title: MED4 P-SSP7 Infected High Light 0.5h Replicate 2

description:
Library name: Inf-hl-05h-2
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 0.5h Replicate 2

value: prokaryotic cell

value: WT

value: High Light


title: ATAC-seq_P_4

status: Public on Jun 17 2026

type: SRA

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: genomic

data_processing:
FASTQ files were output using standard Illumina protocols and software.
FASTQ files  from technical replicates are first concatenated
ATAC-seq reads were aligned to the human genome assembly (hg38) using Bowti2 v2.2.5
For each sample, mitochondrial reads are removed from the aligned bam using the removeChrom python script developed by Harvard Informatics (https://github.com/harvardinformatics/ATAC-seq), and only properly paired reads were used for downstream analysis
PCR duplicates were then removed using Picard MarkDuplicates
Peak calling was then carried out using MCAS2  and ATAC-seq reads overlapping the peaks were summarized using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files; columns represent genomic location and the number of reads mapping to the peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol: As previously described   Corces et al.  2017(OMNI ATAC-seq protocol)

tag: tissue

value: Peripheral blood

tag: progressed to t1d

value: Progressors

tag: Sex

value: M

tag: age

tag: cell type

value: CD4+ T lymphocyte cells


title: ATAC-seq_P_3


title: MED4 P-SSP7 Infected Dark 4h Replicate 1

city: Richland

first: Lindsey

last: Anderson

state: WA

address: 902 Battelle Boulevard

country: USA

institute: Pacific Northwest National Laboratory

description:
Library name: Inf-dk-4h-1
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 4h Replicate 1

library_source: transcriptomic

data_processing:
Read trimming / QC (TrimGalore v0.6.10; CutAdapt v5.0)
Read mapping & quantification (Rsubread v2.20)
Assembly: GCF_000011465.1 (26-JAN-2024), GCF_000858745.1 (11-JAN-2023)
Supplementary files format and content: rna_seq_counts.csv, comma-separated values table with raw RNA-seq counts

molecule: total RNA

source_name: prokaryotic cell

growth_protocol: MED4 cells grown on Pro99 substituting Salish Seawater for Sargasso Seawater. For optimal growth, the medium was supplemented with 2× Pro99 nitrogen and phosphorus while maintaining 1× trace metals. Cultures were maintained at 21°C and 45 µmol photons m⁻² s⁻¹ (standard light conditions) in a 12 h light: 12 h dark photocycle.

extract_protocol:
RNA was extracted from exponentially growing cells using the Qiagen RNeasy Plus Mini Kit according to the manufacturer’s instructions. Samples underwent DNase treatment and rRNA depletion
Paired-end sequencing (2 × 150 bp) with single-indexing on an Illumina NovaSeq X

treatment_protocol: P-SSP7 infection experiments were conducted under three light regimes: standard light (45 µmol photons m⁻² s⁻¹), high light (200-250 µmol photons m⁻² s⁻¹), and darkness. MED4 cultures were infected with P-SSP7 (MOI = 10).  Samples were collected in biological triplicate. Sampling was performed at eight time points (0, 0.5, 1, 2, 4, 8, and 24 h post-infection), with additional time points at 26 and 32 h for the dark treatment to capture transcriptional responses upon return to standard light. For standard and high-light conditions, an uninfected control was processed in parallel with the infection experiment.

tag: genotype

tag: agent

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7

tag: light regime

value: Dark

tag: time point


title: RNA-seq hippocampus, SAL-LPS, female, replicate 4-4

city: la jolla

first: Yanmiao

last: Du

state: CA

address: 4254 Urey Hall, 9500 Gilman Drive

department: Department of Chemistry and Biochemistry/Cellular and Molecular Medicine

institute: UCSD

description: Library name: RNA_Hippo_SAL-LPS_F_4-4

data_processing:
Sequencing reads were trimmed for adapters and quality using Trim Galore (v0.6.7, --paired).
Trimmed reads were aligned to the Mus musculus mm10 reference genome using STAR (v2.7.10a) with --quantMode GeneCounts.
Gene-level counts were validated with HTSeq-count (v0.12.4) using GENCODE vM25 annotation. Genes with total counts <= 10 across all samples were excluded prior to analysis.
Differential expression was performed with DESeq2 (v1.40.2) using median-of-ratios normalization and Wald tests; pairwise contrasts: MOR-SAL vs SAL-SAL and MOR-LPS vs SAL-LPS per brain region. Significance: FDR < 0.05 (Benjamini-Hochberg).
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts per gene for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: hippocampus

growth_protocol: Male and female C57BL/6NTac mice (Taconic, Hudson, NY) were bred at the University of Pennsylvania and group-housed (3-5/cage) under a 12-h light/dark cycle (lights on at 0700) with ad libitum access to food and water. All procedures were approved by the University of Pennsylvania Animal Care and Use Committee.

extract_protocol:
Brain tissues (PFC, hippocampus, hypothalamus, striatum) were collected by bilateral punch (2.0 mm) and flash-frozen at -80C. Nuclei were isolated in cold extraction buffer using a Dounce tissue grinder, filtered (40 um), and enriched by iodixanol gradient centrifugation. NeuN+ neuronal nuclei were labeled with anti-NeuN Alexa Fluor 488 (MAB377X, EMD Millipore) at 4C for 1 h, then sorted by FACS (BD Biosciences). Nuclear RNA was extracted from ~5,000 NeuN+ nuclei per sample using RNeasy Mini Kit (74104, Qiagen) with on-column DNase digestion (RNase-Free DNase Set 79254, Qiagen).
RNA-seq libraries were prepared from ~5,000 NeuN+ sorted nuclei using a modified Smart-seq3 protocol with tagmentation-based library construction. Reverse transcription was performed on nuclear RNA, followed by tagmentation with custom P5/P7-adapter-loaded Tn5 transposase (Diagenode) and PCR amplification with KAPA HiFi ReadyMix and barcoded primers. Libraries were size-checked on a TapeStation (G2992AA, Agilent) using the High Sensitivity DNA Analysis Kit (5067-4626), primer-dimers removed with SPRIselect beads, quantified with KAPA Library Quantification Kit (4824, Roche), pooled, and sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 bp, ~15 million reads per library).

treatment_protocol: Perinatal morphine exposure: 8-12-week-old female mice were implanted with osmotic minipumps (Alzet model 1004) delivering morphine sulfate (10 mg/kg/day, NIDA Drug Supply) or saline, then co-housed with drug-naive males. Pups were transferred to drug-naive surrogates within 4-8 hours of birth. Postnatal morphine (10 mg/kg SC, 10 mL/kg) or saline was administered twice daily (09:00 and 17:00) from PND1 through the morning of PND14, after which mice underwent spontaneous opioid withdrawal. In adulthood, mice were assigned to four groups: SAL-SAL (saline/saline), SAL-LPS (saline/LPS challenge), MOR-SAL (morphine/saline), or MOR-LPS (morphine/LPS challenge). Brain tissues were collected 2 hours after adult LPS or saline injection.

value: hippocampus

value: wild type

tag: treatment

value: SAL-LPS


title: RNA-seq hippocampus, SAL-LPS, female, replicate 4-0

description: Library name: RNA_Hippo_SAL-LPS_F_4-0


title: ATAC-seq_NP_3

value: Non-progressors

value: F


title: RNA_COAH_T3_NKcell

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the human genome by Rsubread version 1.32.2
Fragment (read-pair) counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function
Genes were identified using Gencode annotation v35
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Ensembl Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

extract_protocol:
RNA was isolated using the miRNeasy Micro Kit (QIAGEN, cat. no. 217084) following manufacturer's protocol
Libraries were made following manufactur's protocol for Illumina's TruSeq Total Stranded RNA kitwith Ribo-zero Gold

value: peripheral blood

tag: donor

value: COAH

value: No

tag: data set

value: B

tag: sequencing batch data set a

tag: sequencing batch data set b

value: NK lymphocyte cells


title: MED4 P-SSP7 Infected Dark 2h Replicate 3

description:
Library name: Inf-dk-2h-3
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 2h Replicate 3

organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

value: prokaryotic cell

value: WT


title: RNA-seq hippocampus, SAL-LPS, female, replicate 3-1

description: Library name: RNA_Hippo_SAL-LPS_F_3-1


title: RNA-seq hippocampus, SAL-SAL, male, replicate 3-0

description: Library name: RNA_Hippo_SAL-SAL_M_3-0

value: SAL-SAL


title: ATAC-seq_NP_2

value: Peripheral blood

value: M


title: MED4 P-SSP7 Infected Dark 2h Replicate 2

description:
Library name: Inf-dk-2h-2
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 2h Replicate 2

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7


title: ATAC-seq_P_1

value: Progressors

value: CD4+ T lymphocyte cells


title: ATAC-seq_P_2


title: RNA-seq hippocampus, SAL-LPS, female, replicate 2-2

description: Library name: RNA_Hippo_SAL-LPS_F_2-2

value: hippocampus

value: wild type


title: RNA_COAH_T1_nCD8

value: CD8+ T lymphocyte cells


title: MED4 P-SSP7 Infected Dark 2h Replicate 1

description:
Library name: Inf-dk-2h-1
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 2h Replicate 1

value: Dark


title: Genewiz seq, vtRNA1-3 knockout, bio rep 2

city: Boulder

first: Wayne

last: Hemphill

state: Colorado

address: 3415 Colorado Ave

department: Biochemistry

institute: University of Colorado Boulder

description:
Library name: Genewiz_KO3s2
molecule is rRNA-depleted RNA

library_source: other

data_processing:
Processed with custom R scripts uploaded to github.com/whemphil/vtRNA_Manuscript
index building was performed with the “BSgenome.Hsapiens.UCSC.hg38” package
FASTQ quality filtering with the “Rfastp” package
alignment and feature counting with the “Rsubread” package “subjunc” and “featureCounts” functions and Ensembl release 115 GRCh38 GTF file
differential expression analysis with the “DESeq2” package
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files giving the counts per million (CPM) of each transcript for each sample

molecule: other

growth_protocol: HEK293T (ATCC #CRL-11268, Lot #63696280) cells were incubated at 37°C, 5% CO2, and ≥80% humidity in DMEM (Gibco) with 10% v/v FBS, 1X GlutaMAX (Gibco), and 1% w/v penicillin/streptomycin.

extract_protocol:
Cells were cultured in T25 flasks (Corning #430639) until ~80% confluency, then washed with PBS, lysed in 1 mL TRIzol (Invitrogen), and their RNA purified (with DNase treatment) via the Direct-zol RNA Miniprep Plus kit (Zymo Research #R2070) according to manufacturer guidelines.
Libraries were prepared by Genewiz with rRNA depletion or by Plasmidsaurus with poly-A enrichment

tag: cell line

value: vtRNA1-3 knockout


title: RNA-seq hippocampus, SAL-LPS, female, replicate 2-0

description: Library name: RNA_Hippo_SAL-LPS_F_2-0

value: SAL-LPS


title: ATAC-seq_NP_1

value: Non-progressors

value: F


title: RNA-seq hippocampus, SAL-SAL, male, replicate 11-1

description: Library name: RNA_Hippo_SAL-SAL_M_11-1


title: RNA-seq hippocampus, SAL-LPS, female, replicate 10-4

description: Library name: RNA_Hippo_SAL-LPS_F_10-4


title: Genewiz seq, vtRNA1-3 knockout, bio rep 1

description:
Library name: Genewiz_KO3s1
molecule is rRNA-depleted RNA


title: MED4 P-SSP7 Infected Dark 1h Replicate 3

description:
Library name: Inf-dk-1h-3
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 1h Replicate 3


title: Genewiz seq, vtRNA1-2 knockout, bio rep 3

description:
Library name: Genewiz_KO2s3
molecule is rRNA-depleted RNA

value: vtRNA1-2 knockout


title: Genewiz seq, vtRNA1-2 knockout, bio rep 2

description:
Library name: Genewiz_KO2s2
molecule is rRNA-depleted RNA


title: Genewiz seq, vtRNA1-3 knockout, bio rep 3

description:
Library name: Genewiz_KO3s3
molecule is rRNA-depleted RNA


title: Genewiz seq, vtRNA1-2 knockout, bio rep 1

description:
Library name: Genewiz_KO2s1
molecule is rRNA-depleted RNA


title: MED4 P-SSP7 Infected Dark 1h Replicate 2

description:
Library name: Inf-dk-1h-2
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 1h Replicate 2

value: prokaryotic cell


title: RNA-seq hippocampus, SAL-LPS, female, replicate 10-0

description: Library name: RNA_Hippo_SAL-LPS_F_10-0


title: MED4 P-SSP7 Infected Dark 0.5h Replicate 3

description:
Library name: Inf-dk-05h-3
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 0.5h Replicate 3

