title: snATACseq for Fasted mouse Hypothalmus 3.1

description:
Library name: C57_snATACseq_FFR_Fasted3.1
snATACseq to identify cell type level accessibility peaks across diet states


title: BTRC_98_10X _multiome_snRNAseq

status: Public on Aug 04 2025

type: SRA

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street, HITS 5001

country: USA

institute: Indiana University School of Medicine

description: BTRC_98 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay

library_source: transcriptomic single cell

data_processing:
For libraries containing 'multiome': Cell Ranger ARC Analysis Cell Ranger ARC (cellranger-arc-2.0.0, http://support.10xgenomics.com/) was utilized to process the raw sequence data derived from the single-cell multiome libraries. Both the ATAC and gene expression FASTQ files were processed with the cellranger-arc count algorithm. The reference refdata-cellranger-arc-GRCh38-2020-A-2.0.0 (10x Genomics) was used. Demultiplexing: Cells from each of the sequencing pools were demultiplexed back into their samples of origin using the tool Demuxlet with default parameters. A Signac object, containing both RNA and ATAC-seq data, was created for each pool from the multiome assay from the hdf5 file from the Cell Ranger output. Data from multiple sequencing runs of the same pool were merged. Sample-level metadata were then added to the Signac objects, which were saved as .rds files.
For libraries containing 'HT': Cell ranger Count Analysis: Cell Ranger Count (cellranger-count-7.0.1, http://support.10xgenomics.com/) was utilized to process the raw sequence data derived from the single-cell multiome libraries. The gene expression FASTQ files were processed with the cellranger count algorithm. The reference refdata-cellranger-GRCh38-2020-A (10x Genomics) was used. The filtered gene-cell barcode matrices were used for further analysis. Demultiplexing: Cells from each of the sequencing pools were demultiplexed back into their samples of origin using the tool Demuxlet with default parameters. The data from the technical replicates were then combined. A Seurat object was created from the data from each pool from the HT assay using the gene expression count matrix from the Cell Ranger output. Data from multiple sequencing runs of the same pool were merged. Sample-level metadata was then added to each Seurat object, which were then saved as .rds files.
Assembly: GRCh38
Supplementary files format and content: .RDS files are Seurat objects containing unnormalized count matrices and metadata for each barcode, including sample assignments and sample-level information, such as age, gender, and AUD classification. For HT RNA-seq objects, gene expression counts are included. For multiome objects, counts for gene expression and chromatin peaks are included.

molecule: polyA RNA

organism: Homo sapiens

source_name: caudate nucleus (postmortem brain)

extract_protocol:
For libraries containing 'multiome': 184 fresh-frozen post-mortem caudate brain samples were utilized in the assay. The 184 specimens were divided into 23 pools, with 8 in each pool. The donors in each pool were both condition (with or without AUD) and sex balanced. For each pool, around 20 mg tissue from each donor specimen was collected and combined into a sterilized 2 ml Dounce homogenizer. 2 ml chilled NP40 lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 Substitute, 1mM DTT, 1 U/µl RNase inhibitor) was added to the Dounce homogenizer before the tissues were thawed. The tissues were homogenized 15x using pestle A, and 10x using pestle B, and were transferred into a centrifuge tube to incubate for 2 minutes on ice. After that, 2 ml wash buffer containing PBS, 1% BSA and 1 U/µl RNase inhibitor was added and mixed well. The lysed tissue was centrifuged at 500 rcf for 5 minutes at 4°C, then washed twice more with wash buffer and filtered through 70 µm and then 40 µm cell strainer separately. The pellet was resuspended in 2 ml wash buffer and mixed with 3.6 ml Sucrose Cushion Buffer I (nuclei PURE prep isolation kit, Sigma) containing 1 U/µl RNase inhibitor. 2 ml Sucrose Cushion Buffer I with 1 U/µl RNase inhibitor was added into one 15 ml Beckman Coulter centrifuge tube.  After that, the 5.6 ml nuclei suspensions were gently added to the top of Sucrose Cushion Buffer I without mixing, and followed by centrifuging at 13,000 x rpm (30,000 rcf) (Beckman Coulter ultracentrifuge) with rotor SW40Ti for 45 minutes at 4°C. The purified nuclei pellet was washed by centrifuging at 300 rcf for 5 min at 4°C with wash buffer, and the washed nuclei pellets was resuspended in wash buffer to target ~ 1000 nuclei/μl. For libraries containing HT: Nuclei Isolation for Single-nuclei RNA-seq: 163 fresh-frozen post-mortem caudate brain samples (same individuals as in Multiome assay) were grouped into 17 pools, with roughly 10 in each pool. The donors in each pool were both condition (with or without alcohol use disorder) and sex balanced. For each pool, around 20 mg tissue from each donor specimen was collected and combined into a sterilized 2 ml Dounce homogenizer. 2 ml chilled NP40 lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 Substitute, 1mM DTT, 1 U/µl RNase inhibitor) was added to the Dounce homogenizer before the tissues were thawed. The tissues were homogenized 15x using pestle A, and 10x using pestle B, and were transferred into a centrifuge tube to incubate for 2 minutes on ice. After that, 2 ml wash buffer containing PBS, 1% BSA and 1 U/µl RNase inhibitor was added and mixed well. The lysed tissue was centrifuged at 500 rcf for 5 minutes at 4°C, then washed twice more with wash buffer and filtered through 70 µm and then 40 µm cell strainer separately. The pellet was resuspended in 2 ml wash buffer and mixed with 3.6 ml Sucrose Cushion Buffer I (nuclei PURE prep isolation kit, Sigma).  Zero point two (or One fifth) unit per microliter of RNase inhibitor was used in the buffers. This was followed by centrifuging at 13,000 x rpm (30,000 rcf) (Beckman Coulter ultracentrifuge) with rotor SW40Ti for 45 minutes at 4°C. The purified nuclei pellet was washed by centrifuging at 300 rcf for 5 min at 4°C with wash buffer, and the washed nuclei pellets was resuspended in wash buffer to target ~ 1000 nuclei/μl.
For libraries containing 'multiome': 10X Single-cell Multiome Library Preparation and Sequencing: Paired ATAC and gene expression libraries were generated following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide CG000338_RevB (10X Genomics, Inc). In brief, the isolated nuclei from a pool of samples were first incubated in a transposition mix. The single nuclei master mixture containing tagmented single nuclei suspension was loaded into two well of a Next GEM Chip J, along with the single cell multiome gel beads and partition oil. The chip was then loaded to the Chromium X Controller for GEM generation and barcoding. Barcoded transposed DNA and cDNA were amplified after GEMs being released. At each step, the quality of cDNA, ATAC library and cDNA library was examined by Bioanalyzer 2000. The final single indexed ATAC libraries and the dual indexed gene expression libraries were sequenced on an Illumina Novaseq 6000, with index reads of 10 bp + 24 bp, and 100 bp paired-end reads. The libraries were sequenced twice (2 technical replicates for each BioSample). For libraries containing 'HT': 10X HT Single-nuclei RNA-seq Library Preparation and Sequencing: The Chromium Next GEM single cell 3’ HT reagent kits v3.1 (user guide CG000416, 10X Genomics, Inc.) was used for the single-nuclei RNA-seq assay. The single nuclei suspension from a pool of 10 donor tissue samples were loaded into two wells of a Chromium Next GEM chip M to target 60,000 cell recovery per well. The chip was run on a Chromium X (10x Genomics). Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated. cDNA was synthesized and amplified following cell capture and cell lysis, The quality and quantity of cDNA and resulting libraries were examined by Bioanalyzer. The final libraries were sequenced on an Illumina NovaSeq 6000. 100-bp reads including cell barcode and UMI sequences and 100-bp RNA reads were generated. The libraries were sequenced two or three times for each BioSample.
For libraries containing 'multiome', 10X single nucleus multiome assay (RNA+ATAC-seq). For libraries contatining 'HT', single nucleus RNA-seq.

tag: tissue

value: caudate nucleus (postmortem brain)


title: snATACseq for Fasted mouse Hypothalmus 2.1

city: Salt Lake City

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

institute: University of Utah

description:
Library name: C57_snATACseq_FFR_Fasted2.1
snATACseq to identify cell type level accessibility peaks across diet states

library_source: genomic single cell

data_processing:
CellRanger Fragments files subset with cell types categorized in snRNAseq analysis.
Peaks called with Genrich with the following parameters-r -l 140 -e chrM,chrY -j -d 100 -q 0.05 -v -f.
Assembly: mm10
Supplementary files format and content: NarrowPeak: BED file output by the peak caller Genrich.

molecule: genomic DNA

organism: Mus musculus

source_name: Hypothalamus

extract_protocol:
10x Nuclei Isolation Kit.
10x Genomics Chromium Next GEM Single cell Multiome ATAC preparation.

treatment_protocol: Fed, Fasted 72 hours, Refed 12 hours.

