title: 6614 VDJ

city: Gainesville

first: Todd

middle: M

last: Brusko

state: FL

address: 1275 Center Dr BMSB J515

department: Pathology

institute: University of Florida

description:
Library name: 6614 VDJ
T cell receptor (VDJ), read 1 file contains cell barcode and UMI, read 2 file contains T cell receptor sequence information
filtered_contig_annotations_6614.csv
clonotypes_6614.csv

data_processing:
BCL files were processed to fastq files using the cellranger mkfastq pipeline (10X genomics). Fastq files from gene expression, surface protein, and TCR libraries were processed to matrices using the cellranger multi (10X genomics) count pipeline in order to maximize counting of cells with all three modalities.
scRNAseq data were subject to quality control (QC) by removing doublets using the doubletfinder package, and cells were removed based on cutoffs of reads/cell ≤2000 and percent mitochondrial reads ≤10%, then normalized using the DSB package to remove background noise and ambient signal. After this initial filtering, data were log normalized with NormalizeData() and scaled with ScaleData(), then variable features were calculated and dimensionality reduction performed in seurat. For the antibody-derived tag data, variable features were set to all antibodies included, data were scaled, and principal component analysis (PCA) was run using dimensions 1:6 with reduction.name=“apca”. Data were integrated in Seurat using IntegrateLayers() with rpca as the integration method. Integration of TCR with gene expression data was performed using scRepertoire in R.
Assembly: GRCh38
Supplementary files format and content: Paired end fastq files for gene expression, feature barcode and VDJ libraries
Supplementary files format and content: Sample barcode, feature and matrix files generated by cellranger
Supplementary files format and content: filtered contig annotation files and clonotype files with TCR sequence information

source_name: Pancreatic lymph node

extract_protocol:
Cryopreserved pLN single cell suspensions were thawed and stained with a cocktail of 7 oligo-barcoded TotalSeq antibodies (Biolegend, Table S1) to aid in clustering naïve and memory CD8+ and CD4+ T cell phenotypes. Prior to use, Totalseq antibodies were centrifuged at 14000g for 10 minutes at 4C to avoid antibody aggregates, as recommended by the manufacturer. Cell viability was assessed using acridine orange and propidium iodide (AO/PI) staining on a Nexcelom Cellometer or CellDrop. For six samples with viability <70%, the Dead Cell Removal Kit (Stemcell) was used. 1x106 cells per sample (viability >70%) were resuspended in 100uL volume of PBS + 1% BSA and stained with TruStain FcX (5uL/test) to block Fc receptors for 10 minutes at 4oC prior to incubation with the antibody master mix (0.5uL of each antibody/test) for 30 minutes at 4C. Cells were washed four times with 3mL of chilled PBS + 1% BSA, after which live cells were counted using AO/PI on a Nexcelom Cellometer or CellDrop and volumes adjusted to obtain a targeted recovery of 10,000 cells.
Libraries prepared according to the 5’ v1.1, 5’ v2, and 5’ HT v2 kit protocols (10x Genomics). Libraries were sequenced on an Illumina Novaseq instrument with a target of 50,000 paired reads for gene expression, 10,000 paired reads for surface protein, and 5,000 paired reads for TCR libraries.

value: Pancreatic lymph node

tag: library type

value: VDJ

value: lymphocytes

tag: disease state

value: ND


title: 5-day_cultured_EPCR_High_HSC_1

status: Public on Jul 17 2026

type: SRA

city: Kumamoto

first: Terumasa

last: Umemoto

address: 2-2-1, Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description:
Library name: Sample9
Culture_High-1

library_source: transcriptomic

data_processing:
Trimming, alignment (to mouse genome mm10), and Read counts were performed by Trimmomatic, Hisat2, and featureCounts, respectively. The normalization and comparison between groups were performed using DESeq2.
Assembly: mm10
Supplementary files format and content: Comma-separated values (CSV) file containing DESeq2-normalized gene expression values

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Sorted HSCs were cultured for 5 or 30 days.

extract_protocol:
One hundred cells were directly sorted into lysis buffer.
We performed RNA sequence as previously reported (Hayashi et al., 2018) with minor modification. Briefly, using one hundred sorted cells, the first strand of cDNA was synthesized by using PrimeScript RT reagent Kit (TAKARA Bio Inc., Kusatsu, Japan) and not-so random primers. Following the synthesis of the 1st strand, the 2nd strand was synthesized by using Klenow Fragment (3’-5’ exo-) (New England Biolabs Inc., Ipswich, MA) and complement chains of not-so random primers. Using purified double-strand cDNA, the library for RNA-Seq was prepared and amplified using Nextera XT DNA sample Prep Kit (Illumina Inc., San Diego, CA).

treatment_protocol: R162 was added during the culture.

tag: tissue

value: Bone marrow

tag: cell line

value: Primary cells

tag: cell type

value: Hematopoietic stem cells


title: 5-day_cultured_EPCR_High_HSC_2

description:
Library name: Sample10
Culture_High-2


title: C240221002 - Healthy control 1

city: Belval

first: Matthieu

last: Gobin

address: 6, avenue du Swing

country: Luxembourg

institute: LCSB

description: Library name: C240221002

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using CeleScope (Singleron Biotechnologies; www.github.com/singleron-RD/CeleScope). The dataset was processed with CeleScope v1.15.0. Barcode recognition, correction, and chemistry assignment were performed automatically. Reads were aligned using STARsolo (STAR v2.7.11a) against the GRCh38 human reference genome (Ensembl 92) to generate nucleus-by-gene expression matrices. Downstream quality control, normalization, clustering, and cell-type annotation were performed using standard single-nucleus RNA-sequencing workflows.
Assembly: GRCh38 human reference genome (Ensembl 92)
Supplementary files format and content: The processed data are split in 3 files (barcodes.tsv, genes.tsv, matrix.mtx) for each sample.

organism: Homo sapiens

source_name: brain

extract_protocol:
Microtome-cut human midbrain tissue sections mounted on glass slides. All samples were handled on dry ice upon arrival. Nuclei were isolated following the manufacturer’s instructions using the GEXSCOPE® Single Nucleus RNA Library Kit V2 (Singleron Biotechnologies; cat. nos. 1185011/2) and the included Nucleus Separation Solution V2. Briefly, tissue was minced on ice, incubated in Nucleus Separation Mix, mechanically dissociated, and filtered through a 40-µm strainer. The nuclei-containing flow-through was washed in PBS supplemented with EGTA, pelleted at low speed, and gently resuspended. Nuclear integrity and concentration were assessed microscopically using exclusion dyes such as DAPI or Trypan Blue.
Sequencing libraries were generated using the GEXSCOPE® Single Nucleus RNA Library Kit V2 (cat. nos. 1185011/2). For all samples, 50 ng of amplified cDNA was used as input. cDNA was enzymatically fragmented, end-repaired, A-tailed, and ligated to truncated Illumina adapters. Adapter-ligated fragments were indexed by PCR using Unique Dual Indexes Set A (UDI Set A, included in the kit) and purified by dual size selection with AMPure XP beads. Library concentrations were quantified using a Qubit™ 4 Fluorometer (Thermo Fisher Scientific; cat. Q33238), and library fragment size distributions were evaluated using an Agilent TapeStation system (Agilent Technologies). Final libraries showed an average insert size of approximately 400–700 bp, with <5% of fragments below 300 bp, consistent with expectations for SCOPE-chip SD–derived single-nucleus RNA-seq libraries.

value: brain

tag: genotype

value: Healthy

tag: Sex

value: Female


title: 6614 Feature Barcode

country: USA

description:
Library name: 6614  FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6614.tsv.gz
features_6614.tsv.gz
matrix_6614.mtx.gz

library_source: other

molecule: protein

value: Feature Barcode

tag: batch


title: Uncultured_EPCR_Low_HSC_4

description:
Library name: Sample8
Fresh_Low-4

value: Hematopoietic progenitor cells


title: 6614 Gene Expression

description:
Library name: 6614 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6614.tsv.gz
features_6614.tsv.gz
matrix_6614.mtx.gz

value: Gene Expression


title: 30-day_cultured_EPCR_High_HSC_7

description:
Library name: Sample23
R162-30d-7


title: Uncultured_EPCR_Low_HSC_3

description:
Library name: Sample7
Fresh_Low-3


title: 6610 VDJ

description:
Library name: 6610 VDJ
T cell receptor (VDJ), read 1 file contains cell barcode and UMI, read 2 file contains T cell receptor sequence information
filtered_contig_annotations_6610.csv
clonotypes_6610.csv


title: Uncultured_EPCR_Low_HSC_2

description:
Library name: Sample6
Fresh_Low-2


title: Uncultured_EPCR_Low_HSC_1

description:
Library name: Sample5
Fresh_Low-1


title: 6610 Feature Barcode

description:
Library name: 6610  FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6610.tsv.gz
features_6610.tsv.gz
matrix_6610.mtx.gz


title: 6610 Gene Expression

description:
Library name: 6610 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6610.tsv.gz
features_6610.tsv.gz
matrix_6610.mtx.gz


title: Uncultured_EPCR_High_HSC_4

description:
Library name: Sample4
Fresh_High-4


title: Uncultured_EPCR_High_HSC_3

description:
Library name: Sample3
Fresh_High-3


title: 6579 Feature Barcode

description:
Library name: 6579 FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6579.tsv.gz
features_6579.tsv.gz
matrix_6579.mtx.gz


title: Uncultured_EPCR_High_HSC_1

description:
Library name: Sample1
Fresh_High-1


title: KAT7KO_BMDM_biol_rep3

city: Hefei

first: Xianshe

last: Meng

state: Anhui

address: No. 96 Jinzhai Road

country: China

institute: University of Science and Technology of China

description:
Library name: KC3
KAT7KO BMDMs, biological replicate 3

data_processing:
Raw reads were quality-checked with FastQC and filtered with fastp to remove adapters, reads with >10% N bases, and low-quality reads
Clean reads were aligned to the Mus musculus reference genome using HISAT2.
Gene-level read counts were generated using featureCounts.
Gene-level expression was quantified as read counts, FPKM, and TPM.
Differential expression analysis was performed with DESeq2 for KAT7KO_vs_Ctrl.
Assembly: Mus_musculus.GRCm39.109
Supplementary files format and content: Excel file containing gene-level read counts and FPKM values for Ctrl and KAT7KO samples, together with differential expression results for the KAT7KO_vs_Ctrl comparison

source_name: bone marrow

growth_protocol: Bone marrow cells were isolated from mice and differentiated into BMDMs with M-CSF (20 ng/mL) for 7 days.