value: WT


title: Genewiz seq, vtRNA1-1 knockout, bio rep 3

description:
Library name: Genewiz_KO1s3
molecule is rRNA-depleted RNA

value: vtRNA1-1 knockout


title: strep_WT_minus-glucose_1h_rep3

status: Public on Jun 18 2026

city: Chicago

first: Hoang Anh

middle: V

last: Tran

state: IL

address: 5801 S Ellis Ave

institute: University of Chicago

description: Library name: Sample S3

data_processing:
[Sample T1-T16] The methods of the previously published pipeline (PMID 30559359) were used with some modifications. Raw paired-end sequence reads of 75 or 100 nucleotides were processed by Illumina-utils (PMID 23799126). Inserts contained a 7 nucleotide sample barcode and a random 6 nucleotide unique molecular identifier (UMI). Given that tRNA molecules range in length from 74-96 nucleotides, forward and reverse 100 nucleotide reads fully covered some tRNA sequences and partially overlapped for others. We upgraded the Illumina-utils ‘iu-merge-pairs’ command to merge both fully and partially overlapping reads, while trimming overhanging adapter sequences in the case of more than full overlap (the command line flag, ‘--marker-gene-stringent’, enables consideration of full as well as partial overlap). We minimized erroneous base calls, important for our analysis of modification-induced mutations, by retaining reads that matched with zero mismatches in the overlapping region (option ‘--max-num-mismatches 0’)
[Sample T1-T16] The procedure for de novo profiling of full-length and fragmentary tRNA reads introduced in tRNA-seq-tools (PMID 30559359) was modified as follows. tRNA structural features were identified from the 3’ end of the read. The minimum criteria for tRNA identification were the correct distance to the 7 canonically conserved nucleotides in the T arm, of which 5 must be found, and base pairing in of the T stem. A full-length read must contain a base-paired acceptor stem and all features in between.
[Sample S1-S24] Raw sequences reads were demultiplexed using Je to detect encoded barcode reads. Following this, reads were aligned to a curated Streptococcus mutans tRNA, rRNA and reference genome.
[Sample S1-S24] The aligned reads were then used to determine RNA sequence abundance using custom python script. RNA modifications were detected based on aligned reads using samtools sort (http://www.htslib.org/, Li et al., 2009) feature sort the reads in a bam file format. Then IGVtools count (https://software.broadinstitute.org/software/igv/igvtools) count feature was utilized to output a wig files using the following parameters: -z 5 -w 1 -e 250 —bases. The resulting wig files were processed using a custom python script to identify nucleotide mutations as well as coverage of aligned reads.
Assembly: [Sample T1-T16] tRNA sequences were taxonomically annotated by using the Global Alignment for Sequence Taxonomy (GAST) tool (PMID 19023400) to search a set of reference tRNA sequences that tRNAscan-SE (v1.3.1) (PMID 9023104) identified from 4,235 gold-standard bacterial genomes (non-endosymbiont genomes with an assembly level of “chromosome”) stored in the Ensembl Genomes 2016 database (PMID 26553803).
Assembly: [Sample S1-S24] ASM746v2
Supplementary files format and content: [Sample T1-T16] .tsv files with family taxonomy and tRNA anticodon counts per sample
Supplementary files format and content: [Sample S1-S24] .tsv files with gene name and abundance per sample
Supplementary files format and content: [Sample S1-S24] .sam.tsv files with mutation, deletion, coverage for each gene position per sample

organism: Streptococcus mutans

source_name: bacterial cells

growth_protocol: [Sample S1-S24] S. mutans strains were cultured in Brain Heart Infusion Broth without Dextrose (BHI-D; Alpha Biosciences) at 37°C.

extract_protocol:
[Sample T1-T16] The tongue dorsum scrapings were combined with RNAlater Stabilization solution (Invitrogen) and stored at −80°C. For extraction, RNAlater was first removed by centrifugation. Pelleted material was lysed in 0.3M NaOAc/HOAc,10mM EDTA, pH 4.8 with an equal volume of acetate-saturated phenol:chloroform pH 4.5 (Invitrogen). After addition of 1.0 mm glass lysing beads (Bio-Spec Products) in a 1:1 ratio (bead:sample weight), samples were placed in a reciprocating bead beater (Mini-Beadbeater-16, Bio-Spec Products) for two 1-min intervals on maximum intensity. Samples were centrifuged before re-extraction and isopropanol precipitation of total RNA. Pellets were washed with 75% ethanol before resuspension in an acid-buffered elution buffer (10mM NaOAc, 1mM EDTA, pH 4.8). 1 ug of total RNA was used for the construction of sequencing libraries. RNA quality and quantity were assessed using the Agilent bio-analyzer.
[Sample S1-S24] RNA was isolated using the Quick-RNA Fungal/Bacterial Microprep Kit (Zymo) and treated with DNAse I according to the DNAfree kit (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries. RNA quality and quantity were assessed using the Agilent bio-analyzer.
MSR-seq (PMID 35513407)
[Sample T1-T16] Standard MSR-seq protocol was used with additional chemical treatment. Specifically, after the first ligation and streptavidin bead binding of all CHO, samples were split in two: one mock-treated, and the other subjected to AlkB demethylase reaction (PMID 35513407).

treatment_protocol: [Sample S1-S24] A starter culture for each strain was thawed, resuspended in BHI-D, and used to inoculate BHI-D or BHI-D + 0.15% glucose before incubation. Cells were harvested by centrifugation at 1 h and at early stationary phase (3 h for BHI-D, or 6.5 h for BHI-D + 0.15% glucose).

value: bacterial cells

value: minus-glucose, 1h


title: Genewiz seq, vtRNA1-1 knockout, bio rep 2

description:
Library name: Genewiz_KO1s2
molecule is rRNA-depleted RNA


title: Genewiz seq, vtRNA1-1 knockout, bio rep 1

description:
Library name: Genewiz_KO1s1
molecule is rRNA-depleted RNA


title: RNA-seq hippocampus, MOR-SAL, male, replicate 6-1

description: Library name: RNA_Hippo_MOR-SAL_M_6-1

value: MOR-SAL


title: RNA-seq hippocampus, MOR-SAL, male, replicate 8-0

description: Library name: RNA_Hippo_MOR-SAL_M_8-0


title: MED4 P-SSP7 Infected Dark 1h Replicate 1

description:
Library name: Inf-dk-1h-1
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 1h Replicate 1

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7


title: Genewiz seq, wild-type, bio rep 3

description:
Library name: Genewiz_WTs3
molecule is rRNA-depleted RNA

value: wild-type


title: MED4 P-SSP7 Infected Dark 0.5h Replicate 2

description:
Library name: Inf-dk-05h-2
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 0.5h Replicate 2


title: Genewiz seq, wild-type, bio rep 2

description:
Library name: Genewiz_WTs2
molecule is rRNA-depleted RNA


title: Genewiz seq, wild-type, bio rep 1

description:
Library name: Genewiz_WTs1
molecule is rRNA-depleted RNA


title: MED4 P-SSP7 Infected Dark 0.5h Replicate 1

description:
Library name: Inf-dk-05h-1
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 0.5h Replicate 1


title: Plasmidsaurus seq, control deletion, bio rep 3

description: Library name: Plasmidsaurus_CTRLs3

value: vtRNA1 control deletions


title: RNA-seq hippocampus, MOR-SAL, male, replicate 17-4

description: Library name: RNA_Hippo_MOR-SAL_M_17-4

value: hippocampus

value: wild type


title: Plasmidsaurus seq, control deletion, bio rep 2

description: Library name: Plasmidsaurus_CTRLs2


title: RNA-seq hippocampus, MOR-SAL, male, replicate 17-2

description: Library name: RNA_Hippo_MOR-SAL_M_17-2


title: MED4 P-SSP7 Infected Dark 0h Replicate 3

description:
Library name: Inf-dk-0h-3
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 0h Replicate 3

value: Dark


title: Plasmidsaurus seq, control deletion, bio rep 1

description: Library name: Plasmidsaurus_CTRLs1


title: RNA-seq hippocampus, MOR-SAL, male, replicate 13-3

description: Library name: RNA_Hippo_MOR-SAL_M_13-3


title: Plasmidsaurus seq, vtRNA1 triple-knockout, clone 3, bio rep 3

description: Library name: Plasmidsaurus_KO4c3s3

value: vtRNA1 triple-knockout


title: MED4 P-SSP7 Infected Dark 0h Replicate 2

description:
Library name: Inf-dk-0h-2
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 0h Replicate 2


title: RNA-seq hippocampus, MOR-SAL, male, replicate 13-1

description: Library name: RNA_Hippo_MOR-SAL_M_13-1


title: S5_ChP_Ctrl

city: Boston

first: Maria

last: Lehtinen

state: MA

address: 300 Longwood Ave, Mailcode Bch3400

institute: Boston Children's Hospital

description: Library name: S5

data_processing:
Novogene aligned with STAR2
Reads were quantified with featurecounts 2.0.8
Assembly: GRCh39
Supplementary files format and content: tab delimited text file with each sample as a column

source_name: Choroid Plexus

extract_protocol:
Qiagen RNAEasy miniprep
, total RNA extracted from ChP tissue was submitted to Novogene for library preparation with poly A selection and mRNA directional sequencing

value: Choroid Plexus


title: Plasmidsaurus seq, vtRNA1 triple-knockout, clone 2, bio rep 3

description: Library name: Plasmidsaurus_KO4c2s3


title: Plasmidsaurus seq, vtRNA1 triple-knockout, clone 3, bio rep 2

description: Library name: Plasmidsaurus_KO4c3s2


title: MED4 P-SSP7 Infected Dark 0h Replicate 1

description:
Library name: Inf-dk-0h-1
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 0h Replicate 1


title: RNA-seq hippocampus, MOR-SAL, female, replicate 7-3

description: Library name: RNA_Hippo_MOR-SAL_F_7-3


title: RNA-seq hippocampus, MOR-SAL, female, replicate 7-2

description: Library name: RNA_Hippo_MOR-SAL_F_7-2


title: Plasmidsaurus seq, vtRNA1 triple-knockout, clone 1, bio rep 3

description: Library name: Plasmidsaurus_KO4c1s3


title: Plasmidsaurus seq, vtRNA1 triple-knockout, clone 1, bio rep 2

description: Library name: Plasmidsaurus_KO4c1s2


title: Plasmidsaurus seq, vtRNA1 triple-knockout, clone 3, bio rep 1

description: Library name: Plasmidsaurus_KO4c3s1


title: RNA-seq hippocampus, MOR-SAL, female, replicate 18-0

description: Library name: RNA_Hippo_MOR-SAL_F_18-0


title: Plasmidsaurus seq, vtRNA1-3 knockout, bio rep 3

description: Library name: Plasmidsaurus_KO3s3

value: vtRNA1-3 knockout


title: Plasmidsaurus seq, vtRNA1 triple-knockout, clone 2, bio rep 1

description: Library name: Plasmidsaurus_KO4c2s1


title: Plasmidsaurus seq, vtRNA1-3 knockout, bio rep 2

description: Library name: Plasmidsaurus_KO3s2


title: Plasmidsaurus seq, vtRNA1 triple-knockout, clone 1, bio rep 1

description: Library name: Plasmidsaurus_KO4c1s1


title: RNA-seq hippocampus, MOR-SAL, female, replicate 16-1

description: Library name: RNA_Hippo_MOR-SAL_F_16-1


title: 1379-IDSH3(B)_2

type: protein

city: Vancouver

first: Xiaoyan

last: Jiang

state: BC

address: 675 w10th Ave

department: TFL

country: Canada

institute: BC Cancer Research Center

scan_protocol: Scanned at 543nM using a ScanArray GX Microarray scanner

data_processing: Fluorescent signals from the antibody microarray were quantified with ImaGene 9.0 microarray image analysis software (BioDiscovery). Antibody signal intensity was calculated as a function of the net median signal and spot size, and normalized to the sum of the top 20% of total signals.

label: antibody

molecule: protein

source_name: Pro-B cell line lysate

label_protocol: The Kinex KAM-1325 antibody microarray (Kinexus Bioinformatics Corporation, Vancouver, BC) featured 1325 pan- and phosphosite-specific antibodies that focused on cell signalling proteins, especially protein kinases and their targets. Use of this antibody microarray is described in detail [Yue L, Pelech S. Applications of high content antibody microarrays for biomarker discovery and trafficking cellular signaling Adv Proteomics Bioinform. 2018;APBI-107]. In the data set provided to GEO, BCR-ABL1+ BA cells co-expressing AHI-1 with or without Imatinib were examined. In brief, cells were lysed in homogenizing buffer with ice-cold Tris (2-carboxyethyl)phosphosine (TCEP), within 10 minutes 6 mM 2-nitro-5-thiocyanatobenzoic acid (NTCB) was added, and the samples sonicated for 40 seconds in intervals of 10 seconds with 10 seconds intermissions over ice. The resulting homogenates were further incubated for 30 minutes during ultracentrifugation for at 20°C at 50,000 RPM. Approximately 100 µg (protein) of each samples were then labeled with 20 μg of NHS-Biotin (APExBIO) for 1 hour. The resulting biotin-labeled protein fragments were then purified using Sephadex G-25 Spin columns (Sigma-Aldrich) and eluted. These samples (~100 µg) were then diluted to 400 μL with phosphate-buffered saline (PBS) with 0.05% Tween and 50 mM ethanolamine, and then applied to the antibody microarray slides and incubated in a humidity chamber for 2 hours. Slides were then washed, and anti-biotin antibody labelled with Alex546/Cy3 dye was then applied over the slides for 10 minutes in the humidity chamber. The slides were then washed, dried under nitrogen, and scanned at 543 nM using a ScanArray GX Microarray scanner (Perkin-Elmer).

