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

description: Library name: 200


title: 2351916_CMY_ATAC_3

status: Public on Jul 17 2026

type: SRA

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

country: USA

institute: St. Jude Childrens Research Hospital

description: Library name: 2351916_CMY_ATAC_3

library_source: genomic

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).

molecule: genomic DNA

organism: Homo sapiens

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.

tag: tissue

value: cell line

tag: cell line

value: CMY

tag: cell type

value: human acute myeloid leukemia (AML) cell line

tag: genotype

value: RAD21 Y3*

tag: batch


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

city: Boston

first: Stephanie

last: Ragland

state: MA

address: 1 Blackfan Circle

department: Gastroenterology

institute: Boston Children's Hospital

description: Library name: 199

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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: 2351915_CMY_ATAC_2

description: Library name: 2351915_CMY_ATAC_2


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

description: Library name: 198

value: S. epidermidis


title: 2351914_CMY_ATAC_1

description: Library name: 2351914_CMY_ATAC_1


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

description: Library name: 197

value: S. aureus


title: Healthy blood plasma cfDNA, Male 18

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
Library name: Healthy_Male_18
YNG.bw

data_processing:
Illumina cfDNA datasets were processed with Cutadapt in paired-end mode to remove Illumina adapters. Only reads at least 35 bp after removal of adapters were retained. Reads were trimmed down to a maximum of 130 bp using Cutadapt. Trimmed reads were aligned to the human reference genome (T2T CHM13v2.0/hs1) using bowtie2 (with parameters “--local --very-sensitive-local  --no-unal --no-mixed --no-discordant -I 10 -X 500”). Samtools and bedtools were used for processing aligned reads from SAM to BED files. Duplicate reads were discarded for further analysis if the reads had the same start and end coordinates. For Nanopore data, base-calling was performed with Dorado. Since P5/P7 adapters were ligated before ONT library preparation, we could use them as anchors to precisely define read lengths. Hence, we wrote custom python script to trim P5 and P7 adapters from ONT reads. Reads were also aligned to the CHM13 T2T hs1 v2 human reference genome using minimap2. Alignments with SAM flags of 0 and 16 were selected and used for constructing BigWig files.
For Illumina libraries, BigWig files were created using centers of fragments between 120 and 160 bp. Selected fragment centers were extended by 30 bp upstream and downstream, and coverage was calculated  at 10 bp windows genome-wide, which was calculated as the number of extended fragment centers that mapped at that window, normalized by the factor N: N = 3117275501/(Total number of mapped reads). 3117275501 was a number chosen arbitrarily. For Nanopore reads, BigWig files were created for fragments (with an upper limit of 100 kb in length). Coverage was calculated at 100 bp windows genome-wide, which is number of fragments that map at a window normalized by a factor N: 3117275501/(Total number of mapped reads). 3117275501 was a number chosen arbitrarily.
Assembly: Telomere to Telomere (T2T) CHM13 hs1 v2
Supplementary files format and content: bw

source_name: plasma

extract_protocol:
Human plasma (1 to 10 ml) was thawed from −80°C storage. Plasma samples were spun at maximum speed [21,000 rcf (relative centrifugal force)] at 4°C for 5 to 10 min to pellet any cell debris. The blood plasma supernatant was transferred to new tubes. For 1 mL blood plasma cfDNA extractions the following steps were followed. 1 mL of blood plasma was transferred to a 5 mL conical and 10 µL of proteinase K (20 mg/mL) was added to each donor sample. 650 µL of Digestion Buffer (5M GITC, 25% Tween 20, 50 mM Tris pH 8.0, and 25 mM EDTA) was added to the blood plasma and mixed well by pipetting. The samples incubated at 56°C for 1 hour. 3.3 mL of Binding Buffer (3.5M GITC, 45% Isopropanol, 2.5% Tween 20, 10 mM Tris pH 8.0, and 1mM EDTA) was added to each sample. 40 µL of 400 nm SPHERO Silica Superparamagnetic beads were added to each blood plasma sample and mixed well by vortexing. The bead-plasma slurry incubated for 10 minutes at RT. The tubes were placed on a magnetic rack and when the supernatant was clear (~ 5 min) the blood plasma supernatant was discarded. The tubes were then removed from the magnetic rack, the beads were resuspended and washed with 500 µL of Wash Buffer 1 (3M GITC, 30% Isopropanol, 5% Tween 20, 40 mM Bis-Tris pH 6.0, and 2 mM EDTA). The tubes were placed back on the magnetic rack and once the slurry was clear the supernatant was discarded. The tubes were removed again and were resuspended and washed with 500 µL of Wash Buffer 2 (50 mM Tris pH 8.0, 0.5 mM EDTA, and 80% EtOH). The tubes were placed back on the magnetic rack and once the slurry was clear the supernatant was discarded. The tubes were removed and resuspended with 100 µL of 100% EtOH. The new sample slurries were moved to 1.5 mL tubes. The tubes were then placed on a 1.5 mL magnetic rack and when the slurry cleared the supernatant was discarded. The tubes were spun down briefly and returned to the magnetic rack to remove the remaining EtOH. With the tube caps open they were air dried at 37°C for 2 minutes in a bead bath. 30 µL of nuclease free H2O were added to each sample and carefully mixed by pipetting. The tubes incubated at RT for 5 minutes and were returned to the magnetic rack. Once the supernatant was clear the DNA was eluted to a new tube for each sample. DNA fragments were then checked for quality using the Invitrogen Qubit dsDNA HS Assay kit.
UltraPrep cfDNA Isolation: cfDNA extraction was performed using the UltraPrep method. Briefly, human plasma (1 to 10 mL) was thawed from −80°C and spun at 21,000 rcf (relative centrifugal force), 4°C for 5 to 10 min to pellet any cell debris. The blood plasma supernatant was transferred to new tubes. 1 mL of blood plasma was transferred to a 5 mL conical tube, and 10 µL of proteinase K (20 mg/mL) was added to each donor sample. 650 µL of Digestion Buffer (5M guanidine thiocyanate (GITC), 25% Tween 20, 50 mM Tris pH 8.0, and 25 mM ethylenediaminetetraacetic acid (EDTA)) was added to the plasma and mixed well by pipetting. The samples were incubated at 56°C for 1 hour. 3.3 mL of Binding Buffer (3.5M GITC, 45% isopropanol, 2.5% Tween 20, 10 mM Tris pH 8.0, and 1 mM EDTA) was added to each sample. 40 µL of 400 nm SPHERO Silica Superparamagnetic beads (Spherotech) were added to each blood plasma sample and mixed well by vortexing. The bead-plasma slurry was incubated for 10 minutes at room temperature (RT). The tubes were placed on a magnetic rack, and when the supernatant was clear (~ 5 minutes), it was discarded. The tubes were then removed from the magnetic rack, the beads were resuspended and washed with 500 µL of Wash Buffer 1 (3M GITC, 30% isopropanol, 5% Tween 20, 40 mM bis-tris pH 6.0, and 2 mM EDTA). The tubes were placed back on the magnetic rack, and once the slurry was clear, the supernatant was discarded. The beads were resuspended and washed with 500 µL of Wash Buffer 2 (50 mM Tris pH 8.0, 0.5 mM EDTA, and 80% ethanol). The tubes were placed back on the magnetic rack, and once the slurry was clear, the supernatant was discarded. The beads were resuspended with 100 µL of 100% EtOH. The new sample slurries were moved to 1.5 mL tubes. The tubes were then placed on a 1.5 mL magnetic rack, and when the slurry cleared, the supernatant was discarded. The tubes were spun down briefly and returned to the magnetic rack to remove the remaining EtOH. With the tube caps open, they were air dried at 37°C for 2 minutes in a bead bath. 30 µL of nuclease-free H2O was added to each sample and carefully mixed by pipetting. The tubes were incubated at RT for 5 minutes and returned to the magnetic rack. Once the supernatant was clear, the DNA was eluted into a new tube for each sample. Extracted DNA was quantified using the Invitrogen Qubit dsDNA HS Assay. Sequencing Libraries: cfDNA libraries were generated using the SRSLY PicoPlus Base Kit (cat. CBS-K250B-96). 1 to 10 ng of cfDNA per sample was combined with Nuclease-Free (NF) H2O and SRSLY ss Enhancer in a 0.5 mL Axygen PCR tube (Fisher Scientific cat. 14-222-290) on ice. Following incubation on ice for 2 minutes, tubes were moved into a 0.5 mL PCR block for a heat shock at 98°C (lid 105°C) for 3 minutes to allow denaturation. The tubes were then incubated on ice for 2 minutes and the PCR block was set to 37°C (lid temp 45°C). A phosphorylation master mix was created by combining the SRSLY Master Mix, SRSLY Adapter A, and SRSLY Adapter B, all provided from the SRSLY Base Kit. To each sample, a phosphorylation master mix was added for a final volume of 50 μL. Once the tubes were mixed well via vortex, they were incubated for 1 hour in a PCR block at 37°C (lid temp 45°C). cfDNA was isolated after incubation using AMPure XP Beads (Beckman Coulter cat. A63881) at a ratio of 0.54x, mixed with 100% Isopropanol at a ratio of 0.24x, and NF-H2O.  A 0.5 mL magnetic rack was used to capture and wash cfDNA with 80% EtOH. cfDNA-beads were suspended in 15 μL of NF-H2O, and cfDNA was eluted into new 0.5 mL Axygen PCR Tubes. Purified cfDNA libraries were amplified via PCR with a master SRSLY PCR Mix (provided in the base kit) and NF-H2O. Uniquely barcoded primers, P5 and P7, with a final concentration of 0.25 μM each, were added to each sample. Samples were initially incubated at 98°C (lid 105°C) for 3 minutes, followed by 10 cycles of amplification [98°C for 20 seconds, 65°C for 30 seconds, 72°C for 30 seconds], 72°C for 1 minute, then a final hold at 12°C. After PCR, cfDNA libraries were captured and washed with AMPure XP beads at a ratio of 0.95x. The final elution was in 20 μL 0.1X TE buffer and transferred to 1.5 mL Eppendorf LoBind tubes (cat. 022431021).  Eluted libraries were quantified via Qubit (dsDNA Quantitation, High Sensitivity kit cat. Q32854) and quality checked using an Agilent Tapestation (D1000 tape cat. 5067-5582).  Sequencing libraries were stored at -20°C until shipped for sequencing on the Novaseq. All libraries contained dual barcodes and were subjected to 150 bp paired-end sequencing. PCR enrichment of telomere sequences from SRSLY cfDNA libraries: cfDNA libraries until the PCR amplification step were generated as described above. To enrich for telomeric sequences for long-read sequencing, the libraries were amplified using CloneAmp HiFi PCR premix, which accurately amplifies long amplicons. Either standard P5/P7 primers or primers that recognize the junction between Illumina adapters and telomeric repeats were used for amplification (primer sequences below). We used three primer sets: 1. P5 standard primer sequence and P7 standard primer sequence 2. P5 standard primer sequence and P7 + telomere repeat sequence 3. P7 standard primer sequence and P5 + telomere repeat sequence The PCR conditions were (lid temp 105°C), 98°C 10 seconds, 52°C 15 seconds, 72°C 5 seconds, repeated for 12 total cycles, and a 10°C holding temperature. The cfDNA PCR product was purified using a 2X AMPure bead clean. Eluted libraries were quantified using Qubit (dsDNA Quantitation, High Sensitivity kit cat. Q32854) and quality-checked using an Agilent Tapestation (D1000 tape cat. 5067-5582).  Sequencing libraries were stored at -20°C until utilized for Nanopore sequencing. P5 standard primer sequence: 5’ TTTCCCTACACGACGCTCTT 3’ P7 standard primer sequence: 5’ GTTCAGACGTGTGCTCTTCC 3’ P5 + telomere repeat sequence: 5’ TCTTCCGATCTCCCTAACCCTA 3’ P7 + telomere repeat sequence: 5’ CTCTTCCGATCTCCCTAACCC 3’ Oxford Nanopore Long Read Sequencing: The Nanopore Ligation Sequencing DNA SQK-LSK 110 and SQK-LSK 114 kits were used to generate cfDNA Nanopore sequencing libraries, which were sequenced on R9.4.1 MinION and R10.4.1 PromethION flow cells, respectively.

