing:
The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and PE 100/150 bases reads are generated on G400/T7/T10 platform (BGI-Shenzhen, China).
The sequencing data was filtered with SOAPnuke (v2.2.1) by  Removing reads containing sequencing adapter;Removing reads whose low-quality base ratio;Removing reads whose unknown base ('N' base) ratio is more than 5%;afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
The clean reads were mapped to the reference genome using HISAT2 (v2.2.1). After that, Ericscript (v0.5.5)  and rMATS (V4.1.2)  were used to detect fusion genes and differential splicing genes (DSGs), respectively
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.12)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) (or DEGseq （v1.48.0） or PoissonDis )with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: skin

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

value: skin


title: gDNA RRBS, tumor, patient #6

description: Library name: RRBS_T6

data_processing:
After trimming the TruSeq sequencing adapters from the 3′ ends of read 1 and read 2 via the Cutadapt (v4.9) tool, low-quality and short reads were filtered out. The clean reads were then aligned to the spike-in sequences (the 164 bp and 200 bp synthetic dsDNA spike-ins in Supplementary Table 1 and GenBank J02459.1 for λ-DNA) and reference genomes (mouse reference mm10 for mESC samples; human hg38 for cfDNA samples and CRC samples) via HISAT2 (v2.2.1). The sorted mapped reads in the mESC, cfDNA and CRC samples were then processed to remove PCR duplicates via the Picard tool. Finally, the reads were summed via the featureCounts (v2.0.8) tool for each TSS upstream 2000 bp region downloaded from the UCSC genome browser.
For RRBS samples, after trimming the TruSeq sequencing adapters from the 3′ ends of read 1 and read 2 via the Cutadapt (v4.9) tool, low-quality and short reads were filtered out. The clean reads were then aligned to the human hg38 reference genome via HISAT3N (v2.2.1-3n-0.0.3) with the ‘--no-splice-alignment' argument. The sorted mapped reads in the cfDNA and CRC samples were then processed to remove PCR duplicates via the Picard tool. Finally, the number of converted and unconverted reads at all C sites was counted using the hisat-3n-table command, and the methylation ratio was calculated as the number of unconverted reads divided by total coverage.
Assembly: hg38
Supplementary files format and content: The sum of reads number in 2000 bp region, or the bigwig of sites.

source_name: colon

extract_protocol:
A total of 10 ng of gDNA from CRC patient cohort tumor tissue and adjacent healthy colon tissue was used as the untreated sample, whereas 40 ng was used as the DME-treated sample. All gDNA samples were prepared, fragmented, and end-repaired in the same way as those used for methylated DNA enrichment. 1 ng, 0.5 ng. A total of 0.1 ng of cfDNA from CRC patients and healthy controls was used as the untreated sample, whereas 2 technical replicates of the same input level were used as DME-treated samples. The cfDNA samples were directly end-repaired without fragmentation.
Library were prepared following DMN+ and DMN- protocol same as the methods part of the paper. RRBS libraries were processed using Zymo-seq RRBS Library Kit (Zymo Research) following the following the manufacturer’s protocol

value: colon


title: Huh7

description:
Library name: SSTX-Huh7
TotalX


title: spleen, Ko2

description: Library name: Ko2

value: Efnb1 ai3 KO


title: DLBCL Patient_1

value: Female

value: Dead

value: GCB


title: M+NSPCC1_M03

description: Library name: M+NSPCC1_M03


title: spleen, Ko4

description: Library name: Ko4

value: spleen

value: CD19 cre B KO


title: LWHR85


title: HEK293T, TotalX

description:
Library name: SSTX-HEK293T
TotalX


title: LWHR83


title: M+NSPCC1_M02

description: Library name: M+NSPCC1_M02


title: spleen, EV2

description: Library name: EV2

value: EV


title: M+NSPCC1_M01

description: Library name: M+NSPCC1_M01


title: gDNA RRBS, tumor, patient #4

description: Library name: RRBS_T4


title: gDNA RRBS, tumor, patient #5

description: Library name: RRBS_T5


title: gDNA RRBS, tumor, patient #3

description: Library name: RRBS_T3


title: LWHR77

value: PTEN(i)pe-/-


title: LWHR72

value: 1 month after gene inactivation


title: LWHR74


title: LWHR75


title: gDNA RRBS, tumor, patient #2

description: Library name: RRBS_T2


title: Spleen, Wt3

description: Library name: Wt3

value: CD83+ly75+GCB cells

value: WT

value: SRBCs (i.p.)


title: Spleen, Wt4

description: Library name: Wt4


title: LWHR73

value: prostate

value: luminal cells


title: spleen, EV4

description: Library name: EV4


title: gDNA RRBS, tumor, patient #1

description: Library name: RRBS_T1


title: Model02

description: Library name: Model02


title: Model03

description: Library name: Model03


title: Model01

description: Library name: Model01


title: LWHR69


title: gDNA RRBS, control, patient #3

description: Library name: RRBS_N3


title: Model04

description: Library name: Model04


title: Spleen, Wt1

description: Library name: Wt1


title: gDNA RRBS, control, patient #6

description: Library name: RRBS_N6


title: Spleen, Ko4

description: Library name: Ko4

value: KO


title: LWHR78

value: 3 months after gene inactivation


title: Spleen, Ko3

description: Library name: Ko3


title: Spleen, Wt2

description: Library name: Wt2


title: All 3 neutrophil cultures (Figure 6) FB

city: Birmingham

first: Paran

last: Goel

state: Alabama

address: Department of Hematology and O, 701 20th Street South

institute: University of Alabama, Birming

description: Library name: Sample6

data_processing:
Bcl2fastq files were pre-processed with Cell Ranger mkfastq using a pipeline recommended by 10x Genomics. Cell Ranger multi, software v6.1.1, was used to align reads to reference mouse genome (mm10), assemble transcriptomic count matrices, and de-multiplex hashed samples. Partek Flow (https://www.partek.com/partek-flow/) was used for further analysis and data visualization, including QA/QC, normalization, noise reduction, DEG, clustering, and pathway enrichment analysis.
Assembly: Mouse mm10
Supplementary files format and content: h5 files

source_name: Bone marrow

extract_protocol:
For pooling purposes, bone marrow from control and AML mice were stained with TotalSeq-B hashtaging antibodies as per the protocol provided by BioLegend. Live singlets gated on host neutrophils were sorted in DPBS 0.04% BSA before loading onto 10x Genomics instrument according to the manufacturer’s protocol. SImilarly, all three neutrophil culture conditions were pooled together along with hashtaging antibodies and processed as above.
Gene expression and feature barcode libraries for single-cell RNA-seq were prepared using the Chromium Next GEM Single Cell 3’ Gene Expression v3 with modifications for hashtag libraries. Quality control for amplified cDNA libraries and sequencing libraries was performed using a BioAnalyzer High Sensitivity DNA kit (Agilent). GEX and Cell Hashing libraries were sequenced on Illumina NextSeq 500 with a sequencing depth of at least 50,000 reads per cell for 3’ GEX and 5,000 reads per cell for feature barcode.

value: Bone marrow

value: mouse neutrophil


title: LWHR70


title: Ctrl04

description: Library name: Ctrl04

value: skin


title: gDNA RRBS, control, patient #5

description: Library name: RRBS_N5

value: colon


title: LWHR67


title: All 3 neutrophil cultures (Figure 6) GEX

description: Library name: Sample5


title: gDNA RRBS, control, patient #4

description: Library name: RRBS_N4


title: Spleen, Ko1

description: Library name: Ko1


title: gDNA RRBS, control, patient #2

description: Library name: RRBS_N2


title: Spleen, Ko2

description: Library name: Ko2


title: gDNA RRBS, control, patient #1

description: Library name: RRBS_N1


title: Ctrl01

description: Library name: Ctrl01


title: Bone marrow neutrophils from control and AML mice (Figure 6) FB

description: Library name: Sample4


title: Ctrl03

description: Library name: Ctrl03


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #6, DMN

description: Library name: gDNA_T6-1


title: B1-8 B cells

data_processing:
The Cell Ranger software was obtained from 10x Genomics websitehttps://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters
Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively
Assembly: mm10
Supplementary files format and content: txt files include raw counts for each cells

source_name: spleens

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3.

value: spleens

value: antigen-specific B cells


title: DMN-seq input of mES DNA hypomethylation enrichment

description:
Library name: input_enrich
Mouse embryonic stem cell (mESC) genomic DNA supplemented with 0.1% -DNA, was fragmented using dsDNA Fragmentase, spiked with 200bp dsDNA oligos, and end-repaired/dA-tailed. After ligation with a customized DME adaptor, the DNA was digested with exonucleases to remove unligated or incorrectly processed fragments. The cleaned DNA was treated with recombinant DME enzyme under defined buffer conditions to excise 5mC. Resulting 5-phosphorylated fragments were ligated to a customized ssDNA adaptor using the TACS ligation method. Libraries were PCR-amplified, purified, and sequenced on the Illumina NoveSeqX platform.

