title: 10E_ap2hsKO_plusCHO_rep2_IP

description:
Library name: 10E_ap2hsKO_plusCHO_rep2_IP
10E_ap2hsKO_plusCHO_rep2_IP

tag: genotype

tag: treatment

value: H3K9me3 (Diagenode, C15410193)


title: ASD mouse PFC snRNA-seq [P131_HvM_2 + P131_HfM_2 + P131_HLM_2 + TBR1_HvM_2] (4-plex OCM)

status: Public on Jul 28 2026

type: SRA

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

description:
Library name: 1020-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

library_source: transcriptomic single cell

data_processing:
Per-library FASTQ files were demultiplexed in silico into the four constituent mice using the Cell Ranger multi pipeline (10x Genomics), with mouse-specific reads assigned via OCM barcodes and aligned to the mouse reference genome to generate per-nucleus gene count matrices.
Downstream processing was performed in Seurat v5.0. Low-quality nuclei were filtered (<750 or >8000 detected genes, <1000 or >30000 UMI counts, >5% mitochondrial reads). Top 3000 highly variable genes per sample were used; expression values were normalised and scaled.
Principal component analysis was performed and sequencing-batch effects were corrected with Harmony. Visualisation used UMAP and clustering used a shared nearest-neighbour graph at resolution 0.3.
Clusters were annotated by reference-based label transfer using Seurat MapQuery against the Allen Brain Cell Atlas scRNA-seq reference (GSE246717; 3 donors, 64,409 isocortex cells, 12 cell classes), followed by manual curation. The 19 clusters were mapped to 10 major cell classes.
Relative cell-class proportions were computed per mouse, stratified by genotype, sex, treatment, and Group 1 / Group 2 transcriptomic class.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Each GSM (tube) is associated with four per-sample MEX triplets (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) produced by Cell Ranger multi `per_sample_outs/`, one set per multiplexed mouse. File naming convention: <mouse_id>__barcodes.tsv.gz, <mouse_id>__features.tsv.gz, <mouse_id>__matrix.mtx.gz (double underscore between mouse_id and file type).
Supplementary files format and content: 10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing (OCM). Four mouse-specific nuclei suspensions per GEM well; demultiplexed in silico via Cell Ranger multi. OCM barcodes are hardware-encoded in the chip (not antibody-based CMO/HTO), so feature_reference.csv is not applicable. Mouse <-> OCM-slot mapping per tube is provided in mouse_to_pool.tsv.

molecule: nuclear RNA

organism: Mus musculus

source_name: prefrontal cortex

growth_protocol: All mice were housed under a 12 h light/dark cycle with ad libitum access to food and water. Procedures were approved by the Committee of Animal Research and Ethics at KAIST (KA2024-093-v1) and followed the Korean Laboratory Animal Act.

extract_protocol:
Nuclei were isolated from frozen prefrontal cortex tissue using a lysis buffer of 0.25 M sucrose, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 25 mM KCl, 0.1% Triton X-100, 1 mM DTT and 0.2 U/uL RNAse inhibitor (Protector, Sigma). Tissue was homogenised in 1 mL lysis buffer using a Nano pestle, incubated 5 min on ice and filtered through a 70 um strainer (MACS SmartStrainer, Miltenyi). Filtered samples were centrifuged at 500 g for 5 min at 4 C, resuspended in 1 mL lysis buffer, filtered through a 30 um strainer, centrifuged again at 500 g for 5 min at 4 C, and resuspended in PBS with 0.04% BSA. Nuclei were counted on a Countess 3 (Thermo Fisher).
Four mouse-specific nuclei suspensions were tagged with 10x Genomics On-Chip Multiplexing (OCM) barcodes and pooled prior to loading. Libraries were prepared with the Chromium GEM-X Universal 3' Gene Expression kit v4 with 4-plex On-Chip Multiplexing (10x Genomics) according to the manufacturer's instructions, yielding one paired Gene Expression library per GEM well (tube).

treatment_protocol: From P3 to P25, dams received drinking water containing vehicle (0.2% saccharin), fluoxetine (10 mg/L in saccharin water), or lithium carbonate (600 mg/L in saccharin water). Pups were exposed via maternal milk.

tag: tissue

value: prefrontal cortex

tag: cell type

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

tag: age

value: postnatal day 25

tag: sex (pool_composition)

value: male; male; male; male

tag: genotype (pool_composition)

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

tag: treatment (pool_composition)

value: vehicle; fluoxetine; lithium; vehicle

tag: mouse line_(pool_composition)

value: Pten; Pten; Pten; Tbr1

tag: multiplexed mouse_ids

tag: n samples_per_pool

tag: sequencing batch


title: 3_HKM7VBGXT.3.GCGTAGTA_TATGCAGT

city: Helsinki

first: Olli

last: Pietilainen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: 3_SM-NBW84_plate1
DHMT_2hr_c

library_source: transcriptomic

data_processing:
To identify cell-type-specific gene expression profiles, the fastq files of the bulk RNA-seq data were aligned to a mixed human-mouse reference genome (GRCh37/hg19 and GRCm38/mm10, GSE63269) using STAR65 (v.2.5). As quality control, Illumina adapters and low-quality base bares were trimmed using Trimmomatic66 (v.0.36) and short reads (< 36 base pairs) were removed. Next the reads were annotated with GENCODE GTF annotation version 19 and a custom GTF file for the mixed genome (GSE63269) for the mixed genome. A raw counts matrix was generated using featureCounts67 by Rsubread (v.1.32). Genes with a total read count less than 10 were filtered using filterByExpr function in edgeR68 (v. 4.2.0). Read counts were then normalized for library size (method = TMM) and transformed to log2 counts-per-million (logCPM) estimates using the voom function by limma69 (v. 3.60.3) package. The normalized logCPM gene expression matrices were used as input for all the following analyses.
Assembly: GRCh37/hg19 and GRCm38/mm10, GSE63269
Supplementary files format and content: counts_raw_all.txt contain raw counts for each sample (link: barcode).
Supplementary files format and content: counts_logCPM_human.txt contain logCPM values for all iPCS WT samples.
Supplementary files format and content: counts_logCPM_mouse.txt contain logCPM values for all astrocyte samples that have not been co-cultured CRISPRi-neurons.
Supplementary files format and content: counts_logCPM_CRISPRi_human.txt contain logCPM values for all CRISPRi-edited iPCS  samples.
Supplementary files format and content: counts_logCPM_CRISPRi_mouse.txt contain logCPM values for all astrocyte samples that have been co-cultured with CRISPRi-neurons.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow

tag: cell line

value: iPSC-derived excitatory neuron, astrocyte

value: WT

tag: day

tag: guide rna

value: no guide

tag: barcode


title: GR1395_rep2

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

description: Library name: 4031X6

data_processing:
RNA-seq data was mapped to the C. elegans genome (ce11) using the align (qAlign) function from the QuasR (version 1.34.0) package in R with splicedAlignement = TRUE, using the aligner HISAT2 (version 1.10.0) including an exon-exon junction database. Gene expression levels were quantified using the qCount() function. For annotations, coding transcript info from WormBase WS270 was used. We further compensated for differences in library sizes by scaling each library to the average library size, and log2-transformed the data using a pseudocount of 8 (log2(x+8)). Given that fragments of the genes of mlt-10, ttx-3 and col-19 occur in the arrays, we removed the affected exons from those genes to only count reads that originated from the endogenous genes as opposed to the array. To determine those affected exons, we inspected the read alignments at those loci and removed the exons at the 5' end that overlapped sections with extensive read amplification.
Assembly: ce11
Supplementary files format and content: tab-delimited text file with raw gene expression read counts
Supplementary files format and content: tab-delimited text file with normalized gene expression read counts

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole animals

growth_protocol: Starved N2, GR1935 mgIs49 [mlt-10p::gfp::pest; ttx-3::gfp] and VT1367 maIs105 [col-19::gfp] L1 animals were synchronized in M9 buffer overnight and allowed to develop for 4 hours at 25˚C.

extract_protocol:
The animals were washed three times and lysed in Trizol by repeated freeze thawing. RNA was extracted using the Direct-zol RNA Microprep kit (Zymo, R2062).
mRNA-seq libraries were generated using the Illumina Stranded mRNA Prep solution, according to the manufacturer’s protocol. Libraries were sequenced on a NovaSeq6000 flowcells, paired-end 2x56cycles. Demultiplexing was performed using bcl2fastq2.

value: whole animals

value: mgIs49 [mlt-10p::gfp::pest; ttx-3::gfp]


title: ASD mouse PFC snRNA-seq [TBR1_HfM_1 + ADNP_HLM_1 + SdC_HfM_1 + TBR1_HfM_2] (4-plex OCM)

description:
Library name: 1017-4
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: fluoxetine; lithium; fluoxetine; fluoxetine

value: Tbr1; Adnp; Shank3-deltaC; Tbr1

value: TBR1_HfM_1; ADNP_HLM_1; SdC_HfM_1; TBR1_HfM_2


title: ASD mouse PFC snRNA-seq [B6J_WvM_2 + ADNP_HvM_2 + ADNP_HfM_2 + ADNP_HLM_2] (4-plex OCM)

description:
Library name: 1020-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: wild-type; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: vehicle; vehicle; fluoxetine; lithium

value: C57BL/6J background WT; Adnp; Adnp; Adnp

value: B6J_WvM_2; ADNP_HvM_2; ADNP_HfM_2; ADNP_HLM_2


title: ASD mouse PFC snRNA-seq [Na_HvM_1 + ADNP_HfM_1 + TBR1_HvM_1 + P131_HLM_1] (4-plex OCM)

description:
Library name: 1017-3
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: prefrontal cortex

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

value: postnatal day 25

value: vehicle; fluoxetine; vehicle; lithium

value: Naa15; Adnp; Tbr1; Pten

value: Na_HvM_1; ADNP_HfM_1; TBR1_HvM_1; P131_HLM_1


title: 2_HKM7VBGXT.2.GCGTAGTA_TATGCAGT

description:
Library name: 2_SM-NBW84_plate1
DHMT_2hr_c

value: iPSC-derived excitatory neuron, astrocyte

value: WT


title: GR1395_rep1

description: Library name: 4031X5

value: whole animals


title: ASD mouse PFC snRNA-seq [Na_HfM_1 + SdC_HvM_1 + B6J_WvM_1 + P131_HfM_1] (4-plex OCM)

description:
Library name: 1017-2
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: male; male; male; male

value: heterozygous mutant; heterozygous mutant; wild-type; heterozygous mutant

value: fluoxetine; vehicle; vehicle; fluoxetine

value: Naa15; Shank3-deltaC; C57BL/6J background WT; Pten

value: Na_HfM_1; SdC_HvM_1; B6J_WvM_1; P131_HfM_1


title: 1_HKM7VBGXT.1.GCGTAGTA_TATGCAGT

description:
Library name: 1_SM-NBW84_plate1
DHMT_2hr_c

value: no guide


title: HW3826_rep2

description: Library name: 4031X4

value: maIs105 [col-19::gfp]


title: ASD mouse PFC snRNA-seq [SdC_HLM_1 + P131_HvM_1 + ADNP_HvM_1 + Na_HLM_1] (4-plex OCM)

description:
Library name: 1017-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

value: lithium; vehicle; vehicle; lithium

value: Shank3-deltaC; Pten; Adnp; Naa15

value: SdC_HLM_1; P131_HvM_1; ADNP_HvM_1; Na_HLM_1


title: TM2_male_injured72_ipsi

city: Tempe

first: Christopher

middle: L

last: Plaisier

state: Arizona

department: SBHSE

country: USA

institute: Arizona State University

description: Library name: TM2I

data_processing:
Quality control of raw reads was performed to remove low-quality reads and reads containing adapter or poly-N sequences using an in-house Perl script.
Clean RNA-sequencing data were aligned using Hisat2 v2.0.5 to the mouse genome mm10 (GCF_000001635.20).
Assembly: mm10 (GCF_000001635.20)
Supplementary files format and content: Count file for each sample.

source_name: Brain cortical punch

growth_protocol: All experiments involving animals were performed in accordance with established procedures approved by the Institutional Animal Care and Use Committee of Arizona State University (Protocol #23-1998R). Male and female 7-week-old C57BL/6J mice were purchased from Charles River Laboratories and housed under standard conditions. Upon arrival, mice were housed two per cage on ventilated racks on a 12-hr light/dark cycle. Mice had free access to a standard diet and water and were habituated for 7 days prior to experiments.