value: Hypothalamus

tag: treatment

value: Fasted


title: Colon, control, sample 3

city: Madrid

first: María

last: Mittelbrunn

state: Madrid

address: C/ Nicolás Cabrera, 1

country: Spain

institute: Centro de Biología Molecular Severo Ochoa

library_source: transcriptomic

data_processing:
RNA-sequencing reads were mapped to the Mus musculus reference genome, GRCm39, using Hisat2 v2.2.1 software.
Reads were then preprocessed with SAMtools v1.13 to transform Sequence Alignment/Map files into Binary Alignment/Map files and sorted.
The number of reads covered by each gene is calculated by HTSeq-Count v1.99.2.
The normalized counts was obtained using DESeq2 v1.40.2.
Assembly: grcm39
Supplementary files format and content: comma-separated value file with the DESeq2 normalized counts for each sample
Supplementary files format and content: comma-separated value file the metadata for each sample

source_name: Colon

extract_protocol:
RNA from mouse colon was purified using the RNeasy Mini Kit (QIAGEN)
cDNA libraries were prepared from total RNA and, then, validated and quantified by an Agilent 4150 Bioanalyzer in BGI Genomics.

value: Colon

tag: genotype

value: Tfam fl/fl


title: BTRC_97_10X _multiome_snRNAseq

description: BTRC_97 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snATACseq for Fasted mouse Hypothalmus 2

description:
Library name: C57_snATACseq_FFR_Fasted2
snATACseq to identify cell type level accessibility peaks across diet states


title: BTRC_96_10X _multiome_snRNAseq

description: BTRC_96 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snATACseq for Fed mouse Hypothalmus 2.1

description:
Library name: C57_snATACseq_FFR_Fed2.1
snATACseq to identify cell type level accessibility peaks across diet states

value: Fed


title: BTRC_95_10X _multiome_snRNAseq

description: BTRC_95 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_93_10X _multiome_snRNAseq

description: BTRC_93 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snATACseq for Fasted mouse Hypothalmus 3.2

description:
Library name: C57_snATACseq_FFR_Fasted3.2
snATACseq to identify cell type level accessibility peaks across diet states


title: BTRC_92_10X _multiome_snRNAseq

description: BTRC_92 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_9_10X _multiome_snRNAseq

description: BTRC_9 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_89_10X _multiome_snRNAseq

description: BTRC_89 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_87_10X _multiome_snRNAseq

description: BTRC_87 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snATACseq for 12h refed mouse Hypothalmus 1

description:
Library name: C57_snATACseq_FFR_12hrRefed1
snATACseq to identify cell type level accessibility peaks across diet states


title: BTRC_86_10X _multiome_snRNAseq

description: BTRC_86 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snATACseq for Fed mouse Hypothalmus 1.1

description:
Library name: C57_snATACseq_FFR_Fed1.1
snATACseq to identify cell type level accessibility peaks across diet states


title: snATACseq for Fasted mouse Hypothalmus 1.1

description:
Library name: C57_snATACseq_FFR_Fasted1.1
snATACseq to identify cell type level accessibility peaks across diet states


title: snATACseq for Fed mouse Hypothalmus 1

description:
Library name: C57_snATACseq_FFR_Fed1
snATACseq to identify cell type level accessibility peaks across diet states


title: snATACseq for Fasted mouse Hypothalmus 1

description:
Library name: C57_snATACseq_FFR_Fasted1
snATACseq to identify cell type level accessibility peaks across diet states


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Refed 3

description:
Library name: snRNAseq_12hrRefed_3
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types

data_processing:
The CellRanger - arc version 2.0.2 pipeline (10X Genomics) was used to process the scRNA-seq and scATAC-seq FASTQC files.
R packager Seurat (V5.0.0).
Assembly: mm10
Supplementary files format and content: Seurat object
Supplementary files format and content: Processed Seurat object

molecule: total RNA

extract_protocol:
10x Nuclei Isolation Kit.
10x Genomics Chromium Next GEM Single Cell Multiome Gene Expression Library Preparation.


title: BTRC_79_10X _multiome_snRNAseq

description: BTRC_79 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_85_10X _multiome_snRNAseq

description: BTRC_85 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_76_10X _multiome_snRNAseq

description: BTRC_76 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Refed 2.1

description:
Library name: snRNAseq_Refed_12hr_2.1
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: BTRC_83_10X _multiome_snRNAseq

description: BTRC_83 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Fed 3

description:
Library name: snRNAseq_Fed_3
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Refed 2

description:
Library name: snRNAseq_Refed_12hr_2
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: BTRC_72_10X _multiome_snRNAseq

description: BTRC_72 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted 3.1

description:
Library name: snRNAseq_Fasted_3.1
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted 3

description:
Library name: snRNAseq_Fasted_3
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: snATACseq for Fed mouse Hypothalmus 2

description:
Library name: C57_snATACseq_FFR_Fed2
snATACseq to identify cell type level accessibility peaks across diet states


title: BTRC_71_10X _multiome_snRNAseq

description: BTRC_71 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_7_10X _multiome_snRNAseq

description: BTRC_7 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snATACseq for 12h refed mouse Hypothalmus 1.1

description:
Library name: C57_snATACseq_FFR_12hrRefed1.1
snATACseq to identify cell type level accessibility peaks across diet states


title: BTRC_69_10X _multiome_snRNAseq

description: BTRC_69 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted 2.1

description:
Library name: snRNAseq_Fasted_2.1
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted 2

description:
Library name: snRNAseq_Fasted_2
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: BTRC_6_10X _multiome_snRNAseq

description: BTRC_6 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: WT P2 [p2-3]

city: New Haven

first: Jay

last: Humphrey

state: CT

address: 55 Prospect St

department: Department of Biomedical Engineering

institute: Yale University

description:
Library name: Sample 3
p2-3_264_313_S69_L001

data_processing:
Sequenced reads were imported into CLC Genomics Workbench V23 (Qiagen).
Following quality control, reads were trimmed and aligned/mapped to a Mus musculus reference genome.
Reads were then automatically processed using trimmed mean of M values (TMM) normalization, log counts per million (CPM) transformation, and Z-Score normalization to generate principal component analysis (PCA) and heat map plots (Euclidean distance and complete linkage for clustering).
Assembly: GRCm39
Supplementary files format and content: csv files include raw counts for each sample

source_name: Aorta

extract_protocol:
RNA was isolated using an RNeasyMini Kit (Qiagen) according to manufacturer's specifications.
Whole-transcriptome sequencing was performed by The Yale Center for Genome Analysis using a NovaSeq 6000 System (Illumina, Inc.).

value: Aorta

value: WT

tag: developmental stage


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Fed 2.1

description:
Library name: snRNAseq_Fed_2.1
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Fed 2

description:
Library name: snRNAseq_Fed_2
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: BTRC_58_10X _multiome_snRNAseq

description: BTRC_58 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_54_10X _multiome_snRNAseq

description: BTRC_54 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_5_10X _multiome_snRNAseq

description: BTRC_5 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_51_10X _multiome_snRNAseq

description: BTRC_51 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Fasted 1

description:
Library name: snRNAseq_Fasted _1
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Fed 1

description:
Library name: snRNAseq_Fed1
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: BTRC_47_10X _multiome_snRNAseq

description: BTRC_47 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snRNA-seq for fed, fasted, or refed mouse hypothalamus Refed 1

description:
Library name: snRNAseq_12hrRefed_1
snRNA-seq for fed, fasted, or refed mouse hypothalamus to assess cell type level expression and categorized cell types


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 12hRefed 2

description:
Library name: Mouse_ATACseq_Rep2_Refed_12hr_2
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Refed_12hr
20799X6

library_source: genomic

data_processing:
Trimmed with cutadapt with the following parameters —minimum-length 20 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT ).
Aligned to mm10 index with bowtie2 with the following parameter: —very-sensitive).
Peaks called with Genrich with the following parameters-r -l 140 -e chrM,chrY -j -d 100 -q 0.05 -v -f.
Assembly: mm10
Supplementary files format and content: BigWig
Supplementary files format and content: NarrowPeak: BED file output by the peak caller Genrich

source_name: hypothalamus

extract_protocol: Corces et al. 2017 OMNI-ATAC protocol.

treatment_protocol: Fed, Fasted 72 hours, Refed 12 hours (after fasting), Refed 1 week (after fasting).

value: hypothalamus

tag: batch


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 1wkRefed 1

description:
Library name: Mouse_ATACseq_Rep2_Refed_1wk_1
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Refed_1wk
20799X7


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 1wkRefed 2

description:
Library name: Mouse_ATACseq_Rep2_Refed_1wk_2
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Refed_1wk
20799X8


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 Fed 3

description:
Library name: Mouse_ATACseq_Rep2_Fed_3
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fed
20799X9


title: BTRC_44_10X _multiome_snRNAseq

description: BTRC_44 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_42_10X _multiome_snRNAseq

description: BTRC_42 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 12hRefed 1

description:
Library name: Mouse_ATACseq_Rep2_Refed_12hr_1
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Refed_12hr
20799X5