growth_protocol: BCR::ABL1+ cells were maintained in RPMI1640 supplemanted with 10%FBS, 2mM L-glutamine, 100u/ml penicillin, 0.1 mg/ml streptomycin, 0.1 mM β-ME. 37°C, 5% CO2

extract_protocol: Cells were lysed in homogenizing buffer with ice-cold TCEP, within 10 minutes 6mM NTCB was added. The samples are sonicated for 40 seconds

treatment_protocol: Cells were treated with or without 5uM Imatinib for 3 hours in the culture medium

tag: group

value: untreated

value: Pro-B cell line lysate


title: 1379-IDSH3IM(T)

description: Order4020-KAM1325-K01803-1379-IDSH3-IM(T)

value: IM-treated


title: 1379-IDSH3(B)


title: RNA-seq hippocampus, MOR-SAL, female, replicate 15-4

description: Library name: RNA_Hippo_MOR-SAL_F_15-4


title: Plasmidsaurus seq, vtRNA1-2 knockout, bio rep 3

description: Library name: Plasmidsaurus_KO2s3

value: vtRNA1-2 knockout


title: Plasmidsaurus seq, vtRNA1-3 knockout, bio rep 1

description: Library name: Plasmidsaurus_KO3s1


title: RNA-seq hippocampus, MOR-SAL, female, replicate 15-2

description: Library name: RNA_Hippo_MOR-SAL_F_15-2


title: Plasmidsaurus seq, vtRNA1-2 knockout, bio rep 2

description: Library name: Plasmidsaurus_KO2s2


title: 1377-IDSH3IM(T)_2

description: Order4020-KAM1325-K01803-1377-IDSH3-IM(T)


title: Plasmidsaurus seq, vtRNA1 triple-knockout, clone 2, bio rep 2

description: Library name: Plasmidsaurus_KO4c2s2


title: Plasmidsaurus seq, vtRNA1-1 knockout, bio rep 1

description: Library name: Plasmidsaurus_KO1s1

value: vtRNA1-1 knockout


title: 1379-IDSH3IM(T)_2


title: 1377-IDSH3IM(T)


title: Plasmidsaurus seq, vtRNA1-1 knockout, bio rep 2

description: Library name: Plasmidsaurus_KO1s2


title: Plasmidsaurus seq, vtRNA1-2 knockout, bio rep 1

description: Library name: Plasmidsaurus_KO2s1


title: Plasmidsaurus seq, wild-type, bio rep 3

description: Library name: Plasmidsaurus_WTs3


title: Plasmidsaurus seq, wild-type, bio rep 2

description: Library name: Plasmidsaurus_WTs2


title: RNA-seq hippocampus, MOR-LPS, male, replicate 6-2

description: Library name: RNA_Hippo_MOR-LPS_M_6-2

value: MOR-LPS


title: Plasmidsaurus seq, wild-type, bio rep 1

description: Library name: Plasmidsaurus_WTs1


title: RNA-seq hippocampus, MOR-LPS, male, replicate 17-3

description: Library name: RNA_Hippo_MOR-LPS_M_17-3


title: RNA-seq hippocampus, MOR-LPS, male, replicate 8-3

description: Library name: RNA_Hippo_MOR-LPS_M_8-3


title: 1377-IDS(B)-2


title: 1377-IDS(B)


title: 1367-IDAIM(T)_2


title: RNA-seq hippocampus, MOR-LPS, male, replicate 17-1

description: Library name: RNA_Hippo_MOR-LPS_M_17-1


title: Healthy human donor (3), CAR T cells, BATF2, ChIP, Rep2

city: Stanford

first: Oliver

last: Takacsi-Nagy

address: 234 Pasteur Dr. (BMI 4600)

department: Pathology

institute: Stanford University School of Medicine

description:
Library name: Acute-3K-BATF2-IP-Rep-2
BATF2_peaks.filtered.q3.s8.narrowPeak

data_processing:
Basecalls were performed using bcl-convert Version 4.4.6 from Illumina
Adapters were trimmed from reads prior to mapping to the hg38 reference with  the Burrow-Wheeler Aligner [bwa (v0.7.17-r1188)] and removal of duplicate reads and alignments to artifactual/high signal regions using the nf-core/chipseq pipeline (v2.0.0, doi: 10.5281/zenodo.3240506) with default parameters.
Peaks were called using MACS3 callpeak (v3.0.3) with the following parameters: --gsize 2913022398 -s 150 –nomodel –extsize 200 --bdg. We empirically determined optimal peak calling parameters by examining sites resulting from (1) pooling data from replicates together prior to peak detection with permissive MACS3 q-value of 0.1 (‘oracle peaks’) with post-filtering on q-value and/or signal fold enrichment (FE) and (2) calling peaks separately for each replicate at permissive MACS3 p-value of 1 with post-filtering on p-value (range: 10-3 to 1) and irreducible discovery rate (IDR, v2.0.3) threshold of 1% or 5% with or without restricting to oracle peaks. This analysis identified an acceptable tradeoff between specificity and sensitivity for peaks called from pooled data at MACS3 p-value threshold of 0.1 with post-filtering to retain sites with q-value of 10-3 and FE > 8. The number of unique alignments within peaks for each ChIP dataset was tabulated using subread featureCounts (v2.1.1) with the following parameters: -p –countReadPairs –primary –ignoreDup.
Fold enrichment tracks were generated from ChIP and input signal bedgraph files using MACS3 (v3.0.3) bdgcmp with default parameters.
For visualization, bedgraphs were converted to bigwig using UCSC bedGraphToBigWig (v2.10).
To define a unified set of binding sites across ChIP datasets, peaks were merged using bedtools merge (v2.31.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input samples). A consensus peak set for each TF was generated as described above such that the same peak set is applicable to different human donors/technical replicates.

source_name: Primary Human T Cell

growth_protocol: Primary human T cells were negatively selected from PBMCs isolated from leukoreduction chambers from two healthy blood donors and activated by CD3/28 agonism in X-VIVO 15 supplemented with 5% FBS and 50 IU/mL recombinant human IL-2. 48 hours post-activation, T cells were electroporated with Cas9 ribonucleoprotein and a plasmid homology-directed repair template to enable integration of a multicistronic cassette encoding tNGFR, CD19-28z and variable natural and engineered FLAG-tagged AP-1 transcription factors within the continuous reading frame of the TRAC locus. Pre- and post-editing cells were maintained at 0.5-1e6/ml. Six days post-editing, CAR T cells were challenged with CD19-expressing Nalm6 targets (leukemia cell line, 1:8 Effector:Target ratio, 72-hour co-culture).

extract_protocol:
Up to 1e7 live CAR T cells (NGFR+) were enriched magnetically and cross-linked at RT first in 2 mM disuccinimidyl glutarate in PBS for 30 min and then in 1% methanol-free formaldehyde in PBS for 10 min. Formaldehyde was quenched by adding glycine to 125 mM final concentration. Cross-linked cells were pelleted, snap-frozen in liquid nitrogen, stored at –80ºC. Nuclei were isolated from cryopreserved pellet (1.5 x 1e6 cells) by sequential lysis in LB1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, and 0.25% Triton X-100), LB2 (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), and LB3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% sodium deoxycholate [NaDOC], and 0.5% N-laurylsarcosine) supplemented with 0.5 mM phenylmethylsulfonyl fluoride and 0.5X protease inhibitor cocktail. Chromatin was fragmented to 200-700 bp on a Covaris E220 focused ultrasonicator in microTubes with the following parameters: 140W peak incident power, 5% duty factor, 200 cycles per burst, 6ºC temperature setpoint (range 3-9ºC), run level 6, and time 12-14 min. Triton X-100 was added to final concentration of 1% to clarified chromatin prior to immunoprecipitation for 16h at 4ºC with 2.5 uL of 1 mg/mL mouse monoclonal anti-FLAG M2 antibody bound to a 1:1 mixture of protein A and G magnetic beads. Immunoprecipitated, bead-bound chromatin was washed sequentially with the following buffers supplemented with 0.5 mM PMSF and 0.5X PIC: three times with WB1 (20 mM Tris pH 8, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium dodecyl sulfate [SDS], and 0.1% NaDOC); twice with WB2 (20 mM Tris-HCl pH8, 500 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, and 0.1% NaDOC); twice with WB3 (20 mM Tris-HCl pH 8, 250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630, and 0.5% NaDOC); twice with TET (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.2% Tween-20); and once with TE0.1 (10 mM Tris-HCl pH 8, 0.1 mM EDTA). This mirrors the methods used previously (Umhoefer, et al., Immunity, 2025 and Arce, et al., Nature, 2025).
Beads were brought up in TT (10 mM Tris-HCl pH 8, 0.05% Tween-20) prior to on-bead library preparation using the NEBNext Ultra II DNA Library Prep Kit as previously described (Texari, et al., STAR Protocols, 2021).

treatment_protocol: All T cells in this sample were treated the same, the only difference between the T cells is which healthy human donor they were isolated from and which transcription factor they were edited to express.

value: Primary Human T Cell

tag: individual

value: Healthy Donor 3

tag: tf expressed

tag: chip antibody

value: FLAG (Sigma, F1804)

tag: batch


title: Healthy human donor (3), CAR T cells, BATF2, Input, Rep2

description: Library name: Acute-3K-BATF2-N-Rep-2


title: Healthy human donor (3), CAR T cells, ATF3, Input, Rep2

description: Library name: Acute-3J-ATF3-N-Rep-2


title: Healthy human donor (3), CAR T cells, ATF3, ChIP, Rep2

description:
Library name: Acute-3J-ATF3-IP-Rep-2
ATF3_peaks.filtered.q3.s8.narrowPeak


title: RNA-seq hippocampus, MOR-LPS, male, replicate 14-4

description: Library name: RNA_Hippo_MOR-LPS_M_14-4

tag: tissue


title: 1367-IDAIM(T)

tag: cell type


title: RNA-seq hippocampus, MOR-LPS, male, replicate 14-2

description: Library name: RNA_Hippo_MOR-LPS_M_14-2

tag: genotype


title: Healthy human donor (3), CAR T cells, MAFF, Input, Rep2

description: Library name: Acute-3I-MAFF-N-Rep-2

value: MAFF


title: Healthy human donor (3), CAR T cells, MAFF, ChIP, Rep2

description:
Library name: Acute-3I-MAFF-IP-Rep-2
MAFF_peaks.filtered.q3.s8.narrowPeak


title: S3_ChP_BD

description: Library name: S3


title: RNA-seq hippocampus, MOR-LPS, male, replicate 13-2

description: Library name: RNA_Hippo_MOR-LPS_M_13-2


title: Healthy human donor (3), CAR T cells, FOSL1, Input, Rep2

description: Library name: Acute-3H-FOSL1-N-Rep-2


title: Healthy human donor (3), CAR T cells, FOSL1, ChIP, Rep2

description:
Library name: Acute-3H-FOSL1-IP-Rep-2
FOSL1_peaks.filtered.q3.s8.narrowPeak


title: Healthy human donor (3), CAR T cells, MAFF-ATF3-BATF2, Input, Rep2

description: Library name: Acute-3G-MAFF-ATF3-BATF2-N-Rep-2


title: RNA-seq hippocampus, MOR-LPS, male, replicate 13-0

description: Library name: RNA_Hippo_MOR-LPS_M_13-0


title: 1367-IDA(B)_2


title: Healthy human donor (3), CAR T cells, MAFF-ATF3-BATF2, ChIP, Rep2

description:
Library name: Acute-3G-MAFF-ATF3-BATF2-IP-Rep-2
MAFF-ATF3-BATF2_peaks.filtered.q3.s8.narrowPeak


title: 1367-IDA(B)


title: 1310-IDAIM(T)_2


title: 1310-IDAIM(T)


title: Healthy human donor (3), CAR T cells, FOSL1-BATF-MAFA, Input, Rep2

description: Library name: Acute-3F-FOSL1-BATF-MAFA-N-Rep-2


title: Healthy human donor (3), CAR T cells, FOSL1-BATF-MAFA, ChIP, Rep2

description:
Library name: Acute-3F-FOSL1-BATF-MAFA-IP-Rep-2
FOSL1-BATF-MAFA_peaks.filtered.q3.s8.narrowPeak