extract_protocol:
Mice designated for RNA-sequencing (n=6-9 per sex per timepoint) were transcardially perfused with diethyl pryocarbonate-treated phosphate buffer solution (DEPC PBS) until liquid ran clear from the right atria. Brains were isolated and 4mm cortical biopsy punches centered over the injury site and the contralateral cortex were collected and placed in RNA protect solution (Qiagen RNAprotect Tissue Reagent). For naive animals, the cortical punch from the right hemisphere was labelled as ipsilateral, and the left cortical punch labelled as contralateral. Tissue samples were incubated in RNAprotect overnight at 4°C and then stored at -80°C for later processing. RNA isolation was performed on the cortical tissue using the Qiagen RNeasy Lipid Tissue Mini Kit. Samples were homogenized using Qiazol lysis reagent and 2mL dounce homogenizer. Chloroform was added and mixed, then the mixture was centrifuged to isolate the aqueous phase containing RNA. Purification was performed in accordance with kit procedures, except that centrifuge speeds were increased from 8,000 to 10,000 RPM during washes, and a final wash of the membrane was performed using 80% ethanol followed by a spin at max speed for 5 min using RNAse-free water to collect the purified RNA.
The purified mRNA was isolated using poly-T magnetic beads, fragmented, and reverse transcribed into cDNA using random hexamer primers. Libraries were prepared through end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification. Quality and concentration of libraries were assessed by Qubit and real-time qPCR. Fragment size distribution was quantified using a bioanalyzer. Libraries were then pooled and sequenced on an Illumina platform, yielding ≥20 million reads per sample.

treatment_protocol: Adult 8–9-week-old mice (C57BL/6) underwent unilateral controlled cortical impacts (CCIs) over the right somatosensory cortex as previously described (12,42). Briefly, mice were anesthetized with 1.5-3% isoflurane and the surgical site was shaved. Mice were placed on a homeothermic warming system and secured in a mouse stereotactic frame. The surgical site was prepared with betadine and isopropyl prior to making a midline incision. A 3mm craniotomy was placed approximately 1mm lateral to the midline and 1mm posterior to bregma. The CCI was produced with a Leica Impact One CCI device using the following parameters: 2mm impactor tip, 6.0 m/s, 100ms duration, and 1mm depth. Any bleeding was controlled using cotton-tipped applicators and the incision was closed using 4-0 nylon sutures and subsequent topical application of a triple antibiotic ointment. Mice were given subcutaneous injections of buprenorphine (0.05 mg/kg) and sterile saline (0.5 mL) and moved to a clean warmed cage, where they were observed for 30-60 mins prior to returning to vivarium.

value: Brain cortical punch

tag: animal

tag: strain

tag: Sex

value: male

tag: location of_biopsy

value: ipsi

tag: testosterone log10_(ng/ml)

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)

tag: progesterone log10_(ng/ml)

tag: estradiol log10_(pg/ml)

tag: batch

value: C


title: 4_HKM7VBGXT.4.GGAGCTAC_TATGCAGT

description:
Library name: 4_SM-NBW83_plate1
DHMT_2hr_b

tag: cell type

value: iPSC-derived excitatory neuron, astrocyte

tag: genotype

value: WT


title: TM2_male_injured72_contra

description: Library name: TM2C

tag: tissue

tag: treatment

value: contra


title: HW3826_rep1

description: Library name: 4031X3

value: whole animals


title: Nur77_3_1h

city: Amsterdam

first: Claudia

last: van Tiel

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer 0.2.2
Reads were aligned to the mouse genome mm10 by HISAT2 2.1.0
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.16.1
Raw tag counts per gene were counted using HOMER2's analyzeRepeats.pl script
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts for each sample

growth_protocol: The RAW264.7 macrophage stable cell lines with doxycyclin-inducible expression of Nur77 or GFP were seeded at a density of 3x10^5 cells/ml and the next day Nur77 or GFP expression was induced by incubation with 50ng/ml doxycyclin for 18 h

extract_protocol:
Cells were lysed in RLT buffer and total RNA was isolated using the RNeasy mini kit with on-column DNase treatment (Qiagen)
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol

treatment_protocol: Cells were stimulated with 500 ng/ml LPS for 0, 1 and 5h

tag: cell line

value: macrophages

value: 1h 500 ng/ml LPS


title: TM1_male_injured72_ipsi

description: Library name: TM1I


title: TM1_male_injured72_contra

description: Library name: TM1C


title: 3_HKM7VBGXT.3.GGAGCTAC_TATGCAGT

description:
Library name: 3_SM-NBW83_plate1
DHMT_2hr_b

tag: day

tag: guide rna


title: N2_rep2

description: Library name: 4031X2

value: wild-type


title: TF3_female_injured72_ipsi

description: Library name: TF3I

tag: animal

value: female


title: N2_rep1

description: Library name: 4031X1


title: 2_HKM7VBGXT.2.GGAGCTAC_TATGCAGT

description:
Library name: 2_SM-NBW83_plate1
DHMT_2hr_b

value: no guide

tag: barcode


title: TF3_female_injured72_contra

description: Library name: TF3C

tag: strain

tag: Sex


title: 1_HKM7VBGXT.1.GGAGCTAC_TATGCAGT

description:
Library name: 1_SM-NBW83_plate1
DHMT_2hr_b


title: TF2_female_injured72_contra

description: Library name: TF2C

tag: location of_biopsy

tag: testosterone log10_(ng/ml)


title: Grin2b+/C456Y, Fluoxetine, male, replicate3

description: Library name: G2b_HfM_3

data_processing:
Transcript abundance was estimated with Salmon(v0.11.2) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.0) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.19.11).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

growth_protocol: Mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit  (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Preparation Guide)

value: prefrontal cortex

value: Heterozygous


title: Nrep knockout iWAT biological replicate 3

city: Zunyi

first: Hongkun

last: Li

address: Campus No. 1 Road, Zunyi City, Guizhou Province, China.

country: China

institute: Zunyi Medical University

description:
Library name: KO4_3
iWAT_gene_counts.txt

data_processing:
Raw paired-end reads from both tissue experiments were quality filtered and adapter trimmed using fastp.
Assembly: Liver: Mus musculus GRCm38, Ensembl release 94; iWAT: Mus musculus GRCm39.
Supplementary files format and content: Liver: Microsoft Excel workbook containing a complete gene-level raw read-count matrix for ML1, ML2, ML3, NL1, NL2, and NL3. Rows represent Ensembl gene identifiers, columns represent individual RNA-seq libraries, and values represent gene-level read counts generated using featureCounts.
Supplementary files format and content: iWAT: Tab-delimited matrix containing complete gene-level read counts for WT3_1, WT3_2, WT3_3, KO4_1, KO4_2, and KO4_3. Rows represent Ensembl gene identifiers, columns represent individual RNA-seq libraries, and values represent gene-level read counts.

source_name: inguinal white adipose tissue

extract_protocol:
Liver: total RNA was isolated from frozen liver tissue using TRIzol reagent. RNA degradation and contamination were assessed by agarose gel electrophoresis, and RNA purity and integrity were evaluated using a NanoPhotometer and the RNA Nano 6000 Assay Kit on an Agilent Bioanalyzer 2100. iWAT: Total RNA was extracted from inguinal white adipose tissue using QIAzol Lysis Reagent according to the manufacturer’s instructions. RNA quality was assessed using an Agilent 5300 Fragment Analyzer, and RNA concentration was measured using a NanoDrop spectrophotometer. One microgram of total RNA per sample was used for library preparation.
Liver RNA-seq libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina. Fragmented mRNA was used as the template for first-strand cDNA synthesis with random oligonucleotide primers and M-MuLV reverse transcriptase. The RNA template was subsequently degraded using RNase H, and second-strand cDNA was synthesized using DNA polymerase I and dNTPs. Purified double-stranded cDNA was subjected to end repair, dA-tailing, and sequencing-adapter ligation. cDNA fragments of approximately 250–300 bp were selected using AMPure XP beads, PCR amplified, and purified again using AMPure XP beads to generate the final libraries. Libraries were initially quantified using a Qubit 2.0 fluorometer and diluted to 1.5 ng/µL. Library fragment-size distributions were evaluated using an Agilent 2100 Bioanalyzer, and effective library concentrations were determined by quantitative PCR. Libraries with effective concentrations greater than 3 nM and acceptable fragment-size distributions were sequenced on an Illumina NovaSeq platform using a 150-bp paired-end strategy. iWAT RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep Ligation Kit. Messenger RNA was enriched from 1 microgram of total RNA by poly(A) selection using oligo(dT) magnetic beads and fragmented using fragmentation buffer. Double-stranded cDNA was synthesized using random hexamer primers, followed by end repair, phosphorylation, adapter ligation, and magnetic-bead size selection of approximately 300–400-bp fragments. Libraries were amplified by PCR for 10–15 cycles and quantified using a Qubit 4.0 fluorometer. Qualified libraries were sequenced using a 150-bp paired-end strategy on Illumina NovaSeq X Plus.

value: inguinal white adipose tissue

value: Nrep-/-


title: TF1_female_injured72_ipsi

description: Library name: TF1I

value: Brain cortical punch

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)


title: 4_HKM7VBGXT.4.ACTCGCTA_TATGCAGT

description:
Library name: 4_SM-NBW82_plate1
DHMT_2hr_a


title: Nrep knockout iWAT biological replicate 2

description:
Library name: KO4_2
iWAT_gene_counts.txt


title: 3_HKM7VBGXT.3.ACTCGCTA_TATGCAGT

description:
Library name: 3_SM-NBW82_plate1
DHMT_2hr_a


title: SM2_male_injured72_ipsi

description: Library name: SM2I

value: male

tag: progesterone log10_(ng/ml)

tag: estradiol log10_(pg/ml)


title: SM2_male_injured72_contra

description: Library name: SM2C

tag: batch


title: Nrep knockout iWAT biological replicate 1

description:
Library name: KO4_1
iWAT_gene_counts.txt

tag: genotype


title: 2_HKM7VBGXT.2.ACTCGCTA_TATGCAGT

description:
Library name: 2_SM-NBW82_plate1
DHMT_2hr_a

tag: cell type


title: SM1_male_injured72_ipsi

description: Library name: SM1I

tag: tissue

tag: treatment

value: ipsi


title: SM1_male_injured72_contra

description: Library name: SM1C

value: C


title: WT iWAT biological replicate 3

description:
Library name: WT3_3
iWAT_gene_counts.txt

value: wild type


title: SF3_female_injured72_ipsi

description: Library name: SF3I


title: SF3_female_injured72_contra

description: Library name: SF3C


title: WT iWAT biological replicate 2

description:
Library name: WT3_2
iWAT_gene_counts.txt


title: 4_HKM7VBGXT.4.TCGACGTC_CTCCTTAC

description:
Library name: 4_SM-NBW81_plate1
DHMT_48hr_LRP1_C_d

tag: cell line

value: iPSC-derived excitatory neuron, astrocyte

value: LRP1 knockdown

tag: day


title: SF2_female_injured72_contra

description: Library name: SF2C

tag: animal

value: contra


title: WT iWAT biological replicate 1

description:
Library name: WT3_1
iWAT_gene_counts.txt


title: 3_HKM7VBGXT.3.TCGACGTC_CTCCTTAC

description:
Library name: 3_SM-NBW81_plate1
DHMT_48hr_LRP1_C_d

tag: guide rna

tag: barcode


title: SF1_female_injured72_contra

description: Library name: SF1C

tag: strain

tag: Sex


title: RM2_male_injured24_ipsi

description: Library name: RM2I

tag: location of_biopsy

tag: testosterone log10_(ng/ml)

value: B


title: 2_HKM7VBGXT.2.TCGACGTC_CTCCTTAC

description:
Library name: 2_SM-NBW81_plate1
DHMT_48hr_LRP1_C_d


title: Liver, Npc1 -/-, Co-Npc1:LP, rep 4

city: Oak Ridge

first: Alice

last: Townsend

state: TN

address: 1 Bethel Valley Rd

institute: ORNL

description: Library name: 12725-AC-13

data_processing:
This pool was subjected to 151 bp paired-end sequencing according to the manufacturer’s protocol (Illumina Nova-Seq). BCL Convert Conversion Software v4.3.6 (Illumina) was used to generate de-multiplexed Fastq files.
Sequenced reads were trimmed with Cutadapt v4.8 and the quality of trimmed reads were evaluated with FastQC v0.11.8 while Fastq Screen v0.15.3 was used to screen for various types of contamination.
Trimmed reads were mapped to the mouse reference genome (GRCm38) using the STAR aligner v2.7.9a and quality of alignments was assessed with MultiQC v1.12
featureCounts v2.0.1 was used to construct the raw count matrix
DESeq2 v1.30.1 was used to perform differential expression analysis
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file containing raw counts for all samples

source_name: Liver

extract_protocol:
RNA was isolated from liver tissue using TRIzol Reagent (Ambion 15596018), according to manufacturer’s instructions. 1 ug of total RNA was used for the construction of sequence libraries.
RNA libraries for RNA SEQ were prepared by the Advanced Genomics Core at the University of Michigan with manufacuters protocol for Poly-A enrichment.