value: Embryonic stem cell


title: UBS-seq of mES DNA, batch 2

description:
Library name: UBS_2
200 ng of mESC gDNA supplemented with 0.1% (w:w) -DNA were fragmented and purified with a DNA Clean & Concentrate Kit (Zymo Research). The fragmented mESC gDNA/-DNA mixture was supplemented with 0.01% (w:w) 200 bp dsDNA oligo and 0.01% (w:w) 164 bp dsDNA oligo as spike-ins. The DNA mixture was then added to reagents from the NEBNext Ultra II End Repair/dA-Tailing Module (NEB) and incubated sequentially at 20 C for 30 mins and 65 C for 30 mins. Using the NEBNext Ultra II Ligation Module (NEB), 1/4 of the DNA mixture, which serves as the UBS-seq control samples, was ligated with 15 M methylated NEBNext adaptor (NEB), while the rest was ligated with 15 M customized DME dsDNA adaptor with phosphorothioate modifications (IDT, Table S1) at 20 C for 15 mins. The ligated DNA samples were purified with 1.0 AMPure XP beads and eluted in H2O. The UBS-seq sample was subjected to UBS-1 conditions and desulphonated via DNA Methylation-Gold Kit (Zymo Research) following the UBS-seq procedure [28].


title: Bone marrow neutrophils from control and AML mice (Figure 6) GEX

description: Library name: Sample3


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #5, DMN

description: Library name: gDNA_T5-1


title: Ctrl02

description: Library name: Ctrl02


title: Bone marrow neutrophils from control and AML mice (Figure 3) GEX

description: Library name: Sample1


title: Spleen germinal center B cells, K27NB

data_processing:
Raw paired-end sequenced reads were first cut for adapter sequences and trimmed using trim_galore (v.0.6.6).
Cleaned fastq data were mapped to the mm10 reference genome for sample from mouse using Bowtie 2 (v.2.4.2).
SAMtools (v.1.11) was used to convert and sort the SAM files into BAM format.
DeepTools was used to normalize signals from sorted BAM files via bamCoverage.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

value: spleen

value: Spleen germinal center B cells


title: Spleen germinal center B cells, K27LZ


title: Spleen germinal center B cells, K27Non_DP


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #4, DMN

description: Library name: gDNA_T4-1


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #6, input

description: Library name: gDNA_T6-0


title: Spleen germinal center B cells, K27DP


title: Twist1 EC-KO mouse 4

first: Paul

last: Evans

address: Charterhouse square

institute: QMUL

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode and UMI. Read 2 was assigned 60 base pairs and used to map to the Mouse GRCm38 reference genome with BWA-MEM 0.7.15. Briefly, mapping and generation of count tables was automated using MapAndGO. Unsupervised clustering and differential expression analysis was performed with the Seurat R toolkit
Assembly: mm10 (GRCm38)
Supplementary files format and content: *.TranscriptCounts.tsv: Tab-separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the cell number of the experiment. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. TranscriptCounts files show the estimated original transcript counts, based on the fact that you are randomly sampling from a small fraction of the original pool of molecules.
Supplementary files format and content: *.BarcodeCounts.tsv: Tab-separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the cell number of the experiment. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. BarcodeCounts files show the number of UMI-corrected read counts.
Supplementary files format and content: *.ReadCounts.tsv: Tab-separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the cell number of the experiment. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. ReadCounts files shows the number of raw read counts.

source_name: aorta

extract_protocol:
Mice were given intraperitoneal injections of 100 μl pentobarbital. The mouse chest was dissected, revealing the heart. The vasculature was perfused with 10 ml phosphate buffered saline (PBS) containing 2% heparin. The aorta was dissected and cleaned and the adipose and connective tissue surrounding the aorta were removed. To digest the aorta, (which included the aortic arch, ascending, descending, thoracic, and abdominal portions) the sample was placed in a 35mm dish containing 125 U/mL collagenase type XI, 60 U/mL hyaluronidase type 1-s, 60 U/mL DNase I, 450 U/mL collagenase type I and 0.5 mg/ml elastase in 2.5 ml of PBS, at 37ºC for 1h. After the first 10 mins of incubation, the adventitia was removed using forceps. Following the incubation, single cell suspensions from the digested aorta were prepared by pipetting the solution through a 40 μm cell strainer. Cells were washed and resuspended in FACS buffer (PBS with 1% BSA) and stained with CD31-AF488 and CD45-APC antibodies and TOPRO3. Alive, CD45-, CD31+ cells were sorted using a BDFACSMelody cell sorter (BD Biosciences) into single wells of 384-well plates containing reverse transcription primers, deoxyribonucleotide triphosphates, External RNA Controls Consortium (ERCC) RNA Spike-Ins, and mineral oil.
scRNA-seq libraries were generated using the SORT-seq protocol (Muraro et al., 2016) a partially robotized method based on the CEL-Seq2 protocol (Hashimshony et al., 2016). Single cells were lysed at 65°C for 5 min, and second-strand mixers and reverse transcriptase were added to the wells using the Nanodrop II liquid handling platform (GC Biotech). The mRNA of each cell was reserve-transcribed, double-stranded complementary DNAs (cDNAs) from single cells were pooled, and in vitro transcription was performed for linear amplification, resulting in amplified RNA. The Illumina sequencing libraries were prepared using TruSeq small RNA primers (Illumina), and the DNA libraries were then sequenced paired-end at 75–base pair read length using the Illumina NextSeq 500 by Single Cell Discoveries (Utrecht, The Netherlands). The RNA yield of the amplified RNA and the quality and concentration of the final cDNA libraries were assessed by Bioanalyzer (Agilent).

value: aorta

value: endothelial cells (CD45-, CD31+ cells)

value: Twist1fl/fl, ApoE-/-, Cdh5Cre/+


title: DMN-seq of mES DNA hypomethylation enrichment

description:
Library name: DMN_enrich
Mouse embryonic stem cell (mESC) genomic DNA supplemented with 0.1% -DNA, was fragmented using dsDNA Fragmentase, spiked with 200bp dsDNA oligos, and end-repaired/dA-tailed. After ligation with a customized DME adaptor, the DNA was digested with exonucleases to remove unligated or incorrectly processed fragments. The cleaned DNA was treated with recombinant DME enzyme under defined buffer conditions to excise 5mC. Resulting 5-phosphorylated fragments were ligated to a customized ssDNA adaptor using the TACS ligation method. Libraries were PCR-amplified, purified, and sequenced on the Illumina NoveSeqX platform.


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #4, input

description: Library name: gDNA_T4-0


title: Spleen germinal center B cells, K27PC

value: WT


title: CDM with iron, biol rep1

city: Charlottesville

first: Camille

middle: Shea

last: Westlake

state: Virginia

address: 1340 Jefferson Park Avenue, Pinn Hall Room 7213

department: Microbiology, Immunology, Cancer Biology

institute: University of Virginia

description: Library name: FE1

data_processing:
Sequence reads were trimmed for quality and adaptor sequences using Trimmomatic(v.0.39) with parameters ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True \ LEADING: 3 \ TRAILING:3 \ SLIDINGWINDOW:4:15 \ MINLENGTH: 36
Reads were mapped to the FA1090 Neisseria gonorrhoeae genome using Bowtie2 (v2.5.3) with parameters  -I 0 -X 600 --fr
Gene-level read counts were generated from aligned RNA-seq reads using HTSeq(v2.0.5) with parameters htseq-count --mode=union --stranded=reverse --minaqual=10 --type=CDS  --idattr=ID
Assembly: N. gonorrhoeae FA1090 with GenBank annotations (GCA_009757095.1, ASM975709v1)
Supplementary files format and content: tab-delimited files include counts for each sample (.tabular)

organism: Neisseria gonorrhoeae

source_name: FA1090 OpaDnv

growth_protocol: Gc were prepared for experiments by inoculating -80 °C stocks onto gonococcal base (GCB) medium (Difco) containing Kellogg’s supplements I (105) and 1.25 μM Fe(NO3)3. Gc were cultured at 37 °C with 5% CO2 for 16 hours. Gc colonies from GCB plates were inoculated to a final optical density at 600 nm (OD600) of 0.05 in 5mL of defined medium that was pretreated with Chelex-100 resin (Bio-Rad) (Chelex-treated defined medium [CDM]) (Maurakis & Cornelissen, 2020) in metal free 15 mL conical tubes (VWR 89049-170). Cultures were grown at 37 °C for 2 hours, during which they doubled to an OD ≥0.10 and were then treated.

