title: 92_PBS, Follicular, D7

city: Gold Coast

first: Laurelle

last: Jackson

state: Queensland

address: 1 Parklands Dr, Southport

department: Pharmacy and Medical Sciences

country: Australia

institute: Griffith University

description:
Library name: DSP-1001660034484-A-E09
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

data_processing:
GeoMx DSP sequencing data were processed using the NanoString GeoMx NGS Pipeline to generate digital count (DCC) files for each region of interest (ROI).
Assembly: Whole Transcriptome Atlas based on mm10
Supplementary files format and content: geomx_counts_matrix.txt
Supplementary files format and content: geomx_AOI_metadata.txt
Library strategy: Spatial Transcriptomics

source_name: lymph node

growth_protocol: Female BALB/c mice were maintained under specific pathogen-free conditions with ad libitum access to food and water. Animals were housed and handled in accordance with institutional animal ethics and biosafety guidelines. No in vitro cell culture growth conditions applied to this study, as tissues were collected directly from vaccinated animals for downstream spatial transcriptomic analyses.

extract_protocol:
Injection site muscle and draining lymph nodes were harvested, formalin-fixed, paraffin-embedded (FFPE), and sectioned for spatial transcriptomic analysis. For GeoMx DSP profiling, FFPE sections were deparaffinised, subjected to antigen retrieval and proteinase K digestion according to the manufacturer’s protocol for the GeoMx Whole Transcriptome Atlas assay. Regions of interest were selected based on guidance of morphology marker staining and histological evaluation, followed by UV photocleavage of indexing oligonucleotides for collection and sequencing.
For GeoMx DSP samples, photocleaved oligonucleotide tags released from selected regions of interest were collected and used for library preparation according to the NanoString GeoMx DSP Whole Transcriptome Atlas workflow. Sequencing libraries were generated by PCR amplification with sample-specific Illumina i5 and i7 dual-index primers, followed by purification and quantification prior to next-generation sequencing.

treatment_protocol: Groups of three female BALB/c mice per treatment group were immunised intramuscularly in the quadriceps with either AF03-adjuvanted recombinant haemagglutinin (rHA) protein vaccine or phosphate-buffered saline (PBS) control on Days 0 and 21. Blood was collected longitudinally on Days 0, 14, and 35 for serum-based immunogenicity analyses. For spatial transcriptomic profiling, injection site muscle and draining lymph nodes were collected on Days 1 and 7 following vaccination.

value: lymph node

value: healthy BALB/c mice

tag: region of_interest

value: Follicular

value: PBS


title: LN229,GFP,rep1

status: Public on Apr 16 2026

type: SRA

city: New York

first: Thomas

last: O'Loughlin

state: NY

address: Hess CSM Building, 1470 Madison Avenue

department: Neuroscience

country: USA

institute: Mount Sinai

description: Library name: Sample_1

library_source: transcriptomic

data_processing:
By Plasmidsaurus: "Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file. Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation. Differential expression was done with edgeR v4.0.16 using standard practice including filtering for low-expressed genes with edgeR::filterByExprwith default values. Functional enrichment, when available, is performed using gene set enrichment analysis with gseapy v0.12 using the MSigDB Hallmark gene set."
Assembly: hg38
Supplementary files format and content: .tsv file of raw counts and cpm

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: LN229 cells were cultured in DMEM (Gibco # 11965-084) supplemented with 10% FBS (VWR Seradigm # 97068-085), 1 mM sodium pyruvate (Gibco # 11360-070), and 100 U/mL penicillin plus 100 µg/mL streptomycin (Gibco # 15140-122). Cells were cultured at 37°C and 5% CO2 in a humidified atmosphere.

extract_protocol:
By Plasmidsaurus: Total RNA extracted using a bead-based extraction approach from cells preserved in Zymo DNA/RNA Shield. Post-extraction RNA concentration assessed using a fluorescence based plate reader assay.
By Plasmidsaurus: mRNA converted into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification. cDNA generated using a poly(dT)VN primer

treatment_protocol: Cells were transduced with GFP or SREBP1 cDNA, puro selected to purity, and then harvested in DNA/RNA shield for RNA extraction

tag: cell line

tag: cell type

value: glioblastoma

tag: genotype

value: GFP


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 4

city: Austin

first: Rebecca

middle: L

last: Young

state: TX

address: 2415 Speedway

department: Integrative Biology

institute: University of Texas at Austin

description: Library name: TUB-4

data_processing:
Custom perl scripts using the FASTX-toolkit and CUTADAPT v. 2.8 were used to remove reads with a homo-polymer run of “A”≥8 bases, retain reads with minimum 20 bases, removal PCR duplicates – defined as sequences sharing the same degenerate header and 20 bases of sequence – and filtered for quality (Phred quality score > 20 for 90% of the nucleotides).
We aligned preprocessed reads using the Burrows-Wheeler Aligner (bwa-mem) and process reads using samtools.
Assembly: Oreochromis niloticus reference (Orenil1.0 Ensembl cdna) and Labroides dimidiatus genome (Accession: PRJNA937036)
Supplementary files format and content: Processed data .counts are raw counts aligned to the Oreochromis niloticus reference
Supplementary files format and content: Processed data .LdimAlign.counts are raw counts aligned to the Labroides dimidiatus genome

molecule: total RNA

organism: Labrichthys unilineatus

source_name: Female, forebrain section

extract_protocol:
Total RNA was extracted using Maxwell 16LEV simplyRNA tissue kit (Promega Corporation, Madison, WI, USA) following manufacturer instructions, including DNase treatment. RNA samples were then eluted into 40uL of nuclease-free water.
Libraries are constructed using the University of Texas Genome Sequencing Analysis Facility protocol for 3'tag-seq. Total RNA was fragmented via Mg+ buffer and cDNA was synthesized with poly-dT oligo. cDNA was amplified using PCR and purified with DNA-binding magnetic beads. Sequencing was perfored on an Illumina HiSeq 2000 instrument.

treatment_protocol: Whole heads were transferred into 30 mL conical tubes with RNAlater (ThermoFischer, Waltham, MA, USA) to preserve the integrity of the RNA. The elapsed time between capture and death ranged from 6 to 28 minutes. After 3 hours (on average) in RNAlater, the samples were transferred into O.C.T. Compound (Sakura, Torrance, CA, USA) and flash frozen in liquid nitrogen and shipped to The University of Texas at Austin for RNA isolation.frozen heads were sectioned on a cryostat microtome into 300µm thick slices. The second most rostral slice of the brain, containing pallial areas Dl and Dm (i.e., the putative teleost homologs of the mammalian hippocampus and basolateral amygdala (areas Dl and Dm, respectively), along with partial portions of septal and striatal territories, was collected and stored in 200ul of ice-cold homogenization buffer with 1-thioglycerol (Promega Corporation, Madison, WI, USA) and stored at -80C until further processing.

tag: tissue

value: Female, forebrain section


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 2

description: Library name: TUB-2


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 1

description: Library name: TUB-1


title: LN229,CRISPRa,RSL3,rep2

description:
Library name: Sample_27
CRISPRa_counts_raw.txt
i20a

library_source: genomic

data_processing:
ScreenPro2 package (v0.2.10) used for processing dual-guide (V3) CRISPRa/i screens – https://github.com/ArcInstitute/ScreenPro2. Paired-end deep sequencing FASTQ files are first processed using the `GuideCounter` module to capture guide pairs counts mapped to the reference guide sequences provided in a library table. Then, the output count matrix per sample is then used to calculate drug screen phenotypes using the `PhenoScore` module.
Supplementary files format and content: .txt file of raw counts
Library strategy: CRISPR Screen

molecule: genomic DNA

source_name: LN229 dCas9-Suntag

extract_protocol:
Genomic DNA was purified from cell pellets using NucleoSpin Blood L gDNA extraction kits (Nacherey-Nagel # 740954) in accordance with the manufacturer’s instructions and yields and purity were confirmed by nanodrop.
Amplicons were generated by PCR to introduce sequencing adaptors and sample-specific indexes using a common forward primer within the U6 promoter and reverse primers which bind the sgRNA constant region downstream of the second sgRNA and contain the sample-specific indexes. PCR reactions comprised 2x NEB Next Ultra II Q5 polymerase (NEB # M0544), 10 µg of purified gDNA and 1 µl of each 100 µM primer per 100 μl reaction. PCR amplification was performed with the following cycling conditions: denaturation at 98ºC for 30 secs, 22 cycles of denaturation at 98ºC for 10 secs then annealing and extension at 67ºC for 75 secs, and a final extension at 72ºC for 5 mins. All gDNA was PCR amplified and all reactions for each sample were mixed post-amplification. 300 µl of amplified PCR was subject to a 0.5-0.65X double-sided SPRI selection to enrich for the amplicon and remove excess primer. Sample purity and concentration were determined using an Agilent Tapestation and used to calculate equimolar sample pooling. Pooled libraries were sequenced on a NextSeq550 or NovaSeq 6000 platform with paired end reads using custom read 1, read 2 and index read 1 primers and 10% PhiX achieving a minimum of 6 million reads per sample (i.e. ≥300 reads/library element).

treatment_protocol: LN229 CRISPRi or CRISPRa cells were transduced with compact genome-scale dual-sgRNA libraries generously donated by Jonathan Weissman. Cells were transduced at an MOI of ~0.3 to achieve representation of each sgRNA in an average of >500 cells (500x coverage). At 48 and 72 hrs post-transduction cells were dosed with 3 µg/ml puromycin to select for sgRNA-positive cells. Following selection, sgRNA-positive cells were subsequently recovered in fresh medium for an additional 3 days. 6 days post-transduction cells pellets of 25 million cells were frozen to determine sgRNA composition at selection initiation (T0). Remaining cells were split into treatment conditions in triplicate. For CRISPRi screens conditions were: DMSO, RM-006 1.56 nM, and RM-006 0.098 nM. For CRISPRa screens conditions were: DMSO, RM-006 1.56 nM, RSL3 46.875 nM, and RM-006 1.56 nM+RSL3 46.875 nM. Cells were maintained under selection pressure at 1000x library coverage with passaging every 1 to 4 days as necessary for a total of 14-15 days for the CRISPRi and 12 days for the CRISPRa screens. At the screen endpoint cells were harvested and frozen in 25 million cell pellets prior to library preparation for sequencing.

