title: B. pertussis infected (4-dpi) and treated with AALR drug 2

city: Baltimore

first: Ciaran

last: Skerry

state: MD

address: 685 W. Baltimore Street

department: Microbiology and Immunology

institute: University of Maryland School of Medicine

description:
Library name: AALR2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger software, administered by Maryland Genomics to produce matrices for downstream analysis.
Assembly: Mouse mm
Supplementary files format and content: Matrix files

extract_protocol:
Mouse lungs were minced, incubated in digestion buffer composed of collagenase (2.7 mg/mL), hyaluronidase (0.25 mg/mL), and DNase (0.1 mg/mL) for one hour while undergoing gentlemacs lung dissociation at 37C (Miltenyi Biotec), and then 30 seconds of rapid dissaocciation by gentlemacs lung single cell protocol (Miltenyi Biotec). Cell solution was run through a 40 micron filter, pelleted and then resuspended in 1mL of ACK lysing solution for 5 minutes for lysis and removal of red blood cells. Resulting cell mixture was pelleted and resuspended in HBSS buffer w/ 0.04% BSA. Cells were counted by Countess cell counter and aliquoted for downstream processing.
Cells were counted using a Thermo Fisher Countess II.  Single cell gene expression libraries were prepared according to manufacturer protocol using the Chromium  Next GEM Single Cell 3' v 3.1 kit.

treatment_protocol: Mice challenged intranasally with 50 uLs of PBS-sham or B. pertussis (2x10^6 CFU). One hour before challenge with B. pertussis, mice in the AALR group were treated with S1P agonist, AALR. Four days after infection, mice were euthanized, perfused, and lungs were collected.

value: Lung

tag: age

value: 6 weeks

tag: Sex

value: Female

value: B. pertussis infected + AALR

tag: bacterial strains


title: Multiome_wt_120h_scRNA

status: Public on Mar 11 2026

type: SRA

city: Paris

first: Hocine

last: Rekaik

address: 11, Place Marcelin Berthelot

department: CIRB

country: France

institute: College de France

description: Library name: Multiome_wt_120h_scRNA

library_source: transcriptomic single cell

data_processing:
All scripts are in https://github.com/hrekaik/scriptsForRekaikEtAl2025.
scRNAseq: Mapping and demultiplexing of cell barcode were performed using RNA STARSolo v2.7.10b against the mouse reference genome mm10 and a motified gtf file based on Ensembl 102 (doi:zenodo.org/doi/10.5281/zenodo.10079672) with the following parameters --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 -- soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_CR --soloUMIfiltering - --quantMode TranscriptomeSAM GeneCounts --outSAMattributes NH HI AS nM GX GN CB UB --outSAMtype BAM SortedByCoordinate --soloCellFilter None --soloOutFormatFeaturesGeneField3 'GeneExpression' --outSAMunmapped None --outSAMmapqUnique 60 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000  --limitSjdbInsertNsj 1000000.Then the matrices have been filtered with DropletUtils version 1.10 (Method EmptyDrops, lower-bound threshold = 100, FDR threshold = 0.01).
For scATAC data processing, first, the I2 fastq was reverse complemented with seqtk seq version 1.3.3. Then cell barcodes were added to fastq reads using Sinto barcode v0.10.1. After adapters removal with cutadapt version 4.9, mapping was performed with BWA-MEM v0.7.18 against the mouse reference genome mm10. ATAC fragments with the associated cell barcode were retrieved with Sinto fragments version 0.9.0. The barcodes were translated to match the one from the gene expression. These translated fragment files were sorted and bgzipped to be used by Signac. On the other hand, the fragment file was duplicated and attributed to the + and - strand in order to use both extremities in the peak calling. This duplicated fragment file was used to call peaks with MACS2 v 2.2.9.1 with options --format BED --gsize 1870000000 --call-summits --keep-dup all --bdg --nomodel --extsize 200 --shift -100. The peaks from wt and from Hox-/- samples were concatenated, sorted and merged with bedtools version 2.31.1 in order to create a single comprehensive peak list.
Downstream analysis was done in R with Signac. Individual chromatin assays were created using the ATAC fragment object and the comprehensive list of peaks, then added to the RNA Seurat object. wt and Hox-/- Seurat objects were then merged. The combined Seurat object was filtered to remove low quality cells using ATAC counts (below 1800 or above 100'000), RNA counts (below 1'000 and above 25'000), nucleosome signal (above 2) and TSS enrichment (below 1) values. RNA layer was normalized with SCTransform regressing the percentage of mitochondrial genes and the cell cycle. PCA was also performed on selected genes using the average expression, excluding Hox genes. For the ATAC layer, the all features with more than 5 counts were considered as top features and data normalized using the RunTFID function. The singular value decomposition (SVD) was computed with exclusion of genomic ranges spanning the deleted Hox regions. The joint neighbor graph using RNA and ATAC assays was performed with the FindMultiModalNeighbors function with the 50 first PC for SCT (RNA) and the second to fortieth for lsi (ATAC). The UMAP was computed using this 'weighted.nn' and clustering was computed using the grah 'wknn' with a resolution of 0.5. For motif analysis, chromVAR v1.26.0  was used with the JASPAR 2022 motif collection, the motifs from Berger et al. 2008, the ISMARA motif collection available at https://swissregulon.unibas.ch/data/mm10_f5/mm10_weight_matrices_v2 and the HOMER motifs.
For RNA velocity, velocyto v0.17.17 was used to pre-processes datasets and generate loom files. scVelo v1.10.2  was used to estimate and project RNA velocity and compute the pseudotime.
Assembly: mm10
Supplementary files format and content: .txt: fragment file for ATACseq generated by Sinto fragment and translated so the barcodes match the barcodes from RNAseq part
Supplementary files format and content: tar.gz: scRNAseq filtered matrix in 3 files (barcodes.tsv, genes.tsv, matrix.mtx)
Supplementary files format and content: loom: velocyto output
Supplementary files format and content: merged_peaks.bed.gz: comprehensive list of peaks
Supplementary files format and content: RDS: R seurat object with both samples

molecule: polyA RNA

organism: Mus musculus

source_name: Gastruloid

growth_protocol: For gastruloid differentiation, 300 mES cells were resuspended in 40μl of prewarmed N2B27 medium (50% DMEM/F12 and 50% Neurobasal supplemented with 0.5x N2 and 0.5x B27), and seeded into each well of a low-attachment, rounded-bottom 96-well plate. After 48h, 150µl of N2B27 medium supplemented with 3μM of GSK-3 inhibitor was added to each well. Medium was then replaced every 24h.

extract_protocol:
Gastruloid at 96h and 120h were collected, pooled and dissociated. Nuclei isolation for the single-cell Multiome ATAC and gene expression procedure was per-formed following the manufacture’s instruction of the Chromium Nuclei Isolation Kit (10X Genomics). Dissociated cells were resuspended in cold lysis buffer and incubated for 10min on ice, then transferred to the nuclei isolation column and centrifuged at 16’000 rcf for 20sec at 4°C to re-move cellular debris. The Flowthrough was centrifuged to retrieve the nuclei pellet, then washed with cold Debris Removal Buffer and two rounds of centrifugation, and wash with cold Wash Buffer. Purified nuclei were resuspended in cold Resuspension Buffer, counted and their nuclear membrane assessed.
Samples were immediately processed according to 10X Genomics recommendations of the v1.0 Multiome ATAC + Gene Expression kit. The 10X ATAC and GEX libraries were sequenced

tag: tissue

value: Gastruloid

tag: cell type

value: whole gastruloid

tag: genotype

value: wt

tag: Stage


title: S953_J_0.1_1 rep3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

description: Library name: d5412.S953_J_0.1_1

library_source: transcriptomic

data_processing:
Sequencing using v3 chemistry. Software: Control v2.2.1.1645, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Komagataella phaffi transcripts and exogenous transgenes were quantified using salmon 1.6.0
Gene-level summaries created with tximport 1.24.0
Assembly: Komagataella phaffi WT (strain Y11430) with transcriptome phaffi_plus_240408Lov_transgenes
Supplementary files format and content: phaffi_plus_240408Lov_transgenes.fa.gz is fasta format transcriptome used in salmon quantitation
Supplementary files format and content: 240408Lov_transcript2gene.txt.gz is a tab-delimited file that associates transcript and gene identifiers
Supplementary files format and content: 240408Lov_annotation.txt.gz is a tab-delimited annotation file associating gene names with gene IDs.
Supplementary files format and content: 240408Lov_intCt.txt.gz is a tab delimited file of integrer count data
Supplementary files format and content: 240408Lov_l2tpm.txt.gz is a tab-delimited file of log2 TPM data with a +1 offset.

organism: Komagataella phaffii

source_name: K. phaffii S-953

growth_protocol: Strains were grown in 3 mL cultures in 24-deep well plates (toom temperature, 600 RPM, 3 mm orbit). Cells were cultivated in complex media (potassium phosphate buffer pH 6.5, 1.34% nitrogen base w/o amino acids, 1% yeast extract, 2% peptone). Cultures were inoculated at 0.1 OD600, outgrown for 24 h with 4% glycerol feed, pelleted, and cells resuspended in fresh media with the described quantity of methanol and corresponding co-feed, with 10 mM glutathione. Supernatant samples were collected after 18 hrs and 24 hrs of production for the co-feed screen and the knockout screen respectively, and analyzed.

extract_protocol:
Qiagen RNeasy 96 kit
Nextera XT DNA Library Preparation Kit with the Illumina DNA/RNA UD Indexes

tag: strain

tag: co-feed

value: Xylose

tag: cofeed concentration_(m)

tag: meoh concentration_(v/v_%)


title: B. pertussis infected (4-dpi) and treated with AALR drug 1

description:
Library name: AALR1
10x Genomics

molecule: total RNA

source_name: Lung

tag: treatment


title: S953_J_0.5_1 rep2

description: Library name: d5408.S953_J_0.5_1


title: CMK_IKZF1_2

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

country: China

institute: Children’s Hospital of Soochow University

description:
Library name: Sample 8
CUT&Tag DNA

library_source: genomic

data_processing:
Raw data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.2.5)
Peaks were identified using MACS3 (v3.0.1)
Assembly: hg38
Supplementary files format and content: bw files for each Sample
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: CMK

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

tag: cell line

value: CMK

value: AML cell line

value: WT

tag: antibody

value: IKZF1 (proteintech, #12016-1-AP)


title: S953_J_0.5_1 rep1

description: Library name: d5407.S953_J_0.5_1


title: S953_J_std_1 rep1

description: Library name: d5404.S953_J_std_1


title: B. pertussis infected (4-dpi) 2

description:
Library name: bp2
10x Genomics

value: B. pertussis infected


title: CMK_ERG_2

description:
Library name: Sample 4
CUT&Tag DNA

value: ERG (proteintech, #14356-1-AP)


title: S953_J_std_1 rep2

description: Library name: d5405.S953_J_std_1


title: S953_J_std_1 rep3

description: Library name: d5406.S953_J_std_1


title: B. pertussis infected (4-dpi) 1

description:
Library name: bp1
10x Genomics


title: CMK_ERG_1

description:
Library name: Sample 3
CUT&Tag DNA


title: S953_H_0.1_1 rep1

description: Library name: d5401.S953_H_0.1_1

value: Sorbitol


title: PBS-sham 1

description:
Library name: pbs1
10x Genomics

value: PBS


title: CMK_ETV6_1

description:
Library name: Sample 5
CUT&Tag DNA

value: ETV6 (Abclonal, #A1637)


title: CMK_ELF1_2

description:
Library name: Sample 2
CUT&Tag DNA

value: ELF1 (Abcam, #ab64937)


title: PBS-sham 2

description:
Library name: pbs2
10x Genomics

value: Lung

value: 6 weeks


title: CMK_ELF1_1

description:
Library name: Sample 1
CUT&Tag DNA


title: S953_H_0.5_1 rep2

description: Library name: d5399.S953_H_0.5_1


title: S953_H_std_1 rep1

description: Library name: d5395.S953_H_std_1


title: S953_G_0.1_1 rep2

description: Library name: d5393.S953_G_0.1_1

value: D-Arabinose


title: SH-SY5Y wild type, untreated, rep3

city: Albuquerque

first: Kiran

last: Bhaskar

state: New Mexico

address: 915 Camino De Salud NE

department: Molecular Genetics and Microbiology

institute: University of New Mexico

description: Library name: WT_3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the homo sapiens reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by Deseq2 software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text file includes raw counts and FPKM values for each Sample

growth_protocol: SH-SY5Y WT/OTULIN KO cells were grown in DMEM-F12 (1:1) culture medium supplemented with 10% FBS and 1X concentration of penicillin-streptomycin (10,000 U/mL, stock) in humidified cell culture incubator with 5% CO2 at 37° C.

