title: 2nd non-stressed wild-type mouse

description:
Library name: Wt Control 2
column N in the processed data file


title: 2nd stressed 5xFAD mouse

status: Public on Jun 04 2026

type: SRA

city: Jerusalem

first: Tamir

last: Ben-Hur

address: Hadassah Hospital

department: Department of Neurology

country: Israel

institute: Hadassah – Hebrew University Medical Center

description:
Library name: 5xFAD CMS 2
column W in the processed data file

library_source: transcriptomic

data_processing:
Raw reads in FASTQ format were generated using bcl2fastq v2.20.0.422, with default parameters. Adapter sequences, polyA tails, and low-quality regions were removed using cutadapt v3.5, keeping reads of length 15 and above after trimming. Subsequently, low-quality reads were filtered out with the fastq_quality_filter tool from the FASTX package, v0.0.14, applying a quality threshold of 20 for at least 90% of the read positions. Processed reads were aligned to the mouse genome with STAR(35), using genome version GRCm39 with annotations from Ensembl release 106. Raw counts per gene per sample were obtained with htseq-count, using the parameter --stranded=reverse.
Assembly: GRCm39
Supplementary files format and content: DESeq2_final.xlsx- normalized counts, Log 2fold changes, p values and adjusted p values for differential expression

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
ice were terminally anesthetized and decapitated, and the brains were excised into Earl’s based salt solution. The brains were dissociated to a single-cell suspension using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, 130–092–628) according to the manufacturer’s protocol. For myelin removal, Percoll (Cytiva) protocol was performed. CNS myeloid cells were isolated from myelin-free single-cell suspension using CD11b-conjugated beads (Miltenyi Biotec, 130–093-634) according to the manufacturer’s protocol followed by depletion with MS columns (Miltenyi Biotec, 130-042-201). The procedure resulted in > 90% CD11b + cells.RNA was produced immediately from isolated brain microglia of 5XFAD and wt mice using RNeasy Mini Kit 50 (Qiagen) according to the manufacturer's instructions. High quality RNA (RNA integrity number [RIN] > 9.3) was extracted from all groups.
Libraries were prepared by the Center for Genomic Technologies at the Hebrew University of Jerusalem, using the KAPA Stranded mRNA-Seq Kit (KR0960, Roche) with poly-A selection, according to the manufacturer's protocol. Single-end sequencing was conducted on an Illumina NextSeq 500 machine using 76 cycles. Sequencing depth ranged between 32 and 40 million reads, with an average of 36 million reads per sample.

treatment_protocol: stressed and non-stressed wt (C57Bl) and 5xFAD mice

tag: tissue

value: Brain

tag: cell line

value: CD11b+ cells

tag: cell type

value: CNS myeloid cell

tag: genotype

tag: strain

tag: treatment

value: Chronic Mild Stress (CMS)


title: B.sub_CBS/CSE/TST3

status: Public on Jun 06 2026

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

description: Library name: MCC_3

data_processing:
read trimming with Trimmomatic
read alignment with STAR
read couning with featureCounts
Assembly: Drosophila melanogaster BDGP6.54
Supplementary files format and content: Tab-separated files, with 1st column – Flybase gene identifier, and 2nd – number of reads spanning into exonic regions of genome

organism: Drosophila melanogaster

source_name: whole body

growth_protocol: D.melanogaster flies were maintained on standard yeast-agar medium, at 24 Celsius temperature, with 12/12 light/dark incubator.

extract_protocol:
Total RNA was isolated using RNAzol RT reagent (Molecular Research Center, USA). Briefly, 10–20 flies were homogenized in 200 μL of RNAzol reagent, after which 80 μL of dH₂O was added, and the mixture was incubated on ice for 10 minutes. The homogenate was then centrifuged at 15,000×g for 10 minutes at 4°C. The resulting supernatant was collected and transferred to a new sterile 1.5-mL tube. An additional purification step was performed by adding 1 μL of 4-bromoanisole (MRC, BN 191). The mixture was incubated at room temperature for 3 minutes and centrifuged again at 15,000×g for 10 minutes at +4°C. The supernatant was transferred to a new sterile tube, and 200 μL of isopropyl alcohol was added to precipitate the RNA. The mixture was incubated on ice for 30 min and then centrifuged at 20,000×g for 20 min at +4°C. The RNA pellet was washed twice with chilled 75% ethanol and dissolved in RNase-free water.
RNA-seq libraries were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (cat# NR605-01, Vazyme Biotech, China) according to the manufacturer’s protocol. Sequencing was performed on an Illumina NextSeq 500 platform

treatment_protocol: 5 day old flies were infected with bacteria (Bacillus subtilis) by needle pricking method. Gram-positive bacterium Bacillus Subtilis with a (DAP)-type peptidoglycan  at a concentration of 5 OD was used.

value: whole body

value: CBS/CSE/TST1 deletion

value: B.subtilis inoculated


title: UPS09

city: Zurich

first: Lara

last: Planas-Paz

address: Schmelzbergstrasse 12

department: Pathology and Molecular Pathology

country: Switzerland

institute: University Hospital Zurich

description: Library name: LR2022_165

data_processing:
Dragen RNA
Assembly: Homo_sapiens_assembly38.fasta.gz, hg38.ncbiRefSeq.gtf.gz
Supplementary files format and content: tab-delimited text file includes fpkm values for each sample

organism: Homo sapiens

source_name: undifferentiated pleomorphic sarcoma

growth_protocol: Cells were maintained in advanced Dulbecco’s modified Eagle medium (DMEM; Gibco, 12634028) supplemented with 10% heat-inactivated horse serum (Gibco, 260500888), 1x Glutamax (Gibco 35050038) and 0.2 % Primocin (InvivoGen, ant-pm-2). For cell expansion, the previous media was mixed 1:1 with DMEM containing 1 mM N-acetylcyteine (Sigma-Aldrich, A9165), 50 ng/ml recombinant human epidermal growth factor (Sigma-Aldrich, E9644), 100 ng/ml recombinant human fibroblast growth factor 10 (PeproTech, 100-26), 10 µM Y-27632 (Sellekchem, S1049), 5 µM A-83-01 (Sigma-Aldrich, SLM0788), 10 mM nicotinamide (Sigma-Aldrich, N0636), 10 % R-Spondin conditioned media (self-produced), B27 supplement (Gibco, 17504001), 10 mM HEPES (Gibco, 15630-080), 36 ng/ml hydrocortisone (Sigma-Aldrich, H6909) and 500 ng/ml epinephrine (Sigma-Aldrich, E4250). All cells were passaged when subconfluent  conditions were reached in cell culture‐treated flasks, incubated at 37°C in a humidified atmosphere with 5% CO2, and routinely tested for Mycoplasma.