extract_protocol:
Bacteria from 3 replicate wells (12 mL total) were pooled together in a 15-mL conical tube and pelleted at 4,000 x g for 11 minutes. Gc was resuspended in 200 μL RNAprotect bacteria reagent (Qiagen 76506) and stored at -80 °C until processed to purify RNA. Samples were lysed according to the “Enzymatic Lysis and Proteinase K Digestion of Bacteria” protocol from Qiagen before proceeding with RNeasy Plus minikit (Qiagen 74134) per manufacturer’s instructions. DNase treatment was completed using a TURBO DNAfree kit (Invitrogen AM1907). rRNA reduction was completed using NEBNext rRNA Depletion Kit (Bacteria) (NEB E7850).
Strand specific RNA libraries were prepared for sequencing using standard Illumina protocols using NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760).

treatment_protocol: Gc (2x10^7 CFU/mL) was inoculated into 4 wells of a 6-well plate containing 4mL of CDM alone, with 12.5 µM Fe(NO3)3, or with 10 µM NE at 37 °C in 5% CO2. Incubations were for 1 hour.

value: FA1090 OpaDnv

value: iron

tag: biological replicate


title: CDM with iron, biol rep3

description: Library name: FE3


title: Bone marrow neutrophils from control and AML mice (Figure 3) FB

description: Library name: Sample2

tag: tissue


title: Spleen germinal center B cells, K4nonDP


title: CDM with iron, biol rep2

description: Library name: FE2


title: Twist1 EC-WT mouse 4

value: Twist1fl/fl, ApoE-/-, Cdh5+/+


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #3, input

description: Library name: gDNA_T3-0


title: Twist1 EC-WT mouse 5


title: CDM with norepinephrine, biol rep2

description: Library name: NE2

value: norepinephrine


title: Twist1 EC-KO mouse 2


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #5, input

description: Library name: gDNA_T5-0


title: Twist1 EC-WT mouse 3


title: Spleen germinal center B cells, K4PC


title: Twist1 EC-WT mouse 2


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #3, DMN

description: Library name: gDNA_T3-1


title: Spleen germinal center B cells, K4DP


title: CDM, biol rep3

description: Library name: CDM3


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #2, DMN

description: Library name: gDNA_T2-1


title: Spleen germinal center B cells, K4LZ


title: Spleen germinal center B cells, K4NB


title: Twist1 EC-KO mouse 3


title: CDM with norepinephrine, biol rep1

description: Library name: NE1


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #1, DMN

description: Library name: gDNA_T1-1


title: CDM with norepinephrine, biol rep3

description: Library name: NE3


title: Pre-Plasma germinal center B cells, WT4

value: SRBCs (i.p.)


title: Twist1 EC-WT mouse 1


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #2, input

description: Library name: gDNA_T2-0


title: Pre-Plasma germinal center B cells, WT3


title: Pre-Plasma germinal center B cells, WT7


title: gDNA hypomethylation enrichment DMN-seq, control, patient #6, input

description: Library name: gDNA_C6-0


title: gDNA hypomethylation enrichment DMN-seq, tumor, patient #1, input

description: Library name: gDNA_T1-0


title: Twist1 EC-KO mouse 1


title: gDNA hypomethylation enrichment DMN-seq, control, patient #6, DMN

description: Library name: gDNA_C6-1


title: gDNA hypomethylation enrichment DMN-seq, control, patient #5, DMN

description: Library name: gDNA_C5-1


title: 250_KO_8_3

city: Shanghai

first: Wanxing

last: Xu

address: 227 South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

description:
NA5
250k_ph8_vs_ph7_gene_counts.tsv

data_processing:
Adapter and quality trimming were performed by Trim galore v0.6.6. Filtered reads were mapped with STAR v2.6.1d to reference genome. The expression profile of each gene was obtained by StringTie v2.1.4.
Assembly: GCA_002759435.2, GCA_000182965.3
Supplementary files format and content: tab-delimited, raw count

organism: Candida albicans

source_name: SC5314 RIM101 KO

extract_protocol:
Total RNA was extracted using TRIZOL (Invitrogen) according to the manufacturer’s directions and stored at -80 ̊C.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: SC5314 RIM101 KO

value: pH8 KO3


title: 7C4_diffdTAG_6h, replica 2

city: Memphis

first: Te

last: Ling

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

description:
Library name: 7C4_diffdTAG_6h_2
Clones 6F8 and 7C4 were combined for analysis.

data_processing:
All custom scripts described herein are available on the AdelmanLab GitHub (https://github.com/AdelmanLab/NIH_scripts). Dual, 6nt Unique Molecular Identifiers (UMIs) were extracted from read pairs using UMI-tools [10.1101/gr.209601.116]. Read pairs were trimmed using cutadapt 1.14 to remove adapter sequences (-O 1 --match-read-wildcards -m {20,26}). The UMI length was trimmed off the end of both reads to prevent read-through into the mate’s UMI, which will happen for shorter fragments. An additional nucleotide was removed from the end of read 1 (R1), using seqtk trimfq (https://github.com/lh3/seqtk), to preserve a single mate orientation during alignment. The paired end reads were then mapped to a combined genome index, including both the spike (genome build) and primary (genome build) genomes, using bowtie2 [10.1038/nmeth.1923]. Properly paired reads were retained. These read pairs were then separated based on the genome (i.e. spike-in vs primary) to which they mapped, and both these spike and primary reads were independently deduplicated, again using UMI-tools. Reads mapping to the reference genome were separated according to whether they were R1 or R2, sorted via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl). We note that this script counts each read once at the exact 3’ end of the nascent RNA. Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-“ strands were swapped to generate bedGraphs representing 3’ end positions at single nucleotide resolution.
https://doi.org/10.5281/zenodo.18175046
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: PRO-Seq

molecule: nuclear RNA

growth_protocol: Expansion condition: SFEM II containing 3 U/mL EPO, 50 ng/mL hSCF, 1 μM dexamethasone and 1 μg/mL doxycycline; Differentiation condition: IMDM containing 2% FBS, 3% human AB serum, 3 U/mL EPO, 10 μg/mL insulin, 3 U/mL heperin, 1mg/mL human holo-transferrin, 50 ng/mL hSCF and 1 μg/mL doxycline.

extract_protocol:
PRO-seq was performed based on the protocol provided by the Nascent Transcriptomics Core at Harvard Medical School, with some modifications. All procedures were carried out on ice, and all buffers were kept pre-chilled prior to sample preparation. In detail, HUDEP2 cell lines (clones 6F8 and 7C4), engineered to express the dTAG system, were seeded at a density of 0.5 × 106 cells/m in IMDM-based differentiation medium supplemented with cytokines and incubated for 24 hours. After differentiation, cells were treated with 100 nM dTAG-13 for 0.5, 3, or 6 hours. At each time point, cells were immediately harvested into 10 mL of ice-cold 1X DPBS and centrifuged at 1,500 rpm for 7 minutes at 4°C. The supernatant was discarded, and the pellet was resuspended in 250 μL of Buffer W (10 mM Tris-HCl pH 8.0, 10 mM KCl, 250 mM sucrose, 5 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 10% glycerol, and 0.2 μL/mL SUPERase·In RNase inhibitor). Next, 10 mL of permeabilization Buffer P (Buffer W supplemented with 0.1% IGEPAL CA- 630, 0.05% Tween-20, and 0.2 μL/mL SUPERase-IN) was added carefully. Samples were incubated on ice for 5 minutes and centrifuged at 800 × g for 8 minutes at 4°C. The resulting permeabilized cells were washed with 10 mL Buffer W, centrifuged again under the same conditions, and resuspended in 400 μL of Buffer F (50 mM Tris-HCl pH 8.0, 40% glycerol, 5 mM MgCl2, 1.1 mM EDTA, 0.5 mM DTT, and 1 μL/mL SUPERase-IN RNase inhibitor; Thermo Fisher, Cat. No. AM26976). Cells were counted and QC at this step. Finally, cells were pelleted by centrifugation at 800 × g for 8 minutes at 4°C and resuspended in Buffer F at a concentration of 1 × 106 cells per 40 μL. Samples were flashfrozen immediately in liquid nitrogen (LN2) and stored at −80°C until further analysis.
The Nascent Transcriptomics Core at Harvard Medical School, Boston, Massachusetts, conducted PRO-Seq library construction and data analysis, as previously reported  (Mimoso & Goldman, 2023).

value: erythroid progenitor cell line

value: differentiation, 100 nM dTAG-13


title: 250_KO_7_3

description:
FRAS220043247-1r
250k_ph8_vs_ph7_gene_counts.tsv

value: pH7 KO3


title: 7C4_diffdTAG_6h, replica 1

description:
Library name: 7C4_diffdTAG_6h_1
Clones 6F8 and 7C4 were combined for analysis.


title: CDM, biol rep2

description: Library name: CDM2


title: gDNA hypomethylation enrichment DMN-seq, control, patient #5, input

description: Library name: gDNA_C5-0

value: colon


title: 7C4_diffdTAG_3h, replica 2

description:
Library name: 7C4_diffdTAG_3h_2
Clones 6F8 and 7C4 were combined for analysis.


