title: T47D_E2_rep2

description:
Library name: T47D_E2_rep2
T47D_E2_overlap.optimal_peak.narrowPeak.gz
T47D_E2_idr.optimal_peak.narrowPeak.gz


title: H3K27ac_mg_WT_8mo_rep2

status: Public on Aug 13 2026

type: SRA

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

country: USA

institute: University of California, San Diego

description: ChIP-seq

library_source: genomic

data_processing:
FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert reads aligning to a single genomic location into “tag directories” for subsequent analysis using the command makeTagDirectory (Heinz et al., 2010). To annotate H3K27ac signal around ATAC-seq peaks, the parameter -size 800 was used with the annotatePeaks command. To annotate MITF/TFE tags around ATAC-seq peaks, the parameter -size 200 was used. DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal with > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text. For TFE3-bound promoter and enhancer analyses, promoters were defined as ±500 bp from the TSS and enhancers as outside this region, both having a minimum of ≥16 normalized merged tags for H3K27ac and ≥64 normalized tags for TFE3 IDR peaks. To identify motifs enriched in differential peak regions over background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. Background sequences were comprised of random GC-matched genomic sequences.
Assembly: mm10
Supplementary files format and content: Tab-separated text file that contains the H3K27ac-annotated ATAC IDR peaks for microglia. Microglia ATAC-Seq IDR peak regions were annotated with normalized tag counts from H3K27Ac ChIP-seq data. Peak annotation with H3K27ac tag directories was performed with HOMER annotatePeaks command with option -size 800. All genomic coordinates are relative to mm10 mouse assembly.
Supplementary files format and content: Tab-separated text file that contains the H3K27ac-annotated ATAC IDR peaks for neurons. Neuron ATAC-Seq IDR peak regions were annotated with normalized tag counts from H3K27Ac ChIP-seq data. Peak annotation with H3K27ac tag directories was performed with HOMER annotatePeaks command with option -size 800. All genomic coordinates are relative to mm10 mouse assembly.
Supplementary files format and content: Tab-separated text file that contains the H3K27ac-annotated ATAC IDR peaks for oligodendrocytes. Oligodendrocyte ATAC-Seq IDR peak regions were annotated with normalized tag counts from H3K27Ac ChIP-seq data. Peak annotation with H3K27ac tag directories was performed with HOMER annotatePeaks command with option -size 800. All genomic coordinates are relative to mm10 mouse assembly.
Supplementary files format and content: Tab-separated text file that contains MITF/TFE tag-annotated ATAC IDR peaks for microglia. Microglia ATAC-Seq IDR peak regions were annotated with normalized tag counts from merged MITF/TFE ChIP-seq data. Peak annotation with merged MITF/TFE tag directories was performed with HOMER annotatePeaks command with option -size 200. All genomic coordinates are relative to mm10 mouse assembly.
Supplementary files format and content: Tab-separated text file that contains MITF/TFE-annotated ATAC IDR peaks for oligodendrocytes. Oligodendrocyte ATAC-Seq IDR peak regions were annotated with normalized tag counts from merged MITF/TFE ChIP-seq data. Peak annotation with merged MITF/TFE tag directories was performed with HOMER annotatePeaks command with option -size 200. All genomic coordinates are relative to mm10 mouse assembly.

molecule: genomic DNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Brain nuclei were isolated as previously described (Nott et al., 2019,2021), with initial homogenization and crosslinking performed with either 1% formaldehyde in Dulbecco’s PBS for 10 minutes (H3K27ac) or 2mM DSG (Proteochem) in Dulbecco’s PBS for 30 minutes then 1% formaldehyde for 10 minutes (TF ChIP) at room temperature. Nuclei were stained overnight with PU.1-PE (Cell Signaling 81886S), OLIG2-AF488 (Abcam 225099), or NEUN-AF488 (Millipore MAB 377X). Nuclei were stained with DAPI (BioLegend 422801) the next day then sorted with a Beckman Coulter MoFlo Astrios EQ or BD Influx Cell Sorter. Nuclei were sorted as DAPI positive singlets, additionally with microglia as PU.1+/OLIG2-/NEUN-/DAPI+, neurons as PU.1-/OLIG2-/NEUN+/DAPI+, and oligodendrocytes as PU.1-/OLIG2+/NEUN-/DAPI+. Chromatin immunoprecipitation sequencing was performed as previously described (Heinz et al, 2010, Texari et al, 2021). For H3K27ac ChIP-seq, ~500,000 fixed nuclei were quickly thawed on ice and resuspended in ice-cold LB3 buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and 1x protease inhibitor cocktail. Nuclei / chromatin was sheared by sonication using the PIXUL Multi-Sample Sonicator (Active Motif) in low bind 96 well plates following the manufacturer’s instructions. Samples were sonicated with the following settings: Pulse (N): 50, PRF [kHz]: 1.00, Process time: 60 min, Burst Rate [Hz]: 20.00. Samples were pulse spun to 600xg at 4°C in the 96-well plate, transferred to low-bind tubes, and chromatin was recovered by retaining the supernatant following a spin at 21,000xg at 4°C for 10 minutes. The supernatant was then diluted 1.1-fold with ice-cold 10% Triton X-100. Two percent of the lysate was kept as ChIP input control. 10 μL of Dynabead Protein A and 10 μL of Protein G were added per sample, in addition to 2 μg of a specific antibody for H3K27ac (Active Motif 39685). The samples were rotated overnight at 4°C and were washed as follows the next day: 3x with Wash Buffer I (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) + 1x protease inhibitor cocktail, 3x with Wash Buffer III (10 mM Tris-HCl pH 7.5, 250 mM LiCl, 1% Triton X-100, 1 mM EDTA, 0.7% Sodium Deoxycholate) + 1x protease inhibitor cocktail, 2x with TET (0.2% Tween-20/TE) + 1/3x protease inhibitor cocktail, and 1x with IDTET (0.2% Tween-20, 10 mM Tris pH 8, 0.1 mM EDTA). Samples were finally resuspended in 25 μL TT buffer (10 mM Tris pH 8 + 0.05% Tween 20) prior to on-bead library preparation. For MITF, TFEB, and TFE3 ChIP-seq, one million nuclei were thawed on ice and resuspended in ice-cold RLNR1 buffer (20mM Tris HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 1% NP-40, 0,1% SDS, 0.5 mM DTT) + 1x protease inhibitor cocktail/PMSF. Nuclei / chromatin was sheared and recovered with the same method employed for H3K27ac. 10 μL of Dynabead Protein A and 10 μL of Protein G beads per sample were then coupled to either 2 μg of MITF antibody (ActiveMotif, 91201), 2 μg each of two TFEB antibodies (Abcam ab2636, Cell Signaling CST 37785 (D2O7D), or 2 μg each of two TFE3 antibodies (Abcam ab93808, Millipore  Sigma HPA023881). Bead/antibody complexes were added to each sample and rotated overnight at 4°C. The samples were washed with the following buffers: 2x RLNR1 + PIC/PMSF/DTT buffer, 3x LWB-RCNR1 buffer (10 mM Tris HCl pH 7.5, 1 mM EDTA, 0.7% sodium deoxycholate, 1% NP-40, 250 mM LiCl) + PIC/PMSF, 2x TET buffer, 1x IDTET buffer, and then resuspended in 25 μL TT for on-bead library preparation.
Sequencing libraries for ChIP and input samples were prepared with NEBNext Ultra II DNA library prep kit (NEB, E7645) reagents according to the manufacturer’s protocol on beads suspended in 25 μL TT (10 mM Tris/HCl pH 7.5, 0.05% Tween-20), with reagent volumes reduced by half. DNA was eluted and crosslinks reversed by adding 4 μL 10% SDS, 4.5 μL 5 M NaCl, 3 μL EDTA, 4 μL EGTA, 1 μL proteinase K (20 mg/ml), 16 μL water, incubating for 1 h at 55°C, then 30 minutes to overnight at 65°C. DNA was purified using 2 μL of SpeedBeads (Cytiva GE45152105050250) in a 20% PEG8000 / 1.5M NaCl solution to final concentration of 12% PEG, then eluted with 25 μL TT. DNA contained in the eluate was then amplified for 12-14 cycles in 25 μL PCR reactions using NEBNext High-Fidelity Q5 2X PCR Master Mix (NEB) and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. Resulting libraries were size selected by gel excision to 200-500 bp, purified, and single or paired-end sequenced using an Illumina NovaSeq instrument.

tag: tissue

value: Brain

tag: strain

tag: cell type

value: PU.1+ nuclei

tag: genotype

value: WT

tag: chip antibody

value: ActiveMotif #39685


title: 1737S4 - H3K4me1 - CC282

city: Summit

first: Junfei

last: Zhao

state: NJ

address: 556 Morris Ave

institute: Bristol Myers Squibb

description: Library name: 1737S4-CC282_H3K4me1

data_processing:
We used MACS version 3.0.1 to call peaks.
Assembly: GRCh38
Supplementary files format and content: narrowpeak

organism: Homo sapiens

source_name: cell line

extract_protocol:
DNA was extracted and purified using the standard phenol chloroform method, followed by ethanol precipitation.
Library was prepared using an automated system (Apollo 342, Wafergen Biosystems/Takara).

value: cell line

tag: cell line

tag: treatment


title: Extended Data Fig. 6I,fifth-dose,Myeloid cells,SY9031-USR-17565-057,rep3

city: shanghai

first: xu

middle: sai

last: juan

address: DongchuanRoad

country: China

institute: East china normal university

description: Library name: SY9031-USR-17565-057

data_processing:
Next-generation sequencing (NGS) data were initially processed by demultiplexing and filtering raw reads to remove background noise and low-quality sequences. Cleaned reads were then aligned to the reference sequence using alignment software. CRISPR editing efficiency was analyzed with CRISPResso2, specifying the sgRNA sequence and PCR amplicon region as input. The analysis focused on the defined editing window surrounding the target site. A-to-G conversion rates were quantified to assess the efficiency of base editing at the intended locus.
Assembly: NCBI
Supplementary files format and content: Format: TSV, Content: Editing Efficiency

source_name: BM

extract_protocol:
Genomic DNA was extracted from edited or unedited HSPCs of patient or healthy donors.
Specifically, target loci were amplified with corresponding primers first. After another round of PCR with primers containing adapter, amplicons were sequenced for 2x247 paired-end reads with the Illumina Sequencing System.

value: BM

tag: batch


title: H3K27ac_mg_WT_8mo_rep1

description: ChIP-seq


title: T47D_E2_rep1

city: Basel

first: Fabian

last: Wu

department: Biomedical Research

country: Switzerland

institute: Novartis Pharma

description:
Library name: T47D_E2_rep1
T47D_E2_overlap.optimal_peak.narrowPeak.gz
T47D_E2_idr.optimal_peak.narrowPeak.gz

data_processing:
Raw paired-end reads were processed using the ENCODE ATAC-seq pipeline (v2.0.3).
Reads were trimmed and aligned to the human reference genome (hg38) using Bowtie2.
Aligned reads were filtered to remove duplicates, mitochondrial reads, and low-quality mappings (MAPQ ≥ 30).
Accessible chromatin regions were identified using MACS2, and overlap peak sets across replicates were generated.
Reproducible peaks were further defined using IDR analysis (threshold ≤ 0.05).
Assembly: hg38
Supplementary files format and content: narrowPeak files (overlap optimal set): BED6+4 format containing genomic coordinates of peaks identified by MACS2 and reproducibly observed across replicates.
Supplementary files format and content: narrowPeak files (IDR optimal set): BED6+4 format containing high-confidence peaks passing IDR filtering (threshold ≤ 0.05) across biological replicates.
Supplementary files format and content: bigWig files (per replicate): genome-wide signal tracks representing normalized fold-enrichment over background calculated by MACS2.

growth_protocol: T47D cells were cultured in phenol-red-free RPMI medium supplemented with 10% charcoal-stripped fetal bovine serum under standard conditions.

extract_protocol:
Cells were harvested and nuclei were isolated for transposition-based chromatin accessibility profiling using the ATAC-seq workflow.
ATAC-seq libraries were generated by Tn5 transposase-mediated tagmentation of accessible chromatin, followed by PCR amplification and sequencing library preparation according to standard protocols.

treatment_protocol: Cells were seeded 24 h prior to treatment and then treated with either 1 nM E2 or 1.56 μM CS-1-103 for 24 h.