extract_protocol:
RNA from fresh frozen sarcoma patient samples or patient-derived cells was extracted using the Maxwell RSC simplyRNA Tissue kit (Promega AS1340). The extracted RNA was quantified with a Nanodrop (ThermoFisher Scientific) and the High Sensitivity RNA ScreenTape Assay for TapeStation systems (Agilent 5067).
RNA sequencing libraries were prepared using the Illumina Stranded mRNA sample preparation protocol

value: undifferentiated pleomorphic sarcoma


title: 2nd stressed wild- type mouse

description:
Library name: Wt CMS 2
column T in the processed data file

value: wildtype


title: RNAseq of Model6

city: Hefei

first: Jingjing

last: Hu

address: NO.117 Meishan Road

country: China

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

description: Library name: Model6

data_processing:
Clean reads were aligned to the mouse reference genome (GRCm39) using HISAT2, and gene-level counts were obtained with featureCounts. Differential expression analysis was performed with DESeq2, defining differentially expressed genes as those with Benjamini–Hochberg–adjusted p < 0.05 and absolute log2(fold change) ≥ 0.585. Functional enrichment of differentially expressed genes for Gene Ontology and KEGG pathways was carried out with the clusterProfiler package. Gene set enrichment analysis (GSEA) using MSigDB c2 (curated) and c5 (GO) gene sets with 1,000 permutations was also performed; pathways with |normalised enrichment score (NES)| > 1.5 and FDR q < 0.25 were regarded as significantly enriched, whereas those with 0.25 ≤ FDR q < 0.40 were considered to show a suggestive trend and are reported as exploratory findings.
Assembly: GRCm39
Supplementary files format and content: txt file including Reads count for each sample

source_name: kidney

extract_protocol:
Total RNA was isolated from kidney tissue with TRIzol reagent (Invitrogen, USA) and treated with DNase I; RNA integrity was verified by Bioanalyzer 2100.
Libraries were prepared using the VAHTS mRNA-seq V3 kit (Vazyme, China) and sequenced as 150-bp paired-end reads on an Illumina NovaSeq 6000 platform.

value: kidney


title: 2nd non-stressed 5xFAD mouse

description:
Library name: 5xFAD Control 2
column Q in the processed data file

value: Control


title: UPS08

description: Library name: LR2022_164


title: 1st stressed 5xFAD mouse

description:
Library name: 5xFAD CMS 1
column V in the processed data file


title: RNAseq of Model5

description: Library name: Model5


title: UPS07

description: Library name: LR2022_163


title: 1st stressed wild- type mouse

description:
Library name: Wt CMS 1
column S in the processed data file


title: RNAseq of Model4

description: Library name: Model4


title: 1st non- stressed wild- type mouse

description:
Library name: Wt Control 1
column M in the processed data file


title: UPS06

description: Library name: LR2022_162


title: RNAseq of Model3

description: Library name: Model3


title: shCTRL tumor samples

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

description:
Library name: 1271_2
10x Chromium platform (10x Genomics)

library_source: transcriptomic single cell

data_processing:
Raw reads from FASTQ files were demultiplexed with the mkfastq application (Cell Ranger v.4.0.0). Libraries were mapped to the mouse genome using the cellranger count application and the mm10-2020-A reference packages (Cell Ranger v.4.0.0). The resulting count matrices were imported into the R environment (v.4.3.3.) and analyzed with the Seurat package (v.4.4.0). Each sample was first processed individually following the standard Seurat pipeline.
Assembly: Mouse mm10
Supplementary files format and content: raw and processed files of RNA extracted from single cells
Supplementary files format and content: tab-separated values files and matrix files

molecule: total RNA

source_name: 6- to 8-week BALB/c mice

extract_protocol:
Mice were euthanized when primary tumors reached similar sizes in the cohorts analyzed (14 days post-implantation). Tumor were then excised, minced in RPMI and enzymatically digested in RPMI supplemented with 0.25 mg/ml collagenase (Merck C7657) and 50 U DNase in gentleMACS™ Dissociators with heaters, following the manufacturer’s protocol. Cell suspensions were then filtered through a 70 µl strainer, treated with erythrocyte lysis buffer (ACK, Lonza) for 10 min on ice and then resuspended in RPMI for sorting.
Cells were prepared for single-cell RNA sequencing using the 10x Chromium platform (10x Genomics) following the manufacturer's protocol for cell capture, barcoding, and cDNA library preparation.

treatment_protocol: 4T1 cells expressing shCTRL or shPml were resuspended in 50 μl of PBS and ectopically injected in the mammary fat pad of 6- to 8-week BALB/c mice

value: 6- to 8-week BALB/c mice

value: 4T1 cells expressing shCTRL were  ectopically injected in the mammary fat pad


title: Blood_4

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

country: USA

institute: BU Single Cell Sequencing Core

data_processing:
BaseCalls performed using Illumina
Demultiplexing performed using Cell Ranger v3.1.0 with default settings
Reads were aligned to mm10 reference genome using Cell Ranger v3.1.0 with --expect-cells=5000
Assembly: mm10
Supplementary files format and content: matrix table with raw gene counts for all genes and samples

source_name: Peripheral blood neutrophil

growth_protocol: Male, 8 week old C57BL/6J mice were obtained from Jackson Laboratories at 6-7 weeks of age. Prior to infection, they were housed at the Boston University animal facility and provided with an ad libitum supply of standard chow. Mice were infected at 8 weeks of age. All animal protocols were approved by the BU Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
Cell concentration and viability of mouse samples were measured using the Countess II instrument and ranged from 8 – 9 x 105 cells/mL with ~90% viability (Thermofisher Scientific, USA).  Cell samples were input into 10x Genomics Single Cell 3′ v3 workflow and processed according to the manufacturer’s instructions for a targeted recovery of 5000 cells (10X Genomics, USA).  Resulting cDNA libraries were sequenced on an Illumina NextSeq 500 instrument with 1.8pM input and 1% PhiX control library spike-in (Illumina, USA).
scRNA-seq libraries were generated in BU DOM Single Cell sequencing core facility and sequenced by BU Microarray and Sequencing Resource Core Facility according to 10x Genomics protocol

treatment_protocol: After anesthetization with ketamine and xylazine, the left lung lobes of C57Bl/6J mice were intratracheally infected with 1.0 x 10^6 CFU S. Pneumoniae. After 24 hours of infection, mice were euthanized and BALF and peripheral blood was collected. Red cells were lysed using BD cell lysis buffer and neutrophils were enriched using an EasySep magnetic bead negative selection kit.

