title: E19Diaphragm_AGO2_PN4

description:
Library name: E19Diaphragm_AGO2_PN4
stranded
E19Diaphragm_CDNvPN_DESeq2.csv

tag: Stage

tag: background

value: C57BL/6J and C57BL/6N


title: T342, ChIP-seq, H3K27ac

status: Public on Aug 13 2026

type: SRA

city: Shanghai

first: Zixian

last: Wang

address: 130 Dong'an Road, Xuhui District, Shanghai

country: China

institute: Fudan University

description: Library name: T342-H3K27ac

library_source: genomic

data_processing:
ChIP-seq: Raw reads were assessed with FastQC (v0.11.9) and adapter/low-quality sequences removed using TrimGalore (v0.6.7). Clean reads were aligned to the GRCh38 reference genome with Bowtie2 (v2.2.5) under default parameters. Alignments with mapping quality < 30 or flagged as unmapped, secondary, or PCR/optical duplicates (−F 3844) were discarded using SAMtools (v1.9). Duplicate reads were further marked and removed with Picard (v2.25.1). Library complexity and enrichment were evaluated with ENCODE's Phantompeakqualtools (run_spp.R), providing fragment-length estimates for downstream analyses. Peak calling was performed with MACS3 (v3.0.0a6) using the options “--nomodel --shift 0 --extsize <fragment_length>” and a significance threshold of p < 1 × 10-3.
RNA-seq: The raw data quality was evaluated with FastQC (v0.11.9). Adapter sequences and low-quality bases were removed using AdapterRemoval (v2.3.2). The resulting clean reads were aligned to the human reference genome (GRCh38) with STAR (v2.7.9a), and the alignments were sorted with SAMtools (v1.13). Gene-level read counts were generated from the sorted BAM files using htseq-count (v0.13.5). Differentially expressed genes (DEGs) were identified with DESeq2, applying thresholds of |fold change| > 2 and FDR < 0.05. Transcript abundance in transcripts per million (TPM) was quantified using StringTie (v2.2.1).
scRNA-seq: The raw sequencing data were processed using Fastp to trim adapter sequences and low-quality bases, followed by alignment to the human GRCh38 reference genome using SeekOne®Tools for gene expression matrix generation. Subsequent analysis was performed using 10x Genomics Cell Ranger and the Seurat package (v5.2.1) in R (v4.4.2), beginning with stringent quality control to select high-quality cells based on the following criteria: 200 < nFeature_RNA < 7000, nCount_RNA > 1000 (excluding the top 3% of cells by nCount_RNA), mitochondrial gene content < 10%, and ribosomal gene content between 0-60%.
Assembly: hg38
Supplementary files format and content: bigwig and narrowPeak for ChIP-seq data (except for input sample); gene expression matrix for RNA-seq and scRNA-seq data.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human prostate cancer tissue

extract_protocol:
The immunoprecipitated and input DNA was purified using the MinElute PCR Purification Kit (#28006, Qiagen). Total RNA was isolated using the EZ-10 DNAaway RNA Mini-Preps Kit (#B618133, Sangon Biotech). Single-cell RNA-Seq RNA extracted were prepared using SeekOne® Digital Droplet Single Cell 3’ library preparation kit (No.K00202, SeekGene Catalog).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (#E7103L, NEB) according to the manufacturer’s instructions. RNA-seq libraries were prepared using the Stranded mRNA-seq Lib Prep Module (RK20349, Abclonal). Single-cell RNA-Seq libraries were prepared using SeekOne® Digital Droplet Single Cell 3’ library preparation kit (No.K00202, SeekGene Catalog).

tag: tissue

value: Human prostate cancer tissue


title: SM20_NFIX_THcontrol_2x

city: HOUSTON

first: Sanjana

last: Murali

state: TX

address: 7600 Kirby Drive

country: USA

institute: Baylor College of Medicine

description: Library name: SAMPLE 20

library_source: transcriptomic

data_processing:
Quality control was performed using fastQC (v0.10.1) and MultiQC (v0.9) . Reads were mapped to the mouse genome mm10 assembly using STAR (v2.5.0a). In R(v3.5.2) Bioconductor packages GenomicAlignments (v1.16.0) and GenomicFeatures (v1.32.2) were used to build count matrices (Lawrence et al., 2013). UCSC transcripts were downloaded from Illumina iGenomes in GTF file format. Normalization and differential gene expression analysis were performed using DESeq2 (v1.20.0). Gene Ontologies were determined using Enrichr and visualized using GOplot (v1.0.2).
Assembly: Reads were mapped to the mouse genome mm10 assembly using STAR (v2.5.0a).
Supplementary files format and content: csv file with raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Thalamus

extract_protocol:
RNA was extracted from sorted cells using RNeasyMicro Kit (Cat.No. 4004, QIAGEN). RNA integrity (RINR8.0) was assessed using the High Sensitivity RNA Analysis Kit (DNF-472-0500, Agilent) on a 12-Capillary Fragment Analyzer.
cDNA synthesis and Illumina sequencing libraries with 8-bp single indices were constructed from 10 ng total RNA using the Revelo RNA-seq High Sensitivity kit (Cat.No. 30184149, TECAN).

value: Thalamus

tag: genotype

value: WT


title: SM1_NFIX_Obcontrol 1x

description: Library name: SAMPLE 1

source_name: Olfactory Bulb

value: Olfactory Bulb


title: Spatial transcriptomics of mus musculus: old male lung mouse 6

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

description: Library name: AGE_6_112_Lung_GEX5_A1

data_processing:
We stitched the image series from the Axio Imager KMAT brightfield microscope using the Zeiss ZEN software (v3.6) and cropped and rotated the resulting high-resolution TIFF files using Fiji. Individual sample images were color corrected where needed to match the other images.
In the next step, we ran Spaceranger (v2.1) with the demultiplexed FASTQ files and the corresponding TIFF images. In brief, Spaceranger aligns the reads to a reference genome (refdata-gex-mm10-2020-A), detects tissue under spots and the fiducial frame in the image, to create a spot x UMI count matrix. For the infection cohort, we additionally built a custom Spaceranger reference genome combining mouse (GRCm39) and Plasmodium berghei -ANKA genome (PBANKA01). For two samples the alignment of the fiducial frame was manually corrected after the automatic detection had failed initially. For the manual image QC of Visium samples we used the 10x Loupe browser tool (v6.5.0).
Based on the Spaceranger reports, we either excluded a sample completely from further analysis, or using the 10x Cloupe tool manually selected small spot regions to exclude from downstream analysis where necessary (e.g. removing corners with uneven permeabilization), and further applied criteria-based spot filtering on each sample, to eventually obtain a high-quality data set. To this end, we inspected the variable distributions for the number of UMIs, the number of read counts, mitochondrial content, as well as spot complexity (=log10(Number of features) / log10(Number of counts)) for each tissue separately, and applied the following filtering criteria on the filtered spot count matrix from Spaceranger after loading into Seurat objects: (Maximum percentage of mitochondrial read content; Minimum number of UMIs; Maximum number of UMIs; Minimum number of detected features; Maximum number of detected features; Minimum spot complexity) Brain: (35; 500; 70,000; 300; 10,000; 0.75), Bulb: (35; 500; 70,000; 300; 10,000; 0.75), Heart: (60; 1000; 25,000; 300; 5000; 0.75), Kidney: (30; 1000; 50,000; 300; 8000; 0.75) Liver: (15; 1000; 40,000; 500; 8000; 0.75), Lung: (10; 1000; 30,000; 300; 8000; 0.75) Spleen: (10; 500; 35,000; 300; 8000; 0.75).
We then rotated the images of the remaining samples to best match the desired orientation for each tissue. We then followed the default Seurat (v4.4) workflow to preprocess each sample by applying NormalizeData, FindVariableFeatures with variance stabilizing transformation for 2000 features, followed by SCTransform (v1), regressing out the percentage of mitochondrial reads and subsetting to 3000 variable features. Subsequently, we performed RunPCA on the SCT assay, FindNeighbors on up to 30 PCs, FindClusters with leiden clustering followed by RunUMAP with up to 30 dimensions. Using the cleaned list of Visium samples, we created one Seurat object for each tissue using the SCT-based integration workflow as follows: set the default assay to SCT, run SelectIntegrationFeatures with 3000 features, then PrepSCTIntegration, and FindIntegrationAnchors followed by IntegrateData, each with “SCT” set as normalization method and up to 30 dimensions. Next, we performed the standard dimension reduction workflow consisting of RunPCA, RunUMAP, FindNeighbors, and FindClusters again with up to 30 dimensions and fixed random seeds.
In case of the STOmics Stereo-seq samples, images were obtained and stitched with the Zeiss Moticam Pro 500i. Combined QC and primary analysis of sequencing and image data was performed using the STOmics analysis workflow (SAW) v1.0 to obtain quantification matrices for the mouse genome (GRCm38). The SAW pipeline was also used to accumulate DNB spot gene expression counts into the specific area and cell binnings.
For the STOmics Stereo-seq samples, we first converted the outputs of the Stereo-Seq Analysis Workflow (SAW) pipeline90 into Seurat objects for both bin200 (200x200 Stereo-seq spots) and cell bins. This is done by using the io.stereo_to_anndata function in the Stereopy package91 (v1.1.0), followed by applying the h5ad2rds.R script provided by BGI. Cell bins were obtained using image-based cell segmentation of the corresponding ssDNA-stained images. Filtering was performed using the following criteria: (Maximum percentage of mitochondrial read content; Minimum number of UMIs; Maximum number of UMIs; Minimum number of detected features; Maximum number of detected features; Minimum spot complexity) Brain (bin200): (35; 500; 100,000; 300; 10,000; 0.75), Brain (cell bin): (35; 100; 10,000; 100; 3,000; 0.75).
In line with the Visium 10x samples we applied a default Seurat preprocessing workflow for each sample. Using the cleaned list of STOmics Stereo-Seq samples, we performed the Harmony-based integration workflow as follows: set the default assay to SCT, run SelectIntegrationFeatures with 5000 features, merge the sample list into one Seurat sample, run RunPCA with 50 components, run RunHarmony on SCT assay and the PCA reduction using Sample_ID and Age as latent variables, run JoinLayers on the RNA assay. Then, we performed the sample dimension reduction workflow as in the Visium samples with up to 50 dimensions.
Assembly: GRCm39
Supplementary files format and content: tif image of H&E stained tissue slice on capture area in high resolution
Supplementary files format and content: jpg image of spaceranger aligned fiducials
Supplementary files format and content: jpg image of spaceranger detected tissue
Supplementary files format and content: h5 of filtered spot barcode-to-feature count matrix from spaceranger
Supplementary files format and content: h5 of raw spot barcode-to-feature count matrix from spaceranger
Supplementary files format and content: json of spaceranger image scale factors
Supplementary files format and content: csv of spatial enrichment results for gene features
Supplementary files format and content: png image of tissue slice on visium capture area in high resolution
Supplementary files format and content: png image of tissue slice on visium capture area in low resolution
Supplementary files format and content: csv of spaceranger spot tissue positions
Supplementary files format and content: tif image of adjacent (before or after) H&E stained tissue slice in high resolution
Supplementary files format and content: cellbin.gef cellbin feature expression matrix records the information of cells individually, including the centroid coordinate, boundary coordinates, expression of genes, and cell area.
Supplementary files format and content: gef feature expression matrix includes the whole information over a complete chip region. It only has bin1 expression counts.
Supplementary files format and content: gem gene expression matrix (GEM) stores gene spatial expression data. SAW generates multiple gene expression matrix files in the workflow, the basic format requires six columns with a header row that shows the column names. The six columns are gene ID, gene name, x coordinate, y coordinate, MID count and exon count. When it comes to cellbin GEM, the seventh column is for cell ID. The header of the expression matrix for the maximum area enclosing rectangle region has several annotation rows starting with "#" before the column rows.
Supplementary files format and content: tissue.gef Feature expression matrix under the tissue coverage region. It is also a visualization GEF that includes expression counts for bin1, 5, 10, 20, 50, 100, 150, 200.
Supplementary files format and content: tissue.gem gene expression matrix (GEM) stores gene spatial expression data for spots under tissue. SAW generates multiple gene expression matrix files in the workflow, the basic format requires six columns with a header row that shows the column names. The six columns are gene ID, gene name, x coordinate, y coordinate, MID count and exon count. When it comes to cellbin GEM, the seventh column is for cell ID. The header of the expression matrix for the maximum area enclosing rectangle region has several annotation rows starting with "#" before the column rows.
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: Lung

growth_protocol:
For the aging cohort, male C57BL/6JN mice were shipped from the National Institute on Aging colony (Charles River) to the Stanford ChEM-H animal facility, where they were housed at 12/12h light/dark cycle in cages of 2-3 mice. Water and food were provided ad libitum.
For the infection cohort, C57BL/6 mice were bred at the animal facility of the Bernhard Nocht Institute. P. berghei ANKA parasites were obtained from the blood of sporozoite-infected C57BL/6 mice provided by the Parasitology Section of the Bernhard Nocht Institute. Male C57BL/6 mice (6–8 weeks old) were infected i.p. with 1×10^5 parasitized red blood cells. Parasitemia was determined in Giemsa-stained blood smears from tail blood. Body weight was determined at different time points.