value: Liver


title: RM1_male_injured24_contra

description: Library name: RM1C

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)


title: RM2_male_injured24_contra

description: Library name: RM2C

tag: progesterone log10_(ng/ml)

tag: estradiol log10_(pg/ml)


title: RF2_female_injured24_ipsi

description: Library name: RF2I

tag: batch


title: 1_HKM7VBGXT.1.TCGACGTC_CTCCTTAC

description:
Library name: 1_SM-NBW81_plate1
DHMT_48hr_LRP1_C_d

tag: cell type

tag: genotype


title: RF2_female_injured24_contra

description: Library name: RF2C

tag: tissue

tag: treatment


title: Liver, Npc1 -/-, Co-Npc1:LP, rep 3

description: Library name: 12725-AC-12


title: 4_HKM7VBGXT.4.TGCAGCTA_CTCCTTAC

description:
Library name: 4_SM-NBW7Z_plate1
DHMT_48hr_LRP1_C_c

tag: cell line

tag: day


title: RF1_female_injured24_ipsi

description: Library name: RF1I

tag: animal


title: Liver, Npc1 -/-, Co-Npc1:LP, rep 2

description: Library name: 12725-AC-11


title: RF1_female_injured24_contra

description: Library name: RF1C


title: 3_HKM7VBGXT.3.TGCAGCTA_CTCCTTAC

description:
Library name: 3_SM-NBW7Z_plate1
DHMT_48hr_LRP1_C_c

tag: guide rna

tag: barcode


title: 2_HKM7VBGXT.2.TGCAGCTA_CTCCTTAC

description:
Library name: 2_SM-NBW7Z_plate1
DHMT_48hr_LRP1_C_c


title: Liver, Npc1 -/-, GFP, rep 4

description: Library name: 12725-AC-9


title: QM2_male_injured24_contra

description: Library name: QM2C

tag: strain

tag: Sex


title: QM2_male_injured24_ipsi

description: Library name: QM2I

tag: location of_biopsy

tag: testosterone log10_(ng/ml)


title: 1_HKM7VBGXT.1.TGCAGCTA_CTCCTTAC

description:
Library name: 1_SM-NBW7Z_plate1
DHMT_48hr_LRP1_C_c


title: TF1_female_injured72_contra

description: Library name: TF1C

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)


title: QM1_male_injured24_ipsi

description: Library name: QM1I

tag: progesterone log10_(ng/ml)

tag: estradiol log10_(pg/ml)


title: Liver, Npc1 -/-, GFP, rep 3

description: Library name: 12725-AC-8


title: QF2_female_injured24_ipsi

description: Library name: QF2I

tag: batch


title: QF2_female_injured24_contra

description: Library name: QF2C


title: 4_HKM7VBGXT.4.CGATCAGT_CTCCTTAC

description:
Library name: 4_SM-NBW7Y_plate1
DHMT_48hr_LRP1_C_b

tag: cell type

tag: genotype


title: 1_HKM7VBGXT.1.ACTCGCTA_TATGCAGT

description:
Library name: 1_SM-NBW82_plate1
DHMT_2hr_a

value: WT


title: SF2_female_injured72_ipsi

description: Library name: SF2I

tag: tissue

tag: treatment

value: female


title: 3_HKM7VBGXT.3.CGATCAGT_CTCCTTAC

description:
Library name: 3_SM-NBW7Y_plate1
DHMT_48hr_LRP1_C_b

tag: cell line

tag: day


title: Liver, Npc1 -/-, GFP, rep 2

description: Library name: 12725-AC-7


title: QF1_female_injured24_ipsi

description: Library name: QF1I

tag: animal


title: SF1_female_injured72_ipsi

description: Library name: SF1I


title: QF1_female_injured24_contra

description: Library name: QF1C


title: Liver, Npc1 -/-, Co-Npc1:LP, rep 5

description: Library name: 12725-AC-14


title: Liver, Npc1 -/-, GFP, rep 1

description: Library name: 12725-AC-6


title: PM2_male_injured72_ipsi

description: Library name: PM2I


title: 2_HKM7VBGXT.2.CGATCAGT_CTCCTTAC

description:
Library name: 2_SM-NBW7Y_plate1
DHMT_48hr_LRP1_C_b

tag: guide rna

tag: barcode


title: PM1_female_injured72_ipsi

description: Library name: PM1I

tag: strain

tag: Sex


title: 1_HKM7VBGXT.1.CGATCAGT_CTCCTTAC

description:
Library name: 1_SM-NBW7Y_plate1
DHMT_48hr_LRP1_C_b


title: Liver, Npc1+/+, Veh, rep 5

description: Library name: 12725-AC-5

value: Veh


title: PM1_male_injured72_contra

description: Library name: PM1C

tag: location of_biopsy

tag: testosterone log10_(ng/ml)


title: PM2_male_injured72_contra

description: Library name: PM2C

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)


title: RM1_male_injured24_ipsi

description: Library name: RM1I

tag: progesterone log10_(ng/ml)

tag: estradiol log10_(pg/ml)


title: PF2_female_injured72_ipsi

description: Library name: PF2I

tag: batch


title: Liver, Npc1+/+, Veh, rep 4

description: Library name: 12725-AC-4

tag: genotype


title: PF2_female_injured72_contra

description: Library name: PF2C

tag: tissue


title: Liver, Npc1+/+, Veh, rep 3

description: Library name: 12725-AC-3

tag: treatment


title: 4_HKM7VBGXT.4.CCTAAGAC_CTCCTTAC

description:
Library name: 4_SM-NBW7X_plate1
DHMT_48hr_LRP1_C_a

tag: cell line

tag: cell type


title: PF1_female_injured72_ipsi

description: Library name: PF1I

tag: animal


title: PF1_female_injured72_contra

description: Library name: PF1C


title: Liver, Npc1+/+, Veh, rep 2

description: Library name: 12725-AC-2


title: LM2_male_injured72_ipsi

description: Library name: LM2I


title: 2_HKM7VBGXT.2.CCTAAGAC_CTCCTTAC

description:
Library name: 2_SM-NBW7X_plate1
DHMT_48hr_LRP1_C_a

tag: day

tag: guide rna


title: 3_HKM7VBGXT.3.CCTAAGAC_CTCCTTAC

description:
Library name: 3_SM-NBW7X_plate1
DHMT_48hr_LRP1_C_a

tag: barcode


title: LM2_male_injured72_contra

description: Library name: LM2C

tag: strain

tag: Sex


title: Liver, Npc1+/+, Veh, rep 1

description: Library name: 12725-AC-1


title: LF3_female_injured72_Ipsi

description: Library name: LF3I

tag: location of_biopsy

tag: testosterone log10_(ng/ml)


title: 1_HKM7VBGXT.1.CCTAAGAC_CTCCTTAC

description:
Library name: 1_SM-NBW7X_plate1
DHMT_48hr_LRP1_C_a


title: LF3_female_injured72_contra

description: Library name: LF3C

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)


title: Liver, Npc1 -/-, Co-Npc1:LP, rep 1

description: Library name: 12725-AC-10


title: IRF5_FL5_UUO

city: Hangzhou

first: Jia

last: Wei

state: Zhejiang

address: Binsheng Road 3333

institute: Zhejiang University School of medicine Children's hospital

description: Library name: sample19

data_processing:
Raw reads were first processed using fastp software. In this step, clean reads were obtained by removing reads containing adapters, reads containing poly-N, and low-quality reads from the raw data.
The reference genome and gene model annotation files were downloaded from a genome website. An index of the reference genome was built using HISAT2 (2.2.1), and paired-end clean reads were aligned to the reference genome using HISAT2.
The reads mapped to each gene were counted using featureCounts (2.0.6). Then, FPKM for each gene was calculated based on gene length and the number of reads mapped to that gene.
Assembly: Mouse reference genome GRCm39/mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from mouse kidney tissues using TRIzol® Reagent.
mRNA was enriched from total RNA using Oligo dT magnetic beads. After fragmentation, first‑strand cDNA was synthesized using random hexamer primers, followed by second‑strrand cDNA synthesis. After end repair, A‑tailing, adapter ligation, size selection, amplification, and purification, the library was ready.The library was quantified using a Qubit fluorometer and real‑time PCR, and its fragment size distribution was assessed using a bioanalyzer.

value: kidney


title: KM3_male_naive_ipsi

description: Library name: KM3I

value: naive

tag: progesterone log10_(ng/ml)

tag: estradiol log10_(pg/ml)


title: KM3_male_naive_contra

description: Library name: KM3C

tag: batch


title: 4_HKM7VBGXT.4.ACTGAGCG_CTCCTTAC

description:
Library name: 4_SM-NBW7W_plate1
DHMT_72hr_d

tag: genotype

value: no guide


title: IRF5_FL4_UUO

description: Library name: sample18

tag: tissue


title: KM2_male_naive_ipsi

description: Library name: KM2I

tag: treatment


title: WT_18hLPS_rep3

description: Library name: ATAC17

library_source: genomic

data_processing:
Sequencing reads were de-multiplexed and trimmed using cutadapt v2.6
Mapping to mm10 genome and downstream analyses were performed using the snakeATAC v0.1.1 pipeline using default configuration parameters
Differential binding sites were defined using diffBind v3.0.15
Assembly: mm10
Supplementary files format and content: narrowPeak files, bigWig files

molecule: genomic DNA

source_name: bone marrow

growth_protocol: Bone marrow cells were isolated from the femurs and tibias of male WT and Nur77-KO mice aged 6-12 weeks. The cells were differentiated into macrophages by culturing them in RPMI 1640 medium supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine, 15% L929-conditioned medium, 1 mM sodium pyruvate, 1x MEM Non-Essential Amino Acids Solution, and 1x MEM Vitamin Solution for a period of 7 days. After the differentiation process, the cells were lifted, counted, and re-seeded at a density of   1 × 10^6 cells per ml.

extract_protocol:
Nuclei were isolated from 0.5x10^5 cells. Tagmentation was performed for 45 min at 37°C
Tagmented DNA was aplified by two rounds of PCR using the KAPA kit amplification protocol and Nextera dual-indexing sequencing adapters. Fragments smaller than 700bp were purified using SPRI beads (Beckman Coulter). Library quality was assed using the 2100 Bioanalyzer system (Agilent)

treatment_protocol: Cells were stimulated with 100 ng/ml LPS for 0, 1 and 18h

value: bone marrow

tag: cell type

value: bone marrow-derived macrophages

value: wt

value: 18h 100 ng/ml LPS


title: IRF5_FL3_UUO

description: Library name: sample17


title: 3_HKM7VBGXT.3.ACTGAGCG_CTCCTTAC

description:
Library name: 3_SM-NBW7W_plate1
DHMT_72hr_d

tag: cell line


title: WT_18hLPS_rep2

description: Library name: ATAC16


title: 2_HKM7VBGXT.2.ACTGAGCG_CTCCTTAC

description:
Library name: 2_SM-NBW7W_plate1
DHMT_72hr_d

tag: day


title: IRF5_FL2_UUO

description: Library name: sample16


title: WT_18hLPS_rep1

description: Library name: ATAC15


title: KM2_male_naive_contra

description: Library name: KM2C

value: Brain cortical punch

tag: animal

value: male


title: QM1_male_injured24_contra

description: Library name: QM1C


title: 4_HKM7VBGXT.4.TAGCGCTC_CTCCTTAC

description:
Library name: 4_SM-NBW7V_plate1
DHMT_72hr_c

value: iPSC-derived excitatory neuron, astrocyte

tag: guide rna

tag: barcode


title: 1_HKM7VBGXT.1.ACTGAGCG_CTCCTTAC

description:
Library name: 1_SM-NBW7W_plate1
DHMT_72hr_d


title: IRF5_FL1_UUO

description: Library name: sample15


title: IRF5_MKO6_UUO

description: Library name: sample14


title: KF3_female_naive_contra

description: Library name: KF3C

tag: strain

tag: Sex


title: KF3_female_naive_ipsi

description: Library name: KF3I

tag: location of_biopsy

value: ipsi

tag: testosterone log10_(ng/ml)


title: WT_1hLPS_rep3

description: Library name: ATAC14

value: 1h 100 ng/ml LPS


title: WT_1hLPS_rep1-2

description: Library name: ATAC13


title: 3_HKM7VBGXT.3.TAGCGCTC_CTCCTTAC

description:
Library name: 3_SM-NBW7V_plate1
DHMT_72hr_c


title: IRF5_MKO5_UUO

description: Library name: sample13


title: KF2_female_naive_ipsi

description: Library name: KF2I

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)

value: B


title: WT_ctrl_rep3

description: Library name: ATAC12

value: untreated


title: 2_HKM7VBGXT.2.TAGCGCTC_CTCCTTAC

description:
Library name: 2_SM-NBW7V_plate1
DHMT_72hr_c

value: WT


title: IRF5_MKO4_UUO

description: Library name: sample12


title: 1_HKM7VBGXT.1.TAGCGCTC_CTCCTTAC

description:
Library name: 1_SM-NBW7V_plate1
DHMT_72hr_c


title: HM2_male_injured24_ipsi

description: Library name: HM2I

tag: progesterone log10_(ng/ml)