value: 24h S. pneumoniae

value: neutrophil

tag: Sex

value: Male

tag: location

value: peripheral blood


title: RNAseq of Model2

description: Library name: Model2


title: Blood_1


title: UPS04

description: Library name: LR2022_157


title: BAL_4

source_name: BALF neutrophil

value: alveolus


title: RNAseq of Model1

description: Library name: Model1


title: UPS03

description: Library name: LR2022_156


title: pancreatic CTC sample 531, GKB202-treated

city: Taichung

first: Ruey-Hwang

last: Chou

address: No. 350, Section 1, Jingmao Road, Xinpeng Village, Beitun District

department: The Ph.D. Program of Biotechnology and Biomedical Industry Associate Professor

country: Taiwan

institute: China medicine univercity

description:
Library name: G531_01
Patient-derived pancreatic CTC sample 531 treated with 2 ug/mL GKB202 for 3 days. Corresponding matrix column: G531_01.

data_processing:
Sequencing data in FASTQ format were generated using Welgene Biotech's pipeline based on Illumina bcl2fastq v2.20.
Adaptor clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach.
Trimmed reads were aligned to the reference genome using HISAT2.
Gene-level expression values were quantified and summarized as read counts and TPM values.
Assembly: Trimmed reads were aligned to the Homo sapiens reference genome assembly GRCh38.p14 using HISAT2.
Supplementary files format and content: Tab-delimited text file containing gene-level TPM expression values for all samples.

source_name: peripheral blood

growth_protocol: Peripheral blood samples were collected from patients with non-small cell lung cancer (NSCLC) or pancreatic cancer in EDTA-anticoagulated tubes. Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Paque Plus density gradient centrifugation, and circulating tumor cells (CTCs) were enriched using the RosetteSep CTC Enrichment Kit according to the manufacturer's instructions. The enriched CTCs were resuspended in high-glucose DMEM supplemented with EGF (20 ng/mL), bFGF (20 ng/mL), and B27 (1x), and cultured on binary colloidal crystal matrices for short-term expansion. The culture medium was changed every four days.

extract_protocol:
Total RNA was extracted from patient-derived CTC samples using TRIzol reagent according to the manufacturer's instructions. RNA concentration and purity were assessed using a NanoDrop ND-1000 spectrophotometer. RNA integrity was assessed using an Agilent 2100 Bioanalyzer with the RNA 6000 LabChip kit.
RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Cat. No. 20020598) according to Illumina's official protocol. Fragment size selection was performed using AMPure XP magnetic beads.

treatment_protocol: CTCs isolated from NSCLC and pancreatic cancer patients were treated with either vehicle control or 2 ug/mL GKB202 for 3 days before RNA extraction.

value: circulating tumor cells

value: 2 ug/mL GKB202 for 3 days

tag: batch

value: pancreatic CTC


title: pancreatic CTC sample 531, vehicle control

description:
Library name: D531_01
Patient-derived pancreatic CTC sample 531 treated with vehicle control for 3 days. Corresponding matrix column: D531_01.

value: vehicle control


title: pancreatic CTC sample 414, GKB202-treated

description:
Library name: G414_01
Patient-derived pancreatic CTC sample 414 treated with 2 ug/mL GKB202 for 3 days. Corresponding matrix column: G414_01.


title: RNAseq of Ctrl5

description: Library name: Ctrl5


title: pancreatic CTC sample 414, vehicle control

description:
Library name: D414_01
Patient-derived pancreatic CTC sample 414 treated with vehicle control for 3 days. Corresponding matrix column: D414_01.


title: UPS01

description: Library name: LR2022_56


title: pancreatic CTC sample 318, GKB202-treated

description:
Library name: G318_01
Patient-derived pancreatic CTC sample 318 treated with 2 ug/mL GKB202 for 3 days. Corresponding matrix column: G318_01.


title: RNAseq of Ctrl4

description: Library name: Ctrl4


title: pancreatic CTC sample 318, vehicle control

description:
Library name: D318_01
Patient-derived pancreatic CTC sample 318 treated with vehicle control for 3 days. Corresponding matrix column: D318_01.


title: SS12

description: Library name: LR2022_196

source_name: synovial sarcoma

value: synovial sarcoma


title: Lung cancer CTC sample R24082001, GKB202-treated

description:
Library name: R24082001_Test
Patient-derived lung cancer CTC sample R24082001 treated with 2 ug/mL GKB202 for 3 days. Corresponding matrix column: R24082001_Test.

value: lung CTC


title: RNAseq of Ctrl3

description: Library name: Ctrl3


title: Lung cancer CTC sample R24082001, vehicle control

description:
Library name: R24082001_Ctrl
Patient-derived lung cancer CTC sample R24082001 treated with vehicle control for 3 days. Corresponding matrix column: R24082001_Ctrl.


title: SS11

description: Library name: LR2022_193


title: Lung cancer CTC sample R24091001, GKB202-treated

description:
Library name: R24091001_Test
Patient-derived lung cancer CTC sample R24091001 treated with 2 ug/mL GKB202 for 3 days. Corresponding matrix column: R24091001_Test.


title: Lung cancer CTC sample R24091001, vehicle control

description:
Library name: R24091001_Ctrl
Patient-derived lung cancer CTC sample R24091001 treated with vehicle control for 3 days. Corresponding matrix column: R24091001_Ctrl.