value: plasma

tag: age

value: 24 yo

tag: sample type

value: Blood plasma cfDNA


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

description: Library name: 191

value: Sting-/-


title: Healthy blood plasma cfDNA, Male 17

description:
Library name: Healthy_Male_17
YNG.bw

value: 19 yo


title: Healthy blood plasma cfDNA, Male 09

description:
Library name: Healthy_Male_09
OLD.bw

value: 71 yo


title: Healthy blood plasma cfDNA, Male 08

description:
Library name: Healthy_Male_08
OLD.bw


title: Healthy blood plasma cfDNA, Male 07

description:
Library name: Healthy_Male_07
YNG.bw

value: 25 yo


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

description: Library name: 188

value: Cgas-/-


title: Healthy blood plasma cfDNA, Male 05

description:
Library name: Healthy_Male_05
OLD.bw

value: 58 yo


title: WT iBMDMs, 16hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 187

value: WT


title: Healthy blood plasma cfDNA, Male 04

description:
Library name: Healthy_Male_04
OLD.bw

value: 68 yo


title: WT iBMDMs, 16hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 186

value: iBMDMs


title: Healthy blood plasma cfDNA, Female 11

description:
Library name: Healthy_Female_11
OLD.bw

value: 75 yo


title: WT iBMDMs, 16hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 185

value: macrophage


title: Healthy blood plasma cfDNA, Female 10

description:
Library name: Healthy_Female_10
OLD.bw

value: 73 yo


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 8hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 184

value: L. innocua

value: same batch for all


title: Healthy blood plasma cfDNA, Female 09

description:
Library name: Healthy_Female_09
YNG.bw

value: plasma

value: 27 yo


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 8hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 182

value: S. aureus


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 181


title: Healthy blood plasma cfDNA, Female 07

description:
Library name: Healthy_Female_07
OLD.bw

value: 70 yo

value: Blood plasma cfDNA


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 180

value: S. epidermidis


title: Healthy blood plasma cfDNA, Female 06

description:
Library name: Healthy_Female_06
OLD.bw

value: 71 yo


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 8hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 179


title: Healthy blood plasma cfDNA, Female 05

description:
Library name: Healthy_Female_05
YNG.bw

value: 25 yo


title: Control TAZMYF TEAD4 Rep4

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description: Library name: 20221230_MYF2DFTEAD4-12-14-22-3-08ng-ul_SLV10651_S115

data_processing:
Sequence tags were aligned with Burrows-Wheeler Aligner (BWA) (53) to build hg19 and uniquely mapped, non-redundant reads were retained
Reads were used to generate binding sites with Model-Based Analysis of ChIP-Seq 2 (MACS v2.1.1.20160309), with a q-value (FDR) threshold of 0.01
Assembly: GRCh37/hg19

growth_protocol: MSTO-211H cells were maintained in RPMI supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2  at 37oC

extract_protocol:
For profiling TEAD4 and EZH2, cells were crosslinked first with 2 mM of disuccinimidyl glutarate (DSG, Pierce) for 45 minutes at room temperature and then with 1 mL of 1% formaldehyde for 10 minutes. After quenching and lysis, chromatin was sonicated using Covaris E220 sonicator
ChIP-seq libraries were made using Swift DNA Library Prep Kit (Swift Biosciences 10024). 75 bp paired end reads were sequenced on a NextSeq instrument (Illumina)

treatment_protocol: MSTO-211H malignant pleural mesothelioma cells were transiently transfected with Cas9 and either an sgRNA control guide (sgCTRL) or a guide targeting EZH2 (EZH2-KO). sgCTRL and EZH2-KO cells were treated with DMSO or a TEAD inhibitor, MYF-03-69 for 24h.

value: Malignant Pleural Mesothelioma

value: Tazemetotstat+MYF-03-69 (TEADi)

tag: antibody


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 177


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 176


title: Control TAZMYF TEAD4 Rep3

description: Library name: 20221230_MYF1DFTEAD4-12-14-22-3-98ng-ul_SLV10651_S114


title: Control TAZ TEAD4 Rep4

description: Library name: 20221230_TAZ2DFTEAD4-12-14-22-4-26ng-ul_SLV10651_S111

value: Tazemetotstat


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 174

value: iBMDMs


title: Control TAZ TEAD4 Rep3

description: Library name: 20221230_TAZ1DFTEAD4-12-14-22-4-14ng-ul_SLV10651_S110


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 173


title: Control DMSO TEAD4 Rep4

description: Library name: 20221230_DMSO2DFTEAD4-12-14-22-5-74ng-ul_SLV10651_S107

value: DMSO


title: Control DMSO TEAD4 Rep3

description: Library name: 20221230_DMSO1DFTEAD4-12-14-22-3-60ng-ul_SLV10651_S106


title: Sting-/- iBMDMs, 8hr time point, L. innocua, biological replicate 1

description: Library name: 169

value: macrophage

value: Sting-/-


title: Healthy blood plasma cfDNA, Female 04

description:
Library name: Healthy_Female_04
YNG.bw

value: 31 yo


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 8hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 178

value: L. innocua

value: same batch for all


title: Unwounded 5 dpf Replicate 3

city: Madison

first: Anna

last: Huttenlocher

state: WI

address: 1550 Linden Drive

department: Pediatrics

institute: University of Wisconsin School of Medicine and Public Health

description: Library name: Sample9

data_processing:
Raw sequencing data were aligned to zebrafish genome GRCz11 with an improved gene annotation, published in "improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes” using RSEM v1.3.3 with parameters “-p 16 --paired-end --star --estimate-rspd --append-names --output-genome-bam” and STAR version 2.7.11b.
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files

organism: Danio rerio

source_name: tail half of the larvae

growth_protocol: Adult fish were maintained on a 14-hour light, 10-hour dark cycle. Following breeding, embryos were transferred to E3 medium (5 mM NaCl, 0.17 mM KCl, 0.44 mM CaCl2, 0.33 mM MgSO4, 0.025 mM NaOH, and 0.0003% methylene blue) and maintained at 28.5°C until sample collection.  For all experiments, larval zebrafish were anesthetized in 0.2 mg/mL tricaine (ethyl 3-aminobnzoate) in E3 medium prior to use.

extract_protocol:
RNA extraction was performed on collected tail fin tissues using TRIzol reagent and RNAqueous Micro Kit (Invitrogen) following manufacturer's instructions
Sequencing libraries were constructed by GENEWIZ

treatment_protocol: To perform burn injury, zebrafish larvae were transferred to a 60 mm tissue-culture treated dish containing 0.2 mg/mL tricaine in E3 medium. A fine tip cautery pen (Geiger Medical Instruments) was used to burn the caudal fin of larval zebrafish. Burn wounds were applied until the wounded region bordered but did not touch the posterior notochord boundary. In all cases, larvae were washed to remove tricaine immediately following injury until ready for use.