value: breast cancer cell line


title: Extended Data Fig. 6I,fifth-dose,Myeloid cells,SY9031-USR-17565-055,rep3

description: Library name: SY9031-USR-17565-055


title: 1736S4 - H3K4me1 - BMS158

description: Library name: 1736S4-BMS158_H3K4me1


title: H3K27ac_mg_WT_4mo_rep2

description: ChIP-seq


title: THP-1 cells, deltalpg1666::p4HA Legionella  infection, 6 h post-infection, biol rep 3

city: Clayton

first: Kathleen

last: McCaffrey

state: VIC

address: 25-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Research

description:
Library name: Sample 6
P2 100cycle kit
PureCLIP_HA-Lpg1666minusHA_RBS.bed
PureCLIP_HA-Lpg1666minusHA_crosslink sites.bed

library_source: transcriptomic

data_processing:
On-board Denaturing and clustering using 700pM of library pool with 10% PhiX. Illumina Protocol 1000000109376 v3 Nov2020.
Trimmed reads were mapped to the human genome (hg38) using RNA STAR
Deduplicated reads for replicates were merged prior to PureCLIP analysis.
Assembly: Homo sapiens genome (hg38)
Supplementary files format and content: BAM files including deduplicated mapped reads for each sample
Supplementary files format and content: BED files with cross-linking sites or RNA-binding sites identified using PureCLIP

molecule: total RNA

source_name: Blood

growth_protocol: THP-1 monocytes [Homo sapiens, male] (ATCC Cat#TIB-202) were cultured in RPMI 1640 supplemented with Glutamax (Gibco Cat#61870036) and 10 % foetal bovine serum (FBS) (Bovagen Cat#SFBS-AU) at 37C and 5 % CO2. THP-1 monocytes were seeded at 2.5x105 cells/cm2 in tissue-culture dishes and differentiated for 48 h prior to infection using 50 ng/mL phorbol 12-myristate 13-acetate (PMA) (Sigma Aldrich Cat#P8139).

extract_protocol:
At 6 h post-infection, cell monolayers were irradiated with at UV 254 nm prior to harvesting, cell lysis and immunoprecipitation of Lpg1666 with anti-HA (5D8) magnetic beads. Bound RNA was isolated according to the iCLIP2 protocol.
iCLIP2 library preparation protocol.

treatment_protocol: THP-1 cell monolayers were infected with either L. pneumophila delta1666::p4HA-Lpg1666 or delta1666::p4HA-control at a MOI of 10. At 2 h post-infection, cell monolayers were incubated with gentamicin at 100 g/mL (Gibco Cat#15750060) for 1 h to kill any remaining extracellular bacteria followed by washing and the addition of fresh media. Cross linking was performed using UV 254 nm prior to cell harvesting and lysis. Immunoprecipitation using anti-HA (5D8) magentic beads were used to isolate Lpg1666 and bound RNA. RNA was extracted according to the iCLIP2 protocol for downstream sequencing.

value: Blood

value: Monocyte

value: PMA differentiated, 48 h


title: Extended Data Fig. 6I,fifth-dose,Myeloid cells,SY9031-USR-17565-017,rep3

description: Library name: SY9031-USR-17565-017


title: 1735S4 - H3K4me1 - DMSO

description: Library name: 1735S4-DMSO_H3K4me1

value: DMSO


title: Extended Data Fig. 6I,fifth-dose,Erythroid cells,SY9031-USR-17565-061,rep3

description: Library name: SY9031-USR-17565-061


title: THP-1 cells, deltalpg1666::p4HA Legionella  infection, 6 h post-infection, biol rep 2

description:
Library name: Sample 5
P2 100cycle kit
PureCLIP_HA-Lpg1666minusHA_RBS.bed
PureCLIP_HA-Lpg1666minusHA_crosslink sites.bed


title: ATAC_olig2_SgshKO_4mo_rep2

description: ATAC-seq

data_processing:
ATAC-seq files were trimmed to 30 bp and then mapped to the mouse mm10 genome using Bowtie2 with default parameters (Langmead and Salzberg, 2012). After mapping, tag directories were created using the HOMER command makeTagDirectory (Heinz et la., 2010). For IDR analysis (Brown et al., 2011) to test for reproducibility between replicates, peaks were called with HOMER for each tag directory with relaxed peak finding parameters “-L 0 -C 0 -fdr 0.9 -minDist 200 -size 200”. Only peaks with an IDR<0.05 were used for downstream analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated text files that contain the merged IDR ATAC peaks from WT and SgshKO samples annotated with normalized tag counts.

extract_protocol:
Mouse forebrains were homogenized as previously described by gentle mechanical dissociation (Gosselin et al, 2014) and stained with anti-mouse anti-CD11b-APC (BioLegend 101212), anti-CD45-Alexa488 (BioLegend 103122), and anti-CX3CR1-PE (BioLegend 149006). Microglia were sorted as DAPI negative, singlets, and CD11b+/CD45low/CX3CR1+. For neurons and oligodendrocytes, ~200K nuclei were isolated as previously described (Nott et al, 2019,2021), with initial homogenization performed with 0.1% formaldehyde in PBS for 10 minutes (light fixation). Nuclei were stained with PU.1-PE (Cell Signaling 81886S), OLIG2-AF488 (Abcam 225099) or NEUN-AF488 (Millipore MAB 377X), and DAPI (BioLegend 422801) and sorted with a Beckman Coulter MoFlo Astrios EQ or BD Influx Cell Sorter. Neurons and oligodendrocytes were sorted as DAPI positive, singlets, and PU.1-/OLIG2-/NEUN+ or PU.1-/OLIG2+/NEUN-, respectively.
Pelleted nuclei were resuspended in 50 uL transposase reaction mix (1x Tagment DNA Buffer (Illumina 15027866), 2.5 uL DNA enzyme I (Illumina 15027865), and incubated at 37°C for 30 minutes. DNA was purified with Zymo ChIP DNA concentrator columns (Zymo Research D5205), eluted with 11 uL of elution buffer, and amplified using NebNext High-fidelity 2x PCR MasterMix (New England BioLabs M0541) with the Nextera primer Ad1 (1.25 uM) and a unique Ad2.n barcoding primer (1.25 uM) for 8-12 cycles Resulting libraries were size selected by gel excision to 155-250 bp, purified, and single end sequenced using a HiSeq 4000 or NovaSeq 6000 (Illumina) according to the manufacturer’s instructions.

value: Olig2+ nuclei

value: SgshKO


title: 1742W2 - H3K27Ac - Combo

description: Library name: 1742W2-Combo_H3K27Ac

value: Combo


title: H3K27ac_mg_WT_4mo_rep1

description: ChIP-seq


title: THP-1 cells, deltalpg1666::p4HA Legionella  infection, 6 h post-infection, biol rep 1

description:
Library name: Sample 4
P2 100cycle kit
PureCLIP_HA-Lpg1666minusHA_RBS.bed
PureCLIP_HA-Lpg1666minusHA_crosslink sites.bed


title: 1741W2 - H3K27Ac - CC282

description: Library name: 1741W2-CC282_H3K27Ac


title: Extended Data Fig. 6I,fifth-dose,Erythroid cells,SY9031-USR-17565-058,rep3

description: Library name: SY9031-USR-17565-058


title: ATAC_olig2_SgshKO_4mo_rep1

description: ATAC-seq


title: Extended Data Fig. 6I,fifth-dose,Erythroid cells,SY9031-USR-17565-043,rep3

description: Library name: SY9031-USR-17565-043


title: THP-1 cells, deltalpg1666::p4HA-Lpg1666 Legionella  infection, 6 h post-infection, biol rep 3

description:
Library name: Sample 3
P2 100cycle kit
PureCLIP_HA-Lpg1666minusHA_RBS.bed
PureCLIP_HA-Lpg1666minusHA_crosslink sites.bed


title: 1740W2 - H3K27Ac - BMS158

description: Library name: 1740W2-BMS158_H3K27Ac


title: ATAC_olig2_WT_4mo_rep2

description: ATAC-seq


title: Extended Data Fig. 6I,fifth-dose,Erythroid cells,SY9031-USR-17565-035,rep3

description: Library name: SY9031-USR-17565-035


title: THP-1 cells, deltalpg1666::p4HA-Lpg1666 Legionella  infection, 6 h post-infection, biol rep 2

description:
Library name: Sample 2
P2 100cycle kit
PureCLIP_HA-Lpg1666minusHA_RBS.bed
PureCLIP_HA-Lpg1666minusHA_crosslink sites.bed


title: 1739W2 - H3K27Ac - DMSO

description: Library name: 1739W2-DMSO_H3K27Ac


title: ATAC_olig2_WT_4mo_rep1

description: ATAC-seq


title: THP-1 cells, deltalpg1666::p4HA-Lpg1666 Legionella  infection, 6 h post-infection, biol rep 1

description:
Library name: Sample 1
P2 100cycle kit
PureCLIP_HA-Lpg1666minusHA_RBS.bed
PureCLIP_HA-Lpg1666minusHA_crosslink sites.bed


title: Extended Data Fig. 6I,fifth-dose,CD34 cells,SY9031-USR-17565-059,rep3

description: Library name: SY9031-USR-17565-059


title: ATAC_neun_SgshKO_4mo_rep2

description: ATAC-seq

value: NeuN+ nuclei


title: Extended Data Fig. 6I,second-dose,CD34 cells,SY9031-USR-17565-089,rep3

description: Library name: SY9031-USR-17565-089


title: Extended Data Fig. 6I,fifth-dose,CD34 cells,SY9031-USR-17565-052,rep3

description: Library name: SY9031-USR-17565-052


title: 1738S4 - H3K27Ac - Combo

description: Library name: 1738S4-Combo_H3K27Ac


title: 1737S4 - H3K27Ac - CC282

description: Library name: 1737S4-CC282_H3K27Ac


title: B Cells Run 2 - AbSeq, Sample Tag

city: Wellington

first: Lisa

last: Connor

address: Kelburn Parade

country: New Zealand

institute: Malaghan Institute of Medical Research

description:
Library name: VON14091
Combined AbSeq, Sample Tag sequencing

library_source: transcriptomic single cell

data_processing:
1) reads were aligned to the mouse Gencode M36 transcriptome using bowtie2 to generate per-gene transcript counts
2) reads were processed with the Velsera / BD Rhapsody Sequence Analysis Pipeline to quantify Sample Tag indices (vaccine group) and AbSeq antibody-derived tag counts (surrogate labelling of B cell polyreactivity tiers)
3) reads were analysed with TRUST4 to reconstruct BCR sequences and assign BCR clonotypes
intermediate datasets (1, 2, 3) were merged using BD cell barcode sequences as a primary key, resulting in a single combined dataset that categorised each cell based on its vaccine type (via AbSeq tags) and associated BCR clonotype
Circos plots were created that linked cells to other cells that shared the same clonotype. We removed genes with < 250 total molecules across the dataset and cells with <250 total molecules, as well as cells with >= 35% mitochondrial or >= 90% immunoglobulin reads
Expression values were normalised and scaled with SCTv2 using Seurat v5.3.0 and cells were clustered at resolution of 0.8. Clusters 5-8 showed undetectable BCR sequences and were excluded from subsequent analysis as likely contaminant cells
Assembly: Gencode Mouse M36
Supplementary files format and content: AA_distances_haplotypes_2025-11-25.csv: assembled haplotype differences from mapped reference haplotypes
Supplementary files format and content: counts_annotated_mBcells1_R2_vs_M36_withIg.csv.gz: Transcript and gene counts per cell barcode
Supplementary files format and content: Haplotype_information_2024-09-03.csv: Haplotype and tag count summaries per cell barcode
Supplementary files format and content: IG_hapSeqs_2000MostExpressed.tsv.gz: Parsed data from TRUST; IG haplotype sequences per cell barcode
Supplementary files format and content: IgxJ_hapSeqs_2000MostExpressed.tsv.gz: Parsed data from TRUST; IgxJ haplotype sequences per cell barcode
Supplementary files format and content: IgxV_hapSeqs_2000MostExpressed.tsv.gz: Parsed data from TRUST; IgxV haplotype sequences per cell barcode
Supplementary files format and content: mBcells1_SCTV2_2025-09-17.rds: Seurat single-cell dataset containing transcript and tag counts
Supplementary files format and content: VON13847_mapCounts_R2_vs_AbSeq.txt.gz: AbSeq mapping counts for library VON13847 per cell barcode
Supplementary files format and content: VON14091_mapCounts_R2_vs_AbSeq.txt.gz: AbSeq mapping counts for library VON14091 per cell barcode

molecule: polyA RNA

source_name: lymph nodes

growth_protocol: Specific pathogen-free C57BL/6J mice were bred and housed at the Malaghan Institute of Medical Research.