title: SS10

description: Library name: LR2022_192


title: male, perigonadal white adipose tissue, Tacr2null, high fat diet chronic, biological replicate 4

city: La Jolla

first: Supriya

last: Srinivasan

state: CA

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

description: Library name: Sample 96

data_processing:
Raw sequencing reads were quality-assessed using FastQC, and adapters were removed using Cutadapt.
Trimmed reads were aligned to the mouse reference genome (ENSEMBL GRCm38) using STAR aligner version 2.6.1d.
The distribution of mapped reads across genomic features was analyzed with RSeQC v3.0.1.
Differential gene expression analysis was performed using DESeq2 (v2.11.40.8) implemented in R (v4.2.2) via the Galaxy platform.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: perigonadal white adipose tissue

extract_protocol:
NOTE for intestinal intestinal epithelium: the small intestine was cut longitudanally, and the intestinal epithelium was scraped using microscope slides from the middle of the length of the entire intestine (roughly 16-20 cm in a typical 34 cm small intestine). The tissues (isolated intestinal epithelium or perigonadal white adipose tissues) were processed via commercial RNeasy RNA purification kits using manufacturers protocols.
Total RNA samples were prepared into RNA-Seq libraries using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommended protocol. Briefly, for each sample, 200 ng total RNA was polyA selected, and converted to double-stranded cDNA followed by fragmentation and ligation of sequencing adapters. The libraries were then PCR amplified 12 cycles using barcoded PCR primers, purified, and size selected using AMPure XP Beads before loading onto an Illumina NextSeq 2000 for 100 base single-read sequencing.

treatment_protocol: Mice (8-12 weeks) were maintained on a low fat diet. Test mice were then given an high fat diet for 1 or 12 weeks. The intestines and perigonadal tissues were collected and flash frozen.

value: perigonadal white adipose tissue

value: male

value: high fat diet 12 weeks


title: RNAseq of Ctrl2

description: Library name: Ctrl2

value: kidney


title: BAL_1


title: RNAseq of Ctrl1

description: Library name: Ctrl1


title: male, perigonadal white adipose tissue, Tacr2null, high fat diet chronic, biological replicate 3

description: Library name: Sample 95


title: SS09

description: Library name: LR2022_191


title: UPS02

description: Library name: LR2022_63

value: undifferentiated pleomorphic sarcoma


title: RNAseq of Ctrl6

description: Library name: Ctrl6


title: male, perigonadal white adipose tissue, Tacr2null, high fat diet chronic, biological replicate 2

description: Library name: Sample 94


title: TR1_400nM_BLU667

city: Aurora

first: Lynn

last: Heasley

state: CO

department: Craniofacial Biology

institute: University of Colorado, Anschutz Medical Campus

description: Library name: Sample 14

data_processing:
Fastq files were quality checked with FastQC
illumina adapters trimmed with bbduk, and mapped to the mouse mm10 genome with STAR aligner
Counts were generated by STAR’s internal counter and reads were normalized to counts per million (CPM) using the edgeR R package
Assembly: Mus musculus mm10
Supplementary files format and content: excel files include CPM values for each sample.
Supplementary files format and content: matrix table excel file (.xls) includes CPM values for all samples

growth_protocol: Cells were cultured and maintained at 37oC in RPMI-1640 media (Corning) with 5% fetal bovine serum (FBS; Gibco) and 1% penicillin/streptomycin (Corning) in a humidified incubator with 5% CO2

extract_protocol:
Total RNA was isolated using Quick-RNA MiniPrep Kit (Zymo Research), including the Dnase I treatment step
Libraries were constructed using an Illumina TruSEQ stranded mRNA Sample Prep Kit (Cat# RS-122-2101). Total RNA was combined with RNA purification beads to bind PolyA RNA to oligodT magnetic beads. mRNA was eluted and converted to double stranded DNA. A-tailing, adapter ligation, and PCR amplification using 15 cycles was performed to complete the library construction.

treatment_protocol:
(samples 1-8) Murine Trim24-Ret cell line cultured in 10 cm dishes in full growth media were treated for 1,2,3,5 days with 0.1% DMSO or 100 nM selpercatinib
(samples 9-14) Murine Trim24-Ret cell line cultured in 10 cm dishes in full growth medium containing 0.1% DMSO as a passage control or 30 nM selpercatinib or pralsetinib. Over the course of ~60 days, the TKI concentrations were increased until cultures that readily grew in the presence of 400 to 500 nM TKI were obtained

value: lung adenocarcinoma

value: Trim24-RET fusion

value: 400nM pralsetinib

value: resistant


title: male, perigonadal white adipose tissue, Tacr2null, high fat diet chronic, biological replicate 1

description: Library name: Sample 93


title: TR1_200nM_BLU667

description: Library name: Sample 13

value: 200nM pralsetinib


title: SS08

description: Library name: LR2022_190


title: male, perigonadal white adipose tissue, Tacr2null, high fat diet, acute, biological replicate 4

description: Library name: Sample 92

value: high fat diet one week


title: RNAseq_dNifA_NWH036_rep2

city: Bloomington

first: James

last: McKinlay

address: 1001 E 3rd Street

institute: Indiana University

description: Library name: RNAseq_dNifA_NWH036_rep2

data_processing:
See PMID: 38452196. Raw reads were preprocessed using Trim Galore v.0.6.6 (https://github.com/FelixKrueger/TrimGalore#readme), a Perl script employing Cutadapt v.1.18 [https://doi.org/10.14806/ej.17.1.200], and FastQC v.0.11.5 [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/] for trimming of adapter sequences, and removal of low-quality base calls, and quality control, respectively. Processed reads were aligned to the to the V. natriegens ATCC 14048 genome (GCA_001456255.1) by HISAT2 v.2.1.0 with options −p, −dta, −no-spliced-alignment, and —rna-strandness RF [PMID: 31375807]. Samtools v.1.15.1 was used to convert the sequence alignment and map (SAM) files output from HISAT2 into binary alignment and map (BAM) format. Aligned reads in BAM format were annotated and the transcript abundance was estimated using StringTie v.1.3.3b [PMID: 27560171].
Assembly: V. natriegens ATCC 14048 genome (NCBI RefSeq: GCA_001456255.1)
Supplementary files format and content: Files ending with .csv files have comma-separated values of RNA-seq (FPKM) results.

organism: Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759

source_name: Vibrio natriegens ATCC 14048

growth_protocol: Non-growing cell suspensions were incubated in nitrogen-free VMDC175 (argon headspace) for 2h to induce nitrogen starvation and nitrogenase expression. Cell suspensions were incubated at 30C, laid horizontally with shaking at 150 rpm.