value: tail half of the larvae


title: Unwounded 6 dpf Replicate 1

description: Library name: Sample10


title: Burn 6 hpb Replicate 3

description: Library name: Sample15


title: Burn 6 hpb Replicate 2

description: Library name: Sample14


title: Burn 48 hpb Replicate 1

description: Library name: Sample19


title: SF TAZMYF H3K27me3 Rep2

description: Library name: 20221230_TAZMYF2_SF_H3K27me3_12-07-22_1-32_ng-ul_SLV10636_S84


title: Sting-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 168


title: Sting-/- iBMDMs, 8hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 167

value: S. aureus


title: SF TAZMYF H3K27me3 Rep1

description: Library name: 20221230_TAZMYF1_SF_H3K27me3_12-07-22_1-54_ng-ul_SLV10636_S83


title: Myd88-/-Trif-/- iBMDMs, 8hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 175


title: Cgas-/- iBMDMs, 8hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 166

value: Cgas-/-


title: SF TAZ H3K27me3 Rep2

description: Library name: 20221230_TAZ2_SF_H3K27me3_12-07-22_2-50_ng-ul_SLV10636_S80


title: SF TAZ H3K27me3 Rep1

description: Library name: 20221230_TAZ1_SF_H3K27me3_12-07-22_1-17_ng-ul_SLV10636_S79


title: Cgas-/- iBMDMs, 8hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 165


title: Cgas-/- iBMDMs, 8hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 164


title: WT iBMDMs, 8hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 163

value: WT


title: SF DMSO H3K27me3 Rep2

description: Library name: 20221230_DMSO2_SF_H3K27me3_12-07-22_11_ng-ul_SLV10636_S76


title: 2692148_CMY_Rad21_001

description:
Library name: 2692148_CMY_Rad21_001
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

source_name: CMY

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.

value: CMY

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

value: RAD21 Y3*

value: GeneTex GTX106012


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

description: Library name: 226


title: WT iBMDMs, 8hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 162

value: S. epidermidis


title: 2692145_CMY_GATA1s_001

description:
Library name: 2692145_CMY_GATA1s_001
Spike-in species: Drosophila melanogaster

value: Abcam Ab11852


title: SF DMSO H3K27me3 Rep1

description: Library name: 20221230_DMSO1_SF_H3K27me3_12-07-22_13-7_ng-ul_SLV10636_S75

value: Malignant Pleural Mesothelioma


title: SF MYF H3K27Ac Rep1

description: Library name: 20221230_TAZMYF1_SF_H3K27Ac_12-07-22_2-64_ng-ul_SLV10636_S81

value: Tazemetotstat+MYF-03-69 (TEADi)


title: SF MYF H3K27Ac Rep2

description: Library name: 20221230_TAZMYF2_SF_H3K27Ac_12-07-22_1-81_ng-ul_SLV10636_S82


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 160

value: iBMDMs

value: macrophage


title: WT iBMDMs, 8hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 161


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 158


title: SF TAZ H3K27Ac Rep2

description: Library name: 20221230_TAZ2_SF_H3K27Ac_12-07-22_3-14_ng-ul_SLV10636_S78

value: Tazemetotstat


title: SF TAZ H3K27Ac Rep1

description: Library name: 20221230_TAZ1_SF_H3K27Ac_12-07-22_2-04_ng-ul_SLV10636_S77


title: 2276154_CMY3D11_003

description: Library name: 2276154_CMY3D11_003

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: 2276152_CMY3D11_001

description: Library name: 2276152_CMY3D11_001


title: SF DMSO H3K27Ac Rep2

description: Library name: 20221230_DMSO2_SF_H3K27Ac_12-07-22_2-14_ng-ul_SLV10636_S74

value: DMSO


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

description: Library name: 213

value: untreated

value: same batch for all


title: 2276151_CMY2B10_003

description: Library name: 2276151_CMY2B10_003


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, untreated, biological replicate 1_exp2

description: Library name: 157


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 156

value: L. innocua


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 155


title: SF DMSO H3K27Ac Rep1

description: Library name: 20221230_DMSO1_SF_H3K27Ac_12-07-22_3-64_ng-ul_SLV10636_S73


title: KO Myf TEAD4 Rep2

description: Library name: 20230106_ko_myf2_tead4_SK10681_S122


title: KO Myf TEAD4 Rep1

description: Library name: 20230106_ko_myf1_tead4_SK10681_S121


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 154

value: S. aureus


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, untreated, biological replicate 1_exp2

description: Library name: 153


title: KO DMSO TEAD4 Rep2

description: Library name: 20230106_ko_dmso2_tead4_SK10681_S118


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 151


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 152


title: KO DMSO TEAD4 Rep1

description: Library name: 20230106_ko_dmso1_tead4_SK10681_S117


title: Control Myf TEAD4 Rep2

description: Library name: 20230106_ctrl_myf2_tead4_SK10681_S120


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

description: Library name: 204


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, untreated, biological replicate 1_exp2

description: Library name: 149


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 148


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 147


title: Control Myf TEAD4 Rep1

description: Library name: 20230106_ctrl_myf1_tead4_SK10681_S119


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 150


title: Control DMSO TEAD4 Rep1

description: Library name: 20230106_ctrl_dmso1_tead4_SK10681_S115


title: Control DMSO TEAD4 Rep2

description: Library name: 20230106_ctrl_dmso2_tead4_SK10681_S116


title: 2351922_CMY_2B10_ATAC_3

description: Library name: 2351922_CMY_2B10_ATAC_3

value: cell line

value: CMY

value: human acute myeloid leukemia (AML) cell line


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 146


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, untreated, biological replicate 1_exp2

description: Library name: 145


title: KO MYF H3K27me3 Rep1

description: Library name: 20221230_KOMYF1SFH3K27me3-12-16-22-0-778ng-ul_SLV10661_S53


title: Sting-/- iBMDMs, 4hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 140

value: Sting-/-


title: Sting-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 139

value: S. epidermidis


title: KO DMSO H3K27me3 Rep2

description: Library name: 20221230_KODMSO2SFH3K27me3-12-16-22-0-662ng-ul_SLV10661_S46


title: KO DMSO H3K27me3 Rep1

description: Library name: 20221230_KODMSO1SFH3K27me3-12-16-22-0-646ng-ul_SLV10661_S45


title: Control DMSO H3K27me3 Rep2

description: Library name: 20221230_CTRLDMSO2SFH3K27me3-12-16-22-9-48ng-ul_SLV10661_S42


title: Sting-/- iBMDMs, 4hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 138


title: Control MYF H3K27me3 Rep2

description: Library name: 20221230_CTRLMYF2SFH3K27me3-12-16-22-6-94ng-ul_SLV10661_S50


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

description: Library name: 193


title: Healthy blood plasma cfDNA, Male 19

description:
Library name: Healthy_Male_19
YNG.bw

value: plasma

value: 30 yo

value: Blood plasma cfDNA


title: KO MYF H3K27me3 Rep2

description: Library name: 20221230_KOMYF2SFH3K27me3-12-16-22-1-14ng-ul_SLV10661_S54

value: Malignant Pleural Mesothelioma


title: Cgas-/- iBMDMs, 4hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 136

value: iBMDMs

value: macrophage

value: Cgas-/-


title: KO MYF H3K27Ac Rep2

description: Library name: 20221230_KOMYF2SFH3K27Ac-12-16-22-5-44ng-ul_SLV10661_S52


title: Cgas-/- iBMDMs, 4hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 134


title: Sting-/- iBMDMs, 4hr time point, untreated, biological replicate 1_exp2

description: Library name: 137


title: KO MYF H3K27Ac Rep1

description: Library name: 20221230_KOMYF1SFH3K27Ac-12-16-22-5-34ng-ul_SLV10661_S51


title: KO DMSO H3K27Ac Rep2

description: Library name: 20221230_KODMSO2SFH3K27Ac-12-16-22-5-56ng-ul_SLV10661_S44


title: Control DMSO H3K27me3 Rep1

description: Library name: 20221230_CTRLDMSO1SFH3K27me3-12-16-22-13-5ng-ul_SLV10661_S41

value: DMSO


title: pWER::H2B:GFP_rdr126_Roots_TuYV-GFP

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: Library name: ID11_DA368_TuYV-GFP

data_processing:
Raw reads were quality filtered using fastp (default parameters, --length_required 15, --trim_poly_x, --poly_x_min_len 10) to remove low-quality reads, polyX tails, and reads shorter than 15 nt. Filtered reads were aligned to viral reference genomes (TuYV-wt and TuYV-GFP) or plasmid sequence (pG7_pWER_H2B_eGFP_LB-RB) using Bowtie2 (default parameters, --no-unal) in end-to-end mode. Aligned reads were filtered by read length (21 nt, 22 nt, 24 nt representing DCL4, DCL2, and DCL3 activities respectively) and visualised as strand-specific coverage plots normalised to reads per million (RPM).
Assembly: Custom viral and plasmid reference sequences: TuYV-wt (Turnip yellow mosaic virus wild type), TuYV-GFP (TuYV with GFP insertion), and pG7_pWER_H2B_eGFP_LB-RB (pWER::H2B:GFP transgene plasmid). Reference sequences available upon request.
Supplementary files format and content: Processed data files are tab-delimited text files containing raw counts for small RNA classes (miRNA, snoRNA, snRNA, tRNA, rRNA, ncRNA, Transposon, Pseudogene, ProteinCoding, Intergenic) mapped to the Arabidopsis thaliana TAIR10 genome and TuYV virus, followed by read size distributions (18-30nt) and first nucleotide statistics.