extract_protocol:
cDNA Libraries were prepared using the Mouse TCR/BCR Full Length, mRNA Whole Transcriptome Analysis (WTA), BD AbSeq, and Sample Tag Protocol (BD Biosciences, 23-24367(01)), mRNA WTA and Sample Tag Library kits according to the manufacturer’s instructions.
BCR, WTA, AbSeq and Sample Tag libraries were diluted to 2 nM and mixed together at a ratio of 52.2%, 42.0%, 4.2%, and 1.3% respectively. Additional reads were obtained for the AbSeq and Sample Tag library to make up for the imbalance of read depth among Sample Tags and AbSeq antibodies.

treatment_protocol: Mice were anaesthetised by intraperitoneal injection of ketamine/xylazine (ProVet NZ) and immunised intramuscularly in both hind legs (50 µL per leg) with 5 µg mRNA–LNP vaccine diluted in DPBS (Gibco) using 0.5 mL insulin syringes (BD Biosciences). Boosts were given 21 days after the primary dose, and the response was measured one week post-boost.

value: lymph nodes

value: B-cell

tag: age

value: 9-14 weeks old

tag: host strain

value: MIMR C57BL/6J


title: ATAC_neun_SgshKO_4mo_rep1

description: ATAC-seq

value: Brain


title: Extended Data Fig. 6I,fifth-dose,CD34 cells,SY9031-USR-17565-006,rep3

description: Library name: SY9031-USR-17565-006


title: B Cells Run 1 - WTA, AbSeq, Sample Tag, BCR

description:
Library name: VON13847
Combined AbSeq, WTA, Sample Tag, targeted BCR sequencing


title: ATAC_neun_WT_4mo_rep2

description: ATAC-seq

value: WT


title: SW1353, RNA, rep 3

city: Gainesville

first: Darius

last: Ramkhalawan

address: 1200 Newell Drive

institute: University of Florida

description: Library name: SW_RNA_rep3

library_source: other

data_processing:
MPRA barcode association and counting were performed using MPRAflow
Statistical analyses on the MPRA counts were performed using MPRAnalyze
Assembly: hg19
Supplementary files format and content: Files containing "dna_counts" in the name are DNA barcode counts.
Supplementary files format and content: Files containing "rna_counts" in the name are RNA barcode counts.
Supplementary files format and content: Files containing "RefAlt_annot" in the name are annotation files that attribute the columns present in the DNA/RNA count matrix files to their respective allele, barcode number, replicate number, and condition.
SW1353 and TC28a2 in the file names refer to the cell line in which the experiment was carried out.

molecule: other

extract_protocol:
DNA and RNA was simultaneously isolated from cells using the AllPrep DNA/RNA mini kit (Qiagen).
To associate barcodes with CRSs, the CRS-barcode region was amplified by PCR using custom primers appended with Illumina flowcell adapters. To generate the barcode sequencing library, a P5 flowcell sequence and unique sample indexes were added to each DNA/RNA sample from each replicate by 3 cycles of PCR. Then, a second round of PCR was carried out with P5 and P7 primers. The number of PCR cycles for the second round PCR was determined by qPCR; i.e. the cycle where the amplification curve nearly plateaus. The second round PCR product was gel extracted and purified using the NucleoSpin Gel & PCR Clean-up mini kit (Macherey-Nagel, cat no. 740609.50) and quantified using a Qubit 3.0 fluorometer with the high sensitivity dsDNA kit (Life Technologies, cat no. Q33230). Finally, DNA and cDNA libraries were pooled in a 1:3 ratio before sequencing. Sequencing was performed on an Illumina NextSeq (PE75) with custom primers corresponding to the barcode, sample index, and UMI.

treatment_protocol: Cells were infected with the lentiMPRA library of AIS risk variants and incubated for 48 hours.

value: chondrocyte

value: AIS lentiMPRA library


title: 1736S4 - H3K27Ac - BMS158

description: Library name: 1736S4-BMS158_H3K27Ac

value: cell line


title: Extended Data Fig. 6I,fifth-dose,CD34 cells,SY9031-USR-17565-005,rep3

description: Library name: SY9031-USR-17565-005

value: BM


title: SW1353, DNA, rep 3

description: Library name: SW_DNA_rep3


title: 1735S4 - H3K27Ac - DMSO

description: Library name: 1735S4-DMSO_H3K27Ac


title: ATAC_neun_WT_4mo_rep1

description: ATAC-seq


title: Extended Data Fig. 6I,fifth-dose,B cells,SY9031-USR-17565-042,rep3

description: Library name: SY9031-USR-17565-042


title: 1742W2 - BRD4 - Combo

description: Library name: 1742W2-Combo_BRD4


title: SW1353, RNA, rep 2

description: Library name: SW_RNA_rep2


title: PDGFRaGFPpos 316 n=3

city: montpellier

first: Jean-Philippe

last: Hugnot

address: 141 rue de la Cardonille

country: France

institute: Institut de génomique fonctionnelle

description:
GFPpos316n_3
PDGFRaGFPpos316n_3

data_processing:
Image analyses and base calling were performed using the NovaSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing was performed using Illumina's conversion software bcl2fastq (v2.20.0.422, default parameters). The quality of the raw data was assessed using FastQC (v0.11.8) and summarized using MultiQC (v1.9) from the Babraham Institute. Potential contamination was assesed using FastQ Screen (v0.14.0) from the Babraham Institute.
Reads were mapped to the Mus musculus genome using TopHat2 (v2.1.1) with a set of gene model annotations (gff file downloaded from UCSC on February 8, 2021). Alignments were processed using Samtools (v1.9) and gene counts were obtained using featureCounts (v2.0.0, with parameter -s 2).
Assembly: mm39
Supplementary files format and content: Tab-delimited text file includes raw counts for all samples (names in the “Gene” column are formated as “Symbol|NCBI Gene ID”)

source_name: Spinal cord

growth_protocol: Spinal cord neural stem cells were maintained in DMEM-F12 medium supplemented  with N2, L-glutamine, Ciprofloxaine, Gentamycin, B27, Hepraine, Funzine, EGF and FGF2.

extract_protocol:
Cells were collected and lysate according to the RNeasy kit from QIAGEN.
cDNA libraries were prepared from total RNA using the SMART-Seq Stranded Kit from Takara Bio according to the manufacturer’s instructions.

treatment_protocol: Cells were facs sorted to isolate GFP+ and GFP- cells.

value: Spinal cord

tag: strain background

value: Neural stem cells

value: PDGFRaGFP/+


title: 1741W2 - BRD4 - CC282

description: Library name: 1741W2-CC282_BRD4


title: Extended Data Fig. 6I,fifth-dose,B cells,SY9031-USR-17565-040,rep3

description: Library name: SY9031-USR-17565-040


title: PDGFRaGFPpos 315 n=2

description:
GFPpos315n_2
PDGFRaGFPpos315n_2


title: SW1353, DNA, rep 2

description: Library name: SW_DNA_rep2


title: Extended Data Fig. 6I,fifth-dose,B cells,SY9031-USR-17565-036,rep3

description: Library name: SY9031-USR-17565-036


title: 1740W2 - BRD4 - BMS158

description: Library name: 1740W2-BMS158_BRD4


title: PDGFRaGFPpos 314 n=1

description:
GFPpos314n_1
PDGFRaGFPpos314n_1


title: SW1353, RNA, rep 1

description: Library name: SW_RNA_rep1


title: Extended Data Fig. 6I,fifth-dose,B cells,SY9031-USR-17565-009,rep3

description: Library name: SY9031-USR-17565-009


title: 1739W2 - BRD4 - DMSO

description: Library name: 1739W2-DMSO_BRD4

value: DMSO


title: PDGFRaGFPneg 316 n=3

description:
GFPneg316n_3
PDGFRaGFPneg316n_3

value: PDGFRaGFP/-


title: Extended Data Fig. 6,Extended Data Fig. 6D,second-dose,SY6452-USR-12799-049,rep4

description: Library name: SY6452-USR-12799-049


title: SW1353, DNA, rep 1

description: Library name: SW_DNA_rep1


title: 1738S4 - BRD4 - Combo

description: Library name: 1738S4-Combo_BRD4

value: Combo


title: PDGFRaGFPneg 315 n=2

description:
GFPneg315n_2
PDGFRaGFPneg315n_2


title: Extended Data Fig. 6,Extended Data Fig. 6D,second-dose,SY6452-USR-12799-020,rep4

description: Library name: SY6452-USR-12799-020


title: TC28a2, RNA, rep 3

description: Library name: TC_RNA_rep3


title: 1737S4 - BRD4 - CC282

description: Library name: 1737S4-CC282_BRD4


title: TC28a2, DNA, rep 3

description: Library name: TC_DNA_rep3


title: PDGFRaGFPneg 314 n=1

description:
GFPneg314n_1
PDGFRaGFPneg314n_1


title: Extended Data Fig. 6,Extended Data Fig. 6D,second-dose,SY6452-USR-12799-016,rep4

description: Library name: SY6452-USR-12799-016


title: H-Met Replicate 4

type: RNA

city: Harbin

first: Hong

last: Hu

state: 黑龙江

address: youzheng street

institute: Harbin medical university

description: T4: Biological replicate 4 of 4. PMA-differentiated THP-1 macrophage-like cells treated with high-methionine medium.

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human m6A-mRNA & lncRNA Epitranscriptomic microarray(8×60K,Arraystar) at 65℃ for 17 hours in an Aglient Hybridization Oven.

scan_protocol: The arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software. The probe signals passing P or M QC flags in at least 6 samples were retained for futher analysis.  “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities of RNA.

label_protocol: The “IP” and “Sup” RNAs were supplemented with equal amounts of calibration spike-in control RNA, separately amplified into cRNAs, and labeled with Cy5 for “IP” and Cy3 for “Sup” using the Arraystar Super RNA Labeling Kit (Arraystar, AL-SE-005). The synthesized cRNAs were purified using the RNeasy Mini Kit (QIAGEN). The concentration and specific activity (pmol dye/μg cRNA) were measured using NanoDrop ND-1000.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: group

value: High methionine


title: 1736S4 - BRD4 - BMS158

description: Library name: 1736S4-BMS158_BRD4


title: Patient S10 pan-T cells

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description: Library name: S10_Pan

data_processing:
Sequencing data were preprocessed separately using Cell Ranger 2.1.1, which included generating fastq files, aligning reads, and calculating gene-cell expression matrices. TCR reads were aligned to the GRCh38 reference genome, and consensus TCR annotation was performed using the cellranger vdj program. Barcodes with a higher number of Unique Molecular Identifier (UMI) counts than simulated background were identified as cell barcodes. For each barcode, cellranger performed de novo assembly and identified productive contigs along with their corresponding CDR3 regions and V, D, J, C genes. The single-cell gene expression results were processed using Cell Ranger v8 multi and aligned to the GRCh38p.14 reference genome.
Assembly: GRCh38
Supplementary files format and content: Seurat object in RDS format

source_name: PBMCs

extract_protocol:
Freshly thawed PBMCs were washed twice in RPMI with 10% FBS and resuspended in PBS containing 0.04% BSA. Cell suspensions were filtered through a 35-µm strainer to eliminate aggregates, and viability was assessed by Trypan Blue exclusion. Only preparations with at least 85% viability and minimal debris were used for downstream single-cell capture. For neoantigen-specific T cell samples, short-term (3-day) neoAg-stimulated PBMCs were stained with MHC class I dextramers loaded with the five recurrent frameshift-derived neoantigen peptides together with antibodies against CD3 and CD8 and a live–dead discriminator, as described in the flow cytometry section. For pan-T cell samples, PBMCs were stained with CD3 and the same viability dye. Live, single CD3⁺CD8⁺ lymphocytes, dextramer⁺ neoAg-specific T cells, and pan-T cells were isolated by high-speed fluorescence-activated cell sorting under sterile, low-pressure conditions. Sorted cells were collected directly into PBS with 0.04% BSA and maintained on ice. Immediately after sorting, cells were counted using an automated cell counter, viability was re-confirmed, and 30,000 live T cells per sample were used for Chromium processing. Cell suspensions were adjusted to 700–1,200 cells/µL in PBS + 0.04% BSA according to 10x Genomics recommendations. The adjusted live T cell suspensions were loaded onto Chromium Next GEM chips for partitioning and library preparation using the Single Cell Immune Profiling workflow.
Single-cell RNA-seq (scRNA) and single-cell TCR-seq (scTCR) analyses were performed using the 10x Genomics Single Cell Immune Profiling Solution V1.0 according to the manufacturer’s protocols (10x Genomics V(D)J + 5′ Gene Expression).