extract_protocol:
We followed the standard protocol for fresh frozen tissues (compare document CG000239 - Rev F) using the Visium Spatial Gene Expression (GEX) Slide & Reagent Kits with recommended reagents (10x Genomics, PN-1000193). In brief, after H&E staining and imaging (10x magnification, Axio Imager KMAT - ZEISS), tissues were permeabilized with the previously defined permeabilization time. After reverse transcription on the slide and denaturation, second strand synthesis is performed. For further processing, cDNA is released via denaturation. To determine cycle number for amplification the KAPA SYBER FAST qPCR Master Mix Kit (KAPA Biosystems) is used in a qPCR. All samples in this study were amplified using 14 – 19 PCR cycles. After bead purification using SPRIselect beads (Beckman Coulter, Product No. B233318), cDNA is quantified via 2100 Bioanalyzer using the Bioanalyzer High Sensitivity DNA kit (Agilent, cat.no.:5067-4626).
For each brain, five 10µm sections (Bregma: –1.7, -2.06, -2.7, -3.52 and -4.72) identical to the Visium cohort were collected and loaded onto the StereoSeq Chip T-Slide according to manufacturer´s protocol. In short, after fixation of the tissue using ice-cold methanol, cell nuclei were stained using the ssDNA Qubit dye (Thermo Fisher) and imaged in 10x resolution in FITC channel. Subsequently, brain tissue was permeabilized for 14 min at 37°C, releasing mRNAs from the cells onto the Chip T-Slide. Reverse transcription of mRNAs was conducted for 3 hours at 42°C generating cDNA with sequence barcodes indicating their unique location on the T-Slide. Afterwards, the tissue was removed using tissue removal buffer for 10 min at 55°C and cDNA was collected from the chip o/n at 55°C. CDNA was then purified, amplified and size distribution was checked using High Sensitivity DNA Bioanalyser Kit (Agilent).
The library construction was either performed manually or using the MGISP-100 liquid handling system according to the 10x Visium user guide. In short, the following steps were performed: fragmentation, end repair, A-tailing, double sided size selection, adaptor ligation, post ligation cleanup, sample index PCR, double sided size selection; followed by post library construction QC performed using the Bioanalyzer High Sensitivity DNA kit (Agilent, cat.no.:5067-4626) and KAPA Library Quantification Kit (Roche, KK4824). Libraries were pooled in an equimolar fashion with up to 15 samples in one library, pooling only samples originating from the same organ whenever possible. All libraries were sequenced using NovaSeq 6000 (Illumina).
Library Preparation was performed using Stereo-seq Library Preparation Kit (MGI) using 30ng of cDNA and 13 cycles of amplification following the manufacturer´s protocol. Final quality check of the size distribution of the library was performed using High Sensitivity DNA Bioanalyzer Kit.

treatment_protocol:
For the aging cohort, tissues from brain, heart, kidney, liver, lung and spleen were collected after anaesthetization with 2.5% v/v Avertin and transcardial perfusion with 20 mL cold PBS and flash frozen in isopentane cooled with liquid nitrogen, all between 10:15 AM- 12:00 PM on a single day. For brain samples, the right and left hemisphere were separated before freezing and stored separately. Samples were stored at -80°C until embedding in OCT. Samples were embedded for sectioning in precooled OCT on dry ice.
For the infection cohort, tissues samples were collected on consecutive days, from 9:30 AM (Ctrl.) and 10:30 AM (day 6 post-infection) until 12 PM. To prevent lung deflation, the tracheae were sutured, and the lungs were inflated with a 1:1 mixture of PBS and OCT. The small lung lobe was separated and frozen separately from the residual lung tissue. Brains were frozen without separating the hemispheres. All tissues were simultaneously frozen while embedded in OCT, in an isopentane bath cooled with liquid nitrogen and stored at -80°C.
Cryosectioning and section mounting were performed according to the manufacturer’s protocol, in a Leica cryostat (LEICA CM3050 S) set to -15°C with a slice thickness of 16 µm (except for the spleen of the infection cohort; 10 µm). For the aging cohort, five brain sections were mounted using visual landmarks and the Allen Mouse Brain Atlas, resulting in sections from bregma –1.7, -2.06, -2.7, -3.52 and -4.72. For the infection cohort, two brain sections were mounted, namely from bregma –2.06 and bregma 3.89 (Olfactory bulb). Sections were mounted on designated capture areas and stored at -80°C until further processing. After tissue mounting on the slide, an additional 10-15 sections were collected for RNA Quality assessment. All samples used in this study had a RIN value between 3.0 and 9.0.

value: Lung

tag: strain

tag: mouse id

tag: Sex

value: male

tag: age

value: 112 weeks

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

value: Aging

tag: technology

value: 10x Visium

value: Wildtype

tag: treatment

tag: disease

tag: disease stage


title: TEX_DMSO_24h-2

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

description: Library name: S6577Nr2

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2). The quality of the FASTQ files was analyzed with FastQC (version 0.11.5)
The resulting fastq files were mapped to the reference genome (hg38) using STAR aligner (PMID: 23104886) version 2.7.10a with default parameters.
The read assignments per gene were counted using htseq-count (version 0.11.1), using default counting mode and reverse string assignment to genes.
Assembly: hg38
Supplementary files format and content: htseq-count files

source_name: TEX

growth_protocol: TEX cells were cultured in a humidified 5% CO₂ atmosphere at 37°C  in IMDM medium, supplemented with 15% FBS, 20 ng/ml SCF, and 2 ng/ml IL-3 (PeproTech, Cranbury, NJ, USA).

extract_protocol:
Total RNA was isolated from 1 million cells TEX using the DirektZol kit (Zymo Research), all samples were DNase-treated, and eluted with 50 µl of water.  The quality and quantity of isolated RNA was analyzed using the 2100 Bioanalyzer System (Agilent 2100 bioanalyzer Eukaryote Total RNA Nano Series II Kit). RNA sequencing was performed by the CeGaT company (≥ 1 µg of RNA with a concentration of ≥ 40 ng/µl in at least 25 µl total volume)
The libraries were prepared at CeGaT using 100ng of input mRNA and the TruSeq Stranded mRNA kit and then sequenced there on NovaSeq 6000 using 2x 100bp sequencing.

treatment_protocol: TEX cells were treated with RVU120 (0.5mM), CCT251921 (0.5mM), or DMSO (5%) for 3h, 24h, and 72h in three biological replicates.

tag: cell line

value: TEX

value: DMSO

tag: time point


title: SM19_NFIX_THcontrol_1x

description: Library name: SAMPLE 19

tag: tissue

tag: genotype


title: T329, ChIP-seq, Input

description: Library name: T329-Input


title: E19Diaphragm_AGO2_CDN2

city: New York

first: Benjamin

last: Kleaveland

state: NY

address: 1300 York Ave

department: Pathology and Lab Medicine

institute: Weill Cornell Medicine

description:
Library name: E19Diaphragm_AGO2_CDN2
stranded
E19Diaphragm_CDNvPN_DESeq2.csv

data_processing:
Alignment and differential expression of the RNA-seq libraries was performed using the nf-core pipeline. Briefly, the default RNAseq pipeline was used, specifying STAR alignment and using a salmon counter. Reads were aligned to the mouse genome (mm39) using STAR v2.7.1a and Gencode annotations (m39.gencode.vM25.basic.annotation.gtf; downloaded 7/10/23). For mouse tissues, the gtf file was modified to include Rtl1as using the same coordinates as Rtl1 exon 2. For C2C12 cell lines, the mouse genome and gtf annotation file were modified to include the corresponding piggyBac sequences and either Rtl1, RTL1, or Halo transgenes as an artificial chromosome. As no reads mapped to the endogenous Rtl1 locus in Halo-expressing C2C12 cells, we excluded endogenous Rtl1 from any downstream analysis. Count files were merged to generate tables of gene counts for each tissue organized by genotype. For mouse tissue libraries, salmon.merged.gene_counts_length_scaled.tsv were imported directly into DESeq2; for C2C12 libraries, salmon.merged.gene_counts.tsv and salmon.merged.gene_lengths.tsv were imported into DESeq2 via tximport. Differential expression was performed using DESeq2 without the lfcShrink function.80
Assembly: mm39
Supplementary files format and content: comma-separated text file of DESeq2 output includes gene name, baseMean, log2 fold change, lfcSE, stat, p-value, adjusted p-value, raw counts, and normalized counts

source_name: Diaphragm

extract_protocol:
Total RNA was extracted from mouse tissues using TRI Reagent (ThermoFisher) according to the manufacturer’s protocol with the following modifications. Mouse tissues were rapidly dissected after CO2-based euthanasia and flash frozen in Eppendorf tubes in liquid N2. Tissue was transferred to a 15 mL conical tube, 1–2 mL of TRI Reagent was added, and the tissue was homogenized with a TissueRuptor (Qiagen) and disposable probes. Samples were transferred to Eppendorf tubes (1 mL per tube) and phase separated with 200 μL chloroform (J.T. Baker Analytical). After isopropanol precipitation and two 70% ethanol washes, total RNA was resuspended in water. Small-RNA sequencing libraries were prepared with 2 μg of total RNA from each diaphragm (n = 2–3 biological replicates per genotype). RNAs that co-migrated within the range of 17 and 32 nt radiolabeled internal standards run in adjacent lanes were isolated on a 15% polyacrylamide urea gel. Gel slices were macerated and RNA was eluted overnight at 4C in 400 μL of 0.3 M NaCl. After Spin-X column (Corning CLS8170) cleanup, RNA was precipitated for >2 hours at –20C with 3 μL of GlycoBlue (ThermoFisher AM9515) and 1 mL of 100% ethanol and then resuspended in 8 μL RNase-free H2O.
NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760) was used to generate stranded, poly(A)-selected RNA-seq libraries. Briefly, 1 μg of total RNA was poly(A) enriched and then reverse transcribed into double-strand cDNA. The cDNA samples were fragmented, end-repaired, and polyadenylated before ligation of TruSeq adapters containing an index sequence for multiplex sequencing. Multiplexing fragments containing TruSeq adapters on both ends were selectively enriched with 8–9 PCR cycles. All libraries were sequenced on the NovaseqX (Illumina) with 100 nt paired-end reads and ~20 million reads per sample.