organism: Arabidopsis thaliana

source_name: Roots

extract_protocol:
Small RNA were purified using the TraPR Small RNA Isolation Kit (Lexogen)
Small RNA-seq Library Preparation Kit (Lexogen)

value: Roots

value: pWER::H2B:GFP (rdr1-rdr2-rdr6)

value: TuYV-GFP


title: Control MYF H3K27Ac Rep2

description: Library name: 20221230_CTRLMYF2SFH3K27Ac-12-16-22-2-76ng-ul_SLV10661_S48


title: KO DMSO H3K27Ac Rep1

description: Library name: 20221230_KODMSO1SFH3K27Ac-12-16-22-3-44ng-ul_SLV10661_S43


title: Cgas-/- iBMDMs, 4hr time point, untreated, biological replicate 1_exp2

description: Library name: 133

value: untreated

value: same batch for all


title: pWER::H2B:GFP_rdr126_Roots_Mock

description: Library name: ID1_DA368_mock

value: Mock


title: Cgas-/- iBMDMs, 4hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 135


title: HR5_TCR_510

city: Pittsburgh

first: Alyxzandria

last: Gaydosik

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

description: Library name: HR5_TCR_510

library_source: other

data_processing:
Chromium scRNA-seq data produced by the 10X Chromium Platform were processed to generate sample-specific fastq files.
Processed reads were then examined by quality metrics, mapped to a reference human genome using RNA-seq aligner STAR and assigned to individual cells of origin according to the cell specific barcodes, using the Cell Ranger 3 pipeline (10X Genomics).
Assembly: mm10
Supplementary files format and content: H5 files for gene expression, CSV files for TCR outputs

molecule: other

source_name: muscle

extract_protocol:
Mice Treatment : 100 uL of affinity-purified, filter-sterilized recombinant HRS (3-5 mg/mL) was administered via bilateral, intramuscular hamstring injection (50 ul/side) of 8-10 week old female C57BL/6 mice to induce myositis; control mice received PBS only. Mice were sacrificed 2 weeks or 6 weeks post-immunization for collection of muscle tissue. Physical and enzymatic digestion of groups of 2-3 pooled muscle samples yielded single cell preparations that were then subjected to scRNAseq using the 10X Genomics platform.
Experimental procedures followed established techniques using the Chromium Single Cell 5’ Library V1 kit +V(D)J Enrichment Kit, Mouse T Cell (10x Genomics).

value: muscle

value: HRS (3-5 mg/mL)


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

description: Library name: 192

value: Sting-/-

value: S. epidermidis


title: pWER::H2B:GFP_Roots_TuYV-GFP

description: Library name: ID6_ED335_TuYV-GFP


title: pWER::H2B:GFP_Roots_Mock

description: Library name: ID4_ED335_mock


title: WT iBMDMs, 4hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 132

value: WT

value: L. innocua


title: WT iBMDMs, 4hr time point, S. epidermidis, biological replicate 1_exp2

description: Library name: 131


title: HR5_TCR_411

description: Library name: HR5_TCR_411


title: HR5_GEX_510

description: Library name: HR5_GEX_510


title: Control DMSO H3K27Ac Rep2

description: Library name: 20221230_CTRLDMSO2SFH3K27Ac-12-16-22-6-56ng-ul_SLV10661_S40

value: Malignant Pleural Mesothelioma


title: Control MYF H3K27Ac Rep1

description: Library name: 20221230_CTRLMYF1SFH3K27Ac-12-16-22-4-6ng-ul_SLV10661_S47


title: HR5_GEX_411

description: Library name: HR5_GEX_411


title: WT iBMDMs, 4hr time point, untreated, biological replicate 1_exp2

description: Library name: 129

value: iBMDMs


title: CON510

description: Library name: CON510

value: PBS


title: CON411

description: Library name: CON411


title: Control DMSO H3K27Ac Rep1

description: Library name: 20221230_CTRLDMSO1SFH3K27Ac-12-16-22-4-54ng-ul_SLV10661_S39


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, CV-Cglr4+, biological replicate 4

description: Library name: 128

value: macrophage


title: GrnKO; Rosa26; 15

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

description: Library name: HSA-000050037

data_processing:
Data was processed using nf-core/rnaseq (v3.14.0) of the nf-core collection of workflows, using STAR (v2.7.9a) and salmon (v1.10.1) for alignment of reads to the GRCm39 mouse reference genome and quantification of Gencode (M31) gene models, respectively.
UMIs were extracted from each aligned reads using the following regular expression: ^(?P.{6})(?P.{4}).* . The following extra arguments were provided to STAR to account for the 3’ tag nature of the library: --alignIntronMax 1000000 --alignIntronMin 20 -- alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 -- outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA. Salmon quantification was performed without length correction by specifying the –noLengthCorrection argument.
Downstream analysis was performed with the edgeR (v4.6.2) Bioconductor package using R v4.5.1. Normalized log2 transformed counts per million (CPMs) were obtained by subsetting the raw count matrix to protein-coding genes, calculating library size factors with edgeR's normLibSizes function using the TMM method, and exporting CPMs with edgeR's cpm function.
Assembly: GRCm39
Supplementary files format and content: excel file with four worksheets containing 1) sample annotations, 2) gene annotations, 3) raw gene-level counts and 4) TMM normalized counts (log2 counts per million)

molecule: polyA RNA

source_name: BMDMs

growth_protocol: Frozen BMDM stocks were generated from 12-week-old male Grn+/+ (WT) and Grn-/- (Grn KO) mice (on a C57Bl/6J background with hTfRmu/hu knock-in).

extract_protocol:
RNA was harvested in RLT buffer with B-mercaptoethanol, collected into low-bind eppendorfs, and stored at -80oC until use.
For each of the 16 biological samples, a sequencing library was prepared with the QuantSeq 3′ mRNA-Seq V2 Library Prep Kit FWD (Lexogen 193.384). The UMI second strand synthesis module was used to introduce unique molecular identifiers (UMIs), following the protocol defined by the manufacturer.  Briefly, oligo dT primers were hybridized to total RNA for reverse transcription, followed by RNA removal after first strand synthesis. UMIs were introduced during second strand synthesis and cDNA was purified using magnetic beads, followed by 18 cycles of PCR with dual indexes and PCR purification. Library concentration and fragment size distribution were assessed using the Agilent TapeStation D1000 Screentape system (5067-5582). Libraries were pooled in equimolar ratios and sequenced across two lanes of an Illumina NovaSeq X Series 10B flowcell.

treatment_protocol: CRISPR/Cas9 was used to selectively knock-out Mitf, Tfe3, and Tfeb, in BMDMs taken from WT or Grn KO mice. Briefly, BMDMs were thawed and plated on uncoated 6-well tissue culture-treated dishes at a density of 2 million cells per well in BMDM medium supplemented with 50ng/mL M-CSF (Life Technologies; Cat# PMC2044). On the following day, ribonucleoproteins (RNPs) containing 1.5μL per target gene of 100μM single-guide RNA (sgRNAs) (IDT; Mm.Cas9.MITF.1.AA, Mm.Cas9.TFE3.1.AC, Mm.Cas9.TFEB.1.AC) and 4.5μL of Alt-RTM S.p. Cas9 Nuclease V3, 500 μg (IDT; Cat# 1081059) per reaction were assembled. BMDMs were lifted using Accutase (Stem Cell Technologies, Cat.# 07920), centrifuged at 400xg for 5 minutes, resuspended in BMDM medium containing M-CSF, and counted. Cell suspensions were separated into individual tubes containing 500,000 cells per reaction and pelleted again at 400xg for 5 minutes. Following centrifugation, the supernatant was removed, cell pellets were resuspended in 20μL P3 nucleofection buffer with supplement (Lonza; Cat# V4SP-3960), added to the RNP mix containing sgRNAs and SpCas9, and transfected using program CM-137 on the 4D-Nucleofector Platform (Lonza; Cat# AAF-1003S). Immediately after transfection, 180μL of BMDM medium containing 50ng/mL M-CSF was added to each reaction, cells were mixed by pipetting 3 times, and transfected cells were plated evenly across 10 wells of poly-D-lysine-coated 96-well PhenoPlates (PerkinElmer; Cat# 6055508). Half-media changes of BMDM medium containing 50ng/mL M-CSF were performed every other day and endpoints were assessed at 10 days after transfection.

tag: treatment duration

value: 10 days

value: BMDMs

value: GrnKO


title: GrnKO; Mitf_Tfe3_Tfeb; 16

description: Library name: HSA-000050038


title: 6536 slice 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: 6536 slice 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_6536_slice.csv
clonotypes_6536_slice.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: Pancreas

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: Pancreas

tag: library type

value: VDJ

tag: disease state


title: WT; Mitf_Tfe3_Tfeb; 14

description: Library name: HSA-000050036


title: WT; Rosa26; 13

description: Library name: HSA-000050035


title: 6536 slice Gene Expression

description:
Library name: 6536 slice GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6536_slice.tsv.gz
features_6536_slice.tsv.gz
matrix_6536_slice.mtx.gz

library_source: transcriptomic single cell

value: Gene Expression


title: 6536 slice Feature Barcode

description:
Library name: 6536 slice FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6536_slice.tsv.gz
features_6536_slice.tsv.gz
matrix_6536_slice.mtx.gz

molecule: protein

value: Feature Barcode


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

description: Library name: 126

value: clearcoli

value: same batch for all


title: GrnKO; Rosa26; 11

description: Library name: HSA-000050033


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

description: Library name: 125

value: untreated


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, CV-Cglr4+, biological replicate 4

description: Library name: 124


title: GrnKO; Mitf_Tfe3_Tfeb; 8

description: Library name: HSA-000050030


title: WT; Mitf_Tfe3_Tfeb; 10

description: Library name: HSA-000050032


title: WT; Rosa26; 9

description: Library name: HSA-000050031


title: GrnKO; Rosa26; 7

description: Library name: HSA-000050029


title: 6536 pLN Feature Barcode

description:
Library name: 6536 pLN FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6536_pLN.tsv.gz
features_6536_pLN.tsv.gz
matrix_6536_pLN.mtx.gz