title: Healthy human donor (3), CAR T cells, GFP, Input, Rep2

description: Library name: Acute-3E-GFP-N-Rep-2

value: GFP


title: RNA-seq hippocampus, MOR-LPS, female, replicate 7-1

description: Library name: RNA_Hippo_MOR-LPS_F_7-1

value: hippocampus


title: 1310-IDA(B)_2


title: Healthy human donor (3), CAR T cells, BATF, Input, Rep2

description: Library name: Acute-3D-BATF-N-Rep-2

value: BATF


title: RNA-seq hippocampus, MOR-LPS, female, replicate 18-1

description: Library name: RNA_Hippo_MOR-LPS_F_18-1

value: wild type


title: RNA-seq hippocampus, MOR-LPS, female, replicate 16-4

description: Library name: RNA_Hippo_MOR-LPS_F_16-4


title: 1310-IDA(B)


title: Healthy human donor (3), CAR T cells, GFP, ChIP, Rep2

description:
Library name: Acute-3E-GFP-IP-Rep-2
GFP_peaks.filtered.q3.s8.narrowPeak


title: Healthy human donor (3), CAR T cells, FOS, Input, Rep2

description: Library name: Acute-3C-FOS-N-Rep-2

value: FOS


title: Pig ESC-derived cells, at day 20, directed myogenic differentiation

city: Seoul

first: Jinsol

last: Jeong

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
Library name: Sample 4
Cell viability: 82.7%, Loaded cell number: 30,000, Estimated cell number: 23,324, Library QC (Average yield: 168.85 nM, Fragment size peak: 535 bp), Sequencing depth (Mean reads/cell: 13,346, Median UMI/cell: 6,204, Median genes/cell: 2,460, Total gene detected: 19,379)

library_source: transcriptomic single cell

data_processing:
Data processing:  Raw scRNA-seq reads were de-multiplexed into FASTQ files using cellranger mkfastq (Cell Ranger v7.0.1, 10x Genomics). Read alignment and gene counting were performed with the cellranger count pipeline (v7.0.1) against the pig reference genome Sus scrofa 11.1 (Ensembl release 108), with the option “--include-introns” enabled. Feature-barcode and gene-barcode expression matrices were generated following cellular barcode and UMI processing.
Data filtering:  Processed data were imported into R (v4.3.3) and analyzed using Seurat (v4.3.0). Quality control was performed at the single-cell level, and low-quality cells were excluded based on the following thresholds: <200 detected genes, <1,000 UMI counts, or >20% mitochondrial reads.
Assembly: Sus scrofa 11.1
Supplementary files format and content: Tab-separated values files and matrix files.

organism: Sus scrofa

source_name: not applicable (in vitro culture)

growth_protocol: Pig embryonic stem cells derived from in vitro-fertilized embryos were cultured in ESC medium [DMEM/F12 (Gibco; 11320-033) containing 15% (v/v) KnockOut™ Serum Replacement (Gibco; KSR; cat.10828028), 0.1% (v/v) chemically defined lipid concentrate (Gibco; LC; cat.11905031), 1× GlutaMAX™ supplement (Gibco; cat.10565-018), 0.1 mM β-mercaptoethanol (Gibco; cat.21985023), 1× MEM nonessential amino acids (Gibco; cat.11140050), 1× antibiotic–antimycotic (Gibco; cat.15240-062), 20 ng/mL FGF2 (R&D Systems; cat.233-FB), 5 ng/mL activin A (R&D Systems; cat.338-AC), 1.5 µM CHIR99021 (Cayman Chemical; cat.13122), and 2.5 µM IWR-1 (Sigma-Aldrich; cat. I0161)]. Medium was changed every 24 h and cells were maintained at 37°C with 5% CO2 under humidified conditions.

extract_protocol:
The cells pretreated with 10 µM Y-27632 for 24 h were dissociated using TrypLE™ Express and filtered using a 100 µm Cell Strainer (Corning Inc., cat.CLS431752). After centrifugation at 300g for 5 min at RT and removal of the supernatant, cells were washed twice with cold Ca2+ and Mg2+-free 0.04% BSA (Sigma-Aldrich; cat.A6003)/PBS (Welgene; cat.LB 001-02) at 300 × g for 5 min at 4°C, resuspended in the same buffer, and filtered through a 40 µm Flowmi Cell Strainer (SP Bel-Art; cat.H13680-0040). Viability was assessed using acridine orange and propidium iodide staining (Logos Biosystems; cat.F23001) on a LUNA-FX7™ cell counter (Logos Biosystems). RNA was not extracted separately; poly(A)+ RNA was captured directly from single cells within GEMs using the 10x Genomics Single Cell 3' v3.1 workflow.
Single-cell RNA-seq libraries were prepared using the 10x Chromium iX Controller and Next Gem Single cell 3’ Kit v3.1 (10x Genomics; PN-1000268) according to the 10x Chromium Next GEM Single Cell 3’ v3.1 protocol (10x Genomics; doc.CG000315). Cells were loaded per channel into a Next GEM Chip G (10x Genomics; PN-1000120) with reverse transcription reagents (PN-1000123), partitioning oil (PN-1000190), and Next GEM Single Cell 3ʹ Gel Bead (10x Genomics; PN-1000122) to generate GEMs. Barcoded cDNA was synthesized and amplified according to the Next GEM Single Cell 3’ Kit v3.1 protocols (doc.CG000315). Library preparation was performed using the Single Cell 3’ Library Kit v3.1 (PN-1000190), including fragmentation (Fragmentation Enzyme, PN-2000090; Fragmentation Buffer PN-2000091), end-repair/A-tailing with P5/P7 sequences, adaptor ligation (Ligation Buffer, PN-2000092; Adaptor Oligos, PN-2000094; DNA Ligase, PN-220110), and index PCR with i5/i7 sequences, according to the manufacturer’s protocol (10x Genomics; doc.CG000315). Libraries were quantified using qPCR (LightCycler Instrument) according to the qPCR Quantification Protocol Guide (KAPA Biosystems) and qualified with an Agilent 4200 TapeStation (Agilent Technologies).

treatment_protocol:
To induce myogenic differentiation, pig ESCs were pretreated with 10 µM Y-27632 (Santa Cruz Biotechnology; cat. sc-281642) for 24 h, dissociated into small colonies using TrypLE Express (Gibco; cat.12605010), and seeded at a 1:4 ratio onto Geltrex-coated dishes. From the following day, cells were cultured in DMEM/F12 with 15% KSR, 0.1% LC, 1× GlutaMAX, 0.1 mM β-mercaptoethanol, 1× MEM nonessential amino acids, and 1× antibiotic–antimycotic, supplemented sequentially as follows:
- Day 0–4: 3 µM CHIR99021 + 0.05 µM LDN193189  (Cayman Chemical; cat.11802)
- Day 5–6: 3 µM CHIR99021 + 0.05 µM LDN193189 + 20 ng/mL FGF2
- Day 7–8: 10 ng/mL HGF (R&D Systems; cat.294-HG) + 2 ng/mL IGF1(R&D Systems; cat.291-G1) + 20 ng/mL FGF2 + 0.05 µM LDN193189
- Day 9–12: 2 ng/mL IGF1
- Day 13–25: 2 ng/mL IGF1 + 10 ng/mL HGF
Medium was replaced every 24 h throughout differentiation.

value: not applicable (in vitro culture)

value: pig ESC line, IVF-ES-11

value: differentiated pig embryonic stem cells

value: myogenic differentiation for 20 days


title: RNA-seq hippocampus, MOR-LPS, female, replicate 16-2

description: Library name: RNA_Hippo_MOR-LPS_F_16-2


title: Healthy human donor (3), CAR T cells, JUN, Input, Rep2

description: Library name: Acute-3B-JUN-N-Rep-2

value: JUN


title: RNA-seq hippocampus, MOR-LPS, female, replicate 15-3

description: Library name: RNA_Hippo_MOR-LPS_F_15-3


title: Healthy human donor (3), CAR T cells, FOS, ChIP, Rep2

description:
Library name: Acute-3C-FOS-IP-Rep-2
FOS_peaks.filtered.q3.s8.narrowPeak


title: Plasmidsaurus seq, vtRNA1-1 knockout, bio rep 3

description: Library name: Plasmidsaurus_KO1s3


title: Pig ESC-derived cells, at day 25, directed myogenic differentiation

description:
Library name: Sample 5
Cell viability: 82.4%, Loaded cell number: 30,000, Estimated cell number: 19,394, Library QC (Average yield: 85.93 nM, Fragment size peak: 585 bp), Sequencing depth (Mean reads/cell: 17,809, Median UMI/cell: 7,904, Median genes/cell: 3,092, Total gene detected: 19,411)

value: myogenic differentiation for 25 days


title: Healthy human donor (3), CAR T cells, JUN, ChIP, Rep2

description:
Library name: Acute-3B-JUN-IP-Rep-2
JUN_peaks.filtered.q3.s8.narrowPeak


title: Healthy human donor (3), CAR T cells, JUN-FOS-BATF, Input, Rep2

description: Library name: Acute-3A-JUN-FOS-BATF-N-Rep-2

value: JUN-FOS-BATF


title: 1362_IDIM(T)

value: IM-treated

value: Pro-B cell line lysate


title: Undifferentiated pig ESCs

description:
Library name: Sample 1
Cell viability: 83.8%, Loaded cell number: 30,000, Estimated cell number: 21,361, Library QC (Average yield: 155.05 nM, Fragment size peak: 480 bp), Sequencing depth (Mean reads/cell: 13,816, Median UMI/cell: 4,477, Median genes/cell: 2,215, Total gene detected: 19,160)

source_name: embryo (blastocyst inner cell mass, ICM)

value: pig embryonic stem cells

value: maintained in ESC medium


title: Healthy human donor (3), CAR T cells, JUN-FOS-BATF, ChIP, Rep2

description:
Library name: Acute-3A-JUN-FOS-BATF-IP-Rep-2
JUN-FOS-BATF_peaks.filtered.q3.s8.narrowPeak

value: Primary Human T Cell

value: Healthy Donor 3

value: FLAG (Sigma, F1804)


title: 1362-ID(B)_2

value: untreated


title: sample_87

type: genomic

city: Tampere

first: Keijo

last: Viiri

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

description: GFDp

hyb_protocol: Aliquots of 1 µg of DNA were subjected to bisulfite conversion, and 4 µl of bisulfite-converted DNA underwent whole-genome application, enzymatic fragmentation, and hybridization onto the MethylationEPIC BeadChip (EPICv2).

scan_protocol: The arrays were scanned using the iScan system (Illumina, San Diego, CA, USA).

data_processing:
The DNA methylation data was pre-processed using the default meffil pipeline, with a p-value threshold of 0.05. Probes that failed quality control (QC) were removed from further analysis. One saple was removed from processed data afte QC
Average Beta values

label: biotin

source_name: Whole blood

label_protocol: DNA methylation profiling was performed using the Illumina Infinium MethylationEPIC version 2 BeadChip at Helmholtz Zentrum, Munich, Germany

extract_protocol: Genomics DNA was extracted from whole blood samples with Chemagic 360 robot with CMG-1091 kit (Revvity, Waltham, MA, USA) in combination with chemagic™ DNA Blood 400 kit H96 (Cat. No. CMG-1091), following the manufacture’s protocol (VD190913.che).