extract_protocol:
Total RNA was extracted from BMDMs and used for bulk RNA-seq library preparation.
RNA-seq libraries were prepared from total RNA and sequenced using a paired-end sequencing strategy.

value: bone marrow


title: 6566 Feature Barcode

description:
Library name: 6566 FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6566.tsv.gz
features_6566.tsv.gz
matrix_6566.mtx.gz


title: Uncultured_EPCR_High_HSC_2

description:
Library name: Sample2
Fresh_High-2


title: KAT7KO_BMDM_biol_rep2

description:
Library name: KC2
KAT7KO BMDMs, biological replicate 2


title: 6566 Gene Expression

description:
Library name: 6566 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6566.tsv.gz
features_6566.tsv.gz
matrix_6566.mtx.gz


title: KAT7KO_BMDM_biol_rep1

description:
Library name: KC1
KAT7KO BMDMs, biological replicate 1


title: 6457 VDJ

description:
Library name: 6457 VDJ
T cell receptor (VDJ), read 1 file contains cell barcode and UMI, read 2 file contains T cell receptor sequence information
filtered_contig_annotations_6457.csv
clonotypes_6457.csv


title: 6457 Feature Barcode

description:
Library name: 6457 FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6457.tsv.gz
features_6457.tsv.gz
matrix_6457.mtx.gz


title: Ctrl_BMDM_biol_rep2

description:
Library name: C2
Ctrl BMDMs, biological replicate 2

value: Ctrl


title: 6457 Gene Expression

description:
Library name: 6457 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6457.tsv.gz
features_6457.tsv.gz
matrix_6457.mtx.gz


title: 6374 VDJ

description:
Library name: 6374 VDJ
T cell receptor (VDJ), read 1 file contains cell barcode and UMI, read 2 file contains T cell receptor sequence information
filtered_contig_annotations_6374.csv
clonotypes_6374.csv


title: Ctrl_BMDM_biol_rep1

description:
Library name: C1
Ctrl BMDMs, biological replicate 1


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 16hr time point, L. innocua, biological replicate 4_exp2

city: Boston

first: Stephanie

last: Ragland

state: MA

address: 1 Blackfan Circle

department: Gastroenterology

institute: Boston Children's Hospital

description: Library name: 448

data_processing:
Galaxy Server
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: iBMDMs

extract_protocol:
RNA was extraced from infected iBMDMs using 300 μL lysis buffer with 1% BME, followed by isolation with the Thermo Fisher Scientific PureLink kit (#12183025). RNA  was treated with Turbo DNase (Thermo #AM190) according to manufacturer's instructions. Illumina RNA-sequencing was performed by Azenta/Genewiz.
NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module

value: iBMDMs

value: macrophage

tag: treatment

value: L. innocua

value: same batch for all


title: 6374 Feature Barcode

description:
Library name: 6374  FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6374.tsv.gz
features_6374.tsv.gz
matrix_6374.mtx.gz

value: Pancreatic lymph node

value: lymphocytes


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 16hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 446

value: S. aureus


title: 6374 Gene Expression

description:
Library name: 6374 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6374.tsv.gz
features_6374.tsv.gz
matrix_6374.mtx.gz

value: ND


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 16hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 445


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 444

value: S. epidermidis


title: Immunocult_Donor D

city: Cambridge, MA

first: Praveen Krishna

last: Veerasubramanian

address: 1 Portland Street

institute: Pfizer Inc.

description: Library name: SH14181_SA339756

data_processing:
Adapters were trimmed using Cutadapt (v4.9), reads were aligned using STAR (v2.7.9a) using the GRCh38 assembly (release 111) and quantiﬁed using Salmon (v1.10.1). Downstream analysis was performed in R (v4.4.1). Genes were ﬁltered using the ﬁlterByExpr function in EdgeR (v4.4.2), and voom function in Limma (v3.62.2) was used for normalization and differential gene expression analysis with an absolute fold change of 1.5 and FDR-adjusted P-value of 0.05 being set as the threshold for determining differential expression. Gene Ontology (GO) enrichment analysis of the differentially expressed genes was conducted using clusterProﬁler (v4.14.6). Signiﬁcance was deﬁned by an FDR-adjusted p-value of less than 0.05.
Assembly: Human GRCh38 assembly (release 111)
Supplementary files format and content: Raw counts used for downstream analysis in the publication have been provided as a tsv file.

molecule: polyA RNA

source_name: CD3+ T cells derived from PBMCs, flow sorted from MLR assay

extract_protocol:
Cells were dissolved in RLT buffer (Qiagen, Cat. 79216) with 1% 2-mercaptoethanol for RNA isolation. RNA was isolated using NucleoSpin RNA Plus kits (Takara, Cat. 740984.50).
Poly-A enrichment (stranded mRNA) library construction was performed, and an average of 30 million paired end reads were sequenced per sample.

value: Immunocult

value: Donor D


title: Dapiro + IgG4_Donor D

description: Library name: SH14181_SA339755

value: CD3+ T cells derived from PBMCs, flow sorted from MLR assay

value: Dapiro + IgG4


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 16hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 443


title: Immunocult_Donor C

description: Library name: SH14181_SA339754

value: Donor C


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 16hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 442


title: Dapiro + IgG4_Donor C

description: Library name: SH14181_SA339753


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 441


title: Immunocult_Donor B

description: Library name: SH14181_SA339752

value: Donor B


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 16hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 440


title: 6579 VDJ

description:
Library name: 6579 VDJ
T cell receptor (VDJ), read 1 file contains cell barcode and UMI, read 2 file contains T cell receptor sequence information
filtered_contig_annotations_6579.csv
clonotypes_6579.csv

value: VDJ


title: Dapiro + IgG4_Donor B

description: Library name: SH14181_SA339751


title: Myd88-/-Trif-/- iBMDMs, 16hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 439


title: Myd88-/-Trif-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 438


title: Immunocult_Donor A

description: Library name: SH14181_SA339750

value: Donor A


title: 6579 Gene Expression

description:
Library name: 6579 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6579.tsv.gz
features_6579.tsv.gz
matrix_6579.mtx.gz

value: Gene Expression


title: 6566 VDJ

description:
Library name: 6566 VDJ
T cell receptor (VDJ), read 1 file contains cell barcode and UMI, read 2 file contains T cell receptor sequence information
filtered_contig_annotations_6566.csv
clonotypes_6566.csv


title: Dapiro + IgG4_Donor A

description: Library name: SH14181_SA339749


title: CTLA4-Fc_Donor D

description: Library name: SH14181_SA339748


title: Sting-/- iBMDMs, 16hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 433

value: iBMDMs

value: macrophage

value: Sting-/-


title: Myd88-/-Trif-/- iBMDMs, 16hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 437

value: same batch for all


title: BxPC-3,sgMETTL1,input,rep1

city: Monrovia

first: Ajay

last: Goel

state: CA

address: 1218 south 5th avenue

department: Molecular Diagnostics and Experimental Therapeutics

institute: City of Hope National Medical Center

description:
Library name: BSM_I_rep1
1_all sample.xlsx

data_processing:
Paired-end raw sequencing reads were initially assessed for quality using FastQC. Adapter trimming and quality filtering were performed with Trim Galore. Processed reads were first aligned to a custom reference index containing human rRNA and tRNA sequences (GENCODE v26) using STAR. Unmapped reads were then aligned to the human reference genome (GRCh38/hg38) using STAR with the same alignment parameters. Count tables were generated by extracting the relevant columns from featureCounts output.
Assembly: hg38
Supplementary files format and content: xlsx file include raw counts for each sample from BxPC-3 cells.
Supplementary files format and content: xlsx file include raw counts for each sample from MiaPaCa-2 cells.

extract_protocol:
RNA was extracted from polysome fractions and input using QIAzol Lysis Reagent (Qiagen).
Libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB).

value: Pancreatic Ductal Adenocarcinoma cell

value: METTL1 knockout

value: input


title: Dapiro + IgG1_Donor D

description: Library name: SH14181_SA339747

value: Dapiro + IgG1


title: Sting-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 432

value: S. epidermidis


title: MSU, 22 hours, replicate 3 [HSA-000022240]

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

data_processing:
Data was processed using nf-core/rnaseq v3.11.2 (doi:https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewelset al., 2020) using Gencode M31 gene annotations. Because the QuantSeq data only captures 3' tags from transcripts, the following custom parameters were supplied: extra_star_align_args: '--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA' and extra_salmon_quant_args: '--noLengthCorrection'.
Assembly: GRCm39
Supplementary files format and content: File raw_and_normalized_counts.xlsx is a Microsoft Excel file with four worksheets: 1. sample information, 2. gene information, 3. raw count table, 4. normalized count table (log2 counts per million).

source_name: BMDM

growth_protocol: Animals were sacrificed and the femur and tibia bones were collected into cold HBSS (Gibco; Cat# 14175095). Bones from multiple mice (6 for WT only studies) were pooled for each individual biological replicate and sterilized with 70% isopropanol, washed three times with HBSS, and cracked in HBSS using a mortar and pestle. The cell suspension containing bone marrow cells was filtered through a 70mm strainer to remove cracked bone pieces and centrifuged at 300xg for 5 minutes. The supernatant was removed, and the pellet was resuspended in ACK Lysing Buffer (ThermoFisher; Cat# A1049201) for 2 minutes at room temperature to remove red blood cells. Then, BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] was added to stop the ACK lysis reaction. Cells were pelleted at 300xg for 5 minutes and the supernatant was discarded. Then, the cell pellet was resuspended in BMDM medium, counted, and plated onto 15cm non-tissue culture treated petri dishes at a density of 20 million cells/plate in BMDM medium containing murine M-CSF (Life Technologies; Cat# PMC2044) at 50ng/mL. Four days after seeding the cells, an additional 50ng/mL fresh M-CSF was added to each plate. On day 7, differentiated BMDMs were washed once with PBS and harvested in BMDM medium using a cell scraper. Cells were pelleted at 300xg for 5 minutes, resuspended in BMDM medium, and counted. Finally, cells were centrifuged at 300xg for 5 minutes, resuspended in Recovery Cell Culture Freezing Medium (Gibco; Cat# 12648010) at a density of 10 million cells/mL, and cryopreserved for later use. Differentiated BMDMs were thawed, counted, and seeded at 75k cells/well onto poly-D-lysine-coated plates in BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] with supplemental M-CSF (50ng/mL). Fresh BMDM medium was changed 24 hours after seeding of the cells.