tag: estradiol log10_(pg/ml)

value: A


title: IRF5_MKO3_UUO

description: Library name: sample11


title: WT_ctrl_rep1

description: Library name: ATAC10

tag: genotype


title: KF2_female_naive_contra

description: Library name: KF2C

tag: tissue

value: female

value: contra

tag: batch


title: WT_ctrl_rep2

description: Library name: ATAC11

tag: cell type

tag: treatment


title: 4_HKM7VBGXT.4.ATGCGCAG_CTCCTTAC

description:
Library name: 4_SM-NBW7U_plate1
DHMT_72hr_b

tag: cell line

tag: day


title: HM2_male_injured24_contra

description: Library name: HM2C

tag: animal


title: IRF5_MKO2_UUO

description: Library name: sample10

value: kidney


title: KO_18hLPS_rep3

description: Library name: ATAC9

value: cre


title: 3_HKM7VBGXT.3.ATGCGCAG_CTCCTTAC

description:
Library name: 3_SM-NBW7U_plate1
DHMT_72hr_b

tag: guide rna

value: no guide

tag: barcode


title: IRF5_KO2_UUO

description: Library name: sample9


title: GM2_male_naive_ipsi

description: Library name: GM2I

tag: strain

value: naive

tag: Sex


title: KO_18hLPS_rep2

description: Library name: ATAC8

value: bone marrow

value: bone marrow-derived macrophages


title: 2_HKM7VBGXT.2.ATGCGCAG_CTCCTTAC

description:
Library name: 2_SM-NBW7U_plate1
DHMT_72hr_b


title: GM2_male_naive_contra

description: Library name: GM2C

value: Brain cortical punch

tag: location of_biopsy

tag: testosterone log10_(ng/ml)


title: 1_HKM7VBGXT.1.ATGCGCAG_CTCCTTAC

description:
Library name: 1_SM-NBW7U_plate1
DHMT_72hr_b


title: GF3_female_naive_ipsi

description: Library name: GF3I

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)


title: IRF5_KO1_UUO

description: Library name: sample7


title: KO_1hLPS_rep3

description: Library name: ATAC6


title: KO_18hLPS_rep1

description: Library name: ATAC7

value: 18h 100 ng/ml LPS


title: 4_HKM7VBGXT.4.TACGCTGC_CTCCTTAC

description:
Library name: 4_SM-NBW7T_plate1
DHMT_72hr_a

value: iPSC-derived excitatory neuron, astrocyte


title: IRF5_KO4_UUO

description: Library name: sample8


title: WT4_SHAM

description: Library name: sample6


title: 3_HKM7VBGXT.3.TACGCTGC_CTCCTTAC

description:
Library name: 3_SM-NBW7T_plate1
DHMT_72hr_a


title: KO_1hLPS_rep2

description: Library name: ATAC5


title: GF3_female_naive_contra

description: Library name: GF3C

tag: progesterone log10_(ng/ml)

tag: estradiol log10_(pg/ml)


title: GF2_female_naive_ipsi

description: Library name: GF2I

tag: tissue

value: ipsi


title: WT5_SHAM

description: Library name: sample5


title: KO_1hLPS_rep1

description: Library name: ATAC4

tag: genotype

value: 1h 100 ng/ml LPS


title: WT2_SHAM

description: Library name: sample4


title: GF2_female_naive_contra

description: Library name: GF2C

tag: batch


title: KO_ctrl_rep3

description: Library name: ATAC3

tag: cell type

tag: treatment


title: 1_HKM7VBGXT.1.TACGCTGC_CTCCTTAC

description:
Library name: 1_SM-NBW7T_plate1
DHMT_72hr_a

tag: cell line

tag: day


title: 2_HKM7VBGXT.2.TACGCTGC_CTCCTTAC

description:
Library name: 2_SM-NBW7T_plate1
DHMT_72hr_a

tag: guide rna


title: FM3_male_injured24_ipsi

description: Library name: FM3I

tag: animal

value: male


title: WT4_UUO

description: Library name: sample3


title: 4_HKM7VBGXT.4.CGGAGCCT_CTCCTTAC

description:
Library name: 4_SM-NBW7S_plate1
DHMT_1hr_d

tag: barcode


title: FM3_male_injured24_contra

description: Library name: FM3C

tag: strain

tag: Sex


title: KO_ctrl_rep2

description: Library name: ATAC2

value: untreated


title: WT3_UUO

description: Library name: sample2


title: KO_ctrl_rep1

description: Library name: ATAC1


title: FM2_male_injured24_ipsi

description: Library name: FM2I

tag: location of_biopsy

tag: testosterone log10_(ng/ml)


title: WT1_UUO

description: Library name: sample1


title: RNA-seq in Egr2 knock-out alveolar macrophages (plated, IL-4-treated, rep3)

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

description: Library name: mm_RNA_AM_Egr2KO_IL4_rep4

data_processing:
alignment to mm10 reference genome with HISAT2 (v2.1.0) using default parameters
transcript assembly with StringTie (v1.3.4d)
BAM file indexing with SAMtools (v1.7)
coverage (bigwig) file generation with bamCoverage program of deepTools (v3.0.2)
Assembly: mm10
Supplementary files format and content: bigwig

source_name: alveolar macrophage

growth_protocol: We applied mouse alveolar macrophages from C57BL6 background control and Egr2 myeloid-specific conditional knock-out mice.

extract_protocol:
The murine alveolar macrophages were isolated by bronchoalveolar lavage (BAL) from Egr2+/+ and Egr2fl/fl mice. To collect BAL samples, animals were euthanized by isoflurane inhalation and their tracheas were cannulated. Lavage was performed with 2 aliquots of 0.7 ml of ice-cold PBS (pH 7.3). The BAL cells were centrifuged at 400 g for 10 minutes at 4 °C and the supernatants were removed. BAL cells were suspended in ACK buffer (4.012 g NH4Cl, 0.5 g KHCO3, 18.61 mg Na2EDTA x 2H2O, and 0.5 L milliQ; pH 7.2-7.4) to lyse red blood cells for 2 minutes at room temperature and then adding 1 mL of MACS buffer (2 mM EDTA and 0.5 % BSA in 1x PBS (pH: 7.2)). The alveolar macrophages were purified with CD45 magnetic bead selection according to the manufacturer’s protocol (CD45 bead isolation kit; Order No. 130-052-301; Miltenyi). We cultured isolated cells at 24-well plates in 0.5 mL RPMI medium containing 1% penicillin/streptomycin/amphotericin B (A5955; Sigma), and 10% FBS (F7524, Sigma). After attachment, we added 20 ng/ml IL-4 (Peprotech; 214-14). For RNA-seq experiments, upon 24-hour incubation total RNA was isolated by Trizol reagent (Zymo Research; R2050-1-200). RNA-seq was completed as described earlier (Kolostyak et al. JCI Insight (2024); Czimmerer et al. Immunity (2018).
From total RNA, Ultra II RNA Sample Preparation Kit (New England BioLabs) was used for library preparation following the manufacturer’s protocol.

treatment_protocol: We have generated untreated or 20 ng/ml IL-4-treated (Peprotech; 214-14) cells.

value: alveolar macrophage

value: Egr2 knock-out


title: FM2_male_injured24_contra

description: Library name: FM2C

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)

value: A


title: TF2_female_injured72_ipsi

description: Library name: TF2I

value: female

tag: progesterone log10_(ng/ml)

tag: estradiol log10_(pg/ml)

value: C


title: RNA-seq in Egr2 knock-out alveolar macrophages (plated, IL-4-treated, rep2)

description: Library name: mm_RNA_AM_Egr2KO_IL4_rep3

tag: genotype


title: 2_HKM7VBGXT.2.CGGAGCCT_CTCCTTAC

description:
Library name: 2_SM-NBW7S_plate1
DHMT_1hr_d

value: WT


title: 3_HKM7VBGXT.3.CGGAGCCT_CTCCTTAC

description:
Library name: 3_SM-NBW7S_plate1
DHMT_1hr_d

value: no guide


title: 1_HKM7VBGXT.1.CGGAGCCT_CTCCTTAC

description:
Library name: 1_SM-NBW7S_plate1
DHMT_1hr_d


title: FF3_female_injured24_ipsi

description: Library name: FF3I

tag: tissue

tag: batch


title: WT-1hLPS-input

description: Library name: ChIP41

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer 0.2.2
Reads were aligned to the mouse genome mm10 by HISAT2 2.1.0
Tag directories were created using the makeTagDirectory command in HOMER
BigWigs were produced from HOMER tag directories
Pol II and H3K27ac binding peaks were identified by using HOMER peak calling using the regions setting (broad peaks)
For the peak files, the reproducible peaks in 3 biological replicates were merged using HOMER’s mergePeaks.pl script. The BigWigs were merged using bigwigAverage from deepTools2
Assembly: mm10
Supplementary files format and content: tab-delimited text files with identiified peaks, bigWig files

growth_protocol: Bone marrow cells were isolated from the femurs and tibias of male WT and Nur77-KO mice aged 6-12 weeks. The cells were differentiated into macrophages by culturing them in RPMI 1640 medium supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine, 15% L929-conditioned medium, 1 mM sodium pyruvate, 1x MEM Non-Essential Amino Acids Solution, and 1x MEM Vitamin Solution for a period of 7 days. After the differentiation process, the cells were lifted, counted, and re-seeded at a density of 1 × 10^6 cells per ml.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, the chromatin was sonicated into approximately 400bp fragments using a Bioruptor Pico (Diagenode) for 3 cycles of 10sec on and 50sec off. Immunoprecipitation was performed using RNA polymerase II, or H3K27ac antibody
Strrand-specific ChIP seq libraries were prepared using the KAPA hyperprep kit protocol. Concentration and fragment size of chromatin was confirmed using the Tapestation4200 (Agilent).

treatment_protocol: Cells were stimulated with 100 ng/ml LPS for 0, 1, 5 and 18h

tag: cell type

value: wt

tag: treatment

tag: chip antibody


title: WT-18hLPS-input

description: Library name: ChIP42

value: bone marrow


title: RNA-seq in Egr2 knock-out alveolar macrophages (plated, IL-4-treated, rep1)

description: Library name: mm_RNA_AM_Egr2KO_IL4_rep2


title: 4_HKM7VBGXT.4.GCGTAGTA_CTCCTTAC

description:
Library name: 4_SM-NBW7R_plate1
DHMT_1hr_c

tag: cell line

tag: day

tag: guide rna


title: FF3_female_injured24_contra

description: Library name: FF3C

tag: animal

tag: strain

value: contra


title: RNA-seq in Egr2 knock-out alveolar macrophages (plated, untreated, rep3)

description: Library name: mm_RNA_AM_Egr2KO_ctrl_rep4


title: 3_HKM7VBGXT.3.GCGTAGTA_CTCCTTAC

description:
Library name: 3_SM-NBW7R_plate1
DHMT_1hr_c

tag: barcode


title: WT-0hLPS-input

description: Library name: ChIP40

value: bone marrow-derived macrophages


title: WT-18hLPS-polII-3

description: Library name: ChIP39

value: 18h 100 ng/ml LPS

value: RNA Pol II (Diagenode,C15200253)


title: EM3_male_naive_ipsi

description: Library name: EM3I

value: Brain cortical punch

value: naive

tag: Sex

tag: location of_biopsy

value: ipsi

tag: testosterone log10_(ng/ml)


title: RNA-seq in Egr2 knock-out alveolar macrophages (plated, untreated, rep2)

description: Library name: mm_RNA_AM_Egr2KO_ctrl_rep3

value: untreated


title: 2_HKM7VBGXT.2.GCGTAGTA_CTCCTTAC

description:
Library name: 2_SM-NBW7R_plate1
DHMT_1hr_c

value: iPSC-derived excitatory neuron, astrocyte


title: EM3_male_naive_contra

description: Library name: EM3C

value: male

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)

tag: progesterone log10_(ng/ml)


title: WT-18hLPS-polII-2

description: Library name: ChIP38

tag: tissue

tag: genotype


title: RNA-seq in Egr2 knock-out alveolar macrophages (plated, untreated, rep1)

description: Library name: mm_RNA_AM_Egr2KO_ctrl_rep1

tag: cell type

value: alveolar macrophage

value: Egr2 knock-out


title: 1_HKM7VBGXT.1.GCGTAGTA_CTCCTTAC

description:
Library name: 1_SM-NBW7R_plate1
DHMT_1hr_c


title: WT-18hLPS-polII-1

description: Library name: ChIP37

tag: treatment


title: EM2_male_naive_ipsi

description: Library name: EM2I

tag: estradiol log10_(pg/ml)