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 Fasted 2

description:
Library name: Mouse_ATACseq_Rep2_Fasted_2
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fasted
20799X4


title: BTRC_33_10X _multiome_snRNAseq

description: BTRC_33 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 Fed 2

description:
Library name: Mouse_ATACseq_Rep2_Fed_2
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fed
20799X2


title: BTRC_34_10X _multiome_snRNAseq

description: BTRC_34 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_41_10X _multiome_snRNAseq

description: BTRC_41 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_35_10X _multiome_snRNAseq

description: BTRC_35 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 1wkRefed 4

description:
Library name: Mouse_ATACseq_Rep2_Refed_1wk_4
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Refed_1wk
20799X16


title: BTRC_57_10X _multiome_snRNAseq

description: BTRC_57 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 1wkRefed 3

description:
Library name: Mouse_ATACseq_Rep2_Refed_1wk_3
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Refed_1wk
20799X15


title: BTRC_321_10X _multiome_snRNAseq

description: BTRC_321 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_326_10X _multiome_snRNAseq

description: BTRC_326 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 12hRefed 4

description:
Library name: Mouse_ATACseq_Rep2_Refed_12hr_4
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Refed_12hr
20799X14


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 12hRefed 3

description:
Library name: Mouse_ATACseq_Rep2_Refed_12hr_3
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Refed_12hr
20799X13


title: BTRC_318_10X _multiome_snRNAseq

description: BTRC_318 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_45_10X _multiome_snRNAseq

description: BTRC_45 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 Fasted 4

description:
Library name: Mouse_ATACseq_Rep2_Fasted_4
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fasted
20799X12


title: BTRC_313_10X _multiome_snRNAseq

description: BTRC_313 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 Fasted 3

description:
Library name: Mouse_ATACseq_Rep2_Fasted_3
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fasted
20799X11


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 Fed 4

description:
Library name: Mouse_ATACseq_Rep2_Fed_4
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fed
20799X10


title: BTRC_309_10X _multiome_snRNAseq

description: BTRC_309 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_304_10X _multiome_snRNAseq

description: BTRC_304 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 Fasted 1

description:
Library name: Mouse_ATACseq_Rep2_Fasted_1
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fasted
20799X3


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fasted 4

description:
Library name: Mouse_ATACseq_Rep2_Starved4
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Starved
19924x8

value: Starved


title: BTRC_302_10X _multiome_snRNAseq

description: BTRC_302 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Rep 2 Fed 1

description:
Library name: Mouse_ATACseq_Rep2_Fed_1
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fed
20799X1


title: BTRC_303_10X _multiome_snRNAseq

description: BTRC_303 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fasted 3

description:
Library name: Mouse_ATACseq_Rep2_Starved3
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Starved
19924x7


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fasted 2

description:
Library name: Mouse_ATACseq_Rep2_Starved2
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Starved
19924x6


title: BTRC_30_10X _multiome_snRNAseq

description: BTRC_30 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_3_10X _multiome_snRNAseq

description: BTRC_3 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_299_10X _multiome_snRNAseq

description: BTRC_299 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fed 5

description:
Library name: Mouse_ATACseq_Rep2_Fed5
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fed
19924x4


title: BTRC_295_10X _multiome_snRNAseq

description: BTRC_295 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fed 4

description:
Library name: Mouse_ATACseq_Rep2_Fed4
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fed
19924x3


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fed 3

description:
Library name: Mouse_ATACseq_Rep2_Fed3
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fed
19924x2


title: BTRC_291_10X _multiome_snRNAseq

description: BTRC_291 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


description:
Library name: Mouse_ATACseq_Rep2_Fed1
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fed
19924x1


title: BTRC_29_10X _multiome_snRNAseq

description: BTRC_29 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_289_10X _multiome_snRNAseq

description: BTRC_289 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_282_10X _multiome_snRNAseq

description: BTRC_282 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 1wk Refed 4

description:
Library name: C57_ATACseq_FFR_1WkRefeed_4
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 1wk Refed
20057X8

value: 1 week refed


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 1wk Refed 3

description:
Library name: C57_ATACseq_FFR_1WkRefeed_3
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 1wk Refed
20057X7


description:
Library name: C57_ATACseq_FFR_1WkRefeed_2
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 1wk Refed
20057X6


title: BTRC_311_10X _multiome_snRNAseq

description: BTRC_311 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_284_10X _multiome_snRNAseq

description: BTRC_284 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_280_10X _multiome_snRNAseq

description: BTRC_280 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_281_10X _multiome_snRNAseq

description: BTRC_281 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 12h Refed 4

description:
Library name: C57_ATACseq_FFR_12hrRefeed_4
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 12h Refed
20057X4

value: 12 hours refed


title: BTRC_28_10X _multiome_snRNAseq

description: BTRC_28 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_276_10X _multiome_snRNAseq

description: BTRC_276 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


description:
Library name: C57_ATACseq_FFR_12hrRefeed_2
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 12h Refed
20057X2


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 12h Refed 3

description:
Library name: C57_ATACseq_FFR_12hrRefeed_3
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 12h Refed
20057X3


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 12h Refed 1

description:
Library name: C57_ATACseq_FFR_12hrRefeed_1
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 12h Refed
20057X1


title: BTRC_273_10X _multiome_snRNAseq

description: BTRC_273 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Fasted 1

description:
Library name: Mouse_ATACseq_Rep2_Starved1
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus Starved
19924x5


title: BTRC_269_10X _multiome_snRNAseq

description: BTRC_269 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_272_10X _multiome_snRNAseq

description: BTRC_272 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 14

description:
Library name: PLACseq_B6_Fasted72h_7
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18905X2

data_processing:
Aligned with HiC-Pro.
Matrices Created with FitHiChIP.
Assembly: mm10
Supplementary files format and content: _10000_locus_pairs.bed: BED file of 10 kb binned genomic locus pairs with interaction counts, generated by HiC-Pro.
Supplementary files format and content: _10000_locus_pairs_sort.bed: Sorted version of the above, used for downstream FitHiChIP analysis.
Supplementary files format and content: _ontarget_10000_abs.bed: BED file listing genomic bins (10 kb resolution) that overlap ChIP-seq anchor regions used for targeted PLAC-seq contact inference.
Supplementary files format and content: _ontarget_10000.matrix: Sparse matrix of interaction counts between on-target bins at 10 kb resolution.
Supplementary files format and content: .bwt2pairs.validPairs.txt.gz: Gzipped list of valid read pairs aligned and filtered by HiC-Pro; includes mapping positions and quality information.
Supplementary files format and content: Loops_EdgeR_Default.bed.gz: Gzipped BEDPE-format file of statistically significant differential chromatin loops identified by FitHiChIP using EdgeR-based differential analysis.
Library strategy: PLAC-seq

extract_protocol:
AMPure XP beads, DNA eluted with ARIMA elution buffer.
Arima Hi-C Library Prep with single index.

tag: antibody

value: Active Motif AbFlex rAb H3K27ac Cat# 91193


title: BTRC_27_10X _multiome_snRNAseq

description: BTRC_27 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 10

description:
Library name: PLACseq_B6_Fasted72h_4
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18904X4


title: BTRC_264_10X _multiome_snRNAseq

description: BTRC_264 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 11

description:
Library name: PLACseq_B6_Fasted72h_5
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18904X5


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 9

description:
Library name: PLACseq_B6_Fed_6
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18904X3


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 8

description:
Library name: PLACseq_B6_Fed_5
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18904X2


title: BTRC_261_10X _multiome_snRNAseq

description: BTRC_261 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_267_10X _multiome_snRNAseq

description: BTRC_267 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 7

description:
Library name: PLACseq_B6_Fed_4
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18904X1


title: BTRC_266_10X _multiome_snRNAseq

description: BTRC_266 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 1wk Refed 1

description:
Library name: C57_ATACseq_FFR_1WkRefeed_1
ATAC-seq of Fed Fasted Refed Adult B6 Mouse Hypothalamus 1wk Refed
20057X5


title: BTRC_274_10X _multiome_snRNAseq

description: BTRC_274 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 6

description:
Library name: PLACseq_B6_Fasted72h_1.2
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18878X6


title: BTRC_26_10X _multiome_snRNAseq

description: BTRC_26 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 5

description:
Library name: PLACseq_B6_Fasted72h_1.1
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18878X5


title: BTRC_262_10X _multiome_snRNAseq

description: BTRC_262 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_256_10X _multiome_snRNAseq

description: BTRC_256 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_259_10X _multiome_snRNAseq

description: BTRC_259 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 4

description:
Library name: PLACseq_B6_Fasted72h_1
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18878X4


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 2

description:
Library name: PLACseq_B6_Fed_2
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18878X2


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 13

description:
Library name: PLACseq_B6_Fed_7
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18905X1


title: BTRC_251_10X _multiome_snRNAseq

description: BTRC_251 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 12

description:
Library name: PLACseq_B6_Fasted72h_6
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18904X6