extract_protocol:
RNA was extracted with TRIzolTM (Thermo Fisher) /chloroform as described [PMID: 21325136]. Samples were treated with 4 U Turbo DNase (Invitrogen) in 100 µL at 37oC for 1 h, then purified using a QIAGEN RNeasy MinElute Cleanup Kit.
RNA was quantified using an Agilent 2200 TapeStation at the Indiana University Center for Genomics and Bioinformatics, then submitted to SeqCoast Genomics where rRNA was depleted and libraries prepared using the Illumina Stranded Total RNA Prep Ligation Kit with Ribo-Zero Plus Microbiome.

treatment_protocol: Cell suspensions were chilled on ice and pelleted by centrifugation at 4C. Supernatants were discarded and pellets frozen using dry ice before storing at -80C.

value: Vibrio natriegens ATCC 14048

value: bacterial cell

value: delta-nifA, delta-dns::KmR

value: Non-growing cell suspensions incubated in nitrogen-free VMDC175 (argon headspace) for 2h to induce nitrogen starvation and nitrogenase expression


title: SS07

description: Library name: LR2022_189

value: synovial sarcoma


title: RNAseq_dNifA_NWH036_rep1

description: Library name: RNAseq_dNifA_NWH036_rep1


title: TR1_500nM_LOXO292_2

description: Library name: Sample 12

value: 500nM Selpercatinib


title: RNAseq_dNtrBC_NWH014_rep2

description: Library name: RNAseq_dNtrBC_NWH014_rep2

value: delta-ntrBC, delta-dns::KmR


title: TR1_500nM_LOXO292_1

description: Library name: Sample 11


title: SS06

description: Library name: LR2022_186


title: male, perigonadal white adipose tissue, Tacr2null, high fat diet, acute, biological replicate 3

description: Library name: Sample 91

value: perigonadal white adipose tissue

value: male


title: male, perigonadal white adipose tissue, Tacr2null, high fat diet, acute, biological replicate 2

description: Library name: Sample 90


title: TR1_DMSO_2

description: Library name: Sample 10

value: DMSO

value: parental


title: RNAseq_dNtrBC_NWH014_rep1

description: Library name: RNAseq_dNtrBC_NWH014_rep1


title: SS04

description: Library name: LR2022_181


title: male, perigonadal white adipose tissue, Tacr2null, high fat diet, acute, biological replicate 1

description: Library name: Sample 89


title: TR1_DMSO_1

description: Library name: Sample 9

value: lung adenocarcinoma


title: MPNST08

description: Library name: LR2022_174

source_name: malignant peripheral nerve sheath tumor

value: malignant peripheral nerve sheath tumor


title: MPNST10

description: Library name: LR2022_177


title: MPNST06

description: Library name: LR2022_172


title: male, perigonadal white adipose tissue, Tacr2null, low fat diet, biological replicate 4

description: Library name: Sample 88

value: low fat diet


title: SS03

description: Library name: LR2022_180


title: RNAseq_WT_NWH003_rep1

description: Library name: RNAseq_WT_NWH003_rep1


title: TR1_LOXO_5day

description: Library name: Sample 8

value: Trim24-RET fusion

value: 100nM Selpercatinib


title: MPNST05

description: Library name: LR2022_171


title: male, perigonadal white adipose tissue, Tacr2null, low fat diet, biological replicate 3

description: Library name: Sample 87


title: RNA-seq of HCASMC: DDIT4 overexpression, replicate 1

city: Guangzhou

first: Fengfeng

last: Li

address: 253 Gongye Dadao Zhong, Haizhu District

department: Department of Cardiovascular Medicine

institute: ZhuJiang Hospital, Southern Medical University

description: Library name: sample 3

data_processing:
Raw Data Filtering: Use SOAPnuke to remove adapter-contaminated, low-quality (≥20% Q≤15 bases), and high-N-content (≥5%) reads, generating clean FASTQ data.
Genome Alignment: Align clean reads to the reference genome using HISAT2 with sensitive mode and strand-specific parameters
Transcript Assembly & Quantification: Assemble transcripts and quantify gene expression (FPKM) via RSEM after mapping clean reads to the reference gene set with Bowtie2.
Differential Expression Analysis: Identify differentially expressed genes using DESeq2 (or DEGseq/PoissonDis) with a threshold of Q value ≤0.05 or FDR ≤0.001.
Functional Enrichment: Perform GO and KEGG enrichment analysis on differentially expressed genes using Phyper with hypergeometric testing (Q value ≤0.05).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: Homo sapiens coronary artery smooth muscle cell (HCASMC)

growth_protocol: Human coronary artery smooth muscle cells (HCASMCs, ATCC PCS-100-021) were cultured in Vascular Cell Basal Medium (ATCC PCS-100-030) supplemented with Vascular Smooth Muscle Cell Growth Kit (ATCC PCS-100-042) at 37°C in a humidified 5% CO₂ atmosphere.

extract_protocol:
Total RNA was isolated from HCASMCs using a combined TRIzol-RNeasy Micro Kit method. Cells were lysed in TRIzol reagent (Invitrogen, 15596026) and stored at -80°C until processing. Thawed lysates were mixed with 0.2 volumes of chloroform/iso-amyl alcohol (24:1), followed by centrifugation at 12,000×g for 10 min. The aqueous phase was collected and combined with an equal volume of 75% ethanol. This mixture was then applied to an RNeasy MinElute spin column (QIAGEN, Germany). Subsequent steps included membrane washing with RW1 and RPE buffers, and on-column DNase I digestion using Buffer RDD for 15 min at room temperature to remove genomic DNA contamination. Purified RNA was eluted in 20 µL RNase-free water and assessed for integrity and concentration using Fragment Analyzer, Agilent 2100 Bioanalyzer, or Qseq-400 systems with fluorescent dye-based quantification.
RNA libraries were prepared from total RNA using the Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China) according to the manufacturer's instructions. mRNA was enriched through polyA selection and subsequently fragmented. First-strand cDNA synthesis was carried out using random hexamer primers, followed by second-strand synthesis to generate double-stranded cDNA. The cDNA then underwent end repair, A-tailing, and adapter ligation. Finally, the libraries were amplified by PCR, assessed for quality, and sequenced on the BGISEQ-500 platform.