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, dacA+, biological replicate 4

description: Library name: 123

value: dacA+


title: WT; Mitf_Tfe3_Tfeb; 6

description: Library name: HSA-000050028

value: WT


title: WT; Rosa26; 5

description: Library name: HSA-000050027


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

description: Library name: 122


title: 6551 slice VDJ

description:
Library name: 6551 slice 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_6551_slice.csv
clonotypes_6551_slice.csv


title: 6551 slice Feature Barcode

description:
Library name: 6551 slice FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6551_slice.tsv.gz
features_6551_slice.tsv.gz
matrix_6551_slice.mtx.gz


title: 6551 slice Gene Expression

description:
Library name: 6551 slice GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6551_slice.tsv.gz
features_6551_slice.tsv.gz
matrix_6551_slice.mtx.gz


title: GrnKO, 12, low

description: Library name: HSA-000050062

data_processing:
Data was processed using nf-core/rnaseq (v3.14.0) of the nf-core collection of workflows, using STAR (v2.7.9a) and salmon (v1.10.1) for alignment of reads to the GRCm39 mouse reference genome and quantification of Gencode (M31) gene models, respectively.
The following extra arguments were provided to STAR to account for the 3’ tag nature of the library: --alignIntronMax 1000000 --alignIntronMin 20 -- alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 -- outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA. Salmon quantification was performed without length correction by specifying the –noLengthCorrection argument.
Downstream analysis was performed with the edgeR (v4.6.2) Bioconductor package using R v4.5.1. Normalized log2 transformed counts per million (CPMs) were obtained by subsetting the raw count matrix to protein-coding genes, calculating library size factors with edgeR's normLibSizes function using the TMM method, and exporting CPMs with edgeR's cpm function.
Assembly: GRCm39
Supplementary files format and content: Microsoft Excel file with four worksheets containing 1) sample annotations, 2) gene annotations, 3) raw gene-level counts and 4) TMM normalized counts (log2 counts per million)

source_name: brain

growth_protocol: Brains were extracted from 19-month-old Grn+/+ and Grn-/- mice (on a C57Bl/6J background with hTfRmu/hu knock-in, n = 6/genotype). Tissue was dissociated with the Miltenyi MACS adult brain dissociation kit Miltenyi Biotec; Cat# 130-107-677) with hyaluronidase (Worthington; Cat#LS005474), actinomycin D (CST; Cat#15021; 5μM) and anisomycin (CST, Cat#2222; 2μM) present during the dissociation. Additionally, hibernate A buffer (BrainBits; Cat#NC0176976) with supplemental B-27 (Thermo-Fisher; Cat#12587010) and Glutamax (Gibco; Cat#35050-061) was also used during the debris removal step. Dissociated tissue was filtered with 70μm MACS SmartStrainers (Miltenyi Biotec; Cat#130-098-462) prior to debris removal. After this point, microglia were stained for 30 minutes on ice in the dark with additional Fc block (Biolegend; Cat# 101320; 1:100). The following antibodies were used: Live/Dead-780 (Thermo; Cat# 65-0865-14; 1:1000), Cd11b-BV421 (BD; Cat#562605; 1:100), CD45-PE/Cy7 (Biolegend; Cat# 103114; 1:100).

extract_protocol:
Samples were sorted using a BD Aria III sorter. Lipofuscinosis was assessed by 488-autofluorescence, and Cd11b+/CD45+ cells were sorted into ‘high’ and ‘low’ autofluorescence populations. 1,000 cells were sorted per sample into 57.5ul  ClonTech Lysis/RT buffer (Takara; Cat# 635013) with RNase inhibitor (Takara; Cat#2313A) in 1.5mL DNA lo-bind tubes, snap frozen, and stored at -80 oC until use.
Samples were processed using the Clontech SMARTSeq v4 3′ DE (Takara Bio USA, Inc. 635040 ) kit for cDNA synthesis and the Nextera XT DNA Library Prep Kit (Illumina FC-131-1096) for library generation. 1000 microglia per sample was sorted directly into lysis/RT buffer, and an aliquot of the lysate was used for reverse transcription followed by cDNA amplification to produce full length cDNA. cDNA was normalized to 300 pg of input for library preparation. The tagmentation step simultaneously fragmented and introduced adaptors to the DNA strands, followed by 15 cycles of PCR amplification. Library quantity and quality were assessed with TapeStation D1000 screentape (Agilent 5067-5582). Libraries were pooled in equimolar ratios for sequencing on one lane of an Illumina NovaSeq X Series 10B flowcell, 100 bp; single end reads were generated.

value: brain

tag: Sex

value: female

value: microglia

tag: animal id

tag: lipofuscin bin

value: low


title: 6586 VDJ

description:
Library name: 6586 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_6586.csv
clonotypes_6586.csv

source_name: Pancreatic lymph node

value: Pancreatic lymph node

value: lymphocytes

value: ND


title: TSC1 TFEB DKO3

city: Kansas City

first: chen

last: zhang

state: KS

address: 3901 Rainbow Blvd, MS-1018

institute: University of Kansas Medical Center

description:
Library name: Tsc1 TFEB DKO-3
2M

data_processing:
Raw FASTQ files were assessed for quality using FastQC.
Reads were aligned to the mouse reference genome using STAR aligner.
Gene-level read counts were generated using featureCounts.
Count matrices were imported into R for downstream analysis.
Assembly: Mouse reference genome GRCm38 (mm10).
Supplementary files format and content: Processed data files include a comma-separated values (CSV) file containing gene-level raw read counts. Rows correspond to gene symbols and columns correspond to individual samples.

source_name: Liver

extract_protocol:
Livers were removed and snap frozen in liquid nitrogen. Total RNA was extracted using Trizol reagent and the quality was checked with Qubit quantification and TapeStation gel analysis
RNA libraries were prepared for sequencing using the NEBNext Stranded mRNA library kit with polyA selection of the mRNA

value: Liver

value: hepatic TSC1 and TFEB DKO


title: TSC1 TFEB DKO2

description:
Library name: Tsc1 TFEB DKO-2
2M


title: 6586 Feature Barcode

description:
Library name: 6586  FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6586.tsv.gz
features_6586.tsv.gz
matrix_6586.mtx.gz


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

description: Library name: 118

value: iBMDMs

value: macrophage


title: GrnKO, 12, high

description: Library name: HSA-000050061

value: GrnKO

value: high


title: TSC1 KO4

description:
Library name: Tsc1 KO-4
2M

value: hepatic TSC1 KO


title: WT, 11, high

description: Library name: HSA-000050059


title: TSC1 KO3

description:
Library name: Tsc1 KO-3
2M


title: 6578 VDJ

description:
Library name: 6578 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_6578.csv
clonotypes_6578.csv

value: VDJ


title: GrnKO, 10, low

description: Library name: HSA-000050058

value: male


title: TSC1 KO2

description:
Library name: Tsc1 KO-2
2M


title: 6578 Feature Barcode

description:
Library name: 6578  FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6578.tsv.gz
features_6578.tsv.gz
matrix_6578.mtx.gz

value: Feature Barcode


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, dacA+, biological replicate 4

description: Library name: 127

value: dacA+

value: same batch for all


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

description: Library name: 114

value: clearcoli


title: 6536 pLN VDJ

description:
Library name: 6536 pLN 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_6536_pLN.csv
clonotypes_6536_pLN.csv

value: Pancreas


title: GrnKO, 10, high

description: Library name: HSA-000050057

value: brain

value: microglia


title: 6578 Gene Expression

description:
Library name: 6578 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6578.tsv.gz
features_6578.tsv.gz
matrix_6578.mtx.gz

value: Pancreatic lymph node

value: Gene Expression

value: lymphocytes


title: 6536 pLN Gene Expression

description:
Library name: 6536 pLN GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6536_pLN.tsv.gz
features_6536_pLN.tsv.gz
matrix_6536_pLN.mtx.gz


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

description: Library name: 113

value: iBMDMs

value: untreated


title: TSC1 KO1

description:
Library name: Tsc1 KO-1
2M

value: Liver


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

description: Library name: 121

value: macrophage


title: GrnKO; Rosa26; 3

description: Library name: HSA-000050025

value: 10 days

value: BMDMs

value: GrnKO


title: GrnKO; Mitf_Tfe3_Tfeb; 4

description: Library name: HSA-000050026


title: WT; Mitf_Tfe3_Tfeb; 2

description: Library name: HSA-000050024

value: WT


title: WT, 9, low

description: Library name: HSA-000050056

value: male

value: low


title: 6551 VDJ

description:
Library name: 6551 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_6551.csv
clonotypes_6551.csv

value: VDJ


title: TSC1 WT4

description:
Library name: Tsc1 WT-4
2M

value: wild type


title: TSC1 TFEB DKO4

description:
Library name: Tsc1 TFEB DKO-4
2M

value: hepatic TSC1 and TFEB DKO


title: WT; Rosa26; 1

description: Library name: HSA-000050023


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, CV-Cglr4+, biological replicate 4

description: Library name: 120

value: same batch for all


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, dacA+, biological replicate 4

description: Library name: 119

value: dacA+


title: Sting-/- iBMDMs, 4hr time point, CV-Cglr4+, biological replicate 4

description: Library name: 108

value: Sting-/-


title: WT, 9, high

description: Library name: HSA-000050055

value: brain

value: microglia

value: high


title: 6551 Feature Barcode

description:
Library name: 6551  FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6551.tsv.gz
features_6551.tsv.gz
matrix_6551.mtx.gz

value: Pancreatic lymph node

value: Feature Barcode

value: lymphocytes


title: GrnKO, 8, low

description: Library name: HSA-000050054

value: female


title: TSC1 WT3

description:
Library name: Tsc1 WT-3
2M

value: Liver


title: 6551 Gene Expression

description:
Library name: 6551 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6551.tsv.gz
features_6551.tsv.gz
matrix_6551.mtx.gz

value: Gene Expression


title: Sting-/- iBMDMs, 4hr time point, dacA+, biological replicate 4

description: Library name: 107

value: iBMDMs

value: macrophage


title: TSC1 WT2

description:
Library name: Tsc1 WT-2
2M


title: GrnKO, 8, high

description: Library name: HSA-000050053

value: GrnKO


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

description: Library name: 106

value: clearcoli


title: TSC1 TFEB DKO1

description:
Library name: Tsc1 TFEB DKO-1
2M

value: hepatic TSC1 and TFEB DKO


title: 6550 VDJ

description:
Library name: 6550 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_6550.csv
clonotypes_6550.csv

value: VDJ


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

description: Library name: 105

value: untreated

value: same batch for all


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

description: Library name: 117


title: WT, 7, low

description: Library name: HSA-000050052

value: brain

value: WT

value: low


title: WT, 11, low

description: Library name: HSA-000050060

value: microglia


title: 6550 Feature Barcode

description:
Library name: 6550 FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6550.tsv.gz
features_6550.tsv.gz
matrix_6550.mtx.gz

value: Pancreatic lymph node

value: Feature Barcode


title: Supernatant_3

city: Fuzhou

first: Qingxiang

last: Gao

state: FuJian

address: Qiuyang Road No1.