title: CDM, biol rep1

description: Library name: CDM1


title: 7C4_diffdTAG_3h, replica 1

description:
Library name: 7C4_diffdTAG_3h_1
Clones 6F8 and 7C4 were combined for analysis.


title: 250_KO_7_2

description:
FRAS220043246-1r
250k_ph8_vs_ph7_gene_counts.tsv

value: pH7 KO2


title: Pre-Plasma germinal center B cells, KO7

value: spleen

value: Spleen germinal center B cells

value: KO


title: 7C4_diffdTAG_0.5h, replica 2

description:
Library name: 7C4_diffdTAG_0.5h_2
Clones 6F8 and 7C4 were combined for analysis.


title: 7C4_diffdTAG_0.5h, replica 1

description:
Library name: 7C4_diffdTAG_0.5h_1
Clones 6F8 and 7C4 were combined for analysis.


title: Pre-Plasma germinal center B cells, WT2


title: gDNA hypomethylation enrichment DMN-seq, control, patient #3, DMN

description: Library name: gDNA_C3-1


title: 250_KO_8_2

description:
NA4
250k_ph8_vs_ph7_gene_counts.tsv

value: pH8 KO2


title: Pre-Plasma germinal center B cells, KO2


title: Pre-Plasma germinal center B cells, KO1


title: gDNA hypomethylation enrichment DMN-seq, control, patient #3, input

description: Library name: gDNA_C3-0


title: 250_KO_7_1

description:
FRAS220043245-1r
250k_ph8_vs_ph7_gene_counts.tsv

value: pH7 KO1


title: gDNA hypomethylation enrichment DMN-seq, control, patient #4, input

description: Library name: gDNA_C4-0


title: Pre-Plasma germinal center B cells, KO6


title: gDNA hypomethylation enrichment DMN-seq, control, patient #2, DMN

description: Library name: gDNA_C2-1


title: 250_WT_8_3

description:
NA2
250_ph8_vs_ph7_gene_counts.tsv

value: pH8 WT3


title: 250_WT_8_2

description:
FRAS220043248-1r
250_ph8_vs_ph7_gene_counts.tsv

value: pH8 WT2


title: Pre-Plasma germinal center B cells, WT1

value: WT


title: gDNA hypomethylation enrichment DMN-seq, control, patient #4, DMN

description: Library name: gDNA_C4-1


title: 250_KO_8_1

description:
NA3
250k_ph8_vs_ph7_gene_counts.tsv

value: pH8 KO1


title: 7C4_diffDMSO_0.5h, replica 1

description:
Library name: 7C4_diffDMSO_0.5h_1
Clones 6F8 and 7C4 were combined for analysis.

value: differentiation, DMSO


title: Pre-Plasma germinal center B cells, 8KO

value: SRBCs (i.p.)


title: Pre-Plasma germinal center B cells, 7KO


title: 7C4_diffDMSO_6h, replica 2

description:
Library name: 7C4_diffDMSO_6h_2
Clones 6F8 and 7C4 were combined for analysis.


title: 7C4_dTAG_6h, replica 2

description:
Library name: 7C4_dTAG_6h_2
Clones 6F8 and 7C4 were combined for analysis.

value: expansion, 100 nM dTAG-13


title: 250_WT_8_1

description:
NA1
250_ph8_vs_ph7_gene_counts.tsv

value: pH8 WT1


title: gDNA hypomethylation enrichment DMN-seq, control, patient #2, input

description: Library name: gDNA_C2-0


title: 7C4_diffDMSO_6h, replica 1

description:
Library name: 7C4_diffDMSO_6h_1
Clones 6F8 and 7C4 were combined for analysis.

value: erythroid progenitor cell line


title: 7C4_diffDMSO_3h, replica 2

description:
Library name: 7C4_diffDMSO_3h_2
Clones 6F8 and 7C4 were combined for analysis.


title: Germinal center B cells, DP4

value: SRBC (i.p.)

tag: subcluster

value: DP


title: 7C4_diffDMSO_3h, replica 1

description:
Library name: 7C4_diffDMSO_3h_1
Clones 6F8 and 7C4 were combined for analysis.


title: 7C4_diffDMSO_0.5h, replica 2

description:
Library name: 7C4_diffDMSO_0.5h_2
Clones 6F8 and 7C4 were combined for analysis.


title: Pre-Plasma germinal center B cells, 6WT


title: Germinal center B cells, DN4

value: DN


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 16

description: Library name: cfDNA_T3-16

source_name: plasma

value: plasma


title: gDNA hypomethylation enrichment DMN-seq, control, patient #1, input

description: Library name: gDNA_C1-0

value: colon


title: gDNA hypomethylation enrichment DMN-seq, control, patient #1, DMN

description: Library name: gDNA_C1-1


title: 250_WT_7_1

description:
FRAS220043242-1r
250_ph8_vs_ph7_gene_counts.tsv

value: pH7 WT1


title: Germinal center B cells, DP3

value: spleen

value: Spleen germinal center B cells


title: Germinal center B cells, DP2


title: 250_WT_7_2

description:
FRAS220043243-1b
250_ph8_vs_ph7_gene_counts.tsv

value: pH7 WT2


title: Input chromatin low nuclei RNA 60hr embryo rep1

city: Knoxville

first: Maxim

last: Zagoskin

address: 1311 Cumberland Avenue

department: BCMB

institute: University of Tennessee Knoxville

description:
Library name: INPUT_60hr_chromatinLN_rep1
Small RNA sequencing library prepared from Ascaris suum.

library_source: other

data_processing:
Adapter trimming and length filtering of raw sequencing reads were performed using FASTX-Toolkit (v0.0.14). Reads were separated into small RNA (18–30 nt) and longer RNA fragment (31–150 nt) fractions.
Small RNA reads were mapped using Bowtie allowing one mismatch to Ascaris suum reference databases including rRNAs, tRNAs, mitochondrial genome, miRNAs, repetitive elements, and annotated transcripts. RNA fragments (31–150 nt) were mapped using Bowtie2 against the same reference databases.
Reads mapping to rRNAs and reads without genomic matches were excluded. Expression levels were quantified as counts per million mapped reads (CPM). Reads were classified as sense or antisense relative to annotated transcripts and assigned to intronic or intergenic regions as appropriate.
ChIP-seq reads were aligned to the reference genome using Bowtie2. Duplicate reads were removed prior to peak calling. Enriched regions were identified using MACS3 (v3.0.1) with default parameters and a significance threshold of q < 0.05.
Biological replicates were combined using MSPC to generate reproducible consensus peak sets based on statistical significance. Genome browser tracks were generated in BigWig format for visualization.
Assembly: Ascaris suum reference genome (v37)
Supplementary files format and content: Processed data include genome-wide coverage tracks in BigWig (.bw) format representing normalized read coverage derived from merged biological replicates. Additional processed files include peak coordinates in BED format for ChIP-seq experiments. BigWig files are intended for visualization in genome browsers such as UCSC.
Supplementary files format and content: Raw sequencing data (FASTQ files) are available through the Sequence Read Archive (SRA) and linked to individual GEO Sample (GSM) records. Processed files provided at the Series level correspond to merged biological replicates.

molecule: other

organism: Ascaris suum

source_name: embryo

growth_protocol: Ascaris suum embryos were obtained and staged as previously described. Embryos were collected at defined developmental time points corresponding to programmed DNA elimination (PDE) stages and maintained under standard laboratory conditions prior to subcellular fractionation, immunoprecipitation, or chromatin immunoprecipitation.

extract_protocol:
Subcellular fractionation was performed to isolate cytoplasmic, nuclear, and chromatin-associated fractions from Ascaris suum embryos. Argonaute-containing ribonucleoprotein complexes were immunoprecipitated using specific antibodies. For DuoRIP-seq, RNase-assisted co-immunoprecipitation was performed to recover Argonaute-bound small RNAs (18–30 nt) and protected target RNA fragments (18–150 nt). For ChIP-seq, embryos were cross-linked with formaldehyde, chromatin was isolated, and DNA was sheared to ~300–800 bp prior to immunoprecipitation with AsWAGO-specific antibodies.
RNA recovered from immunoprecipitated complexes was used for library preparation with the Lexogen Small RNA-Seq Kit (catalog #052), which enables simultaneous capture of Argonaute-bound small RNAs and their associated target RNA fragments without size selection. Libraries were prepared using a 5′-end independent strategy to capture RNAs with non-canonical 5′ ends. ChIP-seq libraries were prepared from purified immunoprecipitated DNA as previously described. Sequencing was performed as paired-end (2 × 150 bp) on an Illumina NovaSeq 6000 platform.