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 1

description:
Library name: PLACseq_B6_Fed_1
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18878X1


title: BTRC_245_10X _multiome_snRNAseq

description: BTRC_245 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_241_10X _multiome_snRNAseq

description: BTRC_241 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_242_10X _multiome_snRNAseq

description: BTRC_242 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: PLAC-seq to identify chromatin contacts in hybrid mice 8

description:
Library name: HybridPLACseq_BC10_0259
PLAC-seq to identify chromatin contacts in hybrid mice
18517X1

data_processing:
Aligned and contacts called with MAPS pipeline.
Assembly: mm10
Supplementary files format and content: feather.qc.tsv: Tab-delimited summary file reporting quality control metrics for each chromatin interaction bin pair. Includes fields such as bin coordinates, raw interaction counts, expected counts, normalized signals, and statistical significance (e.g., FDR or p-value).
Supplementary files format and content: _paired.hic.input.gz: Gzipped BEDPE file containing all valid paired-end reads used as input for MAPS interaction calling.
Supplementary files format and content: _paired.long.intra.bedpe.gz: Gzipped BEDPE file containing intra-chromosomal long-range paired-end reads (>10 kb), used for loop detection.
Supplementary files format and content: _basic10kb.10k.2.peaks: Tab-delimited text file listing statistically significant chromatin contacts (loops) identified by MAPS at 10 kb resolution.
Supplementary files format and content: BEDPE, significant MAPS pipeline defined contacts.
Library strategy: PLAC-seq

value: BC


title: PLAC-seq to identify chromatin contacts in hybrid mice 9

description:
Library name: HybridPLACseq_BC15_0259
PLAC-seq to identify chromatin contacts in hybrid mice
18517X2


title: BTRC_24_10X _multiome_snRNAseq

description: BTRC_24 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: PLAC-seq to identify chromatin contacts in hybrid mice 7

description:
Library name: HybridPLACseq_CB6_0218
PLAC-seq to identify chromatin contacts in hybrid mice
18117X6

value: CB


title: PLAC-seq to identify chromatin contacts in hybrid mice 6

description:
Library name: HybridPLACseq_CB4_0218
PLAC-seq to identify chromatin contacts in hybrid mice
18117X4


title: BTRC_235_10X _multiome_snRNAseq

description: BTRC_235 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: PLAC-seq to identify chromatin contacts in hybrid mice 5

description:
Library name: HybridPLACseq_BC7_0218
PLAC-seq to identify chromatin contacts in hybrid mice
18117X3


title: BTRC_234_10X _multiome_snRNAseq

description: BTRC_234 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_258_10X _multiome_snRNAseq

description: BTRC_258 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_231_10X _multiome_snRNAseq

description: BTRC_231 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_232_10X _multiome_snRNAseq

description: BTRC_232 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: PLAC-seq to identify chromatin contacts in hybrid mice 4

description:
Library name: HybridPLACseq_CB3_0218
PLAC-seq to identify chromatin contacts in hybrid mice
18117X2


title: PLAC-seq to identify chromatin contacts in hybrid mice 2

description:
Library name: HybridPLACseq_CB1_0201
PLAC-seq to identify chromatin contacts in hybrid mice
18003X2


description:
Library name: HybridPLACseq_BC1_0201
PLAC-seq to identify chromatin contacts in hybrid mice
18003X1


title: BTRC_230_10X _multiome_snRNAseq

description: BTRC_230 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: knock out

city: Zurich

first: Christoph

last: Schneider

address: Winterthurerstrasse 190

department: Physiology

country: Switzerland

institute: University of Zurich

description: Library name: 2-KO_Library_409137

data_processing:
The two 10X libraries were processed with CellRanger 7.0.0
Assembly: GRCm39
Supplementary files format and content: count matrices

source_name: lung

extract_protocol:
For single cell RNA analysis of pulmonary dendritic cells and their precursors, lungs of 3 individual Csf2ra+/– or Csf2ra–/– mice, neonatally reconstituted with AM, were homogenized as described above and sorted using a FACSymphony S6 (BD Bioscience). After debris and doublet exclusion, live CD45+CD3–CD19–Ly6G–SiglecF–CD11c+ cells were sorted into PBS containing 0.05% BSA for the 10X Genomics protocol.
Sorted cells were loaded into 10X Genomics Chromium. Libraries were prepared following the manufacturer’s protocol (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 protocol)

value: lung


title: Fed and Fasted PLAC-seq to define differential contacts in hypothalamus 3

description:
Library name: PLACseq_B6_Fed_3
Fed and Fasted PLAC-seq to define differential contacts in mouse hypothalamus
18878X3


title: BTRC_228_10X _multiome_snRNAseq

description: BTRC_228 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_227_10X _multiome_snRNAseq

description: BTRC_227 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_225_10X _multiome_snRNAseq

description: BTRC_225 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Ribo-seq from KO heart replicate 1

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

country: China

institute: Harbin Institute of Technology

description:
Library name: KO-1
SURFSeq 5000

data_processing:
The raw sequencing data is first processed using Cutadapt (v3.7) to remove adapter sequences. Then, FastQC (v0.11.9) is used for sequencing quality assessment.
The cleaned reads are aligned to an rRNA reference sequence using Bowtie (v1.3.1), and the aligned reads are removed. The remaining reads are then mapped to the reference genome using STAR (v2.7.4a), with parameters suitable for short reads.
Open reading frame (ORF) prediction is performed using PRICE (v1.0.6).
For Ribo-seq specific analyses, such as P-site estimation and ribosomal frame periodicity analysis, riboWaltz (v1.2.0) is utilized. Read counts for each gene are obtained using HTSeq (v0.13.5).
Gene expression levels are calculated in terms of FPKM using Cufflinks (v2.2.1), and translation efficiency (TE) is evaluated by integrating RNA-seq signals.Differential expression or translation of genes is subjected to functional annotation and pathway enrichment analysis using clusterProfiler (v4.6.0) to interpret their potential biological significance.
Assembly: (GRCm38/mm10)
Supplementary files format and content: Ribosome-bound FPKM file,This file contains the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values representing ribosome-bound RNA for all samples,Format: Tab-delimited
Supplementary files format and content: Translation Efficiency (TE) file,This file contains the translation efficiency (TE) values for all genes across all samples, calculated by integrating Ribo-seq and RNA-seq signals,Format: Tab-delimited
Library strategy: Ribo-seq

source_name: heart

growth_protocol: Approximately 100 mg of fresh mice heart tissue was collected and immediately frozen in liquid nitrogen.

extract_protocol:
Cells or pulverized tissue samples were lysed in lysis buffer containing 100 μg/mL cycloheximide on ice. Lysates were clarified by centrifugation and treated with RNase I to generate ribosome-protected fragments (RPFs). RPFs were isolated using the Epi™ Ribosome Profiling Kit (Epibiotek, R1814), followed by purification using the RNA Clean & Concentrator-5 kit (ZYMO, R1016). rRNA was removed using the Epi™ RiboRNA Depletion Kit (Human/Mouse/Rat) (Epibiotek, R1805).
Sequencing libraries were constructed from purified ribosome-protected fragments (RPFs) using the QIAseq miRNA Library Kit (QIAGEN, 1103679) according to the manufacturer’s protocol. Final libraries were quantified, quality-checked, and subjected to high-throughput sequencing on the SURFSeq 5000 platform.

treatment_protocol: Mice were sacrificed at day 15 after birth. Mice heart was harvested directly for lysis. Cycloheximide (100 μg/mL) was used to freeze translating ribosomes in place before lysis.

value: heart

tag: cell type

value: cardiomyocytes

value: KO


title: Ribo-seq from KO heart replicate 2

description:
Library name: KO-2
SURFSeq 5000


title: BTRC_223_10X _multiome_snRNAseq

description: BTRC_223 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay

value: caudate nucleus (postmortem brain)


title: BTRC_219_10X _multiome_snRNAseq

description: BTRC_219 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_221_10X _multiome_snRNAseq

description: BTRC_221 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_220_10X _multiome_snRNAseq

description: BTRC_220 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: B6 Mouse Hypothalamus H3K27ac ChIP-seq sample2

description:
Library name: Mm_ChIPseq_H3K27ac_CB12
B6 Mouse Hypothalamus H3K27ac ChIP-seq

data_processing:
Aligned with the following parameters -p 2 -q --local
Sorted and indexed with Samtools.
Peaks called with MACS2 with the following parameters: --format BAMPE -g 1.87e9 -B -t -q 0.05
BigWig created with deeptools bamCoverage with the parameter ‘-of bigwig’.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: BED files

extract_protocol:
AMPure XB beads.
Arima Hi-C Library Prep with single index.