value: Diaphragm

tag: Stage

tag: background


title: Spatial transcriptomics of mus musculus: old male liver mouse 6

description: Library name: AGE_6_112_Liver_GEX37_D1

source_name: Liver

value: Liver

tag: strain

tag: mouse id

tag: Sex

tag: age


title: KO5

city: Boston

first: Diana

middle: L

last: Carlone

state: MA

address: 300 Longwood Avenue

department: Endocrinology

institute: Boston Children's Hospital

description: Library name: PC18_KO

data_processing:
RNA-seq counts were generated by bcbio (bcbio-nextgen,0.9.1a-b73c090) and bcbioRNASeq v.0.0.26 using salmon v0.8.2. Counts were imported into R v.3.4.1 using tximport v.1.4.0 and differentially expressed genes identified using DESeq2 v1.16.1. Gene annotations were obtained from Ensembl.
Assembly: mm10 genome
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files includes FPKM values for each Sample.

source_name: E11.5-E12 forelimb bud

growth_protocol: Forelimbs from 5 control and cKOPrx1 E11.5-E12 embryos were collected. Embryos were obtained from four different breeding pairs.

extract_protocol:
RNA was extracted from E11.5 forelimb buds from control and KO mice using Direct-zol RNA kit per manufacturer's instructions.  RNA quality was assessed using a 2100 Agilent Bioanalyzer.
Libraries were prepared using a TrueSeq RNA Library Prep Kit per manufacturer's protocol.

value: E11.5-E12 forelimb bud

tag: somite stage

tag: litter #

value: D


title: T329, ChIP-seq, H3K27ac

description: Library name: T329-H3K27ac


title: E19Diaphragm_AGO2_PN3

description:
Library name: E19Diaphragm_AGO2_PN3
stranded
E19Diaphragm_CDNvPN_DESeq2.csv

value: C57BL/6J and C57BL/6N


title: Spatial transcriptomics of mus musculus: old male kidney mouse 6

description: Library name: AGE_6_112_Kidney_GEX40_D1

source_name: Kidney

value: Kidney

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: T123, ChIP-seq, Input

description: Library name: T123-Input

value: Human prostate cancer tissue


title: KO4

description: Library name: PC13_KO

value: C


title: E19Diaphragm_AGO2_CDN1

description:
Library name: E19Diaphragm_AGO2_CDN1
stranded
E19Diaphragm_CDNvPN_DESeq2.csv


title: Spatial transcriptomics of mus musculus: old male brain4 mouse 6

description: Library name: AGE_6_112_Brain4_GEX24_D1

source_name: Brain

value: Brain

tag: technology

tag: treatment

tag: disease

tag: disease stage


title: PC3, RNA-seq, TKT-siRNA2

description:
Library name: PC3-TKT-siRNA2
PC3-RNAseq.count.tsv
PC3-RNAseq.tpm.tsv

tag: cell line

tag: cell type

value: Prostate cancer cell line


title: KO3

description: Library name: PC7_KO

tag: tissue

tag: genotype

value: B


title: T123, ChIP-seq, H3K27ac

description: Library name: T123-H3K27ac


title: E19Diaphragm_AGO2_PP3

description:
Library name: E19Diaphragm_AGO2_PP3
stranded
E19Diaphragm_CDPvPP_DESeq2.csv

tag: Stage

tag: background


title: KO2

description: Library name: PC4_KO

tag: somite stage

tag: litter #

value: A


title: KO1

description: Library name: PC3_KO


title: E19Diaphragm_AGO2_PP2

description:
Library name: E19Diaphragm_AGO2_PP2
stranded
E19Diaphragm_CDPvPP_DESeq2.csv


title: E19Diaphragm_AGO2_PP1

description:
Library name: E19Diaphragm_AGO2_PP1
stranded
E19Diaphragm_CDPvPP_DESeq2.csv


title: N728, ChIP-seq, Input

description: Library name: N728-Input

source_name: Human adjacent normal prostate tissue

value: Human adjacent normal prostate tissue


title: N342, ChIP-seq, Input

description: Library name: N342-Input


title: Spatial transcriptomics of mus musculus: old male brain3 mouse 6

description: Library name: AGE_6_112_Brain3_GEX24_C1

tag: strain

tag: mouse id

tag: Sex

value: male

tag: age

value: 112 weeks

tag: slide

tag: area

value: Aging

value: 10x Visium


title: E19Diaphragm_AGO2_CDP1

description:
Library name: E19Diaphragm_AGO2_CDP1
stranded
E19Diaphragm_CDPvPP_DESeq2.csv

value: Diaphragm


title: Spatial transcriptomics of mus musculus: old male brain2 mouse 6

description: Library name: AGE_6_112_Brain2_GEX24_B1

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: technology

value: Wildtype

tag: treatment


title: Spatial transcriptomics of mus musculus: middle-aged male spleen mouse 5

description: Library name: AGE_5_73_Spleen_GEX34_B1

source_name: Spleen

tag: tissue

value: Spleen

value: 73 weeks

tag: genotype

tag: disease

tag: disease stage


title: N728, ChIP-seq, H3K27ac

description: Library name: N728-H3K27ac


title: Control5

description: Library name: PC19_control

value: E11.5-E12 forelimb bud

tag: somite stage

tag: litter #

value: D


title: Control3

description: Library name: PC8_control


title: N342, ChIP-seq, H3K27ac

description: Library name: N342-H3K27ac


title: N329, ChIP-seq, Input

description: Library name: N329-Input


title: Control4

description: Library name: PC12_control


title: E19Diaphragm_AGO2_CDN3

description:
Library name: E19Diaphragm_AGO2_CDN3
stranded
E19Diaphragm_CDNvPN_DESeq2.csv

tag: Stage

tag: background

value: C57BL/6J and C57BL/6N


title: Control1

description: Library name: PC1_control


title: Control2

description: Library name: PC2_control


title: Spatial transcriptomics of mus musculus: middle-aged male heart mouse 5

description: Library name: AGE_5_73_Heart_GEX41_D1

source_name: Heart

value: Heart

tag: strain

tag: mouse id

tag: Sex

tag: age


title: E15Placenta_AGO2_CDN2

description:
Library name: E15Placenta_AGO2_CDN2
stranded
E15Placenta_CDNvPN_DESeq2.csv

source_name: Placenta

value: Placenta


title: Spatial transcriptomics of mus musculus: middle-aged male brain5 mouse 5

description: Library name: AGE_5_73_Brain5_GEX26_B1

value: Brain

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)


title: N329, ChIP-seq, H3K27ac

description: Library name: N329-H3K27ac


title: E15Placenta_AGO2_CDN1

description:
Library name: E15Placenta_AGO2_CDN1
stranded
E15Placenta_CDNvPN_DESeq2.csv


title: Spatial transcriptomics of mus musculus: middle-aged male brain4 mouse 5

description: Library name: AGE_5_73_Brain4_GEX23_D1

tag: slice thickness_(um)

tag: cohort

tag: technology

tag: treatment


title: E15Placenta_AGO2_PN2

description:
Library name: E15Placenta_AGO2_PN2
stranded
E15Placenta_CDNvPN_DESeq2.csv

tag: tissue

tag: genotype


title: N123, ChIP-seq, H3K27ac

description: Library name: N123-H3K27ac


title: Spatial transcriptomics of mus musculus: middle-aged male brain3 mouse 5

description: Library name: AGE_5_73_Brain3_GEX23_C1

tag: disease

tag: disease stage


title: WT_aso_grp4_tfeb_rep4

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

description: RNA-seq

data_processing:
RNA-seq FASTQ files were mapped using STAR (v2.5.3a) using the mm10 genome and default parameters. For ASO RNA-seq experiments, FASTQ files were pseudomapped using Kallisto (v0.44.0) with --single -l 200 -s 30 --rf-stranded --single-overhang -b 50 parameters. After mapping, HOMER (v4.11) was used to convert reads aligning to a single genomic location into “tag directories” for subsequent analysis using the command makeTagDirectory. Raw gene expression counts from tag directories were quantified by HOMER’s analyzeRepeats command with parameters “-condenseGenes -count exons -noadj”, and TPM counts with parameters ‘‘-count exons -tpm’’. TPM counts were matched to raw counts using accession numbers. Small RNAs (<200 bp) and genes with TPM<4 in all conditions were removed from analysis. Differential gene expression was calculated with the HOMER command ‘getDiffExpression.pl’ utilizing DESeq2 (v1.36.0) and DEGs were accessed at FC>2 and p.adj<0.05 where indicated. For ASO RNA-seq experiments, abundance files from Kallisto pseudoalignment were imported with tximport (v1.24.0)116 and processed with DESeq2 (v1.36.0) controlling for batch (design = ~batch + treatment) and keeping genes where the sum of normalized counts in each treatment group was >50. Resulting filtered matrices were further analyzed in R v4.2.3.
Assembly: mm10
Supplementary files format and content: Tab-separated or comma-separated text files that contain raw counts, TPM counts, or normalized batched-corrected counts for RNA-seq samples.

extract_protocol:
Mouse forebrains were homogenized as previously described by gentle mechanical dissociation (Gosselin et al, 2014) and stained with anti-mouse anti-CD11b-APC (BioLegend 101212), anti-CD45-Alexa488 (BioLegend 103122), and anti-CX3CR1-PE (BioLegend 149006). Microglia were sorted as DAPI negative, singlets, and CD11b+/CD45low/CX3CR1+. RNA was isolated from sorted microglia using RNeasy Plus micro (Qiagen, 74034) or Direct-zol RNA MicroPrep (Zymo Research, R2052) kits.
RNA libraries were constructed as previously described in Heinz et al. 2010 and Gosselin et al. 2017. Briefly, polyA mRNA was enriched by two successive rounds of incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and then fragmented/eluted by incubation at 94°C for 9 min. cDNA was then synthesized with Superscript III (first-strand synthesis; Life Technologies kit 18080-044) and then DNA Polymerase I (second-strand synthesis; Enzymatics P7050L) with dUTP. Resulting cDNA libraries were prepared for sequencing by blunting/end repair, A-tailing, and barcoded adapter ligation (NEXTflex, Bioo Scientific/PerkinElmer). The resulting RNA-seq libraries were digested by incubation with Uracil DNA Glycosylase for 30 min at 37°C. Libraries were then PCR amplified for 11-14 cycles, size selected for 200-500 bp fragments by gel excision, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and single-end sequenced on a HiSeq 4000 or NextSeq 500 (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: For in vivo knockdown experiments using ASOs, ASOs were administered via single bolus intracerebroventricular (ICV) injections and microglia harvested 14 days later.