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Neuroblastoma

value: Untreated

tag: batch


title: S953_H_std_1 rep3

description: Library name: d5397.S953_H_std_1


title: SH-SY5Y wild type, untreated, rep1

description: Library name: WT_1


title: S953_G_0.1_1 rep1

description: Library name: d5392.S953_G_0.1_1


title: S953_H_0.5_1 rep1

description: Library name: d5398.S953_H_0.5_1


title: Single-cell RNA sequencing of bone metastatic tissue

city: Houston

first: Li

last: Yang

address: 6565 Fannin Street

department: Department of System Medicine and Bioengineering (SMAB)

institute: METHODIST HOSPITAL RESEARCH INSTITUTE

description:
Library name: scRNA_lib1
10x Genomics single-cell RNA-seq library from bone metastasis tissue

data_processing:
Single-cell RNA-seq: Raw FASTQ files were processed using Cell Ranger v7.1.0 (10x Genomics) with alignment to the mouse reference genome refdata-gex-mm10-2020-A. Gene-barcode count matrices were generated using default Cell Ranger parameters. Downstream quality control and analysis were performed using Seurat. Cells with fewer than 200 or more than 2,500 detected genes, or with mitochondrial gene content exceeding 5%, were excluded. Expression data were normalized using Seurat’s LogNormalize method with a scale factor of 10,000, followed by log transformation. Data were scaled, and dimensionality reduction was performed using principal component analysis (PCA). Cell clustering was conducted using Seurat’s FindClusters graph-based algorithm, and UMAP was used for visualization. Differentially expressed genes were identified using FindMarkers, and cell types were annotated based on established marker genes.
Spatial transcriptomics: Spatial transcriptomics FASTQ files were processed using Space Ranger v2.1.0 (10x Genomics) with alignment to the mouse reference genome refdata-gex-mm10-2020-A. Spot-by-gene count matrices were generated using default parameters. Downstream preprocessing, normalization, and integration were performed using Seurat. Four samples were integrated using FindIntegrationAnchors with reciprocal PCA (RPCA) and mutual nearest neighbors (MNN) to correct for batch effects. Dimensionality reduction, clustering, and visualization were performed using PCA and UMAP, consistent with the single-cell RNA-seq analysis workflow.
Assembly: Mouse reference genome: GRCm38 (mm10) Reference package: refdata-gex-mm10-2020-A (10x Genomics)
Supplementary files format and content: Single-cell RNA-seq: Processed data files include: --Gene-barcode count matrices in Matrix Market format (.mtx) with accompanying gene and barcode annotation files (.tsv) --Filtered and unfiltered expression matrices generated by Cell Ranger --Cell-level metadata and cluster annotations provided as tab-delimited text files --Normalized expression matrices and dimensionality reduction coordinates (PCA, UMAP) provided as processed data files
Supplementary files format and content: Spatial transcriptomics: Processed data files include: --Spot-by-gene expression matrices generated by Space Ranger --Spatial coordinates and image alignment metadata --Integrated and normalized expression matrices --Spot-level metadata, cluster assignments, and dimensionality reduction results (PCA, UMAP)

source_name: bone metastatic tissue

growth_protocol: Mouse bone metastasis samples were generated using an internal iliac artery (IIA) injection model. Mice were maintained under standard laboratory housing conditions with ad libitum access to food and water. Bone metastases were induced by injection of LLC1 tumor cells, and animals were monitored post-procedure until full recovery. Bone tissues were harvested at defined experimental endpoints for downstream single-cell RNA sequencing and spatial transcriptomics analysis. For the details, please refer to Wang, H. et al. The osteogenic niche promotes early-stage bone colonization of disseminated breast cancer cells. Cancer Cell 27, 193-210 (2015).

extract_protocol:
For single-cell RNA sequencing, bone metastatic tissues were carefully dissected and processed into single-cell suspensions following previously established protocols as described in “Unbiased metastatic niche-labeling identifies estrogen receptor-positive macrophages as a barrier of T cell infiltration during bone colonization” (Xu et al., bioRxiv, 2024). Briefly, tissues were mechanically minced and enzymatically dissociated under controlled conditions to preserve cell viability. The resulting cell suspensions were filtered to remove debris and cell aggregates, washed, and counted prior to downstream single-cell library preparation, as previously reported  2024.05.07.593016v1.full .  For spatial transcriptomics, bone tissues were freshly harvested and processed according to the 10x Genomics Visium Spatial Gene Expression demonstrated tissue preparation protocol (CG000240, Rev A). When necessary, bone tissues were decalcified using an RNA-preserving EDTA-based protocol prior to embedding. Samples were embedded in optimal cutting temperature (OCT) compound, snap-frozen, cryosectioned, and mounted onto 10x Genomics Visium Spatial Gene Expression Slides. Tissue handling, cryosectioning, and slide preparation were performed following the Visium Spatial Protocols – Tissue Preparation Guide to preserve tissue morphology and RNA integrity. All procedures were carried out under RNase-free conditions prior to library preparation according to the manufacturer’s instructions
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Gene Expression platform following the manufacturer’s protocol. Briefly, single cells were encapsulated into gel bead-in-emulsions (GEMs), followed by reverse transcription, cDNA amplification, and library construction. For the details, please refer to “Unbiased metastatic niche-labeling identifies estrogen receptor-positive macrophages as a barrier of T cell infiltration during bone colonization” (Xu et al., bioRxiv, 2024)  Spatial transcriptomics libraries were generated using the 10x Genomics Visium Spatial Gene Expression protocol (CG000240). Tissue sections were fixed, stained, imaged, permeabilized, and reverse-transcribed on-slide. Spatially barcoded cDNA was collected, amplified, and converted into sequencing libraries following the manufacturer’s instructions.

treatment_protocol: Bone metastasis was established by internal iliac artery injection of LLC1 cells suspended in PBS. Mice were anesthetized, and a surgical incision was made to expose the common iliac artery. Tumor cells were injected using a 31-gauge needle, followed by hemostasis and surgical closure. Tumor progression was monitored using IVIS imaging. No additional pharmacological treatments were applied unless otherwise specified.

value: bone metastatic tissue

value: mixed cell populations


title: S953_G_0.1_1 rep3

description: Library name: d5394.S953_G_0.1_1


title: Spatial transcriptomics of bone metastatic tissue section 3

description:
Library name: Bone_ST_24666
10x Genomics Visium spatial transcriptomics library from bone metastasis tissue

data_processing:
Single-cell RNA-seq: Raw FASTQ files were processed using Cell Ranger v7.1.0 (10x Genomics) with alignment to the mouse reference genome refdata-gex-mm10-2020-A. Gene-barcode count matrices were generated using default Cell Ranger parameters. Downstream quality control and analysis were performed using Seurat. Cells with fewer than 200 or more than 2,500 detected genes, or with mitochondrial gene content exceeding 5%, were excluded. Expression data were normalized using Seurat’s LogNormalize method with a scale factor of 10,000, followed by log transformation. Data were scaled, and dimensionality reduction was performed using principal component analysis (PCA). Cell clustering was conducted using Seurat’s FindClusters graph-based algorithm, and UMAP was used for visualization. Differentially expressed genes were identified using FindMarkers, and cell types were annotated based on established marker genes.
Spatial transcriptomics: Spatial transcriptomics FASTQ files were processed using Space Ranger v2.1.0 (10x Genomics) with alignment to the mouse reference genome refdata-gex-mm10-2020-A. Spot-by-gene count matrices were generated using default parameters. Downstream preprocessing, normalization, and integration were performed using Seurat. Four samples were integrated using FindIntegrationAnchors with reciprocal PCA (RPCA) and mutual nearest neighbors (MNN) to correct for batch effects. Dimensionality reduction, clustering, and visualization were performed using PCA and UMAP, consistent with the single-cell RNA-seq analysis workflow.
Assembly: Mouse reference genome: GRCm38 (mm10) Reference package: refdata-gex-mm10-2020-A (10x Genomics)
Supplementary files format and content: Single-cell RNA-seq: Processed data files include: --Gene-barcode count matrices in Matrix Market format (.mtx) with accompanying gene and barcode annotation files (.tsv) --Filtered and unfiltered expression matrices generated by Cell Ranger --Cell-level metadata and cluster annotations provided as tab-delimited text files --Normalized expression matrices and dimensionality reduction coordinates (PCA, UMAP) provided as processed data files
Supplementary files format and content: Spatial transcriptomics: Processed data files include: --Spot-by-gene expression matrices generated by Space Ranger --Spatial coordinates and image alignment metadata --Integrated and normalized expression matrices --Spot-level metadata, cluster assignments, and dimensionality reduction results (PCA, UMAP)
Library strategy: Spatial Transcriptomics


title: S953_H_0.1_1 rep2

description: Library name: d5402.S953_H_0.1_1


title: SH-SY5Y OTULIN knockout, untreated, rep2

description: Library name: KO_2

value: OTULIN KO


title: S953_G_0.5_1 rep3

description: Library name: d5391.S953_G_0.5_1


title: Spatial transcriptomics of bone metastatic tissue section 1

description:
Library name: Bone_ST_24664
10x Genomics Visium spatial transcriptomics library from bone metastasis tissue


title: Spatial transcriptomics of bone metastatic tissue section 4

description:
Library name: Bone_ST_24667
10x Genomics Visium spatial transcriptomics library from bone metastasis tissue


title: S953_H_0.1_1 rep3

description: Library name: d5403.S953_H_0.1_1


title: SH-SY5Y OTULIN knockout, untreated, rep3

description: Library name: KO_3


title: Td-pos, hashtagged

city: St. Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

description:
Library name: PLX3X-pos_multi
hashtagged immune cells from pooled old and young tdTomato+ mice, multiplex files
td-pos_raw_feature_bc_matrix.tar.gz