value: Whole blood

value: placebo

tag: age

tag: Sex

value: F

tag: timepoint

value: baseline


title: RNA-seq hippocampus, MOR-LPS, female, replicate 12-2

description: Library name: RNA_Hippo_MOR-LPS_F_12-2

value: hippocampus

value: wild type

tag: treatment

value: MOR-LPS


title: Healthy human donor (3), CAR T cells, BATF2, ChIP, Rep1

description:
Library name: Acute-3K-BATF2-IP-Rep-1
BATF2_peaks.filtered.q3.s8.narrowPeak


title: 1362-ID(B)


title: Healthy human donor (3), CAR T cells, ATF3, Input, Rep1

description: Library name: Acute-3J-ATF3-N-Rep-1


title: Healthy human donor (3), CAR T cells, ATF3, ChIP, Rep1

description:
Library name: Acute-3J-ATF3-IP-Rep-1
ATF3_peaks.filtered.q3.s8.narrowPeak


title: Healthy human donor (3), CAR T cells, MAFF, Input, Rep1

description: Library name: Acute-3I-MAFF-N-Rep-1

value: MAFF


title: H3K27ac ChIP-seq prefrontal cortex, SAL-SAL, male, replicate 5-1

description:
Library name: ChIP_PFC_SAL-SAL_M_5-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

data_processing:
Adapters and low-quality bases were trimmed using Trim Galore (v0.6.7, --paired --fastqc).
Reads were aligned to Mus musculus mm10 using Bowtie2 (v2.4.5). PCR duplicates were removed with SAMtools (v1.15.1) markdup. Reads overlapping ENCODE mm10 blacklist (v2) were excluded with BEDTools subtract (v2.30.0). Coverage profiles were generated with bedtools genomecov and converted to BigWig with bedGraphToBigWig.
Peak calling: MACS2 (v2.2.7.1; -q 0.05 -g mm) against matched pooled Input controls.
Differential H3K27ac analysis: consensus peak set constructed in DiffBind (v3.10.1) with condition-aware merging. Read counts quantified with DiffBind (dba.count, summarizeOverlaps); peaks retained if >= 15 reads in >= 80% of samples within any condition. Differential peaks identified via DESeq2 (dba.analyze); FDR < 0.05. Peaks annotated with ChIPpeakAnno (v3.32.1) and EnsDb.Mmusculus.v79.
Transcription factor regulatory influence assessed with Taiji (v1.2.0) integrating H3K27ac enhancers and RNA-seq expression. TF activity quantified as personalized PageRank scores (z-score normalized, capped at +/-2).
Assembly: mm10
Supplementary files format and content: narrowPeak files (MACS2 peak calls); bigWig coverage tracks (bedtools genomecov + bedGraphToBigWig)

source_name: prefrontal cortex

extract_protocol:
Brain tissues (PFC, hippocampus, hypothalamus, striatum) were collected by bilateral punch (2.0 mm) and flash-frozen at -80C. Nuclei were isolated in cold extraction buffer using a Dounce tissue grinder, filtered (40 um), and enriched by iodixanol gradient centrifugation. NeuN+ neuronal nuclei were labeled with anti-NeuN Alexa Fluor 488 (MAB377X, EMD Millipore) at 4C for 1 h, then sorted by FACS (BD Biosciences). ~10,000 NeuN+ nuclei per replicate were lysed and digested with MNase (88216, Thermo Fisher) in the presence of CaCl2; reaction quenched with EDTA. Chromatin IP was performed using 0.125 ug anti-H3K27ac antibody (39135, Active Motif) coupled to 5 uL protein A Dynabeads (10001D, Thermo Fisher), following the MOWChIP-seq protocol.
ChIP-seq libraries were constructed from purified ChIP DNA (~10,000 NeuN+ nuclei) and input DNA (~2,000 nuclei). PFC libraries used xGen 2S DNA Library Prep Kit (10009877, IDT); hippocampus, hypothalamus, and striatum libraries used ThruPLEX DNA-Seq kit (R400674, Takara Bio). Fragment size verified on TapeStation (Agilent) with High Sensitivity DNA Analysis Kit; primer-dimers removed with SPRIselect beads. Libraries quantified with KAPA Library Quantification Kit (4824, Roche), pooled, and sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 nt, ~15 million reads per library).

value: prefrontal cortex

value: SAL-SAL


title: Healthy human donor (3), CAR T cells, MAFF, ChIP, Rep1

description:
Library name: Acute-3I-MAFF-IP-Rep-1
MAFF_peaks.filtered.q3.s8.narrowPeak


title: RNA-seq hippocampus, MOR-LPS, female, replicate 12-0

description: Library name: RNA_Hippo_MOR-LPS_F_12-0


title: 1350-IDIM(T)_2

value: IM-treated

value: Pro-B cell line lysate


title: Healthy human donor (3), CAR T cells, FOSL1, Input, Rep1

description: Library name: Acute-3H-FOSL1-N-Rep-1


title: H3K27ac ChIP-seq prefrontal cortex, SAL-SAL, male, replicate 3-4

description:
Library name: ChIP_PFC_SAL-SAL_M_3-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Healthy human donor (3), CAR T cells, MAFF-ATF3-BATF2, Input, Rep1

description: Library name: Acute-3G-MAFF-ATF3-BATF2-N-Rep-1


title: Input control prefrontal cortex, SAL-SAL, male

description:
Library name: Input_PFC_SAL-SAL_M
Input control (pooled)


title: 1350-ID(B)_2


title: Healthy human donor (3), CAR T cells, FOSL1, ChIP, Rep1

description:
Library name: Acute-3H-FOSL1-IP-Rep-1
FOSL1_peaks.filtered.q3.s8.narrowPeak


title: Healthy human donor (3), CAR T cells, FOSL1-BATF-MAFA, Input, Rep1

description: Library name: Acute-3F-FOSL1-BATF-MAFA-N-Rep-1


title: 1350-ID(B)


title: Healthy human donor (3), CAR T cells, FOSL1-BATF-MAFA, ChIP, Rep1

description:
Library name: Acute-3F-FOSL1-BATF-MAFA-IP-Rep-1
FOSL1-BATF-MAFA_peaks.filtered.q3.s8.narrowPeak


title: NESCs, PD2 cell line, aged, biological replicate 2

city: Maastricht

first: Silvia

last: Bolognin

address: Universiteitssingel 40

country: Netherlands

institute: Maastricht University

description:
Library name: PD2_A_B2
Column name in gene_counts.tsv: T4M_P18_O

data_processing:
Raw sequencing data were processed into gene expression matrices using CeleScope v2.7.4 (multi_bulk_rna workflow with customized chemistry; https://github.com/singleron-RD/CeleScope). R2 FASTQ files containing transcript sequences were demultiplexed using well-specific barcodes extracted from the corresponding R1 FASTQ files. Reads were aligned to the Homo sapiens reference genome (GRCh38, Ensembl release 99) using STAR.
Assembly: GRCh38, Ensembl release 99
Supplementary files format and content: Tab-separated values file includes raw counts for each Sample

source_name: hiPSC-derived Neural Epithelial Stem Cells

growth_protocol: As described in Reinhardt et al., 2013 Plos ONE doi.org/10.1371/journal.pone.0059252

extract_protocol:
Total RNA was extracted from NESCs and snap-frozen. RNA quantity and integrity were assessed using the Qubit RNA High Sensitivity Assay Kit (Invitrogen) and the High Sensitivity RNA ScreenTape system (Agilent Technologies). Polyadenylated mRNA was isolated using paramagnetic bead-based capture.
Library preparation was performed using the AccuraCode RNA-Seq Kit V2 (Singleron Biotechnologies GmbH) according to the manufacturer’s instructions. During reverse transcription, 100 ng mRNA was converted to cDNA and labeled with sample-specific barcodes and unique molecular identifiers. Barcoded cDNA from all samples was pooled and amplified. A total of 50 ng cDNA was used for library construction. Libraries were sequenced on a NovaSeq X platform (Illumina) using paired-end 150-bp sequencing by GENEWIZ (Leipzig, Germany).

treatment_protocol: NESCs were cultured and passaged to generate two experimental conditions. Cells were either maintained at low passage number (P < 8), referred to as “young” (Y), or extensively passaged (P > 16), referred to as “aged” (A), to model cellular aging. Extensive passaging was used to induce replicative exhaustion and age-associated cellular changes. Apart from differences in passage number, all culture conditions and handling procedures were identical between groups.

value: aged


title: NESCs, PD2 cell line, aged, biological replicate 1

description:
Library name: PD2_A_B1
Column name in gene_counts.tsv: T4M_P17_O

value: hiPSC-derived Neural Epithelial Stem Cells


title: Healthy human donor (3), CAR T cells, GFP, ChIP, Rep1

description:
Library name: Acute-3E-GFP-IP-Rep-1
GFP_peaks.filtered.q3.s8.narrowPeak

value: Primary Human T Cell

value: Healthy Donor 3

value: GFP


title: H3K27ac ChIP-seq prefrontal cortex, SAL-SAL, female, replicate 9-2

description:
Library name: ChIP_PFC_SAL-SAL_F_9-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Healthy human donor (3), CAR T cells, FOS, Input, Rep1

description: Library name: Acute-3C-FOS-N-Rep-1

value: FOS


title: H3K27ac ChIP-seq prefrontal cortex, SAL-SAL, female, replicate 9-0

description:
Library name: ChIP_PFC_SAL-SAL_F_9-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Healthy human donor (3), CAR T cells, BATF, ChIP, Rep1

description:
Library name: Acute-3D-BATF-IP-Rep-1
BATF_peaks.filtered.q3.s8.narrowPeak

value: BATF

value: FLAG (Sigma, F1804)


title: NESCs, PD2 cell line, control, biological replicate 2

description:
Library name: PD2_Y_B2
Column name in gene_counts.tsv: T4M_P6_Y

value: control


title: Healthy human donor (3), CAR T cells, JUN, Input, Rep1

description: Library name: Acute-3B-JUN-N-Rep-1

value: JUN


title: IPSC-microglia, AD22, sncRNA

city: Galveston

first: Xiaoyong

last: Bao

state: TX

address: 301 University Boulevard

department: Pediatrics

institute: University of Texas Medical Branch

description:
Library name: S22_CN
small RNAseq of sample 22 (CN)

data_processing:
To analyze the seq data, adaptor sequences were first removed using Cutadapt and reads with a length of more than 15 bp were extracted. We further filtered out RNAs with counts <10 and all rRNA sequences, using the remaining reads as the cleaned input. In terms of the mapping databases, we prepared mRNA database downloaded from UCSC genome browser, extracted sequences with NM accession, and added official gene symbols after the RefSeq accession number. For small RNA database, we prepared tRF5 and tRF3 databases using the identical sequences derived from different tRNAs (sequences downloaded from tRNA genes using the Table Browser of the UCSC genome browser). We also prepared tRF1 sequences using the genome locations of tRNAs. Our inhouse small RNA database includes (1) these tRFs, (2) miR/snoR sequences downloaded from the UCSC genome browser, and (3) piRNA sequences downloaded from piRBase. The cleaned input reads were mapped to our in-house small RNA database using bowtie2 (v2.4.1), allowing two mismatches (option N-1). After we mapped the cleaned input reads to the small RNA database, the unmapped sequences were then mapped to the hg38 genome using the bowtie2 pre-built index (GRCh38_noalt_as) to detect all human sequences.
Assembly: hg38
Supplementary files format and content: csv file include raw counts mapping to mRNAs for all samples
Supplementary files format and content: csv file include raw counts mapping to sncRNAs for all samples

source_name: Human IPSC-derived microglia cells

growth_protocol: Induced pluripotent stem cells were obtained from the Coriell Institute and cultured in mTeSR Plus medium on Matrigel-coated 6-well plates. Induced pluripotent stem cells were differentiated into HPCs using the STEMdiff Hematopoietic Kit following the manufacturer’s instructions. Non-adherent cells harvested on Day 12 were confirmed as HPCs and used immediately for microglial differentiation. Hematopoietic progenitor cells were further differentiated using the STEMdiff Microglia Differentiation Kit and matured with the STEMdiff Microglia Maturation Kit, per the manufacturer’s protocol. On Day 12, cells were collected by centrifugation, resuspended in 2 mL fresh Differentiation Medium, and replated onto Matrigel-coated 6- well plates; medium was topped up every other day. On Day 24, cells were again collected, resuspended in Microglia Maturation Medium, and seeded onto Matrigel-coated 6-well plates. They were then fed every other day for an additional 6 days to complete maturation.

extract_protocol:
After 6 days of maturation, iPSC-derived microglia (iMG) cells were harvested, and RNA was extracted using TRIzol Reagent with the PureLink RNA Mini Kit, according to the manufacturer’s instructions. In brief, after adding chloroform and phase separation, the aqueous phase containing RNA was transferred to the Spin Cartridge provided in the kit.
RNA samples were submitted to RealSeq Biosciences (Santa Cruz, CA) for library preparation and RNA sequencing. Libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Kit with 8 uL of total RNA input and 13 PCR cycles. Libraries were pooled at equal concentrations and profiled using a DNA Tapestation and dsDNA High Sensitivity Qubit assay before sequencing on the Singular G4 platform. We further examined small noncoding RNA (sncRNA) expression in iMGs from sporadic AD and healthy controls, using T4 PNKsncRNA-seq, a modified sequencing method designed to overcome barcode ligation biases inherent in standard library preparations. Many sncRNAs, including tRFs, lack 3’-hydroxyl ends required for efficient barcode ligation, leading to their underrepresentation in conventional methods (Wu et al., 2022). Therefore, before sncRNA seq, we pretreated RNAs with T4-PNK to make sncRNAs homogeneously with 3’-hydroxyl ends. In brief, 15 mL of RNAs was pretreated with 10 units of T4 PNK (New England Biolabs, Ipswich, MA) in a final reaction volume of 50 mL. After incubating them at 37 _x000E_C for 30 min, followed by heat inactivation at 65 C for 20 min, the treated RNAs were purified into 15 mL of nuclease-free water using the Zymo RNA Clean and Concentrator-5 kit, following the small RNA enrichment protocol according to the manufacturer’s instructions. RealSeq-Biofluids libraries were then prepared using 10 mL of treated RNA input and 20 PCR cycles. Libraries were pooled at equal concentrations and profiled using a DNA Tapestation and dsDNA High Sensitivity Qubit assay before sequencing on the NextSeq 550 platform.