treatment_protocol: HCASMCs were infected with recombinant adenoviruses at a multiplicity of infection (MOI) of 100 for 48 hours to achieve genetic manipulation. The specific viruses used included:Empty adenoviral vector (serving as negative control); Adenovirus encoding full-length human DDIT4 (for overexpression); Adenovirus encoding a non-targeting shRNA (for knockdown control); Adenovirus encoding a DDIT4-targeting shRNA (for knockdown).


city: Kanazawa

first: Tomohiro

last: Iba

state: Ishikawa

address: 13-1, Takara-machi

country: Japan

institute: Kanazawa University School of Medicine

description:
Library name: Vascular endothelial cells of mouse lung #2
Lung_No2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Seurat (v4.4.0) for downstream single cell analysis.
Assembly: GRCm38/GRCh38
Supplementary files format and content: barcodes, features, matrix files

source_name: lung

extract_protocol:
Fluorescence-activated cell sorting (FACS)-purified cells were processed using the Chromium Single Cell 3’ Kit v3.1 (10X Genomics, Pleasanton, CA) in accordance with the standard protocol.
Chromium Single Cell 3’ Kit v3.1 (10X Genomics, Pleasanton, CA)

value: lung


title: MPNST02

description: Library name: LR2022_64


title: SS02

description: Library name: LR2022_62


title: TR1_LOXO_3day

description: Library name: Sample 7


title: SS01

description: Library name: LR2022_57


title: SS05

description: Library name: LR2022_185


title: TR1_LOXO_2day

description: Library name: Sample 6


title: male, perigonadal white adipose tissue, Tacr2null, low fat diet, biological replicate 1

description: Library name: Sample 85


title: MFS14

description: Library name: LR2022_65

source_name: myxofibrosarcoma

value: myxofibrosarcoma


description:
Library name: Vascular endothelial cells of mouse lung #1
Lung_No1


title: male, perigonadal white adipose tissue, Tacr2null, low fat diet, biological replicate 2

description: Library name: Sample 86


title: 4th stressed 5xFAD mouse

description:
Library name: 5xFAD CMS 4
column Y in the processed data file

value: Brain

value: CD11b+ cells

value: CNS myeloid cell

value: Chronic Mild Stress (CMS)


description:
Library name: Vascular endothelial cells of mouse limb #2
Muscle_No2

source_name: limb

value: limb


title: TR1_LOXO_1day

description: Library name: Sample 5


title: female, perigonadal white adipose tissue, Tacr2null, high fat diet chronic, biological replicate 4

description: Library name: Sample 84

value: female

value: high fat diet 12 weeks


title: MFS13

description: Library name: LR2022_55


description:
Library name: Vascular endothelial cells of mouse limb #1
Muscle_No1


description:
Library name: Vascular endothelial cells of mouse liver #2
Liver_No2

source_name: liver

value: liver


title: female, perigonadal white adipose tissue, Tacr2null, high fat diet chronic, biological replicate 3

description: Library name: Sample 83

value: perigonadal white adipose tissue


title: TR1_DMSO_5day

description: Library name: Sample 4

value: DMSO


title: MFS12

description: Library name: LR2022_54


title: MFS11

description: Library name: LR2022_53


title: RNAseq of TCM1

description: Library name: TCM1

value: kidney


title: TR1_DMSO_3day

description: Library name: Sample 3

value: lung adenocarcinoma


title: female, perigonadal white adipose tissue, Tacr2null, high fat diet chronic, biological replicate 2

description: Library name: Sample 82


title: RNAseq_WT_NWH003_rep2

description: Library name: RNAseq_WT_NWH003_rep2

value: Vibrio natriegens ATCC 14048

value: bacterial cell

value: Non-growing cell suspensions incubated in nitrogen-free VMDC175 (argon headspace) for 2h to induce nitrogen starvation and nitrogenase expression


title: TR1_DMSO_2day

description: Library name: Sample 2

value: Trim24-RET fusion


title: female, perigonadal white adipose tissue, Tacr2null, high fat diet chronic, biological replicate 1

description: Library name: Sample 81


title: MFS10

description: Library name: LR2022_52

value: myxofibrosarcoma


title: IgG, astrocyte

city: beijing

first: yani

last: zhang

state: beijing

address: tsinghua

institute: tsinghua university

description: Library name: sample3

library_source: genomic

data_processing:
Raw ChIP–seq reads were quality-checked (FastQC v0.11.5), aligned to the mouse genome (GRCm39) using BWA (v0.7.15), and peaks were called with MACS3 (v3.0.3). Signal heatmaps centered on peak summits were generated with deepTools (v3.5.5). Peaks were annotated with ChIPseeker (v1.38.0) by assigning each peak to the nearest transcription start site (TSS). Genes linked to peaks were analyzed for Gene Ontology (GO) and KEGG enrichment with clusterProfiler (v4.10.1). Protein–protein interaction (PPI) networks for genes annotated to neurodevelopmental and differentiation-related GO terms were built using STRING (v12.0) and visualized in Cytoscape (v3.10.3). Hopx ChIP-seq peaks were visualized by IGV (v2.16.2).
Assembly: GRCm39
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: primary astrocyte

extract_protocol:
Astrocytes were crosslinked first with 5 mM ethylene glycol bis (EGS) for 20 min at room temperature, followed by 1.11% formaldehyde for 10 min. Crosslinking was quenched in 140 mM glycine for 5 min at room temperature. Cells were washed in cold PBS and lysed in 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl, 1% NP-40, 1% SDS, 0.5% sodium deoxycholate, supplemented with protease inhibitors. Chromatin was sheared to 200–500 bp fragments  and incubated overnight at 4 °C with anti-Flag or control IgG. Protein G agarose beads were added for 1 h at 4 °C, washed sequentially in low-salt buffer, high-salt buffer, LiCl buffer, and TE. Complexes were eluted in 1% SDS, 0.1 M NaHCO3.
After reverse crosslinking, DNA was purified and ChIP–seq library preparation  was performed using NEBNext Ultra DNA Library Prep Kit.