tag: cell type

value: Microglia (CD45+ CD11b+, CX3CR1+)

value: WT


title: E15Placenta_AGO2_PN1

description:
Library name: E15Placenta_AGO2_PN1
stranded
E15Placenta_CDNvPN_DESeq2.csv

tag: Stage

tag: background


title: WT_aso_grp4_mitf_rep4

description: RNA-seq

tag: strain


title: Spatial transcriptomics of mus musculus: middle-aged male brain2 mouse 5

description: Library name: AGE_5_73_Brain2_GEX23_B1

tag: mouse id

tag: Sex

tag: age


title: Figure 5b,Erythroid differentiation,SY7131-USR-14100-101,rep3

city: shanghai

first: xu

middle: sai

last: juan

address: DongchuanRoad

institute: East china normal university

description: Library name: SY7131-USR-14100-101

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

source_name: BM

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

value: BM

tag: cell line

value: Erythroid

tag: batch

value: Figure 5b,Erythroid differentiation


title: E15Placenta_AGO2_CDN4

description:
Library name: E15Placenta_AGO2_CDN4
stranded
E15Placenta_CDNvPN_DESeq2.csv


title: Spatial transcriptomics of mus musculus: middle-aged male brain1 mouse 5

description: Library name: AGE_5_73_Brain1_GEX23_A1

value: male

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

value: Aging


title: WT_aso_grp4_ntc_rep4

description: RNA-seq

tag: tissue

tag: genotype

tag: treatment


title: Figure 5b,Erythroid differentiation,SY7131-USR-14100-100,rep3

description: Library name: SY7131-USR-14100-100

tag: cell type


title: E15Placenta_AGO2_CDN3

description:
Library name: E15Placenta_AGO2_CDN3
stranded
E15Placenta_CDNvPN_DESeq2.csv

tag: Stage


title: WT_aso_grp4_pbs_rep4

description: RNA-seq


title: Spatial transcriptomics of mus musculus: young male spleen mouse 4

description: Library name: AGE_4_17_Spleen_GEX33_C1

value: 17 weeks

tag: cohort

tag: technology

value: 10x Visium

tag: disease

tag: disease stage


title: Figure 5b,BM cells,SY6155-USR-12152-012,rep3

description: Library name: SY6155-USR-12152-012

value: Figure 5b,BM cells


title: Spatial transcriptomics of mus musculus: old male brain1 mouse 6

description: Library name: AGE_6_112_Brain1_GEX24_A1

tag: strain

tag: mouse id

tag: Sex

tag: age

value: 112 weeks

value: Wildtype


title: E15Placenta_AGO2_PN4

description:
Library name: E15Placenta_AGO2_PN4
stranded
E15Placenta_CDNvPN_DESeq2.csv

tag: background


title: Spatial transcriptomics of mus musculus: young male liver mouse 4

description: Library name: AGE_4_17_Liver_GEX38_D1

value: Liver

tag: slide

tag: area

tag: sequencing primer


title: E19Diaphragm_AGO2_PN1

description:
Library name: E19Diaphragm_AGO2_PN1
stranded
E19Diaphragm_CDNvPN_DESeq2.csv

tag: tissue

value: Diaphragm

value: C57BL/6J and C57BL/6N


title: WT_aso_grp3_tfe3_rep3

description: RNA-seq

tag: genotype


title: Spatial transcriptomics of mus musculus: middle-aged male lung mouse 5

description: Library name: AGE_5_73_Lung_GEX4_C1

value: Lung

value: 73 weeks

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: treatment


title: Figure 5b,BM cells,SY6155-USR-12152-010,rep3

description: Library name: SY6155-USR-12152-010

tag: cell line

tag: batch


title: E15Placenta_AGO2_PN3

description:
Library name: E15Placenta_AGO2_PN3
stranded
E15Placenta_CDNvPN_DESeq2.csv

value: Placenta

tag: Stage


title: Spatial transcriptomics of mus musculus: young male heart mouse 4

description: Library name: AGE_4_17_Heart_GEX2_A1

value: Heart

tag: cohort

tag: technology

tag: disease

tag: disease stage


title: WT_aso_grp3_tfeb_rep3

description: RNA-seq

value: Brain

tag: strain

tag: cell type

value: Microglia (CD45+ CD11b+, CX3CR1+)

value: WT


title: Figure 5b,BM cells,SY5761-USR-11364-008,rep3

description: Library name: SY5761-USR-11364-008

value: BM


title: E15Liver_AGO2_CDP1

description:
Library name: E15Liver_AGO2_CDP1
stranded
E15Liver_CDPvPP_DESeq2.csv

tag: background


title: WT_aso_grp3_mitf_rep3

description: RNA-seq


title: Spatial transcriptomics of mus musculus: young male brain5 mouse 4

description: Library name: AGE_4_17_Brain5_GEX30_C1

tag: mouse id

tag: Sex

value: male

tag: age

tag: slide

tag: area

value: Aging


title: Figure 3l,second-dose,SY5920-USR-11709-033,rep3

description: Library name: SY5920-USR-11709-033

tag: tissue

value: Figure 3l,second-dose


title: E15Liver_AGO2_CDN2

description:
Library name: E15Liver_AGO2_CDN2
stranded
E15Liver_CDNvPN_DESeq2.csv

tag: genotype


title: N123, ChIP-seq, Input

description: Library name: N123-Input

value: Human adjacent normal prostate tissue


title: WT_aso_grp3_ntc_rep3

description: RNA-seq

tag: treatment


title: Spatial transcriptomics of mus musculus: young male brain4 mouse 4

description: Library name: AGE_4_17_Brain4_GEX22_D1

value: 17 weeks

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

value: 10x Visium


title: Figure 3l,second-dose,SY5920-USR-11709-023,rep3

description: Library name: SY5920-USR-11709-023

tag: cell line

tag: batch


title: E15Liver_AGO2_CDN1

description:
Library name: E15Liver_AGO2_CDN1
stranded
E15Liver_CDNvPN_DESeq2.csv

value: Liver

tag: Stage


title: Spatial transcriptomics of mus musculus: young male brain3 mouse 4

description: Library name: AGE_4_17_Brain3_GEX22_C1

tag: strain

tag: cohort

tag: technology

value: Wildtype

tag: disease

tag: disease stage


title: WT_aso_grp3_pbs_rep3

description: RNA-seq

tag: cell type


title: Figure 3l,second-dose,SY5920-USR-11709-022,rep3

description: Library name: SY5920-USR-11709-022


title: E15Liver_AGO2_PP2

description:
Library name: E15Liver_AGO2_PP2
stranded
E15Liver_CDPvPP_DESeq2.csv

tag: background

value: C57BL/6J and C57BL/6N


title: WT_aso_grp4_tfe3_rep4

description: RNA-seq


title: WT_aso_grp2_tfe3_rep2

description: RNA-seq


title: Spatial transcriptomics of mus musculus: young male brain2 mouse 4

description: Library name: AGE_4_17_Brain2_GEX22_B1

tag: mouse id

tag: Sex

tag: age

tag: slide

tag: area


title: Figure 3l,second-dose,SY5920-USR-11709-019,rep3

description: Library name: SY5920-USR-11709-019

tag: tissue


title: E15Liver_AGO2_PP1

description:
Library name: E15Liver_AGO2_PP1
stranded
E15Liver_CDPvPP_DESeq2.csv

tag: genotype


title: WT_aso_grp2_tfeb_rep2

description: RNA-seq

tag: treatment


title: Spatial transcriptomics of mus musculus: young male brain1 mouse 4

description: Library name: AGE_4_17_Brain1_GEX22_A1

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)


title: Figure 3l,fifth-dose,SY9031-USR-17565-062,rep3

description: Library name: SY9031-USR-17565-062

tag: cell line

tag: batch

value: Figure 3l,fifth-dose


title: Figure 5b,Erythroid differentiation,SY7131-USR-14100-102,rep3

description: Library name: SY7131-USR-14100-102

value: Erythroid

value: Figure 5b,Erythroid differentiation


title: E15Liver_AGO2_PN2

description:
Library name: E15Liver_AGO2_PN2
stranded
E15Liver_CDNvPN_DESeq2.csv

tag: Stage


title: Spatial transcriptomics of mus musculus: old male spleen mouse 3

description: Library name: AGE_3_112_Spleen_GEX44_D1

value: Spleen

tag: strain

value: 112 weeks

tag: cohort

tag: technology

tag: disease

tag: disease stage


title: Figure 3l,fifth-dose,SY9031-USR-17565-053,rep3

description: Library name: SY9031-USR-17565-053


title: WT_aso_grp2_mitf_rep2

description: RNA-seq

value: Brain

tag: cell type

value: Microglia (CD45+ CD11b+, CX3CR1+)


title: E15Liver_AGO2_PN1

description:
Library name: E15Liver_AGO2_PN1
stranded
E15Liver_CDNvPN_DESeq2.csv

tag: background


title: WT_aso_grp2_ntc_rep2

description: RNA-seq

value: WT


title: Spatial transcriptomics of mus musculus: old male liver mouse 3

description: Library name: AGE_3_112_Liver_GEX38_C1

tag: mouse id

tag: Sex

value: male

tag: age

tag: slide

tag: area


title: E15Liver_AGO2_CDP3

description:
Library name: E15Liver_AGO2_CDP3
stranded
E15Liver_CDPvPP_DESeq2.csv

tag: tissue

tag: genotype


title: Figure 3l,fifth-dose,SY9031-USR-17565-004,rep3

description: Library name: SY9031-USR-17565-004

value: BM

tag: cell line


title: WT_aso_grp2_pbs_rep2

description: RNA-seq

tag: treatment


title: Figure 3l,fifth-dose,SY9031-USR-17565-001,rep3

description: Library name: SY9031-USR-17565-001

tag: batch


title: Spatial transcriptomics of mus musculus: old male kidney mouse 3

description: Library name: AGE_3_112_Kidney_GEX40_A1

value: Kidney

tag: strain

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

value: Aging


title: E15Liver_AGO2_CDN4

description:
Library name: E15Liver_AGO2_CDN4
stranded
E15Liver_CDNvPN_DESeq2.csv

tag: Stage


title: WT_aso_grp1_tfe3_rep1

description: RNA-seq

tag: cell type


title: Spatial transcriptomics of mus musculus: old male heart mouse 3

description: Library name: AGE_3_112_Heart_GEX41_C1

value: Heart

tag: cohort

tag: technology

tag: disease

tag: disease stage


title: Figure 3k,second-dose,Myeloid cells,SY5920-USR-11709-039,rep3

description: Library name: SY5920-USR-11709-039

value: Myeloid cells

value: Figure 3k,second-dose,Myeloid cells


title: E15Liver_AGO2_CDN3

description:
Library name: E15Liver_AGO2_CDN3
stranded
E15Liver_CDNvPN_DESeq2.csv

value: Liver

tag: background


title: Spatial transcriptomics of mus musculus: old male brain5 mouse 3

description: Library name: AGE_3_112_Brain5_GEX21_B1

tag: mouse id

tag: Sex

tag: age

tag: slide

tag: area

value: 10x Visium

value: Wildtype


title: WT_aso_grp1_tfeb_rep1

description: RNA-seq

tag: tissue

tag: genotype

tag: treatment


title: Figure 3k,second-dose,Myeloid cells,SY5920-USR-11709-037,rep3

description: Library name: SY5920-USR-11709-037

tag: cell line

tag: batch


title: E15Liver_AGO2_PN4

description:
Library name: E15Liver_AGO2_PN4
stranded
E15Liver_CDNvPN_DESeq2.csv

tag: Stage

value: C57BL/6J and C57BL/6N


title: WT_aso_grp1_mitf_rep1

description: RNA-seq

tag: strain

tag: cell type


title: Figure 3k,second-dose,Erythroid,SY5920-USR-11709-036,rep3

description: Library name: SY5920-USR-11709-036

value: Erythroid

value: Figure 3k,second-dose,Erythroid


title: Spatial transcriptomics of mus musculus: middle-aged male spleen mouse 2

description: Library name: AGE_2_73_Spleen_GEX34_A1

value: Spleen

value: 73 weeks

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: technology


title: E15Liver_AGO2_PP4

description:
Library name: E15Liver_AGO2_PP4
stranded
E15Liver_CDPvPP_DESeq2.csv

tag: background


title: WT_aso_grp1_ntc_rep1

description: RNA-seq

value: Brain

value: Microglia (CD45+ CD11b+, CX3CR1+)