extract_protocol:
RNA was harvested from cells using the RNeasy Micro Kit (Qiagen), following the manufacturer’s protocol. RNA integrity (RIN) and concentration were measured by High Sensitivity RNA Screen Tape Analysis (Agilent) on a 4200 TapeStation System (Agilent). Libraries were generated using the QuantSeq 3’ mRNA-seq Library Prep Kit FWB for Illumina (Lexogen A01173) with the UMI second strand synthesis module in order to identify and remove PCR duplicates, following the protocol defined by the manufacturer. Library quantity and quality were assessed with TapeStation High Sensitivity D1000 Screen Tape (Agilent 5067-5592) using High Sensitivity D1000 reagents (Agilent 5067-5593). Libraries were pooled in equimolar ratios and sent to SeqMatic for sequencing on a NovaSeq S1 (75bp, single-end reads).
Libraries were generated using the QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173) with the UMI second strand synthesis module in order to identify and remove PCR duplicates, following the protocol defined by the manufacturer. Library quantity and quality were assessed with TapeStation High Sensitivity D1000 ScreenTape (Agilent 5067-5592) using High Sensitivity D1000 reagents (Agilent 5067-5593).

treatment_protocol: Cells were treated with DMSO, 25nM BafA1, 6uM U18666A, 2uM VPS34IN1, 50uM E64 + 50uM leupeptin + 50uM pepstatin (E/LP), or 200ug/mL monosodium urate (MSU) for 1, 7, or 22h to RNA extraction. Total DMSO concentration was equal across all different treatments.

tag: replicate

value: BMDM

value: WT

value: MSU

tag: treatment dose

value: 200 ug/ml

tag: treatment duration

value: 22 hours

tag: rin


title: Ctrl_BMDM_biol_rep3

description:
Library name: C3
Ctrl BMDMs, biological replicate 3

value: bone marrow

value: Ctrl


title: CTLA4-Fc_Donor C

description: Library name: SH14181_SA339746

value: CD3+ T cells derived from PBMCs, flow sorted from MLR assay

value: Donor C


title: MiaPaCa-2,sgMETTL1,polysome,rep1

description:
Library name: MSM_P_rep1
2_all sample.xlsx

value: polysome


title: Sting-/- iBMDMs, 16hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 431

value: iBMDMs

value: macrophage

value: Sting-/-

value: S. aureus


title: WT, DMSO, replicate 3 [HSA-000022461]

growth_protocol: Animals were sacrificed and the femur and tibia bones were collected into cold HBSS (Gibco; Cat# 14175095). Bones from multiple mice (3 for KO studies) were pooled for each individual biological replicate and sterilized with 70% isopropanol, washed three times with HBSS, and cracked in HBSS using a mortar and pestle. The cell suspension containing bone marrow cells was filtered through a 70mm strainer to remove cracked bone pieces and centrifuged at 300xg for 5 minutes. The supernatant was removed, and the pellet was resuspended in ACK Lysing Buffer (ThermoFisher; Cat# A1049201) for 2 minutes at room temperature to remove red blood cells. Then, BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] was added to stop the ACK lysis reaction. Cells were pelleted at 300xg for 5 minutes and the supernatant was discarded. Then, the cell pellet was resuspended in BMDM medium, counted, and plated onto 15cm non-tissue culture treated petri dishes at a density of 20 million cells/plate in BMDM medium containing murine M-CSF (Life Technologies; Cat# PMC2044) at 50ng/mL. Four days after seeding the cells, an additional 50ng/mL fresh M-CSF was added to each plate. On day 7, differentiated BMDMs were washed once with PBS and harvested in BMDM medium using a cell scraper. Cells were pelleted at 300xg for 5 minutes, resuspended in BMDM medium, and counted. Finally, cells were centrifuged at 300xg for 5 minutes, resuspended in Recovery Cell Culture Freezing Medium (Gibco; Cat# 12648010) at a density of 10 million cells/mL, and cryopreserved for later use. Differentiated BMDMs were thawed, counted, and seeded at 75k cells/well onto poly-D-lysine-coated plates in BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] with supplemental M-CSF (50ng/mL). Fresh BMDM medium was changed 24 hours after seeding of the cells.

treatment_protocol: Cells were treated with 25nM BafA1 or equal percentage of DMSO (vehicle) for 22h prior to RNA extraction.

value: DMSO

value: 0 nM


title: Cgas-/- iBMDMs, 16hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 430

value: Cgas-/-

value: L. innocua

value: same batch for all


title: Dapiro + IgG1_Donor C

description: Library name: SH14181_SA339745

value: Dapiro + IgG1


title: MiaPaCa-2,sgNC,polysome,rep2

description:
Library name: MSN_P_rep2
2_all sample.xlsx

value: Pancreatic Ductal Adenocarcinoma cell

value: WT


title: Cgas-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 429

value: S. epidermidis


title: CTLA4-Fc_Donor B

description: Library name: SH14181_SA339744

value: Donor B


title: Dapiro + IgG1_Donor B

description: Library name: SH14181_SA339743

value: CD3+ T cells derived from PBMCs, flow sorted from MLR assay


title: MiaPaCa-2,sgNC,polysome,rep1

description:
Library name: MSN_P_rep1
2_all sample.xlsx


title: Cgas-/- iBMDMs, 16hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 428


title: WT iBMDMs, 16hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 427


title: CTLA4-Fc_Donor A

description: Library name: SH14181_SA339742

value: Donor A


title: WT iBMDMs, 16hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 426


title: Dapiro + Bam_Donor D

description: Library name: SH14181_SA339740

value: Dapiro + Bam

value: Donor D


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 8hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 424

value: iBMDMs

value: macrophage


title: WT iBMDMs, 16hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 425

value: S. aureus


title: Dapiro + IgG1_Donor A

description: Library name: SH14181_SA339741


title: Ada + IgG4_Donor D

description: Library name: SH14181_SA339739

value: Ada + IgG4


title: Dapiro + Bam_Donor C

description: Library name: SH14181_SA339738

value: Donor C


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 8hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 422


title: Ada + IgG4_Donor C

description: Library name: SH14181_SA339737


title: Dapiro + Bam_Donor B

description: Library name: SH14181_SA339736


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 420


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 421


title: Ada + IgG4_Donor B

description: Library name: SH14181_SA339735


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 419


title: Dapiro + Bam_Donor A

description: Library name: SH14181_SA339734


title: Ada + IgG4_Donor A

description: Library name: SH14181_SA339733


title: Dapiro + Amlite_Donor D

description: Library name: SH14181_SA339732

value: Dapiro + Amlite


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 418

value: L. innocua


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 416

value: same batch for all


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 417


title: Ada + IgG1_Donor D

description: Library name: SH14181_SA339731

value: Ada + IgG1


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 415


title: Dapiro + Amlite_Donor C

description: Library name: SH14181_SA339730


title: Ada + IgG1_Donor C

description: Library name: SH14181_SA339729


title: U18666A, 22 hours, replicate 1 [HSA-000022223]

value: BMDM

value: 6 uM

value: 22 hours


title: BafA1, 22 hours, replicate 1 [HSA-000022218]

value: WT

value: 25 nM


title: Dapiro + Amlite_Donor B

description: Library name: SH14181_SA339728

value: CD3+ T cells derived from PBMCs, flow sorted from MLR assay

value: Donor B


title: VPS34IN-1, 22 hours, replicate 4 [HSA-000022231]

value: 2 uM


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 413

value: iBMDMs


title: Sting-/- iBMDMs, 8hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 409

value: macrophage

value: Sting-/-


title: Ada + IgG1_Donor B

description: Library name: SH14181_SA339727


title: Sting-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 408

value: S. epidermidis


title: Dapiro + Amlite_Donor A

description: Library name: SH14181_SA339726

value: Donor A


title: Sting-/- iBMDMs, 8hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 407

value: S. aureus


title: Ada + IgG1_Donor A

description: Library name: SH14181_SA339725


title: Cgas-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 405

value: Cgas-/-


title: IgG1+IgG4_Donor D

description: Library name: SH14181_SA339723

value: Donor D


title: Ada + Amlite_Donor C

description: Library name: SH14181_SA339722

value: Ada + Amlite

value: Donor C


title: Cgas-/- iBMDMs, 8hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 404

value: same batch for all


title: WT iBMDMs, 8hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 403

value: L. innocua


title: Cgas-/- iBMDMs, 8hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 406


title: WT iBMDMs, 8hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 402

value: WT


title: IgG1+IgG4_Donor C

description: Library name: SH14181_SA339721


title: WT iBMDMs, 8hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 401


title: IgG1+IgG4_Donor B

description: Library name: SH14181_SA339719


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 400


title: Ada + Amlite_Donor B

description: Library name: SH14181_SA339720


title: Ada + Amlite_Donor D

description: Library name: SH14181_SA339724


title: Ada + Amlite_Donor A

description: Library name: SH14181_SA339718


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 398


title: IgG1+IgG4_Donor A

description: Library name: SH14181_SA339717


title: Ada + Dapiro_Donor D

description: Library name: SH14181_SA339716

value: Ada + Dapiro


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, untreated, biological replicate 4_exp2

description: Library name: 397

value: untreated


title: IgG1+IgG1_Donor D

description: Library name: SH14181_SA339715

value: CD3+ T cells derived from PBMCs, flow sorted from MLR assay


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 396


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 395


title: Ada + Dapiro_Donor C

description: Library name: SH14181_SA339714


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 394


title: IgG1+IgG1_Donor C

description: Library name: SH14181_SA339713


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 392


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, untreated, biological replicate 4_exp2

description: Library name: 393


title: Ada + Dapiro_Donor A

description: Library name: SH14181_SA339710


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 390


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 391


title: IgG1+IgG1_Donor B

description: Library name: SH14181_SA339711

value: Donor B


title: IgG1+IgG1_Donor A

description: Library name: SH14181_SA339709


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, untreated, biological replicate 4_exp2