country: China

institute: Fujian University of Traditional Chinese Medicine

description: Library name: Supernatant_3

data_processing:
Reads were trimmed with Cutadapt v3.3, aligned to mm10 (GRCm38, Gencode M25) using STAR v2.7.9a with gene counting, and quantified with featureCounts.
Low-count genes were filtered, and differential m6A enrichment between m6A-bound and Unbound fractions was analyzed with DESeq2 (~group). Functional annotation and pathway enrichment were performed using g: Profiler, GSEA, and Metascape. Quality control confirmed high replicate consistency and clear separation among Input, Unbound, and m6A-bound samples, supporting reliable downstream peak calling and comparative analyses.
Assembly: mm10 (GRCm38, Gencode M25)
Supplementary files format and content: ttest_all_genes.xlsx
Library strategy: MeRIP-Seq

source_name: mouse esophagus

extract_protocol:
EpCAM⁺/CD45⁻ epithelial cells were isolated from wildtype mouse esophagus via single-cell dissociation and magnetic-activated cell sorting (MACS) enrichment. Total RNA was extracted  with miRNeasy Micro (Qiagen) according to the manufacturer’s instructions, with a portion retained as Input and the remainder subjected to m6A immunoprecipitation. Anti-m6A antibody (1.25 µg/reaction) was pre-bound to Protein A/G magnetic beads (Millipore) for 1 h, then incubated with RNA at 4 °C for 2 h. Beads were sequentially washed (low salt ×2, high salt ×2, RIPA ×2), with washes collected as Unbound. m6A-bound RNA was specifically eluted using 20 mM m6A 5′-monophosphate sodium salt at 4°C for 1 h, followed by ethanol precipitation.
Libraries for Input, Unbound, and m6A-bound fractions were prepared using NEBNext Single Cell/Low Input RNA Library Prep and sequenced on Illumina HiSeq 2500 (PE150) with three biological replicates per fraction.

value: mouse esophagus

value: Mouse esophageal epithelial cells

value: Wild Type

tag: merip antibody

tag: fraction

value: Unbound


title: 6586 Gene Expression

description:
Library name: 6586 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6586.tsv.gz
features_6586.tsv.gz
matrix_6586.mtx.gz

tag: tissue

value: Gene Expression

value: lymphocytes

value: ND


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, CV-Cglr4+, biological replicate 4

description: Library name: 116

tag: cell line

value: iBMDMs

value: macrophage


title: Cgas-/- iBMDMs, 4hr time point, CV-Cglr4+, biological replicate 4

description: Library name: 104

tag: cell type

value: Cgas-/-


title: 6550 Gene Expression

description:
Library name: 6550 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6550.tsv.gz
features_6550.tsv.gz
matrix_6550.mtx.gz


title: WT, 7, high

description: Library name: HSA-000050051

value: female

tag: genotype

value: high


title: GrnKO, 6, low

description: Library name: HSA-000050050

value: brain

value: male

value: GrnKO


title: Cgas-/- iBMDMs, 4hr time point, dacA+, biological replicate 4

description: Library name: 103

value: dacA+

tag: batch

value: same batch for all


title: Supernatant_1

description: Library name: Supernatant_1

value: mouse esophagus


title: Supernatant_2

description: Library name: Supernatant_2

value: Mouse esophageal epithelial cells


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

description: Library name: 102

tag: treatment

value: clearcoli


title: 6548 VDJ

description:
Library name: 6548 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_6548.csv
clonotypes_6548.csv

value: Pancreatic lymph node

value: VDJ


title: 6548 Feature Barcode

description:
Library name: 6548 FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6548.tsv.gz
features_6548.tsv.gz
matrix_6548.mtx.gz

value: Feature Barcode

value: lymphocytes


title: GrnKO, 6, high

description: Library name: HSA-000050049

value: microglia


title: Immunoprecipitation_3

description: Library name: Immunoprecipitation_3

value: Wild Type


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

description: Library name: 101

value: iBMDMs

value: macrophage

value: Cgas-/-

value: untreated


title: 6548 Gene Expression

description:
Library name: 6548 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6548.tsv.gz
features_6548.tsv.gz
matrix_6548.mtx.gz

value: Gene Expression

value: ND


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, dacA+, biological replicate 4

description: Library name: 115

value: dacA+


title: Immunoprecipitation_1

description: Library name: Immunoprecipitation_1


title: 6493 VDJ

description:
Library name: 6493 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_6493.csv
clonotypes_6493.csv


title: Immunoprecipitation_2

description: Library name: Immunoprecipitation_2


title: WT, 5, high

description: Library name: HSA-000050047

value: brain

value: male

value: WT

value: high


title: WT iBMDMs, 4hr time point, CV-Cglr4+, biological replicate 4

description: Library name: 100

value: same batch for all


title: 6493 Feature Barcode

description:
Library name: 6493 FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6493.tsv.gz
features_6493.tsv.gz
matrix_6493.mtx.gz

value: Pancreatic lymph node


title: WT iBMDMs, 4hr time point, dacA+, biological replicate 4

description: Library name: 99


title: 6493 Gene Expression

description:
Library name: 6493 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6493.tsv.gz
features_6493.tsv.gz
matrix_6493.mtx.gz


title: Input_2

description: Library name: Input_2

value: mouse esophagus

value: Mouse esophageal epithelial cells

value: Input


title: WT iBMDMs, 4hr time point, clearcoli, biological replicate 4

description: Library name: 98

value: clearcoli


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

description: Library name: 97

value: iBMDMs


title: Input_1

description: Library name: Input_1

value: Wild Type


title: TSC1 WT1

description:
Library name: Tsc1 WT-1
2M

value: Liver

value: wild type


title: 6482 VDJ

description:
Library name: 6482 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_6482.csv
clonotypes_6482.csv

value: VDJ

value: lymphocytes


title: WT, 3, low

description: Library name: HSA-000050044

value: female

value: microglia

value: low


title: Myd88-/-Trif-/-Lrrc8a-/- iBMDMs, 4hr time point, CV-Cglr3+, biological replicate 3

description: Library name: 96

value: macrophage


title: 6482 Feature Barcode

description:
Library name: 6482  FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6482.tsv.gz
features_6482.tsv.gz
matrix_6482.mtx.gz

value: Feature Barcode

value: ND


title: WT, 3, high

description: Library name: HSA-000050043

value: brain

value: WT

value: high


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

description: Library name: 95

value: dacA+

value: same batch for all


title: 6482 Gene Expression

description:
Library name: 6482 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6482.tsv.gz
features_6482.tsv.gz
matrix_6482.mtx.gz

value: Pancreatic lymph node

value: Gene Expression


title: GrnKO, 2, low

description: Library name: HSA-000050042

value: male

value: GrnKO


title: RA 2

city: Cincinnati

first: Theresa

last: Alenghat

state: Ohio

address: 3333 Burnet Avenue

department: Division of Immunobiology

institute: Cincinnati Children's Hospital Medical Center

description: Library name: sample 5

data_processing:
Sequence reads were aligned to the mm10 genome using the Illumina sequence analysis pipeline.
Differentially expressed genes between Vehicle control and RA-treated stem cell orgnaoids were identified using DSeq2.
Assembly: mm10
Supplementary files format and content: text files with Dseq2 output for each sample

source_name: stem cell enteroid

growth_protocol: Organoids were dervied from the ileum (enteroids) of WT C57Bl/6 and maintained at 37C, 5% CO2, in organoid growth media.

extract_protocol:
Organoids were harvested and RNA was isolated using the RNeasy Kit (Qiagen) according to manufacturer's instructions
Directional polyA RNAseq according to standard Illumina protocols

treatment_protocol: Stem cell-enriched organoids were cultured in organoid growth media supplemented with 10 μM CHIR99021 for 96 hours, followed by treatment with 10 μM retinoic acid or vehicle control for 24 hours

value: stem cell enteroid

value: organoid

value: intestinal stem cells

value: 10 µM all-trans retinoic acid


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

description: Library name: 94

value: iBMDMs

value: clearcoli


title: GrnKO, 2, high

description: Library name: HSA-000050041

value: microglia


title: 6461 VDJ

description:
Library name: 6461 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_6461.csv
clonotypes_6461.csv

value: VDJ

value: lymphocytes

value: ND


title: RA 1

description: Library name: sample 4


title: WT, 1, low

description: Library name: HSA-000050040

value: brain

value: WT

value: low


title: 6461 Feature Barcode

description:
Library name: 6461  FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6461.tsv.gz
features_6461.tsv.gz
matrix_6461.mtx.gz

value: Pancreatic lymph node

value: Feature Barcode


title: Myd88-/-Trif-/-Sting-/- iBMDMs, 4hr time point, CV-Cglr3+, biological replicate 3

description: Library name: 92

value: macrophage

value: same batch for all


title: WT, 1, high

description: Library name: HSA-000050039

value: male

value: high


title: 6461 Gene Expression

description:
Library name: 6461 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6461.tsv.gz
features_6461.tsv.gz
matrix_6461.mtx.gz

value: Gene Expression


title: Veh 2

description: Library name: sample 2

value: stem cell enteroid

value: organoid

value: intestinal stem cells

value: Vehicle/DMSO


title: 3A10t Treg, rep3

city: San Francisco

first: Huiyun

last: Lyu

state: CALIFORNIA

address: 513 Parnassus Ave

department: Diabetes Center

institute: University of California, San Francisco

description: Library name: 3A10t-3

data_processing:
Raw fastq reads were trimmed by Cutadapt (version 1.18) to trim adapter and low-quality sequence. Reads were aligned to the mouse genome (mm10) using STAR (version 2.5.3). The number of reads within each gene in each sample were counted using RSEM (version 1.3.0) with gene annotation file from GENCODE (GRCm38.m23). Differential expression was estimated by using DESeq2 package (version 1.26).
Assembly: GENCODE (GRCm38.m23)
Supplementary files format and content: csv file include TPM value for each sample

source_name: lymph node

growth_protocol: Cells were cultured in DMEM-high glucose no glutamine media supplemented with 10% heat-inactivated fetal calf serum, 100 IU/ml penicillin and streptomycin, 10mM of HEPES, GlutaMax, sodium pyruvate, non-essential amino acids, and beta-mercaptoethanol.