value: primary astrocyte


title: TR1_DMSO_1day

description: Library name: Sample 1


title: MFS09

description: Library name: LR2022_51


title: Tim4- 10wpi rerun [Hash]

city: Freiburg

first: Philipp

last: Henneke

state: Baden-Württemberg

address: Breisacher Straße 115 B

department: Institute for Infection Prevention and Control (IIK)

country: Germany

institute: University Hospital Freiburg

description:
Library name: TIM4NEG10WPIRERUNHash
rerun of the same named population, due to potential low recovery
TIM4NEG10WPIRERUNHash
runharmonysubsettedres07.rds
tim4neg10wpire_barcodes.tsv.gz
tim4neg10wpire_features.tsv.gz
tim4neg10wpire_matrix.mtx.gz

data_processing:
FastQ files were aligned with CellRanger (7.2.0) and downstream processing was perfomed in R (4.3.2) with the seurat package (5.0.1). Cell were excluded with more than 5% mitochondrial transcripts, less than 200 or more than 5000 detectable genes.
For batch effect correction harmony was used.
First a FindNeighbours and FindClusters were performed with the top 30 harmony dimensions and a resolution of 0.6. This led to the exclusion of clusters not containing macrophages or monocytes. Further subclusering was then performed with a resolution of 0.7 and the top 30 harmony dimensions.
Assembly: mm10
Supplementary files format and content: Unprocessed but mm10 aligned data

growth_protocol: SPF animal facility

extract_protocol:
Livers were isolated and digested 4 weeks after injection of PBS or BCG-BFP. Kupffer cells were sorted by flow cytometry. Hashing antibodies were used to identify KCs isolated from the same mouse
ScRNAseq was performed using the Chromium Next GEM Single Cell 5’ Kit v2, and libraries were constructed with the Library Construction Kit and Chromium Next GEM Single Cell 5’ Gel Bead Kit v2 by 10X

treatment_protocol: Mice received either i.v. injection of BCG-BFP (107 cfu) or PBS in 100µl and livers were extracted after 4 or 10 weeks of injection

value: Kupffer cell

tag: time

value: 10 weeeks post injection

value: contains 3 infected and one PBS sample

tag: pbs3 totalseq_hash_ab_biolegend

tag: bcg4 totalseq_hash_ab_biolegend

tag: bcg5 totalseq_hash_ab_biolegend

tag: bcg6 totalseq_hash_ab_biolegend

value: batch 3


title: anti-flag, astrocyte

description: Library name: sample2


title: female, perigonadal white adipose tissue, Tacr2null, high fat diet, acute, biological replicate 4

description: Library name: Sample 80

value: female

value: high fat diet one week


title: MFS08

description: Library name: LR2022_50


title: female, perigonadal white adipose tissue, Tacr2null, high fat diet, acute, biological replicate 2

description: Library name: Sample 78


title: Tim4- 10wpi [Hash]

description:
Library name: TIM4NEG10WPIHash
TIM4NEG10WPIHash
runharmonysubsettedres07.rds
tim4neg10wpi_barcodes.tsv.gz
tim4neg10wpi_features.tsv.gz
tim4neg10wpi_matrix.mtx.gz

value: liver

value: batch 2


title: biological replicate-2 Cyc8-non-Anchor-away Snf2-HA (IP)

city: Dublin 2

first: Alastair

last: Fleming

address: College Green

department: Microbiology Dept.

country: Ireland

institute: Trinity College Dublin

description: Library name: 2-Cyc8-AA-Snf2-HA-noRap-IP

data_processing:
NovaSeq 2x150 v2.0.0
Sequencing reads were first trimmed using TrimGalore (v0.6.10) with cutadapt (v2.6) and FastQC (v0.12.1), applying the parameters: `-q 25 --length 25 -e 0.1 --stringency 4 --paired -o trimmed/ "$R1" "$R2"`.
The resulting trimmed reads were aligned to the R64-1-1 reference genome using Bowtie2 with pari-end mode '-1 "$R1" -2 "$R2"' (v2.5.2). Alignment files in SAM format were converted to BAM format with SAMtools suite (v1.19.2).
2 replicates each of IP and Input BAM files were merged repectively using the samtools merge function. Both merged and non-merged BAM files were then transformed into bigWig format using BamCoverage function from the deepTools suite (v3.5.4) (parameter '--binSize 10'), for visualization in JBrowse2 (v2.10.2).
Peak calling was performed with MACS2(v 2.2.6) (using the parameters '-BAMPE -q 0.01`) using ChIP as test group and IP as control
Assembly: R64-1-1
Supplementary files format and content: bigWig

organism: Saccharomyces cerevisiae

source_name: log Phase yeast cells

growth_protocol: All samples were grown in YPD (2% glucose) media at 30° C.

extract_protocol:
Following ChIP protocol (used anti-HA antibody from Abcam (ab9110)), input and IP chromatin samples had cross-links reversed at 65oC with high salt in the presence of Pronase to digest protein. Input and IP DNA was finally purified through a Quiagen QIAquick PCR purification kit.
The extracted DNA was sent to Azenta life sciences for library preparation and pair end sequecing using Illumina NovaSeq 6000 platform

treatment_protocol: Rapamycin (1μg/ ml, dissolved in DMSO) was added to the relevant samples at early exponential growth phase (OD600 = ~0.4) and samples for ChIP were taken after 1 hour. The control group, (without rapamycin addition (no Rap)) were treated the same as above, except only DMSO was added. The collected samples were subsequently cross-linked with formaldehyde. Two biological replicate experiments were performed for each condition (+ Rap / - Rap)

value: log Phase yeast cells

value: YBL29; MAT a; tor1-1; fpr1::loxP-LEU2-loxP; RPL13A-2XFKBP12::loxP; CYC8-FRB::HIS3; SNF2::hphNT1-3HA

value: no rapamycin addition

value: HA antibody


title: MFS07

description: Library name: LR2022_49


title: LG815_C_132

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description:
Library name: Sample 16
mRNA expression in mouse hippocampus