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 9.0.1. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
see methods for more details
Assembly: mm10
Supplementary files format and content: gzipped files containing raw feature, barcode, and matrix files
Supplementary files format and content: feature reference csv files

source_name: immune cells

extract_protocol:
10X Genomics Chromium Single Cell preparation
NGS Illumina NextSeq

value: immune cells

value: tdTomato+

tag: age group

value: old, young

tag: library type

value: HTO


title: SH-SY5Y OTULIN knockout, untreated, rep1

description: Library name: KO_1


title: S953_G_std_1 rep3

description: Library name: d5388.S953_G_std_1


title: S953_G_0.5_1 rep1

description: Library name: d5389.S953_G_0.5_1


title: S953_G_0.5_1 rep2

description: Library name: d5390.S953_G_0.5_1


title: Spatial transcriptomics of bone metastatic tissue section 2

description:
Library name: Bone_ST_24665
10x Genomics Visium spatial transcriptomics library from bone metastasis tissue


title: S953_H_0.5_1 rep3

description: Library name: d5400.S953_H_0.5_1


title: SH-SY5Y wild type, untreated, rep2

description: Library name: WT_2

value: WT


title: S953_G_std_1 rep2

description: Library name: d5387.S953_G_std_1


title: S953_H_std_1 rep2

description: Library name: d5396.S953_H_std_1

value: Sorbitol


title: Td-neg, hashtagged

description:
Library name: PLX3X-neg_multi
hashtagged immune cells from pooled old and young tdTomato- mice, multiplex files
td-neg_raw_feature_bc_matrix.tar.gz

value: tdTomato-


title: S953_G_std_1 rep1

description: Library name: d5386.S953_G_std_1


title: S953_F_0.1_1 rep3

description: Library name: d5385.S953_F_0.1_1

value: Rhamnose


title: Td-neg, GEX

description:
Library name: PLX3X-neg
hashtagged immune cells from pooled old and young tdTomato- mice, GEX files
td-neg_raw_feature_bc_matrix.tar.gz

value: mRNA


title: CMK-USP20-2

description:
Library name: Sample 2
CUT&Tag DNA

data_processing:
Raw data of CUT-TAG was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.1)
Peaks were identified using MACS3 (v3.0.2)
Assembly: hg38
Supplementary files format and content: bw files for each Sample
Library strategy: CUT&Tag

value: CMK

value: AML

value: USP20 (proteintech,# 17491-1-AP)


title: untreated, hashtagged

description:
Library name: sham
hashtagged blood and misc from untreated mice

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 9.0.1. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
see methods for more details
Assembly: mm10
Supplementary files format and content: gzipped files containing feature, barcode, and matrix files
Supplementary files format and content: feature reference csv files

source_name: blood, other

value: blood, other

value: parabiosis


title: Td-pos, GEX

description:
Library name: PLX3X-pos
hashtagged immune cells from pooled old and young tdTomato+ mice, GEX files
td-pos_raw_feature_bc_matrix.tar.gz


title: CMK-USP20-1

description:
Library name: Sample 1
CUT&Tag DNA


title: S953_F_0.5_1 rep3

description: Library name: d5382.S953_F_0.5_1


title: S953_F_0.1_1 rep2

description: Library name: d5384.S953_F_0.1_1


title: S953_F_0.5_1 rep1

description: Library name: d5380.S953_F_0.5_1


title: S953_F_0.5_1 rep2

description: Library name: d5381.S953_F_0.5_1


title: S953_F_0.1_1 rep1

description: Library name: d5383.S953_F_0.1_1


title: CMK-IgG

description:
Library name: Sample 3
CUT&Tag DNA

value: IgG (Abcam，#ab172730)


title: S953_F_std_1 rep2

description: Library name: d5378.S953_F_std_1


title: S953_E_0.1_1 rep3

description: Library name: d5376.S953_E_0.1_1

value: Sucrose


title: S953_F_std_1 rep1

description: Library name: d5377.S953_F_std_1


title: S953_F_std_1 rep3

description: Library name: d5379.S953_F_std_1


title: CMK cells, NC-2

description:
Library name: Sample 6
CMK sample with no treatment

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: CMK cells, sh-USP20-1

description:
Library name: Sample 7
CMK sample with USP20 knockdown

value: USP20 knockdown


title: S953_E_0.1_1 rep2

description: Library name: d5375.S953_E_0.1_1


title: skull, hashtagged

description:
Library name: skull
hashtagged skull from pooled mice

source_name: skull

value: skull


title: WT

description:
Library name: WT
hashtagged skull, blood, and misc from pooled untreated mice

source_name: skull, blood, other

value: skull, blood, other

value: skull transplant, parabiosis


title: blood, hashtagged

description:
Library name: blood
hashtagged blood from pooled mice

source_name: blood

value: blood

value: skull transplant


title: S953_E_0.1_1 rep1

description: Library name: d5374.S953_E_0.1_1


title: CMK cells, NC-1

description:
Library name: Sample 5
CMK sample with no treatment

value: WT


title: FIRE

description:
Library name: FIRE
hashtagged skull and blood from pooled FIRE mice

source_name: skull, blood

value: skull, blood


title: S953_E_0.5_1 rep3

description: Library name: d5373.S953_E_0.5_1


title: CMK cells, sh-USP20-2

description:
Library name: Sample 8
CMK sample with USP20 knockdown


title: Febrile_16

type: RNA

city: Taipei

first: Shan-Chi

last: Yu

address: No 7 Chung Shan S Rd

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: not provided by submitter

scan_protocol: not provided by submitter

data_processing:
Raw counts were processed using nSolver Analysis Software (version 4.0). Background subtraction was performed by calculating a threshold based on the mean plus two standard deviations (Mean + 2SD) of the internal negative control probes. Data normalization followed a two-step transformation: (1) Technical normalization using the geometric mean of internal positive control probes (factor range 0.3–3.0), and (2) Biological normalization using the geometric mean of housekeeping genes (factor range 0.1–10.0) to account for variations in RNA input and quality
Normalized counts (counts that have undergone background subtraction, positive control normalization, and housekeeping gene normalization).

label_protocol: not provided by submitter

extract_protocol: not provided by submitter

tag: tag

value: FFPE LN tissue


title: MV4-11 cells, sh-USP20-2

description:
Library name: Sample 4
MV4-11 sample with USP20 knockdown


title: S953_E_0.5_1 rep1

description: Library name: d5371.S953_E_0.5_1


title: Febrile_15


title: YSM2, ATACseq

description: Library name: LIB038997_22CCF3LT4_S149

data_processing:
ATAC-seq reads were trimmed with Trimmomatic (v0.39) to remove Nextera adapters and aligned to the mm10 genome with Bowtie2 (v2.2.5). Duplicate reads were removed with Picard MarkDuplicates, and tag directories and peaks were generated, merged, and annotated with HOMER.
see methods in paper for more details
Assembly: mm10
Supplementary files format and content: BED and BigWig files included

source_name: brain parenchymal macrophages

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol with minor adjustments for low-input sorted cells, as described in Grandi et al.
Libraries were pooled at equimolar ratios to a final concentration of 10 nM and sequenced on an Illumina NovaSeq 6000 by the Genome Technology Access Center at Washington University in St. Louis

value: brain parenchymal macrophages


title: MDM2, ATACseq

description: Library name: LIB038996_22CCF3LT4_S148


title: Febrile_14


title: S953_E_0.5_1 rep2

description: Library name: d5372.S953_E_0.5_1


title: Febrile_13


title: MV4-11 cells, NC-2

description:
Library name: Sample 2
MV4-11 sample with no treatment


title: S953_E_std_1 rep2

description: Library name: d5369.S953_E_std_1


title: MV4-11 cells, NC-1

description:
Library name: Sample 1
MV4-11 sample with no treatment


title: Febrile_12


title: YSM1, ATACseq

description: Library name: LIB038995_22CCF3LT4_S147


title: Tonsil B-cells, Left Feature Barcode

city: Clayton

first: Nitika

last: Kandhari

state: VIC

address: Wellington Road

country: Australia

institute: Monash University

description:
Library name: DH_HF20_FB2_L
Left feature barcode library: FB read1 contains cell barcode, UMI ; read2 contains feature barcode for GAC and SpyCEP

library_source: other

data_processing:
Raw 10X GEX, FB and VDJ fastq files were first aligned with CellRanger multi (version 7.2.0) which allows for simultaneous profiling of the V(D)J repertoire, cell surface protein, antigen, and gene expression (GEX) data.
Cellranger output was demultiplexed for 4 donors using VireoSNP including: cellular genotyping with cellSNP-lite v1.2.3 (Huang et al.) and 7.4 SNPs (with MAF > 0.05) from the 1000 genomes project. Donor deconvolution was done with Vireo v0.5.6 (Huang et al).
The counts generated were processed and analysed using the Seurat package (version 5.1.0) in R
Assembly: The reads were mapped to the Human GRCh38 (GENCODE v32/Ensembl98, refdata-gex-GRCh38-2020-A) reference genome, and the VDJ sequences were mapped to vdj-GRCh38-alts-ensembl-5.0.0 reference transcriptome.
Supplementary files format and content: 10X filtered counts (filtered_feature_bc_matrix) for 4 donors (donor0, donor1, donor2, donor3)

molecule: protein

source_name: Tonsil

extract_protocol:
Cryopreserved human tonsil cells from 4 Strep A-colonised paediatric donors were thawed, stained with GAC and SpyCEP antigen tetramers separately, and magnetically enriched for tetramer-binding cells. These cells were stained with surface marker antibodies and either TotalSeq™-C0252 anti-human Hashtag 2 Antibody (for SpyCEP tetramer-binding cells) or TotalSeq™-C0254 anti-human Hashtag 4 Antibody (for GAC tetramer-binding cells). Antigen tetramer-binding isotype switched (IgD–) B cells were isolated by Fluorescence-activated cell sorting (FACS) and sequenced by single cell sequencing using the Chromium Next GEM Chip K Single Cell Kit (10X Genomics, PN-1000286), the Chromium Next GEM single Cell 5’ v2 dual index kit (10X Genomics, PN-1000263).
Sequencing libraries were generated following the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping protocol (10X Genomics, CG000330 Rev C). Single cell RNA, VDJ, and feature barcode sequencing libraries were generated using the Chromium Next GEM Chip K Single Cell Kit (10X Genomics, PN-1000286), the Chromium Next GEM single Cell 5’ v2 dual index kit (10X Genomics, PN-1000263), the 10X Chromium Single Cell Human BCR Amplification Kit (10X Genomics, PN-1000253), and the 5' Feature Barcode Kit (10X Genomics, PN-1000256). Libraries were indexed using the Dual Index Kit TT Set A (10X Genomics, PN-1000215) and the Dual Index Kit TN Set A (10X Genomics, PN-1000250), pooled for sequencing at a molar ratio of 3:1:1 (GEX:VDJ:feature barcode), and sequenced with the Illumina Novaseq 6000 on an S1 flowcell. 10X single cell RNAseq sequneced for GEX, VDJ and Feature barcoding. Cells were spread across two lanes (L= left, R = right) and were further spread across two lanes, L001 and L002.

value: Tonsil

value: Human pediatric tonsil

value: Antigen Tetramer positive CD19posIgDneg B cells

value: mixed sample (GAC treated and SpyCEP treated from 4 donors)


title: Febrile_11


title: MV4-11 cells, sh-USP20-1

description:
Library name: Sample 3
MV4-11 sample with USP20 knockdown


title: S953_E_std_1 rep1

description: Library name: d5368.S953_E_std_1


title: S953_D_std_1 rep3

description: Library name: d5367.S953_D_std_1

value: NoCofeed


title: CUT&Tag anti-YY1 of BV2 microglial cell line, mock-transduced

city: Yushima, Bunkyo-ku

first: Jun

last: Tsuyama

state: Tokyo

department: Medical Research Laboratory

country: Japan

institute: Institute of Science Tokyo

description:
Library name: CutTag_BV2_YY1_MCS
CUT&Tag with anti-YY1 antibody (Abcam, ab109237) in mock-transduced BV2 microglial cell line. Sequenced on Illumina NovaSeq 6000 (PE150).