value: LN229 dCas9-Suntag

tag: treatment


title: LN229,CRISPRa,RM6RSL3,rep1

description:
Library name: Sample_29
CRISPRa_counts_raw.txt
i22a


title: On-d GLUT3 EGFRvIII targeting CAR-T cell-rep 2, 0.5 mM glucose condition, day 7

city: Tokyo

first: Hiroyoshi

last: Nishikawa

state: Tokyo

address: 5-1-1 Tsukiji, Chuo-ku

department: 3Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC)

country: Japan

institute: National Cancer Center Japan

description: Library name: Sample 16

data_processing:
RNA-seq reads were processed using the Genomon RNA-seq pipeline. Adapter sequences and low-quality bases were trimmed prior to alignment. Reads were aligned to the human reference genome (hg38), and gene-level read counts were generated for downstream analysis.
Assembly: Reads were aligned to the human reference genome (GRCh38/hg38).
Supplementary files format and content: tab-delimited text file includes raw counts for each samples.

source_name: Human CD3+ T cell

extract_protocol:
RNA was extracted using an RNeasy kit according to the manufacturer’s instructions (QIAGEN, Hilden, Germany). 1.0μg of total RNA was used for the construction of sequencing libraries.
Sample 1-4: Libraries were prepared using theNEBNext Ultra II Directional RNA Library Prep Kit  (New England BioLabs, Ipswich, MA) Sample 5-16: Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA)

value: Human CD3+ T cell

value: 0.5 mM glucose


title: LN229,CRISPRa,RSL3,rep3

description:
Library name: Sample_28
CRISPRa_counts_raw.txt
i21a


title: On-d GLUT3 EGFRvIII targeting CAR-T cell-rep 1, 0.5 mM glucose condition, day 7

description: Library name: Sample 15


title: LN229,CRISPRa,RM6,rep3

description:
Library name: Sample_25
CRISPRa_counts_raw.txt
i18a


title: LN229,CRISPRa,RSL3,rep1

description:
Library name: Sample_26
CRISPRa_counts_raw.txt
i19a


title: 89_PBS, B220, D7

description:
Library name: DSP-1001660034484-A-E06
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

organism: Mus musculus

tag: time


title: LN229,CRISPRa,RM6,rep2

description:
Library name: Sample_24
CRISPRa_counts_raw.txt
i17a


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 10

description: Library name: TUB-10


title: 88_PBS, Follicular, D7

description:
Library name: DSP-1001660034484-A-E05
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 90_PBS, Follicular, D7

description:
Library name: DSP-1001660034484-A-E07
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 6

description: Library name: LYR-6

organism: Thalassoma lunare


title: GLUT3 EGFRvIII targeting CAR-T cell-rep 2, 0.5 mM glucose condition, day 7

description: Library name: Sample 14


title: 91_PBS, Non-follicular, D7

description:
Library name: DSP-1001660034484-A-E08
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: Non-follicular


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 9

description: Library name: LYR-9


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 8

description: Library name: LYR-8


title: 87_PBS, Follicular, D7

description:
Library name: DSP-1001660034484-A-D11
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 85_PBS, Follicular, D7

description:
Library name: DSP-1001660034484-A-D09
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: LN229,CRISPRa,RM6RSL3,rep2

description:
Library name: Sample_30
CRISPRa_counts_raw.txt
i23a


title: On-d GLUT3 EGFRvIII targeting CAR-T cell-rep 2, 0.5 mM glucose condition, day 3

description: Library name: Sample 10


title: GLUT3 EGFRvIII targeting CAR-T cell-rep 1, 0.5 mM glucose condition, day 7

description: Library name: Sample 13


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 7

description: Library name: LYR-7


title: conventional EGFRvIII targeting CAR-T cell-rep 2, 0.5 mM glucose condition, day 7

description: Library name: Sample 12


title: 86_PBS, Non-follicular, D7

description:
Library name: DSP-1001660034484-A-D10
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: conventional EGFRvIII targeting CAR-T cell-rep 1, 0.5 mM glucose condition, day 7

description: Library name: Sample 11


title: 84_PBS, Non-follicular, D7

description:
Library name: DSP-1001660034484-A-D08
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 4

description: Library name: LYR-4


title: LN229,CRISPRa,RM6,rep1

description:
Library name: Sample_23
CRISPRa_counts_raw.txt
i16a


title: LN229,CRISPRa,veh,rep3

description:
Library name: Sample_22
CRISPRa_counts_raw.txt
i15a

value: DMSO


title: LN229,CRISPRa,veh,rep2

description:
Library name: Sample_21
CRISPRa_counts_raw.txt
i14a


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 5

description: Library name: LYR-5


title: On-d GLUT3 EGFRvIII targeting CAR-T cell-rep 1, 0.5 mM glucose condition, day 3

description: Library name: Sample 9


title: GLUT3 EGFRvIII targeting CAR-T cell-rep 1, 0.5 mM glucose condition, day 3

description: Library name: Sample 7


title: LN229,CRISPRa,veh,rep1

description:
Library name: Sample_20
CRISPRa_counts_raw.txt
i13a


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 2

description: Library name: LYR-2


title: LN229,CRISPRa,T0,rep3

description:
Library name: Sample_19
CRISPRa_counts_raw.txt
i12a


title: conventional EGFRvIII targeting CAR-T cell-rep 2, 0.5 mM glucose condition, day 3

description: Library name: Sample 6


title: 82_PBS, Follicular, D7

description:
Library name: DSP-1001660034484-A-D06
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: LN229,CRISPRa,T0,rep2

description:
Library name: Sample_18
CRISPRa_counts_raw.txt
i11a


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 1

description: Library name: LYR-1


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 3

description: Library name: LYR-3


title: conventional EGFRvIII targeting CAR-T cell-rep 1, 0.5 mM glucose condition, day 3

description: Library name: Sample 5


title: 81_PBS, B220, D7

description:
Library name: DSP-1001660034484-A-D05
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 83_PBS, Follicular, D7

description:
Library name: DSP-1001660034484-A-D07
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: GLUT3 EGFRvIII targeting CAR-T cell-rep 2, 0.5 mM glucose condition, day 3

description: Library name: Sample 8


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 10

description: Library name: LYR-10


title: 79_rHA protein vaccine, Non-follicular, D7

description:
Library name: DSP-1001660034484-A-D03
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: rHA protein vaccine


title: 3tj1FM white tot RNA

city: Planegg

first: Luca

last: Salvi

state: Please select

address: Semmelweisstr. 3

country: Germany

institute: ViGeneron GmbH

data_processing:
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichment was calculated with our house Perl scripts
Normalization to reads per million or to background
Assembly: Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary files format and content: Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv

organism: Schizosaccharomyces pombe

growth_protocol: cells were grown in liquid, rich YES medium

extract_protocol:
ChIP libraries: IP of crosslinked (1% formaldehyde, 15 min) sonycated lysate, followed by decrosslinking and protein and RNA degradation. DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). DNA sequencing via Illumina: Cells were lysed by bead beating and lysate was sonycated and RNAse-treated. DNA isolated via phenol-chloroform-isoamylalcohol purification followed by ethanol precipitation. DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). DNA sequencing via Nanopore: DNA extraction was performed with Genomic Tip 500/G kit (Qiagen) following the manufacturer’s instruction, but using Lallzyme MMX for lysis. Sequencing was performed using Oxford Nanopore (MinION). RNA sequencing: RNA was isolated applying the hot phenol method. Total RNA and polyA RNA Libraries made with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB). In the polyA library preparation, isolation of the polyA RNA from the total RNA was performed using polyT beads. Small RNA sequencing: strains with the endogenous Ago1 3xFLAG tagged were grown in YES and 2.5l of log phase cells were collected. Cells were resuspended in lysis buffer (50 mM HEPES pH 7.5, 1.5 M NaOAc, 5 mM MgCl2, 2 mM EDTA pH 8, 2 mM EGTA pH 8, 0.1% Nonidet P-40, 20% glycerol) supplemented with 1mM PMSF and Complete EDTA free Protease Inhibitor Cocktail (Roche), keeping a 1:1 ratio between the cell volume and the buffer. Cells were fragmented using glass beads and the bead beater as described for the ChIP protocol. The cell debris was eliminated by cetrifugation at 13000g and the crude lysate was incubated with 30μl of FLAG-M2 agarose resin (Sigma-Aldrich A2220) at 4°C for 2h with gentle rotation. The IP was washed five times with the lysis buffer and Ago1 was eluted from the resin mixing 1% SDS with 300 mM NaOAc and phenol-chloroform-isoamylalcohol (25:24:1, Roth). The sRNAs were concetrated by ethanol precipitation, run on an 18% polyacrylamide urea gel together with 22, 26 and 30 nt RNA markers and the bands of sizes between 20 and 30 nt were excised from the gel. A 3’ linker was ligated to the sRNAs (5 rAppCTGTAGGCACCATCAAT–N ′ H2 3’, NEB, reaction concentration 2μM). The 3' ligated products were purified on an 18% acrylamide urea gel with subsequent phenol-chloroform purification and ethanol purification. The 5' adaptor (5'-ACACUCUUUCCCUACACGACGCUC UUCCGAUCU-3', Metabion) ligation was performed, followed by reverse transcription (RT primer: 5’- GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCGATTGATGGTGCCTACAG -3’, Metabion). The cDNA was amplified with 12-20 PCR cycles using the Phusion hot start II DNA polymerase kit (ThermoFisher) and the Illumina P5 5' primer (5' -AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC G -3') together with the Illumina P7 3' primer with inserted barcode (5'-CAA GCA GAA GAC GGC ATA CGA GAT XXXXXX GTG ACT GGA GTT CAG ACG TG -3'). The sRNA library was purified from an 8% polyacrylamide gel, ethanol precipitated and Single end sequencing was performed on an Illumina GAIIX sequencer.
Libraries were prepared using NEBnext Ultra Directional RNA or DNA Ultra II Library Prep Kit for Illumina (NEB), following the manufacturer instruction.