extract_protocol:
Cells were lysed using TCL buffer (Qiagen, 1070498), and RNA was extracted using VAHTS RNA Clean Beads (Vazyme, N412), then eluted in 10 µL of nuclease-free water.
For first strand cDNA synthesis and amplification, the Discover-sc WTA kit V2 (Vazyme, N711) was used. Briefly, 5 µL of extracted RNA was mixed with 1 µL of 10x sample buffer, oligo dT primer, and dNTP mix. Samples were incubated at 72°C for 3 minutes and immediately placed on ice for 2 minutes cooling. First strand cDNA synthesis was then performed by adding FS buffer V2, DTT, RNase inhibitor, oligo, and transcriptase to the previous 10 µL mixture. Samples were incubated at 42°C for 90 minutes, followed by 70°C for 15 minutes. Full-length cDNA was subsequently amplified for 15 cycles by adding Discover-sc PCR mix and primer. The products were purified using 1x VAHTS DNA Clean Beads (Vazyme, N411), and the yield of DNA was quantified using Qubit. For DNA fragmentation and adaptor ligation, the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) was used. 50 ng of amplified cDNA were mixed with 5x TTBL, TTE Mix V50, and ddH2O by pipetting 20 times, followed by incubation at 55C for 10 minutes for fragmentation. The products were purified using 2x VAHTS DNA Clean Beads, and the eluted samples were amplified for total 9 cycles using a different combination of i7 and i5 index primers (TruePrep Index Kit V2 for Illumina, Vazyme, TD202). Size selection of the PCR product was performed using 0.55x VAHTS DNA Clean Beads. Finally, 20 ng of each sample were pooled for subsequent second-generation sequencing on the Illumina NovaSeq X, with a read length of 50 bp for paired end.

treatment_protocol: Lymph nodes from 16 NOD.Foxp3-GFP mice were collected, enriched for CD4+ T cells, split into 3 equal parts, and FACS purified for Foxp3.GFP+CD25+ expressing Tregs on 3 separate sorting machines. These samples were activated separately and treated as experimental replicates. Each of the experimental replicates further split into 3 parts on day 2 after activation and transduced with either CD25t tether construct (1G12t or 3A10t) or EV as a control construct. On day 4, 2 days after transduction, cells were washed to remove exogenous IL-2 and cultured for 5 additional days. Half of the EV transduced culture was left in IL-2-containing medium as a positive control. The transduced cells were FACS purified based on the expression of the Thy1.1 at day 9.

value: lymph node

value: Treg

value: Rest


title: 6418 VDJ

description:
Library name: 6418 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_6418.csv
clonotypes_6418.csv

value: VDJ

value: lymphocytes


title: Veh 1

description: Library name: sample 1


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

description: Library name: 90

value: iBMDMs

value: clearcoli


title: 3A10t Treg, rep2

description: Library name: 3A10t-2


title: 6418 Feature Barcode

description:
Library name: 6418 FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6418.tsv.gz
features_6418.tsv.gz
matrix_6418.mtx.gz

value: Pancreatic lymph node

value: Feature Barcode


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

description: Library name: 89

value: macrophage

value: untreated

value: same batch for all


title: BT549-mimicNC

city: Daejeon

first: Sugi

last: Lee

address: 125, Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea

country: South Korea

institute: KRIBB

description:
Library name: BT549-mimicNC
Reads were aligned to the human reference genome GRCh38

data_processing:
Sequence reads were assessed for quality using FastQC (v0.11.4)
Sequence reads were trimmed for adapter sequences and low-quality bases using cutadapt (v1.8.3)
Trimmed sequence reads were aligned to the appropriate reference genome (GRCh38) using HISAT2 (v2.1.0)
Transcript assembly and expression quantification were performed using StringTie(v2.2.1) with the reference annotation.
Assembly: GRCh38(Genome Reference Consortium Human Build 38)
Supplementary files format and content: tab-delimited text file includes TPM for each Sample

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74106) according to the manufacturer's instructions.
RNA libraries for RNA-Seq were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer's protocols.

value: Breast Cancer


title: 3A10t Treg, rep1

description: Library name: 3A10t-1


title: 6418 Gene Expression

description:
Library name: 6418 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6418.tsv.gz
features_6418.tsv.gz
matrix_6418.mtx.gz

value: Gene Expression


title: BT549-miR1290

description:
Library name: BT549-miR1290
Reads were aligned to the human reference genome GRCh38


title: Myd88-/-Trif-/-Cgas-/- iBMDMs, 4hr time point, CV-Cglr3+, biological replicate 3

description: Library name: 88


title: 6414 VDJ

description:
Library name: 6414 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_6414.csv
clonotypes_6414.csv


title: 1G12t Treg, rep3

description: Library name: 1G12t-3


title: WT_185

city: Baltimore

first: Jin-Young

last: Koh

state: MD

address: 670 W Baltimore Street

department: Otorhinolaryngology-Head & Neck Surgery

institute: University of Maryland, Baltimore

description: Library name: Sample 12

data_processing:
Nanopore sequencing reads were demultiplexed and aligned to the mm10 genome (GRCm38) by Mandalorion (commit c2b369e plus local modification) using BLAT version 35 and GMAP version 2018-07-04.  Mandalorion then quality filtered the aligned reads and used the filtered alignments to define and quantify isoforms.
Assembly: mm10
Supplementary files format and content: PSL file produced by Mandalorion for each sample

source_name: cochlear lateral wall

extract_protocol:
After euthanasia by CO2, the temporal bones were removed and placed into DPBS. The temporal bone was removed and opened under a dissecting microscope to access the cochlear membranous labyrinth. Once the cochlea was accessible, the stria vascularis tissue was extracted from the temporal bone and incubated for 5min at 37°C with collagenase from clostridium histolyticum solution at a working concentration of 0.3mg/500µl. The cell dissociation was completed by gently pipetting up and down. The disrupted stria vascularis tissues were placed under an inverted microscope equipped with 20x and 40x objectives and two 3D micromanipulators, each driving a pulled-glass micropipette attached to a nitrogen gas-powered Pico-Injector to control aspiration pressure. The dissociated cells were examined under the inverted microscope and were aspirated into the first pulled-glass micropipette in a slow and controlled manner then washed in fresh DPBS to remove residual collagenase solution and debris.
Nextera XT DNA sample preparation kits, including Tn5 enzymes for tagmentation, were used together with Nextera XT index kits for multiplexing.

value: cochlear lateral wall

value: root cell

tag: strain

tag: age


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

description: Library name: 87

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

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: dacA+


title: 1G12t Treg, rep2

description: Library name: 1G12t-2

value: lymph node


title: 6414 Feature Barcode

description:
Library name: 6414 FB
FB (feature barcode), read 1 file contains cell barcode and UMI, read 2 file contains feature barcode derived reads
barcodes_6414.tsv.gz
features_6414.tsv.gz
matrix_6414.mtx.gz


title: WT_198

description: Library name: Sample 11

value: spindle cell


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

description: Library name: 86


title: 1G12t Treg, rep1

description: Library name: 1G12t-1

value: Treg

value: Rest


title: 6414 Gene Expression

description:
Library name: 6414 GEX
GEX (5' RNA), read 1 file contains cell barcode and UMI, read 2 file contains transcript
barcodes_6414.tsv.gz
features_6414.tsv.gz
matrix_6414.mtx.gz

value: lymphocytes


title: WT_173

description: Library name: Sample 10


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

description: Library name: 85

value: iBMDMs


title: EV Treg with IL2, rep3

description: Library name: EM-3

value: Rest with IL-2


title: WT_172

description: Library name: Sample 9


title: WA09_invivo_undiff_DAPI-

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

description: Library name: Sample_WA09_undiff_1

data_processing:
Alignment and gene counting were accomplished using STARsolo with the following flags: “--twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --soloType CB_UMI_Simple --soloCBwhitelist 3M-february-2018.txt --soloUMIlen 12 --soloUMIfiltering MultiGeneUMI --soloCBmatchWLtype 1MM_multi_pseudocounts --limitSjdbInsertNsj 2000000”. Samples produced using 10X Genomics scRNA 2.0 chemistry were aligned using the following STARsolo flags: “--twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --soloType CB_UMI_Simple --soloCBwhitelist 737K-august-2016.txt --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 10 --soloBarcodeReadLength 0 --soloUMIfiltering MultiGeneUMI --soloCBmatchWLtype 1MM_multi_pseudocounts --limitSjdbInsertNsj 2000000.”
Assembly: A custom chimeric reference comprised of concatenating GRCh38 ensembl 106 to GRCm39 ensembl 106 and filtering for transcript types: “protein_coding”, “lncRNA”, or “miRNA”.
Supplementary files format and content: Contains two 10X sparse matrixes with gene counts per cell. One for the mouse fraction and one for the human fraction. The mouse fraction of invivo cultures consist of the small subset of genes with homology great enough that the chimeric aligner cannot distinguish them.