tag: batch

value: A


title: 4_HKM7VBGXT.4.GGAGCTAC_CTCCTTAC

description:
Library name: 4_SM-NBW7Q_plate1
DHMT_1hr_b

tag: cell line

value: WT

tag: day


title: RNA-seq in wild-type alveolar macrophages (plated, IL-4-treated, rep3)

description: Library name: mm_RNA_AM_WT_IL4_rep3

value: wild-type


title: EM2_male_naive_contra

description: Library name: EM2C

tag: animal


title: RNA-seq in wild-type alveolar macrophages (plated, IL-4-treated, rep2)

description: Library name: mm_RNA_AM_WT_IL4_rep2


title: EF3_female_naive_ipsi

description: Library name: EF3I

tag: strain

value: female


title: WT-1hLPS-polII-3

description: Library name: ChIP36

value: bone marrow

value: wt

value: 1h 100 ng/ml LPS

tag: chip antibody


title: 3_HKM7VBGXT.3.GGAGCTAC_CTCCTTAC

description:
Library name: 3_SM-NBW7Q_plate1
DHMT_1hr_b

tag: guide rna

value: no guide

tag: barcode


title: 2_HKM7VBGXT.2.GGAGCTAC_CTCCTTAC

description:
Library name: 2_SM-NBW7Q_plate1
DHMT_1hr_b


title: WT-1hLPS-polII-2

description: Library name: ChIP35

value: bone marrow-derived macrophages

value: RNA Pol II (Diagenode,C15200253)


title: RNA-seq in wild-type alveolar macrophages (plated, IL-4-treated, rep1)

description: Library name: mm_RNA_AM_WT_IL4_rep1


title: EF3_female_naive_contra

description: Library name: EF3C

value: Brain cortical punch

value: naive

tag: Sex

tag: location of_biopsy

value: contra

tag: testosterone log10_(ng/ml)


title: WT-1hLPS-polII-1

description: Library name: ChIP34


title: 1_HKM7VBGXT.1.GGAGCTAC_CTCCTTAC

description:
Library name: 1_SM-NBW7Q_plate1
DHMT_1hr_b

value: iPSC-derived excitatory neuron, astrocyte


title: RNA-seq in wild-type alveolar macrophages (plated, untreated, rep3)

description: Library name: mm_RNA_AM_WT_ctrl_rep3

value: untreated


title: DM2_male_injured24_ipsi

description: Library name: DM2I

value: male

value: ipsi

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)

tag: progesterone log10_(ng/ml)


title: WT-0hLPS-polII-3

description: Library name: ChIP33

tag: tissue

tag: cell type

tag: genotype


title: RNA-seq in wild-type alveolar macrophages (plated, untreated, rep2)

description: Library name: mm_RNA_AM_WT_ctrl_rep2

value: alveolar macrophage

tag: treatment


title: 4_HKM7VBGXT.4.ACTCGCTA_CTCCTTAC

description:
Library name: 4_SM-NBW7P_plate1
DHMT_1hr_a

tag: cell line

value: WT


title: WT-0hLPS-polII-2

description: Library name: ChIP32


title: 3_HKM7VBGXT.3.ACTCGCTA_CTCCTTAC

description:
Library name: 3_SM-NBW7P_plate1
DHMT_1hr_a

tag: day


title: RNA-seq in wild-type alveolar macrophages (plated, untreated, rep1)

description: Library name: mm_RNA_AM_WT_ctrl_rep1

value: wild-type


title: WT-0hLPS-polII-1

description: Library name: ChIP31


title: DM2_male_injured24_contra

description: Library name: DM2C

tag: animal

tag: estradiol log10_(pg/ml)

tag: batch

value: A


title: ATAC-seq in Egr2 knock-out alveolar macrophages (plated, 24h IL-4-treated, rep2)

description: Library name: mm_ATAC_AM_Egr2KO_IL4_24h_rep2

data_processing:
alignment to mm10 reference genome with BWA v0.7.10 using default parameters
bam generation with SAMtools v1.7 using default parameters
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile using -fsize 1e50 -norm parameters
peak prediction with callpeak function of MACS2
Assembly: mm10
Supplementary files format and content: bedgraph

extract_protocol:
The murine alveolar macrophages were isolated by bronchoalveolar lavage (BAL) from Egr2+/+ and Egr2fl/fl mice. To collect BAL samples, animals were euthanized by isoflurane inhalation and their tracheas were cannulated. Lavage was performed with 2 aliquots of 0.7 ml of ice-cold PBS (pH 7.3). The BAL cells were centrifuged at 400 g for 10 minutes at 4 °C and the supernatants were removed. BAL cells were suspended in ACK buffer (4.012 g NH4Cl, 0.5 g KHCO3, 18.61 mg Na2EDTA x 2H2O, and 0.5 L milliQ; pH 7.2-7.4) to lyse red blood cells for 2 minutes at room temperature and then adding 1 mL of MACS buffer (2 mM EDTA and 0.5 % BSA in 1x PBS (pH: 7.2)). The alveolar macrophages were purified with CD45 magnetic bead selection according to the manufacturer’s protocol (CD45 bead isolation kit; Order No. 130-052-301; Miltenyi). We cultured isolated cells at 24-well plates in 0.5 mL RPMI medium containing 1% penicillin/streptomycin/amphotericin B (A5955; Sigma), and 10% FBS (F7524, Sigma). After attachment, we added 20 ng/ml IL-4 (Peprotech; 214-14). ATAC-seq was performed as previously (Kolostyak et al. JCI Insight (2024).
Libraries were prepared from 10ng DNA withTruSeq ChIP library systems (Illumina) according to the manufacturer's instructions.

value: Egr2 knock-out


title: DF3_female_injured24_ipsi

description: Library name: DF3I

tag: strain

value: female


title: 2_HKM7VBGXT.2.ACTCGCTA_CTCCTTAC

description:
Library name: 2_SM-NBW7P_plate1
DHMT_1hr_a

tag: guide rna

tag: barcode


title: DF3_female_injured24_contra

description: Library name: DF3C

tag: Sex

tag: location of_biopsy


title: WT-18hLPS-H3k27ac-3

description: Library name: ChIP30

value: bone marrow

value: wt

value: 18h 100 ng/ml LPS

tag: chip antibody

value: H3K27ac (Diagenode, C15410196)


title: ATAC-seq in Egr2 knock-out alveolar macrophages (plated, 24h IL-4-treated, rep1)

description: Library name: mm_ATAC_AM_Egr2KO_IL4_24h_rep1


title: 1_HKM7VBGXT.1.ACTCGCTA_CTCCTTAC

description:
Library name: 1_SM-NBW7P_plate1
DHMT_1hr_a

value: no guide


title: DF2_female_injured24_ipsi

description: Library name: DF2I

value: Brain cortical punch

tag: testosterone log10_(ng/ml)

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)


title: WT-18hLPS-H3k27ac-2

description: Library name: ChIP29

tag: tissue

tag: cell type

value: bone marrow-derived macrophages


title: DF2_female_injured24_contra

description: Library name: DF2C

tag: treatment

value: contra

tag: progesterone log10_(ng/ml)


title: 4_HKM7VBGXT.4.TCGACGTC_AGAGGATA

description:
Library name: 4_SM-NBW7O_plate1
DHMT_48hr_LRP1_B_d

tag: cell line

value: iPSC-derived excitatory neuron, astrocyte

tag: genotype

value: LRP1 knockdown

tag: day


title: ATAC-seq in Egr2 knock-out alveolar macrophages (plated, untreated, rep2)

description: Library name: mm_ATAC_AM_Egr2KO_ctrl_rep2

value: untreated


title: WT-18hLPS-H3k27ac-1

description: Library name: ChIP28


title: ATAC-seq in Egr2 knock-out alveolar macrophages (plated, untreated, rep1)

description: Library name: mm_ATAC_AM_Egr2KO_ctrl_rep1

value: alveolar macrophage


title: 3_HKM7VBGXT.3.TCGACGTC_AGAGGATA

description:
Library name: 3_SM-NBW7O_plate1
DHMT_48hr_LRP1_B_d


title: CM1_male_naive_ipsi

description: Library name: CM1I

tag: animal

value: naive

value: male

value: ipsi

tag: estradiol log10_(pg/ml)

tag: batch


title: WT-1hLPS-H3k27ac-3

description: Library name: ChIP27

tag: strain

value: 1h 100 ng/ml LPS


title: ATAC-seq in wild-type alveolar macrophages (plated, 24h IL-4-treated, rep2)

description: Library name: mm_ATAC_AM_WT_IL4_24h_rep2

value: wild-type


title: 2_HKM7VBGXT.2.TCGACGTC_AGAGGATA

description:
Library name: 2_SM-NBW7O_plate1
DHMT_48hr_LRP1_B_d

tag: guide rna

tag: barcode


title: CM1_male_naive_contra

description: Library name: CM1C

tag: Sex

tag: location of_biopsy

value: A


title: WT-1hLPS-H3k27ac-2

description: Library name: ChIP26

value: bone marrow

value: wt

tag: chip antibody


title: 1_HKM7VBGXT.1.TCGACGTC_AGAGGATA

description:
Library name: 1_SM-NBW7O_plate1
DHMT_48hr_LRP1_B_d


title: ATAC-seq in wild-type alveolar macrophages (plated, 24h IL-4-treated, rep1)

description: Library name: mm_ATAC_AM_WT_IL4_24h_rep1


title: CF3_female_naive_ipsi

description: Library name: CF3I

value: female

tag: testosterone log10_(ng/ml)

tag: androstenedione log10_(ng/ml)

tag: dhea log10_(ng/ml)


title: ATAC-seq in wild-type alveolar macrophages (plated, untreated, rep2)

description: Library name: mm_ATAC_AM_WT_ctrl_rep2

tag: cell type

tag: treatment


title: WT-1hLPS-H3k27ac-1

description: Library name: ChIP25

tag: tissue

value: H3K27ac (Diagenode, C15410196)


title: 4_HKM7VBGXT.4.TGCAGCTA_AGAGGATA

description:
Library name: 4_SM-NBW7N_plate1
DHMT_48hr_LRP1_B_c

tag: cell line

tag: genotype


title: CF3_female_naive_contra

description: Library name: CF3C

value: Brain cortical punch

tag: animal

tag: progesterone log10_(ng/ml)


title: 3_HKM7VBGXT.3.TGCAGCTA_AGAGGATA

description:
Library name: 3_SM-NBW7N_plate1
DHMT_48hr_LRP1_B_c

tag: day


title: ATAC-seq in wild-type alveolar macrophages (plated, untreated, rep1)

description: Library name: mm_ATAC_AM_WT_ctrl_rep1


title: WT-0hLPS-H3k27ac-3

description: Library name: ChIP24

tag: strain

value: bone marrow-derived macrophages


title: CF2_female_naive_ipsi

description: Library name: CF2I

tag: estradiol log10_(pg/ml)

tag: batch


title: WT-0hLPS-H3k27ac-2

description: Library name: ChIP23


title: TD006769-9187

city: NEW YORK

first: Alexander

last: Tsankov

state: New York

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 6
10x Genomics

data_processing:
We initiated our analysis by aligning the raw fastq files to the customized mouse genome reference mm10, which included the Rfp sequence. This alignment process was executed using CellRanger v5.0.0 by 10X Genomics. Following alignment, we used the CellRanges algorithm to filter count matrices. Cells with less than 400 genes, fewer than 1000 UMI (unique molecular identifier), or over 25% mitochondrial gene expression were excluded. Subsequent data processing and analysis were conducted using the Seurat v4.2.2 R package. The data was normalized using the NormalizeData function, utilizing the normalization.method = 'LogNormalize' parameter. For dimensionality reduction, we focused on the top 2,000 variable features, using functions such as FindVariableFeatures, ScaleData, and RunPCA. Ultimately, we generated UMAPs based on the top 15 principal components (PCs).
To subcluster the immune compartment, we employed the R package Harmony to address batch effects stemming from technical variations across replicates. De novo clustering was carried out using the Louvain algorithm at multiple resolutions (0.2, 0.4, 0.8, 2, 3, 5, 8) within the KNN graph space. For high-level cell type annotation, we iteratively and semi-supervisedly assigned de novo discovered clusters to cell types based on the expression of established marker genes defining each cluster. The annotation of cell subtypes at a lower level followed a similar approach to the high-level annotation, with additional assistance from de novo marker discovery utilizing the Seurat FindMarkers function and Wilcoxon Rank Sum test.
To identify clusters enriched with doublets, we searched for cell clusters that exhibited the expression of canonical markers for two or more distinct cell types and a higher count of genes/UMI. These identified clusters were subsequently excluded from further analysis.
Cell-level proliferation analysis was performed using the Seurat function CellCycleScoring, which utilized a curated list of murine cell cycle genes. Subsequently, cells were categorized as 'cycling' or 'non-cycling' based on whether their S-phase score or G2M-score exceeded a threshold of 0.10 for the tumor compartment and immune compartment.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain tumor

extract_protocol:
Tumors were dissected from the brain, minced into pieces < 1 mm3, and digested with an enzymatic mixture that includes papain (0.94 mg/ml, Worthington, LS003120), EDTA (0.18 mg/ml, Sigma, E6758), cysteine (0.18 mg/ml, Sigma, A8199), and DNase I (60 μg/ml, Roche, 11284932001) in 2 ml HBSS (Gibco, 14175-095). Tumor tissues were kept at 37°C for 15 minutes with occasional agitation. The digestion was terminated with the addition of 2 ml Ovomucoid (0.7 mg/ml, Worthington, LS003086). Following digestion, single cells were passed through a 70 μm cell strainer, centrifuged, and resuspended in 30% Percoll (GE Healthcare, 17-0891-01) solution containing 10% FBS (Hyclone SH30396.03). Cells were separated by centrifugation at 800g for 15 minutes at 4°C. The pellet was resuspended in RBC lysis buffer (BioLegend, 420301) for 1 min at 37°C before they were centrifuged at 450g for 5 min. The pellet was resuspended in PBS and immediately delivered for GEM preparation.
Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (ThermoFisher) analyses.