description: Library name: 389

value: iBMDMs


title: Bam + IgG1_Donor D

description: Library name: SH14181_SA339708

value: Bam + IgG1


title: Ada + Dapiro_Donor B

description: Library name: SH14181_SA339712


title: MSU, 7 hours, replicate 3 [HSA-000022210]

value: BMDM

value: MSU

value: 200 ug/ml

value: 7 hours


title: E/L/P, 7 hours, replicate 2 [HSA-000022204]

value: E/L/P

value: 50 uM


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 387

value: macrophage

value: S. epidermidis


title: DMSO, 22 hours, replicate 2 [HSA-000022214]

value: DMSO

value: 0 nM

value: 22 hours


title: Bam + IgG1_Donor C

description: Library name: SH14181_SA339706

value: Donor C


title: No drug_Donor D

description: Library name: SH14181_SA339707

value: No drug

value: Donor D


title: MSU, 7 hours, replicate 5 [HSA-000022212]

value: WT


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 388

value: iBMDMs

value: L. innocua

value: same batch for all


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 414


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 386

value: S. aureus


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, untreated, biological replicate 4_exp2

description: Library name: 385

value: untreated


title: Bam + IgG1_Donor B

description: Library name: SH14181_SA339704

value: CD3+ T cells derived from PBMCs, flow sorted from MLR assay

value: Bam + IgG1

value: Donor B


title: 5-day_cultured_EPCR_Low_HSC_3

description:
Library name: Sample15
Culture_Low-3

value: Bone marrow

value: Primary cells

value: Hematopoietic progenitor cells


title: No drug_Donor B

description: Library name: SH14181_SA339703


title: Sting-/- iBMDMs, 4hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 380

value: macrophage

value: Sting-/-


title: No drug_Donor A

description: Library name: SH14181_SA339701

value: Donor A


title: Bam + IgG1_Donor A

description: Library name: SH14181_SA339702


title: Amlite + IgG1_Donor D

description: Library name: SH14181_SA339700

value: Amlite + IgG1


title: Sting-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 379

value: S. epidermidis


title: Unstim_Donor D

description: Library name: SH14181_SA339699

value: Unstim

value: Donor D


title: Cgas-/- iBMDMs, 4hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 374

value: iBMDMs

value: Cgas-/-


title: Unstim_Donor C

description: Library name: SH14181_SA339697

value: Donor C


title: Amlite + IgG1_Donor B

description: Library name: SH14181_SA339696


title: Cgas-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 375

value: same batch for all


title: WT iBMDMs, 4hr time point, untreated, biological replicate 4_exp2

description: Library name: 369

value: WT

value: untreated


title: Unstim_Donor A

description: Library name: SH14181_SA339693

value: CD3+ T cells derived from PBMCs, flow sorted from MLR assay


title: Colonoid-A10-4

city: Ann Arbor

last: Schmidt

state: Michigan

address: 1150 W Medical Ctr 1520C MSRB I

department: Medical School Internal Medicine Infectious Diseases

institute: University of Michigan

description: Library name: 12396-NC-8

data_processing:
Data was pre-filtered to remove genes with 0 counts in all samples.
Differential gene expression analysis was performed using DESeq2,[22] using a negative binomial generalized linear model (thresholds: linear fold change >1.5 or <-1.5, Benjamini-Hochberg FDR (Padj <0.05).
Annotation data from ENSEMBL 113 was used, and genes were additionally annotated with Entrez GeneIDs and text descriptions.
Gene counts were provided after using DESeq2 regularized log transformation to normalize to sequencing depth.
Assembly: GRCh38
Supplementary files format and content: gene_expected_count.annot.txt: Raw counts of genes per sample.  A tab-separated text file with table headers.  The first four columns identify the gene, followed by one column with the abundance for each sample.
Supplementary files format and content: gene_FPKM.annot.txt: Normalized gene abundance per sample.  A tab-separated text file with table headers.  The first four columns identify the gene, followed by one column with abundance (fragments per kilobase per million) for each sample.

source_name: Ascending colon

growth_protocol: Organoids were maintained in transwells with 2DM medium basolaterally and CCM medium apically at 37°C with a 5% CO2 atmosphere.

extract_protocol:
Extraction was done using RNeasy Micro kit (Cat# 74004) according to manufacturers instructions.
Library preparation was performed using polyA RNA ultra II (NEB) following manufacturers instructions

treatment_protocol: Cells were maintained in either a ambient oxygen (~20%) incubator; or within an anaerobic chamber, mounted in a co-culture apparatus (Coy Laboratories) with 10% oxygen gas delivered basolaterally.

value: Ascending colon

value: 81-CA/Sigma SCC313

value: Epithelium

value: Physiological hypoxia


title: Colonoid-A10-3

description: Library name: 12396-NC-7


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 16hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 366

value: macrophage

value: S. aureus


title: Colonoid-S21-4

description: Library name: 12396-NC-4

value: Ambient oxygen


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 16hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 363


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 364

value: S. epidermidis


title: Colonoid-S21-3

description: Library name: 12396-NC-3


title: Colonoid-S21-2

description: Library name: 12396-NC-2


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 16hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 360


title: No drug_Donor C

description: Library name: SH14181_SA339705

value: No drug


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 361


title: Myd88-/-Trif-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 358


title: Myd88-/-Trif-/- iBMDMs, 16hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 359

value: L. innocua


title: HASMC_Stretch_Rep2

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

description:
Library name: HASMC_Stretch_Rep2
HASMC_Exp2A

data_processing:
Primary processing and expression quantification of the reads were performed by DataPrudence (Carboctet). FASTQ files were trimmed using TrimGalore! in “paired” mode to remove Illumina adaptor sequences and low-quality reads. Paired, trimmed reads were then aligned with STAR (v 2.7.10b) to Homo sapiens  reference genome version GRCh38.p14, GENCODE 44 (http://Jul2023.archive.ensembl.org/Homo_sapiens/Info/Annotation), using the STAR alignment tool (v2.7.10b) with “--quantMode TranscriptomeSAM” option. We obtained approximately 21-34 million reads per sample (FastQ). Approximately >90% of reads uniquely mapped to the reference human genome. Gene expression was quantified by obtaining gene-level and transcriptome-level count estimates from transcriptome-aligned BAM using RSEM (v1.3.1) and differential gene expression analysis achieved using DESeq2 (v 1.34.0). Genes with an adjusted P < 0.05 and log2Fold Change > |1| were considered differentially expressed.
Assembly: Homo sapiens  reference genome version GRCh38.p14
Supplementary files format and content: csv file, raw counts for all the samples

source_name: Human iPSC

extract_protocol:
Total RNA was collected from both NOTCH1+/- and WT iVSMCs using the Total RNA Purification Kit (Norgen Biotek) per published manufacturer’s instructions for cell line at baseline and following 24 hours of exposure to mechanical strain.
RNA samples were prepared for sequencing via provider’s instructions (Novogene Corporation) and sequenced on a NovaSeq 6000 (Illumina).

value: Human iPSC

value: Commercially available human aortic smooth muscle cells

value: Wildtype

value: Mechanical strain


title: HASMC_Stretch_Rep1

description:
Library name: HASMC_Stretch_Rep1
HASMC_Exp1A


title: Myd88-/-Trif-/- iBMDMs, 16hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 357

value: iBMDMs

value: same batch for all


title: HASMC_Baseline_Rep3

description:
Library name: HASMC_Baseline_Rep3
HASMC_Con3A

value: No treatment


title: Sting-/- iBMDMs, 16hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 353

value: Sting-/-


title: HASMC_Baseline_Rep2

description:
Library name: HASMC_Baseline_Rep2
HASMC_Con2A


title: Sting-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 352


title: HASMC_Baseline_Rep1

description:
Library name: HASMC_Baseline_Rep1
HASMC_Con1A


title: Sting-/- iBMDMs, 16hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 351


title: NOTCH1_Stretch_Rep3

description:
Library name: NOTCH1_Stretch_Rep3
N1_Het_Exp3A

value: vascular smooth muscle cells


title: Cgas-/- iBMDMs, 16hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 350

value: Cgas-/-


title: NOTCH1_Stretch_Rep2

description:
Library name: NOTCH1_Stretch_Rep2
N1_Het_Exp2A


title: Cgas-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 349


title: NOTCH1_Stretch_Rep1

description:
Library name: NOTCH1_Stretch_Rep1
N1_Het_Exp1A


title: Cgas-/- iBMDMs, 16hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 348


title: Sting-/- iBMDMs, 4hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 378


title: Sting-/- iBMDMs, 4hr time point, untreated, biological replicate 4_exp2

description: Library name: 377

value: untreated


title: NOTCH1_Baseline_Rep3

description:
Library name: NOTCH1_Baseline_Rep3
N1_Het_Con3A


title: Amlite + IgG1_Donor C

description: Library name: SH14181_SA339698

value: CD3+ T cells derived from PBMCs, flow sorted from MLR assay

value: Amlite + IgG1

value: Donor C


title: WT iBMDMs, 4hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 372

value: macrophage

value: WT


title: Cgas-/- iBMDMs, 4hr time point, untreated, biological replicate 4_exp2

description: Library name: 373


title: WT iBMDMs, 16hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 347

value: L. innocua


title: NOTCH1_Baseline_Rep2

description:
Library name: NOTCH1_Baseline_Rep2
N1_Het_Con2A

value: Human iPSC


title: Cgas-/- iBMDMs, 4hr time point, L. innocua, biological replicate 4_exp2

description: Library name: 376


title: Unstim_Donor B

description: Library name: SH14181_SA339695

value: Unstim

value: Donor B


title: WT iBMDMs, 4hr time point, S. aureus, biological replicate 4_exp2

description: Library name: 370

value: S. aureus


title: WT iBMDMs, 4hr time point, S. epidermidis, biological replicate 4_exp2

description: Library name: 371

value: iBMDMs

value: S. epidermidis


title: Amlite + IgG1_Donor A

description: Library name: SH14181_SA339694

value: Donor A


title: WT iBMDMs, 16hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 346

value: same batch for all


title: NOTCH1_Baseline_Rep1

description:
Library name: NOTCH1_Baseline_Rep1
N1_Het_Con1A

value: vascular smooth muscle cells

value: No treatment


title: WT iBMDMs, 16hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 345


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 16hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 368


title: Wildtype_Stretch_Rep3

description:
Library name: Wildtype_Stretch_Rep3
WT_Exp3A

value: Wildtype

value: Mechanical strain


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 8hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 344


title: Wildtype_Stretch_Rep2

description:
Library name: Wildtype_Stretch_Rep2
WT_Exp2A


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 8hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 342


title: Colonoid-A10-1

description: Library name: 12396-NC-5

value: Ascending colon

value: 81-CA/Sigma SCC313

value: Epithelium

value: Physiological hypoxia


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 16hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 365

value: macrophage

value: L. innocua


title: Colonoid-A10-2

description: Library name: 12396-NC-6


title: Wildtype_Stretch_Rep1

description:
Library name: Wildtype_Stretch_Rep1
WT_Exp1A

value: Human iPSC


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 341


title: Wildtype_Baseline_Rep3

description:
Library name: Wildtype_Baseline_Rep3
WT_Con3A


title: Wildtype_Baseline_Rep2

description:
Library name: Wildtype_Baseline_Rep2
WT_Con2A


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 340


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 16hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 362