value: PBMCs

value: T cells


title: Extended Data Fig. 6,Extended Data Fig. 6D,Non-Mobilization,SY6452-USR-12799-014,rep4

description: Library name: SY6452-USR-12799-014


title: H-Met Replicate 3

description: T3: Biological replicate 3 of 4. PMA-differentiated THP-1 macrophage-like cells treated with high-methionine medium.


title: Patient P7 pan-T cells

description: Library name: P7_Pan


title: 1735S4 - BRD4 - DMSO

description: Library name: 1735S4-DMSO_BRD4


title: Extended Data Fig. 6,Extended Data Fig. 6D,Non-Mobilization,SY6452-USR-12799-003,rep4

description: Library name: SY6452-USR-12799-003


title: 1742W2 - Aiolos - Combo

description: Library name: 1742W2-Combo_Aiolos


title: Patient S2 pan-T cells

description: Library name: S2_Pan


title: H-Met Replicate 2

description: T2: Biological replicate 2 of 4. PMA-differentiated THP-1 macrophage-like cells treated with high-methionine medium.


title: Extended Data Fig. 6,Extended Data Fig. 6D,Non-Mobilization,SY6452-USR-12799-001,rep4

description: Library name: SY6452-USR-12799-001


title: 1741W2 - Aiolos - CC282

description: Library name: 1741W2-CC282_Aiolos


title: Patient P5 pan-T cells

description: Library name: P5_Pan


title: Extended Data Fig. 6,Extended Data Fig. 6D,Mobilization,SY6452-USR-12799-045,rep4

description: Library name: SY6452-USR-12799-045


title: 1740W2 - Aiolos - BMS158

description: Library name: 1740W2-BMS158_Aiolos


title: NC Replicate 4

description: N4: Biological replicate 4 of 4. PMA-differentiated THP-1 macrophage-like cells cultured under normal methionine conditions.

value: Normal methionine


title: H-Met Replicate 1

description: T1: Biological replicate 1 of 4. PMA-differentiated THP-1 macrophage-like cells treated with high-methionine medium.


title: Patient P1 pan-T cells

description: Library name: P1_Pan


title: 1739W2 - Aiolos - DMSO

description: Library name: 1739W2-DMSO_Aiolos


title: Extended Data Fig. 6,Extended Data Fig. 6D,Mobilization,SY6452-USR-12799-031,rep4

description: Library name: SY6452-USR-12799-031


title: NC Replicate 3

description: N3: Biological replicate 3 of 4. PMA-differentiated THP-1 macrophage-like cells cultured under normal methionine conditions.


title: Patient S8 pan-T cells

description: Library name: S8_Pan


title: Extended Data Fig. 6,Extended Data Fig. 6D,Mobilization,SY6452-USR-12799-002,rep4

description: Library name: SY6452-USR-12799-002


title: NC Replicate 2

description: N2: Biological replicate 2 of 4. PMA-differentiated THP-1 macrophage-like cells cultured under normal methionine conditions.


title: 1738S4 - Aiolos - Combo

description: Library name: 1738S4-Combo_Aiolos


title: Patient S10 TGFBR2 antigen-specific T cells

description: Library name: S10-TGFBR2


title: 1737S4 - Aiolos - CC282

description: Library name: 1737S4-CC282_Aiolos


title: 1736S4 - Aiolos - BMS158

description: Library name: 1736S4-BMS158_Aiolos


title: NC Replicate 1

description: N1: Biological replicate 1 of 4. PMA-differentiated THP-1 macrophage-like cells cultured under normal methionine conditions.


title: Patient S10 RNF43_2 antigen-specific T cells

description: Library name: S10-RNF43_2


title: Extended Data Fig. 6,Extended Data Fig. 6D,fifth-dose,SY6452-USR-12799-011,rep4

description: Library name: SY6452-USR-12799-011


title: Patient P7 BMPR2 antigen-specific T cells

description: Library name: P7_BMPR2


title: Extended Data Fig. 6,Extended Data Fig. 6D,fifth-dose,SY6452-USR-12799-012,rep4

description: Library name: SY6452-USR-12799-012


title: Female Sprague‑Dawley rat, SUI modeling followed by transvaginal PFES treatment rep3

city: Beijing

first: Chen

last: Li

state: Beijing

address: No. 10 North Jiaomen Road

department: School of Rehabilitation

institute: Capital Medical University

description: Library name: stimll3

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: mRatBN7.2 (GCA_015227675.2)
Supplementary files format and content: Tab‑delimited text files include gene‑count and FPKM values for each sample.

organism: Rattus norvegicus

source_name: Pubococcygeus muscle

extract_protocol:
1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into a tissue grinding tube (tissue ≤ 30 mg, cells ≤ 1×10⁷). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the sample using a rotor–stator homogenizer, and incubate the lysate at room temperature for 5 min. 1.1.3 Centrifuge at 12,000× g for 3 min at room temperature, then transfer the supernatant onto the AllPrep DNA spin column. 1.1.4 Centrifuge at 12,000× g for 30 s at room temperature. Retain the flow-through in the collection tube for subsequent RNA purification. 1.1.5 Transfer the AllPrep DNA spin column into a new collection tube for DNA purification.  1.2 DNA Purification 1.2.1 Add 500 μL Buffer AW1 to the AllPrep DNA spin column, centrifuge at 10,000× g for 30 s, and discard the flow-through. 1.2.2 Add 500 μL Buffer AW2 to the AllPrep DNA spin column, centrifuge at 10,000× g for 30 s, and discard the flow-through. 1.2.3 Perform a dry spin at 16,000× g for 2 min. Transfer the AllPrep DNA spin column into a 1.5 mL microcentrifuge tube. 1.2.4 Add 50 μL Buffer EB onto the column membrane, and incubate at room temperature for 1 min. 1.2.5 Centrifuge at 16,000× g for 2 min to elute DNA.  1.3 RNA Purification 1.3.1 Add an equal volume of 70% ethanol to the flow-through collected in step 1.1.4 and mix thoroughly by pipetting. 1.3.2 Transfer up to 700 μL of the mixture onto an RNeasy spin column placed in a 2 mL collection tube. 1.3.3 Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.4 Add 700 μL Buffer RW1 to the RNeasy spin column. Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.5 Add 500 μL Buffer RPE to the RNeasy spin column. Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.6 Add another 500 μL Buffer RPE to the RNeasy spin column. Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.7 Centrifuge at 16,000× g for 2 min to dry the column membrane, then transfer the RNeasy spin column into a 1.5 mL microcentrifuge tube. 1.3.8 Add 35 μL RNase-free water onto the column membrane and incubate at room temperature for 1 min. 1.3.9 Centrifuge at 16,000× g for 2 min at room temperature to elute purified RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Pubococcygeus muscle


title: Extended Data Fig. 6,Extended Data Fig. 6D,fifth-dose,SY6452-USR-12799-010,rep4

description: Library name: SY6452-USR-12799-010


title: Patient S2 RNF43_3 antigen-specific T cells

description: Library name: S2_RNF43_3


title: 1735S4 - Aiolos - DMSO

description: Library name: 1735S4-DMSO_Aiolos


title: Female Sprague‑Dawley rat, SUI modeling followed by transvaginal PFES treatment rep2

description: Library name: stimll2


title: INPUT.

description: Library name: Pooled_Input


title: Extended Data Fig. 10b,Mock,On-target,SY9031-USR-17565-073,rep3

description: Library name: SY9031-USR-17565-073

value: Extended Data Fig. 10b,Mock,On-target


title: Patient P5 MSH3 antigen-specific T cells

description: Library name: P5_MSH3


title: Extended Data Fig. 10b,Mock,On-target,SY9031-USR-17565-072,rep3

description: Library name: SY9031-USR-17565-072


title: Female Sprague‑Dawley rat, SUI modeling followed by transvaginal PFES treatment rep1

description: Library name: stimll1


title: Patient P5 RNF43_3 antigen-specific T cells

description: Library name: P5_RNF43_3


title: WSUDLCL2 - BMS158_2.5_CC282_5 - D3 - rep3

description: Library name: 7357-CH-0307

data_processing:
We used featureCounts 2.0.6 to count the number of reads on gene level.
Assembly: GRCh38
Supplementary files format and content: readcount on gene level

extract_protocol:
Cells for RNAseq were prepared according to instructions from Discovery Life Sciences.
Five million cells per sample were collected, washed, fixed, and stored at -80 C prior to shipping to Discovery Life Sciences where downstream RNAseq was carried out.


title: Female Sprague‑Dawley rat, SUI modeling (bilateral ovariectomy + vaginal distension), no additional treatment rep3

description: Library name: sham3


title: Extended Data Fig. 10b,Mock,On-target,SY9031-USR-17565-071,rep3

description: Library name: SY9031-USR-17565-071


title: WSUDLCL2 - BMS158_2.5_CC282_5 - D3 - rep2

description: Library name: 7357-CH-0306


title: Patient P1 BMPR2 antigen-specific T cells

description: Library name: P1_BMPR2


title: Extended Data Fig. 10a,On-target,Mock,SY12253-USR-23993-070,rep3

description: Library name: SY12253-USR-23993-070

value: Extended Data Fig. 10a,On-target,Mock


title: Female Sprague‑Dawley rat, SUI modeling (bilateral ovariectomy + vaginal distension), no additional treatment rep2

description: Library name: sham2


title: WSUDLCL2 - BMS158_2.5_CC282_5 - D3 - rep1

description: Library name: 7357-CH-0305


title: Female Sprague‑Dawley rat, SUI modeling (bilateral ovariectomy + vaginal distension), no additional treatment rep1

description: Library name: sham1


title: WSUDLCL2 - BMS158_2.5 - D3 - rep3

description: Library name: 7357-CH-0304


title: Patient S8 RNF43_3 antigen-specific T cells

description: Library name: S8_RNF43_3


title: Extended Data Fig. 10a,On-target,Mock,SY12253-USR-23993-066,rep3

description: Library name: SY12253-USR-23993-066


title: WSUDLCL2 - BMS158_2.5 - D3 - rep2

description: Library name: 7357-CH-0303


title: scTCR_Patient S10 pan-T cells

description: Library name: S10_Pan

data_processing:
Sequencing data were preprocessed separately using Cell Ranger 2.1.1, which included generating fastq files, aligning reads, and calculating gene-cell expression matrices. TCR reads were aligned to the GRCh38 reference genome, and consensus TCR annotation was performed using the cellranger vdj program. Barcodes with a higher number of Unique Molecular Identifier (UMI) counts than simulated background were identified as cell barcodes. For each barcode, cellranger performed de novo assembly and identified productive contigs along with their corresponding CDR3 regions and V, D, J, C genes. The single-cell gene expression results were processed using Cell Ranger v8 multi and aligned to the GRCh38p.14 reference genome.
Assembly: GRCh38
Supplementary files format and content: xxx_filtered_contig_annotations.csv is the cell-level (or contig-level) detailed file. It contains information for every high-confidence V(D)J transcript (contig) assembled in each cell.
Supplementary files format and content: xxx_clonotypes.csv is the clonotype-level summary file.