data_processing:
Reads were mapped to the mm10 (genome file) by Bowtie2, as for ATAC-seq.
Duplicate reads were removed with picard-tools-1.119.
For primary microglia samples, peaks were called with SEACR. Peaks with only one unique read count were then removed. For BV2 cell line samples, peaks were called with MACS2 (narrowPeak).
Signal tracks were plotted by deepTools. BigWig files were generated for visualization.
Assembly: mm10 (GRCm38)
Supplementary files format and content: BigWig signal track files.
Library strategy: CUT&Tag

source_name: BV2 microglial cell line

growth_protocol: All mice were maintained in a conventional facility at the Institute of Science Tokyo or Tokyo Metropolitan Institute of Medical Science in Tokyo, Japan. All experiments were approved by the Institutional Animal Research Committee of the Institute of Science Tokyo (approval number: A2025-011C2) and Tokyo Metropolitan Institute of Medical Science (approval number: 21-004). C57BL/6J mice were used for WT mice. BV2, a microglial cell line, was supplied by Prof. Kazuhide Inoue at Kyushu University, Japan.

extract_protocol:
For primary microglia: Sham-operated mice or mice after MCAO were transcardially perfused with saline, and then the forebrain was removed. After homogenization with RPMI-1640, 1 mg ml–1 collagenase (Sigma-Aldrich) and 50 mg ml–1 DNase I (Sigma-Aldrich) were added to the homogenates. Brain homogenates were digested for 25 min and subjected to Percoll (GE Healthcare) gradient centrifugation. From the interlayer between 37% and 70% Percoll, cells were isolated and stained with anti-CD45 FITC (30-F11, eBioscience), anti-CD11b PerCP-Cy5.5 (M1/70, eBioscience), and anti-CD31 PE/Cyanine7 (390, eBioscience). CD45(int)CD11b(int) cells were sorted using a FACSAria III cell sorter (BD/Thermo Fisher Scientific). For BV2 cells: BV2 cells were harvested from culture.
CUT&Tag libraries were prepared using a bench top CUT&Tag V.2 protocol with slight modifications, as described previously (Nakamura et al., Neuron 2023). BV2 cells or CD45(int)CD11b(int) cells (100,000–200,000 cells from the sham-operated or ischemic hemisphere) were pelleted for 3 min at 600×g at room temperature. Anti-YY1 (Abcam, ab109237) and anti-ZNF384 (Sigma, HPA004051) antibodies were used for primary antibodies. Sequencing was performed using the PE150 strategy on Illumina HiSeq 2500 for primary microglia and BV2 IgG samples, or Illumina NovaSeq 6000 for BV2 anti-ZFP384 and anti-YY1 antibody samples.

treatment_protocol: Transient brain ischemia, induced by middle cerebral artery occlusion (MCAO), was generated in male mice between 8 and 24 weeks of age, with a weight range of 20 to 30 g. Anesthesia was induced by 3% isoflurane with a mixture of 70% nitrous oxide and 30% oxygen, and maintained by 1% isoflurane during the operation. Silicone-coated monofilaments were inserted through the common carotid artery to occlude the origin of the middle cerebral artery. Reperfusion was facilitated by withdrawing the inserted monofilaments 60 minutes after MCAO. Head temperature was maintained at 36°C. Inclusion criteria required confirmation of a >60% reduction in cerebral blood flow using laser Doppler flowmetry. Sham-operated mice underwent the same surgical procedure without occlusion.

value: BV2 microglial cell line

value: wild-type

value: untreated


title: S953_D_std_1 rep1

description: Library name: d5365.S953_D_std_1


title: S953_E_std_1 rep3

description: Library name: d5370.S953_E_std_1

value: Sucrose


title: CUT&Tag anti-ZFP384 of BV2 microglial cell line, Zfp384 overexpression

description:
Library name: CutTag_BV2_Zfp384_Z384OE
CUT&Tag with anti-ZNF384 antibody (Sigma, HPA004051) in Zfp384-overexpressing BV2 microglial cell line. Sequenced on Illumina NovaSeq 6000 (PE150).

value: Zfp384 overexpression (lentiviral)


title: MDM1, ATACseq

description: Library name: LIB038994_22CCF3LT4_S146


title: CUT&Tag anti-YY1 of BV2 microglial cell line, Zfp384 overexpression

description:
Library name: CutTag_BV2_YY1_Z384OE
CUT&Tag with anti-YY1 antibody (Abcam, ab109237) in Zfp384-overexpressing BV2 microglial cell line. Sequenced on Illumina NovaSeq 6000 (PE150).


title: Febrile_9


title: Tonsil B-cells, Right Gene Expression

description:
Library name: DH_HF20_GEX_R
Right gene expression library: GEX (3' mRNA library) , read1 contains cell barcodes, UMI; read2 contains transcript


title: Tonsil B-cells, Right Feature Barcode

description:
Library name: DH_HF20_FB2_R
Right feature barcode library: FB read1 contains cell barcode, UMI; read2 contains feature barcode for GAC and SpyCEP


title: Febrile_10


title: CUT&Tag anti-ZFP384 of BV2 microglial cell line, mock-transduced

description:
Library name: CutTag_BV2_Zfp384_MCS
CUT&Tag with anti-ZNF384 antibody (Sigma, HPA004051) in mock-transduced BV2 microglial cell line. Sequenced on Illumina NovaSeq 6000 (PE150).


title: Tonsil B-cells, Left Gene Expression

description:
Library name: DH_HF20_GEX_L
Left gene expression library: GEX (3' mRNA library) , read1 contains cell barcodes, UMI; read2 contains transcript


title: S953_C_0.1_1 rep3

description: Library name: d5364.S953_C_0.1_1

value: Citrate


title: Febrile_8


title: RNA-seq of mouse microglia, MCAO day 14, Igf1-Egfp EGFP+

description:
Library name: bulkRNA_Day14_Igf1pos
RNA-seq of FACS-sorted CD45(int)CD11b(int) EGFP+ microglia from Igf1-Egfp transgenic mouse brain on day 14 after stroke onset. Libraries were sequenced on Illumina NovaSeq 6000.
bulkRNA_Day14Igf1_gene_counts.txt

data_processing:
Reads were aligned to the mm10 annotation file using STAR, and the read counts for each gene were determined through featureCounts.
Normalization and differential expression analysis were performed using edgeR. DEGs were identified by edgeR.
Gene ontology analysis was performed using DAVID (https://david.ncifcrf.gov/).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited text file containing gene-level raw counts (rows: genes, columns: samples).

source_name: brain

growth_protocol: All mice were maintained in a conventional facility at the Institute of Science Tokyo or Tokyo Metropolitan Institute of Medical Science in Tokyo, Japan. All experiments were approved by the Institutional Animal Research Committee of the Institute of Science Tokyo (approval number: A2025-011C2) and Tokyo Metropolitan Institute of Medical Science (approval number: 21-004). C57BL/6J mice were used for WT mice.

extract_protocol:
Sham-operated mice or mice after MCAO were transcardially perfused with saline, and then the forebrain was removed. After homogenization with RPMI-1640, 1 mg ml–1 collagenase (Sigma-Aldrich) and 50 mg ml–1 DNase I (Sigma-Aldrich) were added to the homogenates. Brain homogenates were digested for 25 min and subjected to Percoll (GE Healthcare) gradient centrifugation. From the interlayer between 37% and 70% Percoll, cells were isolated and stained with anti-CD45 FITC (30-F11, eBioscience), anti-CD11b PerCP-Cy5.5 (M1/70, eBioscience), and anti-CD31 PE/Cyanine7 (390, eBioscience). The cells were sorted using a FACSAria III cell sorter (BD/Thermo Fisher Scientific).
Total RNA was purified using a RNeasy micro kit (Qiagen) and used for the preparation of RNA-seq libraries by an Ovation SoLo RNA-Seq Library Preparation Kit (Tecan), according to the manufacturer's procedure. Following the assessment of quantity and fragment size distribution of cDNA libraries by Agilent TapeStation 4150, the libraries were sequenced by Illumina HiSeq 2500. Libraries for the Day 14 Igf1 cohort were sequenced on Illumina NovaSeq 6000.

value: brain

value: microglia

value: MCAO (Igf1-EGFP positive)


title: S953_D_std_1 rep2

description: Library name: d5366.S953_D_std_1


title: Febrile_7


title: S953_C_0.1_1 rep1

description: Library name: d5362.S953_C_0.1_1


title: S953_C_0.1_1 rep2

description: Library name: d5363.S953_C_0.1_1


title: F-1746-4Gy

city: Philadelphia

first: Kai

last: Tan

state: PA

address: 3501 Civic Center Boulevard

department: Pediatrics

institute: Children's Hospital of Philadelphia

description:
Library name: Sample18
IDH/H3-WT pHGG

data_processing:
Reads were aligned to the human genome (GRCh38) using STAR aligner(v2.7.3a) with default parameters. Gene-count matrices were produced by featureCounts (v2.0.1).
Assembly: GRCh38
Supplementary files format and content: Sample by gene matrix of read counts

source_name: pHGG

extract_protocol:
RNA extraction and sequencing was performed by GeneWiz
Pooled libraries were then sequenced with paired-end 2x150 bp format

value: pHGG

value: 4 Gy


title: Febrile_6

value: FFPE LN tissue


title: E-1746-4Gy

description:
Library name: Sample17
IDH/H3-WT pHGG


title: RNA-seq of mouse microglia, MCAO day 14, Igf1-Egfp EGFP–

description:
Library name: bulkRNA_Day14_Igf1neg
RNA-seq of FACS-sorted CD45(int)CD11b(int) EGFP– microglia from Igf1-Egfp transgenic mouse brain on day 14 after stroke onset. Libraries were sequenced on Illumina NovaSeq 6000.
bulkRNA_Day14Igf1_gene_counts.txt

value: MCAO (Igf1-EGFP negative)


title: D-1746-4Gy

description:
Library name: Sample16
IDH/H3-WT pHGG


title: ATAC-seq of mouse microglia, MCAO day 28, Igf1-CreER;Ai14 homeostatic (EGFP–tdTomato–)

description:
Library name: ATAC_Day28_Igf1-CreER_Ai14_control
ATAC-seq of FACS-sorted CD45(int)CD11b(int) EGFP–tdTomato– microglia (homeostatic state) from Igf1-CreER;Ai14 mouse brain on day 28 after stroke onset. Libraries were sequenced on Illumina NovaSeq 6000.

data_processing:
Reads were mapped to mm10 (genome file) by Bowtie2.
ATAC-seq signal peaks were detected by MACS2 default parameters.
BigWig signal track files were generated using deepTools bamCoverage with RPGC normalization.
Assembly: mm10 (GRCm38)
Supplementary files format and content: BigWig signal track files (RPGC-normalized coverage).

extract_protocol:
Sham-operated mice or mice after MCAO were transcardially perfused with saline, and then the forebrain was removed. After homogenization with RPMI-1640, 1 mg ml–1 collagenase (Sigma-Aldrich) and 50 mg ml–1 DNase I (Sigma-Aldrich) were added to the homogenates. Brain homogenates were digested for 25 min and subjected to Percoll (GE Healthcare) gradient centrifugation. From the interlayer between 37% and 70% Percoll, cells were isolated and stained with anti-CD45 FITC (30-F11, eBioscience), anti-CD11b PerCP-Cy5.5 (M1/70, eBioscience), and anti-CD31 PE/Cyanine7 (390, eBioscience). The cells were sorted using a FACSAria III cell sorter (BD/Thermo Fisher Scientific).
An ATAC-seq library was prepared according to the protocol described previously (Nakamura et al., Neuron 2023). For the fragmentation and tagmentation of genomic DNA, 50,000 nuclei isolated from CD45(int)CD11b(int) cells were treated with Tn5 transposase (Illumina, Nextera DNA Library Preparation Kit). The DNA fragments were amplified using KAPA HiFi HS ReadyMix (Kapa Biosystems) and purified using SPRI select beads (Beckman). Library quality and fragment size distribution were assessed by Agilent TapeStation 4150. Libraries were sequenced using the Illumina HiSeq 2500 for wild-type time-course samples or Illumina NovaSeq 6000 for Igf1-CreER;Ai14 samples.