tag: chip antibody


title: B6 Mouse Hypothalamus H3K27ac ChIP-seq sample3

description:
Library name: Mm_ChIPseq_H3K27ac_CB13
B6 Mouse Hypothalamus H3K27ac ChIP-seq


title: Ribo-seq from WT heart replicate 1

description:
Library name: FF-1
SURFSeq 5000


title: BTRC_216_10X _multiome_snRNAseq

description: BTRC_216 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: PLAC-seq to identify chromatin contacts in hybrid mice 3

description:
Library name: HybridPLACseq_BC6_0218
PLAC-seq to identify chromatin contacts in hybrid mice
18117X1

value: Hypothalamus


title: BTRC_215_10X _multiome_snRNAseq

description: BTRC_215 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: B6 Mouse Hypothalamus H3K27ac ChIP-seq input3

description:
Library name: Mm_ChIPseq_H3K27ac_CB13 input
B6 Mouse Hypothalamus H3K27ac ChIP-seq


title: B6 Mouse Hypothalamus H3K27ac ChIP-seq sample1

description:
Library name: Mm_ChIPseq_H3K27ac_BC13
B6 Mouse Hypothalamus H3K27ac ChIP-seq


title: B6 Mouse Hypothalamus H3K27ac ChIP-seq input1

description:
Library name: Mm_ChIPseq_H3K27ac_BC13 input
B6 Mouse Hypothalamus H3K27ac ChIP-seq


title: BTRC_214_10X _multiome_snRNAseq

description: BTRC_214 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: B6 Mouse Hypothalamus H3K27ac ChIP-seq input2

description:
Library name: Mm_ChIPseq_H3K27ac_CB12 input
B6 Mouse Hypothalamus H3K27ac ChIP-seq


title: BTRC_211_10X _multiome_snRNAseq

description: BTRC_211 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_210_10X _multiome_snRNAseq

description: BTRC_210 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_218_10X _multiome_snRNAseq

description: BTRC_218 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_207_10X _multiome_snRNAseq

description: BTRC_207 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Ribo-seq from WT heart replicate 2

description:
Library name: FF-2
SURFSeq 5000


title: BTRC_21_10X _multiome_snRNAseq

description: BTRC_21 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Blood LM + sq

city: Ann Arbor

first: Ashley

last: Pearson

state: MI

address: 1301 Catherine St

institute: University of Michigan

description: Library name: Sample 3

data_processing:
FASTQ files were aligned to the mouse genome (GRCm38.p6) using CellRanger (version 7.0.0) (10x Genomics). The barcodes, features, and matrix output from CellRanger were used for downstream analysis via Seurat (version 4.3.0.1) in R (version 4.3.1).
Assembly: mice genome (GRCm38.p6)
Supplementary files format and content: barcodes, features. Matrix

source_name: Blood

growth_protocol: On day 0, mice were either intrasplenically injected with 800,000 B16F10 cells or saline, followed by immediate splenectomy. All mice were then subcutaneously injected with 250,000 B16F10 cells. On day 7, lungs and blood were collected.

extract_protocol:
Single cell sequencing was performed on the lungs and blood of mice with or without liver metastasis. Lungs were homogenized through a 70 uM filter then passed through two Live/Dead columns, sequentially. Blood was collected and CD45+ cells were collected via density centrifugation.
This pool was subjected to 28x151bp of sequencing according to the manufacturer’s protocol (Illumina NovaSeq). BCL Convert Conversion Software v3.9.3 (Illumina) was used to generate de-multiplexed Fastq files.

value: Blood

tag: cell line

value: Blood immune cells

value: strain:C57/Bl6 age:6-8 weeks Sex:female

value: Liver metastasis and subcutaneous tumor


title: Lung sq

description: Library name: Sample 2

source_name: Lung

value: Lung

value: Pulmonary

value: Subcutaneous tumor


title: BTRC_204_10X _multiome_snRNAseq

description: BTRC_204 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_212_10X _multiome_snRNAseq

description: BTRC_212 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Blood sq

description: Library name: Sample 4


title: Colon, KO, sample 5

data_processing:
RNA-sequencing reads were mapped to the Mus musculus reference genome, GRCm39, using STAR v2.5.2 software.
Reads were then preprocessed with STAR v2.5.2 to transform Sequence Alignment/Map files into Binary Alignment/Map files and sorted.
The number of reads covered by each gene is calculated by HTSeq-Count v1.99.2.
The normalized counts was obtained using DESeq2 v1.44.
Assembly: grcm39
Supplementary files format and content: tab-separated value file with the DESeq2 normalized counts for each sample
Supplementary files format and content: tab-separated value file the metadata for each sample

value: Colon

value: Tfam fl/fl Cd4 Cre


title: Colon, KO, sample 4


title: BTRC_205_10X _multiome_snRNAseq

description: BTRC_205 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Colon, KO, sample 2


title: Colon, control, sample 5

value: Tfam fl/fl


title: Colon, KO, sample 1


title: BTRC_2_10X _multiome_snRNAseq

description: BTRC_2 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Colon, KO, sample 3


title: BTRC_20_10X _multiome_snRNAseq

description: BTRC_20 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Colon, control, sample 3


title: BTRC_197_10X _multiome_snRNAseq

description: BTRC_197 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_196_10X _multiome_snRNAseq

description: BTRC_196 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_195_10X _multiome_snRNAseq

description: BTRC_195 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_193_10X _multiome_snRNAseq

description: BTRC_193 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Colon, control, sample 1


title: Colon, control, sample 4


title: Lung LM + sq

description: Library name: Sample 1


title: BTRC_191_10X _multiome_snRNAseq

description: BTRC_191 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Colon, control, sample 2


title: BTRC_190_10X _multiome_snRNAseq

description: BTRC_190 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_201_10X _multiome_snRNAseq

description: BTRC_201 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_183_10X _multiome_snRNAseq

description: BTRC_183 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Colon, KO+adoptive transfer, sample 3

value: Treg cell therapy


title: BTRC_182_10X _multiome_snRNAseq

description: BTRC_182 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_198_10X _multiome_snRNAseq

description: BTRC_198 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Colon, KO+adoptive transfer, sample 2


title: mouse heart RIP

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low- quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome ( grcm39-110) was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed. The interaction between Intracellular RNA and protein binding were not random, while they show some specific sequence preference.
Homer（v4.9.1） was used to detect the denovo sequence motif and the matched known motifs. Peak related genes can be confirmed by Peak Annotator.
GO enrichment analysis was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered significantly enriched by peak related genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other highthrough put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS (3.0) software to test the statistical enrichment of peak related genes in KEGG pathways.
Assembly: mouse reference genome( grcm39-110)
Supplementary files format and content: Processed data files; excel; RIP_summits_table

extract_protocol:
Heart tissues (～60 mg) were homogenized in a lysis buffer(100 mM KCl, 5 mM MgCl2, 10 mM HEPES (pH 7.0), 0.5% NP40, 1 mM DTT, 100 units/mL RNaseOut) that was made in DEPC H2O. 10% of cell lysate was used for input. The left cell lysate was immunoprecipitated with 50 μL anti-FLAG M2 magnetic beads (M8823, Millipore) at 4 ℃ for 2 hours. The immunoprecipitated samples were washed using lysis buffer for 4 times. Total RNA was extracted from the immunoprecipitated and input samples using the TriPure Isolation Reagent (Roche, Mannheim, Germany). Message RNA was purified by using  Hieff NGS® mRNA Isolation Master Kit (12603, Yeasen Biotechnology).
The fragment distribution and concentration of RNAs（after immunoprecipitation） were detected using an Agilent 2100 bioanalyzer (Agilent) and simpliNano spectrophotometer (GE Healthcare). Then, immunoprecipitated RNA or Input was used for library construction with NEB NextR Ultra™ RNA Library Prep Kit (New England Biolabs). Library quality was assessed on the Agilent Bioanalyzer 2100 system.
The libraries were sequenced on an Illumina Novaseq 6000 platform with a paired-end read length of 150 bp according to the standard protocols.

treatment_protocol: At day 1 after birth, WT mice were injected with AAV9-cTnT-FLAG-NAT10 (3X 1011 VP/mouse) subcutaneously. Mice were sacrificed at day 20 after injection.


title: BTRC_180_10X _multiome_snRNAseq

description: BTRC_180 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_18_10X _multiome_snRNAseq

description: BTRC_18 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_176_10X _multiome_snRNAseq

description: BTRC_176 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: mouse heart Input

value: At day 1 after birth, WT mice were injected with AAV9-cTnT-FLAG-NAT10 (3X 1011 VP/mouse) subcutaneously. Mice were sacrificed at day 20 after injection.


title: BTRC_179_10X _multiome_snRNAseq

description: BTRC_179 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_174_10X _multiome_snRNAseq

description: BTRC_174 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_171_10X _multiome_snRNAseq

description: BTRC_171 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: K209A_KO2