title: Spatial transcriptomics of mus musculus: middle-aged male lung mouse 2

description: Library name: AGE_2_73_Lung_GEX4_D1

value: Lung

tag: mouse id

tag: Sex

value: male

tag: age

tag: disease

tag: disease stage


title: Figure 3k,second-dose,Erythroid,SY5920-USR-11709-034,rep3

description: Library name: SY5920-USR-11709-034

tag: tissue

value: BM


title: E15Liver_AGO2_CDP4

description:
Library name: E15Liver_AGO2_CDP4
stranded
E15Liver_CDPvPP_DESeq2.csv

tag: genotype


title: Spatial transcriptomics of mus musculus: middle-aged male kidney mouse 2

description: Library name: AGE_2_73_Kidney_GEX40_C1

value: Kidney

tag: slide

tag: area

value: Aging

tag: treatment


title: WT_aso_grp1_pbs_rep1

description: RNA-seq

tag: strain

tag: cell type

value: WT


title: Figure 3k,second-dose,CD34,SY5920-USR-11709-029,rep3

description: Library name: SY5920-USR-11709-029

tag: cell line

tag: batch

value: Figure 3k,second-dose,CD34


title: Spatial transcriptomics of mus musculus: middle-aged male heart mouse 2

description: Library name: AGE_2_73_Heart_GEX41_B1

value: Heart

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: E15Liver_AGO2_CDP2

description:
Library name: E15Liver_AGO2_CDP2
stranded
E15Liver_CDPvPP_DESeq2.csv

value: Liver

tag: Stage

tag: background


title: E15Liver_AGO2_PP3

description:
Library name: E15Liver_AGO2_PP3
stranded
E15Liver_CDPvPP_DESeq2.csv


title: SgshKO_aso_grp2_combo_rep4

description: RNA-seq

value: SgshKO


title: Spatial transcriptomics of mus musculus: middle-aged male brain5 mouse 2

description: Library name: AGE_2_73_Brain5_GEX21_C1

tag: mouse id

tag: Sex

tag: age

tag: technology

value: 10x Visium

value: Wildtype

tag: disease


title: Figure 3k,second-dose,BM,SY5920-USR-11709-009,rep3

description: Library name: SY5920-USR-11709-009

tag: tissue

value: Figure 3k,second-dose,BM


title: Figure 3k,second-dose,CD34,SY5920-USR-11709-028,rep3

description: Library name: SY5920-USR-11709-028


title: E15Liver_AGO2_PN3

description:
Library name: E15Liver_AGO2_PN3
stranded
E15Liver_CDNvPN_DESeq2.csv

tag: genotype

value: C57BL/6J and C57BL/6N


title: SgshKO_aso_grp2_combo_rep3

description: RNA-seq

tag: strain

tag: treatment


title: Spatial transcriptomics of mus musculus: middle-aged male brain4 mouse 2

description: Library name: AGE_2_73_Brain4_GEX19_D1

value: 73 weeks

tag: slide

tag: area

tag: disease stage


title: SgshKO_aso_grp2_combo_rep2

description: RNA-seq

value: Brain

tag: cell type


title: Figure 3k,second-dose,BM,SY5920-USR-11709-007,rep3

description: Library name: SY5920-USR-11709-007

tag: cell line

tag: batch


title: snRNA_cortex_SgshKO_6mo_rep2

description: RNA-seq

data_processing:
Raw FASTQ files for each sample were processed through CellRanger v7.2.0 (10x Genomics) with standard parameters aligning to the mm10-2020-A reference transcriptome. For snRNA-seq, downstream analysis was performed with the single cell analysis suite scRNAsequest (Li et al, 2023). For scRNA-seq, downstream analysis was performed in R v4.2.3 using Seurat v4.4.0 (Butler et al, 2018).
Assembly: mm10-2020-A
Supplementary files format and content: Processed data files are raw and filtered gene count matrices in .h5 format as output by CellRanger.

molecule: nuclear RNA

extract_protocol:
For scRNA-seq, mouse forebrains were homogenized as previously described by gentle mechanical dissociation (Gosselin et al, 2014) and stained with anti-CD45-Alexa488 (BioLegend 103122) and DAPI (1:1,000; BioLegend 422801). Myeloids cells were sorted as DAPI negative, singlets, and CD45+. For snRNA-seq, forebrain was dissected and olfactory bulbs removed. Dissected tissue was homogenized in lysis buffer (10% Triton X-100, 0.1 M DTT, 40 U/μL RNasin (Promega, N2115), protease inhibitor cocktail (Sigma-Aldrich, P8340), and 2% bovine serum albumin (BSA) (Sigma Aldrich, B6917) in PBS) using a Dounce homogenizer for 10 strokes. Samples were incubated for 5 minutes on ice and then centrifuged at 500xg for 5 minutes at 4°C in a tabletop centrifuge. Pellets were resuspended in sorting buffer (0.5 M EDTA, 40 U/μL RNasin, 2% BSA in PBS), transferred to FACS tubes, filtered through a 70 μm mesh strainer, and centrifuged at 800xg for 5 minutes at 4°C in a swinging bucket centrifuge. DAPI (1:1,000; BioLegend 422801) was used to label nuclei. Samples were strained through a 70 μm mesh strainer, washed once more, resuspended in sorting buffer, and kept on ice until nuclei sorting. Nuclei were sorted for DAPI+ singlets on a Beckman Coulter MoFlo Astrios EQ.
For scRNA-seq, CD45+ sorted cells were spun down at 400xg for 5 minutes, supernatant carefully aspirated, and resuspended to 60 μL PBS supplemented with 400 μg/mL BSA. Appropriate volumes of each sample were loaded onto a Chromium Controller (10x Genomics) to target 10,000 cells per sample. Following capture, single cell sequencing libraries were generated using the Chromium Single Cell 3’ Library Reagent Kit (v3 Chemistry, 10X Genomics) following manufacturer’s instructions. For snRNA-seq, sorted purified nuclei were centrifuged at 800xg for 5 minutes at 4°C and then resuspended in PBS supplemented with 400 mg/mL BSA. Appropriate volumes of each sample were loaded onto a Chromium Controller (10x Genomics) to couple to beads targeting 20,000 cells per sample per the manufacturer’s Single Cell 3’ HT v3.1 (HT) protocol. Following capture, single nuclei sequencing libraries were prepared following the standard 10X Genomics HT protocol.

value: Nuclei (DAPI+)


title: SgshKO_aso_grp2_combo_rep1

description: RNA-seq

value: Microglia (CD45+ CD11b+, CX3CR1+)


title: Spatial transcriptomics of mus musculus: middle-aged male brain3 mouse 2

description: Library name: AGE_2_73_Brain3_GEX19_C1

value: male

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: Figure 3k,second-dose,B cells,SY5920-USR-11709-032,rep3

description: Library name: SY5920-USR-11709-032

value: BM

value: B cells

value: Figure 3k,second-dose,B cells


title: snRNA_cortex_SgshKO_6mo_rep1

description: RNA-seq


title: SgshKO_aso_grp2_ntc_rep4

description: RNA-seq


title: Figure 3k,second-dose,B cells,SY5920-USR-11709-031,rep3

description: Library name: SY5920-USR-11709-031


title: Spatial transcriptomics of mus musculus: middle-aged male brain2 mouse 2

description: Library name: AGE_2_73_Brain2_GEX19_B1

tag: mouse id

tag: Sex

tag: age

value: Aging


title: snRNA_cortex_Het_6mo_rep2

description: RNA-seq

tag: tissue

value: Het


title: SgshKO_aso_grp2_ntc_rep3

description: RNA-seq

tag: genotype


title: Spatial transcriptomics of mus musculus: middle-aged male brain1 mouse 2

description: Library name: AGE_2_73_Brain1_GEX19_A1

tag: strain

tag: technology

tag: disease


title: Figure 3k,fifth-dose,Myeloid cell,SY5761-USR-11364-021,rep3

description: Library name: SY5761-USR-11364-021

value: Figure 3k,fifth-dose,Myeloid cell


title: snRNA_cortex_Het_6mo_rep1

description: RNA-seq


title: SgshKO_aso_grp2_ntc_rep2

description: RNA-seq

tag: treatment


title: SgshKO_aso_grp2_ntc_rep1

description: RNA-seq


title: Spatial transcriptomics of mus musculus: young male spleen mouse 1

description: Library name: AGE_1_17_Spleen_GEX33_B1

value: Spleen

value: 17 weeks

tag: slide

tag: area

tag: disease stage


title: Figure 3k,fifth-dose,Myeloid cell,SY5761-USR-11364-019,rep3

description: Library name: SY5761-USR-11364-019

tag: cell line

tag: batch


title: snRNA_cortex_WT_6mo_rep2

description: RNA-seq

tag: cell type

value: WT


title: Spatial transcriptomics of mus musculus: young male lung mouse 1

description: Library name: AGE_1_17_Lung_GEX2_C1

value: Lung

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

value: 10x Visium

value: Wildtype


title: Figure 3k,fifth-dose,Myeloid cell,SY5761-USR-11364-006,rep3

description: Library name: SY5761-USR-11364-006


title: snRNA_cortex_WT_6mo_rep1

description: RNA-seq


title: SgshKO_aso_grp1_combo_rep4

description: RNA-seq

value: SgshKO


title: Spatial transcriptomics of mus musculus: young male kidney mouse 1

description: Library name: AGE_1_17_Kidney_GEX40_B1

value: Kidney

tag: mouse id

tag: Sex

tag: cohort


title: Figure 3k,fifth-dose,Erythroid,SY5761-USR-11364-015,rep3

description: Library name: SY5761-USR-11364-015

tag: tissue

value: Erythroid

value: Figure 3k,fifth-dose,Erythroid


title: scRNA_CD45+_SgshKO_4mo_rep2

description: RNA-seq

value: Brain

tag: strain

value: Myeloid cells (CD45+)

tag: genotype


title: SgshKO_aso_grp1_combo_rep3

description: RNA-seq

value: Microglia (CD45+ CD11b+, CX3CR1+)


title: Figure 3k,fifth-dose,Erythroid,SY5761-USR-11364-013,rep3

description: Library name: SY5761-USR-11364-013

value: BM


title: SgshKO_aso_grp1_combo_rep2

description: RNA-seq


title: scRNA_CD45+_WT_4mo_rep2

description: RNA-seq


title: Spatial transcriptomics of mus musculus: young male brain2 mouse 1

description: Library name: AGE_1_17_Brain2_GEX18_B1

value: male

tag: age

value: Aging

tag: technology

tag: disease


title: SgshKO_aso_grp1_combo_rep1

description: RNA-seq

tag: treatment


title: Spatial transcriptomics of mus musculus: young male brain5 mouse 1

description: Library name: AGE_1_17_Brain5_GEX21_D1

tag: slide

tag: area

tag: disease stage


title: Spatial transcriptomics of mus musculus: young male brain4 mouse 1

description: Library name: AGE_1_17_Brain4_GEX18_D1


title: Figure 3k,fifth-dose,Erythroid,SY5761-USR-11364-002,rep3

description: Library name: SY5761-USR-11364-002

tag: cell line

tag: cell type

tag: batch


title: Spatial transcriptomics of mus musculus: young male brain3 mouse 1

description: Library name: AGE_1_17_Brain3_GEX18_C1

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)