value: brain tumor


title: CF2_female_naive_contra

description: Library name: CF2C

tag: Sex

value: contra


title: 2_HKM7VBGXT.2.TGCAGCTA_AGAGGATA

description:
Library name: 2_SM-NBW7N_plate1
DHMT_48hr_LRP1_B_c

value: iPSC-derived excitatory neuron, astrocyte

value: LRP1 knockdown

tag: guide rna

tag: barcode


title: WT-0hLPS-H3k27ac-1

description: Library name: ChIP22

value: untreated

tag: chip antibody


title: TD006766-9145

description:
Library name: Sample 5
10x Genomics


title: 1_HKM7VBGXT.1.TGCAGCTA_AGAGGATA

description:
Library name: 1_SM-NBW7N_plate1
DHMT_48hr_LRP1_B_c


title: 2DGF

type: RNA

city: Kobe

first: Haruaki

last: Sato

state: Hyogo

address: BldgC #504, 2-2-3, Minatojimaminamimachi, Chuo Ward

department: Biodynamics Research

country: Japan

institute: RIKEN

hyb_protocol: Xenium analysis was performed using the pre-designed Xenium Mouse Brain Gene Expression Panel (247 genes; 10x Genomics, PN-1000462) in combination with a custom add-on panel (100 genes; 10x Genomics, PN-1000651) and reagents (10x Genomics, PN-1000460, 1000461, 1000487, and 1000662) according to the manufacturer’s protocols (CG000580, CG000749, and CG000584).

scan_protocol: Xenium In Situ Analyzer. Instrument software version: 3.2.1.2 for male Ctrl and Cold groups or 4.0.1.4 for other groups. Analysis version xenium-3.2.0.7 for male Ctrl and Cold groups or 3.3.1.1 for other groups.

data_processing:
Xenium Onboard Analysis: 3.2.0.7 for male Ctrl and Cold groups or 3.3.1.1 for other groups., R using Seurat v5.3.0 packages
CentralCanal_coordinate.zip: File names follow the format (# of animal)-(# of segment)-(# of section). The first number indicates the animal ID, the second number indicates the spinal cord segment (1 = T1–4, 2 = T5–7, 3 = T8–10, 4 = T11–13, 5 = L1–3, 6 = L4–5, 7 = L6–S1, 8 = S2–4), and the third number indicates the sequential section number within that segment (the Nth section from thoracic).

label: Xenium probe set

source_name: 2-DG group of three female mice

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: FFPE blocks were sectioned at a 5 μm thickness and mounted onto slides according to the manufacturer’s protocol (10x Genomics, CG000578).

treatment_protocol: RT/saline: Mice injected with saline as controls and maintained at room temperature (RT) for 1.5 hours.   Cold: Mice maintained at cold environment (4 deg C) for 1.5 hours.  2-DG: Mice  injected with 2-DG (400 mg/kg) and sacrificed after 1.5 hours.

value: Spinal cord (from thoracic, lumbar, and sacral parts)

tag: tissue preservation method

value: FFPE

value: Wild type


title: TD006751-9043

description:
Library name: Sample 4
10x Genomics


title: 4_HKM7VBGXT.4.CGATCAGT_AGAGGATA

description:
Library name: 4_SM-NBW7M_plate1
DHMT_48hr_LRP1_B_b


title: 2DGM

source_name: 2-DG group of three male mice


title: KO-1hLPS-input

description: Library name: ChIP20

value: cre

value: 1h 100 ng/ml LPS


title: KO-18hLPS-input

description: Library name: ChIP21

value: 18h 100 ng/ml LPS


title: BS-5856

description:
Library name: Sample 3
10x Genomics


title: 3_HKM7VBGXT.3.CGATCAGT_AGAGGATA

description:
Library name: 3_SM-NBW7M_plate1
DHMT_48hr_LRP1_B_b


title: ColdF

source_name: Cold group of three female mice

value: Cold


title: KO-0hLPS-input

description: Library name: ChIP19

value: bone marrow


title: BS_H3.1K27M-20210804

description:
Library name: Sample 2
10x Genomics


title: 2_HKM7VBGXT.2.CGATCAGT_AGAGGATA

description:
Library name: 2_SM-NBW7M_plate1
DHMT_48hr_LRP1_B_b


title: CtrlF

source_name: RT/saline group of three female mice

value: RT/saline


title: KO-18hLPS-polII-3

description: Library name: ChIP18

value: RNA Pol II (Diagenode,C15200253)


title: 5718-20210810-BS-H3.1K27M

description:
Library name: Sample 1
10x Genomics


title: ColdM3

source_name: Cold group of a male mouse


title: KO-18hLPS-polII-2

description: Library name: ChIP17


title: 1_HKM7VBGXT.1.CGATCAGT_AGAGGATA

description:
Library name: 1_SM-NBW7M_plate1
DHMT_48hr_LRP1_B_b


title: ColdM2


title: 4_HKM7VBGXT.4.CCTAAGAC_AGAGGATA

description:
Library name: 4_SM-NBW7L_plate1
DHMT_48hr_LRP1_B_a


title: Nur77_LPS3

growth_protocol: The RAW264.7 macrophage stable cell lines with doxycyclin-inducible expression of Nur77 or GFP were seeded at a density of 3x10^5 cells/ml and the next day Nur77 or GFP expression was induced by incubation with 1ug/ml doxycyclin for 18 h

treatment_protocol: Cells were stimulated with 500 ng/ml LPS for 0 and 1h

value: macrophages

value: 1h 500 ng/ml LPS


title: KO-18hLPS-polII-1

description: Library name: ChIP16

value: bone marrow-derived macrophages


title: Nur77_LPS2


title: ColdM1


title: 3_HKM7VBGXT.3.CCTAAGAC_AGAGGATA

description:
Library name: 3_SM-NBW7L_plate1
DHMT_48hr_LRP1_B_a


title: KO-1hLPS-polII-3

description: Library name: ChIP15


title: Nur77_LPS1


title: 2_HKM7VBGXT.2.CCTAAGAC_AGAGGATA

description:
Library name: 2_SM-NBW7L_plate1
DHMT_48hr_LRP1_B_a


title: CtrlM3

source_name: RT/saline group of a male mouse


title: KO-1hLPS-polII-2

description: Library name: ChIP14


title: 1_HKM7VBGXT.1.CCTAAGAC_AGAGGATA

description:
Library name: 1_SM-NBW7L_plate1
DHMT_48hr_LRP1_B_a


title: 4_HKM7VBGXT.4.ACTGAGCG_AGAGGATA

description:
Library name: 4_SM-NBW7K_plate1
DHMT_48hr_d

value: WT

value: no guide


title: Nur77_Ctrl2


title: CtrlM2


title: Nur77_Ctrl3


title: KO-1hLPS-polII-1

description: Library name: ChIP13


title: KO-0hLPS-polII-3

description: Library name: ChIP12


title: CtrlM1


title: Nur77_Ctrl1


title: 3_HKM7VBGXT.3.ACTGAGCG_AGAGGATA

description:
Library name: 3_SM-NBW7K_plate1
DHMT_48hr_d

value: iPSC-derived excitatory neuron, astrocyte


title: Xenium spatial transcriptomics of Prf1-/- uninjected mouse 1 (replicate 2)

city: New York

first: Morgan

last: Huse

state: NY

address: 417 E 68th St

institute: Sloan Kettering Institute

hyb_protocol: Spatial transcriptomics was performed using the Xenium In Situ platform (10x Genomics). Targeted RNA probes were hybridized in situ, followed by cyclic  detection of transcripts according to manufacturer protocols.

scan_protocol: Spatial transcriptomic data were acquired using the 10x Genomics Xenium Analyzer, an automated fluorescence imaging platform for in situ RNA detection and spatial gene expression profiling.

data_processing: Raw imaging data were processed using the Xenium analysis pipeline to detect transcripts and assign spatial coordinates.

source_name: Bone

extract_protocol: tissue preparation protocol: Sections for Xenium were prepared according to the Xenium In Situ for FFPE − Tissue Preparation Guide (CG000578 Rev D; 10x Genomics) protocol.  For spatial transcriptomics, a series of 5 μm-thick longitudinal sections were cut across the femur, floated in an RNase-free water bath, then carefully mounted within the probe field of Xenium slides containing the Prime 5K Mouse panel with custom add-ons. Samples were taken from 2 B16F10-injected Prf1-/- mice and 1 uninjected  Prf1-/- control.

value: Bone


title: KO-0hLPS-polII-2

description: Library name: ChIP11

value: untreated


title: GFP_LPS3

value: GFP


title: 2_HKM7VBGXT.2.ACTGAGCG_AGAGGATA

description:
Library name: 2_SM-NBW7K_plate1
DHMT_48hr_d


title: Xenium spatial transcriptomics of  Prf1-/- uninjected mouse 1 (replicate 1)

value: FFPE


title: KO-0hLPS-polII-1

description: Library name: ChIP10

value: cre


title: Xenium spatial transcriptomics of Prf1-/- bone-injected mouse 2 (replicate 2)

value: B16F10 injection


title: 1_HKM7VBGXT.1.ACTGAGCG_AGAGGATA

description:
Library name: 1_SM-NBW7K_plate1
DHMT_48hr_d


title: KO-18hLPS-H3k27ac-3

description: Library name: ChIP9

value: 18h 100 ng/ml LPS

value: H3K27ac (Diagenode, C15410196)


title: GFP_LPS1


title: GFP_LPS2


title: 4_HKM7VBGXT.4.TAGCGCTC_AGAGGATA

description:
Library name: 4_SM-NBW7J_plate1
DHMT_48hr_c


title: KO-18hLPS-H3k27ac-2

description: Library name: ChIP8

value: bone marrow


title: Xenium spatial transcriptomics of Prf1-/- bone-injected mouse 2 (replicate 1)


title: GFP_Ctrl3


title: 3_HKM7VBGXT.3.TAGCGCTC_AGAGGATA

description:
Library name: 3_SM-NBW7J_plate1
DHMT_48hr_c


title: KO-18hLPS-H3k27ac-1

description: Library name: ChIP7


title: Xenium spatial transcriptomics of Prf1-/- bone-injected mouse 1 (replicate 2)


title: GFP_Ctrl2


title: 2_HKM7VBGXT.2.TAGCGCTC_AGAGGATA

description:
Library name: 2_SM-NBW7J_plate1
DHMT_48hr_c


title: Xenium spatial transcriptomics of Prf1-/- bone-injected mouse 1 (replicate 1)


title: KO-1hLPS-H3k27ac-3

description: Library name: ChIP6

value: 1h 100 ng/ml LPS


title: GFP_Ctrl1


title: 3453

city: Palo Alto

first: Michael

middle: Seth

last: Kapiloff

state: California

address: 1651 Page Mill Road, Room 2112

institute: Stanford University

description:
Library name: 53E3
10x Genomics

data_processing:
Cell Ranger software v7.1.0 was used to build a custom reference after adding AAV viral marker genes to the Sscrofa11.1 (Ensembl Pig release-109) reference, following which gene counting was performed
Assembly: Sscrofa11.1 (Ensembl Pig release-109)
Supplementary files format and content: Cell Ranger Feature Barcode Matrices in h5 format

organism: Sus scrofa

source_name: Heart

growth_protocol: Female Ossabaw swines were fed high fat diet as of 2 months of age (heart failure cohorts) or normal chow (control cohort).

extract_protocol:
Total RNA extracted  via RNeasy mini kit (Qiagen #74104)
Frozen pig heart tissues were freshly embedded in OCT compound and sliced for nuclei isolation using Chromium Nuclei Isolation Kit (10x genomics). 7,000-10,000 nuclei were used for each snRNA library construction via Chromium Next GEM Single Cell 3’ v3 Dual Index Reagent Kits (10x genomics). Sample index i7 and i5, and Cellular barcodes were incoporated according to manual instruction.