title: 80_PBS, Follicular, D7

description:
Library name: DSP-1001660034484-A-D04
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 3tj1FM red tot RNA


title: 78_rHA protein vaccine, B220, D7

description:
Library name: DSP-1001660034484-A-D02
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HNRNPA0_lx_3

city: Riverside

first: feng

last: tang

state: CA

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

description: Library name: HNRNPA0_lx_3

data_processing:
High-throughput sequencing reads were processed with our previous easy-CLIP pipeline28 including trimming adapter, identifying reads uniquely mapping to the human genome (hg38), and removing PCR duplicates. Scripts used for CLIP analysis are available at github.com/dfporter/easyCLIP. For the peak distribution used in Figure 4, RNA-protein binding sites were identified with Clipper using default parameters (https://github.com/YeoLab/clipper/wiki/CLIPper-Home). The Integrative Genomics Viewer45 was used to visualize the mapping results. The intersection between bed files was performed using BEDTools.46 Overlapping percentage was calculated as (# of overlapped peaks)/(total # of peaks for the target protein) × 100%.
Assembly: hg38
Supplementary files format and content: bed files were genereated using Clipper
Supplementary files format and content: bw files were generated using deeptools

source_name: HEK293T cells

growth_protocol: Cells were maintained in DMEM (Life Technologies) supplemented with 10% FBS (Invitrogen) and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Cross-linked cells were harvested in ∼1 mL 4°C CLIP lysis buffer (50 mM Tris-HCl, pH 7.5, 200 mM NaCl and 1 mM EDTA, 10% glycerol, 0.1% NP40, 1% Triton X-100, 0.5% N-lauroylsarcosine) per plate.
~2 mg clarified lysate per replicate was combined with 22 μL anti-HA magnetic beads (ThermoFisher, #88837) for 1 h, washed, treated with 0.02 U/μL Ambion RNAse I (ThermoFisher, #AM2294) at 30°C for ∼3 min, 3′ dephosphorylated with PNK and ligated overnight to L3 adapters. Following L3 adapter ligation, replicates were pooled, 5′ phosphorylated, and ligated to L5 adapters. RNA-protein complexes were resolved by SDS-PAGE, transferred to nitrocellulose, and RNA recovered by proteinase K digestion. RNA was purified by using oligo(dT) beads to capture the poly(A) tail on L3 adapters, then reverse transcribed and amplified by PCR following previously described protocol 44. Libraries were sequenced on a NovaSeq X plus (paired-end 150 bp; ~30 M reads per sample).

value: HEK293T cells

value: Human embryonic kidney

value: WT


title: LN229,CRISPRa,T0,rep1

description:
Library name: Sample_17
CRISPRa_counts_raw.txt
i10a


title: HNRNPA0_lx_2

description: Library name: HNRNPA0_lx_2


title: 3tj1EL white tot RNA


title: Human EGFRvIII targeting CAR-T cell-rep 1, 10mM glucose condition

description: Library name: Sample 3

value: 10 mM glucose


title: Human EGFRvIII targeting CAR-T cell-rep 2, 10 mM glucose condition

description: Library name: Sample 4


title: HNRNPA0_lx_1

description: Library name: HNRNPA0_lx_1


title: Human EGFRvIII targeting CAR-T cell-rep 2, 0.5 mM glucose condition

description: Library name: Sample 2


title: 3tj1EL red tot RNA


title: 76_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034484-A-C12
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: lymph node


title: 3tj1EL DNA-seq nanopore

data_processing:
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichment was calculated with our house Perl scripts
Normalization to reads per million or to background
Assembly: Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary files format and content: Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv
Library strategy: DNA-seq


title: 75_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034484-A-C11
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: healthy BALB/c mice


title: 3tj1EL tot RNA


title: TPL_3_IP

city: Fuzhou City

first: xinru

last: liu

state: Fujian Province

address: No. 1, Xuefu North Road, Shangjie Town, Minhou County

department: School of Basic Medical Sciences

country: China

institute: Fujian Medical University

description: Library name: TPL_3_IP

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: hg19
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and m6A methylation status changes for each gene.
Library strategy: MeRIP-seq

source_name: placenta

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: placenta

value: epithelial cells

value: Wild type

value: treat with triptolide


title: 77_rHA protein vaccine, B220, D7

description:
Library name: DSP-1001660034484-A-D01
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 74_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034484-A-C10
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: Follicular


title: 3tj1FM tot RNA


title: 2tj1G DNA-seq nanopore


title: TPL_2_IP

description: Library name: TPL_2_IP


title: 2tj1H DNA-seq


title: 2tj1E white tot RNA


title: 2tj1I DNA-seq


title: 73_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034484-A-C09
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 2tj1E red tot RNA


title: TPL_1_IP

description: Library name: TPL_1_IP


title: 72_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034484-A-C08
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 2tj1J DNA-seq


title: 2tj1C DNA-seq


title: 2tj1F white tot RNA


title: 71_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034484-A-C07
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: Human EGFRvIII targeting CAR-T cell-rep 1, 0.5 mM glucose condition

description: Library name: Sample 1


title: TPL_2_Input

description: Library name: TPL_2_Input


title: TPL_3_Input

description: Library name: TPL_3_Input


title: 2tj1F red tot RNA


title: 2tj1B DNA-seq


title: 70_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034484-A-C06
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: TPL_1_Input

description: Library name: TPL_1_Input


title: 2tj1D white tot RNA


title: 69_PBS, Non-follicular, D7

description:
Library name: DSP-1001660034484-A-B09
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: PBS


title: 2tj1F tot RNA


title: 3Dskin model, RFMN and WHS treatment, d5

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstraße 30

institute: Uniklinik RWTH Aachen

description: Library name: Sample 6

data_processing:
FASTQ files were generated using bcl-convert (Illumina), with demultiplexing performed based on a custom sample sheet and without lane splitting. Subsequent processing was carried out using the nf-core/rnaseq pipeline (v3.18.0), executed via Nextflow (v24.10.5). Reads were trimmed using Trim Galore (v0.6.10) and aligned to the human reference genome (hg38) with STAR (v2.7.11b). Gene-level quantification was performed using featureCounts, with grouping by gene_type. Differential expression analysis was conducted using DESeq2 (v1.42.1) within R (v4.3.3) using default parameters. The resulting differential gene expression data were further subjected to over-representation analysis (ORA) and gene set enrichment analysis (GSEA) using the clusterProfiler package (v4.10.1) in conjunction with the Gene Ontology (GO) database.
Assembly: hg38
Supplementary files format and content: matrix table

source_name: skin

growth_protocol: Full-thickness 3D skin models were generated as followed. Briefly, the dermal compartment was constructed using a collagen-elastin scaffold (MatriDerm®; MedSkin Solutions Dr. Suwelack AG), which was cut into 19 mm circular punches and placed into six-well cell culture inserts (BD Falcon, Bedford, MA, USA). A total of 2 × 10^5 NHDF were seeded onto each scaffold and submerged in fibroblast growth medium. After three hours, 2 × 10^6 NHEK were seeded on top of the dermal equivalents. Two days later, the skin models were raised to the air-liquid interface (ALI). RFMN treatment was applied after the 3D skin models achieved complete epidermal differentiation.

extract_protocol:
Total RNA from 3D skin models was extracted using the NucleoSpin RNA Kit (Macherey-Nagel).
RNA libraries were prepared using Lexogen QuantSeq 3’ mRNA-Seq Kit following the manufacturer´s protocol.

treatment_protocol: 3D skin models were treated with RFMN using the Morpheus8 handpiece with 24-pin microneedle tips (InMode Aesthetics, Düsseldorf, Germany). The penetration depth was 0.5 mm using energy level 8, according to the manufacturer´s and clinical treatment recommendations. Immediately after RFMN part of the models received aftercare treatment with a dexpanthenol-containing ointment (Bepanthen wound and care ointment, Bayer Vital GmbH, Leverkusen Germany). After treatment, the models were cultivated in fresh culture medium and harvested on days 2 and 5 for histological analysis and detection of gene expression. Untreated models were maintained as negative controls.

value: skin

value: 3D skin model

value: fibroblasts and keratinocytes

value: RFMN and WHS treatment


title: 68_PBS, B220, D7

description:
Library name: DSP-1001660034484-A-B08
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 3Dskin model, RFMN and WHS treatment, d2

description: Library name: Sample 5


title: SiSFPQ_3

city: Xiamen

first: Suibin

last: ma

state: Fujian

address: Xiang'an Campus of Xiamen University, Xiamen City, Fujian Province

department: School of Life Sciences

institute: Xiamen university

description:
Library name: Sample 6
SiSFPQ_3

data_processing:
Raw data filtering
Genome alignment/mapping
Distribution of base quality
Gene expression level analysis
Functional enrichment analysis
Assembly: RGch38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: genes.reads.count1.txt

growth_protocol: U-2UOS cells were maintained in McCoy’s 5A supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
The total RNA of  sample was extracted using TRIzol Reagent (Thermo Scientific, cat. #15596026) following the manufacturer's recommended protocol.
A amount of 1μg total RNA per sample was used for stranded RNA sequencing library preparation using polyA selection method and KC-DigitalTM stranded mRNA-seq Library Prep Kit (Cat. no. DR09202, Seqhealth Ltd., Wuhan, China), according to the(Cat. no. DR09202, Seqhealth Ltd., Wuhan, China), according to the manufacturer's instructions.