value: embryo


title: Germinal center B cells, DN2

value: WT


title: 7C4_dTAG_0.5h, replica 2

description:
Library name: 7C4_dTAG_0.5h_2
Clones 6F8 and 7C4 were combined for analysis.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 14

description: Library name: cfDNA_T3-14


title: Germinal center B cells, DP1


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 17

description: Library name: cfDNA_T3-17


title: 7C4_dTAG_6h, replica 1

description:
Library name: 7C4_dTAG_6h_1
Clones 6F8 and 7C4 were combined for analysis.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 15

description: Library name: cfDNA_T3-15


title: 7C4_dTAG_3h, replica 1

description:
Library name: 7C4_dTAG_3h_1
Clones 6F8 and 7C4 were combined for analysis.


title: AsWAGO-3 IP chromatin RNA 60hr embryo X rep1

description:
Library name: WAGO3_60hrX_chromatin_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: 250_WT_7_3

description:
FRAS220043244-1r
250_ph8_vs_ph7_gene_counts.tsv

value: pH7 WT3


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 11

description: Library name: cfDNA_T3-11


title: 7C4_dTAG_3h, replica 2

description:
Library name: 7C4_dTAG_3h_2
Clones 6F8 and 7C4 were combined for analysis.


title: AsWAGO-3 ChIP 60hr RNase embryo rep1

description:
Library name: WAGO3_60hrRNase_rep1
ChIP sequencing library prepared from Ascaris suum.


title: Germinal center B cells, DN3


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 13

description: Library name: cfDNA_T3-13


title: 7C4_dTAG_0.5h, replica 1

description:
Library name: 7C4_dTAG_0.5h_1
Clones 6F8 and 7C4 were combined for analysis.


title: 7C4_DMSO_6h, replica 2

description:
Library name: 7C4_DMSO_6h_2
Clones 6F8 and 7C4 were combined for analysis.

value: expansion, DMSO


title: 107DP

data_processing:
Raw paired-end sequenced reads were first cut for adapter sequences and trimmed using trim_galore (v.0.6.6).
Cleaned fastq data were mapped to the mm10 reference genome for sample from mouse using Bowtie 2 (v.2.4.2).
SAMtools (v.1.11) was used to convert and sort the SAM files into BAM format.
SEACR（1.3）was used for peak calling with default model.
DeepTools was used to normalize signals from sorted BAM files via bamCoverage.
Assembly: mm10
Supplementary files format and content: bigWig, bed

value: KO


title: Input nucleoplasm low nuclei RNA 60hr embryo rep2

description:
Library name: INPUT_60hr_nucleoplasmLN_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 10

description: Library name: cfDNA_T3-10


title: AsWAGO-3 IP chromatin RNA 60hr embryo M rep1

description:
Library name: WAGO3_60hrM_chromatin_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 9

description: Library name: cfDNA_T3-09


title: AsWAGO-3 ChIP 60hr embryo rep2

description:
Library name: WAGO3_60hr_rep2
ChIP sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 12

description: Library name: cfDNA_T3-12


title: 106DP


title: Germinal center B cells, DN1


title: AsWAGO-3 IP nucleoplasm RNA 60hr embryo X rep1

description:
Library name: WAGO3_60hrX_nucleoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: AsWAGO-3 ChIP 60hr embryo rep3

description:
Library name: WAGO3_60hr_rep3
ChIP sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 7

description: Library name: cfDNA_T3-07


title: AsWAGO-3 IP nucleoplasm RNA 60hr embryo M rep1

description:
Library name: WAGO3_60hrM_nucleoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: AsWAGO-3 ChIP 60hr embryo rep1

description:
Library name: WAGO3_60hr_rep1
ChIP sequencing library prepared from Ascaris suum.


title: 7C4_DMSO_3h, replica 1

description:
Library name: 7C4_DMSO_3h_1
Clones 6F8 and 7C4 were combined for analysis.


title: 7C4_DMSO_3h, replica 2

description:
Library name: 7C4_DMSO_3h_2
Clones 6F8 and 7C4 were combined for analysis.


title: 7C4_DMSO_6h, replica 1

description:
Library name: 7C4_DMSO_6h_1
Clones 6F8 and 7C4 were combined for analysis.


title: 110DP


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 8

description: Library name: cfDNA_T3-08


title: Liver, AIMER treated mouse, rep5

city: Cambridge

first: Jigar

last: Desai

state: MA

address: 733 Concord Avenue

institute: Wave Life Science

data_processing:
For differential analysis, fastq files were mapped to mouse genome (GRCm38) that was modified to include human SERPINA1 sequence without replacing the original mouse SERPINA1 sequence. Reads were mapped using STAR aligner (2.7.11b). Counts from the resulting bam files were generated by Salmon (1.10.2). Count plots were normalized by counts per million; however, raw counts were used for differential expression analysis with DESeq2 (v 1.42.0)(insert DESeq citation). Differentially expressed genes (DEGs) between PBS- and AIMer-treated samples were determined by DESeq2’s DESeq function and a contrast between the two treatment groups. The DEGs with a p-value less than 0.05 have been provided as Supplementary Data file 1. The log fold change values from DESseq were used to for Fig. 4A. Finally, the DEGs identified by DESeq were passed to ShinyGO v0.76
Assembly: mm10 modified to include human SERPINA1
Supplementary files format and content: tab delimited raw counts for each sample

source_name: Liver

growth_protocol: Mouse work was performed under a protocol approved by the Institutional Animal Care and Use Committee (IACUC) of Biomere - Biomedical Research Models, Inc. (Worcester, MA). Male NSG-PiZ mice (aged 7-10 weeks) were obtained from Jackson Laboratory (Cat. No. 028842)

extract_protocol:
Each liver punch was transferred to a 2 mL microcentrifuge tube (VWR, 16466-058) containing zirconium oxide beads (Next Advance, ZrOB10). 1 mL of TRIzol was added to each tube, and samples were lysed using Precellys Evolution tissue homogenizer (Bertin, P000062-PEVO0-A). Next, 200 µL of chloroform was added to each tube followed by repeatedly inverting for 30 seconds to ensure thorough mixing, then incubation at room temperature for 10 minutes. Samples were centrifuged at 20,000 × g for 10 minutes at 4°C. After centrifugation, ~400 µL of the top aqueous phase was transferred to a 96-well RNA binding plate and total RNA was again extracted using SV 96 Total RNA Isolation System (Promega, Z3500).
mRNA was isolated from total RNA using poly-A isolation and strand-specific libraries were generated (Novagene, USA)
50M reads (2X 150 bp) per sample were sequenced with the Illumina NovaSeq platform

treatment_protocol: dosed subcutaneously with PBS or with SERPINA1-994

value: Liver

value: NSG

value: AIMER (SERPINA1-994)


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 5

description: Library name: cfDNA_T3-05


title: 7C4_DMSO_0.5h, replica 2

description:
Library name: 7C4_DMSO_0.5h_2
Clones 6F8 and 7C4 were combined for analysis.

value: erythroid progenitor cell line


title: 104DP


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 6

description: Library name: cfDNA_T3-06


title: AsWAGO-3 IP nucleoplasm RNA 60hr embryo rep4

description:
Library name: WAGO3_60hr_nucleoplasm_rep4
Small RNA sequencing library prepared from Ascaris suum.


title: 7C4_DMSO_0.5h, replica 1

description:
Library name: 7C4_DMSO_0.5h_1
Clones 6F8 and 7C4 were combined for analysis.


title: 6F8_diffdTAG_6h, replica 2

description:
Library name: 6F8_diffdTAG_6h_2
Clones 6F8 and 7C4 were combined for analysis.

value: differentiation, 100 nM dTAG-13


title: AsWAGO-3 IP nucleoplasm RNA 60hr embryo rep3

description:
Library name: WAGO3_60hr_nucleoplasm_rep3
Small RNA sequencing library prepared from Ascaris suum.


title: Liver, AIMER treated mouse, rep2


title: Liver, AIMER treated mouse, rep3


title: Liver, AIMER treated mouse, rep4


title: AsWAGO-3 IP nucleoplasm RNA 60hr embryo rep1

description:
Library name: WAGO3_60hr_nucleoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: 6F8_diffdTAG_6h, replica 1

description:
Library name: 6F8_diffdTAG_6h_1
Clones 6F8 and 7C4 were combined for analysis.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 4

description: Library name: cfDNA_T3-04


title: Liver, AIMER treated mouse, rep1


title: AsWAGO-3 IP nucleoplasm RNA 60hr embryo rep2

description:
Library name: WAGO3_60hr_nucleoplasm_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 3

description: Library name: cfDNA_T3-03


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 1

description: Library name: cfDNA_T3-01


title: Liver, PBS treated mouse, rep5

value: PBS


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 2

description: Library name: cfDNA_T3-02

value: plasma


title: AsWAGO-3 IP chromatin RNA 60hr embryo rep4

description:
Library name: WAGO3_60hr_chromatin_rep4
Small RNA sequencing library prepared from Ascaris suum.