value: Igf1-CreER; Ai14

value: MCAO


title: C-1746-0Gy

description:
Library name: Sample15
IDH/H3-WT pHGG

value: Control


title: S953_C_0.5_1 rep3

description: Library name: d5361.S953_C_0.5_1


title: Febrile_5


title: Febrile_4


title: A-1746-0Gy

description:
Library name: Sample13
IDH/H3-WT pHGG


title: ATAC-seq of mouse microglia, MCAO day 28, Igf1-CreER;Ai14 dysfunctional (EGFP–tdTomato+)

description:
Library name: ATAC_Day28_Igf1-CreER_Ai14_dysfunctional
ATAC-seq of FACS-sorted CD45(int)CD11b(int) EGFP–tdTomato+ microglia (dysfunctional state) from Igf1-CreER;Ai14 mouse brain on day 28 after stroke onset. Libraries were sequenced on Illumina NovaSeq 6000.


title: B-1746-0Gy

description:
Library name: Sample14
IDH/H3-WT pHGG


title: Febrile_3


title: L-1763NR-4Gy

description:
Library name: Sample12
H3K27M-altered pHGG


title: Febrile_2


title: MDM_4

description: Library name: 10_MDM_k27ac

data_processing:
H3K27ac CUT&Tag reads were trimmed with Trimmomatic (v0.39) to remove Nextera adapters and aligned to the mm10 genome with Bowtie2 (v2.2.5). Duplicate removal with Picard, and tag directory generation with HOMER.
see methods in paper for more details
Assembly: mm10
Supplementary files format and content: BED and BigWig files included
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed on freshly isolated brain macrophages using a low-input protocol adapted from Kaya-Okur et al.
Libraries were quantified by Qubit, pooled equimolarly, and sequenced on an Illumina NovaSeq platform using paired-end 50-bp reads, targeting 10 million uniquely aligned reads per sample.

value: brain parenchymal macrophages


title: S953_C_std_1 rep3

description: Library name: d5358.S953_C_std_1

data_processing:
Sequencing using v3 chemistry. Software: Control v2.2.1.1645, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Komagataella phaffi transcripts and exogenous transgenes were quantified using salmon 1.6.0
Gene-level summaries created with tximport 1.24.0
Assembly: Komagataella phaffi WT (strain Y11430) with transcriptome phaffi_plus_240408Lov_transgenes
Supplementary files format and content: phaffi_plus_240408Lov_transgenes.fa.gz is fasta format transcriptome used in salmon quantitation
Supplementary files format and content: 240408Lov_transcript2gene.txt.gz is a tab-delimited file that associates transcript and gene identifiers
Supplementary files format and content: 240408Lov_annotation.txt.gz is a tab-delimited annotation file associating gene names with gene IDs.
Supplementary files format and content: 240408Lov_intCt.txt.gz is a tab delimited file of integrer count data
Supplementary files format and content: 240408Lov_l2tpm.txt.gz is a tab-delimited file of log2 TPM data with a +1 offset.


title: YSM_4

description: Library name: 8_YSM_k27ac


title: MDM_3

description: Library name: 9_MDM_k27ac


title: K-1763NR-4Gy

description:
Library name: Sample11
H3K27M-altered pHGG


title: S953_C_0.5_1 rep2

description: Library name: d5360.S953_C_0.5_1


title: S953_C_std_1 rep1

description: Library name: d5356.S953_C_std_1


title: S953_C_std_1 rep2

description: Library name: d5357.S953_C_std_1


title: S953_C_0.5_1 rep1

description: Library name: d5359.S953_C_0.5_1


title: YSM_3

description: Library name: 7_YSM_k27ac


title: Febrile_1


title: J-1763NR-4Gy

description:
Library name: Sample10
H3K27M-altered pHGG


title: FebLAP_4


title: I-1763NR

description:
Library name: Sample9
H3K27M-altered pHGG


title: MDM_k27me3

description: Library name: 10_MDM_k27me3


title: S953_B_0.1_1 rep3

description: Library name: d5355.S953_B_0.1_1

value: Galactose


title: YSM_k27me3

description: Library name: 9_YSM_k27me3


title: S953_B_0.1_1 rep1

description: Library name: d5353.S953_B_0.1_1


title: FebLAP_2


title: FebLAP_1


title: MDM_2

description: Library name: 8_MDM_k27ac


title: F-195NR-4Gy

description:
Library name: Sample6
H3K27M-altered pHGG


title: S953_B_0.1_1 rep2

description: Library name: d5354.S953_B_0.1_1


title: aLAP_15


title: S953_B_0.5_1 rep2

description: Library name: d5351.S953_B_0.5_1


title: G-1763NR

description:
Library name: Sample7
H3K27M-altered pHGG


title: H-1763NR

description:
Library name: Sample8
H3K27M-altered pHGG


title: FebLAP_3


title: YSM_2

description: Library name: 6_YSM_k27ac


title: E-195NR-4Gy

description:
Library name: Sample5
H3K27M-altered pHGG


title: YSM_1

description: Library name: 5_YSM_k27ac


title: aLAP_14


title: aLAP_13


title: aLAP_12


title: D-195NR-4Gy

description:
Library name: Sample4
H3K27M-altered pHGG


title: S953_B_0.5_1 rep3

description: Library name: d5352.S953_B_0.5_1


title: C-195NR

description:
Library name: Sample3
H3K27M-altered pHGG


title: S953_B_0.5_1 rep1

description: Library name: d5350.S953_B_0.5_1


title: S953_B_std_1 rep3

description: Library name: d5349.S953_B_std_1


title: MDM_1

description: Library name: 7_MDM_k27ac


title: aLAP_11


title: B-195NR

description:
Library name: Sample2
H3K27M-altered pHGG


title: S953_B_std_1 rep2

description: Library name: d5348.S953_B_std_1


title: aLAP_10


title: Combined

first: Xiang

last: Zhang

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: Combined
cellranger demultiplexed

data_processing:
Downstream analyses were performed using Seurat v5.2.0 (96). Single-cell objects were created and filtered based on standard quality-control criteria (minimum features per cell: 250–6,000; mitochondrial gene fraction < 15%). Datasets were normalized then, to correct for batch effects, we applied Seurat’s FindIntegrationAnchors and IntegrateData functions prior to generating the final integrated single-cell objects. Standard neighborhood and clustering analyses from Seurat pipeline were used to generate clusters at 0.5 resolution. Clusters were first unbiasedly identified with SingleR Immgen (https://github.com/SingleR-inc/celldex), then verified manually with lineage markers. Differential gene expression was identified with the FindMarkers function from the Seurat package, which used the MAST model testing between two clusters or datasets. Other packages used for downstream analyses include CellChat, UCell, Slingshot, and EnhancedVolcano.
Assembly: GRCm39
Supplementary files format and content: tab-seperarated values files and matrix files

source_name: mammary tumor

extract_protocol:
Day 7 mice were treated 3 hours before euthanasia and harvesting. Tumors were processed, digested, and diluted as mentioned above. Spleens were harvested as mentioned above. Anti-CD16/32 antibody was used to block FcR binding, then incubated with anti-CD45 (BioLegend, 103128 1:250) for 45 min. Cells were then stained in collection buffer (PBS + 20%FBS) with Dapi. Minimally, 150,000 cells were sorted for Dapi-CD45+ on a Sony MA900 in the Cytometry and Cell Sorting Core at Baylor College of Medicine. After sorting, cells were spun, resuspended in PBS, and submitted to the Single Cell Genomics Core at Baylor College of Medicine.
A single cell 3’ Gene Expression Library was prepared according to Chromium Single Cell Gene expression 3’V4 On-Chip Multiplexing kit (10x Genomics). In brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium X (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell is pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified cDNA is fragmented to optimal size and the 3’ Gene Expression (GEX) library was generated via End-repair, A-tailing, Adaptor ligation and PCR amplification. Libraries were sent to the Genomic and RNA Profiling Core for sequencing with a NextSeq 500. Raw sequencing data were processed using Cell Ranger v9.0.1 (10x Genomics) after receiving the raw output files from the Genomic and RNA Profiling Core (GARP) at Baylor College of Medicine. A configuration file was used for sample demultiplexing, containing the correspondence between OCM Barcodes (OB) and sample names (OB1: Combination_CD45; OB2: CTX_CD45; OB3: MRX_CD45; OB4: VC_CD45). The Cell Ranger pipeline generated count matrices and cell barcode files separately for each sample.

value: mammary tumor

value: Combined


title: ctxd18t

description:
Library name: ctxd18t
cellranger demultiplexed


title: S953_B_std_1 rep1

description: Library name: d5347.S953_B_std_1


title: combod18t

description:
Library name: combod18t
cellranger demultiplexed


title: CTX

description:
Library name: CTX
cellranger demultiplexed

value: CTX


title: HG_Ctrl_HiChIP

city: Guangzhou

first: Lei

last: Jiang

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

description: Library name: HG_Ctrl_HiChIP

data_processing:
ChIP-seq: Single-end reads were mapped to the GRCm38/mm10 (or GRCh37/hg19) reference genome using the bwa2 mem. The duplicated reads were removed using the Picard Toolkit (https://broadinstitute.github.io/picard/), whereas the reads with a quality lower than 20 were filtered. The ChIP-seq peaks were called using the default (narrow) setting in MACS2.
ATAC-seq: The adapters were removed and the filtered reads were mapped to GRCm38/mm10 (or GRCh37/hg19) using bwa mem. The duplicated reads were removed using Picard (https://broadinstitute.github.io/picard/) and the reads with quality lower than 20 were filtered.
RNA-seq: The reads were mapped toGRCm38/mm10 (or GRCh37/hg19) using STAR. The reads mapped to gene exon regions were counted using featureCounts. Differential expression was determined using DESeq2.
HiChIP: HiChIP data were processed using HiC-Pro with default parameters with the exception of the LIGATION_SITE being set to GATCGATC, GANTGATC, GANTANTC, GATCANTC and the GENOME_FRAGMENT that was generated using digest_genome.py in HiC-Pro utilities. The following parameters were used: -r ^GATC G ^ANTC -o mm10 (or hg19)_restriction sites.bed hg19.fasta. The raw reads were mapped to the GRCm38/mm10 (or GRCh37/hg19) reference genome and were assigned to restriction fragments. The raw reads were filtered for valid pairs (VI). 1D coverage files for the visualization in bigwig format were converted from bam format using deepTools and RPKM (Reads Per Kilobase per Million reads to normalize the number of reads per bin) normalization was used. The HiC files were generated using hicprotojuiebox.py utilities in HiC-Pro.
Assembly: GRCm38/mm10 (or GRCh37/hg19)
Library strategy: HiChIP

source_name: umbilical vein

growth_protocol: Mouse aortic endothelial cells (isolated from mouse aorta) and human umbilical vein cells (Cell biology) were cultured in endothelial cell growth medium in T12.5 flasks coated with gelatin (0.1%). Incubate the cells at 37 °C, 5% CO2 until they are 85% - 90% confluent. After 2-3 passages, endothelial cells were treated with Trypsin-EDTA (0.25% Trypsin, 0.02 EDTA in PBS) and collected. The cells were washed with sterile 37 °C PBS before subsequent experiments.