extract_protocol:
For invitro samples unsorted PSC and GPC stage cells were incubated in Accutase (Millipore Sigma Cat. A6964) diluted 50% in DPBS for 6 minutes at 37 degrees. Cells were resuspended in DMEM and filtered for FACS. . Cells were selected based on forward and side scatter in addition to negative gating of 4′,6-diamidino-2-phenylindole (DAPI, Thermo Fisher Scientific, D1306) staining to remove dead cells and debri (1 µg ml−1). Cells were then captured for scRNA-seq on a 10X Genomics chromium controller. For Invivo samples the mouse brains were removed and immersed in ice-cold HBSS and their corpora callosa dissected and chopped into small pieces. This tissue was then incubated in a papain/DNase dissociation solution at 37 °C for 50 min. Papain was inactivated with the addition of ovomucoid dissolved in EBSS. A single-cell suspension was then achieved via repeated pipetting. Cells were pelleted, resuspended into MEM, and filtered for FACS. Cells were selected based on forward and side scatter in addition to negative gating of 4′,6-diamidino-2-phenylindole (DAPI, Thermo Fisher Scientific, D1306) staining to remove dead cells and debri (1 µg ml−1). Cells were then captured for scRNA-seq on a 10X Genomics chromium controller.
Libraries were constructed according to manufacturers instructions for either single cell 3' v2 or single cell 3' v3.1 from 10X genomics as noted in the metadata table.

tag: Stage

value: In Vitro - Pluripotent Stem Cell Stage

tag: sort

value: DAPI-

tag: 10x chemistry


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, CV-Cglr3+, biological replicate 3

description: Library name: 84

value: macrophage


title: EV Treg with IL2, rep2

description: Library name: EM-2


title: WT, 5, low

description: Library name: HSA-000050048

value: brain

value: male

value: microglia

value: WT

value: low


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

description: Library name: 91

value: same batch for all


title: WA09_invitro_GPC_DAPI-_2

description: Library name: Sample_Unsorted_WA09_5

value: In Vitro - GPC Stage


title: WT_169

description: Library name: Sample 8

value: cochlear lateral wall


title: Myd88-/-Trif-/- iBMDMs, 4hr time point, dacA+, biological replicate 3

description: Library name: 83

value: dacA+


title: EV Treg with IL2, rep1

description: Library name: EM-1

value: lymph node

value: Treg


title: WA09_invitro_GPC_CD140+_2

description: Library name: Sample_CD140_WA09_5


title: WT_161

description: Library name: Sample 7

value: spindle cell


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

description: Library name: 82

value: iBMDMs

value: clearcoli


title: Input_3

description: Library name: Input_3

value: mouse esophagus

value: Mouse esophageal epithelial cells

value: Wild Type

value: Input


title: WT iBMDMs, 4hr time point, S. aureus, biological replicate 1_exp2

description: Library name: 130

value: macrophage

value: S. aureus


title: GrnKO, 4, low

description: Library name: HSA-000050046

value: brain

value: female

value: microglia

value: GrnKO


title: EV Treg, rep3

description: Library name: E-3

value: Rest


title: WT_215

description: Library name: Sample 6

value: cochlear lateral wall


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

description: Library name: 81

value: untreated

value: same batch for all


title: GrnKO, 4, high

description: Library name: HSA-000050045

value: high


title: C27_invitro_undiff_1

description: Library name: Sample_C27_undiff_1

value: In Vitro - Pluripotent Stem Cell Stage

value: DAPI-


title: C27_invitro_GPC_DAPI-

description: Library name: Sample_C27_DAPI_3

value: In Vitro - GPC Stage


title: EV Treg, rep2

description: Library name: E-2

value: lymph node

value: Treg


title: WT_209

description: Library name: Sample 5

value: pendrin cell


title: EV Treg, rep1

description: Library name: E-1


title: GrnKO; Mitf_Tfe3_Tfeb; 12

description: Library name: HSA-000050034

tag: treatment duration

value: 10 days

value: BMDMs


title: Sting-/- iBMDMs, 4hr time point, dacA+, biological replicate 3

description: Library name: 75

value: iBMDMs

value: macrophage

value: Sting-/-

value: dacA+


title: Sting-/- iBMDMs, 4hr time point, CV-Cglr3+, biological replicate 3

description: Library name: 76


title: WT_143

description: Library name: Sample 4

value: root cell


title: PBMC, replicate 2, scRNAseq

city: Singapore

first: Zexi

last: Guo

address: 90 Tanglin Halt Road

country: Singapore

institute: National Cancer Centre Singapore

description: 10x Genomics

data_processing:
the demultuplexing, barcoded processing, gene counting and aggregation were made using the CellRanger v7.0.1
Assembly: GRCh38
Supplementary files format and content: Tab-separated values, matrix files, Hierarchical Data Formats

source_name: PBMC

extract_protocol:
After isolation of PBMCs and dissociation of tumor into single cells, cells were were cryopreserved in freezing media until day of single cell run. Cells were quickly thawed in a 37C water bath and freezing media was diluted with cold media with no additives before being spun at 300g for 5 min. Cell pellet was washed at least once with MACS buffer before a cell count was performed for single cell isolation.
Library was performed according to the manufacturer's protocol (single cell 3' v2 protocol, 10x Genomics). Briefly, cellsfrom each sample were resuspended in the mastermix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in EMULSION. The poly-A RNA from the cell lysate contained in each GEM was retrotranscripted to cDNA. The pooled barcoded cDNA was cleaned up and amplified for library preparation and the final libraries were sent for sequencing.

value: PBMCs

value: PBMC


title: Pool_C_CMO

description: 10X Genomics cell multiplexing oligo

data_processing:
Raw sequencing data was processed with cellranger multi (10X Genomics) version 7.1.0 with default arguments, aligning reads to the refdata-gex-mm10-2020-A reference provided by 10X Genomics. Cells from the different animals were demultiplexed by providing the CMO identifiers and sequences. (Please consult the feature_config.csv supplementary file included in this submission.)
Assembly: GRcm38
Supplementary files format and content: Tar archives of filtered counts (matrix.mtx.gz), barcodes.tsv.gz and features.tsv.gz for each biological sample (e.g. after demultiplexing).
Supplementary files format and content: The feature_config.csv file contains CMO sequences used for (de)multiplexing samples, as well as metadata for each animal included in each pool.

growth_protocol: Two-year-old mice were anesthetized, transcardially perfused with PBS, and brains were removed for scRNA-seq.

extract_protocol:
Equal numbers of cells from all samples were pelleted and labeled using CellPlex CMO tags (10x Genomics) for multiplexing, following manufacturer protocols. Finally, cells were sorted and CD11b + /CD45 + /CD44 - /CD163 - /Ly6G - cells were collected by FACS, pelleted and counted. Single cell suspensions were labeled with CellPlex CMO per 10X Genomics protocol (CG000391 Rev A.) After each sample was labeled with CMO tags, we prepared two replicate pools of cells, each including cells from all animals (pools A and C). Equal numbers of cells per sample were combined into each pool, and each pool was captured in one channel of the Chromium instrument.
After cell capture, RT and cDNA amplification were performed according to the 10X Genomics protocol (CG000388 Rev B). Afterwards, each sample pool was separated into one gene expression (GEX) library and one sample tag (CMO) library via dual-sided SPRI bead purification. Library preparation was performed per manufacturer’s protocol (CG000388 Rev B). Libraries from the 2 GEMS were pooled in equimolar amounts and sequenced on two lanes of an Illumina NovaSeq X 10B (28X10X10X90).

treatment_protocol: Hemibrains were separated and one half was diced into a fine slurry and dissociated using the Miltenyi Adult Brain Dissociation Kit (Miltenyi Biotec, Cat# 130-107- 677) in the presence of transcription and translation inhibitors 5mg/ml actinomycin D (Cell Signaling Technology; Cat# 15021) and 0.56mg/ml anisomycin (Selleck Chemical; Cat# S7409). After dissociation and debris removal, cells were stained on ice for 30 minutes, protected from light. The following primary antibodies were used: anti-CD11b BV421 (BD; Cat# 562605; 1:100), anti-CD45 APC (Biolegend; Cat# 157606; 1:100), anti-CD44 PE-Cy7 (Sigma-Aldrich; MABF426; 1:100), anti-CD163 PE-Cy7 (BioLegend; Cat# 155320; 1:100), and anti-Ly6G PE-Cy7 (BioLegend; Cat# 127618; 1:100). Total live cell counts were measured using CountBright Plus Absolute Counting Beads (Invitrogen; Cat# C36995) by flow using a FACS Aria III (BD).

value: brain

value: mixed sample (WT, Grn KO)

value: 2 years

tag: library type

value: CMO


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

description: Library name: 74

value: clearcoli

value: same batch for all


title: Pool_C_GEX

description: 10X Genomics gene expression

value: mRNA


title: WT_028

description: Library name: Sample 2

value: cochlear lateral wall


title: PBMC, replicate 1, scRNAseq

description: 10x Genomics


title: WT_075

description: Library name: Sample 3


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

description: Library name: 73

value: untreated


title: Pool_A_CMO

description: 10X Genomics cell multiplexing oligo


title: LN, replicate 1, scRNAseq

description: 10x Genomics

source_name: Lymph node

value: diseased lymph node cells

value: Lymph node


title: Cgas-/- iBMDMs, 4hr time point, CV-Cglr3+, biological replicate 3

description: Library name: 72

source_name: iBMDMs

value: iBMDMs

value: macrophage

value: Cgas-/-


title: Pool_A_GEX

description: 10X Genomics gene expression