title: 6F8_diffdTAG_3h, replica 1

description:
Library name: 6F8_diffdTAG_3h_1
Clones 6F8 and 7C4 were combined for analysis.


title: AsWAGO-3 IP chromatin RNA 60hr embryo rep3

description:
Library name: WAGO3_60hr_chromatin_rep3
Small RNA sequencing library prepared from Ascaris suum.


title: 6F8_diffdTAG_0.5h, replica 1

description:
Library name: 6F8_diffdTAG_0.5h_1
Clones 6F8 and 7C4 were combined for analysis.


title: 6F8_diffDMSO_6h, replica 1

description:
Library name: 6F8_diffDMSO_6h_1
Clones 6F8 and 7C4 were combined for analysis.

value: differentiation, DMSO


title: 6F8_diffdTAG_0.5h, replica 2

description:
Library name: 6F8_diffdTAG_0.5h_2
Clones 6F8 and 7C4 were combined for analysis.


title: Liver, PBS treated mouse, rep2


title: AsWAGO-3 IP cytoplasm RNA 60hr embryo rep1

description:
Library name: WAGO3_60hr_cytoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.5 ng) hypomethylation enrichment DMN-seq, tumor, replicate 4

description: Library name: cfDNA_T2-4


title: Liver, PBS treated mouse, rep4


title: cfDNA low input (0.5 ng) hypomethylation enrichment DMN-seq, tumor, replicate 2

description: Library name: cfDNA_T2-2


title: Liver, PBS treated mouse, rep3


title: 6F8_diffDMSO_6h, replica 2

description:
Library name: 6F8_diffDMSO_6h_2
Clones 6F8 and 7C4 were combined for analysis.


title: Liver, PBS treated mouse, rep1


title: AsWAGO-3 IP chromatin RNA 60hr embryo rep1

description:
Library name: WAGO3_60hr_chromatin_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.5 ng) hypomethylation enrichment DMN-seq, tumor, replicate 5

description: Library name: cfDNA_T2-5


title: cfDNA low input (0.5 ng) hypomethylation enrichment DMN-seq, tumor, replicate 3

description: Library name: cfDNA_T2-3


title: AsWAGO-3 IP chromatin RNA 60hr embryo rep2

description:
Library name: WAGO3_60hr_chromatin_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: Liver, Baseline mouse untreated, rep5

value: Baseline


title: 6F8_diffdTAG_3h, replica 2

description:
Library name: 6F8_diffdTAG_3h_2
Clones 6F8 and 7C4 were combined for analysis.


title: AsWAGO-2 IP nucleoplasm RNA 60hr embryo X rep1

description:
Library name: WAGO2_60hrX_nucleoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.5 ng) hypomethylation enrichment DMN-seq, tumor, replicate 1

description: Library name: cfDNA_T2-1


title: 6F8_diffDMSO_3h, replica 2

description:
Library name: 6F8_diffDMSO_3h_2
Clones 6F8 and 7C4 were combined for analysis.


title: AsWAGO-2 IP chromatin RNA 60hr embryo X rep1

description:
Library name: WAGO2_60hrX_chromatin_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: 6F8_diffDMSO_3h, replica 1

description:
Library name: 6F8_diffDMSO_3h_1
Clones 6F8 and 7C4 were combined for analysis.


title: Liver, Baseline mouse untreated, rep4


title: 6F8_diffDMSO_0.5h, replica 2

description:
Library name: 6F8_diffDMSO_0.5h_2
Clones 6F8 and 7C4 were combined for analysis.


title: cfDNA low input (1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 1

description: Library name: cfDNA_T1-1


title: AsWAGO-2 IP nucleoplasm RNA 60hr embryo rep4

description:
Library name: WAGO2_60hr_nucleoplasm_rep4
Small RNA sequencing library prepared from Ascaris suum.


title: Liver, Baseline mouse untreated, rep2


title: Liver, Baseline mouse untreated, rep1


title: AsWAGO-2 IP nucleoplasm RNA 60hr embryo rep5

description:
Library name: WAGO2_60hr_nucleoplasm_rep5
Small RNA sequencing library prepared from Ascaris suum.


title: 6F8_diffDMSO_0.5h, replica 1

description:
Library name: 6F8_diffDMSO_0.5h_1
Clones 6F8 and 7C4 were combined for analysis.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 19

description: Library name: cfDNA_C3-19


title: AsWAGO-2 IP nucleoplasm RNA 60hr embryo rep3

description:
Library name: WAGO2_60hr_nucleoplasm_rep3
Small RNA sequencing library prepared from Ascaris suum.


title: KO_EM_1

city: Toronto

first: Michael

last: Geuenich

state: Ontario

address: 600 University Ave

country: Canada

institute: Lunenfeld Tanenbaum Research Institute

data_processing:
Basecalling was done with bcl2fastq2 v2.20
fastq files were processed into count matrix using the nf-core rnaseq pipeline version 3.9
Reads were aligned using STAR version 2.6.1d
Read counts were created using salmon version 1.5.2
Assembly: mm38
Supplementary files format and content: tsv
Supplementary files format and content: counts

growth_protocol: T cells were seeded in complete RPMI medium with 10% FBS, antibiotics, glutamax, and 2-mercaptoethanol  in humidified at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen)
Libraries were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: Differentiation was induced by activating T cells with CD3/CD28 microbeads +IL7 & IL15

value: spleen

value: CD8 EM T cell

value: HEB cKO


title: cfDNA low input (1 ng) hypomethylation enrichment DMN-seq, tumor, replicate 2

description: Library name: cfDNA_T1-2


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 20

description: Library name: cfDNA_C3-20


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 16

description: Library name: cfDNA_C3-16


title: 6F8_dTAG_6h, replica 1

description:
Library name: 6F8_dTAG_6h_1
Clones 6F8 and 7C4 were combined for analysis.

value: expansion, 100 nM dTAG-13


title: 6F8_dTAG_6h, replica 2

description:
Library name: 6F8_dTAG_6h_2
Clones 6F8 and 7C4 were combined for analysis.


title: KO_EM_2


title: 6F8_dTAG_3h, replica 2

description:
Library name: 6F8_dTAG_3h_2
Clones 6F8 and 7C4 were combined for analysis.


title: KO_CM_2

value: CD8 CM T cell


title: AsWAGO-2 IP nucleoplasm RNA 60hr embryo rep1

description:
Library name: WAGO2_60hr_nucleoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.

value: embryo


title: AsWAGO-2 IP cytoplasm RNA 60hr embryo rep1

description:
Library name: WAGO2_60hr_cytoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: AsWAGO-2 IP nucleoplasm RNA 60hr embryo rep2

description:
Library name: WAGO2_60hr_nucleoplasm_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: 6F8_dTAG_3h, replica 1

description:
Library name: 6F8_dTAG_3h_1
Clones 6F8 and 7C4 were combined for analysis.


title: KO_CM_1


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 18

description: Library name: cfDNA_C3-18


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 17

description: Library name: cfDNA_C3-17


title: AsWAGO-2 IP chromatin RNA 60hr embryo rep3

description:
Library name: WAGO2_60hr_chromatin_rep3
Small RNA sequencing library prepared from Ascaris suum.


title: Liver, Baseline mouse untreated, rep3


title: 6F8_DMSO_6h, replica 2

description:
Library name: 6F8_DMSO_6h_2
Clones 6F8 and 7C4 were combined for analysis.

value: expansion, DMSO


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 15

description: Library name: cfDNA_C3-15


title: KO_SCM_1

value: CD8 SCM T cell


title: AsWAGO-2 IP chromatin RNA 60hr embryo rep5

description:
Library name: WAGO2_60hr_chromatin_rep5
Small RNA sequencing library prepared from Ascaris suum.


title: 6F8_dTAG_0.5h, replica 2

description:
Library name: 6F8_dTAG_0.5h_2
Clones 6F8 and 7C4 were combined for analysis.


title: AsWAGO-2 IP chromatin RNA 60hr embryo rep4

description:
Library name: WAGO2_60hr_chromatin_rep4
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 13

description: Library name: cfDNA_C3-13


title: 6F8_dTAG_0.5h, replica 1

description:
Library name: 6F8_dTAG_0.5h_1
Clones 6F8 and 7C4 were combined for analysis.


title: KO_Naive_1

value: CD8 Naive T cell


title: 6F8_DMSO_3h, replica 2

description:
Library name: 6F8_DMSO_3h_2
Clones 6F8 and 7C4 were combined for analysis.


title: KO_SCM_2


title: WT_EM_1

value: WT


title: 6F8_DMSO_0.5h, replica 2

description:
Library name: 6F8_DMSO_0.5h_2
Clones 6F8 and 7C4 were combined for analysis.