title: scRNA_CD45+_SgshKO_4mo_rep1

description: RNA-seq


title: SgshKO_aso_grp1_ntc_rep4

description: RNA-seq


title: Figure 3k,fifth-dose,CD34 cell,SY9031-USR-17565-002,rep3

description: Library name: SY9031-USR-17565-002

value: Figure 3k,fifth-dose,CD34 cell


title: SgshKO_8mo_rep7

description: RNA-seq


title: Spatial transcriptomics of mus musculus: young male brain1 mouse 1

description: Library name: AGE_1_17_Brain1_GEX18_A1

tag: mouse id

tag: Sex

tag: cohort


title: scRNA_CD45+_WT_4mo_rep1

description: RNA-seq

tag: tissue

tag: strain

tag: genotype


title: Figure 3k,fifth-dose,CD34 cell,SY9031-USR-17565-003,rep3

description: Library name: SY9031-USR-17565-003


title: SgshKO_aso_grp1_ntc_rep3

description: RNA-seq


title: Figure 3k,fifth-dose,BM,SY6155-USR-12152-011,rep3

description: Library name: SY6155-USR-12152-011

value: Figure 3k,fifth-dose,BM


title: SgshKO_8mo_rep6

description: RNA-seq


title: SgshKO_aso_grp1_ntc_rep2

description: RNA-seq


title: SgshKO_8mo_rep5

description: RNA-seq


title: Figure 3k,fifth-dose,BM,SY5761-USR-11364-007,rep3

description: Library name: SY5761-USR-11364-007


title: SgshKO_8mo_rep4

description: RNA-seq


title: ChIP_olig2_SgshKO_input2

description: ChIP-seq

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

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

value: Olig2+ nuclei


title: SgshKO_8mo_rep3

description: RNA-seq


title: SgshKO_aso_grp1_ntc_rep1

description: RNA-seq


title: Figure 3k,fifth-dose,BM,SY5761-USR-11364-005,rep3

description: Library name: SY5761-USR-11364-005


title: ChIP_olig2_SgshKO_tfe3_rep2

description: ChIP-seq

tag: chip antibody


title: ChIP_olig2_SgshKO_input1

description: ChIP-seq


title: TC28a2, RNA, rep 2

city: Gainesville

first: Darius

last: Ramkhalawan

address: 1200 Newell Drive

institute: University of Florida

description: Library name: TC_RNA_rep2

library_source: other

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

molecule: other

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

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

value: chondrocyte

tag: treatment

value: AIS lentiMPRA library


title: Figure 3k,fifth-dose,B cell,SY6155-USR-12152-009,rep3

description: Library name: SY6155-USR-12152-009

value: Figure 3k,fifth-dose,B cell


title: ChIP_olig2_SgshKO_tfe3_rep1

description: ChIP-seq


title: TC28a2, DNA, rep 2

description: Library name: TC_DNA_rep2


title: Figure 3k,fifth-dose,B cell,SY5761-USR-11364-016,rep3

description: Library name: SY5761-USR-11364-016


title: SgshKO_8mo_rep2

description: RNA-seq


title: TC28a2, RNA, rep 1

description: Library name: TC_RNA_rep1


title: Figure 3k,fifth-dose,B cell,SY5761-USR-11364-014,rep3

description: Library name: SY5761-USR-11364-014


title: SgshKO_8mo_rep1

description: RNA-seq


title: ChIP_olig2_SgshKO_tfeb_rep2

description: ChIP-seq


title: ChIP_olig2_SgshKO_tfeb_rep1

description: ChIP-seq


title: WT_8mo_rep4

description: RNA-seq

value: WT


title: Figure 3i,second-dose,SY5920-USR-11709-027,rep3

description: Library name: SY5920-USR-11709-027

value: Figure 3i,second-dose


title: TC28a2, DNA, rep 1

description: Library name: TC_DNA_rep1


title: ChIP_olig2_SgshKO_mitf_rep2

description: ChIP-seq

value: SgshKO

value: ActiveMotif #91201


title: 3D_OVSAHO_7day

city: Ljubljana

first: Vesna

last: Kokondoska Grgič

address: Brnčičeva ulica 31, Kemomed

department: R&D Kemomed

country: Slovenia

institute: kemomed d.o.o

description:
Library name: 3D_OVSAHO_7day
ULA spheroids

data_processing:
Raw sequencing reads were demultiplexed using DRAGEN BCL Convert v4.2.7.
Read quality was assessed using FastQC. Reads were aligned to the human reference genome.
Gene-level read counts were quantified using a standard RNA-seq quantification pipeline.
Raw counts were used as input for differential gene expression analysis using the limma R package (v3.66). Linear models were fitted per gene with empirical Bayes moderation; p-values were corrected using Benjamini-Hochberg FDR. Genes with adjusted p < 0.05 and |log2FC| > 1 were considered significant.
Raw counts were normalized to log2-transformed counts [log2(norm_count + 1)] and mean centered.
GRCh38 / hg38 (Homo sapiens)
Assembly: Tab-delimited files including raw counts for reach sample
Supplementary files format and content: Csv file containing TPM (Transcripts Per Million) values for each sample

source_name: Ovarian epithelial tissue

growth_protocol: Cell lines OVCAR-4, OVSAHO, COV362, and Kuramochi were maintained in a humidified incubator at 37°C and 5% CO2. Media were changed every 2–3 days and cells were cultured for a maximum of 15 passages. 2D adherent cultures were grown on 12-well and 96-well flat-bottomed plates (TPP, Switzerland) at 40,000 cells/well and 10,000 cells/100 µL/well, respectively. 3D spheroid models were prepared in ultra-low attachment (ULA) plates (Prime Surface, PHCBI, The Netherlands) by seeding 10,000 cells/100 µL/well. Growth media: Kuramochi and OVSAHO – RPMI-1640 (R5886) supplemented with 2 mM L-glutamine (G7153) and 10% FBS (F9665); COV362 – DMEM (D5546) with 10% FBS (F9665) and 2 mM L-glutamine (G7153); OVCAR-4 – RPMI-1640 (R5886) with 10% FBS (F9665), 0.25 U/mL insulin (I9278), and 2 mM L-glutamine (G7153). Cells were regularly tested for mycoplasma contamination using the MycoAlert Mycoplasma Detection Kit (Lonza).

extract_protocol:
Total RNA was isolated from 2D monolayer and 3D spheroid cultures. Spheroids were first dissociated using a 1:1 enzyme mixture of collagenase I (1 mg/mL; StemCell Technologies) and TryPLE (Gibco TrypLE Express Enzyme (1X)) for 15–25 min at 37°C with continuous shaking at 30 ×g, depending on cell line stiffness. RNA was extracted using the NucleoSpin RNA Isolation Kit (Macherey-Nagel). RNA quantity was assessed by NanoDrop (Thermo Fisher Scientific) and RNA integrity by Agilent 2100 Bioanalyzer. Samples with sufficient quantity and integrity were used for library preparation. Input RNA: 250–800 ng per sample (adjusted based on available concentration).
RNA sequencing libraries were prepared using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (96 samples), following the manufacturer's protocol (Illumina, document no. 1000000124514 v04). Ribosomal RNA depletion was performed with the Illumina Ribo-Zero Plus rRNA Depletion Kit. cDNA synthesis and library ligation were performed using Illumina cDNA Synthesis and RNA Prep Ligation kits, respectively. Libraries were indexed with IDT for Illumina RNA UD Indexes Set A (Ligation, 96 samples). Library quality and fragment size distribution were assessed using the Agilent DNA 1000 Kit on the Agilent 2100 Bioanalyzer (average fragment size ~330–420 bp). Library quantity was measured using the Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific). Libraries were diluted to 2 nM and pooled at equimolar ratios. The pooled library was sequenced on the Illumina NextSeq 2000 using a P3 Reagent Cartridge (300 Cycles) with paired-end sequencing. Demultiplexing was performed using DRAGEN BCL Convert v4.2.7 via the Illumina Base Space Sequencing Hub. Sequencing was performed at ELIXIR-SI Centre (Maribor, Slovenia). A minimum of 20 million reads per sample was targeted.

value: Ovarian epithelial tissue

value: OVSAHO

value: High-grade serous ovarian cancer


title: WT_8mo_rep3

description: RNA-seq

value: Brain

value: Microglia (CD45+ CD11b+, CX3CR1+)