value: Human osteosarcoma cells

value: SiSFPQ

value: actinomycin D


title: 2tj1E tot RNA


title: 3Dskin model, RFMN treatment, d5

description: Library name: Sample 4

value: WT

value: RFMN treatment


title: 67_PBS, Follicular, D7

description:
Library name: DSP-1001660034484-A-B07
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: lymph node


title: 2tj1D red tot RNA


title: SiSFPQ_2

description:
Library name: Sample 5
SiSFPQ_2


title: 66_PBS, Follicular, D7

description:
Library name: DSP-1001660034484-A-B06
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: healthy BALB/c mice


title: SiSFPQ_1

description:
Library name: Sample 4
SiSFPQ_1


title: 3Dskin model, RFMN treatment, d2

description: Library name: Sample 3


title: SiCtrl_3

description:
Library name: Sample 3
SiCtrl_3

value: SiCtrl


title: 65_PBS, Follicular, D7

description:
Library name: DSP-1001660034484-A-B05
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 3Dskin model, control, d5

description: Library name: Sample 2

value: control


title: 2tj1G white tot RNA


title: SiCtrl_2

description:
Library name: Sample 2
SiCtrl_2


title: SiCtrl_1

description:
Library name: Sample 1
SiCtrl_1


title: 2tj1B white tot RNA


title: 2tj1G red tot RNA


title: 2_No template control

description:
Library name: DSP-1001660034484-A-A01
Control with no template

source_name: No template control

value: No template control


title: Human_old_3_ATAC

city: Mannheim

first: Fredy

middle: Andres

last: Delgado Lagos

address: Ludolf-Krehl- Straße 13-17

department: Vascular Dysfunction

institute: UMM, Heidelberg University

description: Library name: Sample 6

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 99) with STAR 2.7.3a (Dobin et al., STAR: ultrafast universal RNA-seq aligner). Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 2.1.1 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq). Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded. Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). The raw count matrix was normalized with DESeq2 version 1.26.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 99. Contrasts were created with DESeq2 based on the normalized count peak matrix with all size factors set to one. Peaks were classified as significantly differential at average count > 10 and -1 < log2FC > 1.
Assembly: mm10
Supplementary files format and content: tab-seperated txt file

source_name: Mesenteric artery endothelial cells

extract_protocol:
50.000 cells were used for ATAC library preparation using Tn5 Transposase from Nextera DNA Sample Preparation Kit (Illumina).
Cells were pelleted and resuspended in 50µl Lysis/Transposition reaction (12.5µl THS-TD-Buffer, 2.5µl Tn5, 5µl 0.1% Digitonin and 30µl water) and was incubated at 37°C for 30min with occasional snap mixing. Following purification of the DNA fragments was done by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq500 platform (Illumina) using P3 flowcell with 2x 38bp paired-end setup.

value: Mesenteric artery endothelial cells


title: 64_PBS, Non-follicular, D1

description:
Library name: DSP-1001660034485-B-H10
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: Non-follicular


title: 3Dskin model, control, d2

description: Library name: Sample 1


title: 2tj1B red tot RNA


title: HuH-7, anti-ZEB1, DOT1L_KO, rep2, ChIP

city: Shanghai

first: Siyuan

last: Xu

address: No.131, Dongan Road, Shanghai

institute: Fudan Unversity

description: Library name: HuH-7_anti-ZEB1_DOT1L_KO_rep2

data_processing:
ChIP-seq or fanChIP reads within FASTQ files were trimmed using trim_galore from 3’ end until the final base had a quality score > 25.
ChIP-seq or fanChIP reads were aligned to the human hg38 reference genome using Bowtie 2 version 2.2.5 with the default parameters.
SAMtools version 1.9 was applied to transform SAM into the BAM format and removed PCR duplicates and unmapped reads.
The peak calling was done using MACS2 version 2.1.4 with the default parameters.
DeepTools version 3.5.1 was applied to transform BAM into the bigwig format, normalized using the counts per million (CPM).
DESeq2 package version 1.36.0 was used for differential peak analysis.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: DMEM, 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were cultured at 37°C with 5% (v/v) of CO2

extract_protocol:
For ChIP-seq experiments, cells were cross-linked with 1% formaldehyde at room temperature, followed by quenching with glycine. After cell lysis, the chromatin was sonicated for 100-500 bp at 4°C. For fanChIP assays, cells were lysed with CSK buffer. After that, the cell lysate was resuspended with MNase buffer and incubated with 0.5 unit of MNase at 37°C for 5 mins.
ChIP-seq or fanChIP libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina from Vazyme. The purified DNA was end-repaired and then ligated with adapters. After purified by AMPure XP beads from Beckman, the DNA was amplified using 13 cycles with the PCR program.

value: Hepatocellular carcinoma

tag: chip antibody

value: ZEB1 (Proteintech, #21544-1-AP)


title: Human_old_2_ATAC

description: Library name: Sample 5


title: 2tj1D tot RNA


title: 63_PBS, B220, D1

description:
Library name: DSP-1001660034485-B-H09
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: PBS


title: Human_young_3_ATAC

description: Library name: Sample 3


title: 61_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-H07
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: Follicular


title: hESC-derived HLO-D21

city: Geneva

first: Miranda

last: Türkal

address: 24 rue du Général-Dufour

country: Switzerland

institute: University of Geneva

description: Library name: liver_organoid

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed with Cell Ranger v7.2.0 using the GRCh38-2020-A reference to generate filtered gene–cell count matrices.
Quality control was performed in Seurat, removing genes expressed in fewer than 3 cells and cells with fewer than 200 detected genes. Cells were retained if they contained ≥40,000 UMIs and ≤20% mitochondrial transcripts.
Doublets were identified and removed using scDblFinder.
Dimensionality reduction was performed using PCA and UMAP on the 500 most variable genes. Clustering was conducted using the first 10 PCs at resolution = 0.5.
Cell types were annotated using a pre-trained classifier derived from GEO dataset GSE207889. Predicted identities were assigned when ≥85% of cells in a cluster shared the same classification. Cluster marker genes were identified with FindAllMarkers() (adj. p ≤ 0.05, log₂FC > 0.5, ≥5% expression).
Assembly: GRCh38 (GRCh38-2020-A, 10x Genomics reference)
Supplementary files format and content: Filtered gene–cell count matrices output by Cell Ranger are provided in Matrix Market format (matrix.mtx, barcodes.tsv, features.tsv).

source_name: Human liver organoid (HLO)

extract_protocol:
On D21, HLOs from three wells of an ultra-low attachment 24-well plate were collected and washed 2x with DPBS (-/-). The HLOs were then dissociated using TrypLE Express for 15 minutes at 37 °C. Following dissociation, the cell suspension was passed through a 70 μm MACS SmartStrainer to obtain a single-cell suspension. Cells were collected in 1% BSA in DMEM, centrifuged at 300 × g for 5 minutes, and resuspended again in 1% BSA in DMEM.
The 10× Genomics Chromium equipment and the 3′v3.1 reagent kit were used to create single-cell RNA-Seq libraries in accordance with the manufacturer's instructions. A Qubit fluorometer (ThermoFisher Scientific) and a Tapestation (DNA High sensitivity chip - Agilent Technologies) were used for library quantification and quality evaluation. Libraries were sequenced on an Illumina NovaSeq 6000 for paired-end 28 - 90 reads.

value: Human liver organoid (HLO)

value: hESCs, HS420, BAG-hES-IMP-0046

value: pluripotent


title: 62_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-H08
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 2tj1A white tot RNA


title: 2tj1G tot RNA


title: 59_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-H05
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, anti-ZEB1, DOT1L_KO, rep1, ChIP

description: Library name: HuH-7_anti-ZEB1_DOT1L_KO_rep1


title: Human_young_2_ATAC

description: Library name: Sample 2


title: HuH-7, anti-ZEB1, Neg2, rep1, ChIP

description: Library name: HuH-7_anti-ZEB1_Neg2_rep1


title: Human_old_1_ATAC

description: Library name: Sample 4


title: 2tj1A red tot RNA


title: 58_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-H04
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, anti-H3K79me2, DOT1L_KO, rep1, ChIP

description: Library name: HuH-7_anti-H3K79me2_DOT1L_KO_rep1


title: 2tj1B tot RNA


title: HuH-7, anti-ZEB1, Neg2, rep2, ChIP

description: Library name: HuH-7_anti-ZEB1_Neg2_rep2


title: 60_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-H06
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 2P-seq_PTBP3_WT-2

city: Beijing

first: Zongchang

last: Du

address: 15 Datun Road, Chaoyang District, Beijing, China

institute: IBP

data_processing:
Illumina bcl2fastq-1.8.4 conversion software was used for base calling.
After sequencing of single-cell RNA-seq libraries, adapters and low-qaulity bases were removed by Trimmomatic (Bolger et al., 2014) program. The retained paired-end reads were aligned to the mouse reference genome (mm9) using HISAT2 (Kim et al., 2015) tool with default parameters. The uniquely mapped reads count matrix were subject to DESeq2 (Michael, et al., 2014)  package to identify differentially expressed genes. Alternative splicing events were detected using rMATS (Shihao Shen, et al., 2014) software with defualt parameters.
2P-seq reads were filtered by trimming adaptors and A’s from the end of reads using the Cutadapt (Martin et al., 2014) program. The remaining reads were mapped to the mouse genome, and only uniquely mapped reads were retained. All samples were combined together and reads adjacent to each other were merged to cluster to identify robust polyadenylation sites. The alternative polyadenylation events were detected using DEXSeq (Anders Simon et al,. 2012) package with defualt parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage.

source_name: spleen

growth_protocol: Wild type and PTBP3 knockout mice were bred at six- to eight-weeks-old.

extract_protocol:
Total RNAs were extracted with Trizol regent and chloroform.
RNA-seq libraries were generated with some modifications (Mortazavi et al, 2008), 2P-seq libraries were generated with modification (Spies et al., 2013) .

treatment_protocol: Naive B cells were isolated from spleen using MojoSort™ Mouse Pan-B Cell Isolation Kit (Biolegend, 480052) following the manufacture’s protocol.