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the mouse reference genome(GRCm38/mm10) using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate .
Assembly: mouse reference genome(GRCm38/mm10)
Supplementary files format and content: Processed data files; excel; gene_fpkm

extract_protocol:
At day 1 after birth, Nat10flox/flox mice were injected with AAV9-cTnT-GFP (1X 1011 VP/mouse) subcutaneously, and Nat10-CKO mice were injected with equal amount of AAV9-cTnT-GFP, AAV9-cTnT-NAT10, AAV9-cTnT-NAT10G641E, and AAV9-cTnT-NAT10K209A, respectively. Mice were sacrificed at day 12-14 after injection. Heart tissues were collected. Total RNA was extracted from heart tissues using Tripure Isolation Reagent (Roche, Mannheim, Germany). Three independent biological replicates for each group were used for RNA-seq.
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

value: heart

value: injected with AAV9-cTnT-NAT10K209A


title: BTRC_172_10X _multiome_snRNAseq

description: BTRC_172 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: G641E_KO2

value: injected with AAV9-cTnT-NAT10G641E


title: G641E_KO1


title: BTRC_170_10X _multiome_snRNAseq

description: BTRC_170 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay

value: caudate nucleus (postmortem brain)


title: BTRC_17_10X _multiome_snRNAseq

description: BTRC_17 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: K209A_KO1


title: Colon, KO+adoptive transfer, sample 6


title: WT_KO3

value: injected with AAV9-cTnT-NAT10


title: WT_KO1


title: Colon, KO+adoptive transfer, sample 4


title: BTRC_168_10X _multiome_snRNAseq

description: BTRC_168 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_169_10X _multiome_snRNAseq

description: BTRC_169 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: WT_KO2


title: GFP_KO3

value: injected with AAV9-cTnT-GFP


title: Colon, KO+adoptive transfer, sample 1


title: GFP_KO2


title: BTRC_167_10X _multiome_snRNAseq

description: BTRC_167 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: K209A_KO3


title: BTRC_164_10X _multiome_snRNAseq

description: BTRC_164 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: Control

description: Library name: 1-CTRL_Library_409136

value: lung


title: BTRC_163_10X _multiome_snRNAseq

description: BTRC_163 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_173_10X _multiome_snRNAseq

description: BTRC_173 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: G641E_KO3


title: GFP_KO1


title: GFP_ff3


title: BTRC_162_10X _multiome_snRNAseq

description: BTRC_162 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: GFP_ff2


title: BTRC_16_10X _multiome_snRNAseq

description: BTRC_16 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_159_10X _multiome_snRNAseq

description: BTRC_159 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: GFP_ff1


title: BTRC_158_10X _multiome_snRNAseq

description: BTRC_158 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: CKO_2

extract_protocol:
Nat10flox/flox and Nat10-CKO mice were sacrificed at 15 days old.Total RNA was extracted from heart tissues using Tripure Isolation Reagent (Roche, Mannheim, Germany). Three independent biological replicates for each group were used for RNA-seq.
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.


title: CKO_1


title: flox_3


title: BTRC_149_10X _multiome_snRNAseq

description: BTRC_149 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_148_10X _multiome_snRNAseq

description: BTRC_148 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: flox_2


title: BTRC_147_10X _multiome_snRNAseq

description: BTRC_147 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_146_10X _multiome_snRNAseq

description: BTRC_146 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_145_10X _multiome_snRNAseq

description: BTRC_145 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: stromal_2

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

data_processing:
Sequencing was performed in 2 sequencing unit of NovaSeq 6000 (Illumina) (100-nt-length reads, paired end).
Quality of RNA-seq data was assessed using FastQC (v0.11.9). Reads were aligned to the transcriptome using STAR.
Assembly: mm10
Supplementary files format and content: raw count matrix (csv file)

source_name: skin

extract_protocol:
Total RNA was extracted using the Total RNA purification kit (Norgen) according to the manufacturer’s protocol. cDNA was generated using the SMART-Seq mRNA LP kit (Takara) according to the manufacturer’s protocol.
The integrity of the DNA was confirmed in BioAnalyzer using High Sensitivity DNA kit (Agilent Technologies) (RIN > 8). Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Prep Kit (Illumina).

treatment_protocol: Purified immune and non-immune skin cells were analyzed 6h after application of hypobaric pressure. Unstretched tissue of the same area (control) was used as baseline.

value: skin

value: control


title: stromal_3


title: BTRC_143_10X _multiome_snRNAseq

description: BTRC_143 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_142_10X _multiome_snRNAseq

description: BTRC_142 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: stromal_1


title: immune_7

value: stretched


title: immune_8


title: BTRC_136_10X _multiome_snRNAseq

description: BTRC_136 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: flox_1


title: BTRC_161_10X _multiome_snRNAseq

description: BTRC_161 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_139_10X _multiome_snRNAseq

description: BTRC_139 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_134_10X _multiome_snRNAseq

description: BTRC_134 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: stromal_4


title: BTRC_137_10X _multiome_snRNAseq

description: BTRC_137 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_132_10X _multiome_snRNAseq

description: BTRC_132 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: CKO_3


title: stromal_5


title: BTRC_131_10X _multiome_snRNAseq

description: BTRC_131 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_128_10X _multiome_snRNAseq

description: BTRC_128 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: immune_5


title: immune_4


title: BTRC_127_10X _multiome_snRNAseq

description: BTRC_127 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: immune_6


title: immune_2


title: BTRC_125_10X _multiome_snRNAseq

description: BTRC_125 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: immune_3


title: stromal_6


title: BTRC_124_10X _multiome_snRNAseq

description: BTRC_124 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_123_10X _multiome_snRNAseq

description: BTRC_123 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: immune_1


title: stromal_7


title: C8

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

institute: University of Missouri

data_processing:
The quality of raw sequences was checked using FastQC.
Adaptor trimming was performed using cutadapt. The fastp tool was used to perform base quality trimming (Phred score >30) by sliding window scan (4 nucleotides).
Then the reads were mapped to the pig reference genome GRCm39  using the STAR aligner
Differential gene expression analysis was performed using edgeR
Assembly: GRCm39
Supplementary files format and content: Read counts in tab separated text file.

source_name: Placenta

growth_protocol: Adult male and female mice (7 weeks old) were paired in cages to induce pregnancy. The females were checked for vaginal plug. The start of pregnancy (day 1) was considered when a vaginal plug was observed. The control and Cav-null pregnant mice were euthanized in triplicates on gestation day 15, and the mammary gland and placenta samples were dissected from each mice.  The samples were washed in sterile phosphate buffer saline, snap frozen in liquid nitrogen and stored in -80°C for downstream analyses.

extract_protocol:
Total RNA was isolated from the mammary gland and placenta samples (in triplicates) of control and Cav1-null mice using AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID:80204) following the manufacturers’ instructions.
Each library was sequenced to 20 million paired end reads of 150 bases using a NovaSeq 6000 sequencer.

value: Placenta

tag: time

value: Gestation day 15

tag: strain


title: BTRC_121_10X _multiome_snRNAseq

description: BTRC_121 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay

data_processing:
For libraries containing 'multiome': Cell Ranger ARC Analysis Cell Ranger ARC (cellranger-arc-2.0.0, http://support.10xgenomics.com/) was utilized to process the raw sequence data derived from the single-cell multiome libraries. Both the ATAC and gene expression FASTQ files were processed with the cellranger-arc count algorithm. The reference refdata-cellranger-arc-GRCh38-2020-A-2.0.0 (10x Genomics) was used. Demultiplexing: Cells from each of the sequencing pools were demultiplexed back into their samples of origin using the tool Demuxlet with default parameters. A Signac object, containing both RNA and ATAC-seq data, was created for each pool from the multiome assay from the hdf5 file from the Cell Ranger output. Data from multiple sequencing runs of the same pool were merged. Sample-level metadata were then added to the Signac objects, which were saved as .rds files.
For libraries containing 'HT': Cell ranger Count Analysis: Cell Ranger Count (cellranger-count-7.0.1, http://support.10xgenomics.com/) was utilized to process the raw sequence data derived from the single-cell multiome libraries. The gene expression FASTQ files were processed with the cellranger count algorithm. The reference refdata-cellranger-GRCh38-2020-A (10x Genomics) was used. The filtered gene-cell barcode matrices were used for further analysis. Demultiplexing: Cells from each of the sequencing pools were demultiplexed back into their samples of origin using the tool Demuxlet with default parameters. The data from the technical replicates were then combined. A Seurat object was created from the data from each pool from the HT assay using the gene expression count matrix from the Cell Ranger output. Data from multiple sequencing runs of the same pool were merged. Sample-level metadata was then added to each Seurat object, which were then saved as .rds files.
Assembly: GRCh38
Supplementary files format and content: .RDS files are Seurat objects containing unnormalized count matrices and metadata for each barcode, including sample assignments and sample-level information, such as age, gender, and AUD classification. For HT RNA-seq objects, gene expression counts are included. For multiome objects, counts for gene expression and chromatin peaks are included.


title: stromal_8


title: BTRC_115_10X _multiome_snRNAseq

description: BTRC_115 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_112_10X _multiome_snRNAseq

description: BTRC_112 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_12_10X _multiome_snRNAseq

description: BTRC_12 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: C4


title: BTRC_116_10X _multiome_snRNAseq

description: BTRC_116 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: MAME

source_name: Mammary gland

value: Mammary gland


title: BTRC_107_10X _multiome_snRNAseq

description: BTRC_107 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: C7


title: BTRC_11_10X _multiome_snRNAseq

description: BTRC_11 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: MC

value: Control


title: BTRC_106_10X _multiome_snRNAseq

description: BTRC_106 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: MAMD


title: MAMF


title: BTRC_103_10X _multiome_snRNAseq

description: BTRC_103 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_102_10X _multiome_snRNAseq

description: BTRC_102 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_99_10X _HT_snRNA-seq

description: 'BTRC_99 ' in Seurat object's 'sample' metadata field


title: MA


title: MB


title: WT + AR-ASO6

first: Andrew

middle: P

last: Lieberman

address: 1150 W Medical Center Dr.

description:
Library name: 13493-CK-22
Column name in rsem.merged.gene_counts.annot.csv: 13493-CK-22

data_processing:
151bp paired-end sequencing (Illumina NovaSeqXPlus, System Suite Version: 1.3.0.39308).
De-multiplexed fastq files were generated using BCL Convert Conversion Software v4.3.13 (Illumina).
QC, trimming, alignment, and quantification were performed via the NF-Core RNAseq pipeline in June 2025. Aligner: star_rsem.
Full software version details for the NF-Core RNAseq pipeline used can be found in this publication's supplemental information.
Assembly: GRCm38, ensembl_version: 102
Supplementary files format and content: csv file has the compiled RSEM counts with gene name annotation.