title: Figure 3i,second-dose,SY5345-USR-10689-034,rep3

description: Library name: SY5345-USR-10689-034

value: BM


title: ChIP_olig2_SgshKO_mitf_rep1

description: ChIP-seq


title: 3D_OVSAHO_4_7days

description:
Library name: 3D_OVSAHO_4_7days
ULA spheroids


title: Figure 3i,second-dose,SY5345-USR-10689-032,rep3

description: Library name: SY5345-USR-10689-032


title: WT_8mo_rep2

description: RNA-seq


title: ChIP_olig2_WT_input2

description: ChIP-seq


title: 3D_OVSAHO_3day

description:
Library name: 3D_OVSAHO_3day
ULA spheroids


title: Figure 3i,fifth-dose,SY5761-USR-11364-004,rep3

description: Library name: SY5761-USR-11364-004

value: Figure 3i,fifth-dose


title: WT_8mo_rep1

description: RNA-seq


title: ChIP_olig2_WT_input1

description: ChIP-seq


title: 3D_OVSAHO_3_7days

description:
Library name: 3D_OVSAHO_3_7days
ULA spheroids


title: Figure 3i,fifth-dose,SY5761-USR-11364-003,rep3

description: Library name: SY5761-USR-11364-003


title: SgshKO_4mo_rep2

description: RNA-seq


title: ChIP_olig2_WT_tfe3_rep2

description: ChIP-seq


title: SgshKO_4mo_rep1

description: RNA-seq


title: Figure 3i,fifth-dose,SY5761-USR-11364-001,rep3

description: Library name: SY5761-USR-11364-001


title: 3D_OVSAHO_2_7days

description:
Library name: 3D_OVSAHO_2_7days
ULA spheroids


title: ChIP_olig2_WT_tfe3_rep1

description: ChIP-seq


title: 3D_OVSAHO_10day

description:
Library name: 3D_OVSAHO_10day
ULA spheroids


title: 3D_OVCAR4_7day

description:
Library name: 3D_OVCAR4_7day
ULA spheroids


title: Figure 2h,Myeloid cells,SY1870-USR-3757-003,rep3

description: Library name: SY1870-USR-3757-003

value: Myeloid cells

value: Figure 2h,Myeloid cells


title: Figure 2h,Myeloid cells,SY1870-USR-3757-021,rep3

description: Library name: SY1870-USR-3757-021


title: WT_4mo_rep2

description: RNA-seq


title: ChIP_olig2_WT_tfeb_rep2

description: ChIP-seq

value: Olig2+ nuclei


title: E19Heart_AGO2_PN2

description:
Library name: E19Heart_AGO2_PN2
stranded
E19Heart_CDNvPN_DESeq2.csv

value: Heart

tag: Stage

tag: background

value: C57BL/6J and C57BL/6N


title: 3D_OVCAR4_6

description:
Library name: 3D_OVCAR4_5
ULA spheroids


title: WT_4mo_rep1

description: RNA-seq


title: ChIP_olig2_WT_tfeb_rep1

description: ChIP-seq


title: ChIP_olig2_WT_mitf_rep2

description: ChIP-seq


title: Figure 2h,Myeloid cells,SY12253-USR-23993-004,rep3

description: Library name: SY12253-USR-23993-004


title: 3D_OVCAR4_3_7days

description:
Library name: 3D_OVCAR4_3_7days
ULA spheroids


title: SgshKO_3wks_rep3

description: RNA-seq


title: Figure 2h,Input HSPCs,SY1870-USR-3757-015,rep3

description: Library name: SY1870-USR-3757-015

value: Figure 2h,Input HSPCs


title: SgshKO_3wks_rep4

description: RNA-seq


title: Figure 2h,Input HSPCs,SY1707-USR-3383-002,rep3

description: Library name: SY1707-USR-3383-002


title: SgshKO_3wks_rep2

description: RNA-seq


title: 3D_OVCAR4_2_7days

description:
Library name: 3D_OVCAR4_2_7days
ULA spheroids

value: WT


title: ChIP_mg_SgshKO_input2

description: ChIP-seq

value: PU.1+ nuclei


title: ChIP_olig2_WT_mitf_rep1

description: ChIP-seq


title: Figure 2h,Input HSPCs,SY12253-USR-23993-043,rep3

description: Library name: SY12253-USR-23993-043


title: 3D_OVCAR4_10day

description:
Library name: 3D_OVCAR4_10day
ULA spheroids


title: SgshKO_3wks_rep1

description: RNA-seq

value: SgshKO


title: ChIP_mg_SgshKO_input1

description: ChIP-seq


title: 3D_Kuramochi_7_7days

description:
Library name: 3D_Kuramochi_7_7days
ULA spheroids


title: Figure 2h,Erythroid,SY1870-USR-3757-007,rep3

description: Library name: SY1870-USR-3757-007

value: Erythroid

value: Figure 2h,Erythroid


title: WT_3wks_rep3

description: RNA-seq


title: Figure 2h,Erythroid,SY1707-USR-3383-004,rep3

description: Library name: SY1707-USR-3383-004


title: ChIP_mg_SgshsKO_tfe3_rep2

description: ChIP-seq


title: 3D_Kuramochi_6_7days

description:
Library name: 3D_Kuramochi_6_7days
ULA spheroids

value: Ovarian epithelial tissue


title: WT_3wks_rep2

description: RNA-seq


title: 3D_Kuramochi_5_7days

description:
Library name: 3D_Kuramochi_5_7days
ULA spheroids

value: High-grade serous ovarian cancer


title: ChIP_mg_SgshsKO_tfe3_rep1

description: ChIP-seq

value: Brain


title: Figure 2h,Erythroid,SY12253-USR-23993-044,rep3

description: Library name: SY12253-USR-23993-044


title: ChIP_mg_SgshKO_tfeb_rep2

description: ChIP-seq


title: WT_3wks_rep1

description: RNA-seq

value: Microglia (CD45+ CD11b+, CX3CR1+)


title: 3D_Kuramochi_4_7days

description:
Library name: 3D_Kuramochi_4_7days
ULA spheroids

value: Kuramochi


title: Figure 2h,BM,SY1870-USR-3757-017,rep3

description: Library name: SY1870-USR-3757-017

value: BM

value: Figure 2h,BM


title: ATAC_mg_SgshKO_4mo_rep2

description: ATAC-seq

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

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


title: ChIP_mg_SgshKO_tfeb_rep1

description: ChIP-seq


title: 3D_Kuramochi_3day

description:
Library name: 3D_Kuramochi_3day
ULA spheroids


title: ChIP_mg_SgshKO_mitf_rep2

description: ChIP-seq

value: ActiveMotif #91201


title: Figure 2h,BM,SY1707-USR-3383-003,rep3

description: Library name: SY1707-USR-3383-003


title: ATAC_mg_SgshKO_4mo_rep1

description: ATAC-seq


title: 3D_Kuramochi_3_7days

description:
Library name: 3D_Kuramochi_3_7days
ULA spheroids


title: Figure 2h,BM,SY12253-USR-23993-023,rep3

description: Library name: SY12253-USR-23993-023


title: ChIP_mg_SgshKO_mitf_rep1

description: ChIP-seq


title: ATAC_mg_WT_4mo_rep2

description: ATAC-seq


title: Figure 2h,B cells,SY1870-USR-3757-009,rep3

description: Library name: SY1870-USR-3757-009

value: B cells

value: Figure 2h,B cells


title: 3D_Kuramochi_2_7days

description:
Library name: 3D_Kuramochi_2_7days
ULA spheroids


title: ATAC_mg_WT_4mo_rep1

description: ATAC-seq


title: ChIP_mg_WT_input3

description: ChIP-seq


title: 3D_Kuramochi_10days

description:
Library name: 3D_Kuramochi_10days
ULA spheroids


title: Figure 2h,B cells,SY1707-USR-3383-001,rep3

description: Library name: SY1707-USR-3383-001


title: 3D_Kuramochi_1_7day

description:
Library name: 3D_Kuramochi_1_7day
ULA spheroids


title: Figure 2h,B cells,SY12253-USR-23993-003,rep3

description: Library name: SY12253-USR-23993-003


title: ChIP_mg_WT_input2

description: ChIP-seq


title: KPB25Luv_CD40ag_7Day_Mouse_Tumor_scRNAseq

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files were processed through 10x Genomics Cell Ranger pipeline version 6.1.1
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Tumor

extract_protocol:
Whole mammary tumors were extracted from the mouse and placed into ice cold PBS. The tumors were then cut into 2mm pieces and then placed into digestion buffer provided by Miltenyi's mouse tumor dissasociating kit. The tumor tissue was then incubated on a Miltenyi's octo dissascoiater to obtain a single cell suspension of the tumor tissue. The resulting suspension is then centrifuged at 300xG for 5 minutes. Supernatent was then removed and cells were resuspended in RPMI. Cells were then strained through a 70um cell strainer. Cells were then centrifuged at 300xG for 5 minutes. Supernatant were then removed and cells resupended in suspension buffer (PBS, 2% FBS).
Library was constructed according to 10x Genomics protocol from their single cell 5' v2 kit.

value: Tumor

value: Cancer Cell Line

value: Brca 1 Null/ P53 Null


title: ChIP_mg_WT_input1

description: ChIP-seq

value: PU.1+ nuclei

value: WT


title: WSUDLCL2 - BMS-986158 2.5 nM + CC-99282 50nM

city: Summit

first: Junfei

last: Zhao

state: NJ

address: 556 Morris Ave

institute: Bristol Myers Squibb

description: Library name: ATAC_1937

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

source_name: cell line

extract_protocol:
Cells for ATACseq were prepared according to instructions from Novogene.
Five million cells were collected and cryopreserved prior to shipping to Novogene.