title: Female Sprague‑Dawley rat, no surgical intervention or treatment rep3

description: Library name: Blank3


title: Extended Data Fig. 10a,On-target,Mock,SY12253-USR-23993-062,rep3

description: Library name: SY12253-USR-23993-062


title: scTCR_Patient P7 pan-T cells

description: Library name: P7_Pan


title: Female Sprague‑Dawley rat, no surgical intervention or treatment rep2

description: Library name: Blank2


title: Extended Data Fig. 10,Extended Data Fig. 10a,On-target,SY3893-USR-7940-036,rep3

description: Library name: SY3893-USR-7940-036


title: scTCR_Patient S2 pan-T cells

description: Library name: S2_Pan


title: WSUDLCL2 - BMS158_1.25_CC282_5 - D3 - rep3

description: Library name: 7357-CH-0301


title: Extended Data Fig. 10,Extended Data Fig. 10a,On-target,SY3893-USR-7940-034,rep3

description: Library name: SY3893-USR-7940-034


title: WSUDLCL2 - BMS158_1.25_CC282_5 - D3 - rep2

description: Library name: 7357-CH-0300


title: WSUDLCL2 - BMS158_2.5 - D3 - rep1

description: Library name: 7357-CH-0302


title: Extended Data Fig. 10,Extended Data Fig. 10a,On-target,SY3893-USR-7940-035,rep3

description: Library name: SY3893-USR-7940-035


title: WSUDLCL2 - BMS158_1.25_CC282_5 - D3 - rep1

description: Library name: 7357-CH-0299


title: scTCR_Patient P5 pan-T cells

description: Library name: P5_Pan


title: Female Sprague‑Dawley rat, no surgical intervention or treatment rep1

description: Library name: Blank1


title: Bulk RNA-seq from cryoinjured zebrafish ventricles - replicate 3

city: Fribourg

first: Anna

last: Jaźwińska

address: Chemin du Musée 10

department: Department of Biology

institute: University of Fribourg

description:
Library name: ZF_7dpci_III
ZF_7dpci_III

data_processing:
The quality of the RNA-seq data was assessed using fastqc and RSeQC (v4.0.0).
The reads were mapped to the reference genome using HiSat2 (v2.2.1)
FeatureCounts (v2.0.1) was used to count the number of reads overlapping with each gene as specified in the genome annotation.
DESeq2 (v1.38.3) was used to test for differential gene expression between the experimental groups.
Gene set enrichment analysis were achieved with ClusterProfiler (v4.7.1) using genesets from KEGG and MSigDb
Assembly: Danio_rerio.GRCz11.94 Xiphophorus_maculatus.X_maculatus-5.0-male.95
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: The CSV file includes the normalised read counts, log₂ fold change (log₂FC) and p-value for each gene, obtained using DESeq2.

organism: Danio rerio

source_name: Heart ventricles

growth_protocol: Adult zebrafish and platyfish were raised in system water at a temperature of ~27°C, a pH of ~7.5 and a conductivity of ~485 µS. They were fed twice daily from Monday to Friday (dry food at 9 am and Artemia at 4 pm) and once at the weekend.

extract_protocol:
RNA were extracted using usual Trizol procedure, followed by DNAse treatment.
TruSeq Stranded mRNA library preparation kit (Illumina) was used following the manufacturer's protocol.

treatment_protocol: Twenty-four zebrafish and twenty-four platyfish underwent a ventricular cryoinjury procedure on day 0. On day 7, their hearts were collected and their ventricles were separated from the bulbus arteriosus and atrium. These were then pooled in three tubes, with eight ventricles in each tube. For the control group, the same number of uninjured ventricles from zebrafish and platyfish that had not been manipulated in any way were distributed in three tubes for each species, with eight ventricles per tube.

value: Heart ventricles

value: Mixed

value: WT

value: Cryoinjured zebrafish ventricles

value: replicate 3


title: hTERT-RPE1, PKIA, biological replicate 3

city: Cambridge

first: Yi

middle: Hua

last: Chen-Neumann

state: MA

address: Whitehead Institute 455 Main St, Rm 639 Weissman Lab

institute: Whitehead Institute

description:
Library name: RPE1_PKIA_rep3
Counts for this sample are in column 'RPE1_PKIA_rep3' of raw_counts_matrix.txt.

data_processing:
Data were processed by Plasmidsaurus using their standard RNA-seq pipeline (https://plasmidsaurus.com/technical-documentation/rna).
FASTQ generation and demultiplexing with BCL Convert v4.3.6 and fqtk v0.3.1.
Read filtering with fastp v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, minimum Phred quality score 15, minimum length 50 bp.
Alignment to GRCh38 with STAR v2.7.x, with non-canonical splice junction removal and output of unmapped reads.
Coordinate sorting of BAM files with samtools v1.21.
UMI-based removal of PCR and optical duplicates with UMICollapse v1.1.0.
Mapping QC with RustQC v0.2.1 and summary reporting with MultiQC v1.33.
Gene-level quantification with featureCounts (subread package v2.1.1) using strand-specific counting, fractional assignment of multi-mapping reads, exon and three prime UTR features, grouped by gene_id.
Per-sample gene counts were assembled into a single matrix, raw_counts_matrix.txt.
Assembly: GRCh38
Supplementary files format and content: raw_counts_matrix.txt: tab-delimited text file of gene-level raw (UMI-deduplicated) read counts. Rows are 35,748 genes identified by Ensembl gene ID in the first column ('gene_id'); the remaining 16 columns are the samples, with headers matching the library names in the SAMPLES section.

growth_protocol: hTERT-RPE1 cells were maintained at 37 C and 5% CO2 in DMEM/F-12 supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were preserved in Zymo DNA/RNA Shield and shipped to Plasmidsaurus, where total RNA was extracted using a bead-based method. Post-extraction RNA concentration was measured with a fluorescence-based plate reader assay and normalized across samples prior to library preparation; RNA Integrity Number was not assessed.
3' end counting RNA-seq libraries were prepared by Plasmidsaurus. mRNA was reverse transcribed into cDNA with a poly(dT)VN primer followed by second-strand synthesis, then tagmentation, library indexing and amplification. Libraries are stranded and single-end, sequenced toward the transcript 3' end (read length ~90 bp), with unique molecular identifiers (UMIs) for deduplication and unique dual indices (UDIs) to prevent index hopping.

treatment_protocol: Cells were transduced with lentiviral particles expressing the indicated ORF and selected with 7.5 ug/mL puromycin for at least 5 days to establish stable overexpression prior to harvest.

value: stable overexpression of cAMP-dependent protein kinase inhibitor alpha (PKIA)


title: scTCR_Patient P1 pan-T cells

description: Library name: P1_Pan


title: hTERT-RPE1, PKIA, biological replicate 4

description:
Library name: RPE1_PKIA_rep4
Counts for this sample are in column 'RPE1_PKIA_rep4' of raw_counts_matrix.txt.


title: scTCR_Patient S8 pan-T cells

description: Library name: S8_Pan


title: hTERT-RPE1, PKIA, biological replicate 2

description:
Library name: RPE1_PKIA_rep2
Counts for this sample are in column 'RPE1_PKIA_rep2' of raw_counts_matrix.txt.


title: Bulk RNA-seq from cryoinjured zebrafish ventricles - replicate 2

description:
Library name: ZF_7dpci_II
ZF_7dpci_II

value: replicate 2


title: WSUDLCL2 - CC282_5 - D3 - rep3

description: Library name: 7357-CH-0298

value: cell line


title: Subject ZA0010855, Visit 2

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

description: Library name: ZA0010855.Visit.2

data_processing:
Sequencing data were aligned to a composite reference of GRCh38 with Ensemble annotation version 100 and SARS-CoV-2 reference assembly MN985325.1 using STAR v2.7.3a. Transcript abundance estimates were calculated by using the
STAR “quantMode GeneCounts” option using the algorithm of htseq-count.
Assembly: GRCh38-100, MN985325.1
Supplementary files format and content: Tab delimited text with counts for each sample in columns and transcript in rows.

source_name: Whole blood

growth_protocol: Whole blood collected in Paxgene tubes. No growth

extract_protocol:
Blood was collected into PAXgene Blood RNA tubes (BD Biosciences) and the RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes (ThermoFisher Scientific). RNA quality was assessed using a TapeStation 4200 and one microgram of total RNA was subjected to globin transcript depletion using the human GLOBINclear Kit (ThermoFisher Scientific).
Ten nanograms of the globin-depleted RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent)

treatment_protocol: Whole blood collected 1, 2, 3 or 7 days after primary, secondary or tertiary vaccinations

value: Whole blood

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Primary

tag: infection status

value: Uninfected

tag: infection category

value: Healthy

tag: study

value: NX


title: hTERT-RPE1, PKIA, biological replicate 1

description:
Library name: RPE1_PKIA_rep1
Counts for this sample are in column 'RPE1_PKIA_rep1' of raw_counts_matrix.txt.

tag: genotype


title: scTCR_Patient S10 TGFBR2 antigen-specific T cells

description: Library name: S10-TGFBR2

tag: tissue

value: PBMCs

tag: cell type

value: T cells


title: Bulk RNA-seq from cryoinjured zebrafish ventricles - replicate 1

description:
Library name: ZF_7dpci_I
ZF_7dpci_I

tag: treatment

value: replicate 1


title: WSUDLCL2 - CC282_5 - D3 - rep2

description: Library name: 7357-CH-0297

tag: cell line

tag: batch


title: scTCR_Patient S10 RNF43_2 antigen-specific T cells

description: Library name: S10-RNF43_2


title: hTERT-RPE1, EBV BNLF2b, biological replicate 4

description:
Library name: RPE1_BNLF2b_rep4
Counts for this sample are in column 'RPE1_BNLF2b_rep4' of raw_counts_matrix.txt.

value: stable overexpression of Epstein-Barr virus BNLF2b


title: Bulk RNA-seq from uninjured zebrafish ventricles - replicate 3

description:
Library name: ZF_Uninj_III
ZF_Uninj_III

value: Heart ventricles

value: Uninjured zebrafish ventricles


title: WSUDLCL2 - CC282_5 - D3 - rep1

description: Library name: 7357-CH-0296


title: scTCR_Patient P7 BMPR2 antigen-specific T cells

description: Library name: P7_BMPR2


title: hTERT-RPE1, EBV BNLF2b, biological replicate 3

description:
Library name: RPE1_BNLF2b_rep3
Counts for this sample are in column 'RPE1_BNLF2b_rep3' of raw_counts_matrix.txt.


title: Bulk RNA-seq from uninjured zebrafish ventricles - replicate 2

description:
Library name: ZF_Uninj_II
ZF_Uninj_II

value: Mixed

value: WT


title: WSUDLCL2 - BMS158_1.25 - D3 - rep3

description: Library name: 7357-CH-0295


title: Subject ZA0010998, Visit 1

description: Library name: ZA0010998.Visit.1

value: Tertiary

value: Infected

value: Prior


title: scTCR_Patient S2 RNF43_3 antigen-specific T cells

description: Library name: S2_RNF43_3


title: hTERT-RPE1, EBV BNLF2b, biological replicate 2

description:
Library name: RPE1_BNLF2b_rep2
Counts for this sample are in column 'RPE1_BNLF2b_rep2' of raw_counts_matrix.txt.


title: Bulk RNA-seq from uninjured zebrafish ventricles - replicate 1

description:
Library name: ZF_Uninj_I
ZF_Uninj_I


title: WSUDLCL2 - BMS158_1.25 - D3 - rep2

description: Library name: 7357-CH-0294

value: cell line


title: scTCR_Patient P5 MSH3 antigen-specific T cells

description: Library name: P5_MSH3


title: Subject ZA0010740, Visit 1

description: Library name: ZA0010740.Visit.1

value: Whole blood


title: hTERT-RPE1, EBV BNLF2b, biological replicate 1

description:
Library name: RPE1_BNLF2b_rep1
Counts for this sample are in column 'RPE1_BNLF2b_rep1' of raw_counts_matrix.txt.


title: WSUDLCL2 - BMS158_1.25 - D3 - rep1

description: Library name: 7357-CH-0293


title: scTCR_Patient P5 RNF43_3 antigen-specific T cells

description: Library name: P5_RNF43_3


title: K9_K10

city: Chongqing

first: Zhiwei

last: Chen

address: The Second Affiliated Hospital of Chongqing Medical University, 74  Linjiang Road, Yuzhong District, Chongqing

description:
Library name: K9_K10
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipelineto generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using SpaceRanger's default settings
Gene expression level of Refseg coding genes were quantified using Space Ranger'sdefault settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz:list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene lDs
Supplementary files format and content: matrix.mtx.gz:gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg.gz:image of tissue and spots
Supplementary files format and content: scalefactors json.json.gz:scalefactors in json format
Supplementary files format and content: tissue hires image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue lowres image.png.gz: low-res image of tissue
Supplementary files format and content: spatial_enrichment.csv.gz:list of Gene Expression
Supplementary files format and content: tissue positions list.csv.gz: list of spatial barcodes and the coordinates specifyingspots
Library strategy: Spatial Transcriptomics

organism: Hepatitis B virus

source_name: liver tissue

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics VisiumSpatial Gene Expression Slides & Reagent kit according to manufacturer's construction

tag: host

value: homo sapiens

value: liver tissue


title: hTERT-RPE1, HPV E7, biological replicate 4

description:
Library name: RPE1_E7_rep4
Counts for this sample are in column 'RPE1_E7_rep4' of raw_counts_matrix.txt.