title: WT_EM_2


title: KO_Naive_2


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 14

description: Library name: cfDNA_C3-14


title: AsWAGO-2 IP chromatin RNA 60hr embryo rep2

description:
Library name: WAGO2_60hr_chromatin_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: 6F8_DMSO_3h, replica 1

description:
Library name: 6F8_DMSO_3h_1
Clones 6F8 and 7C4 were combined for analysis.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 12

description: Library name: cfDNA_C3-12


title: AsWAGO-1 IP nuclei RNA 64hr embryo rep1

description:
Library name: WAGO1_64hr_nuclei_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: AsWAGO-1 IP nucleoplasm RNA 60hr embryo rep2

description:
Library name: WAGO1_60hr_nucleoplasm_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: 6F8_DMSO_6h, replica 1

description:
Library name: 6F8_DMSO_6h_1
Clones 6F8 and 7C4 were combined for analysis.


title: AsWAGO-2 IP chromatin RNA 60hr embryo rep1

description:
Library name: WAGO2_60hr_chromatin_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 9

description: Library name: cfDNA_C3-09


title: AsWAGO-1 IP nucleoplasm RNA 60hr embryo rep1

description:
Library name: WAGO1_60hr_nucleoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 8

description: Library name: cfDNA_C3-08


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 11

description: Library name: cfDNA_C3-11


title: WT_CM_2


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 7

description: Library name: cfDNA_C3-07


title: HEK293 total lysate for YBX1 rep 3

city: Bethesda

first: Markus

last: Hafner

state: Maryland

address: 50 South Drive

institute: NIAMS/NIH

description: Library name: YBX1_TOT_rep3

data_processing:
Illumina Nextseq2000 and NextSeq500 platform was used for sequencing
Basecalling was done using bcl2fastq V2.20.0
The reads were aligned to the hg38 genome and peak was called using PCLIPtools v0.7.2
normalized reads and clusters were combined in a tsv file
Assembly: hg38
Supplementary files format and content: PCLIPtools output conaining read depth and T-to-C mismatch information

source_name: KIDNEY

growth_protocol: APEX2 compatible HEK293 cell lines were cultured in DMEM media supplemented with 10% Fetal Bovine Serum, 1% Penicillin-Streptomycin, 100 μg/ml of Hygromycin B and 5 μg/ml of Blastacidin. While HEK293 cells were cultured in complete media without Hygromycin and Blasticidin.

extract_protocol:
Cells were lysed into total lysates and clarified by centrifugation. In the case of YBX1 and ELAVL1: first biotinylated proteins were enriched by immunoprecipitation with anti-biotin antibody and eluted by 2% acetic acid. Eluted lysates were neutralized by NaOH. Then YBX1 and ELAVL1 was enriched by immunoprecipitation with anti-YBX1 and anti-ELAVL1, respectively.  After washing the beads, RNase T1 digestion was performed, 3´ends of the RNA fragments were dephosphorylated using CIP, and RNA was fluorescently 3´end-labeled using T4 Rnl2(1–249)K227Q, followed by dephosporylation with T4 PNK. RNA-protein complexes were separated by SDS-PAGE and excised. After proteinase K treatment, RNA was extracted and 5' end labelled with T4 RNA ligase. Following small RNA cDNA library preparation was performed. In the case of AGO2: first FLAG-AGO2 was immpunoprecipitated, eluted with FLAG-peptide. After washing the beads, RNase T1 digestion was performed, 3´ends of the RNA fragments were dephosphorylated using CIP, and RNA was fluorescently 3´end-labeled using T4 Rnl2(1–249)K227Q, followed by dephosporylation with T4 PNK. RNA-protein complexes were separated by SDS-PAGE and excised and eluted. anti-biotin was immunoprecipitated on the eluted material followed by proteinase K treatment, RNA extraction and 5' end labelling with T4 RNA ligase. Following small RNA cDNA library preparation was performed.
Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: 16 h before cell harvesting, cells were treated with 4-thiouridine (4SU) at a final concentration of 100 μM for all cell lines and additional 2 μg/ml of doxycycline for APEX2 cell lines. Just before harvesting, APEX2 cells biotinylated and washed with quenching solution. HEK293 cells were washed with 1x PBS. The cells were then crosslinked with 312 nm UV-light for 5 min and collect the cells immediately.

value: KIDNEY

value: Doxycycline, biotinylation, 4SU, and 312 nm UV light


title: 6F8_DMSO_0.5h, replica 1

description:
Library name: 6F8_DMSO_0.5h_1
Clones 6F8 and 7C4 were combined for analysis.

value: erythroid progenitor cell line


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 10

description: Library name: cfDNA_C3-10


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 5

description: Library name: cfDNA_C3-05


title: WT_SCM_1


title: HEK293 APEX2 YBX1 nucleolar lysate biol rep3

description: Library name: YBX1_NIK3x_rep3

value: APEX2 expression


title: HEK293 total lysate for YBX1 rep 1

description: Library name: YBX1_TOT_rep1


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 4

description: Library name: cfDNA_C3-04

value: plasma


title: AsWAGO-1 IP chromatin RNA 60hr embryo rep1

description:
Library name: WAGO1_60hr_chromatin_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: AsNRDE-3 IP total RNA 64hr embryo rep1

description:
Library name: NRDE3_64hr_total_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: AsWAGO-1 IP cytoplasm RNA 60hr embryo rep1

description:
Library name: WAGO1_60hr_cytoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: WT_Naive_2


title: HEK293 APEX2 YBX1 nucleolar lysate biol rep1

description: Library name: YBX1_NIK3x_rep1


title: CD4T, WT in situ HiC rep2

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Sequenced using Illumina NovaSeq 6000 platform
Raw reads were processed using HiC-Pro pipeline v2.11.4 with MboI restriction sites
Assembly: mm10
Supplementary files format and content: hic contaning validpairs

growth_protocol: CD4 T cells prepared from CreER or CreER;Ctcffl/fl mice were culutred under the presence of anti-CD3ε and anti-CD28 for 6 days with chaning medium every 2 days. For the deletion of Ctcf allele, 4-OH tamoxifen is added only on the first day of culture.

extract_protocol:
Fixed chromatin was digested using MboⅠ enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, the DNA was sonicated and captured with Streptavidin C-1 beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Purified DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina NovaSeq 6000 platform.

treatment_protocol: CD4 T cells were stimulated with IL-2 at the concentration of 100U/ml every 2 days.

value: T cells

value: 10 weeks old

value: CreER


title: WT_SCM_2

value: spleen


title: WT_CM_1


title: WT_Naive_1


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 6

first: Yang

last: Li

institute: The University of Chicago

description: Library name: cfDNA_C3-06


title: Input total low nuclei RNA 65hr embryo rep2

description:
Library name: INPUT_65hr_totalLN_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 3

description: Library name: cfDNA_C3-03


title: AsWAGO-1 IP chromatin RNA 60hr embryo rep2

description:
Library name: WAGO1_60hr_chromatin_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: CD4T, KO in situ HiC rep2

value: CreER;Ctcf fl/fl


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 2

description: Library name: cfDNA_C3-02


title: HEK293 APEX2 YBX1 cytoplasmic lysate biol rep1

description: Library name: YBX1_NES_rep1


title: HEK293 total lysate for YBX1 rep 2

description: Library name: YBX1_TOT_rep2


title: AsWAGO-1 IP cytoplasm RNA 64hr embryo rep1

description:
Library name: WAGO1_64hr_cytoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: HEK293 APEX2 YBX1 nucleolar lysate biol rep2

description: Library name: YBX1_NIK3x_rep2


title: AsNRDE-3 IP nucleoplasm RNA 60hr embryo rep1

description:
Library name: NRDE3_60hr_nucleoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: HEK293 APEX2 YBX1 cytoplasmic lysate biol rep2

description: Library name: YBX1_NES_rep2


title: Input total RNA 65hr embryo rep2

description:
Library name: INPUT_65hr_total_rep2
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.5 ng) hypomethylation enrichment DMN-seq, control, replicate 3

description: Library name: cfDNA_C2-3


title: cfDNA low input (0.1 ng) hypomethylation enrichment DMN-seq, control, replicate 1

description: Library name: cfDNA_C3-01


title: CD4T, KO in situ HiC rep1


title: Input total RNA 65hr embryo rep3

description:
Library name: INPUT_65hr_total_rep3
Small RNA sequencing library prepared from Ascaris suum.


title: CD4T, WT H3K27ac HiChIP rep2

data_processing:
Sequenced using Illumina NovaSeq 6000 platform
Raw reads were processed using HiC-Pro pipeline v2.11.4 with MboI restriction sites
Assembly: mm10
Supplementary files format and content: hic contaning validpairs
Library strategy: HiChIP

extract_protocol:
Fixed chromatin was digested using MboⅠ enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, the DNA was sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads. Reverse-crosslinked DNA was captured with Streptavidin C-1 beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Purified DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina NovaSeq 6000 platform.