value: Human IPSC-derived microglia cells


title: NESCs, PD2 cell line, control, biological replicate 1

description:
Library name: PD2_Y_B1
Column name in gene_counts.tsv: T4M_P5_Y


title: Healthy human donor (3), CAR T cells, JUN-FOS-BATF, Input, Rep1

description: Library name: Acute-3A-JUN-FOS-BATF-N-Rep-1

value: JUN-FOS-BATF


title: H3K27ac ChIP-seq prefrontal cortex, SAL-SAL, female, replicate 4-1

description:
Library name: ChIP_PFC_SAL-SAL_F_4-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type


title: Healthy human donor (2), CAR T cells, BATF2, Input, Rep1

description: Library name: Acute-2K-BATF2-N-Rep-1

value: Healthy Donor 2


title: NESCs, PD1 GC cell line, aged, biological replicate 2

description:
Library name: PD1GC_A_B2
Column name in gene_counts.tsv: T4GC_P18_O

value: PD1 GC

value: LRRK2-G2019S gene corrected


title: Healthy human donor (2), CAR T cells, BATF2, ChIP, Rep1

description:
Library name: Acute-2K-BATF2-IP-Rep-1
BATF2_peaks.filtered.q3.s8.narrowPeak


title: H3K27ac ChIP-seq prefrontal cortex, SAL-SAL, female, replicate 10-3

description:
Library name: ChIP_PFC_SAL-SAL_F_10-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: prefrontal cortex

value: SAL-SAL


title: Input control prefrontal cortex, SAL-SAL, female

description:
Library name: Input_PFC_SAL-SAL_F
Input control (pooled)


title: Healthy human donor (2), CAR T cells, ATF3, ChIP, Rep1

description:
Library name: Acute-2J-ATF3-IP-Rep-1
ATF3_peaks.filtered.q3.s8.narrowPeak


title: NESCs, PD1 GC cell line, aged, biological replicate 1

description:
Library name: PD1GC_A_B1
Column name in gene_counts.tsv: T4GC_P17_O

value: hiPSC-derived Neural Epithelial Stem Cells

value: aged


title: Healthy human donor (2), CAR T cells, MAFF, Input, Rep1

description: Library name: Acute-2I-MAFF-N-Rep-1

value: Primary Human T Cell

value: MAFF


title: Healthy human donor (2), CAR T cells, MAFF, ChIP, Rep1

description:
Library name: Acute-2I-MAFF-IP-Rep-1
MAFF_peaks.filtered.q3.s8.narrowPeak


title: sample_81

description: GFDp

value: Whole blood

value: placebo

value: F

value: baseline


title: Sprague–Dawley rats, ISO Test3

city: Kunming

first: Kang

last: Luo

state: Yunnan

address: No. 1168, Chunrong West Road, Yuhua Street, Chenggong District, Kunming,

country: China

institute: Kunming Medical University

description: Library name: T84

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster
Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to
the manufacturer’s instructions. After cluster generation, the library preparations were
sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were
generated.
Assembly: mm10
Supplementary files format and content: RNAseq_counts_matrix.csv
Supplementary files format and content: RNAseq_counts_matrix.csv

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 µg RNA oftotal RNA was used for the construction of sequencing libraries
Sequencing libraries were generated using NEBNext® UltraTM.RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Heart

value: WT

value: subcutaneous injection of ISO (1.5 mg/kg/day) for 7 consecutive days


title: NESCs, PD1 GC cell line, control, biological replicate 3

description:
Library name: PD1GC_Y_B3
Column name in gene_counts.tsv: T4GC_P7_Y

value: control


title: H3K27ac ChIP-seq prefrontal cortex, SAL-LPS, male, replicate 1-4

description:
Library name: ChIP_PFC_SAL-LPS_M_1-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type

value: SAL-LPS


title: Healthy human donor (2), CAR T cells, FOSL1, ChIP, Rep1

description:
Library name: Acute-2H-FOSL1-IP-Rep-1
FOSL1_peaks.filtered.q3.s8.narrowPeak

value: Healthy Donor 2

value: FLAG (Sigma, F1804)


title: Input control prefrontal cortex, SAL-LPS, male

description:
Library name: Input_PFC_SAL-LPS_M
Input control (pooled)

value: prefrontal cortex


title: NESCs, PD1 GC cell line, control, biological replicate 1

description:
Library name: PD1GC_Y_B1
Column name in gene_counts.tsv: T4GC_P5_Y

value: PD1 GC

value: hiPSC-derived Neural Epithelial Stem Cells

value: LRRK2-G2019S gene corrected


title: H3K27ac ChIP-seq prefrontal cortex, SAL-LPS, male, replicate 1-0

description:
Library name: ChIP_PFC_SAL-LPS_M_1-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: H3K27ac ChIP-seq prefrontal cortex, SAL-LPS, female, replicate 9-3

description:
Library name: ChIP_PFC_SAL-LPS_F_9-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Mouse 167aL CLE

type: RNA

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

description: Parental strain, expresses autoantigen, still has Merkel cells, lost TLR9 signaling

hyb_protocol: Hybridizations were performed per NanoString manufacturer's protocol overnight for 18h in a BioRad C1000 touch thermocycler

scan_protocol: Cartridges were run on a NanoString Sprint machine.

data_processing: Data were analyzed with nSolver software version 4.0

label: fluorescent probe

source_name: frozen skin

label_protocol: Probe labeling was performed per NanoString manufacturer's protocol.

growth_protocol: For OT2 cultures, CD4+ T cells were isolated from donor spleens, activated with anti-CD3/28 antibodies, skewed with cytokines and antibodies towards Th2, and expanded with IL-2 for a total of 10 days (see also PMIDs: 29889098, 35833127). Ten million OT2 Th2 cells were transfered into recipient mice. Lesional skin tissue was isolated from all recipient mice and frozen for future analysis. Skin was also isolated from littermate injected mice from similar anatomical sites.

extract_protocol: RNA was extracted from skin using Qiagen RNEasy mini kits per the manufacturer's instructions.

tag: cle genotype status

tag: merkel cell genotype status

value: N/A (parental strain)

value: CLE

tag: skin disease score

value: Female

value: frozen skin


title: Healthy human donor (2), CAR T cells, FOSL1-BATF-MAFA, ChIP, Rep1

description:
Library name: Acute-2F-FOSL1-BATF-MAFA-IP-Rep-1
FOSL1-BATF-MAFA_peaks.filtered.q3.s8.narrowPeak

value: Primary Human T Cell


title: Mouse 38R littermate

description: Cannot express autoantigen, lost all Merkel cells, lost TLR9 signaling

value: Atoh1flox/flox K14Cre+

value: littermate


title: NESCs, PD1 cell line, aged, biological replicate 2

description:
Library name: PD1_A_B2
Column name in gene_counts.tsv: C338_P18_O

value: aged


title: NESCs, PD1 cell line, aged, biological replicate 1

description:
Library name: PD1_A_B1
Column name in gene_counts.tsv: C338_P17_O


title: H3K27ac ChIP-seq prefrontal cortex, SAL-LPS, female, replicate 4-4

description:
Library name: ChIP_PFC_SAL-LPS_F_4-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Mouse 38O littermate

description: Cannot express autoantigen, lost half Merkel cells, lost TLR9 signaling

value: Atoh1flox/wt K14Cre+


title: Healthy human donor (3), CAR T cells, BATF, ChIP, Rep2

description:
Library name: Acute-3D-BATF-IP-Rep-2
BATF_peaks.filtered.q3.s8.narrowPeak

value: Healthy Donor 3

value: BATF


title: Healthy human donor (2), CAR T cells, GFP, ChIP, Rep1

description:
Library name: Acute-2E-GFP-IP-Rep-1
GFP_peaks.filtered.q3.s8.narrowPeak

value: Healthy Donor 2

value: GFP


title: RNA-seq hippocampus, MOR-LPS, female, replicate 15-1

description: Library name: RNA_Hippo_MOR-LPS_F_15-1

value: hippocampus

value: wild type

value: MOR-LPS


title: 1362_IDIM(T)_2

value: IM-treated

value: Pro-B cell line lysate


title: NESCs, PD1 cell line, control, biological replicate 3

description:
Library name: PD1_Y_B3
Column name in gene_counts.tsv: C338_P7_Y

value: hiPSC-derived Neural Epithelial Stem Cells

value: control


title: Healthy human donor (3), CAR T cells, BATF2, Input, Rep1

description: Library name: Acute-3K-BATF2-N-Rep-1


title: H3K27ac ChIP-seq prefrontal cortex, SAL-LPS, female, replicate 4-0

description:
Library name: ChIP_PFC_SAL-LPS_F_4-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: prefrontal cortex

value: SAL-LPS


title: NESCs, PD2 cell line, aged, biological replicate 3

description:
Library name: PD2_A_B3
Column name in gene_counts.tsv: T4M_P19_O


title: 1350-IDIM(T)


title: Healthy human donor (3), CAR T cells, MAFF-ATF3-BATF2, ChIP, Rep1

description:
Library name: Acute-3G-MAFF-ATF3-BATF2-IP-Rep-1
MAFF-ATF3-BATF2_peaks.filtered.q3.s8.narrowPeak

value: Primary Human T Cell

value: FLAG (Sigma, F1804)


title: Healthy human donor (2), CAR T cells, BATF, Input, Rep1

description: Library name: Acute-2D-BATF-N-Rep-1


title: NESCs, PD1 cell line, control, biological replicate 2

description:
Library name: PD1_Y_B2
Column name in gene_counts.tsv: C338_P6_Y


title: H3K27ac ChIP-seq prefrontal cortex, SAL-SAL, male, replicate 1-1

description:
Library name: ChIP_PFC_SAL-SAL_M_1-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: SAL-SAL


title: H3K27ac ChIP-seq prefrontal cortex, SAL-LPS, female, replicate 3-1

description:
Library name: ChIP_PFC_SAL-LPS_F_3-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Healthy human donor (3), CAR T cells, GFP, Input, Rep1

description: Library name: Acute-3E-GFP-N-Rep-1


title: Healthy human donor (3), CAR T cells, FOS, ChIP, Rep1

description:
Library name: Acute-3C-FOS-IP-Rep-1
FOS_peaks.filtered.q3.s8.narrowPeak

value: FOS


title: Healthy human donor (3), CAR T cells, BATF, Input, Rep1

description: Library name: Acute-3D-BATF-N-Rep-1

value: Healthy Donor 3


title: NESCs, PD2 cell line, control, biological replicate 3

description:
Library name: PD2_Y_B3
Column name in gene_counts.tsv: T4M_P7_Y


title: Healthy human donor (2), CAR T cells, BATF, ChIP, Rep1

description:
Library name: Acute-2D-BATF-IP-Rep-1
BATF_peaks.filtered.q3.s8.narrowPeak

value: BATF


title: H3K27ac ChIP-seq prefrontal cortex, SAL-LPS, female, replicate 2-0

description:
Library name: ChIP_PFC_SAL-LPS_F_2-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: NESCs, PD1 cell line, control, biological replicate 1

description:
Library name: PD1_Y_B1
Column name in gene_counts.tsv: C338_P5_Y


title: H3K27ac ChIP-seq prefrontal cortex, SAL-SAL, female, replicate 4-3

description:
Library name: ChIP_PFC_SAL-SAL_F_4-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Healthy human donor (2), CAR T cells, FOS, Input, Rep1

description: Library name: Acute-2C-FOS-N-Rep-1

value: Healthy Donor 2


title: Healthy human donor (3), CAR T cells, JUN, ChIP, Rep1

description:
Library name: Acute-3B-JUN-IP-Rep-1
JUN_peaks.filtered.q3.s8.narrowPeak

value: JUN


title: NESCs, HT cell line, aged, biological replicate 3

description:
Library name: HT_A_B3
Column name in gene_counts.tsv: A13_P19_O

value: HT

value: wt

value: aged


title: H3K27ac ChIP-seq prefrontal cortex, SAL-SAL, female, replicate 9-4

description:
Library name: ChIP_PFC_SAL-SAL_F_9-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type


title: H3K27ac ChIP-seq prefrontal cortex, SAL-LPS, female, replicate 2-2

description:
Library name: ChIP_PFC_SAL-LPS_F_2-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Healthy human donor (2), CAR T cells, FOS, ChIP, Rep1

description:
Library name: Acute-2C-FOS-IP-Rep-1
FOS_peaks.filtered.q3.s8.narrowPeak


title: Healthy human donor (3), CAR T cells, JUN-FOS-BATF, ChIP, Rep1

description:
Library name: Acute-3A-JUN-FOS-BATF-IP-Rep-1
JUN-FOS-BATF_peaks.filtered.q3.s8.narrowPeak

value: JUN-FOS-BATF


title: NESCs, PD1 GC cell line, aged, biological replicate 3

description:
Library name: PD1GC_A_B3
Column name in gene_counts.tsv: T4GC_P19_O

value: PD1 GC

value: hiPSC-derived Neural Epithelial Stem Cells

value: LRRK2-G2019S gene corrected


title: Mouse 141O CLE

description: Parental strain, expresses autoantigen, still has Merkel cells, lost TLR9 signaling