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 339


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 338


title: Wildtype_Baseline_Rep1

description:
Library name: Wildtype_Baseline_Rep1
WT_Con1A


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 337


title: HK2 cells, DDX18-116R-3

city: Guangzhou

first: Lijun

last: Dong

address: 1023-1063 Shatai South Road, Baiyun District

institute: Southern Medical University

description:
Library name: Sample 6
DDX18A_3

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: kidney

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: kidney

value: HK2 cells

value: renal tubular epithelial cells

value: hypoxia/reoxygenation


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 336

value: iBMDMs

value: S. aureus


title: HK2 cells, DDX18-116R-2

description:
Library name: Sample 5
DDX18A_2


title: HK2 cells, DDX18-116R-1

description:
Library name: Sample 4
DDX18A_1


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 335

value: same batch for all


title: HK2 cells, DDX18-WT-3

description:
Library name: Sample 3
DDX18_3


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 334

value: S. epidermidis


title: HK2 cells, DDX18-WT-2

description:
Library name: Sample 2
DDX18_2


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 333


title: Colonoid-S21-1

description: Library name: 12396-NC-1

value: Ambient oxygen


title: HK2 cells, DDX18-WT-1

description:
Library name: Sample 1
DDX18_1


title: Sting-/- iBMDMs, 8hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 329

value: Sting-/-


title: PSII + AlkB

city: Chicago

first: Caraline

last: Sepich

state: Illinois

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

description: Library name: A4_PSII_AlkB

data_processing:
Reads were trimmed using the trim command in HomerTools, and low-quality reads were subsequently removed
The remaining high-quality reads were then mapped to spike-in sequences using BWA32 with the following parameters: 'bwa aln -t 4 -n 0.06 -q 20' for downstream analysis.
Assembly: N/A (reads mapped to spike-in sequences)
Supplementary files format and content: For the known  m3C site on each probe, the number of reads which had each mutation type are displayed in each column as labeled by mutation type.

molecule: other

source_name: HeLa

growth_protocol: Hela cells were maintained in RPMI supplemented with 10% FBS as previously described (Mol Cell. 2020 Nov 19;80(4):633-647.e7).

extract_protocol:
Total RNA was isolated from HeLa cells using Trizol (Invitrogen) according to the manufacturer’s instructions. Small RNA was isolated from total RNA using the RNA Clean and Concentrator kit (Zymo) according to the manufacturer protocol for purification of small and large RNAs into separate fractions, saving the small RNA fraction.
Libraries were prepared beginning with a mixture of total RNA (0.5 μg) and small RNA (1.5 μg). RNA was fragmented with 10x fragmentation reagent (100 mM ZnCl2, 10 mM Tris pH 7.5) at 70 °C for 10 minutes and purified using the RNA Clean and Concentrator kit (Zymo), eluting with 45 μL of RNase-free water. 3’-repair was conducted by adding 5 μL T4 PNK 10x buffer and 1 μL T4 PNK (NEB) followed by incubation at 37 °C for 1 hour, purification with the Oligo Clean and Concentrator kit (Zymo) eluting with 13 μL RNase-free water, and measurement of the concentration. 100 ng was then taken for 3-ligation, along with 2 ng of spike-in oligo mixture with sequences indicated at the end of this section. 1 μL of 11.25 μM 3'-adaptor (5'-rApp-NN NNN ATC ACG AG ATC GGA AGA GCA CAC-3') was added to this mixture, and it was heated at 70 °C for 2 minutes and put onto ice. Then, 10 μL 3'-ligation buffer and 3 μL ligation enzyme mix were added (from the NEBNext Multiplex Small RNA Library Prep Set for Illumina). After pipetting, the reactions were incubated at 16 °C for 16 hours. Digestion of excess 3’-adaptor was then performed by adding 28 μL water and 1 μL 5’-deadenylase (NEB #M0331) into the ligation mix and incubating at 30 °C for 1 hour, followed by adding 1 μL RecJF I (NEB) at 37 °C for 1 hour and purification by RNA Clean and Concentrator kit (Zymo) with 120 μL ethanol and elution by 31 μL RNase-free water. The sample was then split to test different reverse transcriptases and conditions. To test each RT, 2 μL of each sample was combined with 1 μL 1.125 μM SR RT primer (NEBNext Small RNA kit) and incubated at 65 °C for 5 minutes then placed on ice. Then, 4 μL of 5x buffer (HIV RT buffer (250 mM Tris-HCl (pH 8.3), 375 mM KCl, 10 mM MgCl2) or 5x ProtoScript® II Reverse Transcriptase Reaction Buffer (NEB), 2 μL 10 mM dNTP, and 2 μL of each RT were added with water to 20 μL. The mixture was incubated at 37 °C (HIV RT and HIV RT-1306) or 42 °C (PSII) for 1 hour. 1 μL murine RNase inhibitor was included in the PSII library. 8 μL of 3'-ligated sample was used for AlkB treatment followed by RT using PSII. AlkB treatment was performed as described previously (Nat Cell Biol. 2021;23(7):684-691). Briefly, RNA was treated in a 50-μL reaction volume with the following reagents: 30mM MES buffer (pH 5.5), 100 µM (NH4)2Fe(SO4)2·6H2O, 300 µM α-ketoglutarate, 2 mM L-ascorbic acid, 150 mM NaCl, 2 mM MgCl2 and 40 µg ml−1 BSA with 2.5 µl SUPERase•In RNase Inhibitor and 1.0 µl of engineered AlkB (Nat Methods. 2015;12(9):835-837, Nat Cell Biol. 2021;23(7):684-691) (D135S, 10 mg ml−1). The mixture was incubated at 25 °C for 2 h and then purified using the Oligo Clean & Concentrator kit (Zymo). 100 ng 90-mer polyT DNA carrier (IDT) was added to the sample and it was purified with the Oligo Clean and Concentrator kit (Zymo). 9 μL was then taken for reverse transcription with PSII similarly to the reaction described above. After the RT reactions, 1 μL RNase H buffer and 1 μL RNase H (NEB) were added to each reaction, with incubation at 37 °C for 30 minutes. 28 μL RNase free water was added followed by purification with the RNA Clean and Concentrator kit (Zymo), using 120 μL ethanol and eluting with 6.5 μL RNase-free water. Next, 3’ cDNA ligation was performed by adding 1 μL 50 μM 3' cDNA linker (5’-/Phos/NNN NNG ATC GTC GGA CTG TAG AAC TCT GAAC /3SpC3) and 1 μL DMSO into 5.5 μL of each cDNA sample. Samples were heated at 70 °C for 2 minutes, chilled on ice immediately, and then a ligation mixture was added consisting of 2 μL 10x RNA ligation buffer (NEB), 0.2 μL 100 mM ATP, 9 μL 50% PEG8000, and 1.5 μL Rnl1 (NEB M0437M, high concentration). Ligation was performed at 25 °C for 12 hours, followed by incubation at 65 °C for 5 minutes and a hold at 4 °C. Purification was performed using the RNA Clean and Concentrator kit (Zymo), using 100 μL ethanol and eluting with 20 μL RNase-free water. qPCR was then conducted to test the cycles needed for library amplification 10 μL FastStart Essential DNA Green Master Mix (Roche), 1 μL index 1 primer (NEB small RNA kit), 1 μL SR primer (NEB), 1 μL cDNA template, and 7 μL RNase-free water on a LightCycler96 (Roche). PCR was performed for each sample using the appropriate number of cycles per sample by combining 12.5 μL 2x LongAmp Taq Mix (NEB small RNA kit), 0.625 μL SR primer (NEB small RNA kit), 1.25 μL RNase-free water, 10 μL cDNA, and 0.625 μL of an index primer unique to each sample (NEB). Samples were pre-incubated at 94°C for 30s, followed by cycling for a number of cycles determined by qPCR at 94°C for 15 seconds, 62 °C for 30 seconds, and 70 °C for 15 seconds, and finishing with a 70°C, 5-minute final extension. Libraries were purified using a 3% low melting agarose gel using 6x loading buffer (NEB #B7024) and the Quick Load pBR322 DNA-MspI Digest NEB #N3032 ladder. Samples were run at 90 V for 1-1.5 hours and purified by MinElute Gel Extraction Kit (Qiagen). Samples were sequenced on a Novaseq 6000 SP flowcell. Spike in oligos: DH-718-5-33mer: 5'-GGA GAC GGU CGG G(m3C)C CAG AUA UUC GUA UCU GUC-3’; DJ-963-11-45mer: CCU CAC CAU CUC AAC CUG AGU CG(m5C) GGC AUG AGG GAG AAG UGG UGA; m4C oligo: GGA ATA AAA TGA ATA (m4C)AG AAT TAA GGA GGA ATA AAA TAT TAG AGG AAT AAA ATA TTA AGG; DO-12-16a-21mer: 5'-ACU CAGATC UCG UG(hm5C) UAC GCU; DJ-963-13-27mer:  5'-UGU CAU CAC GAG G(f5C)A CUA AAG CUG ACU.