tag: method

value: wild type

value: Naive B cells

value: spleen

tag: strain


title: Human_young_1_ATAC

description: Library name: Sample 1


title: HuH-7, anti-H3K79me2, DOT1L_KO, rep2, ChIP

description: Library name: HuH-7_anti-H3K79me2_DOT1L_KO_rep2


title: 2tj1A tot RNA


title: 57_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-H03
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: lymph node


title: 2P-seq_PTBP3_WT-1


title: HuH-7, anti-H3K79me2, Neg2, rep2, ChIP

description: Library name: HuH-7_anti-H3K79me2_Neg2_rep2

value: WT


title: 1tj1 tot RNA


title: 56_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-H02
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: healthy BALB/c mice


title: HuH-7, anti-H3K27ac, DOT1L_KO, rep2, ChIP

description: Library name: HuH-7_anti-H3K27ac_DOT1L_KO_rep2

value: H3K27ac (Abcam, #ab4729)


title: 55_PBS, Non-follicular, D1

description:
Library name: DSP-1001660034485-B-H01
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 2P-seq_PTBP3_KO-1

value: PTBP3 knockout


title: 2P-seq_PTBP3_KO-2


title: 3tj1FM white polyA RNA


title: HuH-7, anti-H3K79me2, Neg2, rep1, ChIP

description: Library name: HuH-7_anti-H3K79me2_Neg2_rep1


title: 3tj1FM red polyA RNA


title: 54_PBS, Non-follicular, D1

description:
Library name: DSP-1001660034485-B-G12
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 3tj1EL white polyA RNA


title: HuH-7, anti-H3K27ac, DOT1L_KO, rep1, ChIP

description: Library name: HuH-7_anti-H3K27ac_DOT1L_KO_rep1


title: HuH-7, anti-H3K27ac, Neg2, rep2, ChIP

description: Library name: HuH-7_anti-H3K27ac_Neg2_rep2


title: 3tj1EL polyA RNA


title: 51_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-G09
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: MG1655 cells, 37˚C, 10 min rifampicin treated, total RNA-seq

city: Urbana

first: Yan

last: Zhang

state: IL

address: 600 S Mathews Ave Roger Adams Laboratory

department: Biochemistry

institute: University of Illinois Urbana-Champaign

description:
Library name: 37C_RNA_t10
Barcode GTCA in raw file

data_processing:
The raw sequencing reads were first demultiplexed based on the 4-base barcode corresponding to individual samples using fastx_barcode_splitter (https://github.com/agordon/fastx_toolkit). The linker sequence was clipped using Cutadapt. The clipped sequences were then mapped to the reference genome NC_000913.3, obtained from the NCBI Reference Sequence Database, using STAR version 2.7.6a. The STAR alignment output files are stranded wiggle files. Multi-mapping signal is distributed equally across loci (e.g., for ribosomal RNA reads). Signal.UniqueMultiple.str1 and Signal.UniqueMultiple.str2 represent signal from both uniquely and multi-mapped reads mapped to the minus and plus strand, respectively. Accordingly, they were renamed 'minus' and 'plus'.
Assembly: NC_000913.3
Supplementary files format and content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position. 'Minus' and 'plus' represent reads mapped to the minus and plus strand, respectively.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacterial cells

growth_protocol: E. coli wild-type cells (MG1655) were grown in MOPS EZ Rich Defined Medium (Teknova, M2105) at 37°C. An overnight culture was diluted into fresh medium to an initial OD600 of 0.005 and grown to mid-log phase (OD600 ~ 0.3).

extract_protocol:
Total RNA was purified from samples using hot acid phenol extraction. Briefly, frozen pellets were resuspended in 500 µL of RNA extraction buffer (0.3M NaOAc, 1mM EDTA, 1% SDS) and mixed with 600 µL hot phenol (Invitrogen, AM9720) at 65°C for 5 min. The mixture was centrifuged at 14000 rpm at 4°C for 10 min, and the upper aqueous layer was transferred to a new tube. A second phenol/chloroform extraction was performed, followed by an additional extraction with an equal volume of chloroform. The upper layer was mixed with 2 µL GlycoBlue coprecipitant (Invitrogen, AM9516) and an equal volume of isopropanol to precipitate RNA. RNA pellets were washed with 750 µL 80% ethanol, dried, and resuspend in 10 mM Tris pH 7. Genomic DNA was removed by Turbo DNase (Invitrogen, AM2238).
Purified RNA was fragmented by mixing with an equal volume of 2x alkaline fragmentation buffer (0.6 volumes of 100 mM Na2CO3 and 4.4 volumes of 100 mM NaHCO3), incubated at 95°C for 13 min, and then purified using Zymo oligo CC kit (Zymo Research, D4060). 600 ng fragmented RNA was dephosphorylated by T4 polynucleotide kinase (New England Biolabs, M0201) at 37°C for 1 hour, followed by ligation to 3’ linker oligos (sequences provided in the publication) using T4 RNA ligase 2 truncated KQ (New England Biolabs, M0373) at 16°C overnight. The ligated products from different samples were pooled and purified by size excision. For samples requiring mRNA enrichment, ribosomal RNAs were removed with Ribo-Zero rRNA depletion kit (Epicentre, MRZGN126). Ligated RNA was reverse transcribed into cDNA by SuperScript IV Reverse Transcriptase (Invitrogen, 18090010). The resulting cDNA was purified and ligated to a second oligo (sequences provided in the publication) using T4 RNA ligase 1 (New England Biolabs, M0204) at 16°C overnight. The final ligation products were purified by size excision. The purified cDNAs were PCR amplified using Phusion polymerase (New England Biolabs, M0530) (PCR primers provided in the publication). The final libraries were size selected and purified. Sequencing was performed on an Illumina HiSeq 4000 system, using single-end 50-nucleotide reads.

treatment_protocol: Rifampicin (Sigma-Aldrich, R3501) was added at a final concentration of 500 µg/mL to inhibit transcription initiation. Samples were collected at t = 0, 0.5, 1, 2, 3, 4, 5, 6, 8, and 10 min after rifampicin treatment, by mixing 2 mL of culture with 250 µL of ice-cold stop solution (225 µL ethanol and 25 µL phenol). Cultures were centrifuged at 8000 rpm for 3 min, and pellets were flash-frozen in liquid nitrogen.

value: bacterial cells

value: Wild type

value: 10 min rifampicin treated


title: 52_PBS, B220, D1

description:
Library name: DSP-1001660034485-B-G10
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: MG1655 cells, 37˚C, 6 min rifampicin treated, total RNA-seq

description:
Library name: 37C_RNA_t6
Barcode TCAG in raw file

value: 6 min rifampicin treated


title: MG1655 cells, 37˚C, 8 min rifampicin treated, total RNA-seq

description:
Library name: 37C_RNA_t8
Barcode CATG in raw file

value: 8 min rifampicin treated


title: 53_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-G11
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: Follicular

value: PBS


title: 3tj1EL red polyA RNA


title: HuH-7, anti-H3K27ac, Neg2, rep1, ChIP

description: Library name: HuH-7_anti-H3K27ac_Neg2_rep1

value: Hepatocellular carcinoma


title: HuH-7, anti-H3K4me3, DOT1L_KO, rep2, ChIP

description: Library name: HuH-7_anti-H3K4me3_DOT1L_KO_rep2

value: H3K4me3 (Abcam, #ab8580)


title: 3tj1FM polyA RNA


title: 50_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-G08
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: MG1655 cells, 37˚C, 5 min rifampicin treated, total RNA-seq

description:
Library name: 37C_RNA_t5
Barcode CTGA in raw file

value: 5 min rifampicin treated


title: MG1655 cells, 37˚C, 4 min rifampicin treated, total RNA-seq

description:
Library name: 37C_RNA_t4
Barcode GACT in raw file

value: 4 min rifampicin treated


title: HuH-7, anti-H3K4me3, Neg2, rep2, ChIP

description: Library name: HuH-7_anti-H3K4me3_Neg2_rep2


title: 2tj1E red polyA RNA


title: MG1655 cells, 37˚C, 3 min rifampicin treated, total RNA-seq

description:
Library name: 37C_RNA_t3
Barcode AGTC in raw file

value: 3 min rifampicin treated


title: HuH-7, anti-H3K4me3, Neg2, rep1, ChIP

description: Library name: HuH-7_anti-H3K4me3_Neg2_rep1


title: MG1655 cells, 37˚C, 2 min rifampicin treated, total RNA-seq

description:
Library name: 37C_RNA_t2
Barcode GCTA in raw file

value: 2 min rifampicin treated


title: 48_rHA protein vaccine, Non-follicular, D7

description:
Library name: DSP-1001660034485-B-F12
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: lymph node

value: Non-follicular

value: rHA protein vaccine


title: 2tj1F white polyA RNA


title: 49_rHA protein vaccine, Non-follicular, D7

description:
Library name: DSP-1001660034485-B-G01
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: healthy BALB/c mice


title: 45_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-F09
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 2tj1D white polyA RNA


title: HuH-7, NPM1, rep2, ChIP

description: Library name: HuH-7_NPM1_rep2

value: WT

value: NPM1 (Proteintech, #10306-1-AP)


title: MG1655 cells, 37˚C, 0.5 min rifampicin treated, total RNA-seq

description:
Library name: 37C_RNA_t05
Barcode TAGC in raw file

value: bacterial cells

value: Wild type

value: 0.5 min rifampicin treated


title: HuH-7, NPM1, rep1, ChIP

description: Library name: HuH-7_NPM1_rep1


title: 2tj1F red polyA RNA


title: 46_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-F10
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: Follicular


title: 2tj1E white polyA RNA


title: HuH-7, IgG, rep1, ChIP

description: Library name: HuH-7_ChIP_IgG_rep1

value: IgG (Abcam, #ab172730)


title: 47_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-F11
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: MG1655 cells, 37˚C, 10 min rifampicin treated, mRNA-seq

description:
Library name: 37C_mRNA_t10
Barcode GTCA in raw file

value: 10 min rifampicin treated


title: MG1655 cells, 37˚C, untreated, total RNA-seq

description:
Library name: 37C_RNA_t0
Barcode ATCG in raw file

value: Untreated


title: 43_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-F07
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, anti-H3K4me3, DOT1L_KO, rep1, ChIP

description: Library name: HuH-7_anti-H3K4me3_DOT1L_KO_rep1

value: Hepatocellular carcinoma

value: H3K4me3 (Abcam, #ab8580)


title: MG1655 cells, 37˚C, 1 min rifampicin treated, total RNA-seq

description:
Library name: 37C_RNA_t1
Barcode CGAT in raw file

value: 1 min rifampicin treated


title: MG1655 cells, 37˚C, 8 min rifampicin treated, mRNA-seq

description:
Library name: 37C_mRNA_t8
Barcode CATG in raw file

value: 8 min rifampicin treated


title: HuH-7, IgG, rep2, ChIP

description: Library name: HuH-7_ChIP_IgG_rep2


title: 2tj1F polyA RNA


title: 2tj1D red polyA RNA


title: 42_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-F06
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: lymph node