value: N/A (parental strain)

value: CLE

value: Female

value: frozen skin


title: H3K27ac ChIP-seq prefrontal cortex, SAL-LPS, female, replicate 10-2

description:
Library name: ChIP_PFC_SAL-LPS_F_10-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: prefrontal cortex

value: SAL-LPS


title: Healthy human donor (2), CAR T cells, ATF3, Input, Rep1

description: Library name: Acute-2J-ATF3-N-Rep-1

value: Primary Human T Cell


title: NESCs, HT cell line, aged, biological replicate 2

description:
Library name: HT_A_B2
Column name in gene_counts.tsv: A13_P18_O


title: NESCs, HT cell line, aged, biological replicate 1

description:
Library name: HT_A_B1
Column name in gene_counts.tsv: A13_P17_O


title: Input control prefrontal cortex, SAL-LPS, female

description:
Library name: Input_PFC_SAL-LPS_F
Input control (pooled)


title: Healthy human donor (2), CAR T cells, JUN, Input, Rep1

description: Library name: Acute-2B-JUN-N-Rep-1

value: Healthy Donor 2


title: Healthy human donor (2), CAR T cells, JUN, ChIP, Rep1

description:
Library name: Acute-2B-JUN-IP-Rep-1
JUN_peaks.filtered.q3.s8.narrowPeak

value: JUN

value: FLAG (Sigma, F1804)


title: NESCs, HT cell line, control, biological replicate 3

description:
Library name: HT_Y_B3
Column name in gene_counts.tsv: A13_P7_Y

value: HT

value: wt

value: control


title: H3K27ac ChIP-seq prefrontal cortex, MOR-SAL, male, replicate 8-0

description:
Library name: ChIP_PFC_MOR-SAL_M_8-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type

value: MOR-SAL


title: H3K27ac ChIP-seq prefrontal cortex, SAL-LPS, male, replicate 3-3

description:
Library name: ChIP_PFC_SAL-LPS_M_3-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Healthy human donor (2), CAR T cells, JUN-FOS-BATF, Input, Rep1

description: Library name: Acute-2A-JUN-FOS-BATF-N-Rep-1

value: JUN-FOS-BATF


title: Mouse 33R Merkel het CLE

description: Expresses autoantigen, lost half Merkel cells, lost TLR9 signaling

value: Atoh1flox/wt K14Cre+

value: Merkel het CLE


title: Mouse 152L CLE

value: N/A (parental strain)

value: CLE


title: NESCs, HT cell line, control, biological replicate 2

description:
Library name: HT_Y_B2
Column name in gene_counts.tsv: A13_P6_Y

value: hiPSC-derived Neural Epithelial Stem Cells


title: Mouse 36L Merkel het CLE

value: Female

value: frozen skin


title: H3K27ac ChIP-seq prefrontal cortex, MOR-SAL, male, replicate 13-1

description:
Library name: ChIP_PFC_MOR-SAL_M_13-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: prefrontal cortex


title: Healthy human donor (2), CAR T cells, JUN-FOS-BATF, ChIP, Rep1

description:
Library name: Acute-2A-JUN-FOS-BATF-IP-Rep-1
JUN-FOS-BATF_peaks.filtered.q3.s8.narrowPeak

value: Primary Human T Cell

value: Healthy Donor 2


title: Mouse 23O littermate

description: Cannot express autoantigen, still has Merkel cells, lost TLR9 signaling

value: Atoh1wt/wt K14Cre-

value: littermate


title: Mouse 23RL littermate

description: Cannot express autoantigen, still has Merkel cells

value: Atoh1flox/flox K14Cre-


title: Healthy human donor (2), CAR T cells, FOSL1, Input, Rep1

description: Library name: Acute-2H-FOSL1-N-Rep-1


title: Healthy human donor (2), CAR T cells, MAFF-ATF3-BATF2, Input, Rep1

description: Library name: Acute-2G-MAFF-ATF3-BATF2-N-Rep-1


title: NESCs, HT cell line, control, biological replicate 1

description:
Library name: HT_Y_B1
Column name in gene_counts.tsv: A13_P5_Y

value: HT

value: wt

value: control


title: Plasmid

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

description: Plasmid

data_processing:
The dual-sgRNA CRISPR screen data were pre-processed to acquire paired spacer sequences of each guide via Cutadapt v3.4 92. Briefly, reads were trimmed in paired-end mode to remove flanking sequences of the sgRNA spacers, first removing the 5’ adaptors (Read 1:  5’-GTTTCAGAGCTATGCTGG; Read 2: 5’-CAAGGCTTTTCTCCAAGG) and then 3’ adaptors (Read 1:  5’-GGAAAGGACGAAACACCG; Read 2: 5’-TATTTCTAGCTCTAAAAC). The paired spacers were then filtered to include those with a length of > 18 nt. The pre-processed spacer sequences were then aligned to the paired sgRNA library reference, comprised of joined spacer sequences without gaps, using Bowtie v1.3.0 93 (parameters: -v2 -m2 --suppress 1,4,5,6,7 -I 26 --chunkmbs 2000 --fr -X 100 --best ).
Assembly: Custom CRISPR library sequences were used for alignment
Supplementary files format and content: Processed data is in a tab-delimited file, where the first column = sgRNA name, second column = gene name, and every other column are the CRISPR library counts for each sample.

organism: synthetic construct

extract_protocol:
Method 1: for cells less than 1 × 105, cells were directly resuspended in 100 μL QuickExtract solution (Epicenter), incubated at 65 °C for 30 min to lyse the cell, and 95 °C for 5 min to denature proteins.
Method 2: for cell number between 1 × 105 to 2 × 106, QIAmp Fast DNA Tissue Kit (QIAGEN) was used in accordance with manufacturer’s protocol.
Genomic DNA of whole tumor or spleen samples were harvested for library readout PCR. CRISPR screen sample sgRNA library readout was performed by a two-step PCR. For PCR #1, two primers were used to pre-amplify the dual-sgRNA containing region:
Forward: AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTTCG
Reverse: GGCTGCAGGAATTCGATATCAAGC
In a 100 μL readout PCR system, 1 μg spleen or cell sample gDNA, or 2 μg tumor gDNA was used as input. 20 PCR reactions were used to ensure the coverage of the library. gDNA was PCR amplified using Phusion Flash 2× PCR Master Mix (ThermoFisher) according to manufacturer’s protocol, in 28 cycles with Tm = 62.4 °C.
The products from PCR #1 were pooled for each sample, then used for a second amplification using barcoded PCR primers (Supplementary information - Oligos). In a 50 μL readout PCR system, at least four PCR #2 reactions were carried out for each sample, using 2 µL of the pooled PCR #1 product for each reaction, in 28 cycles with Tm = 67.2 °C. PCR #2 products were pooled, normalized, and pooled together. The pooled PCR product was purified through a 2% E-gel EX (Life Technologies) and the QiaQuick kit (QIAGEN). The purified, pooled library was quantified using BioAnalyzer (Agilent), and then sequenced by Illumina NovaSeq 6000 system.


title: NESCs, PD1 GC cell line, control, biological replicate 2

description:
Library name: PD1GC_Y_B2
Column name in gene_counts.tsv: T4GC_P6_Y

value: PD1 GC

value: LRRK2-G2019S gene corrected


title: Mouse 23R Merkel het CLE

description: Expresses autoantigen, lost half Merkel cells

value: Atoh1flox/wt K14Cre+

value: Merkel het CLE


title: Mouse 23L Merkel het CLE


title: Blood C038

city: Singapore

first: Jia Ming

last: Low

address: NUHS Tower Block, 1E Kent Ridge Road, Singapore 119228

country: Singapore

institute: National University Hospital

description:
Library name: C038_Mom_PBMC_T1
Blood

data_processing:
Demultiplexed FASTQ files were processed using Cell Ranger (10x Genomics)
Gene expression matrices were imported into Seurat (v4.4.0)
Cells with fewer than 250 detected genes, fewer than 500 UMIs, or greater than 10% mitochondrial transcripts were excluded.
Data were normalized, scaled, and integrated across samples using standard Seurat workflows.
Dimensionality reduction was performed using principal component analysis and Uniform Manifold Approximation and Projection (UMAP).
Cell clusters were identified and annotated on canonical marker gene expression.
Annotated datasets were exported as count matrices, metadata tables, and a Seurat object for public deposition.
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz contains gene expression count matrices;
Supplementary files format and content: barcodes.tsv.gz contains cell barcodes; features.tsv.gz contains gene features;
Supplementary files format and content: cell_metadata.csv.gz contains cell-level annotations;
Supplementary files format and content: sample_metadata.csv.gz contains sample-level metadata;
Supplementary files format and content: MILK_final_annotated_seurat_object_CORRECTED.rds contains the annotated Seurat object used for downstream analyses.

source_name: Peripheral blood mononuclear cells

growth_protocol: Lactating mothers were recruited under an institutional review board approved study. Human breast milk and peripheral blood samples were collected longitudinally across lactation.

extract_protocol:
Cells were isolated from fresh breast milk and peripheral blood mononuclear cells. Single-cell suspensions were processed according to standard laboratory protocols prior to sequencing.
Single-cell libraries were generated using the 10x Genomics Chromium platform according to the manufacturer's instructions.

treatment_protocol: No experimental treatment was administered. Samples were collected observationally.

value: Peripheral blood mononuclear cells

value: female

value: wild type


title: Mouse 167aLL CLE

description: Parental strain, expresses autoantigen, still has Merkel cells, lost TLR9 signaling

value: N/A (parental strain)

value: CLE

value: Female

value: frozen skin


title: Healthy human donor (2), CAR T cells, MAFF-ATF3-BATF2, ChIP, Rep1

description:
Library name: Acute-2G-MAFF-ATF3-BATF2-IP-Rep-1
MAFF-ATF3-BATF2_peaks.filtered.q3.s8.narrowPeak

value: Primary Human T Cell

value: Healthy Donor 2

value: FLAG (Sigma, F1804)


title: H3K27ac ChIP-seq prefrontal cortex, MOR-SAL, male, replicate 17-4

description:
Library name: ChIP_PFC_MOR-SAL_M_17-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: prefrontal cortex

value: MOR-SAL


title: Healthy human donor (3), CAR T cells, ATF3, RNA

description:
Library name: Acute_3J-ATF3_RNA
Column name in both processed data files: 'Acute_3J'

data_processing:
Basecalls were performed using bcl-convert Version 4.4.6 from Illumina
Reads were pre-processed and pseudoaligned for transcript quantification using Salmon (v1.5.2) and the nf-core/rnaseq pipeline (v3.5) with default parameters.
DESeq2 (v1.50.2) was used to variance-stabilize (normalized) Salmon quantifications (raw).
Assembly: hg38
Supplementary files format and content: Two csv files, one for raw counts and one for normalized (DESeq VST) counts; column names correspond to Samples in both.

growth_protocol: Primary human T cells were negatively selected from PBMCs isolated from leukoreduction chambers from three healthy blood donors and activated by CD3/28 agonism in X-VIVO 15 supplemented with 5% FBS and 50 IU/mL recombinant human IL-2. 48 hours post-activation, T cells were electroporated with Cas9 ribonucleoprotein and a plasmid homology-directed repair template to enable integration of a multicistronic cassette encoding tNGFR, CD19-28z and variable natural and engineered FLAG-tagged AP-1 transcription factors within the continuous reading frame of the TRAC locus. Pre- and post-editing cells were maintained at 0.5-1e6/ml. Six days post-editing, CAR T cells were challenged with CD19-expressing Nalm6 targets (leukemia cell line, 1:8 Effector:Target ratio, 72-hour co-culture).

extract_protocol:
2e5-5e5 live CAR T cells (tNGFR+) were enriched magnetically and RNA was isolated using Qiagen RNeasy Micro or Mini Kits, including DNase treatment.
25-100ng of RNA based on Qubit quantification (Thermo Fisher) was inputted into the Illumina Stranded mRNA Prep workflow and resultant libraries were quantified by Qubit and size-verified on an Agilent TapeStation. Sequencing was performed on a NovaSeq X (Illumina) with the following read structure: 151 bp Read 1, 12 bp i7 Index, 24 bp i5 Index, 151 bp Read 2.