value: H3K27ac (Abcam #ab4729)


title: CD4T, WT in situ HiC rep1


title: HEK293 APEX2 YBX1 cytoplasmic lysate biol rep3

description: Library name: YBX1_NES_rep3


title: cfDNA low input (0.5 ng) hypomethylation enrichment DMN-seq, control, replicate 5

description: Library name: cfDNA_C2-5


title: CD4T, WT H3K27ac HiChIP rep1


title: Input total low nuclei RNA 65hr embryo rep1

description:
Library name: INPUT_65hr_totalLN_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: AsNRDE-3 IP chromatin RNA 60hr embryo rep1

description:
Library name: NRDE3_60hr_chromatin_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: Input total RNA 64hr embryo rep1

description:
Library name: INPUT_64hr_total_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: Input total RNA 65hr embryo rep1

description:
Library name: INPUT_65hr_total_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.5 ng) hypomethylation enrichment DMN-seq, control, replicate 1

description: Library name: cfDNA_C2-1


title: HEK293 APEX2 YBX1 nuclear lysate biol rep2

description: Library name: YBX1_H2B_rep2


title: cfDNA low input (0.5 ng) hypomethylation enrichment DMN-seq, control, replicate 4

description: Library name: cfDNA_C2-4


title: CD4T, KO H3K27ac HiChIP rep1


title: HEK293 total lysate for ELAVL1 rep3

description: Library name: ELAVL1_TOT_rep3


title: HEK293 total lysate for ELAVL1 rep2

description: Library name: ELAVL1_TOT_rep2


title: CD4T, WT STAT5 rep2

data_processing:
sequnced using Illumina HiSeq 2500, NovaSeq6000, HiSeq X ten platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the mm10 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD  v2.18.23
peaks were called using macs2 v2.2.7.1 with the following setting: -f BAMPE -g mm (--broad for H3K4me1,H3K27me3 ChIP-seq peak calling and -q 0.001 for H3K27ac ChIP-seq peak calling)
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.5.1
Assembly: mm10
Supplementary files format and content: narrowPeak, broadPeak, CPM normalized bigwig

growth_protocol: CD4 T cells prepared from CreER or CreER;Ctcffl/fl mice were culutred under the presence of anti-CD3ε and anti-CD28 for 6 days with chaning medium every 2 days. For the deletion of CTCF allele, 4-OH tamoxifen is added only on the first day of culture.

extract_protocol:
ChIP-seq was performed using the protocol from Schmidl et al., 2015 with small modifications. Fixed cells were sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Reverse-crosslinked DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq 2500, NovaSeq6000, HiSeq X ten platform.

treatment_protocol: CD4 T cells were stimulated with Il-2 at the concentration of 100U/ml every 2 days.


title: HEK293 APEX2 YBX1 nuclear lysate biol rep3

description: Library name: YBX1_H2B_rep3


title: Input nucleoplasm RNA 60hr embryo M rep1

description:
Library name: INPUT_60hrM_nucleoplasm_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: cfDNA low input (0.5 ng) hypomethylation enrichment DMN-seq, control, replicate 2

description: Library name: cfDNA_C2-2


title: HEK293 total lysate for ELAVL1 rep1

description: Library name: ELAVL1_TOT_rep1


title: Input chromatin RNA 60hr embryo M rep1

description:
Library name: INPUT_60hrM_chromatin_rep1
Small RNA sequencing library prepared from Ascaris suum.


title: HEK293 APEX2 YBX1 nuclear lysate biol rep1

description: Library name: YBX1_H2B_rep1


title: Input nucleoplasm RNA 60hr embryo rep4

description:
Library name: INPUT_60hr_nucleoplasm_rep4
Small RNA sequencing library prepared from Ascaris suum.


title: CD4T, KO H3K27ac HiChIP rep2


title: HCT116, pooled virus infection, 4dpi, biol rep2, GEX

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

description:
Library name: HCT116-pool-GEX-2
multiplexed single cell libraries

data_processing:
scRNAseq libraries were demultiplexed by transgene barcodes, as given in the feature_references.csv file
Assembly: GRCh38
Supplementary files format and content: h5 file (output of cell ranger for each sample)
Supplementary files format and content: h5ad file (anndata object containing all samples)

source_name: HCT 116

growth_protocol: Caco2-et, HT-29-et, RKO-et, SW480-et, HCT116 were cultured in Dubecco´s Modified Eagle´s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) (PanBiotech),1 % stable L-glutamine (PanBiotech), and 1 % penicillin/streptomycin (PanBiotech) at 37 °C and 5 % CO2 and according Puromycin concentration.

extract_protocol:
For single cell RNA sequencing, cells were harvested using TrypLE, resuspended in PBS, filtered through 30 µm  filters, facs sorted into PBS+1% FBS and directly processed into a library.
Gene expression (GEX) libraries were created from 10000-30000 cells, which were sorted using FACSAria (BD Bioscience) and processed right after sorting following the standard Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10X Genomics), following standard dual-index protocols and the Chromium-X controller (10xGenomics). Libraries were sequenced on the Nova Seq X Plus 25B with 150 PE (Illumina, Inc.) Barcode-targeted libraries were generated from amplified cDNA used for GEX libraries. PCR was performed with a primer (5′-GTGGTGTTAATTAACCTAGAGGGC-3′) carrying a specific handle and partial Read One primer to amplify the 10 bp viral barcode. Each 100 µL reaction included 100 ng cDNA, primers, and KAPA HiFi mix, with cycling: 95 °C (3 min), 5 cycles of 98 °C (20 s), 67 °C (60 s), 72 °C (60 s), and a final 72 °C (5 min). PCR products were size-selected with SPRIselect beads (0.6X/1.2X) per 10X Genomics protocol. For index PCR, 30 µL of cleaned product underwent 14 cycles, followed by standard indexing and clean-up. Final product size (~360 bp) was confirmed via TapeStation (Agilent). Sequcing was performed as for GEX libraries.

treatment_protocol: CRC cells at 50% confluency were infected using viral supernatant and 8 µg/mL Polybrene (Santa Cruz Biotechnology) at a maximum MOI of 0.2. HCT116 cells were pre-treated with Ecotropic Receptor Booster (Takara Bio) as per the manufacturer’s instructions before infection. After 20 hours of viral exposure, the medium was replaced. All cells used for single-cell datasets were collected 4 days post-infection (dpi).

value: HCT 116

value: colorectal cancer

value: virus pool


title: CD4T, WT SMC1A rep2

value: SMC1 (Bethyl #A300-055A)


title: cfDNA low input (1 ng) hypomethylation enrichment DMN-seq, control, replicate 2

description: Library name: cfDNA_C1-2

data_processing:
After trimming the TruSeq sequencing adapters from the 3′ ends of read 1 and read 2 via the Cutadapt (v4.9) tool, low-quality and short reads were filtered out. The clean reads were then aligned to the spike-in sequences (the 164 bp and 200 bp synthetic dsDNA spike-ins in Supplementary Table 1 and GenBank J02459.1 for λ-DNA) and reference genomes (mouse reference mm10 for mESC samples; human hg38 for cfDNA samples and CRC samples) via HISAT2 (v2.2.1). The sorted mapped reads in the mESC, cfDNA and CRC samples were then processed to remove PCR duplicates via the Picard tool. Finally, the reads were summed via the featureCounts (v2.0.8) tool for each TSS upstream 2000 bp region downloaded from the UCSC genome browser.
For RRBS samples, after trimming the TruSeq sequencing adapters from the 3′ ends of read 1 and read 2 via the Cutadapt (v4.9) tool, low-quality and short reads were filtered out. The clean reads were then aligned to the human hg38 reference genome via HISAT3N (v2.2.1-3n-0.0.3) with the ‘--no-splice-alignment' argument. The sorted mapped reads in the cfDNA and CRC samples were then processed to remove PCR duplicates via the Picard tool. Finally, the number of converted and unconverted reads at all C sites was counted using the hisat-3n-table command, and the methylation ratio was calculated as the number of unconverted reads divided by total coverage.
Assembly: hg38
Supplementary files format and content: The sum of reads number in 2000 bp region, or the bigwig of sites.


title: cfDNA low input (1 ng) hypomethylation enrichment DMN-seq, control, replicate 1

description: Library name: cfDNA_C1-1


title: CD4T, WT H3K4me3 rep2

value: H3K4me3 (Millipore #04-745)


title: CD4T, WT RPB1-S5P rep1

value: Phospho-Rpb1 CTD (Ser5) (CST #13523)


title: Input nucleoplasm RNA 60hr embryo rep2

description:
Library name: INPUT_60hr_nucleoplasm_rep2
Small RNA sequencing library prepared from Ascaris suum.

value: embryo