value: stable overexpression of human papillomavirus E7 oncoprotein


title: WSUDLCL2 - DMSO - D3 - rep3

description: Library name: 7357-CH-0292

value: DMSO


title: scTCR_Patient P1 BMPR2 antigen-specific T cells

description: Library name: P1_BMPR2

value: PBMCs


title: hTERT-RPE1, HPV E7, biological replicate 3

description:
Library name: RPE1_E7_rep3
Counts for this sample are in column 'RPE1_E7_rep3' of raw_counts_matrix.txt.


title: K8_K7

institute: The Second Affiliated Hospital of Chongqing Medical University

description:
Library name: K8_K7
Fresh frozen Spatial transcriptome sequencing


title: EI2_EI3

description:
Library name: EI2_EI3
Fresh frozen Spatial transcriptome sequencing


title: WSUDLCL2 - DMSO - D3 - rep2

description: Library name: 7357-CH-0291


title: scTCR_Patient S8 RNF43_3 antigen-specific T cells

description: Library name: S8_RNF43_3

value: T cells


title: hTERT-RPE1, HPV E7, biological replicate 2

description:
Library name: RPE1_E7_rep2
Counts for this sample are in column 'RPE1_E7_rep2' of raw_counts_matrix.txt.


title: EH4_EI1

description:
Library name: EH4_EI1
Fresh frozen Spatial transcriptome sequencing


title: WSUDLCL2 - DMSO - D3 - rep1

description: Library name: 7357-CH-0290


title: KO77054_3

city: Ribeirão Preto

first: Matheus

middle: Mertz

last: Ribeiro

state: São Paulo

address: Av. Prof. Dr. Zeferino Vaz - Vila Monte Alegre, Ribeirão Preto - SP, 14040-900

department: Faculty of Pharmaceutical Sciences of Ribeirão Preto

country: Brazil

institute: University of São Paulo

description:
Library name: KO77054_3
Column name in RNAseq_Macrophage.csv : KO77054

data_processing:
Data processing  Raw sequencing data generated from multiple sequencing lanes were concatenated for each biological sample prior to downstream analyses. Sequence quality was assessed using FastQC, and adapter sequences and low-quality bases were removed using fastp. Filtered paired-end reads were aligned to the appropriate reference genome using HISAT2. Fungal reads were aligned against the Aspergillus nidulans FGSC A4 (ASM1142v1) or Aspergillus fumigatus A1163 reference genomes, while host reads were aligned against the *Mus musculu* reference genome (GRCm39). Alignment files were sorted and indexed using SAMtools. Gene-level read counts were generated using featureCounts based on the corresponding genome annotations (GTF/GFF3). Differential gene expression analyses were performed using the DESeq2 package in R. Raw counts were normalized using the median-of-ratios method, and differential expression was assessed using the Wald test with Benjamini–Hochberg correction for multiple testing. Genes with an adjusted *P* value < 0.05 were considered significantly differentially expressed. Genome build:*Mus musculus GRCm39;Aspergillus nidulans FGSC A4 (ASM1142v1); Aspergillus fumigatus A1163.  Supplementary files format and content: Tab-delimited text files containing raw gene counts.
Assembly: GCA_000002655.1 (A. fumigatus Af293) - GCA_000001635.9 (Mus musculus GRCm39) -  GCA_000011425.1 (A. nidulans A4)
Supplementary files format and content: RNAseq_Macrophage.csv
Supplementary files format and content: RNAseq_fumigatus.csv
Supplementary files format and content: RNAseq_nidulans.csv

source_name: murine macrophages

extract_protocol:
Total RNAs of cultures of early dual biofilm interactions of 24 and 48 h were extracted by the TRIzol method, treated with RQ1 RNase-free DNase I (Promega), and purified using the RNAeasy kit (Qiagen) according to the manufacturer’s instructions. The total RNA was quantified using a NanoDrop, and its integrity was analyzed using an Agilent 2100 Bioanalyzer. All RNA had a minimum RNA integrity number value of 8.0. For RNA sequencing, the cDNA libraries were constructed using the TruSeq Total RNA with Ribo Zero (Illumina, San Diego, CA, USA).
mRNA library  preparation (poly A enrichment)

tag: sample group

value: murine macrophages

value: Macrophage CGD + A. nidulans 77054

value: Coculture

tag: time


title: hTERT-RPE1, HPV E7, biological replicate 1

description:
Library name: RPE1_E7_rep1
Counts for this sample are in column 'RPE1_E7_rep1' of raw_counts_matrix.txt.


title: SUDHL4 - BMS158_2.5_CC282_50 - D3 - rep3

description: Library name: 7357-CH-0289


title: KO65034_3

description:
Library name: KO65034_3
Column name in RNAseq_Macrophage.csv : KO65034

value: Macrophage CGD + A. nidulans 65034


title: EH3_EI4

description:
Library name: EH3_EI4
Fresh frozen Spatial transcriptome sequencing


title: Subject ZA0010763, Visit 1

description: Library name: ZA0010763.Visit.1

tag: subject

value: Uninfected

value: Healthy

value: NX


title: hTERT-RPE1, GFP11 control, biological replicate 4

description:
Library name: RPE1_GFP11_rep4
Counts for this sample are in column 'RPE1_GFP11_rep4' of raw_counts_matrix.txt.

value: stable overexpression of GFP11 (split-GFP fragment; negative control)


title: EH1_EH2

description:
Library name: EH1_EH2
Fresh frozen Spatial transcriptome sequencing


title: SUDHL4 - BMS158_2.5_CC282_50 - D3 - rep2

description: Library name: 7357-CH-0288


title: hTERT-RPE1, GFP11 control, biological replicate 3

description:
Library name: RPE1_GFP11_rep3
Counts for this sample are in column 'RPE1_GFP11_rep3' of raw_counts_matrix.txt.


title: KO8425_3

description:
Library name: KO8425_3
Column name in RNAseq_Macrophage.csv : KO8425

value: Macrophage CGD + A. nidulans 8425


title: CRS-barcode association

description: Library name: Association

source_name: synthesized oligonucleotides

value: synthesized oligonucleotides


title: SUDHL4 - BMS158_2.5_CC282_50 - D3 - rep1

description: Library name: 7357-CH-0287

value: cell line


title: KOAFU_3

description:
Library name: KOAFU_3
Column name in RNAseq_Macrophage.csv : KOAFU

value: KOAFU

value: Macrophage CGD + A. fumigatus A1160


title: hTERT-RPE1, GFP11 control, biological replicate 2

description:
Library name: RPE1_GFP11_rep2
Counts for this sample are in column 'RPE1_GFP11_rep2' of raw_counts_matrix.txt.


title: 293T 0h I 3

city: Saarbrücken

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

data_processing:
Sample primary processing was performed with miRMaster (Fehlmann et al., Nucleic Acids Res, 2021) using standard parameters. Mapping to the genome was performed allowing up to 5 mulit-mapping hits with Bowtie. One mismatch was allowed for the quantification of isomiRs.  As output, miRMaster generated a list with the expression of 80,668 RNAs from 10 RNA classes. The data were normalized to expression in one million reads and further processed with R (R 4.0.4 GUI 1.74 Catalina build (7936)). To limit the effect of low-abundance miRNAs, we considered miRNA isoforms as expressed if at least five in 10 million mapped miRNA reads were found for at least three independent samples.
Supplementary files format and content: Reads per million mapped miRNA normalzed counts for each sample and human miRNA from miRBase v22.

growth_protocol: The cell lines HEK293T (ACC 635), SH-SY5Y (ACC 209) and HeLa (ACC 57) were purchased from the German collection of microorganisms and cell cultures (DSMZ). The authenticity of the cell lines was confirmed by STR fingerprinting by the supplier. Cell lines were cultivated in DMEM (Life Technologies, Darmstadt, Germany) supplemented with penicillin (100 U/ml), streptomycin (100 µg/ml) and either 10% [v/v] FCS for 293T and HeLa cells or 20% [v/v] FCS for SH-SY5Y cells. Lund human mesencephalic (LUHMES) cells were purchased from the American Type Culture Collection (ATCC; CRL-2927). The cells were cultured as previously described by Scholz et al. We performed one passage for all cell lines after purchasing them and cryo-conserved them. All cell lines are from female. All cell lines were subcultured two times a week for no more than three months after the start of the culture.

extract_protocol:
0, 4, 8, 24, 48 h after transfections for miR-7 and 48 h for miRNAs miR-34a, -129, -133b, 873, cells were lysed by QIAzol Lysis Reagent (Qiagen, Hilden, Germany), and total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Library preparation for small RNA sequencing was performed using the MGIEasy Small RNA Library Prep Kit according to the manufacturer’s recommendations. In detail, after 3’ and 5’ adapter ligation, RNAs were reverse transcribed and PCR amplified (21 cycles). PCR products were purified using 6% TBE gels, excising only the 110 bp band corresponding to the PCR product of miRNAs. Subsequently, twelve samples were pooled equimolar into one library, and the library was further circularized and purified. Circularized libraries were sent to BGI Hong Kong for sequencing using the standard MPS protocol as described previously (Li et al., Nucleic Acids Res, 2021).

treatment_protocol: Sequence inserts representing miRNA precursor sequences with additional nucleotides up- and downstream of the precursor sequence for mir-129 and mir-873 were either synthesized by Eurofins Genomics (Ebersberg, Germany) or PCR amplified using sequence-specific primers with human genomic DNA as a template and subsequently cloned into the expression plasmid pSG5 (Agilent Technologies, Santa Clara, California) using EcoR I and BamH I restriction sites. The expression plasmid pSG5-miR-129 harbors nucleotides 128207756-128208053[+] of human chromosome 7 (GRCh38/hg38) and pSG5-miR-873 nucleotides 28888786-28889058[-] of human chromosome 9 (GRCh38/hg38). Cloned sequences of miRNA expression plasmids were verified by Sanger sequencing. Cloning of the pSG5-miR-133b, pSG5-miR-34a and pSG5-miR-7 expression vectors was described previously (Alles et al., Nucleic Acids Res, 2019; Hart et al., Oncotarget, 2016; Kern et al., Nucleic Acids Res, 2021).  For ectopic expression of the respective miRNAs for NGS of miR-transfected HEK293T and HeLa cells, 4x105 cells were seeded out in 6-well plates. Twenty-four hours later, the cells were transfected with the respective DNA amounts (0.5 µg, 1 µg, 2 µg for miR-7, 2 µg for mir-34a, -129, -133b, 873) using PolyFect transfection reagent (Qiagen, Hilden, Germany). For the transfection of the different amounts of mir-7 (0.5 µg, 1 µg) in HEK293T cells, the pSG5-miR-7 expression plasmids were supplemented with the respective amount of pSG5 empty vector to achieve equal amounts of transfected DNA in all samples. For ectopic expression of the respective miRNAs of miR-transfected SH-SY5Y (4,5x105 cells/well) and 4x105 LUHMES (4x105 cells/well) cells for NGS, cells were seeded out in 6-well plates. Twenty-four hours later, the cells were transfected with 2 µg of the respective expression plasmids for mir-7, mir-34a, mir-129, mir-133b, mir-873 or the pSG5-empty vector using Lipofectamine™ 2000 transfection reagent (Invitrogen, Karlsbad, USA). All experiments were conducted 3 times.

tag: Sex

value: Female

tag: plasmid

value: unt. Con.

tag: concentration

value: 0 hr


title: KOMO_3

description:
Library name: KOMO_3
Column name in RNAseq_Macrophage.csv : KOMO

value: KOMO

value: Macrophage CGD

value: Monoculture


title: SUDHL4 - BMS158_2.5 - D3 - rep3

description: Library name: 7357-CH-0286


title: 293T 0h II 3


title: hTERT-RPE1, GFP11 control, biological replicate 1

description:
Library name: RPE1_GFP11_rep1
Counts for this sample are in column 'RPE1_GFP11_rep1' of raw_counts_matrix.txt.


title: WT77054_3

description:
Library name: WT77054_3
Column name in RNAseq_Macrophage.csv : WT77054

value: murine macrophages

value: Macrophage WT + A. nidulans 77054

value: Coculture


title: NC2 TCR (NC13,NC11,NC14,NC12,NC10)