value: Healthy Donor 3


title: Healthy human donor (3), CAR T cells, BATF2, RNA

description:
Library name: Acute_3K-BATF2_RNA
Column name in both processed data files: 'Acute_3K'


title: H3K27ac ChIP-seq prefrontal cortex, MOR-SAL, male, replicate 6-1

description:
Library name: ChIP_PFC_MOR-SAL_M_6-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Blood C011

description:
Library name: C011_Blood_T1
Blood


title: Healthy human donor (3), CAR T cells, MAFF, RNA

description:
Library name: Acute_3I-MAFF_RNA
Column name in both processed data files: 'Acute_3I'

value: MAFF


title: Blood C010

description:
Library name: C010_Blood_T1
Blood


title: Healthy human donor (3), CAR T cells, FOSL1, RNA

description:
Library name: Acute_3H-FOSL1_RNA
Column name in both processed data files: 'Acute_3H'


title: H3K27ac ChIP-seq prefrontal cortex, MOR-SAL, male, replicate 14-1

description:
Library name: ChIP_PFC_MOR-SAL_M_14-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: H3K27ac ChIP-seq prefrontal cortex, MOR-SAL, male, replicate 17-2

description:
Library name: ChIP_PFC_MOR-SAL_M_17-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Primary endometrial culture_biologycal rep_3

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

description: Gene expression data from endometrium cells

hyb_protocol: Samples were hybridized to the array at 45°C for 16 hours, followed by washing. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip™ Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 7g GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 7g

data_processing:
The data were analyzed with Transcriptome Analysis Console (TAC) Software  version 4.0.3.14 using Affymetrix default analysis settings and SST RMA algorithm
The data were analyzed with Transcriptome Analysis Console (TAC) Software  version 4.0.2 using Affymetrix default analysis settings and RMA algorithm

source_name: primary endometrial cultureRNA

label_protocol:
Transcriptome analysis was performed using the Clariom™ S Assay human microarray (Applied Biosystems™). After RNA isolation, reverse transcription was performed using the WT Amplification Kit to synthesize first- and second-strand cDNA, cRNA, and single-stranded cDNA, incubating them at appropriate temperatures and purifying them using magnetic beads. Single-stranded cDNA was then fragmented and labeled with biotin.
Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol:
Endometrium supplemented with 50 ng/ml of exosomes  obtained from the conditioned medium of MSCs was collected and lysed in MagZol reagent for subsequent RNA extraction.
Macrophages samples were collected, frozen, lysed in QIAZOL reagent for the following RNA extraction

extract_protocol:
Total RNA was isolated from primary endometrial culture using MagZol reagent according to a standard protocol.
Ordinary extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol:
Primary endometrial culture without exasomes served as a control. Exasomes obtained from the conditioned medium of MSCs were added to the primary endometrial culture at a concentration of 50 ng/ml. The endometrium was incubated with the exosomes for 24 hours.
Macrophages samples were cellected on different time periods after cocultivation with Ito cells, CD146cells, HGF/cultivation with MCSF

value: primary endometrial culture


title: Primary endometrial culture_biologycal rep_2


title: NESCs, PD1 cell line, aged, biological replicate 3

description:
Library name: PD1_A_B3
Column name in gene_counts.tsv: C338_P19_O

value: hiPSC-derived Neural Epithelial Stem Cells

value: aged


title: Healthy human donor (2), CAR T cells, FOSL1-BATF-MAFA, Input, Rep1

description: Library name: Acute-2F-FOSL1-BATF-MAFA-N-Rep-1


title: Input control prefrontal cortex, MOR-SAL, male

description:
Library name: Input_PFC_MOR-SAL_M
Input control (pooled)


title: Blood C008

description:
Library name: C008_Blood_T1
Blood

value: Peripheral blood mononuclear cells


title: Healthy human donor (3), CAR T cells, MAFF-ATF3-BATF2, RNA

description:
Library name: Acute_3G-MAFF-ATF3-BATF2_RNA
Column name in both processed data files: 'Acute_3G'


title: Mature C038

description:
Library name: C038_BM_T3
Mature

source_name: Breast milk

value: Breast milk

value: female

tag: Stage

value: Mature


title: Healthy human donor (3), CAR T cells, FOSL1-BATF-MAFA, RNA

description:
Library name: Acute_3F-FOSL1-BATF-MAFA_RNA
Column name in both processed data files: 'Acute_3F'


title: H3K27ac ChIP-seq prefrontal cortex, MOR-SAL, female, replicate 7-3

description:
Library name: ChIP_PFC_MOR-SAL_F_7-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type


title: Colostrum C038

description:
Library name: C038_BM_T1
Colostrum

value: Colostrum


title: H3K27ac ChIP-seq prefrontal cortex, MOR-SAL, female, replicate 7-2

description:
Library name: ChIP_PFC_MOR-SAL_F_7-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Mature C011

description:
Library name: C011_BM_T3
Mature


title: Healthy human donor (3), CAR T cells, BATF, RNA

description:
Library name: Acute_3D-BATF_RNA
Column name in both processed data files: 'Acute_3D'

value: BATF


title: Colostrum C011

description:
Library name: C011_BM_T1
Colostrum


title: H3K27ac ChIP-seq prefrontal cortex, MOR-SAL, female, replicate 15-2

description:
Library name: ChIP_PFC_MOR-SAL_F_15-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Mature C010

description:
Library name: C010_BM_T3
Mature


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, male, replicate 6-4

description:
Library name: ChIP_PFC_MOR-LPS_M_6-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: MOR-LPS


title: Input control prefrontal cortex, MOR-SAL, female

description:
Library name: Input_PFC_MOR-SAL_F
Input control (pooled)


title: Puck_230807_27

city: New Haven

first: Hattie

last: Chung

address: 300 George St

description: Library name: 2024-03-21_Puck_230807_27

data_processing:
Raw sequencing data were processed using the Slide-seq pipeline following Stickels et al. Nat Biotech 2021.
Assembly: mm10
Supplementary files format and content: [puck_name].h5ad: processed raw counts of beads (rows) and genes (columns)
Library strategy: Spatial Transcriptomics

source_name: Ovary

growth_protocol: Female C57BL/6 mice were maintained under SPF conditions on a 12-hour light-dark cycle with standard chow and water provided ad libitum.

extract_protocol:
10µm frozen sections were cut on the cryostat
Spatial transcriptome libraries were prepared using the Slide-seq V2 protocol

treatment_protocol: Mice were staged near-daily for their estrous cycle and harvested at the estrus or metestrus stage via intracardial perfusion with PBS. Ovaries were fresh frozen embedded in OCT.

value: Ovary

value: Estrus

value: Young


title: Colostrum C010

description:
Library name: C010_BM_T1
Colostrum


title: Transitional C003

description:
Library name: C003_BM_T1
Transitional milk

value: Transitional


title: Puck_240129_33

description: Library name: 2024-03-04_Puck_240129_33

value: Metestrus

value: Middle


title: Healthy human donor (3), CAR T cells, JUN-FOS-BATF, RNA

description:
Library name: Acute_3A-JUN-FOS-BATF_RNA
Column name in both processed data files: 'Acute_3A'

value: Primary Human T Cell

value: Healthy Donor 3

value: JUN-FOS-BATF


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, male, replicate 17-3

description:
Library name: ChIP_PFC_MOR-LPS_M_17-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: prefrontal cortex


title: H3K27ac ChIP-seq prefrontal cortex, SAL-LPS, female, replicate 9-1

description:
Library name: ChIP_PFC_SAL-LPS_F_9-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: SAL-LPS


title: Healthy human donor (2), CAR T cells, BATF2, RNA

description:
Library name: Acute_2K-BATF2_RNA
Column name in both processed data files: 'Acute_2K'

value: Healthy Donor 2


title: Transitional C008

description:
Library name: C008_BM_T1
Transitional milk

value: Breast milk

value: female


title: Primary endometrial culture +50 ng/ml of exosomes_biologycal rep_1

description: Gene expression data from endometrium cells +50 ng/ml of exosomes obtained from the conditioned medium of MSCs

value: primary endometrial culture + 50 ng/ml of exosomes obtained from the conditioned medium of multipotent mesenchymal stromal cells (MMSCs)


title: Primary endometrial culture +50 ng/ml of exosomes_biologycal rep_3


title: Adult mouse brain Xenium cohort

city: Irvine

first: Saurabh

last: Chatterjee

state: California

address: 847 Health Sciences Road

department: Department of Environmental and Occupational Health

institute: University of California, Irvine

description: Adult cohort from Xenium run ChatS_10032025; sample_map.csv includes control_1-control_4 and heatstress_1-heatstress_4 across areas 1-4. Heat-stress mice received periodic heat exposure at approximately 40 deg C for 3 hours/day for 14-15 days; slide ID 0069979; panel Xenium Mouse Brain Gene Expression (mBrain_v1.1); instrument XETG00221; analysis software xenium-4.0.1.0.

hyb_protocol: The Xenium Mouse Brain Gene Expression panel (mBrain_v1.1; 247 predesigned targets; chemistry v1) was used by the UCI Genomics Research and Technology Hub for in situ probe hybridization. Panel probes were hybridized to target RNAs, washed, ligated/circularized, and amplified by rolling-circle amplification according to the 10x Genomics Xenium workflow before imaging and decoding.

scan_protocol: Imaging, decoding, quality score generation, and segmentation were performed using the Xenium Analyzer system. Instrument software version 4.0.1.4; analysis software xenium-4.0.1.0; instrument serial XETG00221; pixel size 0.2125 um; z-step size 3.0 um.

data_processing: Decoded transcripts and cell segmentation outputs were generated by Xenium Onboard Analysis version xenium-4.0.1.0. Processed outputs for each cohort include cell_feature_matrix.h5, MEX matrix files, cells.parquet, cell_boundaries.parquet, nucleus_boundaries.parquet, and coordinates.csv.

source_name: brain

extract_protocol: tissue preparation protocol: FFPE mouse brain tissue sections were processed by the UCI Genomics Research and Technology Hub using the 10x Genomics Xenium FFPE tissue preparation workflow. Sections were mounted on Xenium slides, baked/deparaffinized, rehydrated, subjected to target retrieval and enzymatic permeabilization, post-fixed, and equilibrated for in situ hybridization.

treatment_protocol: Heat-stress mice received periodic heat exposure at approximately 40 deg C for 3 hours/day for 14-15 days. Control and heat-stress sample annotations are recorded in sample_map.csv.

value: brain

tag: tissue preservation method

value: FFPE

value: control and periodic heat exposure (~40 deg C, 3 hours/day for 14-15 days)


title: Healthy human donor (3), CAR T cells, JUN, RNA

description:
Library name: Acute_3B-JUN_RNA
Column name in both processed data files: 'Acute_3B'

value: JUN


title: Puck_240129_37

description: Library name: 2024-03-02_Puck_240129_37

value: Ovary

value: Estrus

tag: group

value: Young


title: Healthy human donor (3), CAR T cells, FOS, RNA

description:
Library name: Acute_3C-FOS_RNA
Column name in both processed data files: 'Acute_3C'

tag: individual

value: FOS


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, male, replicate 6-0

city: la jolla

first: Yanmiao

last: Du

address: 4254 Urey Hall, 9500 Gilman Drive

description:
Library name: ChIP_PFC_MOR-LPS_M_6-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type

value: MOR-LPS


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, male, replicate 17-1

description:
Library name: ChIP_PFC_MOR-LPS_M_17-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Primary endometrial culture_biologycal rep_1

description: Gene expression data from endometrium cells

value: primary endometrial culture


title: Puck_240129_35

description: Library name: 2024-03-04_Puck_240129_35

value: Metestrus

value: Middle


title: Mature C008

description:
Library name: C008_BM_T3
Mature

value: Mature


title: Healthy human donor (2), CAR T cells, ATF3, RNA

description:
Library name: Acute_2J-ATF3_RNA
Column name in both processed data files: 'Acute_2J'

value: Primary Human T Cell

value: Healthy Donor 2

tag: tf expressed


title: Healthy human donor (3), CAR T cells, GFP, RNA

description:
Library name: Acute_3E-GFP_RNA
Column name in both processed data files: 'Acute_3E'

value: Healthy Donor 3

value: GFP


title: Primary endometrial culture +50 ng/ml of exosomes_biologycal rep_2

value: primary endometrial culture + 50 ng/ml of exosomes obtained from the conditioned medium of multipotent mesenchymal stromal cells (MMSCs)


title: Healthy human donor (2), CAR T cells, FOSL1-BATF-MAFA, RNA

description:
Library name: Acute_2F-FOSL1-BATF-MAFA_RNA
Column name in both processed data files: 'Acute_2F'


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, male, replicate 13-2

description:
Library name: ChIP_PFC_MOR-LPS_M_13-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: prefrontal cortex


title: H3K27ac ChIP-seq prefrontal cortex, MOR-LPS, male, replicate 14-4

description:
Library name: ChIP_PFC_MOR-LPS_M_14-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Puck_240129_25

description: Library name: 2024-03-02_Puck_240129_25


title: Input control prefrontal cortex, MOR-LPS, male

description:
Library name: Input_PFC_MOR-LPS_M
Input control (pooled)


title: Puck_240129_31

description: Library name: 2024-03-02_Puck_240129_31


title: Healthy human donor (2), CAR T cells, MAFF-ATF3-BATF2, RNA

description:
Library name: Acute_2G-MAFF-ATF3-BATF2_RNA
Column name in both processed data files: 'Acute_2G'