extract_protocol:
ChIP-seq: Chromatin (8 μg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were precipitated using 4 μg of antibody against H3K27Ac (Active Motif, Cat# 39133) or 10 μg of antibody again JUNB (Activemotif, Cat#39549). The complexes were washed, eluted from the beads with 1% SDS buffer and subjected to RNase and proteinase K treatment overnight at 65°C. The ChIPed DNA was purified by phenol-chloroform extraction and ethanol precipitation. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K in a similar way as ChIPed DNA.
ATAC-seq: Cells grown in tissue culture were pretreated with 200 U/ml DNase (Worthington) for 30 min at 37 °C to remove free-floating DNA and to digest DNA from dead cells. This medium was then washed out, and the cells were resuspended in cold PBS. After the cells were counted, 50,000 cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500 g for 5 min at 4 °C. Supernatant was carefully aspirated. Cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 g at 4 °C. Supernatant was removed and nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2), 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down at least five times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator-5 kit.
RNA-seq: Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
H3K27ac HiChIP: Biotin-labeled proximally-ligated chromatin was prepared using the Arima-HiC kit (Arima Genomics Cat # A510008). Briefly, the crosslinked chromatin was initially digested using a restriction enzyme (RE) cocktail. The 5’-overhangs were subsequently filled in and labeled with a biotinylated nucleotide. Subsequently, the spatially proximal digested ends of DNA were ligated. The resulting proximally-ligated chromatin was fragmented using the Diagenode Bioruptor Pico instrument, bound to an H3K27ac antibody (Abcam Cat # ab4729) overnight and immunoprecipitated on Protein A magnetic beads (Thermo Cat # 10002D). The immunoprecipitated chromatin was reverse crosslinked and purified using the Arima-HiC kit. Subsequently, the Illumina-compatible sequencing libraries were prepared by initial enrichment for biotin using C1 streptavidin beads (Thermo Cat # 65001). The samples were tagmented on-bead utilizing Tagment DNA Enzyme and Buffer (Illumina Cat # 20034197). Subsequently, DNA was ready for PCR enrichment.
ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated. system (Apollo 342, Wafergen Biosystems/Takara). ChIP-Seq libraries were sequenced on Illumina NextSeq 500 as 75-nt single end reads. Adapter sequences were not trimmed during demultiplexing. ATAC-seq: Libraries were prepared as the description (Buenrostro et al., 2015). RNA-seq: After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA form the total RNA with kit. By using the fragmentation buffer, the mRNA and non-coding RNAs are fragmented into short fragments (about 200~700 bp), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand cDNA. The double strand cDNA is purified with QiaQuick PCR extraction kit and then used for end-polishing. Sequencing adapters are ligated to the fragments , then the second strand is degraded using UNG(Uracil-N-Glyosylase)finally. The fragments are purified by Agarose gel electrophoresis and enriched by PCR amplification.The library products are ready for sequencing analysis via Illunima HiSeq 4000 or Hiseq X Ten. HiChIP: Tagmented DNA was PCR amplified utilizing NPM and the indexing primers from the Nextera XT DNA Library Prep kit (Illumina Cat # FC-131-1024). The PCR products were purified and size selected by 0.5X SPRI beads followed by 0.7X SPRI beads before sequencing.

value: umbilical vein

value: Endothelial cell of umbilical vein

value: RBBP6 knocked down

value: high glocose


title: HG_RBBP6-KD_HiChIP

description: Library name: HG_RBBP6-KD_HiChIP


title: aLAP_8


title: A-195NR

description:
Library name: Sample1
H3K27M-altered pHGG


title: VC

description:
Library name: VC
cellranger demultiplexed

value: VC


title: Immortalized Alveolar type 2 Cell  type 2 Cell line 3

city: Los Angeles

first: Anas

last: Rabata

state: CA

address: 127 S. San Vicente Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

description: Library name: Sample 3

data_processing:
We used Cell Ranger version 1.7.0.1 (10x Genomics) to process raw sequencing data and  Seurat suite version 4.1.0 for downstream analysis.
Assembly: mm10
Supplementary files format and content: Matrix files

extract_protocol:
The immortalized AT2 cell lines were collected and trypsinized after 3–4 passages of 2D culture. The cells were then resuspended in Hanks’ balanced salt solution supplemented with 2% fetal bovine serum (FBS), 10 mM HEPES, and 0.1 mM EDTA (HBSS+ buffer). Dead cells were excluded using 7-AAD dye staining. total RNA from the single cells were extracted, reverse transcribed and amplified.
Library preparation was performed according to the manufacturer's instructions using the Chromium Single Cell 3' Reagent Kits v2 protocol (10x Genomics, Pleasanton, CA, USA). Briefly, the cell suspension was resuspended in master mix and, together with partitioning oil and Gel Beads, loaded onto Chromium microfluidic chips to generate Gel Beads-in-Emulsion (GEMs). Within each GEM, poly(A) mRNA from individual cell lysates was reverse transcribed into barcoded, full-length cDNA incorporating an Illumina Read 1 primer sequence, a Unique Molecular Identifier (UMI), and a 10x Cell Barcode. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit for Illumina platforms. Sequencing libraries were loaded onto a NextSeq 500 instrument.

value: Lung

value: Alveolar type 2 Cell


title: aLAP_7

value: FFPE LN tissue


title: Immortalized Alveolar type 2 Cell  type 2 Cell line 2

description: Library name: Sample 2


title: Muscle,control3

city: hefei

last: Wu

state: Anhui

address: Meishan Road 81

institute: Anhui medical university

description:
Library name: control3
10x Genomics

data_processing:
The scRNA-seq libraries were checked for quality using the Agilent Bioanalyzer High Sensitivity chip.
Sequencing results were converted to FASTQ files using Illumina bcl2fastq software (version 5.01).
Raw data were demultiplexed, barcode and mapped to the mouse reference genome using the Cell Ranger package (version 7.0.0).
Feature-barcode raw digital gene expression matrix (UMI counts per gene per cell) was filtered and normalized by using the R package Seurat  (Version 4.1.2).
Genes detected in fewer than one cell were filtered out, and cells were removed if they expressed fewer than 500 detected genes, UMI counts less than Inf, and the percent of mitochondrial-DNA derived gene-expression < 25%. The Doublet Finder package (version 2.0.3) was also used to remove doublets.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tibialis anterior muscle

extract_protocol:
The mouse muscle tissue was added to 1 mL of pre-cooled lysis buffer and minced into approximately 1 mm³ pieces, followed by the addition of 2 mL of pre-cooled lysis buffer. The tissue was then transferred to a Kimble Dounce tissue homogenizer placed on ice and gently homogenized 3–5 times by slowly moving the pestle up and down until complete lysis was achieved. The lysate was incubated on ice for 5 minutes. Subsequently, 4 mL of pre-cooled 2% BSA solution was added for dilution, and the reaction was terminated by pipetting with a Pasteur pipette. The suspension was filtered through a 30 μm cell strainer, and the filtrate was collected and centrifuged at 300 g for 5 minutes at 4 °C. The supernatant was discarded, and the pellet was resuspended in 5 mL of 2% BSA solution. Then, the filtrate was centrifuged at 300 g for 5 minutes at 4 °C. After discarding the supernatant, the nuclei were resuspended in 500 μL of resuspension buffer (1× PBS, 2% BSA, 0.1% RNase inhibitor). The nuclei were stained with propidium iodide, and cell debris was removed by sorting using a BD FACSAria II flow cytometer. A clean nuclear suspension was collected, then counted using CountStar.
The scRNA-seq libraries were constructed with the Chromium Single Cell 3’ Reagent Kits Version 4 (10x Genomics).

value: tibialis anterior muscle

tag: Sex

value: female


title: LG_Ctrl_HiChIP

description: Library name: LG_Ctrl_HiChIP


title: Immortalized Alveolar type 2 Cell  type 2 Cell line 1

description: Library name: Sample 1

source_name: Lung


title: aLAP_9


title: Namalwa scRNA-seq S63845 resistant_L004

city: Charlottesville

first: Jing

last: Gao

state: VA

address: 21 HOSPITAL DR, OMS BLOG RM 4767

department: Pathology

institute: University of Virginia

description:
Library name: Namalwa_S63845_Res_scRNA_L004
Namalwa lymphoma cells treated with S63845 for 8 weeks

data_processing:
Raw base call files were demultiplexed and converted to FASTQ format using Illumina bcl2fastq.
Reads were aligned to the reference genome and gene-level UMI counts were generated using Cell Ranger software (10x Genomics).
Downstream quality control, normalization, and exploratory analyses were performed using standard single-cell RNA-seq analysis workflows.
Assembly: Human: GRCh38; Mouse: GRCm38
Supplementary files format and content: Processed single-cell RNA-seq gene expression data were generated using Cell Ranger and provided in 10x Genomics format. For each sample, the processed data include a sparse gene-cell count matrix (matrix.mtx.gz), corresponding cell barcode annotations (barcodes.tsv.gz), and gene feature annotations (features.tsv.gz).

source_name: Namalwa

growth_protocol: Human Namalwa lymphoma cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and antibiotics at 37°C with 5% CO₂. Eu-Myc mouse lymphoma cells were isolated from spleen tissue and processed immediately for downstream single-cell RNA sequencing.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Single-cell RNA sequencing libraries were generated using the 10x Genomics Chromium Single Cell 3′ platform according to the manufacturer’s instructions.

treatment_protocol: Namalwa cells were treated with the MCL-1 inhibitor S63845 or vehicle control for the indicated durations (12 h, 72 h， 8weeks) or subjected to long-term drug exposure to generate drug-resistant populations. Mouse lymphoma-bearing animals were treated as described in the associated study design.

value: Namalwa

value: B cell lymphoma

value: S63845 8 weeks


title: Muscle,control2

description:
Library name: control2
10x Genomics


title: MRX

description:
Library name: MRX
cellranger demultiplexed

value: MRX


title: LX2 GFP

city: Tokyo

first: Atsushi

last: Nara

address: 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan

description: Library name: Sample 3

data_processing:
Sequence reads were checked by using FastQC.
Sequence reads were mapped to GRCm38/mm10 by using STAR.
Read count extraction was performed by using RSEM.
Normalization and differential expression analysis were performed by using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include expected_count, TPM and FPKM, which were calculated by using RSEM.