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description:
Library name: NC2_TCR
10x Genomics Single Cell 5’ V3 + V(D)J sequencing

data_processing:
Raw FASTQ files were processed using 10x Genomics Cell Ranger version 9.0.1. RNA counts were generated by aligning to the GRCh38 (hg38) reference and the Cell Ranger V(D)J reference dataset (v.7.1) using Cell Range multi.
Assembly: GENCODE human reference genome v38
Supplementary files format and content: Gene expression – Raw counts
Library strategy: TCR-seq

source_name: Bone Marrow T Cell

extract_protocol:
Frozen BMMNC fractions were thawed using X-VIVO medium (Lonza, Cat. # 04-380Q) supplemented with 50% FBS and 100 U/mL DNase. The suspension was centrifuged at 1200 rpm for 8 minutes; cells were resuspended in RPMI with 10% FBS. Four to five million MNC cells were resuspended in staining buffer (2% BSA, 0.01% Tween-20 in PBS) in conical bottom polypropylene FACS tubes. Cells were incubated with Human TruStain FcX (BioLegend, Cat. # 422302) at a dilution of 1:10 for 10 minutes on ice. After blocking, 0.1ug (per 1x106 cells) of unique TotalSeq™-C Hashing antibody (Biolegend) was added and incubated for 30 minutes on ice. Cells were washed 5 times with 1 ml Staining buffer, centrifuged at 4˚C for 5 minutes at 350g. After the final wash, cells were resuspended in FACS buffer (2% FBS in PBS) and stained with the following antibodies: CD45-APC (Biolegend) and CD3-PE (Biolegend) for 1 hour at 4°C. DAPI was used for dead cell exclusion. Cells were filtered and sorted on a BD Aria Fusion. T cells from non-CHIP (n=5-6) and CHIP (n=5-6) patients were sorted and pooled at equal ratios for two independent library preparations.
Pooled samples were delivered to the Princess Margaret Genomics Center (PMGC) for 10x single cell library preparation and sequencing using Chromium Single Cell 5' V3 Reagent Kits and Chromium Single Cell V(D)J Enrichment Kit.

value: Bone Marrow T Cell

tag: disease state

value: Non-CHIP

value: Mixed


title: WT65034_3

description:
Library name: WT65034_3
Column name in RNAseq_Macrophage.csv : WT65034

value: Macrophage WT + A. nidulans 65034


title: SUDHL4 - BMS158_1.25_CC282_50 - D3 - rep3

city: Summit

last: Zhao

institute: Bristol Myers Squibb

description: Library name: 7357-CH-0283


title: 293T 0h I 2


title: WT8425_3

description:
Library name: WT8425_3
Column name in RNAseq_Macrophage.csv : WT8425

value: Macrophage WT + A. nidulans 8425


title: SUDHL4 - BMS158_2.5 - D3 - rep1

description: Library name: 7357-CH-0284

value: cell line


title: SUDHL4 - BMS158_2.5 - D3 - rep2

description: Library name: 7357-CH-0285


title: 293T 0h II 2


title: NC1 TCR (NC01,NC02,NC04,NC07,NC08)

description:
Library name: NC1_TCR
10x Genomics Single Cell 5’ V3 + V(D)J sequencing


title: WTAFU_3

description:
Library name: WTAFU_3
Column name in RNAseq_Macrophage.csv : WTAFU

value: WTAFU

value: Macrophage WT + A. fumigatus A1160


title: CH2 TCR (CH10,CH07,CH08,CH12,CH09,CH11)

description:
Library name: CH2_TCR
10x Genomics Single Cell 5’ V3 + V(D)J sequencing

value: CHIP


title: 293T 0h I 1

value: Female

value: unt. Con.


title: 293T 0h II 1

value: 0 hr


title: CH1 TCR (CH02,CH03,NA,CH05,CH06)

description:
Library name: CH1_TCR
10x Genomics Single Cell 5’ V3 + V(D)J sequencing


title: SUDHL4 - BMS158_1.25_CC282_50 - D3 - rep1

description: Library name: 7357-CH-0281


title: SUDHL4 - BMS158_1.25_CC282_50 - D3 - rep2

description: Library name: 7357-CH-0282


title: WTMO_3

description:
Library name: WTMO_3
Column name in RNAseq_Macrophage.csv : WTMO

value: WTMO

value: Macrophage WT


title: NC2 scRNA-seq (NC13,NC11,NC14,NC12,NC10)

description:
Library name: NC2_scRNA-seq
10x Genomics Single Cell 5’ V3 + V(D)J sequencing

data_processing:
Raw FASTQ files were processed using 10x Genomics Cell Ranger version 9.0.1. RNA counts were generated by aligning to the GRCh38 (hg38) reference and the Cell Ranger V(D)J reference dataset (v.7.1) using Cell Range multi.
Assembly: GENCODE human reference genome v38
Supplementary files format and content: Gene expression – Raw counts


title: 293T 4h pSG5-miR-7 3

value: 4 hr


title: SUDHL4 - CC282_50 - D3 - rep3

description: Library name: 7357-CH-0280


title: NC1 scRNA-seq (NC01,NC02,NC04,NC07,NC08)

description:
Library name: NC1_scRNA-seq
10x Genomics Single Cell 5’ V3 + V(D)J sequencing


title: 293T 4h pSG5 3


title: KO65034_2

description:
Library name: KO65034_2
Column name in RNAseq_Macrophage.csv : KO65034

value: murine macrophages

value: Macrophage CGD + A. nidulans 65034


title: KO77054_2

description:
Library name: KO77054_2
Column name in RNAseq_Macrophage.csv : KO77054

value: Macrophage CGD + A. nidulans 77054

value: Coculture


title: SUDHL4 - CC282_50 - D3 - rep2

description: Library name: 7357-CH-0279


title: 293T 4h pSG5-miR-7 2


title: CH2 scRNA-seq (CH10,CH07,CH08,CH12,CH09,CH11)

description:
Library name: CH2_scRNA-seq
10x Genomics Single Cell 5’ V3 + V(D)J sequencing

value: Bone Marrow T Cell

value: Mixed


title: CH1 scRNA-seq (CH02,CH03,NA,CH05,CH06)

description:
Library name: CH1_scRNA-seq
10x Genomics Single Cell 5’ V3 + V(D)J sequencing


title: 293T 4h pSG5 2


title: SUDHL4 - CC282_50 - D3 - rep1

description: Library name: 7357-CH-0278


title: BM Niche, NC06

description:
Library name: HS_17
10x Genomics Single Cell 3’ V4

data_processing:
Raw FASTQ files were processed using CellRanger version 8.0.1 (10X Genomics). RNA counts were generated by aligning to the GRCh38 (hg38) reference using SC3Pv3 or SC3Pv4 for 10Xv3 or 10Xv4 3’ pair end sequencing respectively. HTO counts were generated using the same method, by aligning to their respective barcodes.
Assembly: GENCODE human reference genome v38
Supplementary files format and content: Gene expression – Raw counts

source_name: Bone Marrow

extract_protocol:
Niche fraction - Digested cell suspension were depleted for hematopoietic cells using automated magnetic cell separation system (AUTOMACS). Cells were stained with biotin anti-human CD45 and biotin anti-human glycophorin A (Biolegend).  Depleted fraction was stained for 1 hour at 4 degrees with the following antibodies: CD45-BUV395 (BD), GlyA-FITC (Biolegend), CD38-PECy7 (Biolegend), CD34-APCCy7 (Biolegend), NGFR-AF647 (Biolegend) and CD31-PE (Biolegend) and FVS575V was used for dead cell exclusion. Cells were sorted on a BD Aria Fusion. Two populations were sorted: CD45-GlyA-CD38-  niche fraction and CD45lowCD34+ HSPC fraction. Niche fraction was resuspended in PBS + 0.04% BSA and loaded into the 10x Genomics Chip G or X.  Hematopoietic fraction - Frozen mononuclear cell fractions were thawed using X-VIVO medium (Lonza) supplemented with 50% FBS and 110 mg/mL DNase. The suspension was centrifuged at 1200 rpm for 8 mins, cells were resuspended in RPMI with 10% FBS and counted. 4-5x106 MNC cells were resuspended in staining buffer (2% BSA,0.01% Tween in PBS) in conical bottom polypropylene FACS tubes. Cells were incubated with Fc Blocking reagent at a dilution of 1:10 (FcX, BioLegend) for 10 minutes on ice. After FcX block incubation, 0.1ug (per 1x106 cells) of unique TotalSeq™-B Hashing antibody (Biolegend) was added and incubated for 30 minutes on ice. Cells were washed 5 times with 1 ml Staining buffer (2%BSA/0.01%Tween, PBS), spined at 4˚C for 5 minutes at 350g. After the final wash, cells were resuspended in FACS buffer (PBS 2% FBS) and stained with the following antibodies: Lineage cocktail-FITC, CD45-PECy7, CD34-APCCy7 for 1 hour at 4 degrees. DAPI was used for dead cell exclusion. Cells were filtered and sorted on a BD Aria Fusion. Three hematopoietic populations were sorted: Mature cells (Lineage+), committed progenitors (Lineage-CD45+) and hematopoieitc progenitors (Lineage-CD45lowCD34+).  Samples were pooled evenly for two library preparations: Mature library (Mature cells and committed progenitors) and HSPC library. Pooled samples were delivered to the Princess Margaret Genomics Center (PMGC) for single cell sequencing preparation using the 10X platform.
We used Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 and Chromium GEM-X Single Cell 3', Library & Gel Bead Kit v4 and followed the protocol as provided by 10x Genomics. Sorted HSPC fraction was frozen until further use.

value: Bone Marrow

value: Non-CHIP

value: Male

tag: compartment

value: BM Niche


title: KOAFU_2

description:
Library name: KOAFU_2
Column name in RNAseq_Macrophage.csv : KOAFU

value: KOAFU

value: Macrophage CGD + A. fumigatus A1160


title: KO8425_2

description:
Library name: KO8425_2
Column name in RNAseq_Macrophage.csv : KO8425

value: Macrophage CGD + A. nidulans 8425


title: SUDHL4 - BMS158_1.25 - D3 - rep3

description: Library name: 7357-CH-0277

value: cell line


title: 293T 4h pSG5-miR-7 1

value: Female


title: KOMO_2

description:
Library name: KOMO_2
Column name in RNAseq_Macrophage.csv : KOMO

value: KOMO

value: Macrophage CGD

value: Monoculture


title: SUDHL4 - BMS158_1.25 - D3 - rep2

description: Library name: 7357-CH-0276


title: 293T 4h pSG5 1

value: 4 hr


title: BM Niche, CH04

description:
Library name: HS_15
10x Genomics Single Cell 3’ V4

value: CHIP


title: WT77054_2

description:
Library name: WT77054_2
Column name in RNAseq_Macrophage.csv : WT77054

value: murine macrophages

value: Macrophage WT + A. nidulans 77054

value: Coculture


title: SUDHL4 - BMS158_1.25 - D3 - rep1

description: Library name: 7357-CH-0275


title: 293T 8h pSG5-miR-7 3

value: 8 hr


title: BM Niche, NC09

description:
Library name: HS_14
10x Genomics Single Cell 3’ V4

value: Bone Marrow

value: Non-CHIP


title: WT65034_2

description:
Library name: WT65034_2
Column name in RNAseq_Macrophage.csv : WT65034

value: Macrophage WT + A. nidulans 65034


title: SUDHL4 - DMSO - D3 - rep3

description: Library name: 7357-CH-0274

value: DMSO


title: SUDHL4 - DMSO - D3 - rep2

description: Library name: 7357-CH-0273


title: Mature Immune, (NC09,CH04,NA,NC06)

description:
Library name: HM_5
10x Genomics Single Cell 3’ V4

value: Mixed

value: Mature Immune


title: 293T 8h pSG5 3


title: 293T 8h pSG5-miR-7 2


title: WT8425_2

description:
Library name: WT8425_2
Column name in RNAseq_Macrophage.csv : WT8425

value: Macrophage WT + A. nidulans 8425


title: HSPC, (NC09,CH04,NA,NC06)

description:
Library name: HH_5
10x Genomics Single Cell 3’ V4

value: HSPC


title: SUDHL4 - DMSO - D3 - rep1

description: Library name: 7357-CH-0272

value: cell line


title: WTAFU_2

description:
Library name: WTAFU_2
Column name in RNAseq_Macrophage.csv : WTAFU

value: WTAFU

value: Macrophage WT + A. fumigatus A1160


title: 293T 8h pSG5 2

value: Female


title: Knockdown (siFKBP5) rep3 - primary human pulmonary microvascular endothelial cells

city: jinan

first: yanan

last: li

state: 山东省

address: lixia

department: medicine

institute: Shandong University

description: Library name: C3

data_processing:
1) Raw sequencing data in FASTQ format were generated by CASAVA base calling. Quality scores are encoded in Qphred+33 format (Illumina 1.8+). 2) Quality control was performed using FastQC (v0.11.9) to assess base quality score distribution, GC content, adapter contamination, and duplicate levels. 3) Adapter trimming and low-quality read filtering (Q < 20) were performed using Trimmomatic (v0.39). 4) Clean reads were aligned to the human reference genome GRCh38 (hg38) using HISAT2 (v2.2.1). 5) Gene expression quantification was performed using featureCounts (v2.0.1) to generate raw read counts.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data files are provided as tab-delimited text files. Each file contains gene-level expression counts: first column is gene symbol/Ensembl ID, subsequent columns represent raw read counts per sample.