treatment_protocol: Obese female Ossabaw swines (Heart failure cohorts) were subjected to aortic banding and immediately treated by peripheral intravenous infusion with 8e12 vg/kg (3e14 vg total) AAV9sc.KBD. Heart tissue were collected 6 months after treatment.

value: Heart

value: Ossabaw

value: strain

value: wildtype

value: control


title: KO-1hLPS-H3k27ac-2

description: Library name: ChIP5

value: bone marrow-derived macrophages


title: 1_HKM7VBGXT.1.TAGCGCTC_AGAGGATA

description:
Library name: 1_SM-NBW7J_plate1
DHMT_48hr_c

value: iPSC-derived excitatory neuron, astrocyte

value: WT

value: no guide


title: 4_HKM7VBGXT.4.ATGCGCAG_AGAGGATA

description:
Library name: 4_SM-NBW7I_plate1
DHMT_48hr_b


title: GS80d-3

city: Guangzhou

first: Delin

last: Mo

address: Xingang Road

institute: Sun Yat-sen University

data_processing:
Clustering of index-encoded samples was performed using KAPA RNA Adapters set1/set2 for Illumina.
After clustering, libraries were sequenced using (2 ×150 bp) paired-end modules on the Illumina HiSeq × Ten platform.
Differentially expressed genes (DEGs) between the two groups were identified through the P-values < 0.05 and fold changes >1.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Adipose tissue

extract_protocol:
Total RNA was extracted from cells and pig adipose tissue samples using TRIzol reagent (Takara Bio, Otsu, Japan) according to the manufacturer's instructions.1.5 ug of total RNA was used for the construction of sequencing libraries.
The transcriptome libraries were generated for sequencing using the KAPA-Stranded RNASeq Library Prep Kit (Illumina).

value: Adipose tissue

tag: breed

value: Guangdong small-eared pigs

value: Adipocyte


title: 3449

description:
Library name: 49E2
10x Genomics

tag: cell type


title: GS80d-2


title: KO-1hLPS-H3k27ac-1

description: Library name: ChIP4

value: cre

tag: treatment


title: 3_HKM7VBGXT.3.ATGCGCAG_AGAGGATA

description:
Library name: 3_SM-NBW7I_plate1
DHMT_48hr_b

data_processing:
To identify cell-type-specific gene expression profiles, the fastq files of the bulk RNA-seq data were aligned to a mixed human-mouse reference genome (GRCh37/hg19 and GRCm38/mm10, GSE63269) using STAR65 (v.2.5). As quality control, Illumina adapters and low-quality base bares were trimmed using Trimmomatic66 (v.0.36) and short reads (< 36 base pairs) were removed. Next the reads were annotated with GENCODE GTF annotation version 19 and a custom GTF file for the mixed genome (GSE63269) for the mixed genome. A raw counts matrix was generated using featureCounts67 by Rsubread (v.1.32). Genes with a total read count less than 10 were filtered using filterByExpr function in edgeR68 (v. 4.2.0). Read counts were then normalized for library size (method = TMM) and transformed to log2 counts-per-million (logCPM) estimates using the voom function by limma69 (v. 3.60.3) package. The normalized logCPM gene expression matrices were used as input for all the following analyses.
Assembly: GRCh37/hg19 and GRCm38/mm10, GSE63269
Supplementary files format and content: counts_raw_all.txt contain raw counts for each sample (link: barcode).
Supplementary files format and content: counts_logCPM_human.txt contain logCPM values for all iPCS WT samples.
Supplementary files format and content: counts_logCPM_mouse.txt contain logCPM values for all astrocyte samples that have not been co-cultured CRISPRi-neurons.
Supplementary files format and content: counts_logCPM_CRISPRi_human.txt contain logCPM values for all CRISPRi-edited iPCS  samples.
Supplementary files format and content: counts_logCPM_CRISPRi_mouse.txt contain logCPM values for all astrocyte samples that have been co-cultured with CRISPRi-neurons.

extract_protocol:
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow


title: 3448

description:
Library name: 48E1
10x Genomics

tag: tissue


title: KO-0hLPS-H3k27ac-3

description: Library name: ChIP3

value: untreated


title: GS80d-1


title: 2_HKM7VBGXT.2.ATGCGCAG_AGAGGATA

description:
Library name: 2_SM-NBW7I_plate1
DHMT_48hr_b

tag: cell line


title: 3390

description:
Library name: 90D8
10x Genomics

tag: genotype

value: AAV9sc.KBD-treated Heart Failure


title: KO-0hLPS-H3k27ac-2

description: Library name: ChIP2

value: bone marrow

value: H3K27ac (Diagenode, C15410196)


title: YK80d-3

value: Yorkshire pigs


title: 1_HKM7VBGXT.1.ATGCGCAG_AGAGGATA

description:
Library name: 1_SM-NBW7I_plate1
DHMT_48hr_b


title: 3389

description:
Library name: 89D7
10x Genomics

value: Heart

value: Ossabaw

value: Saline-treated Heart Failure


title: YK80d-2


title: 4_HKM7VBGXT.4.TACGCTGC_AGAGGATA

description:
Library name: 4_SM-NBW7H_plate1
DHMT_48hr_a


title: KO-0hLPS-H3k27ac-1

description: Library name: ChIP1


title: 3388

description:
Library name: 88D6
10x Genomics

value: strain

value: wildtype


title: 3_HKM7VBGXT.3.TACGCTGC_AGAGGATA

description:
Library name: 3_SM-NBW7H_plate1
DHMT_48hr_a

value: iPSC-derived excitatory neuron, astrocyte


title: YK80d-1

value: WT


title: 3380

description:
Library name: 80D5
10x Genomics


title: WT_18h3

description:
Library name: Sample 31
Column name in raw_read_quant.table.txt: WT_18h3

value: bone marrow-derived macrophages

value: wt

value: 18h 100 ng/ml LPS


title: GS9d-3

value: Adipose tissue

value: Guangdong small-eared pigs

value: Adipocyte


title: 2_HKM7VBGXT.2.TACGCTGC_AGAGGATA

description:
Library name: 2_SM-NBW7H_plate1
DHMT_48hr_a

value: no guide


title: 3369

description:
Library name: 69D4
10x Genomics


title: WT_18h2

description:
Library name: Sample 30
Column name in raw_read_quant.table.txt: WT_18h2

value: bone marrow


title: GS9d-2


title: 1_HKM7VBGXT.1.TACGCTGC_AGAGGATA

description:
Library name: 1_SM-NBW7H_plate1
DHMT_48hr_a


title: 3367

description:
Library name: 67D3
10x Genomics


title: WT_18h1

description:
Library name: Sample 29
Column name in raw_read_quant.table.txt: WT_18h1


title: GS9d-1


title: 4_HKM7VBGXT.4.CGGAGCCT_AGAGGATA

description:
Library name: 4_SM-NBW7G_plate1
DHMT_0.5hr_d


title: WT_5h4

description:
Library name: Sample 28
Column name in raw_read_quant.table.txt: WT_5h4

value: 5h 100 ng/ml LPS


title: 3340

description:
Library name: 40D2
10x Genomics

value: AAV9sc.KBD-treated Heart Failure


title: YK9d-3

value: Yorkshire pigs


title: 3_HKM7VBGXT.3.CGGAGCCT_AGAGGATA

description:
Library name: 3_SM-NBW7G_plate1
DHMT_0.5hr_d


title: 3335

description:
Library name: 35D1
10x Genomics

value: Heart

value: Ossabaw


title: WT_5h3

description:
Library name: Sample 27
Column name in raw_read_quant.table.txt: WT_5h3


title: YK9d-2


title: 2_HKM7VBGXT.2.CGGAGCCT_AGAGGATA

description:
Library name: 2_SM-NBW7G_plate1
DHMT_0.5hr_d


title: Zebrafish embryos at 72 hpf from the  wbp11-MO-3

city: changsha

first: Haochen

last: Wang

address: 183 Lushan Road, Yuelu District, Changsha City, Hunan Province

institute: hunan normal university

description: Library name: W11-3

data_processing:
FastQC (version 0.12.1).
HTSeq-count (version 2.0.5)
Assembly: Danio_rerio.GRCz11.dna.primary_assembly.fa
Supplementary files format and content: FPKM_normalized.tsv.gz: FPKM-normalized expression matrix with identical row/column structure to the raw counts file.

organism: Danio rerio

source_name: embryos

extract_protocol:
Zebrafish embryos at 72 hpf from the Control-MO and wbp11-MO groups were collected, with three biological replicates per group and 50 embryos per replicate. Samples were preserved in RNAlater (Servicebio) and stored at -80 °C prior to being shipped on dry ice to Shanghai Personal Biotechnology Co., Ltd. for library construction, transcriptome sequencing, and bioinformatics analysis. mRNA with polyA tails was enriched from total RNA using Oligo(dT) magnetic beads and fragmented to approximately 300 bp using an ion_x001E_based fragmentation method. Following library construction, PCR amplification was performed to enrich the library fragments, after which size selection was conducted to obtain libraries of approximately 450 bp. Library quality was assessed using an Agilent 2100 Bioanalyzer, and both total concentration and effective concentration of the libraries were determined.
mRNA with polyA tails was enriched from total RNA using Oligo(dT) magnetic beads and fragmented to approximately 300 bp using an ion_x001E_based fragmentation method. Following library construction, PCR amplification was performed to enrich the library fragments, after which size selection was conducted to obtain libraries of approximately 450 bp.

value: embryos

value: KNOCK DOWN


title: WT_5h2

description:
Library name: Sample 26
Column name in raw_read_quant.table.txt: WT_5h2


title: 1_HKM7VBGXT.1.CGGAGCCT_AGAGGATA

description:
Library name: 1_SM-NBW7G_plate1
DHMT_0.5hr_d

value: iPSC-derived excitatory neuron, astrocyte


title: YK9d-1

value: WT


title: Zebrafish embryos at 72 hpf from the  wbp11-MO-2

description: Library name: W11-2


title: AF22, BMI1/COMMD3-BMI1_KD, 1

city: Higashi-Hiroshima

first: boyang

last: An

state: Hirohsima

address: Kagamiyama 1-3-1

institute: Hiroshima University

description: Library name: BMI1/COMMD3-BMI1_KD_1

data_processing:
Adaptor and imcomplete sequences were removed by Trim Galore (ver. 0.6.6)
Short-read sequences were mapped on the human reference genome hg38 by STAR (ver. 2.7.10a)
mapped reads were counted by bedtools (ver. v2.29.2)
Assembly: hg38
Supplementary files format and content: txt

extract_protocol:
RNA was extracted with Sepazol Super G RNA (Nakarai Tesque), followed by Dnase digestion with NucleoSpin RNA column kit. 700 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's protocols.

value: neural stem cells

value: BMI1/COMMD3-BMI1 knockdown


title: WT_18h4

description:
Library name: Sample 32
Column name in raw_read_quant.table.txt: WT_18h4

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer 0.2.2
Reads were aligned to the mouse genome mm10 by HISAT2 2.1.0
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.16.1
Raw tag counts per gene were counted using HOMER2's analyzeRepeats.pl script
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts for each sample

extract_protocol:
Cells were lysed in RLT buffer and total RNA was isolated using the RNeasy mini kit with on-column DNase treatment (Qiagen)
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol

value: bone marrow-derived macrophages

value: wt

value: 18h 100 ng/ml LPS


title: 4_HKM7VBGXT.4.GCGTAGTA_AGAGGATA

description:
Library name: 4_SM-NBW7F_plate1
DHMT_0.5hr_c


title: Zebrafish embryos at 72 hpf from the  wbp11-MO-1

description: Library name: W11-1


title: WT_5h1

description:
Library name: Sample 25
Column name in raw_read_quant.table.txt: WT_5h1


title: WT_1h4

description:
Library name: Sample 24
Column name in raw_read_quant.table.txt: WT_1h4

value: 1h 100 ng/ml LPS


title: AF22, shControl, 1

description: Library name: shControl_1


title: 3_HKM7VBGXT.3.GCGTAGTA_AGAGGATA

description:
Library name: 3_SM-NBW7F_plate1
DHMT_0.5hr_c

value: no guide


title: WT_1h3

description:
Library name: Sample 23
Column name in raw_read_quant.table.txt:

value: bone marrow


title: NF54, HS, rep3

city: Barcelona

first: Elisabet

last: Tinto-Font

address: c/Rossello 153

department: Malaria

country: Spain

institute: ISGlobal

description:
Library name: NF54_HS_rep3
NF54_HS_rep3

data_processing:
RNA-seq data analysis was carried out using custom scripts written in Python (v3.11.5) and R (v4.3.2). Trimming, quality control and contamination check of raw reads were performed as for ChIP-seq. Trimmed reads were mapped to the P. falciparum 3D7 reference transcriptome (PlasmoDB v67) using STAR (v2.7.10b) with the following parameters: --outFilterType Normal --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.05 --alignIntronMin 20 --alignIntronMax 5000 --alignMatesGapMax 10000. Alignments were sorted, compressed and indexed using SAMtools (v1.15).  Gene-level quantification was performed using featureCounts (Rsubread v2.16.1), based on the GTF annotation file from PlasmoDB (v67).
Assembly: Plasmodium falciparum 3D7 reference genome (PlasmoDB v67)
Supplementary files format and content: Raw counts: gene-level quantification in counts. Tab-separated file.