source_name: Liver

extract_protocol:
Total RNA was extracted from cells by using TRIzol Reagent (Thermo Fisher Scientific). Contaminating DNA was removed by digestion with DNA-free DNA Removal Kit (Thermo Fisher Scientific). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).
RNA libraries for RNA-seq were prepared by using NEBNext Ultra Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Liver

value: Hepatic stellate cell

value: SPP1 Wild type


title: aLAP_5


title: LX2 SPP1

description: Library name: Sample 4

value: SPP1 overexpression


title: Namalwa scRNA-seq S63845 resistant_L003

description:
Library name: Namalwa_S63845_Res_scRNA_L003
Namalwa lymphoma cells treated with S63845 for 8 weeks


title: HuH7 SPP1

description: Library name: Sample 2

value: Hepatocellular carcinoma


title: Muscle,case2

description:
Library name: case2
10x Genomics


title: HuH7 GFP

description: Library name: Sample 1


title: aLAP_6


title: Namalwa scRNA-seq S63845 resistant_L002

description:
Library name: Namalwa_S63845_Res_scRNA_L002
Namalwa lymphoma cells treated with S63845 for 8 weeks


title: Immortalized Alveolar type 2 Cell  type 2 Cell line 4

description: Library name: Sample 4


title: Muscle,control1

description:
Library name: control1
10x Genomics


title: aLAP_2


title: Muscle,case1

description:
Library name: case1
10x Genomics


title: Namalwa scRNA-seq S63845 resistant_L001

description:
Library name: Namalwa_S63845_Res_scRNA_L001
Namalwa lymphoma cells treated with S63845 for 8 weeks


title: IR-BMT treated wildtype mouse brain, replicate 3

description: Library name: sample.23_SD_IR

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software. Aligned gene-level counts were processed in R using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: TSV of raw gene counts and CPM for all samples are included

extract_protocol:
Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) following the manufacturer’s protocol with minor modifications.Briefly, frozen forebrain tissue was disrupted in 1 mL QIAzol Lysis Reagent (Qiagen) at room temperature and further homogenized by repeated passage through an insulin syringe. The homogenate was incubated for 5 min at room temperature, followed by addition of 200 µL chloroform and vigorous vortexing for 15 s. After a 2-3 min incubation at room temperature, samples were centrifuged at 12,000 × g for 15 min at 4°C. The upper aqueous phase was carefully transferred to a new tube, mixed with an equal volume of 70% ethanol, and applied (up to 700 µL per load) to a RNeasy Mini spin column in a 2-mL collection tube. Columns were centrifuged at ≥8,000 x g for 15 s at room temperature, the flow-through was discarded, and subsequent wash and elution steps were performed as recommended by the manufacturer.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 TapeStation. Double standard complementary DNA (cDNA) was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, and cycles per burst 50 for 120 s. cDNA was blunt ended, had an A base added to the 3′ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 to 15 cycles using primers, incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: brain

value: WT

value: IR


title: Namalwa scRNA-seq S63845 72h_L004

description:
Library name: Namalwa_S63845_72h_scRNA_L004
Namalwa lymphoma cells treated with S63845 for 72 hours


title: tRNA MeRIP-seq of Control DLD-1 cells - Rep2 - IP

city: GuangZhou

first: Mingzhe

last: Huang

address: Guangzhou, Guangdong

institute: Sun Yat-sen University

description: Library name: Ctrl-2-tRNA.IP

data_processing:
1.Quality Control: Raw reads were generated after sequencing, image analysis, base calling, and quality filtering on the Illumina sequencer. Q30 was used as the quality control metric, ensuring that the majority of bases had a Phred quality score of 30 or higher. 2.Adapter Trimming: Adapter sequences were removed from the raw reads using cutadapt software (version 1.9.3). Only adaptor-trimmed reads of >= 15nt were retained for downstream analysis. 3.Read Alignment: Trimmed reads from all samples were aligned to a custom tRNA library using bowtie2 software with sensitive options. The custom tRNA library was adapted from the tRNAScan-SE library by appending CCA to tRNAs from the genomic tRNA database (GtRNAdb2). Isodecoders with identical scores were consolidated to simplify identity assignment. 4.Read Counting: Mapped reads on each tRNA were counted using samtools. This step quantifies the expression of individual tRNAs across different samples. 5.Differential Expression Analysis: EdgeR software was used to detect statistical differences in tRNA expression between conditions (e.g., control vs. TRMT6 overexpression).
Assembly: The custom tRNA library was adapted from the tRNAScan-SE library available at GtRNAdb2. The human genome assembly GRCh38 (hg38) was also used as the reference genome for read alignment.
Supplementary files format and content: BAM Files: Contain aligned reads mapped to the custom tRNA library and the human genome (GRCh38). Read Counts: Tab-delimited text files listing the number of reads mapped to each tRNA gene. Differential Expression: CSV files with tRNA expression levels and statistical results from EdgeR analysis, including log-fold changes and p-values. Normalized Data: Tab-delimited text files with normalized tRNA expression values (e.g., TPM or RPKM) for downstream analysis and visualization.

source_name: Colon

extract_protocol:
Total RNA was extracted from DLD1 cells using the MirVana Isolation Kit (ThermoFisher, AM1561) following the manufacturer’s protocol. The kit specifically enriches for small RNA fractions (<200nt).Enriched small RNAs were de-aminoacylated in a solution containing 0.1 M Tris–HCl (pH 9.0) and 1 mM EDTA for 30 minutes at 37°C to remove amino acid residues from tRNA molecules.
1.Library Construction: tRNA libraries were constructed using the GenSeq® Small RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. This kit is optimized for generating sequencing libraries from small RNA fractions, including tRNAs. 2.Size Selection: Libraries were size-selected to enrich for the tRNA fraction before sequencing. This step ensures that the sequencing data primarily represent tRNA molecules. 3.Sequencing: All libraries were sequenced on the NovaSeq platform (Illumina, Inc., San Diego, CA, USA), which provides high-throughput sequencing capabilities suitable for small RNA-seq experiments.

value: Colon

value: Colon cancer cells

value: Control


title: tRNA MeRIP-seq of Control DLD-1 cells - Rep2 - Input

description: Library name: Ctrl-2-tRNA.Input


title: aLAP_4

data_processing:
Raw counts were processed using nSolver Analysis Software (version 4.0). Background subtraction was performed by calculating a threshold based on the mean plus two standard deviations (Mean + 2SD) of the internal negative control probes. Data normalization followed a two-step transformation: (1) Technical normalization using the geometric mean of internal positive control probes (factor range 0.3–3.0), and (2) Biological normalization using the geometric mean of housekeeping genes (factor range 0.1–10.0) to account for variations in RNA input and quality
Normalized counts (counts that have undergone background subtraction, positive control normalization, and housekeeping gene normalization).

value: FFPE LN tissue


title: aLAP_1


title: aLAP_3


title: IR-BMT treated wildtype mouse brain, replicate 2

description: Library name: sample.22_SD_IR


title: P795CBm_RNA

city: New Haven

first: Yuting

last: Liu

state: CT

address: 333 Cedar Street

institute: YALE UNIVERSITY

description: Library name: P795CBm_GEX_MAH

data_processing:
Raw base call files were converted to FASTQ format and processed using Cell Ranger ARC (v2.0.1, 10x Genomics). Reads were aligned to species-specific reference genomes. Gene expression matrices and chromatin accessibility peak counts were generated using default Cell Ranger ARC parameters. Nuclei were filtered based on quality control thresholds including UMI counts, feature counts, mitochondrial gene percentage (>5%), total ATAC fragment counts (<1,000), and transcription start site enrichment score (<4). Downstream clustering and cell type annotation were performed using Seurat (v4.0.6).
Assembly: human, GRCh38; chimpanzees, panTro5;rhesus macaque, rheMac10; marmoset, calJac4
Supplementary files format and content: cellranger output: feature_bc_matrix.h5
Supplementary files format and content: cellranger output: atac_fragments.tsv.gz

molecule: nuclear RNA

organism: Pan troglodytes

source_name: cerebellum

extract_protocol:
Frozen cerebellar cortex tissue was homogenized and nuclei were isolated using detergent-based resuspension buffers containing NaCl, MgCl₂, Tris-HCl, NP-40, Tween-20, digitonin, protease inhibitors, DTT, BSA, and RNase inhibitor. Nuclei were filtered through 70 µm strainers, centrifuged at 500 × g at 4°C, and resuspended in nuclei buffer supplemented with DTT and RNase inhibitor. Nuclei concentration was adjusted to 4.5 × 10⁶ nuclei/mL prior to microfluidic capture.
Single-nucleus RNA and chromatin accessibility libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC and Gene Expression kit (10x Genomics, PN-1000283) according to the manufacturer’s instructions. Approximately 10,000 nuclei were targeted per sample using the Chromium microfluidic system with Multiome Gel Bead Kit A and Multiome GEM Kit A. RNA and ATAC libraries were generated in parallel from the same nuclei preparation.

value: cerebellum

tag: developmental stage

value: adult

value: mRNA


title: Namalwa scRNA-seq S63845 72h_L003

description:
Library name: Namalwa_S63845_72h_scRNA_L003
Namalwa lymphoma cells treated with S63845 for 72 hours

value: Namalwa

value: B cell lymphoma


title: Namalwa scRNA-seq S63845 72h_L001

description:
Library name: Namalwa_S63845_72h_scRNA_L001
Namalwa lymphoma cells treated with S63845 for 72 hours


title: P795CBm_ATAC

description: Library name: P795CBm_ATAC_MAH

library_source: genomic single cell

tag: tissue

value: ATAC


title: IR-BMT treated wildtype mouse brain, replicate 1

description: Library name: sample.21_SD_IR


title: Namalwa scRNA-seq S63845 72h_L002

description:
Library name: Namalwa_S63845_72h_scRNA_L002
Namalwa lymphoma cells treated with S63845 for 72 hours

tag: cell type


title: tRNA MeRIP-seq of Control DLD-1 cells - Rep1 - IP

description: Library name: Ctrl-1-tRNA.IP

tag: genotype


title: tRNA MeRIP-seq of Control DLD-1 cells - Rep2 - dma.IP

description: Library name: Ctrl-2-tRNA.dma.IP


title: tRNA MeRIP-seq of Control DLD-1 cells - Rep1 - Input

description: Library name: Ctrl-1-tRNA.Input


title: Namalwa scRNA-seq S63845 12h_L004

description:
Library name: Namalwa_S63845_12h_scRNA_L004
Namalwa lymphoma cells treated with S63845 for 12 hours


title: P166CBm_RNA

description: Library name: P166CBm_GEX_MAH


title: PLX treated wildtype mouse brain, replicate 3

description: Library name: sample.19_SD_PLX3X_CD30

value: PLX


title: PLX treated wildtype mouse brain, replicate 2

description: Library name: sample.18_SD_PLX3X_CD30


title: P166CBm_ATAC

description: Library name: P166CBm_ATAC_MAH


title: PLX treated wildtype mouse brain, replicate 1

description: Library name: sample.17_SD_PLX3X_CD30


title: P165CBm_RNA

description: Library name: P165CBm_GEX_MAH


title: Namalwa scRNA-seq S63845 12h_L003

description:
Library name: Namalwa_S63845_12h_scRNA_L003
Namalwa lymphoma cells treated with S63845 for 12 hours


title: tRNA MeRIP-seq of TRMT6/61A-overexpressing DLD-1 cells - Rep2 - IP

description: Library name: 6-61A-2-tRNA.IP

value: TRMT6/TRMT61A overexpression


title: tRNA MeRIP-seq of TRMT6/61A-overexpressing DLD-1 cells - Rep2 - Input

description: Library name: 6-61A-2-tRNA.Input


title: PLX 3x treated wildtype mouse brain, replicate 3

description: Library name: sample.15_SD_PLX3X_CD0


title: Namalwa scRNA-seq S63845 12h_L002

description:
Library name: Namalwa_S63845_12h_scRNA_L002
Namalwa lymphoma cells treated with S63845 for 12 hours


title: tRNA MeRIP-seq of TRMT6/61A-overexpressing DLD-1 cells - Rep2 - dma.IP

description: Library name: 6-61A-2-tRNA.dma.IP


title: Namalwa scRNA-seq S63845 12h_L001

description:
Library name: Namalwa_S63845_12h_scRNA_L001
Namalwa lymphoma cells treated with S63845 for 12 hours