title: 2tj1E polyA RNA


title: 2tj1G white polyA RNA


title: HuH-7, DOT1L, rep1, fanChIP

description: Library name: HuH-7_DOT1L_rep1

value: DOT1L (Cell Signaling Technology, #77087)


title: 41_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-F05
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: rHA protein vaccine


title: HuH-7, DOT1L, rep2, fanChIP

description: Library name: HuH-7_DOT1L_rep2


title: 2tj1B white polyA RNA


title: 44_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-F08
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: healthy BALB/c mice


title: MG1655 cells, 37˚C, 5 min rifampicin treated, mRNA-seq

description:
Library name: 37C_mRNA_t5
Barcode CTGA in raw file

value: 5 min rifampicin treated


title: MG1655 cells, 37˚C, 4 min rifampicin treated, mRNA-seq

description:
Library name: 37C_mRNA_t4
Barcode GACT in raw file

value: 4 min rifampicin treated


title: 40_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-F04
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, IgG, rep2, fanChIP

description: Library name: HuH-7_fanChIP_IgG_rep2

value: WT


title: 39_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-F03
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, IgG, rep1, fanChIP

description: Library name: HuH-7_fanChIP_IgG_rep1


title: MG1655 cells, 37˚C, 3 min rifampicin treated, mRNA-seq

description:
Library name: 37C_mRNA_t3
Barcode AGTC in raw file

value: bacterial cells

value: Wild type

value: 3 min rifampicin treated


title: 2tj1G red polyA RNA


title: MG1655 cells, 37˚C, 2 min rifampicin treated, mRNA-seq

description:
Library name: 37C_mRNA_t2
Barcode GCTA in raw file

value: 2 min rifampicin treated


title: HuH-7, EPZ-5676_rep3, RNA-seq

description: Library name: HuH-7_EPZ-5676_rep3

data_processing:
RNA-seq reads within FASTQ files were trimmed using trim_galore with default parameters.
Trimmed reads were aligned to the human reference genome hg38 or mm10 using HISAT2 version 2.2.1 with default parameters
SAMtools version 1.9 was applied to transform SAM into the BAM format.
FeautureCounts version 0.6.1 was used to calculate the read counts of each transcript. TEtranscripts version 2.2.3 was applied to calculate the read counts of transposable elements.
DESeq2 package version 1.36.0 was used for differential expression analysis.
Assembly: hg38 or mm10
Supplementary files format and content: Raw counts for each sample

growth_protocol: HuH-7, Hepa1-6, Hep53.4, and LLC cell lines were maintained in 89% DMEM medium , 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were cultured at 37°C with 5% (v/v) of CO2.

extract_protocol:
RNA was harvested using RNeasy Mini Kit from QIAGEN. About 1μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina according to the manufacture’s protocol.

treatment_protocol: HuH-7 cells were treated with EPZ-5676 for 7 days.


title: HuH-7, EPZ-5676_rep2, RNA-seq

description: Library name: HuH-7_EPZ-5676_rep2


title: 38_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-F02
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

data_processing:
GeoMx DSP sequencing data were processed using the NanoString GeoMx NGS Pipeline to generate digital count (DCC) files for each region of interest (ROI).
Assembly: Whole Transcriptome Atlas based on mm10
Supplementary files format and content: geomx_counts_matrix.txt
Supplementary files format and content: geomx_AOI_metadata.txt
Library strategy: Spatial Transcriptomics

value: Follicular


title: 37_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-F01
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: MG1655 cells, 37˚C, 1 min rifampicin treated, mRNA-seq

description:
Library name: 37C_mRNA_t1
Barcode CGAT in raw file


title: 2tj1D polyA RNA


title: HuH-7, EPZ-5676_rep1, RNA-seq

description: Library name: HuH-7_EPZ-5676_rep1


title: 2tj1G polyA RNA


title: 36_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-E12
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, DMSO_rep3, RNA-seq

description: Library name: HuH-7_DMSO_rep3


title: MG1655 cells, 37˚C, 0.5 min rifampicin treated, mRNA-seq

description:
Library name: 37C_mRNA_t05
Barcode TAGC in raw file

value: 0.5 min rifampicin treated


title: 2tj1B red polyA RNA


title: 2tj1A white polyA RNA


title: 35_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-E11
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: MG1655 cells, 37˚C, untreated, mRNA-seq

description:
Library name: 37C_mRNA_t0
Barcode ATCG in raw file

value: Untreated


title: 2tj1A red polyA RNA


title: HuH-7, DMSO_rep2, RNA-seq

description: Library name: HuH-7_DMSO_rep2

value: Hepatocellular carcinoma


title: LN229,CRISPRi,RM6lo,rep3,exp2

description:
Library name: Sample_16
CRISPRi_counts_raw.txt
i18i

source_name: LN229 dCas9-KRAB

value: LN229 dCas9-KRAB

value: glioblastoma


title: HuH-7, DMSO_rep1, RNA-seq

description: Library name: HuH-7_DMSO_rep1


title: 34_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-E04
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: lymph node


title: 2tj1B polyA RNA


title: 32_rHA protein vaccine, Non-follicular, D7

description:
Library name: DSP-1001660034485-B-E02
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: Non-follicular


title: LN229,CRISPRi,RM6lo,rep2,exp2

description:
Library name: Sample_15
CRISPRi_counts_raw.txt
i17i


title: 2tj1A polyA RNA


title: 2tj1C polyA RNA


title: HuH-7, IFN, DOT1L_sgRNA#2_rep2, RNA-seq

description: Library name: HuH-7_DOT1L_IFN_sgRNA#2_rep2


title: LN229,CRISPRi,RM6lo,rep1,exp2

description:
Library name: Sample_14
CRISPRi_counts_raw.txt
i16i


title: 31_rHA protein vaccine, B220, D7

description:
Library name: DSP-1001660034485-B-E01
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: rHA protein vaccine


title: LN229,CRISPRi,veh,rep3,exp2

description:
Library name: Sample_13
CRISPRi_counts_raw.txt
i15i

value: DMSO


title: 30_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-D12
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: healthy BALB/c mice


title: 1tj1 polyA RNA


title: HuH-7, IFN, DOT1L_sgRNA#2_rep1, RNA-seq

description: Library name: HuH-7_DOT1L_IFN_sgRNA#2_rep1


title: 33_rHA protein vaccine, Non-follicular, D7

description:
Library name: DSP-1001660034485-B-E03
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, IFN, DOT1L_sgRNA#1_rep2, RNA-seq

description: Library name: HuH-7_DOT1L_IFN_sgRNA#1_rep2


title: LN229,CRISPRi,veh,rep2,exp2

description:
Library name: Sample_12
CRISPRi_counts_raw.txt
i14i


title: HuH-7, IFN, DOT1L_sgRNA#1_rep1, RNA-seq

description: Library name: HuH-7_DOT1L_IFN_sgRNA#1_rep1


title: LN229,CRISPRi,veh,rep1,exp2

description:
Library name: Sample_11
CRISPRi_counts_raw.txt
i13i


title: 29_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-D11
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 1tj1 red polyA RNA


title: 1tj1 white polyA RNA


title: LN229,CRISPRi,RM6hi,rep3,exp1

description:
Library name: Sample_10
CRISPRi_counts_raw.txt
i12i


title: HuH-7, DOT1L_sgRNA#2_rep2, RNA-seq

description: Library name: HuH-7_DOT1L_sgRNA#2_rep2


title: LN229,CRISPRi,RM6hi,rep2,exp1

description:
Library name: Sample_9
CRISPRi_counts_raw.txt
i11i


title: LN229,CRISPRi,veh,rep3,exp1

description:
Library name: Sample_7
CRISPRi_counts_raw.txt
i09i


title: HuH-7, IFN, sgNeg2_rep1, RNA-seq

description: Library name: HuH-7_DOT1L_IFN_Neg2_rep1


title: 27_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-D09
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, DOT1L_sgRNA#1_rep2, RNA-seq

description: Library name: HuH-7_DOT1L_sgRNA#1_rep2


title: 28_rHA protein vaccine, Follicular, D7

description:
Library name: DSP-1001660034485-B-D10
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, DOT1L_sgRNA#2_rep1, RNA-seq

description: Library name: HuH-7_DOT1L_sgRNA#2_rep1


title: LN229,CRISPRi,veh,rep2,exp1

description:
Library name: Sample_6
CRISPRi_counts_raw.txt
i08i


title: 25_rHA protein vaccine, Non-follicular, D1

description:
Library name: DSP-1001660034485-B-D07
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, DOT1L_sgRNA#1_rep1, RNA-seq

description: Library name: HuH-7_DOT1L_sgRNA#1_rep1


title: 2tj1A red sRNA

tag: antibody used_for_ip

value: anti FLAG M2 affinity gel Sigma, n° A 2220


title: wt sRNA

value: wt


title: 1tj1 white sRNA


title: LN229,CRISPRi,RM6hi,rep1,exp1

description:
Library name: Sample_8
CRISPRi_counts_raw.txt
i10i


title: 1tj1 red sRNA


title: Atpif4_16_10uE_1

status: Public on Apr 21 2026

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

description: Library name: sample7

data_processing:
Raw data quality was assessed by FastQC v.0.11.5 with the default parameters.
The genome indexes were made by HISAT2 v 2.1.0 using the function hisat2-build with the default paraments.
The mapping of short reads in the indexes of the four reference genomes was done with the same software using the function hisat2 with the parameter --dta.
Assembly: The reference genomes and the annotations used for the mapping of the reads were GCF_000001735.4, GCA_009936355.2, GCA_009602735.1 and GCA_000214015.2 for Arabidopsis thaliana, Marchantia polymorpha, Mesotaenium endlicherianum and Ostreococcus tauri, respectively.
Supplementary files format and content: Tab-delimted files include raw counts for each sample.

organism: Arabidopsis thaliana

source_name: 7d seedlings

extract_protocol:
Total RNA extraction from A. thaliana, M. polymorpha and M. endlicherianum were performed with the RNA extraction kit NucleoSpinTM RNA Plant Kit Macherey-Nagel according to the manufacturer's instructions.
Library preparation and sequencing of 100bp pair-end were performed by the company BGI Genomics, Hong Kong. The sequencing platform used was DNBseqTM and the coverage was higher than 50 million reads per sample.