value: HeLa


title: PSII

description: Library name: A3_PSII


title: Sting-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 328


title: Sting-/- iBMDMs, 8hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 327


title: HIV RT-1306

description: Library name: A2_HIV_RT-1306


title: HASMC_Stretch_Rep3

description:
Library name: HASMC_Stretch_Rep3
HASMC_Exp3A

value: Commercially available human aortic smooth muscle cells

value: Wildtype

value: Mechanical strain


title: HIV RT (WT)

description: Library name: A1_HIV_RT


title: Cgas-/- iBMDMs, 8hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 326

value: macrophage

value: Cgas-/-


title: Cgas-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 325


title: TEC subset of stromal-enriched thymic cells, donor pool, scMultiome-seq_GEX

city: Oslo

first: Hanne

middle: Sagsveen

last: Hjorthaug

address: Kirkeveien 166

country: Norway

institute: Oslo University Hospital

description: Library name: Donor_pool_GEX

data_processing:
Raw sequencing data from the scMultiome-seq stromal-enriched sample were processed by the 10x Genomics Cell Ranger ARC v.2.0.2 pipeline, using the GRCh38-2020-A-2.0.0 reference path. Before peak calling, the Cell Ranger ARC fragment file was filtered to remove barcodes unlikely to represent intact nuclei based on low read depth. MACS2 v.2.2.7.1 was used for initial peak calling on the filtered fragment file. The resulting peak set and the filtered fragment file was used to create a peak count matrix. Ambient RNA was removed using SoupX v 1.6.1, and a Seurat object was created to hold cells expressing at least 100 genes, and genes being expressed in at least 3 cells. The ATAC count matrix was added to the object, followed by QC, and filtering. Clusters corresponding to thymic epithelial cells (TECs) were extracted, and the TEC subset was subject to a per-cluster peak call (MACS2). The resulting peaks were combined with the initial peak set to create a new count matrix and Seurat object, which was subject to a final QC, filtering, and cell type labelling.
Assembly: GRCh38
Supplementary files format and content: Fragment file: Cell Ranger ARC fragment file filtered to contain fragments belonging to TECs only
Supplementary files format and content: TECs Seurat object RDS file: A Seurat object filtered to contain TECs only, annotated by cell type

molecule: nuclear RNA

source_name: Thymus

extract_protocol:
Thymic tissue samples were collected in RPMI-1640 w/ 10% FBS and transported on ice. Dissociation was initiated < 1 hr after surgical removal, by enzymatic and mechanical digestion. Dissociated cells were then subject to Optiprep gradient enrichment (Sigma Aldrich), followed by magnetic depletion (STEMcell technologies) of CD45-expressing cells.
Nuclei was isolated from a pool of 25 000 thawed cryopreserved stromal-enriched cells from each donor, following the 10x Genomics’ Demonstrated Protocol - Nuclei Isolation for Single Cell ATAC Sequencing, revision D. ATAC and gene expression (GEX) libraries were prepared according to the 10x Genomics Chromium Next GEM Single Cell ATAC + Gene Expression User Guide, revision E.

value: Thymus

tag: subject status

value: paediatric donors undergoing corrective cardiac surgery


title: TEC subset of stromal-enriched thymic cells, donor pool, scMultiome-seq_ATAC

description: Library name: Donor_pool_ATAC

library_source: genomic single cell

molecule: genomic DNA


title: Cgas-/- iBMDMs, 8hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 324


title: WT iBMDMs, 8hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 323

value: WT

value: L. innocua


title: WT iBMDMs, 8hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 322


title: TEC subset of stromal-enriched thymic cells, donor 5 (3080), scATAC-seq

description: Library name: Donor5_3080

data_processing:
Raw sequencing data were processed by the 10x Genomics Cell Ranger ATAC pipeline v.1.2.0, with alignment to GRCh38. Before peak calling, the Cell Ranger ATAC fragment files were filtered to remove barcodes unlikely to represent intact nuclei based on low read depth. MACS2 v.2.2.7.1 was used for initial peak calling on each filtered fragment file. Filtered fragment files and the combined peak set were used to create a peak count matrix and a Seurat object per donor, which were subsequently integrated into one Seurat object. Following QC and filtering, clusters corresponding to thymic epithelial cells (TECs) were extracted. The TEC subset was subject to a per-cluster peak call (MACS2). The resulting peaks were combined with the initial peak set to create new per-donor count matrices and Seurat objects, which were integrated into one Seurat object and subject to final QC, filtering, and cell type labelling.
Assembly: GRCh38
Supplementary files format and content: Fragment files: Cell Ranger ATAC fragment files filtered to contain fragments belonging to TECs only
Supplementary files format and content: TECs Seurat object RDS file: A Seurat object filtered to contain TECs only, annotated by donor and cell type

extract_protocol:
Thymic tissue samples were collected in RPMI-1640 w/ 10% FBS and transported on ice. Dissociation was initiated < 1 hr after surgical removal, by enzymatic and mechanical digestion. Dissociated cells were then subject to Optiprep gradient enrichment (Sigma Aldrich), followed by magnetic depletion (STEMcell technologies) of CD45-expressing cells.
For each donor, nuclei was isolated from cryopreserved stromal-enriched cells according to the 10x Genomics’ Demonstrated Protocol - Nuclei Isolation for Single Cell ATAC Sequencing, revision D. For donor 1, 2, and 5, sequencing libraries were prepared according to the 10x Genomics Chromium Single Cell ATAC Reagent Kits User Guide Rev B, while donor 3 and 4 were prepared as described in the 10x Genomics Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 User Guide Rev D.

tag: subject id


title: TEC subset of stromal-enriched thymic cells, donor 4 (3073), scATAC-seq

description: Library name: Donor4_3073


title: WT iBMDMs, 8hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 321


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 320


title: TEC subset of stromal-enriched thymic cells, donor 3 (3091), scATAC-seq

description: Library name: Donor3_3091


title: TEC subset of stromal-enriched thymic cells, donor 2 (3077), scATAC-seq

description: Library name: Donor2_3077


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 318


title: TEC subset of stromal-enriched thymic cells, donor 1 (3075), scATAC-seq

description: Library name: Donor1_3075


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, untreated, biological replicate 3_exp2

description: Library name: 317

value: untreated


title: 2574286_3D11_Rep4

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

description: Library name: 2574286_3D11_Rep4

library_source: genomic

data_processing:
Raw paired-end Hi-C sequencing reads were processed using the Juicer pipeline (v1.5) with default parameters, based on hg38 reference (without ALT chromosomes) and MboI ligation sites GATCGATC.
Assembly: Human reference genome GRCh38 (hg38), excluding alternative (ALT) contigs.
Supplementary files format and content: Processed Hi-C data are provided as .hic files generated by Juicer.

source_name: CMY

growth_protocol: CMY and isogenic clones were grown in  RPMI medium supplemented with heat-inactivated fetal bovine serum (10%) and penicillin/streptomycin under standard conditions. Cells were passaged every 2–5 days and confirmed to be mycoplasma-free and authenticated by STR profiling.

extract_protocol:
Hi-C libraries were generated following the in situ Hi-C protocol described by Rao et al. (2014). Briefly, 2 × 10⁷ cells were crosslinked with 1% formaldehyde, quenched with glycine, lysed, and chromatin was digested overnight with MboI restriction enzyme. DNA ends were filled in and labeled with biotin-dATP prior to proximity ligation.
After proximity ligation, crosslinks were reversed and DNA was purified, sheared to 300–500 bp fragments, and biotinylated fragments were isolated by streptavidin pulldown. Sequencing libraries were prepared according to the Hi-C protocol and were compatible with Illumina sequencing platforms. Libraries were sequenced on an Illumina NovaSeq instrument using paired-end reads.

treatment_protocol: Genome-edited and control cell lines were generated using CRISPR/Cas9 ribonucleoprotein (RNP) nucleofection as described. No additional chemical or drug treatments were applied prior to Hi-C sample preparation.

value: CMY

value: Myeloid leukemia of Down syndrome (ML-DS) cell line

value: RAD21 WT


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 316

value: iBMDMs

value: same batch for all


title: 2574285_3D11_Rep3

description: Library name: 2574285_3D11_Rep3


title: 2574284_3D11_Rep2

description: Library name: 2574284_3D11_Rep2


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 314

value: S. aureus


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 315

value: S. epidermidis


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, untreated, biological replicate 3_exp2

description: Library name: 313


title: 2574282_2B10_Rep4

description: Library name: 2574282_2B10_Rep4


title: 2574281_2B10_Rep3

description: Library name: 2574281_2B10_Rep3


title: 2574283_3D11_Rep1

description: Library name: 2574283_3D11_Rep1


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 312


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 311


title: 2574280_2B10_Rep2

description: Library name: 2574280_2B10_Rep2


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 310


title: 2574279_2B10_Rep1

description: Library name: 2574279_2B10_Rep1


title: 2574278_CMY_Rep4

description: Library name: 2574278_CMY_Rep4


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, untreated, biological replicate 3_exp2

description: Library name: 309


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 308


title: 2574277_CMY_Rep3

description: Library name: 2574277_CMY_Rep3

value: RAD21 Y3*


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 307


title: 2574275_CMY_Rep1

description: Library name: 2574275_CMY_Rep1


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, untreated, biological replicate 3_exp2

description: Library name: 305


title: 3276444_3D11_H3K4me1_002

description:
Library name: 3276444_3D11_H3K4me1_002
Spike-in species: Drosophila melanogaster

data_processing:
Raw sequencing reads were quality-filtered and adapter-trimmed using Trim Galore (v0.4.4) with cutadapt (Q20 quality cutoff).
Trimmed reads were aligned to a combined human-Drosophila hybrid reference genome (GRCh38.p12 + dm6) using BWA (v0.7.12-r1039). Alignments were converted to BAM format using samtools (v1.2), and duplicate reads were marked using biobambam2 (v2.0.87).
Spike-in normalization factors were calculated based on the fraction of reads mapping to the Drosophila (dm6) genome relative to all mapped reads. For downstream analyses, only reads mapping to the human genome were retained. Alignments were filtered to uniquely mapped reads (MAPQ ≥1), excluding low-quality, secondary, and supplementary alignments.
Filtered BAM files were name-sorted and converted to paired-end fragment representations (BEDPE) using bedtools (v2.17.0), retaining properly paired fragments. Genome-wide coverage tracks were generated from fragments shorter than 2 kb by extracting the central 80 bp of each fragment (midpoint ±40 bp). Coverage was computed using bedtools genomecov and converted to bigWig format using UCSC bedGraphToBigWig. Coverage tracks were normalized to 10 million fragments and additionally scaled by the spike-in normalization factor.
Peak calling was performed using MACS2 with matched IgG controls. Broad histone targets (H3K4me1) were called with SICER (v1.1; p‑value 1e‑5). Peaks overlapping ENCODE blacklist regions were removed using bedtools.
Assembly: hg38
Supplementary files format and content: Processed data include peak files in narrowPeak BED, for targets with narrow peak profile, and BED format for broad targets; BigWig files containing sample level normalized genome-wide signal tracks and condition level signals (samples average).
Library strategy: CUT&Run

growth_protocol: Cmy cells and isogenic clones were cultured in RPMI (Gibco) supplemented with heat-inactivated fetal bovine serum (10%) and 1× penicillin/streptomycin at 37 °C with 5% CO₂. Cells were passaged every 2–5 days and confirmed to be mycoplasma-free and authenticated prior to experiments.