value: cell line


title: Figure 2g,Myeloid cells,SY3893-USR-7940-061,rep3

description: Library name: SY3893-USR-7940-061

value: Myeloid cells

value: Figure 2g,Myeloid cells


title: WSUDLCL2 - BMS-986158 2.5 nM

description: Library name: ATAC_1936


title: ChIP_mg_WT_tfe3_rep3

description: ChIP-seq


title: 3D_COV362_7day

description:
Library name: 3D_COV362_7day
ULA spheroids

value: Ovarian epithelial tissue

value: High-grade serous ovarian cancer


title: 3D_COV362_5_7days

description:
Library name: 3D_COV362_5_7days
ULA spheroids


title: Figure 2g,Myeloid cells,SY1707-USR-3383-020,rep3

description: Library name: SY1707-USR-3383-020


title: WSUDLCL2 - BMS-986158 1.25 nM + CC-99282 50nM

description: Library name: ATAC_1935


title: ChIP_mg_WT_tfe3_rep2

description: ChIP-seq

value: Brain


title: 3D_COV362_4_7days

description:
Library name: 3D_COV362_4_7days
ULA spheroids


title: WSUDLCL2 - CC-99282 50nM

description: Library name: ATAC_1934


title: ChIP_mg_WT_tfe3_rep1

description: ChIP-seq


title: Figure 2g,Myeloid cells,SY1707-USR-3383-009,rep3

description: Library name: SY1707-USR-3383-009


title: Figure 2g,Input HSPCs,SY3893-USR-7940-050,rep3

description: Library name: SY3893-USR-7940-050

value: Figure 2g,Input HSPCs


title: WSUDLCL2 - BMS-986158 1.25 nM

description: Library name: ATAC_1933


title: 3D_COV362_3day

description:
Library name: 3D_COV362_3day
ULA spheroids


title: 3D_COV362_3_7days

description:
Library name: 3D_COV362_3_7days
ULA spheroids


title: WSUDLCL2 - DMSO

description: Library name: ATAC_1932

value: DMSO


title: ChIP_mg_WT_tfeb_rep3

description: ChIP-seq


title: Figure 2g,Input HSPCs,SY3893-USR-7940-049,rep3

description: Library name: SY3893-USR-7940-049

value: BM


title: Figure 2g,Input HSPCs,SY1870-USR-3757-001,rep3

description: Library name: SY1870-USR-3757-001


title: SUDHL4 - BMS-986158 2.5 nM + CC-99282 50nM

description: Library name: ATAC_2094


title: ChIP_mg_WT_tfeb_rep1

description: ChIP-seq


title: ChIP_mg_WT_tfeb_rep2

description: ChIP-seq


title: ChIP_mg_WT_mitf_rep3

description: ChIP-seq

value: ActiveMotif #91201


title: 3D_COV362_2_7days

description:
Library name: 3D_COV362_2_7days
ULA spheroids


title: Figure 2g,Erythroid,SY3893-USR-7940-062,rep3

description: Library name: SY3893-USR-7940-062

value: Erythroid

value: Figure 2g,Erythroid


title: Figure 2g,Erythroid,SY1707-USR-3383-019,rep3

description: Library name: SY1707-USR-3383-019


title: 2D_OVSAHO_2

description:
Library name: 2D_OVSAHO_2
ULA spheroids

value: OVSAHO


title: SUDHL4 - BMS-986158 2.5 nM

description: Library name: ATAC_2093


title: SUDHL4 - BMS-986158 1.25 nM + CC-99282 50nM

description: Library name: ATAC_2092


title: 2D_OVSAHO_3

description:
Library name: 2D_OVSAHO_3
ULA spheroids


title: 2D_OVSAHO_4

description:
Library name: 2D_OVSAHO_4
ULA spheroids


title: Figure 2g,Erythroid,SY1707-USR-3383-008,rep3

description: Library name: SY1707-USR-3383-008


title: ChIP_mg_WT_mitf_rep2

description: ChIP-seq


title: ChIP_mg_WT_mitf_rep1

description: ChIP-seq


title: 2D_OVSAHO_1

description:
Library name: 2D_OVSAHO_1
ULA spheroids


title: SUDHL4 - CC-99282 50nM

description: Library name: ATAC_2091


title: Figure 2g,BM,SY3894-USR-7940-123,rep3

description: Library name: SY3894-USR-7940-123

value: Figure 2g,BM


title: SUDHL4 - BMS-986158 1.25 nM

description: Library name: ATAC_2090


title: 2D_OVCAR4_2

description:
Library name: 2D_OVCAR4_2
ULA spheroids


title: SUDHL4 - DMSO

description: Library name: ATAC_2089


title: H3K27ac_olig2_WTSgshKO_4mo_input

description: ChIP-seq

value: Olig2+ nuclei


title: Figure 2g,BM,SY1707-USR-3383-017,rep3

description: Library name: SY1707-USR-3383-017


title: 2D_OVCAR4_1

description:
Library name: 2D_OVCAR4_1
ULA spheroids


title: H3K27ac_olig2_SgshKO_4mo_rep2

description: ChIP-seq

value: SgshKO

value: ActiveMotif #39685


title: 1742W2 - Ikaros - Combo

description: Library name: 1742W2-Combo_Ikaros

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

value: cell line

value: Combo


title: Figure 2g,BM,SY1707-USR-3383-006,rep3

description: Library name: SY1707-USR-3383-006


title: H3K27ac_olig2_SgshKO_4mo_rep1

description: ChIP-seq


title: 2D_Kuramochi_4

description:
Library name: 2D_Kuramochi_4
ULA spheroids

value: Kuramochi

value: WT


title: Figure 2g,B cells,SY3893-USR-7940-063,rep3

description: Library name: SY3893-USR-7940-063

value: B cells

value: Figure 2g,B cells


title: 1741W2 - Ikaros - CC282

description: Library name: 1741W2-CC282_Ikaros


title: 2D_Kuramochi_3

description:
Library name: 2D_Kuramochi_3
ULA spheroids

value: Ovarian epithelial tissue

value: High-grade serous ovarian cancer


title: H3K27ac_olig2_WT_4mo_rep2

description: ChIP-seq

value: Brain


title: 1740W2 - Ikaros - BMS158

description: Library name: 1740W2-BMS158_Ikaros


title: H3K27ac_olig2_WT_4mo_rep1

description: ChIP-seq


title: Figure 2g,B cells,SY1707-USR-3383-018,rep3

description: Library name: SY1707-USR-3383-018

value: BM


title: 2D_Kuramochi_2

description:
Library name: 2D_Kuramochi_2
ULA spheroids


title: Figure 2g,B cells,SY1707-USR-3383-007,rep3

description: Library name: SY1707-USR-3383-007


title: 1739W2 - Ikaros - DMSO

description: Library name: 1739W2-DMSO_Ikaros

value: DMSO


title: 2D_Kuramochi_1

description:
Library name: 2D_Kuramochi_1
ULA spheroids


title: 1738S4 - Ikaros - Combo

description: Library name: 1738S4-Combo_Ikaros


title: Extended Data Fig. 6I,second-dose,Myeloid cells,SY9031-USR-17565-075,rep3

description: Library name: SY9031-USR-17565-075


title: H3K27ac_neun_WTSgshKO_4mo_input

description: ChIP-seq

value: NeuN+ nuclei


title: 2D_COV362_4

description:
Library name: 2D_COV362_4
ULA spheroids


title: H3K27ac_neun_SgshKO_4mo_rep2

description: ChIP-seq


title: Extended Data Fig. 6I,second-dose,Myeloid cells,SY9031-USR-17565-068,rep3

description: Library name: SY9031-USR-17565-068


title: 1737S4 - Ikaros - CC282

description: Library name: 1737S4-CC282_Ikaros


title: H3K27ac_neun_SgshKO_4mo_rep1

description: ChIP-seq


title: 2D_COV362_3

description:
Library name: 2D_COV362_3
ULA spheroids


title: 1736S4 - Ikaros - BMS158

description: Library name: 1736S4-BMS158_Ikaros


title: Extended Data Fig. 6I,second-dose,Myeloid cells,SY9031-USR-17565-026,rep3

description: Library name: SY9031-USR-17565-026


title: H3K27ac_neun_WT_4mo_rep2

description: ChIP-seq


title: 2D_COV362_2

description:
Library name: 2D_COV362_2
ULA spheroids


title: Extended Data Fig. 6I,second-dose,Erythroid cells,SY9031-USR-17565-066,rep3

description: Library name: SY9031-USR-17565-066


title: 1735S4 - Ikaros - DMSO

description: Library name: 1735S4-DMSO_Ikaros


title: H3K27ac_neun_WT_4mo_rep1

description: ChIP-seq


title: 2D_COV362_1

description:
Library name: 2D_COV362_1
ULA spheroids


title: 1742W2 - H3K4me3 - Combo

description: Library name: 1742W2-Combo_H3K4me3


title: H3K27ac_mg_SgshKO_8mo_rep2_input

description: ChIP-seq

value: PU.1+ nuclei


title: Extended Data Fig. 6I,second-dose,Erythroid cells,SY9031-USR-17565-065,rep3

description: Library name: SY9031-USR-17565-065


title: Mock, Experimental, IFNB, 72hpi, TIME

city: Pittsburgh

first: Jim

last: Pipas

state: PA

address: 5th and Tennyson

institute: University of Pittsburgh

description: Library name: MposIFN_72HPI

data_processing:
RNAseq: Reads were processed with the nfcore/rnaseq pipeline (version 3.3; https://nf-co.re/rnaseq/3.3). Reads were aligned to a hybrid reference of the human genome (Gencode GRCh38.primary_assembly.genome.fa) and the BKV genome (NC_001538.1) with gene anotations from Gencode V38 GTF.
Assembly: RNAseq: hybrid reference of the human genome (Gencode GRCh38.primary_assembly.genome.fa) and the BKV genome (NC_001538.1) with gene anotations from Gencode V38 GTF.
Supplementary files format and content: RNAseq: The salmon.merged.gene_counts.tsv and salmon.merged.gene_tpm.tsv files are directly output by the nf-core/rnaseq pipeline. They contain the Salmon raw counts and tpm values, respectively, for each gene and each sample.

source_name: Neonatal foreskin microvascular endothelial cells

extract_protocol:
RNAseq: TRIzol (Thermo Fisher) was used to extract RNA from cells in 6 well plates. RNA isolation was completed with Direct-Zol RNA Miniprep (Zymo Research) according to manufacturer instructions.
RNAseq: Quality control (Qubit and TapeStation) and library preparation were done by the Health Sciences Sequencing Core (HSSC) at UPMC Children’s Hospital of Pittsburgh using the Illumina Stranded mRNA Prep kit. Libraries were sequenced on a NextSeq 2000 to an approximate depth of 60 million paired end reads (58bp reads).

value: TIME

value: Endothelial

value: Mock infection


title: Extended Data Fig. 6I,second-dose,Erythroid cells,SY9031-USR-17565-064,rep3

description: Library name: SY9031-USR-17565-064


title: 1741W2 - H3K4me3 - CC282

description: Library name: 1741W2-CC282_H3K4me3


title: Mock, Experimental, IFNB, 16hpi, TIME

description: Library name: MposIFN_16HPI

value: Neonatal foreskin microvascular endothelial cells


title: H3K27ac_mg_SgshKO_8mo_rep1_input

description: ChIP-seq

value: SgshKO


title: H3K27ac_mg_SgshKO_4mo_rep2_input

description: ChIP-seq


title: 1740W2 - H3K4me3 - BMS158

description: Library name: 1740W2-BMS158_H3K4me3

value: cell line


title: Mock, Experimental, no IFNB, 72hpi, TIME

description: Library name: MnegIFN_72HPI


title: Extended Data Fig. 6I,second-dose,CD34 cells,SY9031-USR-17565-095,rep3

description: Library name: SY9031-USR-17565-095


title: Extended Data Fig. 6I,second-dose,Erythroid cells,SY9031-USR-17565-032,rep3

description: Library name: SY9031-USR-17565-032


title: 1739W2 - H3K4me3 - DMSO

description: Library name: 1739W2-DMSO_H3K4me3


title: Mock, Experimental, no IFNB, 16hpi, TIME

description: Library name: MnegIFN_16HPI


title: 1738S4 - H3K4me3 - Combo

description: Library name: 1738S4-Combo_H3K4me3

value: Combo


title: H3K27ac_mg_SgshKO_4mo_rep1_input

description: ChIP-seq


title: H3K27ac_mg_WT_8mo_rep2_input

description: ChIP-seq

value: WT


title: BKV, Experimental, IFNB, 72hpi, TIME

description: Library name: DposIFN_72HPI

value: BKV infection


title: 1737S4 - H3K4me3 - CC282

description: Library name: 1737S4-CC282_H3K4me3


title: 1736S4 - H3K4me3 - BMS158

description: Library name: 1736S4-BMS158_H3K4me3


title: H3K27ac_mg_WT_4mo_rep2_input

description: ChIP-seq


title: H3K27ac_mg_WT_8mo_rep1_input

description: ChIP-seq


title: BKV, Experimental, IFNB, 16hpi, TIME

description: Library name: DposIFN_16HPI


title: BKV, Experimental, no IFNB, 72hpi, TIME

description: Library name: DnegIFN_72HPI


title: Extended Data Fig. 6I,second-dose,CD34 cells,SY9031-USR-17565-031,rep3

description: Library name: SY9031-USR-17565-031


title: 1735S4 - H3K4me3 - DMSO

description: Library name: 1735S4-DMSO_H3K4me3


title: H3K27ac_mg_WT_4mo_rep1_input

description: ChIP-seq


title: BKV, Experimental, no IFNB, 16hpi, TIME

description: Library name: DnegIFN_16HPI


title: Extended Data Fig. 6I,second-dose,CD34 cells,SY9031-USR-17565-083,rep3

description: Library name: SY9031-USR-17565-083


title: Extended Data Fig. 6I,second-dose,B cells,SY9031-USR-17565-096,rep3

description: Library name: SY9031-USR-17565-096


title: 1742W2 - H3K4me1 - Combo

description: Library name: 1742W2-Combo_H3K4me1


title: H3K27ac_mg_SgshKO_8mo_rep2

description: ChIP-seq

value: ActiveMotif #39685


title: T47D_CS-1-103_rep3

city: Basel

last: Wu

department: Biomedical Research

country: Switzerland

institute: Novartis Pharma

description:
Library name: T47D_CS-1-103_rep3
T47D_CS-1-103_overlap.optimal_peak.narrowPeak.gz
T47D_CS-1-103_idr.optimal_peak.narrowPeak.gz

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

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

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

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

value: breast cancer cell line


title: 1741W2 - H3K4me1 - CC282

description: Library name: 1741W2-CC282_H3K4me1


title: Extended Data Fig. 6I,second-dose,B cells,SY9031-USR-17565-025,rep3

description: Library name: SY9031-USR-17565-025


title: H3K27ac_mg_SgshKO_8mo_rep1

description: ChIP-seq


title: T47D_CS-1-103_rep2

description:
Library name: T47D_CS-1-103_rep2
T47D_CS-1-103_overlap.optimal_peak.narrowPeak.gz
T47D_CS-1-103_idr.optimal_peak.narrowPeak.gz


title: Extended Data Fig. 6I,second-dose,B cells,SY9031-USR-17565-021,rep3

description: Library name: SY9031-USR-17565-021


title: H3K27ac_mg_SgshKO_4mo_rep2

description: ChIP-seq


title: 1740W2 - H3K4me1 - BMS158

description: Library name: 1740W2-BMS158_H3K4me1


title: T47D_CS-1-103_rep1

description:
Library name: T47D_CS-1-103_rep1
T47D_CS-1-103_overlap.optimal_peak.narrowPeak.gz
T47D_CS-1-103_idr.optimal_peak.narrowPeak.gz


title: Extended Data Fig. 6I,second-dose,B cells,SY9031-USR-17565-016,rep3

description: Library name: SY9031-USR-17565-016


title: 1739W2 - H3K4me1 - DMSO

description: Library name: 1739W2-DMSO_H3K4me1


title: H3K27ac_mg_SgshKO_4mo_rep1

description: ChIP-seq


title: T47D_E2_rep3

description:
Library name: T47D_E2_rep3
T47D_E2_overlap.optimal_peak.narrowPeak.gz
T47D_E2_idr.optimal_peak.narrowPeak.gz


title: Extended Data Fig. 6I,fifth-dose,Myeloid cells,SY9031-USR-17565-093,rep3

description: Library name: SY9031-USR-17565-093


title: 1738S4 - H3K4me1 - Combo

description: Library name: 1738S4-Combo_H3K4me1