title: PLX 3x treated wildtype mouse brain, replicate 2

description: Library name: sample.14_SD_PLX3X_CD0


title: P165CBm_ATAC

description: Library name: P165CBm_ATAC_MAH


title: SH3

first: Jialing

state: Guangdong

address: Zhongshan No.2 Road 1th, Nonglin Street

institute: Sun Yat-Sen University

description: Library name: SAMPLES6

data_processing:
Base-calling was performed with the MGISEQ-2000RS software.
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were alignment to the reference genome, GRCh38.p13 using HISAT2 (v2.1.0).
Bowtie2 (2.3.4.3) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: FPKM, TPM and read_count values for each sample and each gene

extract_protocol:
Total RNA was extracted from SW480 cells (shNC vs shAURKA) cells using TRIzol reagent.
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads, then fragmented. Then cDNA were sythesized, added A and adaptor ligation, and put into PCR system. Finally, PCR products were circularized and single-stranded circle DNA molecules were replicated via rolling cycle amplificationa to generate a DNA nanoball (DNB), which were then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: colon cancer cells

value: AURKA knockdown


title: PLX 3x treated wildtype mouse brain, replicate 1

description: Library name: sample.13_SD_PLX3X_CD0

value: brain


title: Namalwa scRNA-seq Parental control_L004

description:
Library name: Namalwa_Par_scRNA_L004
Namalwa lymphoma cells, vehicle

value: Vehicle


title: tRNA MeRIP-seq of TRMT6/61A-overexpressing DLD-1 cells - Rep1 - IP

description: Library name: 6-61A-1-tRNA.IP


title: tRNA MeRIP-seq of Control DLD-1 cells - Rep1 - dma.IP

description: Library name: Ctrl-1-tRNA.dma.IP

value: WT


title: Namalwa scRNA-seq Parental control_L002

description:
Library name: Namalwa_Par_scRNA_L002
Namalwa lymphoma cells, vehicle


title: PLX 1x treated wildtype mouse brain, replicate 3

description: Library name: sample.10_SD_PLX1X


title: SH1

description: Library name: SAMPLES4


title: PL3

description: Library name: SAMPLES3


title: tRNA MeRIP-seq of TRMT6/61A-overexpressing DLD-1 cells - Rep1 - Input

description: Library name: 6-61A-1-tRNA.Input

value: Colon


title: tRNA MeRIP-seq of TRMT6/61A-overexpressing DLD-1 cells - Rep1 - dma.IP

description: Library name: 6-61A-1-tRNA.dma.IP

value: Colon cancer cells


title: PLX 1x treated wildtype mouse brain, replicate 1

description: Library name: sample.8_SD_PLX1X


title: Namalwa scRNA-seq Parental control_L003

description:
Library name: Namalwa_Par_scRNA_L003
Namalwa lymphoma cells, vehicle


title: No treatment wildtype mouse brain, replicate 3

description: Library name: sample.3_SD_NT

value: NT


title: SH2

description: Library name: SAMPLES5


title: HeLa siRNA KDEL Receptor 3, replica 5

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

description: Library name: siKR3_E5_R1.fastq.gz

data_processing:
Trimming of the adapter sequences from reads with Trimmomatic
Alignment to the human hg38 genome using the STAR (v2.5.3a)
Counting of genes using featureCounts with the gene annotation from Gencode (version31).
R/Bioconduction package ‘limma’ was used to conduct differential expression analysis using standard procedures.
Assembly: hg38
Supplementary files format and content: count_data.txt: raw counts of expressed genes (cpm>1 in at least 5 samples)
Supplementary files format and content: Palazzo_Differential_Expression_Limma.txt contains the results of the differential expression contrasts result of applying the limma::write.fit() function

source_name: uterine cervix

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco, Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Euroclone) and Penicillin/Streptavidin (Pen/Strep).

extract_protocol:
72 hours after silencing cells were collected and RNA extracted using the RNeasy Plus Kits for RNA Isolation (QIAGEN, ID: 74134) and quantified by Nanodrop.
Libraries of cDNA were prepared with TruSeq mRNA Library Prep Kit (Illumina) and sequenced using the Novaseq instrument (Illumina) 100 bp single-end up to 30 million reads.

treatment_protocol: For silencing assays, cells were plated in 6 wells or 6 cm plates to have about 50-60% confluence on the day of transfection. Five replicates for each condition were used. Following the manufacturer's instruction, cells were transfected using Lipofectamine RNAiMAX (Invitrogen). MISSION® siRNA Universal Negative Control (MERCK) was used as a control. 3 µL duplexes (20 µM) were used for each well of a 6-well plate. Cells were incubated overnight at 37% and 5% CO2. The morning after, the supernatant was replaced with 2 mL of fresh medium. Cells were harvested and lysed 72 hours after silencing.

value: uterine cervix

value: Hela

value: siRNA with duplexes against KDELR3


title: PL2

description: Library name: SAMPLES2


title: HeLa siRNA KDEL Receptor 3, replica 4

description: Library name: siKR3_D5_R1.fastq.gz


title: No treatment wildtype mouse brain, replicate 1

description: Library name: sample.1_SD_NT


title: PL1

description: Library name: SAMPLES1


title: HeLa siRNA KDEL Receptor 3, replica 3

description: Library name: siKR3_C5_R1.fastq.gz


title: K562 CUX1 knock-out, rep 1 H3K9me2 Cut&run

city: Chicago

first: Angela

last: Stoddart

state: IL

address: 900 E. 57th Street

institute: University of Chicago

description: Library name: K562_gCUX1_H3K9me2_rep1

data_processing:
Paired-end reads were aligned to the UCSC hg19 genome using bwa (version 0.7.17). Only uniquely mapped reads with at most two mismatches were retained. Duplicated reads were removed using samtools (version 1.16.1)
Peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=0.1, with input control, broadPeak files were generated using the default MACS2 settings.
deepTools(version 3.5.1) was used to create coverage file in bigWig format. Scores represent normalized to fragments (reads) per kilobase per million (RPKM) at a given genomic coordinate
Assembly: hg19
Supplementary files format and content: broadPeak, bigWig
Library strategy: CUT&Run

source_name: bone marrow

growth_protocol: K562 cells were grown in RPMI 1640 media (Gibco 61870127) supplemented with 10% FBS and 1X Antibiotic-Antimycotic (Gibco 15240062) , at 37 °C and 5% CO2.

extract_protocol:
5x10E5 cells were bound to ConA-coating beads by rotation for 10 minutes at room temperature. Cells were permeabilized (20 mM HEPES pH 7.5, 150 mM NaCL, 0.5 mM Sperimidine, Roche Complete EDTA free 5892953001, 0.05% w/v digitonin) and incubated overnight at 4°C with anti-H3K9me2 (D85B4) 1:50, antibodies. Protein A/G-MNase beads were added and placed on a tube rotator for 1 hour at 4°C. MNAse bound DNA was cleaved and released by adding 1X pA-MNAse mix containing CaCl2 at 0°C for 30 minutes, STOP buffer was added and CUT&RUN fragments were released by incubating for 30 minutes at 37°C.
Library end repair, ligation, and amplification were performed using the Ovation Ultralow System V2 kit (Tecan Genomics Inc. 0344NB-32) and amplified by PCR with the following parameters: 1 cycle of 72°C  2 minutes, 95°C  3 minutes, followed by 13 cycles of 98°C  20 seconds, 65°C  30 seconds, 72°C  30 seconds, and a final extension at 72°C  for 1 min.  Libraries were cleaned up using MinElute PCR purification kit (Qiagen) and a left-sided size selection using SPRI beads (Beckman Coulter B23317). Final libraries were analyzed by Bioanalyzer (Agilent) prior to sequencing.

value: bone marrow

value: human myeloid leukemia

value: CRISPR gCUX1


title: PLX 1x treated wildtype mouse brain, replicate 2

description: Library name: sample.9_SD_PLX1X


title: K562 Control, rep 2 H3K9me2 Cut&run

description: Library name: K562_gHPRT_H3K9me2_rep2

value: CRISPR gHPRT (CTRL)


title: HeLa siRNA KDEL Receptor 3, replica 2

description: Library name: siKR3_B5_R1.fastq.gz


title: Namalwa scRNA-seq Parental control_L001

description:
Library name: Namalwa_Par_scRNA_L001
Namalwa lymphoma cells, vehicle

value: Namalwa

value: B cell lymphoma


title: K562 Control, rep 1 H3K9me2 Cut&run

description: Library name: K562_gHPRT_H3K9me2_rep1


title: K562 CUX1 knock-out, rep 2 H3K9me2 Cut&run

description: Library name: K562_gCUX1_H3K9me2_rep2


title: HeLa siRNA KDEL Receptor 3, replica 1

description: Library name: siKR3_A5_R1.fastq.gz


title: Young tdTomato+ mouse 3

description:
Library name: 21-young-td-pos-3
Young tdTomato+ mouse 3

source_name: Brain

extract_protocol:
Total RNA was then isolated using the RNeasy Micro Plus Kit (Qiagen) according to the manufacturer’s instructions.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 TapeStation. Double standard complementary DNA (cDNA) was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, and cycles per burst 50 for 120 s. cDNA was blunt ended, had an A base added to the 3′ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 to 15 cycles using primers, incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Brain

value: Macrophages

value: Ms4a3-cre, R26-tdTomato

tag: sample group

value: Young tdTomato+ mouse


title: Young tdTomato- mouse 2

description:
Library name: 20-young-td-neg-3
Young tdTomato- mouse 2

value: Young tdTomato- mouse


title: LG-Null-rep2_ATAC

description: Library name: LG-Null-rep2_ATAC

data_processing:
ChIP-seq: Single-end reads were mapped to the GRCm38/mm10 (or GRCh37/hg19) reference genome using the bwa2 mem. The duplicated reads were removed using the Picard Toolkit (https://broadinstitute.github.io/picard/), whereas the reads with a quality lower than 20 were filtered. The ChIP-seq peaks were called using the default (narrow) setting in MACS2.
ATAC-seq: The adapters were removed and the filtered reads were mapped to GRCm38/mm10 (or GRCh37/hg19) using bwa mem. The duplicated reads were removed using Picard (https://broadinstitute.github.io/picard/) and the reads with quality lower than 20 were filtered.
RNA-seq: The reads were mapped toGRCm38/mm10 (or GRCh37/hg19) using STAR. The reads mapped to gene exon regions were counted using featureCounts. Differential expression was determined using DESeq2.
HiChIP: HiChIP data were processed using HiC-Pro with default parameters with the exception of the LIGATION_SITE being set to GATCGATC, GANTGATC, GANTANTC, GATCANTC and the GENOME_FRAGMENT that was generated using digest_genome.py in HiC-Pro utilities. The following parameters were used: -r ^GATC G ^ANTC -o mm10 (or hg19)_restriction sites.bed hg19.fasta. The raw reads were mapped to the GRCm38/mm10 (or GRCh37/hg19) reference genome and were assigned to restriction fragments. The raw reads were filtered for valid pairs (VI). 1D coverage files for the visualization in bigwig format were converted from bam format using deepTools and RPKM (Reads Per Kilobase per Million reads to normalize the number of reads per bin) normalization was used. The HiC files were generated using hicprotojuiebox.py utilities in HiC-Pro.
Assembly: GRCm38/mm10 (or GRCh37/hg19)

value: umbilical vein

value: Endothelial cell of umbilical vein


title: No treatment wildtype mouse brain, replicate 2

description: Library name: sample.2_SD_NT

value: brain

value: WT

value: NT


title: HeLa siRNA KDEL Receptor 2, replica 5

description: Library name: siKR2_E4_R1.fastq.gz

value: uterine cervix

value: Hela

value: siRNA with duplexes against KDELR2


title: Old tdTomato+ mouse 4

description:
Library name: 19-old-td-pos-5
Old tdTomato+ mouse 4

value: Old tdTomato+ mouse