extract_protocol:
Nuclei were isolated from intact cells and chromatin-bound proteins were selectively released using micrococcal nuclease (MNase) digestion following the Epicypher CUTANA CUT&RUN protocol. MNase digestion time was modified to 1.5 hours.
CUT&RUN libraries were prepared using the CUTANA CUT&RUN Library Prep Kit (Epicypher; Cat#14-1001) according to the manufacturer’s protocol following antibody-directed MNase digestion. Libraries were indexed, pooled, and sequenced on an Illumina NovaSeq platform.

treatment_protocol: No chemical treatment was applied prior to CUT&RUN. Genome-edited cell lines were generated by CRISPR-Cas9 nucleofection and clonally expanded prior to chromatin profiling.

tag: antibody

value: Active Motif 39297


title: 3276445_3D11_H3K4me1_003

description:
Library name: 3276445_3D11_H3K4me1_003
Spike-in species: Drosophila melanogaster


title: Sting-/- iBMDMs, 4hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 298

value: Sting-/-


title: Cgas-/- iBMDMs, 4hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 296

value: macrophage


title: 3276440_2B10_H3K4me1_001

description:
Library name: 3276440_2B10_H3K4me1_001
Spike-in species: Drosophila melanogaster


title: Cgas-/- iBMDMs, 4hr time point, untreated, biological replicate 3_exp2

description: Library name: 293

value: Cgas-/-


title: 3276427_3D11_H3K27ac_003

description:
Library name: 3276427_3D11_H3K27ac_003
Spike-in species: Drosophila melanogaster

value: Active Motif 39133


title: WT iBMDMs, 4hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 291


title: 3276437_CMY_H3K4me1_001

description:
Library name: 3276437_CMY_H3K4me1_001
Spike-in species: Drosophila melanogaster


title: 3276426_3D11_H3K27ac_002

description:
Library name: 3276426_3D11_H3K27ac_002
Spike-in species: Drosophila melanogaster


title: WT iBMDMs, 4hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 290


title: 3276425_3D11_H3K27ac_001

description:
Library name: 3276425_3D11_H3K27ac_001
Spike-in species: Drosophila melanogaster


title: WT iBMDMs, 4hr time point, untreated, biological replicate 3_exp2

description: Library name: 289


title: 3276424_2B10_H3K27ac_003

description:
Library name: 3276424_2B10_H3K27ac_003
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 16hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 288


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 16hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 285


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 284


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 16hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 283


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 16hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 282


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 16hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 280


title: Myd88-/-Trif-/- iBMDMs, 16hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 279


title: Sting-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 299


title: 3276415_2B10_RabIgG_003

description:
Library name: 3276415_2B10_RabIgG_003
Spike-in species: Drosophila melanogaster

value: Epicypher 13-0042K


title: WT iBMDMs, 4hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 292

value: WT


title: 3276441_2B10_H3K4me1_002

description:
Library name: 3276441_2B10_H3K4me1_002
Spike-in species: Drosophila melanogaster


title: 3276439_CMY_H3K4me1_003

description:
Library name: 3276439_CMY_H3K4me1_003
Spike-in species: Drosophila melanogaster


title: 3276414_2B10_RabIgG_002

description:
Library name: 3276414_2B10_RabIgG_002
Spike-in species: Drosophila melanogaster


title: 3276423_2B10_H3K27ac_002

description:
Library name: 3276423_2B10_H3K27ac_002
Spike-in species: Drosophila melanogaster


title: Sting-/- iBMDMs, 16hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 273

value: L. innocua


title: Myd88-/-Trif-/- iBMDMs, 16hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 277


title: 3276413_2B10_RabIgG_001

description:
Library name: 3276413_2B10_RabIgG_001
Spike-in species: Drosophila melanogaster


title: 3276412_CMY_RabIgG_003

description:
Library name: 3276412_CMY_RabIgG_003
Spike-in species: Drosophila melanogaster


title: 3276419_CMY_H3K27ac_001

description:
Library name: 3276419_CMY_H3K27ac_001
Spike-in species: Drosophila melanogaster


title: 3276420_CMY_H3K27ac_002

description:
Library name: 3276420_CMY_H3K27ac_002
Spike-in species: Drosophila melanogaster


title: Sting-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 272


title: Sting-/- iBMDMs, 16hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 271


title: 3276411_CMY_RabIgG_002

description:
Library name: 3276411_CMY_RabIgG_002
Spike-in species: Drosophila melanogaster


title: 3276410_CMY_RabIgG_001

description:
Library name: 3276410_CMY_RabIgG_001
Spike-in species: Drosophila melanogaster


title: 3276417_3D11_RabIgG_002

description:
Library name: 3276417_3D11_RabIgG_002
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 281


title: Cgas-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 269


title: 2692186_3D11_RabIgG_003

description:
Library name: 2692186_3D11_RabIgG_003
Spike-in species: Drosophila melanogaster


title: Cgas-/- iBMDMs, 16hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 270


title: 2692185_3D11_RabIgG_002

description:
Library name: 2692185_3D11_RabIgG_002
Spike-in species: Drosophila melanogaster


title: Cgas-/- iBMDMs, 16hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 268


title: 2692184_3D11_RabIgG_001

description:
Library name: 2692184_3D11_RabIgG_001
Spike-in species: Drosophila melanogaster


title: WT iBMDMs, 16hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 267


title: WT iBMDMs, 16hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 266


title: WT iBMDMs, 16hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 265


title: 2692181_3D11_CTCF_001

description:
Library name: 2692181_3D11_CTCF_001
Spike-in species: Drosophila melanogaster

value: Millipore Sigma 07-729


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 8hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 264


title: 2692180_3D11_Rad21_003

description:
Library name: 2692180_3D11_Rad21_003
Spike-in species: Drosophila melanogaster

value: CMY

value: GeneTex GTX106012


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 8hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 262


title: 2692179_3D11_Rad21_002

description:
Library name: 2692179_3D11_Rad21_002
Spike-in species: Drosophila melanogaster

value: Myeloid leukemia of Down syndrome (ML-DS) cell line

value: RAD21 WT


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 261

value: iBMDMs

value: same batch for all


title: 2692178_3D11_Rad21_001

description:
Library name: 2692178_3D11_Rad21_001
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 260

value: S. epidermidis


title: 2692177_3D11_GATA1s_003

description:
Library name: 2692177_3D11_GATA1s_003
Spike-in species: Drosophila melanogaster

value: Abcam Ab11852


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 259

value: S. aureus


title: 2692176_3D11_GATA1s_002

description:
Library name: 2692176_3D11_GATA1s_002
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 258


title: 2692175_3D11_GATA1s_001

description:
Library name: 2692175_3D11_GATA1s_001
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 257


title: Myd88-/-Trif-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 278


title: 2692174_3D11_H3K4me3_003

description:
Library name: 2692174_3D11_H3K4me3_003
Spike-in species: Drosophila melanogaster

value: Epicypher 13-0060K


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 256

value: macrophage


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 255


title: 2692172_3D11_H3K4me3_001

description:
Library name: 2692172_3D11_H3K4me3_001
Spike-in species: Drosophila melanogaster


title: 2692173_3D11_H3K4me3_002

description:
Library name: 2692173_3D11_H3K4me3_002
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 254


title: 2692171_2B10_RabIgG_003

description:
Library name: 2692171_2B10_RabIgG_003
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 253


title: Sting-/- iBMDMs, 8hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 249

value: Sting-/-


title: 2692170_2B10_RabIgG_002

description:
Library name: 2692170_2B10_RabIgG_002
Spike-in species: Drosophila melanogaster


title: 2692169_2B10_RabIgG_001

description:
Library name: 2692169_2B10_RabIgG_001
Spike-in species: Drosophila melanogaster


title: Sting-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 248


title: 2692168_2B10_CTCF_003

description:
Library name: 2692168_2B10_CTCF_003
Spike-in species: Drosophila melanogaster


title: Sting-/- iBMDMs, 8hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 247


title: 2692167_2B10_CTCF_002

description:
Library name: 2692167_2B10_CTCF_002
Spike-in species: Drosophila melanogaster


title: Cgas-/- iBMDMs, 8hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 246

value: Cgas-/-


title: 2692166_2B10_CTCF_001

description:
Library name: 2692166_2B10_CTCF_001
Spike-in species: Drosophila melanogaster


title: Cgas-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 245


title: Cgas-/- iBMDMs, 8hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 244


title: 2692164_2B10_Rad21_002

description:
Library name: 2692164_2B10_Rad21_002
Spike-in species: Drosophila melanogaster


title: WT iBMDMs, 8hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 243


title: 2692165_2B10_Rad21_003

description:
Library name: 2692165_2B10_Rad21_003
Spike-in species: Drosophila melanogaster


title: 2692183_3D11_CTCF_003

description:
Library name: 2692183_3D11_CTCF_003
Spike-in species: Drosophila melanogaster


title: 2692163_2B10_Rad21_001

description:
Library name: 2692163_2B10_Rad21_001
Spike-in species: Drosophila melanogaster


title: WT iBMDMs, 8hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 242


title: 2692182_3D11_CTCF_002

description:
Library name: 2692182_3D11_CTCF_002
Spike-in species: Drosophila melanogaster


title: WT iBMDMs, 8hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 241


title: 2692161_2B10_GATA1s_002

description:
Library name: 2692161_2B10_GATA1s_002
Spike-in species: Drosophila melanogaster


title: 2574276_CMY_Rep2

description: Library name: 2574276_CMY_Rep2

value: RAD21 Y3*


title: 2692162_2B10_GATA1s_003

description:
Library name: 2692162_2B10_GATA1s_003
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 240