value: 7d seedlings

value: 2d under 20˚C and 100 µmol m-2 s-1 of continuous white light followed by 5d under 16˚C and 10 µmol m-2 s-1 of continuous white light


title: 24_rHA protein vaccine, Non-follicular, D1

description:
Library name: DSP-1001660034485-B-D06
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

extract_protocol:
Injection site muscle and draining lymph nodes were harvested, formalin-fixed, paraffin-embedded (FFPE), and sectioned for spatial transcriptomic analysis. For GeoMx DSP profiling, FFPE sections were deparaffinised, subjected to antigen retrieval and proteinase K digestion according to the manufacturer’s protocol for the GeoMx Whole Transcriptome Atlas assay. Regions of interest were selected based on guidance of morphology marker staining and histological evaluation, followed by UV photocleavage of indexing oligonucleotides for collection and sequencing.
For GeoMx DSP samples, photocleaved oligonucleotide tags released from selected regions of interest were collected and used for library preparation according to the NanoString GeoMx DSP Whole Transcriptome Atlas workflow. Sequencing libraries were generated by PCR amplification with sample-specific Illumina i5 and i7 dual-index primers, followed by purification and quantification prior to next-generation sequencing.


title: 23_rHA protein vaccine, Follicular, D1

description:
Library name: DSP-1001660034485-B-D05
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: LN229,CRISPRi,veh,rep1,exp1

description:
Library name: Sample_5
CRISPRi_counts_raw.txt
i07i


title: HuH-7, sgNeg2_rep2, RNA-seq

description: Library name: HuH-7_DOT1L_Neg2_rep2

value: WT


title: 2tj1D  white +plasmids H3K9me2 ChIP

value: anti H3K9me2, Abcam 1220


title: 2tj1D  red +plasmids H3K9me2 ChIP


title: LN229,CRISPRi,T0,rep2,exp2

description:
Library name: Sample_4
CRISPRi_counts_raw.txt
i06i


title: 22_rHA protein vaccine, Follicular, D1

description:
Library name: DSP-1001660034485-B-D04
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: Follicular


title: 21_rHA protein vaccine, B220, D1

description:
Library name: DSP-1001660034485-B-D03
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, sgNeg2_rep1, RNA-seq

description: Library name: HuH-7_DOT1L_Neg2_rep1


title: HuH-7, IFN, sgNeg2_rep2, RNA-seq

description: Library name: HuH-7_DOT1L_IFN_Neg2_rep2


title: 2tj1G  white +plasmids H3K9me2 ChIP


title: LN229,CRISPRi,T0,rep1,exp2

description:
Library name: Sample_3
CRISPRi_counts_raw.txt
i05i


title: 20_rHA protein vaccine, Follicular, D1

description:
Library name: DSP-1001660034485-B-D02
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, DOT1L_KO, rep1, ATAC

description: Library name: HuH-7_DOT1L_KO_rep1

data_processing:
ATAC-seq reads within FASTQ files were trimmed using trim_galore from 3’ end until the final base had a quality score > 25.
ATAC-seq reads were aligned to the human hg38 reference genome using Bowtie 2 version 2.2.5 with the default parameters.
SAMtools version 1.9 was applied to transform SAM into the BAM format and removed PCR duplicates and unmapped reads.
The peak calling was done using MACS2 version 2.1.4 with the default parameters.
DeepTools version 3.5.1 was applied to transform BAM into the bigwig format, normalized using the counts per million (CPM).
DESeq2 package version 1.36.0 was used for differential ATAC peak analysis.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: DMEM, 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were cultured at 37°C with 5% (v/v) of CO2.

extract_protocol:
HuH-7 cells were lysed with lysis buffer containing 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin.
ATAC-seq libraries were prepared using the Hyperactive ATAC-Seq Library Prep Kit for Illumina from Vazyme. The purified DNA was end-repaired and then ligated with adapters. After purified by AMPure XP beads from Beckman, the DNA was amplified using 15 cycles with the PCR program.


title: LN229,CRISPRi,T0,rep2,exp1

description:
Library name: Sample_2
CRISPRi_counts_raw.txt
i04i

data_processing:
ScreenPro2 package (v0.2.10) used for processing dual-guide (V3) CRISPRa/i screens – https://github.com/ArcInstitute/ScreenPro2. Paired-end deep sequencing FASTQ files are first processed using the `GuideCounter` module to capture guide pairs counts mapped to the reference guide sequences provided in a library table. Then, the output count matrix per sample is then used to calculate drug screen phenotypes using the `PhenoScore` module.
Supplementary files format and content: .txt file of raw counts
Library strategy: CRISPR Screen


title: HuH-7, DOT1L_KO, rep2, ATAC

description: Library name: HuH-7_DOT1L_KO_rep2


title: HuH-7, Neg2, rep2, ATAC

description: Library name: HuH-7_Neg2_rep2


title: 19_rHA protein vaccine, Follicular, D1

description:
Library name: DSP-1001660034485-B-D01
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 2tj1G  red +plasmids H3K9me2 ChIP


title: 2tj1G red sRNA


title: LN229,CRISPRi,T0,rep1,exp1

description:
Library name: Sample_1
CRISPRi_counts_raw.txt
i03i


title: 18_PBS, Non-follicular, D1

description:
Library name: DSP-1001660034485-B-C06
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: PBS


title: 3tj1FM white H3K9me2 ChIP


title: 3tj1FM red H3K9me2 ChIP


title: LN229,RM6,0.39nM,rep2

description:
Library name: Sample_8
R6-M2

data_processing:
UMIs were extracted from the fastq files with umi_tools and cutadapt was used to remove short and low-quality reads. The reads were aligned to the human GENCODE v.34 reference genome using STAR aligner and the duplicate reads were collapsed using umi_tools. Gene level counts were measured using HTSeq.
Assembly: GRCh38.p13
Supplementary files format and content: .txt file of raw counts

extract_protocol:
RNA was extracted from cells using Quick-RNA microprep kit (Zymo # R1050) according to the manufacturer's instructions
3’ RNA-seq libraries were generated using a QuantSeq FWD Kit (Lexogen # 015) with UMI add-on module according to the manufacturer’s instructions. Briefly, 350 ng of input RNA was used for first-strand cDNA synthesis with an oligo(dT) primer, RNA was removed, second strand synthesis was performed with random primers containing unique molecular identifiers, and the generated cDNA purified using magnetic beads. Purified cDNA was amplified by 16 cycles of PCR to generate sufficient material for sequencing and to introduce complete sequencing adapters. Amplified libraries were subject to a further purification step and then assessed for yield and composition on an Agilent Bioanalyzer. Samples were pooled equimolarly, and pooled libraries were subsequently sequenced on an Illumina NextSeq550 platform using a High Output Reagent Cartridge v2 (Illumina # 15057934) in single-end 65 bp configuration.

treatment_protocol: Cells were treated with vehicle (DMSO) or 0.098, 0.39, 1.56 nM RM-006 for 72 hours

value: wild-type


title: 17_PBS, Non-follicular, D1

description:
Library name: DSP-1001660034485-B-C05
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: HuH-7, Neg2, rep1, ATAC

description: Library name: HuH-7_Neg2_rep1

value: Hepatocellular carcinoma


title: 3tj1EL  white H3K9me2 ChIP

data_processing:
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichment was calculated with our house Perl scripts
Normalization to reads per million or to background
Assembly: Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary files format and content: Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv


title: WT-3

city: Taizhou

first: yin

last: yuan

state: jiangsu

address: 210 Yingchun Road, Hailing District, Taizhou City, Jiangsu Province

institute: Nanjing Medical University Affiliated Taizhou People's Hospital

description: Library name: Sample9

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: raw counts and RPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Oral squamous cell carcinoma cell lines

tag: sample group


title: LN229,RM6,0.39nM,rep1

description:
Library name: Sample_7
R6-M1

value: glioblastoma


title: WT-1

description: Library name: Sample7


title: LN229,RM6,0.098nM,rep1

description:
Library name: Sample_5
R6-L1


title: 15_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-C03
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: lymph node


title: 3tj1EL H3K9me2 ChIP


title: 14_PBS, B220, D1

description:
Library name: DSP-1001660034485-B-C02
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 3tj1FM H3K9me2 ChIP


title: LN229,RM6,0.098nM,rep2

description:
Library name: Sample_6
R6-L2


title: MPTN-2

description: Library name: Sample6

value: MPTN


title: 3tj1EL  red H3K9me2 ChIP


title: WT-2

description: Library name: Sample8


title: LN229,RM6,1.56nM,rep2

description:
Library name: Sample_4
R6-H2


title: 16_PBS, Non-follicular, D1

description:
Library name: DSP-1001660034485-B-C04
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: Non-follicular


title: LN229,RM6,1.56nM,rep1

description:
Library name: Sample_3
R6-H1


title: MPTN-1

description: Library name: Sample5


title: LN229,veh,rep2

description:
Library name: Sample_2
D-2

value: DMSO


title: 2tj1E white H3K9me2 ChIP


title: MPTN-3

description: Library name: Sample4


title: 13_PBS, Follicular, D1

description:
Library name: DSP-1001660034485-B-C01
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: healthy BALB/c mice


title: 12_rHA protein vaccine, Non-follicular, D1

description:
Library name: DSP-1001660034485-B-B12
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: rHA protein vaccine


title: MG1655 cells, 37˚C, 6 min rifampicin treated, mRNA-seq

description:
Library name: 37C_mRNA_t6
Barcode TCAG in raw file

value: bacterial cells

value: Wild type

value: 6 min rifampicin treated


title: 2tj1E red H3K9me2 ChIP


title: 10_rHA protein vaccine, Follicular, D1

description:
Library name: DSP-1001660034485-B-B10
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 2tj1F white H3K9me2 ChIP


title: MPTN24-3

description: Library name: Sample3


title: 11_rHA protein vaccine, Follicular, D1

description:
Library name: DSP-1001660034485-B-B11
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: MPTN24-2

description: Library name: Sample2


title: LN229,veh,rep1

description:
Library name: Sample_1
D-1


title: SIF_4

city: Chengdu

first: Qiming

last: Duan

state: Sichuan

address: No.211, Huimin Road, Wenjiang District

department: Animal Nutrition Institute

institute: Sichuan Agriculture University

description: Library name: SIF_4

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: Sscrofa11.1
Supplementary files format and content: txt or xlsx, matrix tables containing miRNA raw counts and normalized expression values (e.g., CPM) for all samples

organism: Sus scrofa

source_name: colostrum

growth_protocol: Landrace × Yorkshire sows were maintained under routine commercial production conditions at a commercial pig farm. From gestation day 106 to lactation day 28, animals were assigned to either a basal diet (CON) or the same diet supplemented with 200 mg/kg soy isoflavones (SIF). Sows were moved to a thoroughly disinfected farrowing facility at gestation day 104 and housed individually in farrowing crates on fully slatted floors at 19-25 °C. Feed was provided three times daily, and water was available ad libitum. Colostrum samples used for exosomal miRNA extraction were collected from healthy sows within 1 h postpartum.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare 8 small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: Prior to extract preparation, sows were subjected to two dietary treatments: a control diet (CON) or the same basal diet supplemented with 200 mg/kg soy isoflavones (SIF). Dietary treatment was applied from gestation day 106 to lactation day 28. Colostrum samples for exosomal RNA extraction were collected within 1 h postpartum from healthy sows in each group. No additional treatment was applied to the colostrum samples before exosome isolation and RNA extraction.