source_name: lung

growth_protocol: Primary human pulmonary microvascular endothelial cells (HPMVECs) were obtained from iCell Bioscience Inc, Shanghai. Cells were cultured in endothelial cell medium (ECM, Sciencell) supplemented with 5% fetal bovine serum (FBS, Sciencell), 1% penicillin/streptomycin, and 1% endothelial cell growth factor. Cells were maintained at 37°C in a humidified atmosphere with 5% CO₂ and 95% air. Only cells at passages 3 to 5 and at approximately 80% confluence were used for subsequent experiments.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer's protocol. RNA integrity and concentration were assessed using Agilent 2100 Bioanalyzer. Only samples with RNA integrity number (RIN) ≥ 7.0 were used for library construction.
Library construction was performed using total RNA. Polyadenylated mRNA was enriched using Oligo(dT) magnetic beads. The enriched mRNA was then fragmented using divalent cations in Fragmentation Buffer. First-strand cDNA was synthesized using random oligonucleotides as primers and M-MuLV reverse transcriptase. Second-strand cDNA synthesis was performed using RNaseH and DNA polymerase I. The double-stranded cDNA was purified, end-repaired, A-tailed, and ligated with sequencing adapters. AMPure XP beads were used to select cDNA fragments of 370-420 bp. The final library was amplified by PCR and purified again with AMPure XP beads. Library quality was assessed using Qubit 2.0 Fluorometer and Agilent 2100 Bioanalyzer, and library concentration was quantified by qRT-PCR (effective concentration > 1.5 nM).

treatment_protocol: Cells were divided into three groups: (A) Control group (no treatment), (B) Overexpression group (transduced with adenovirus carrying FKBP5 provided by Vigene Biosciences), and (C) Knockdown group (transfected with siFKBP5 targeting FKBP5 provided by Boshang Biotechnology). Transfection/transduction was performed according to the manufacturers' protocols. Cells were harvested 48 hours post-treatment for RNA extraction.

value: lung

value: primary cell

value: FKBP5 knockdown


title: WSUDLCL2 - BMS158_2.5_CC282_5 - D2 - rep3

first: Junfei

address: 556 Morris Ave

description: Library name: 7357-CH-0183


title: WTMO_2

description:
Library name: WTMO_2
Column name in RNAseq_Macrophage.csv : WTMO

value: WTMO

value: murine macrophages

value: Macrophage WT

value: Monoculture


title: WSUDLCL2 - BMS158_2.5_CC282_5 - D2 - rep2

description: Library name: 7357-CH-0182


title: 293T 8h pSG5-miR-7 1

value: 8 hr


title: KO77054_1

description:
Library name: KO77054_1
Column name in RNAseq_Macrophage.csv : KO77054

value: Macrophage CGD + A. nidulans 77054

value: Coculture


title: Knockdown (siFKBP5) rep2 - primary human pulmonary microvascular endothelial cells

description: Library name: C2


title: 293T 8h pSG5 1


title: Knockdown (siFKBP5) rep1 - primary human pulmonary microvascular endothelial cells

description: Library name: C1


title: KO65034_1

description:
Library name: KO65034_1
Column name in RNAseq_Macrophage.csv : KO65034

value: Macrophage CGD + A. nidulans 65034


title: WSUDLCL2 - BMS158_2.5_CC282_5 - D2 - rep1

description: Library name: 7357-CH-0181


title: 293T 24h pSG5-miR-7 3

value: 24 hr


title: KO8425_1

description:
Library name: KO8425_1
Column name in RNAseq_Macrophage.csv : KO8425

value: Macrophage CGD + A. nidulans 8425


title: Overexpression (FKBP5) rep3 - primary human pulmonary microvascular endothelial cells

description: Library name: B3

value: FKBP5 overexpression


title: Overexpression (FKBP5) rep2 - primary human pulmonary microvascular endothelial cells

description: Library name: B2


title: WSUDLCL2 - BMS158_2.5 - D2 - rep3

description: Library name: 7357-CH-0180

value: cell line


title: 293T 24h pSG5 3


title: WSUDLCL2 - BMS158_2.5 - D2 - rep2

description: Library name: 7357-CH-0179


title: KOAFU_1

description:
Library name: KOAFU_1
Column name in RNAseq_Macrophage.csv : KOAFU

value: KOAFU

value: Macrophage CGD + A. fumigatus A1160


title: Overexpression (FKBP5) rep1 - primary human pulmonary microvascular endothelial cells

description: Library name: B1

value: lung


title: 293T 24h pSG5-miR-7 2

value: Female


title: WSUDLCL2 - BMS158_2.5 - D2 - rep1

description: Library name: 7357-CH-0178


title: WSUDLCL2 - BMS158_1.25_CC282_5 - D2 - rep3

description: Library name: 7357-CH-0177


title: KOMO_1

description:
Library name: KOMO_1
Column name in RNAseq_Macrophage.csv : KOMO

value: KOMO

value: Macrophage CGD


title: WT77054_1

description:
Library name: WT77054_1
Column name in RNAseq_Macrophage.csv : WT77054

value: murine macrophages

value: Macrophage WT + A. nidulans 77054


title: 293T 24h pSG5 2


title: WSUDLCL2 - BMS158_1.25_CC282_5 - D2 - rep2

description: Library name: 7357-CH-0176


title: Control rep2 - primary human pulmonary microvascular endothelial cells

description: Library name: A2

value: primary cell

value: control


title: 293T 24h pSG5 1


title: WSUDLCL2 - BMS158_1.25_CC282_5 - D2 - rep1

description: Library name: 7357-CH-0175


title: Control rep3 - primary human pulmonary microvascular endothelial cells

description: Library name: A3


title: Niche, NC07

description:
Library name: HS_12
10x Genomics Single Cell 3’ V4

value: Bone Marrow

value: Non-Carrier

value: BM Niche


title: WSUDLCL2 - CC282_5 - D2 - rep3

description: Library name: 7357-CH-0174


title: WTAFU_1

description:
Library name: WTAFU_1
Column name in RNAseq_Macrophage.csv : WTAFU

value: WTAFU

value: Macrophage WT + A. fumigatus A1160

value: Coculture


title: WSUDLCL2 - CC282_5 - D2 - rep2

description: Library name: 7357-CH-0173

value: cell line


title: 293T 48h pSG5 2µg 3

value: 48 hr


title: Niche, NC02

description:
Library name: HS_10
10x Genomics Single Cell 3’ V4

value: Male


title: 293T 48h pSG5-miR-7 2µg 2


title: WSUDLCL2 - CC282_5 - D2 - rep1

description: Library name: 7357-CH-0172


title: 293T 48h pSG5 2µg 2


title: WSUDLCL2 - BMS158_1.25 - D2 - rep3

description: Library name: 7357-CH-0171


title: c-MAF CUT&RUN in microglia

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

description: Library name: MG_Maf

data_processing:
Adapter trimming was performed using fastp (v0.20.1), reads were aligned to the mm10 reference genome using hisat2 (v2.1.0), and duplicates were removed using “Picard markDuplicates” (v2.18.29) (https://github.com/broadinstitute/picard).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: brain

extract_protocol:
n=16 brains from P0 Bl6 pups were mechanically dissociated and approximately 100,000 CD206+MHCII− BAMs and microglia were sorted separately and resuspended in PBS at 1,000 cells/µl.
Cell were bound to Concanavalin A-coated magnetic beads and permeabilized with Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and one Roche Complete protein inhibitor tablet per 50 mL) containing 0.05% digitonin (Dig Wash). The cells were incubated with anti-cMAF antibody (Abcam, ab77071 at 1:25 dilution) or IgG negative control antibody (Antibodies-online ABIN101961) or H3K27me3 positive control antibody (Cell Signaling 9733S) overnight at 4°C. The slurry was then washed twice with Dig Wash buffer and incubated with Protein A/G-MNase (Epicypher, 15-1016) for 1 hour at 4°C, followed by two additional washes with Dig Wash. Tubes were placed on ice and incubated with Dig Wash containing 2 mM CaCl₂ to initiate MNase digestion of bound fragments. After 30 minutes incubation, 4X STOP buffer (80 mM EGTA, 0.05% Digitonin, 100 μg/mL RNase A) was added to stop the reaction, and fragments were released by incubation for 30 minutes at 37°C. The supernatant containing cleaved DNA fragments was transferred to a new tube and used directly as input for barcoded Illumina libraries, as previously described109. Libraries were pooled and sequenced on an Illumina NovaSeqX Plus targeting 150M reads.

value: brain

value: primary cells

value: microglia

value: wild-type

tag: antibody

value: Maf


title: Niche, CH01

description:
Library name: HS_8
10x Genomics Single Cell 3’ V4

value: CHIP


title: c-MAF CUT&RUN in BAMs

description: Library name: BAM_Maf

value: macrophages


title: WSUDLCL2 - BMS158_1.25 - D2 - rep2

description: Library name: 7357-CH-0170


title: 293T 48h pSG5 2µg 1

first: Fabian

value: Female


title: WSUDLCL2 - BMS158_1.25 - D2 - rep1

description: Library name: 7357-CH-0169


title: Bulk RNA-seq of brain endothelial cells CTRL-3

description:
Library name: CTRL_3
RNA-seq

data_processing:
Adapter trimming was performed using fastp (v0.20.1) and reads were aligned to the GRCm39 reference genome using hisat2 (v2.1.0). To count reads overlapping genes, featureCounts v2.0.6 was used, and the output was loaded into R (v4.2.2) for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: counts table

source_name: Brain

growth_protocol: 6-week-old C57BL/6 mice mice were anesthetized with a ketamine/xylazine injection and perfused with 20ml of ice-cold PBS. Cortices were homogenized with GentleMACS tissue dissociator (Mylteni Biotech) in prewarmed DMEM supplemented with 2% Bovine Calf Serum (BCS, HyClone), 25µg/ml Liberase DL, 100µg/ml Dispase, 0.5mg/ml Papain, 10µg/ml DNase-I (all enzymes from Sigma) for 30 min at 37°C. After homogenization the cell suspension was filtered through a 70 μm strainer and myelin depletion was performed in 30% isotonic percoll (800g for 20 min at 4°C). Brain cell pellets were stained with anti-CD45-AlexaFluor 647 (1:200), anti-CD31-PE (1:100), and anti-Ly6C-APCCy7 (1:200) for 30 minutes on ice (all antibodies from Biolegend). DAPI was used for live/dead cells discrimination. The DAPI−CD45−CD31+Ly6C+ population was sorted on FACS Aria-III (BD Bioscience) using a 100 µm nozzle. Approximately 600,000 brain endothelial cells (BEC) per sample were sorted (two brains were pooled for each sample). BECs were collected into Endothelial Cell Medium (Cell Biologics, M1168), plated onto a Matrigel-coated 24-well plate and expanded for 12 days in Endothelial Cell Medium at 37°C with 5% CO2. Matrigel was removed using Cell Recovery Solution (Corning) prior to RNA extraction.

extract_protocol:
Cells were lysed in 450µl of lysis buffer for RNA extraction. The lysate was mixed by pipetting and briefly shaken for 1 minute at room temperature. Lysates were collected, and RNA was purified using the RNeasy Micro Kit (Qiagen 74004), following the manufacturer’s protocol. Purified RNA was stored at -80°C until analysis.
Library preparation was performed with 5-10ng of total RNA per sample. ds-cDNA was made using the low-input SMARTseq mRNA kit (Takarabio) according to manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Libraries were pooled and sequenced on an Illumina NovaSeqX Plus (2x150 sequencing recipe), targeting 50M reads per sample. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.

treatment_protocol: On the day of the experiment, cells were incubated in serum-free medium for 2 hours prior to stimulation with recombinant mouse GAS6 (250 ng/mL; R&D Systems) and recombinant mouse IGF-I (200 ng/mL; PeproTech), or PBS as a control. After 6 hours stimulation, the medium was removed, and wells were washed with PBS.

value: Brain

value: Endothelial cells

value: Wild-type

value: PBS


title: Niche, CH03

description:
Library name: HS_6
10x Genomics Single Cell 3’ V3

value: Bone Marrow

value: BM Niche