source_name: Lumbar spinal cord

extract_protocol:
Mice were euthanized at 52 weeks, and lumbar spinal cord was extracted and flash-frozen. Total RNA was then extracted using TRIzol, chloroform, and isopropanol. 500 ng RNA per sample was used for library prep and sequencing.
RNA libraries for RNA-seq were prepared by the University of Michigan Advanced Genomics Core, using the Illumina platform with manufacturer's protocols for polyA-enrichment.

treatment_protocol: Male wild-type C57BL6/J mice were treated between weeks 26 and 52 of age, once weekly, with subcutaneous injection of 25 mg/kg AR-directed (AR-ASO, N = 6 mice) or non-targeting (NT-ASO, N = 5 mice) anti-sense oligonucleotide, dissolved in sterile PBS.

value: Lumbar spinal cord

value: wild-type

value: AR-ASO


title: WT + AR-ASO5

description:
Library name: 13493-CK-20
Column name in rsem.merged.gene_counts.annot.csv: 13493-CK-20


title: BTRC_98_10X _HT_snRNA-seq

description: 'BTRC_98 ' in Seurat object's 'sample' metadata field

extract_protocol:
For libraries containing 'multiome': 184 fresh-frozen post-mortem caudate brain samples were utilized in the assay. The 184 specimens were divided into 23 pools, with 8 in each pool. The donors in each pool were both condition (with or without AUD) and sex balanced. For each pool, around 20 mg tissue from each donor specimen was collected and combined into a sterilized 2 ml Dounce homogenizer. 2 ml chilled NP40 lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 Substitute, 1mM DTT, 1 U/µl RNase inhibitor) was added to the Dounce homogenizer before the tissues were thawed. The tissues were homogenized 15x using pestle A, and 10x using pestle B, and were transferred into a centrifuge tube to incubate for 2 minutes on ice. After that, 2 ml wash buffer containing PBS, 1% BSA and 1 U/µl RNase inhibitor was added and mixed well. The lysed tissue was centrifuged at 500 rcf for 5 minutes at 4°C, then washed twice more with wash buffer and filtered through 70 µm and then 40 µm cell strainer separately. The pellet was resuspended in 2 ml wash buffer and mixed with 3.6 ml Sucrose Cushion Buffer I (nuclei PURE prep isolation kit, Sigma) containing 1 U/µl RNase inhibitor. 2 ml Sucrose Cushion Buffer I with 1 U/µl RNase inhibitor was added into one 15 ml Beckman Coulter centrifuge tube.  After that, the 5.6 ml nuclei suspensions were gently added to the top of Sucrose Cushion Buffer I without mixing, and followed by centrifuging at 13,000 x rpm (30,000 rcf) (Beckman Coulter ultracentrifuge) with rotor SW40Ti for 45 minutes at 4°C. The purified nuclei pellet was washed by centrifuging at 300 rcf for 5 min at 4°C with wash buffer, and the washed nuclei pellets was resuspended in wash buffer to target ~ 1000 nuclei/μl. For libraries containing HT: Nuclei Isolation for Single-nuclei RNA-seq: 163 fresh-frozen post-mortem caudate brain samples (same individuals as in Multiome assay) were grouped into 17 pools, with roughly 10 in each pool. The donors in each pool were both condition (with or without alcohol use disorder) and sex balanced. For each pool, around 20 mg tissue from each donor specimen was collected and combined into a sterilized 2 ml Dounce homogenizer. 2 ml chilled NP40 lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 Substitute, 1mM DTT, 1 U/µl RNase inhibitor) was added to the Dounce homogenizer before the tissues were thawed. The tissues were homogenized 15x using pestle A, and 10x using pestle B, and were transferred into a centrifuge tube to incubate for 2 minutes on ice. After that, 2 ml wash buffer containing PBS, 1% BSA and 1 U/µl RNase inhibitor was added and mixed well. The lysed tissue was centrifuged at 500 rcf for 5 minutes at 4°C, then washed twice more with wash buffer and filtered through 70 µm and then 40 µm cell strainer separately. The pellet was resuspended in 2 ml wash buffer and mixed with 3.6 ml Sucrose Cushion Buffer I (nuclei PURE prep isolation kit, Sigma).  Zero point two (or One fifth) unit per microliter of RNase inhibitor was used in the buffers. This was followed by centrifuging at 13,000 x rpm (30,000 rcf) (Beckman Coulter ultracentrifuge) with rotor SW40Ti for 45 minutes at 4°C. The purified nuclei pellet was washed by centrifuging at 300 rcf for 5 min at 4°C with wash buffer, and the washed nuclei pellets was resuspended in wash buffer to target ~ 1000 nuclei/μl.
For libraries containing 'multiome': 10X Single-cell Multiome Library Preparation and Sequencing: Paired ATAC and gene expression libraries were generated following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide CG000338_RevB (10X Genomics, Inc). In brief, the isolated nuclei from a pool of samples were first incubated in a transposition mix. The single nuclei master mixture containing tagmented single nuclei suspension was loaded into two well of a Next GEM Chip J, along with the single cell multiome gel beads and partition oil. The chip was then loaded to the Chromium X Controller for GEM generation and barcoding. Barcoded transposed DNA and cDNA were amplified after GEMs being released. At each step, the quality of cDNA, ATAC library and cDNA library was examined by Bioanalyzer 2000. The final single indexed ATAC libraries and the dual indexed gene expression libraries were sequenced on an Illumina Novaseq 6000, with index reads of 10 bp + 24 bp, and 100 bp paired-end reads. The libraries were sequenced twice (2 technical replicates for each BioSample). For libraries containing 'HT': 10X HT Single-nuclei RNA-seq Library Preparation and Sequencing: The Chromium Next GEM single cell 3’ HT reagent kits v3.1 (user guide CG000416, 10X Genomics, Inc.) was used for the single-nuclei RNA-seq assay. The single nuclei suspension from a pool of 10 donor tissue samples were loaded into two wells of a Chromium Next GEM chip M to target 60,000 cell recovery per well. The chip was run on a Chromium X (10x Genomics). Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated. cDNA was synthesized and amplified following cell capture and cell lysis, The quality and quantity of cDNA and resulting libraries were examined by Bioanalyzer. The final libraries were sequenced on an Illumina NovaSeq 6000. 100-bp reads including cell barcode and UMI sequences and 100-bp RNA reads were generated. The libraries were sequenced two or three times for each BioSample.
For libraries containing 'multiome', 10X single nucleus multiome assay (RNA+ATAC-seq). For libraries contatining 'HT', single nucleus RNA-seq.


title: WT + NT-ASO5

description:
Library name: 13493-CK-21
Column name in rsem.merged.gene_counts.annot.csv: 13493-CK-21

value: NT-ASO


title: BTRC_97_10X _HT_snRNA-seq

description: 'BTRC_97 ' in Seurat object's 'sample' metadata field


title: WT + NT-ASO4

description:
Library name: 13493-CK-19
Column name in rsem.merged.gene_counts.annot.csv: 13493-CK-19


title: BTRC_96_10X _HT_snRNA-seq

description: 'BTRC_96 ' in Seurat object's 'sample' metadata field


title: BTRC_95_10X _HT_snRNA-seq

description: 'BTRC_95 ' in Seurat object's 'sample' metadata field


title: WT + NT-ASO3

description:
Library name: 13493-CK-17
Column name in rsem.merged.gene_counts.annot.csv: 13493-CK-17


title: WT + AR-ASO4

description:
Library name: 13493-CK-18
Column name in rsem.merged.gene_counts.annot.csv: 13493-CK-18


title: BTRC_92_10X _HT_snRNA-seq

description: 'BTRC_92 ' in Seurat object's 'sample' metadata field


title: WT + AR-ASO3

description:
Library name: 13493-CK-16
Column name in rsem.merged.gene_counts.annot.csv: 13493-CK-16


title: WT + NT-ASO2

description:
Library name: 13493-CK-15
Column name in rsem.merged.gene_counts.annot.csv: 13493-CK-15


title: BTRC_93_10X _HT_snRNA-seq

description: 'BTRC_93 ' in Seurat object's 'sample' metadata field


title: MD901 HDAC3 AZA, rep4

city: Nice

first: Pilar

middle: M

last: Dominguez

state: Provence-Alpes-Côte d'Azur

address: 151 Route de Saint-Antoine

institute: Centre Méditerranéen de Médecine Moléculaire: C3M

description: Library name: Sample 41

data_processing:
QC was performed on FASTQ files using FASTQC (v0.11.9).
FASTQ were trimmed (TrimGalore! v0.6.10) and aligned to the to GRCH38.p14 human genome (NCBI) using Bismark with directional mode enabled (v0.24.0).
Cytosine methylation calls were extracted using the Bismark methylation extractor (v0.24.0).
A complete statistical analysis was performed using methylKit (v1.32.1), including descriptive statistics, data preparation, preliminary statistical analysis, and differential methylation analysis.
Assembly: hg38
Supplementary files format and content: Cov file generated during the methylation extraction step, contains information such as genomic position, methylation percentage, and the number of methylated and unmethylated cytosines

source_name: lymphoma cells

growth_protocol: Cells were passaged every 3-4 days when they were observed to have attained roughly 90% confluency, determined by light microscopy. New frozen vials of cells were thawed every month for use.