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 238


title: 2692159_2B10_H3K4me3_003

description:
Library name: 2692159_2B10_H3K4me3_003
Spike-in species: Drosophila melanogaster


title: 2692160_2B10_GATA1s_001

description:
Library name: 2692160_2B10_GATA1s_001
Spike-in species: Drosophila melanogaster


title: Sting-/- iBMDMs, 4hr time point, L. innocua, biological replicate 3_exp2

description: Library name: 300


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 306


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, untreated, biological replicate 2_exp2

description: Library name: 237

value: untreated


title: 2692158_2B10_H3K4me3_002

description:
Library name: 2692158_2B10_H3K4me3_002
Spike-in species: Drosophila melanogaster


title: 3276443_3D11_H3K4me1_001

description:
Library name: 3276443_3D11_H3K4me1_001
Spike-in species: Drosophila melanogaster

value: Active Motif 39297


title: Sting-/- iBMDMs, 4hr time point, untreated, biological replicate 3_exp2

description: Library name: 297


title: 3276442_2B10_H3K4me1_003

description:
Library name: 3276442_2B10_H3K4me1_003
Spike-in species: Drosophila melanogaster


title: 2692157_2B10_H3K4me3_001

description:
Library name: 2692157_2B10_H3K4me3_001
Spike-in species: Drosophila melanogaster


title: Cgas-/- iBMDMs, 4hr time point, S. aureus, biological replicate 3_exp2

description: Library name: 294


title: Cgas-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 3_exp2

description: Library name: 295


title: 3276438_CMY_H3K4me1_002

description:
Library name: 3276438_CMY_H3K4me1_002
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 236

value: L. innocua


title: 2692155_CMY_RabIgG_002

description:
Library name: 2692155_CMY_RabIgG_002
Spike-in species: Drosophila melanogaster

value: CMY

value: Epicypher 13-0042K


title: 2692156_CMY_RabIgG_003

description:
Library name: 2692156_CMY_RabIgG_003
Spike-in species: Drosophila melanogaster

value: Myeloid leukemia of Down syndrome (ML-DS) cell line


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 235


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 234


title: 2692154_CMY_RabIgG_001

description:
Library name: 2692154_CMY_RabIgG_001
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 232


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, untreated, biological replicate 2_exp2

description: Library name: 233


title: 2692153_CMY_CTCF_003

description:
Library name: 2692153_CMY_CTCF_003
Spike-in species: Drosophila melanogaster

value: Millipore Sigma 07-729


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 231

value: iBMDMs


title: 2692152_CMY_CTCF_002

description:
Library name: 2692152_CMY_CTCF_002
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 230

value: same batch for all


title: 2692151_CMY_CTCF_001

description:
Library name: 2692151_CMY_CTCF_001
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, untreated, biological replicate 2_exp2

description: Library name: 229


title: 2692150_CMY_Rad21_003

description:
Library name: 2692150_CMY_Rad21_003
Spike-in species: Drosophila melanogaster

value: GeneTex GTX106012


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 228


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 16hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 286


title: 2692149_CMY_Rad21_002

description:
Library name: 2692149_CMY_Rad21_002
Spike-in species: Drosophila melanogaster


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 227

value: S. epidermidis


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, untreated, biological replicate 2_exp2

description: Library name: 225


title: Sting-/- iBMDMs, 4hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 220


title: Sting-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 219


title: 2692147_CMY_GATA1s_003

description:
Library name: 2692147_CMY_GATA1s_003
Spike-in species: Drosophila melanogaster

value: Abcam Ab11852


title: 2692144_CMY_H3K4me3_003

description:
Library name: 2692144_CMY_H3K4me3_003
Spike-in species: Drosophila melanogaster

value: Epicypher 13-0060K


title: 2692146_CMY_GATA1s_002

description:
Library name: 2692146_CMY_GATA1s_002
Spike-in species: Drosophila melanogaster


title: Sting-/- iBMDMs, 4hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 218

value: macrophage

value: S. aureus


title: 2692143_CMY_H3K4me3_002

description:
Library name: 2692143_CMY_H3K4me3_002
Spike-in species: Drosophila melanogaster


title: Sting-/- iBMDMs, 4hr time point, untreated, biological replicate 2_exp2

description: Library name: 217

value: Sting-/-


title: Cgas-/- iBMDMs, 4hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 216

value: Cgas-/-


title: 2692142_CMY_H3K4me3_001

description:
Library name: 2692142_CMY_H3K4me3_001
Spike-in species: Drosophila melanogaster

value: RAD21 Y3*


title: Cgas-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 215


title: 2276153_CMY3D11_002

description: Library name: 2276153_CMY3D11_002

data_processing:
Raw sequencing reads were adapter-trimmed and quality-filtered using Trim Galore (v0.4.4) with Cutadapt (Q20).
Trimmed reads were aligned to the human reference genome hg38 (GRCh38.p12) using STAR aligner (v2.7.9a).
PCR duplicates were identified and marked using GATK MarkDuplicates (v4.1.2.0).
Gene-level read quantification was performed using RSEM with GENCODE Release 31 gene annotations.
Assembly: Human reference genome hg38 (GRCh38.p12).
Supplementary files format and content: Processed data files include gene-level read count matrices generated by RSEM, reporting raw counts, TPM and FPKM values per gene for each RNA-seq sample.

growth_protocol: Cells were cultured under standard conditions as described. CMY cells and derived isogenic clones were maintained in RPMI (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1× penicillin/streptomycin. Cells were passaged every 2–5 days, and cell identity was verified by STR profiling and confirmed to be mycoplasma-free.

extract_protocol:
Total RNA was extracted from 1 × 10⁶ cells per sample using the Qiagen RNeasy Kit (Qiagen; Cat#74104) according to the manufacturer’s instructions. RNA quantity and quality were assessed prior to library preparation.
RNA-seq libraries were prepared from total RNA using Illumina-compatible stranded RNA-seq library preparation protocols. Library quality and fragment size distributions were assessed prior to sequencing.

treatment_protocol: No chemical treatment was applied for RNA-seq experiments. Where applicable, cells represent genome-edited clonal lines or control counterparts generated by CRISPR/Cas9 editing and expanded under identical culture conditions prior to RNA extraction.

value: RAD21 WT


title: Cgas-/- iBMDMs, 4hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 214


title: 2276150_CMY2B10_002

description: Library name: 2276150_CMY2B10_002


title: WT iBMDMs, 4hr time point, S. epidermidis, biological replicate 2_exp2

description: Library name: 211

value: WT


title: 2276149_CMY2B10_001

description: Library name: 2276149_CMY2B10_001

value: CMY


title: WT iBMDMs, 4hr time point, L. innocua, biological replicate 2_exp2

description: Library name: 212

value: L. innocua


title: WT iBMDMs, 4hr time point, S. aureus, biological replicate 2_exp2

description: Library name: 210


title: 2276142_CMY_003

description: Library name: 2276142_CMY_003

value: Myeloid leukemia of Down syndrome (ML-DS) cell line


title: WT iBMDMs, 4hr time point, untreated, biological replicate 2_exp2

description: Library name: 209

value: untreated


title: 2276141_CMY_002

description: Library name: 2276141_CMY_002


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 16hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 208

value: iBMDMs


title: 2276140_CMY_001

description: Library name: 2276140_CMY_001


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 16hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 206

value: same batch for all


title: 2351925_CMY_3D11_ATAC_3

description: Library name: 2351925_CMY_3D11_ATAC_3

data_processing:
Raw paired-end ATAC-seq reads were trimmed using Trim Galore (v0.4.4) with cutadapt (Q20). To mitigate GC bias, the first 15 base pairs of each read were clipped prior to alignment.
Trimmed reads were aligned to the human reference genome using BWA-mem (v0.7.17) within the NVIDIA Parabricks fq2bam workflow (v4.3.0-1). PCR duplicates were marked using GATK MarkDuplicates.
Properly paired, uniquely mapped reads (MAPQ ≥1) were retained using samtools (v1.2), and mitochondrial reads were excluded. Paired-end reads were converted to BEDPE format using bedtools (v2.24.0) for fragment length–based classification.
Nucleosome-free fragments (<100 bp, Tn5-adjusted) were selected for downstream analyses. Genome-wide coverage tracks were generated by computing fragment midpoints (±40 bp window), normalized to 20 million nucleosome-free fragments per sample, and converted to bigWig format using UCSC bedGraphToBigWig.
Peak calling was performed on nucleosome-free fragments using MACS2 (v2.1.1.20160309) with parameters “–nomodel –keep-dup all” and genome-specific effective genome sizes. Peaks overlapping ENCODE blacklist regions were removed.
Assembly: hg38
Supplementary files format and content: Processed data include peak files in narrowPeak BED format, BigWig files containing sample level normalized genome-wide signal tracks and condition level signals (samples average).

source_name: cell line

growth_protocol: Cells were cultured under standard conditions as described. Briefly, CMY and isogenic clones were maintained in RPMI supplemented with 10% heat-inactivated fetal bovine serum and 1× penicillin/streptomycin. Cells were passaged every 2–5 days and confirmed to be free of mycoplasma contamination.

extract_protocol:
50,000 cells per sample were washed in PBS, nuclei were isolated, and chromatin was accessed and tagmented following the Omni-ATAC protocol.
ATAC-seq libraries were generated following the Omni-ATAC protocol, including Tn5 transposase-mediated tagmentation of accessible chromatin. Library preparation, quality control, and amplification were performed by the Hartwell Center at St. Jude Children’s Research Hospital following standard Illumina-compatible procedures.

treatment_protocol: No chemical treatments were applied prior to ATAC-seq. Where applicable, genome-edited cell lines were generated using CRISPR/Cas9 technology and expanded prior to chromatin accessibility profiling.

value: cell line

value: human acute myeloid leukemia (AML) cell line


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 16hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 205


title: 2351924_CMY_3D11_ATAC_2

description: Library name: 2351924_CMY_3D11_ATAC_2


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 16hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 203


title: 2351923_CMY_3D11_ATAC_1

description: Library name: 2351923_CMY_3D11_ATAC_1


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 16hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 202


title: 2351921_CMY_2B10_ATAC_2

description: Library name: 2351921_CMY_2B10_ATAC_2


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 201

value: S. epidermidis


title: 2351920_CMY_2B10_ATAC_1

description: Library name: 2351920_CMY_2B10_ATAC_1