value: colostrum

value: soy isoflavone supplemented diet (200 mg/kg)


title: 2tj1F red H3K9me2 ChIP

extract_protocol:
ChIP libraries: IP of crosslinked (1% formaldehyde, 15 min) sonycated lysate, followed by decrosslinking and protein and RNA degradation. DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). DNA sequencing via Illumina: Cells were lysed by bead beating and lysate was sonycated and RNAse-treated. DNA isolated via phenol-chloroform-isoamylalcohol purification followed by ethanol precipitation. DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). DNA sequencing via Nanopore: DNA extraction was performed with Genomic Tip 500/G kit (Qiagen) following the manufacturer’s instruction, but using Lallzyme MMX for lysis. Sequencing was performed using Oxford Nanopore (MinION). RNA sequencing: RNA was isolated applying the hot phenol method. Total RNA and polyA RNA Libraries made with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB). In the polyA library preparation, isolation of the polyA RNA from the total RNA was performed using polyT beads. Small RNA sequencing: strains with the endogenous Ago1 3xFLAG tagged were grown in YES and 2.5l of log phase cells were collected. Cells were resuspended in lysis buffer (50 mM HEPES pH 7.5, 1.5 M NaOAc, 5 mM MgCl2, 2 mM EDTA pH 8, 2 mM EGTA pH 8, 0.1% Nonidet P-40, 20% glycerol) supplemented with 1mM PMSF and Complete EDTA free Protease Inhibitor Cocktail (Roche), keeping a 1:1 ratio between the cell volume and the buffer. Cells were fragmented using glass beads and the bead beater as described for the ChIP protocol. The cell debris was eliminated by cetrifugation at 13000g and the crude lysate was incubated with 30μl of FLAG-M2 agarose resin (Sigma-Aldrich A2220) at 4°C for 2h with gentle rotation. The IP was washed five times with the lysis buffer and Ago1 was eluted from the resin mixing 1% SDS with 300 mM NaOAc and phenol-chloroform-isoamylalcohol (25:24:1, Roth). The sRNAs were concetrated by ethanol precipitation, run on an 18% polyacrylamide urea gel together with 22, 26 and 30 nt RNA markers and the bands of sizes between 20 and 30 nt were excised from the gel. A 3’ linker was ligated to the sRNAs (5 rAppCTGTAGGCACCATCAAT–N ′ H2 3’, NEB, reaction concentration 2μM). The 3' ligated products were purified on an 18% acrylamide urea gel with subsequent phenol-chloroform purification and ethanol purification. The 5' adaptor (5'-ACACUCUUUCCCUACACGACGCUC UUCCGAUCU-3', Metabion) ligation was performed, followed by reverse transcription (RT primer: 5’- GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCGATTGATGGTGCCTACAG -3’, Metabion). The cDNA was amplified with 12-20 PCR cycles using the Phusion hot start II DNA polymerase kit (ThermoFisher) and the Illumina P5 5' primer (5' -AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC G -3') together with the Illumina P7 3' primer with inserted barcode (5'-CAA GCA GAA GAC GGC ATA CGA GAT XXXXXX GTG ACT GGA GTT CAG ACG TG -3'). The sRNA library was purified from an 8% polyacrylamide gel, ethanol precipitated and Single end sequencing was performed on an Illumina GAIIX sequencer.
Libraries were prepared using NEBnext Ultra Directional RNA or DNA Ultra II Library Prep Kit for Illumina (NEB), following the manufacturer instruction.

value: anti H3K9me2, Abcam 1220


title: 8_rHA protein vaccine, Follicular, D1

city: Gold Coast

first: Laurelle

last: Jackson

address: 1 Parklands Dr, Southport

institute: Griffith University

description:
Library name: DSP-1001660034485-B-B08
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing

value: Follicular


title: SIF_3

description: Library name: SIF_3


title: SIF_2

description: Library name: SIF_2


title: kongbai-3

description: Library name: Sample6


title: 9_rHA protein vaccine, B220, D1

description:
Library name: DSP-1001660034485-B-B09
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: MPTN24-1

description: Library name: Sample1


title: 2tj1F H3K9me2 ChIP


title: 7_rHA protein vaccine, Follicular, D1

description:
Library name: DSP-1001660034485-B-B07
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: SIF_1

description: Library name: SIF_1


title: IRF9-3

description: Library name: Sample3

value: overexpressing IRF9


title: kongbai-2

description: Library name: Sample5


title: 6_rHA protein vaccine, Follicular, D1

description:
Library name: DSP-1001660034485-B-B06
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 2tj1D white H3K9me2 ChIP


title: CON_4

description: Library name: CON_4

value: control diet


title: 2tj1E H3K9me2 ChIP


title: CON_3

description: Library name: CON_3


title: IRF9-1

description: Library name: Sample1

value: Oral squamous cell carcinoma cell lines


title: kongbai-1

description: Library name: Sample4


title: IRF9-2

description: Library name: Sample2


title: 2tj1D red H3K9me2 ChIP


title: 2tj1B white H3K9me2 ChIP


title: 3_rHA protein vaccine, Follicular, D1

description:
Library name: DSP-1001660034485-B-B03
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 4_rHA protein vaccine, Non-follicular, D1

description:
Library name: DSP-1001660034485-B-B04
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: CON_1

description: Library name: CON_1


title: 2tj1G white H3K9me2 ChIP


title: CON_2

description: Library name: CON_2


title: 2tj1G red H3K9me2 ChIP


title: 5_rHA protein vaccine, Non-follicular, D1

description:
Library name: DSP-1001660034485-B-B05
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 2_rHA protein vaccine,B220, D1

description:
Library name: DSP-1001660034485-B-B02
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: 26_rHA protein vaccine, Follicular, D1

description:
Library name: DSP-1001660034485-B-D08
Formalin fixed paraffin embedded tissue spatial transcriptomics sequencing


title: Podocyte cell_NG_scr_Rep_5_(20)

first: Ana

last: Ortega

state: VALENCIA

address: Av. Menendez Pelayo 4

institute: Incliva Health Research Institute

description:
Library name: Sample_37_NG_scr_Biol_rep_5_(20)
Colum name in Counts_smallRNA.txt: NG_scr_20

data_processing:
Small RNA levels were quantified with the featureCounts function from the Rsubread package from Bioconductor, R
Trimming was performed with Trim Galore!
Alignment to the GRCh38 reference genome was performed with STAR
Assembly: GRCh38
Supplementary files format and content: .txt files contain raw counts for each sample

source_name: podocyte AB8/13

growth_protocol: Conditionally immortalised human podocytes (cell line AB8/13) were cultured on collagen type I-coated (Gibco, Thermo-Fisher Scientific, Waltham, MA, USA) flasks or plates in the RPMI medium 1640 supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (both from Biowest, Nuaillé, France), and 1% insulin-transferrin-selenium (ITS, Gibco, Thermo-Fisher Scientific, Waltham, MA, USA). They were maintained at 33 °C until reaching 80% confluence, then trypsinised and reseeded at 70% confluence for differentiation that was induced by incubating cells at 37 °C with 2% FBS for 10-14 days. All cultures were kept in a humidified incubator with 5% CO₂ and 95% air (BINDER, VWR International, Radnor, PA, USA). Differentiated podocytes were used to perform all experiments.

extract_protocol:
Total RNA, was isolated from podocyte-derived-EVs using the Total Exosome RNA and Protein Isolation kit (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA), following the manufacturer’s protocol. All RNA preparations were stored at −80 °C until further use.
Libraries were prepared from 6 μL of total RNA per sample using the Small RNA-Seq Library Prep Kit (Lexogen GmbH, Austria), following a protocol optimised for low-input samples. Individual libraries were normalised to 4 nM, pooled, and sequenced on the NextSeq 550 platform (Illumina, USA) using 150-cycle paired-end reads.

treatment_protocol: Podocytes were transiently transfected with siRNA targeting the RAB27A and the RAB3A gene using Lipofectamine 3000 (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA) in serum-free Opti-MEM® Gibco, Thermo-Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s protocol. As control, cells were transfected with a scrambled siRNA (scr) (Silencer™ Select Negative Control, Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA). After 24 hours, the transfection medium was replaced with RPMI containing 1% penicillin-streptomycin and ITS. Cells were then treated with either normal glucose (NG; 5.5 mM) or high glucose (HG; 30 mM) concentrations (D-(+)-Glucose; Sigma Aldrich, St. Louis, MO, USA) and incubated for an additional 24 hours at 37 °C.

value: podocyte AB8/13

value: renal podocyte

tag: sirna transfection

value: scramble transfected

value: normal glucose


title: IRF9-Input

description: Library name: Sample2

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: 2tj1D H3K9me2 ChIP


title: 2tj1A white H3K9me2 ChIP


title: Podocyte cell_HG_scr_Rep_5_(20)

description:
Library name: Sample_38_HG_scr_Biol_rep_5_(20)
Colum name in Counts_smallRNA.txt: HG_scr_20

value: high glucose