extract_protocol:
At day 5, genomic DNA was isolated with the Monarch gDNA purification kit (New England Biolabs)
Bisulfite-conversion

treatment_protocol: Cells were treated daily with 0nM or 200nM 5-AZA from day 0 to day 4; and on day 2 and day 4 they were treated with either 0μM or 10μM HDAC3i

value: lymphoma cells


title: BTRC_9_10X _HT_snRNA-seq

description: 'BTRC_9 ' in Seurat object's 'sample' metadata field


title: WT + AR-ASO2

description:
Library name: 13493-CK-14
Column name in rsem.merged.gene_counts.annot.csv: 13493-CK-14


title: BTRC_89_10X _HT_snRNA-seq

description: 'BTRC_89 ' in Seurat object's 'sample' metadata field


title: BTRC_105_10X _multiome_snRNAseq

description: BTRC_105 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: WT + NT-ASO1

description:
Library name: 13493-CK-13
Column name in rsem.merged.gene_counts.annot.csv: 13493-CK-13


title: MD901 AZA, rep4

description: Library name: Sample 37

value: AZA


title: MD901 HDAC3 AZA, rep1

description: Library name: Sample 38


title: BTRC_87_10X _HT_snRNA-seq

description: 'BTRC_87 ' in Seurat object's 'sample' metadata field

value: caudate nucleus (postmortem brain)


title: MD901 AZA, rep2

description: Library name: Sample 35


title: MD901 AZA, rep3

description: Library name: Sample 36


title: WT + AR-ASO1

description:
Library name: 13493-CK-12
Column name in rsem.merged.gene_counts.annot.csv: 13493-CK-12


title: MD901 AZA, rep1

description: Library name: Sample 34


title: BTRC_86_10X _HT_snRNA-seq

description: 'BTRC_86 ' in Seurat object's 'sample' metadata field


title: CKO_3

description: Library name: CKO_3

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.2.1) and paired-end clean reads were aligned to the mouse reference genome(grcm39) using Hisat2 (v2.2.1). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.42.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate .
Assembly: mouse reference genome(grcm39)
Supplementary files format and content: Processed data files; excel; gene_fpkm

extract_protocol:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina  novaseq x plus. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

treatment_protocol: Nat10flox/flox and Nat10-CKO mice were sacrificed at 10 days old.Total RNA was extracted from heart tissues using Tripure Isolation Reagent (Roche, Mannheim, Germany). Three independent biological replicates for each group were used for RNA-seq.

value: heart


title: MD901 HDAC3i, rep3

description: Library name: Sample 32


title: MD901 HDAC3i, rep4

description: Library name: Sample 33


title: BTRC_85_10X _HT_snRNA-seq

description: 'BTRC_85 ' in Seurat object's 'sample' metadata field


title: CKO_2

description: Library name: CKO_2


title: BTRC_83_10X _HT_snRNA-seq

description: 'BTRC_83 ' in Seurat object's 'sample' metadata field


title: MD901 HDAC3 AZA, rep2

description: Library name: Sample 39


title: MD901 vehicle, rep3

description: Library name: Sample 28

value: vehicle


title: BTRC_79_10X _HT_snRNA-seq

description: 'BTRC_79 ' in Seurat object's 'sample' metadata field


title: MD901 HDAC3i, rep2

description: Library name: Sample 31


title: ff_3

description: Library name: ff_3


title: BTRC_76_10X _HT_snRNA-seq

description: 'BTRC_76 ' in Seurat object's 'sample' metadata field


title: MD901 vehicle, rep2

description: Library name: Sample 27


title: MD901 HDAC3 AZA, rep3

description: Library name: Sample 40


title: MD901 vehicle, rep1

description: Library name: Sample 26


title: MD901 vehicle, rep4

description: Library name: Sample 29


title: MD901 HDAC3i, rep1

description: Library name: Sample 30


title: CKO_1

description: Library name: CKO_1


title: BTRC_73_10X _HT_snRNA-seq

description: 'BTRC_73 ' in Seurat object's 'sample' metadata field


title: ff_2

description: Library name: ff_2


title: INPUT

description: Library name: Sample 25

data_processing:
Bcl2fastq (v2.17.1.14) was used to demultiplex sequencing files and resulting Fastq output was quality checked using FASTQC (v0.11.9).
Sequencing reads were trimmed (Fastp) and mapped to GRCH38.p14 human genome (NCBI) using Bowtie2 with local alignment mode enabled (v2.5.4).
SAM files were converted to BAM format and sorted by genomic coordinates using Samtools (v1.21). Prior to the peak calling step, duplicates were removed with Sambamba (v0.6.6), and multi-mapped or unaligned reads were filtered out using Samtools (v1.21), retaining only uniquely aligned reads. Additionally, genomic artifact regions listed in the ENCODE blacklist were excluded using Bedtools (v2.27.1).
Deeptools bamCoverage function was used for BAM to BigWig file conversion using the following settings (--normalizeUsing CPM --smooth length 150 -bs 50 -e 150).
BAM file peak Calling was performed using MACS2 (v2.2.7.1)  with the following settings (-f BAM --qvalue 0.05 -g hs -c INPUT)
The peak annotation has been performed using ChIPseeker (v4.4) and the statistical analysis was carried out with DiffBind (v3.6.10).
Assembly: hg38
Supplementary files format and content: bigWig generated with the peak Calling step, contains information such as postion, score, Signal Value, qValue

extract_protocol:
At day 5 cells were fixed with 1% formaldehyde for 10min and sonicated using the S220 Focused-ultrasonicator (Covaris) for 15min. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated after immunoprecipitation with the H3K27ac antibody (Abcam Cat# ab4729) using Protein A and Protein G Dyna beads (Invitrogen). Samples were washed prior to overnight reverse crosslinking.Chromatin was isolated with the ChIP DNA Clean and concentrator (Zymo Research) .
Libraries were prepared using the DNA Library Prep NEB (New England Biolabs)

value: INPUT


title: ff_1

description: Library name: ff_1


title: BTRC_72_10X _HT_snRNA-seq

description: 'BTRC_72 ' in Seurat object's 'sample' metadata field


title: MD901 HDAC3 AZA_rep1

description: Library name: Sample 22

value: H3K27ac antibody


title: MD901 HDAC3 AZA_rep3

description: Library name: Sample 24


title: OXA_d16

city: New York

first: Raman

last: Gill

state: NY

address: 1428 Madison Ave

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

description: Library name: OXA16

data_processing:
Samples were sequenced and demultiplexed by Novogene (Novogene, Sacramento, CA) to produce raw fastq files for each sample. Fastq files were mapped to the mm10 mouse genome using the Cellranger (v.8.0) pipeline from 10X Genomics. UMI counts for each gene were quantified per cell to generate feature-barcode counts matrices.
Assembly: mm10
Supplementary files format and content: processed files are filtered cellranger matrix, feature, and barcode output files. Default filtering parameters in cellranger were used

extract_protocol:
ear+neck skin samples were pooled for n=3 mice per library and immediately digested using the Multi Tissue Dissociation Kit 1 (Miltenyi). To enhance the detection rate of fibroblasts, Collagenase Ia (1 mg/mL, Sigma) was used in place of Enzyme D. Digestion was carried out at 37°C for 1 hour with gentle agitation using the GentleMACS Dissociator Program H. The digested cell suspensions were passed sequentially through 100 μm and 35 μm cell strainers to remove undigested tissue fragments. To ensure a high cell viability, the suspension was further processed using the MojoSort™ Mouse Dead Cell Removal Kit (BioLegend) twice. After confirming a cell viability of ≥80%, the cells were resuspended in PBS and proceeded to library preparation according to the protocol provided by 10x Genomics (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index))
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)

treatment_protocol: Neck skin was shaved for each mouse 1 day prior to treatment. For MC903, 1nmol calcipotriol (Tocris Bioscience) dissolved in ethanol, was used to induce AD-like skin in mice. 100uL was applied to the ear and neck skin of the mouse every day for 9 days. For Oxazolone, Oxazolone (Sigma) was used as a hapten. Mice were sensitized with 100 µl of 3% (wt/vol) oxazolone in acetone–mineral oil  4:1 (v/v) on their shaved back and ear skin. Seven days after sensitization, 100 µl of 1.0% (wt/vol) oxazolone was applied every other day. Treated neck/ear skin was harvested at day 10 and day16

value: skin

tag: site

value: neck + ear

value: Oxazolone d16

tag: age

value: 6-8 weeks

tag: Sex

value: female

tag: host strain


title: MD901 HDAC3 AZA_rep2

description: Library name: Sample 23


title: MD901 AZA_rep2

description: Library name: Sample 20


title: MC903_d9

description: Library name: MC903