organism: Plasmodium falciparum

growth_protocol: Parasites were cultured in B+ or O+ erythrocytes at a 3% hematocrit under standard conditions in RPMI-1640-based media, supplemented with 0.5% Albumax II (Gibco, 11021037) and 2 mM choline chloride (Sigma-Aldrich, C7527), and maintained in a shaking incubator with a 5% CO₂, 3% O₂, and balance N₂ atmosphere. All cultures were kept at 37ºC, except for parasite lines in which pfap2-hs was disrupted and control cultures grown in parallel , which were maintained at 35ºC because at 37ºC they show reduced growth (Tintó-Font, E., et al., 2021; PMID:34400833). Tight synchronization to a 5 h age window was achieved by purification of late stages in 63% Percoll gradients (GE Healthcare, 17-0891-01) followed by sorbitol lysis 5 h later (Sigma-Aldrich, S3889). For ChIP-seq experiments, erythrocyte were filtered with Plasmodipur (R-Biopharm Nederland B.V., 8011FILTER) to remove leukocytes before using them for parasite cultures.

extract_protocol:
RNA was harvested from  tyghtly synchronized cultures at the mid trophozoite stage (33–38 hpi, unless stated otherwise) at ~2 % parasitemia using 20 pellet volumes of TRIrizol (Life Technologies, 15596018). RNA of ap2-hs KO was collected at 37-42 hpi to account for their slower IDC progression (Tintó-Font, E., et al., 2021; PMID:34400833). RNA extraction and treatment with DNase was performed as previously described [Casas-Vila, N., Pickford, A., et al. 2021. PMID: 34313989]. rRNA depletion of 5 μg of RNA was performed using the Rneasy Pure mRNA Bead Kit (Qiagen, 180244) following manufacturers’ instructions, and eluted in 18 μl of nuclease-free water. rRNA-depleted RNA was fragmented to ~100-400 bp using the NEBNext Magnesium RNA Fragmentation Module (NEB, E6150S), by adding 2 μl of fragmentation buffer, incubating for 4 min at 94 ºC, placing on ice and immediately adding 2 μl of stop solution. Fragmented RNA was cleaned up using the RNeasy MinElute CleanUp Kit (Qiagen, 74204) and eluted in 11 μl of nuclease-free water. For the first-strand cDNA synthesis, the SuperScript III Reverse Transcriptase kit (Invitrogen, 18080093) was used. Each sample was pre-incubated for 10 min at 70 ºC with 1.25 μl of AT-biased random primers (IDT) and 1 μl of actinomycin (Gibco, 11805017) and then for 2 min at 37 ºC with 8 μl of mastermix containing 1x first-strand buffer, 25 mM DTT, 1.25 mM dNTP (NEB, N0447S) and 1 μl RNasin Plus Ribonuclease inhibitor (40 U/ μl) (Promega, N2611).Next, 1 μl of Superscript III (200 U/ μl) was added to each sample, and incubated for 10 min at 37 ºC, followed by 1 h at 42 ºC. Second-strand cDNA synthesis was achieved by incubating the product of the previous reaction for 2 h at 16 ºC with 55 μl of a mastermix containing 1x second-strand buffer (Invitrogen, 10812014), 0.27 mM dNTP custom mix (10 mM dACG/dU) (Invitrogen, 10297018; Thermo Scientific, R0133), 0.1 μl Ambion RNase H (10 U/μl) (Invitrogen, AM2292), 2 μl DNA Polymerase I (10 U/μl) (Promega, M205A) and 0.5 μl E. coli DNA ligase (10 U/μl) (NEB, M0205S). The final cleanup was performed using the MinElute PCR purification kit (Qiagen, 28006), eluting in 10 μl nuclease-free water. The resultant cDNA was quantified by Qubit HS before library preparation.
Library preparation was performed using 5 ng of DNA, as previously described (Llorà-Batlle, O., 2020. PMID: 32577509). NEBNext multiplex oligonucleotides for Illumina (NEB, E7335, E7500 and E7710) were used, and 9 cycles of amplification were performed with the Kapa HiFi HotStart PCR kit (Roche, 7958889001). All purification steps were carried out using AMPure XP beads (Beckman Coulter, 082A63881). Quality and concentration of all libraries was determined using a Tapestation 4200 (Agilent). We obtained ~8-19 million 150 bp paired-end reads per sample using a NextSeq500 System (Illumina).

treatment_protocol: Sexual conversion was induced by three different methods: choline depletion, dihydroartemisinin (DHA; Sigma-Aldrich, D7439) treatment or heat shock (HS). For induction by choline depletion, the regular RPMI medium with Albumax II and a 2 mM choline supplement was replaced by the same medium without the choline supplement in cultures at the early ring stage (0-5 h post-invasion, hpi) and cultures were placed in static conditions in a hypoxia chamber for the rest of the experiment. For induction of sexual conversion by DHA or HS, tightly synchronized cultures (0-5 hpi) were placed in static conditions in a hypoxia chamber, and left undisturbed until the early trophozoite stage (25-30 hpi for most experiments; 29-34 hpi for experiments with transgenic lines in which ap2hs was disrupted, to account for their slower growth), when they were exposed to a 3 h of 10 nM DHA pulse or maintained for 3 h at 41.5 ºC (placing the full hypoxia chamber in an incubator at 41.5 ºC), respectively. After exposure, DHA was removed from the medium by centrifugation or cultures were placed back in an incubator at the normal growth temperature. Medium  was refreshed at ~33 hpi to all conditions. A control condition was always kept in parallel until the end of the experiment

value: heat shock exposure

tag: biological replicate

tag: time


title: Zebrafish embryos at 72 hpf from the Control-MO-3

description: Library name: control -3

value: CONTROL


title: 2_HKM7VBGXT.2.GCGTAGTA_AGAGGATA

description:
Library name: 2_SM-NBW7F_plate1
DHMT_0.5hr_c

tag: day


title: WT_1h2

description:
Library name: Sample 22
Column name in raw_read_quant.table.txt: WT_1h2

tag: strain


title: Zebrafish embryos at 72 hpf from the Control-MO-2

description: Library name: control -2


title: NF54 ctrl, rep3

description:
Library name: NF54_ctrl_rep3
NF54_ctrl_rep3

value: control heat shock


title: WT_1h1

description:
Library name: Sample 21
Column name in raw_read_quant.table.txt: WT_1h1


title: 1_HKM7VBGXT.1.GCGTAGTA_AGAGGATA

description:
Library name: 1_SM-NBW7F_plate1
DHMT_0.5hr_c


title: Zebrafish embryos at 72 hpf from the Control-MO-1

description: Library name: control -1


title: 4_HKM7VBGXT.4.GGAGCTAC_AGAGGATA

description:
Library name: 4_SM-NBW7E_plate1
DHMT_0.5hr_b


title: HAstV1_Caco2_NAI_rep2

city: singapore

first: YUE

last: WAN

address: 1, #20-10 Fusionopolis Way, Connexis, North Tower, 138632

country: Singapore

institute: Genome Institute of Singapore,A*STAR

description:
Library name: RHX944
HAstV1_Caco2_rep2_processed_profile.txt

library_source: other

data_processing:
Raw reads were trimmed the adapter and poor-quality reads using the software cutadapt.
The trimmed reads were processed by ‘Shapemapper-2.15’ of Weeks et al to calculate the SHAPE values for each position with the minimum effective sequencing depth 5000.
Assembly: GRCh38
Supplementary files format and content: *.txt, the profiles for mutation and reactivity of transcripts, including mitochondrial transcripts
Library strategy: SHAPE-Map

molecule: other

growth_protocol: Caco2 cells were infected with astrovirus HAstV1 viruses at a multiplicity of infection (MOI) = 0.01 for 1 h at 37°C. Following 1 h infection, virus inoculum was removed and replaced with DMEM-5% FBS. Flasks were incubated for 48 h at 37 °C, 5% CO2. At 24 hpi, cells were washed once with PBS and trypsin was added to detach the cells from the flask. The cells were collected and centrifuged at 300 × g for 5 min.

extract_protocol:
The total RNA was extracted from the cells using E.Z.N.A. Total RNA Kit (Omega bio-tek) according to the manufacture’s instructions.
The library preparation following the SHAPE-MaP protocol were performed to generate cDNA libraries compatible for Illumina sequencing.

treatment_protocol: The pellet was resuspended in PBS and the cells were then separated into three reactions: (1) added 1:20 volume of 1 M NAI (03-310, Merck, 25 µL of NAI in 500 µL of infected cells) and incubated for 15 min at 37 °C for structure probing; (2) added 1:20 volume of dimethyl sulfoxide (DMSO) and incubated for 15 min at 37 °C, as negative control; and (3) set aside a third portion of the infected cells without any treatment, for the denaturing control in the downstream library preparation process.

value: HAstV1 infect, NAI


title: DRG, HC, rep2

city: Beijing

first: Tian-Yu

last: Feng

address: 1 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

description: Library name: Sample 4

data_processing:
Raw sequencing data were processed using the DNBelab C Series V2 Single-Cell RNA Analysis pipeline (v3.1.5).
Assembly: GCF_016699485.2
Supplementary files format and content: Tab-separated values files and matrix files

organism: Gallus gallus

source_name: dorsal root ganglia and attached nerves

extract_protocol:
DRG and attached nerves were harvested from chickens, rinsed twice with PBS, and snap-frozen in liquid nitrogen. Tissues were thawed on ice in pre-chilled homogenization buffer for 10 minutes. Samples were homogenized using a sterile pestle, filtered through a 70 µm strainer, and then re-homogenized with a clean pestle. The homogenate was filtered again through a 30 µm strainer and centrifuged at 500 g for 5 minutes at 4 °C. The pellet was washed twice with pre-chilled blocking buffer and resuspended in PBS containing 0.04% BSA.
Single-nucleus suspensions were processed using the DNBelab C Series Single-Cell Library Prep Set following the manufacturer's protocol. Nuclei were encapsulated with barcoded magnetic beads in droplets via microfluidics. After mRNA capture, emulsions were broken and magnetic beads were collected and washed. Reverse transcription was performed on bead-bound mRNA using UMI-tagged primers, followed by second-strand synthesis and PCR amplification. After cDNA quality assessment, fragmentation, end-repair, adapter ligation, and indexing PCR were performed. Final libraries were purified and sequenced on the DNBSEQ-T7 platform using paired-end sequencing.

value: dorsal root ganglia and attached nerves

tag: age

value: TRPA1 inhibitor


title: WT_0h4

description:
Library name: Sample 20
Column name in raw_read_quant.table.txt: WT_0h4

value: untreated


title: HAstV1_Caco2_NAI_rep1

description:
Library name: RHX943
HAstV1_Caco2_rep1_processed_profile.txt


title: 3_HKM7VBGXT.3.GGAGCTAC_AGAGGATA

city: Helsinki

first: Olli

last: Pietilainen

address: Haartmaninkatu 8

institute: University of Helsinki

description:
Library name: 3_SM-NBW7E_plate1
DHMT_0.5hr_b

value: iPSC-derived excitatory neuron, astrocyte


title: HAstV1_Caco2_DMSO_rep2

description:
Library name: RHX942
HAstV1_Caco2_rep2_processed_profile.txt

value: HAstV1 infect, DMSO


title: WT_0h3

description:
Library name: Sample 19
Column name in raw_read_quant.table.txt: WT_0h3


title: 2_HKM7VBGXT.2.GGAGCTAC_AGAGGATA

description:
Library name: 2_SM-NBW7E_plate1
DHMT_0.5hr_b

value: WT


title: DRG, HC, rep1

description: Library name: Sample 3


title: DRG, con, rep2

description: Library name: Sample 2

value: control


title: HAstV1_Caco2_DMSO_rep1

description:
Library name: RHX941
HAstV1_Caco2_rep1_processed_profile.txt


title: 1_HKM7VBGXT.1.GGAGCTAC_AGAGGATA

description:
Library name: 1_SM-NBW7E_plate1
DHMT_0.5hr_b


title: DRG, con, rep1

description: Library name: Sample 1


title: WT_0h1

description:
Library name: Sample 17
Column name in raw_read_quant.table.txt: WT_0h1

value: bone marrow-derived macrophages


title: WT_0h2

description:
Library name: Sample 18
Column name in raw_read_quant.table.txt: WT_0h2

value: wt