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.6.1.2) (10x Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 6.1.2 default parameters were used to call cell barcodes.
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v4 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: hippocampus

value: Male

tag: age

value: Scn1a +/-; cGAS +/+


title: 1st non-stressed 5xFAD mouse

description:
Library name: 5xFAD Control 1
column P in the processed data file

source_name: Brain

value: Brain

value: CD11b+ cells

value: CNS myeloid cell

value: Control


title: biological replicate-2 Cyc8-non-Anchor-away Snf2-HA (Input)

description: Library name: 2-Cyc8-AA-Snf2-HA-noRap-IN


title: high 10wpi [Hash]

description:
Library name: HIGH10WPIHash
HIGH10WPIHash
runharmonysubsettedres07.rds
high10wpi_barcodes.tsv.gz
high10wpi_features.tsv.gz
high10wpi_matrix.mtx.gz

value: Kupffer cell

value: 10 weeeks post injection

value: contains 3 infected and one PBS sample


title: female, perigonadal white adipose tissue, Tacr2null, high fat diet, acute, biological replicate 1

description: Library name: Sample 77

value: perigonadal white adipose tissue

value: female

value: high fat diet one week


title: MFS06

description: Library name: LR2022_48

value: myxofibrosarcoma


title: shPml  tumor samples

description:
Library name: 1271_1
10x Chromium platform (10x Genomics)

source_name: 6- to 8-week BALB/c mice

value: 6- to 8-week BALB/c mice

value: 4T1 cells expressing shPml were  ectopically injected in the mammary fat pad


title: UPS05

description: Library name: LR2022_159

source_name: undifferentiated pleomorphic sarcoma

value: undifferentiated pleomorphic sarcoma


title: MoMacs 10wpi [Hash]

description:
Library name: MOMACS10WPIHash
MOMACS10WPIHash
runharmonysubsettedres07.rds
momacs10wpi_barcodes.tsv.gz
momacs10wpi_features.tsv.gz
momacs10wpi_matrix.mtx.gz

value: liver

value: Monocytes

value: batch 2


description:
Library name: Vascular endothelial cells of mouse liver #1
Liver_No1


title: biological replicate-1 Cyc8-non-Anchor-away Snf2-HA (IP)

description: Library name: 1-Cyc8-AA-Snf2-HA-noRap-IP

value: log Phase yeast cells

value: YBL29; MAT a; tor1-1; fpr1::loxP-LEU2-loxP; RPL13A-2XFKBP12::loxP; CYC8-FRB::HIS3; SNF2::hphNT1-3HA

value: no rapamycin addition

value: HA antibody


title: female, perigonadal white adipose tissue, Tacr2null, low fat diet, biological replicate 4

description: Library name: Sample 76

value: low fat diet


title: MFS05

description: Library name: LR2022_47


title: Tim4- 4wpi [Hash]

description:
Library name: TIM4NEG4WPIHash
TIM4NEG4WPIHash
runharmonysubsettedres07.rds
tim4neg4wpi_barcodes.tsv.gz
tim4neg4wpi_features.tsv.gz
tim4neg4wpi_matrix.mtx.gz

value: Kupffer cell

value: 4 weeks post injection

value: contains 3 infected and two PBS samples

tag: bcg1 totalseq_hash_ab_biolegend

tag: bcg2 totalseq_hash_ab_biolegend

tag: bcg3 totalseq_hash_ab_biolegend

tag: pbs1 totalseq_hash_ab_biolegend

tag: pbs2 totalseq_hash_ab_biolegend

value: batch 1


title: biological replicate-1 Cyc8-non-Anchor-away Snf2-HA (Input)

description: Library name: 1-Cyc8-AA-Snf2-HA-noRap-IN

tag: tissue

tag: genotype


title: female, perigonadal white adipose tissue, Tacr2null, low fat diet, biological replicate 3

description: Library name: Sample 75

value: perigonadal white adipose tissue

value: female

tag: treatment


title: MFS04

description: Library name: LR2022_46

value: myxofibrosarcoma


title: low 4wpi [Hash]

description:
Library name: LOW4WPIHash
LOW4WPIHash
runharmonysubsettedres07.rds
low4wpi_barcodes.tsv.gz
low4wpi_features.tsv.gz
low4wpi_matrix.mtx.gz

tag: cell type


title: female, perigonadal white adipose tissue, Tacr2null, low fat diet, biological replicate 2

description: Library name: Sample 74

tag: Sex


title: biological replicate-2 wild type Pol II ChIP (IP)

description: Library name: 2-wt_IP

extract_protocol:
Following ChIP protocol (used anti-Pol II from Covance, MMS-126R-200), input and IP chromatin samples had cross-links reversed at 65oC with high salt in the presence of Pronase to digest protein. Input and IP DNA was finally purified through a Quiagen QIAquick PCR purification kit.
The extracted DNA was sent to Azenta life sciences for library preparation and pair end sequecing using Illumina NovaSeq 6000 platform

treatment_protocol: Samples were collected at exponential phase(OD600=~0.8). The collected samples were subsequently cross-linked with formaldehyde.


title: MFS03

description: Library name: LR2022_45


title: biological replicate-2 wild type Pol II ChIP (Input)

description: Library name: 2-wt_IN


title: high 4wpi [Hash]

description:
Library name: HIGH4WPIHash
HIGH4WPIHash
runharmonysubsettedres07.rds
high4wpi_barcodes.tsv.gz
high4wpi_features.tsv.gz
high4wpi_matrix.mtx.gz

tag: batch


title: female, perigonadal white adipose tissue, Tacr2null, low fat diet, biological replicate 1

description: Library name: Sample 73


title: female, perigonadal white adipose tissue, Tacr2null, high fat diet, acute, biological replicate 3

description: Library name: Sample 79

value: high fat diet one week


title: MFS02

description: Library name: LR2022_44


title: MoMac 4wpi [Hash]

description:
Library name: MOMACS4WPIHash
MOMACS4WPIHash
runharmonysubsettedres07.rds
momacs4wpi_barcodes.tsv.gz
momacs4wpi_features.tsv.gz
momacs4wpi_matrix.mtx.gz

tag: time


title: biological replicate-1 wild type Pol II ChIP (IP)

description: Library name: 1-wt_IP


title: MFS01

description: Library name: LR2022_43


title: Tim4- 10wpi rerun [Gex]

description:
Library name: TIM4NEG10WPIRERUNGex
rerun of the same named population, due to potential low recovery
TIM4NEG10WPIRERUNGex
runharmonysubsettedres07.rds
tim4neg10wpire_barcodes.tsv.gz
tim4neg10wpire_features.tsv.gz
tim4neg10wpire_matrix.mtx.gz

value: 10 weeeks post injection

value: contains 3 infected and one PBS sample

tag: pbs3 totalseq_hash_ab_biolegend

value: batch 3


title: male, perigonadal white adipose tissue, wildtype, high fat diet chronic, biological replicate 4

description: Library name: Sample 72

value: male

value: wildtype

value: high fat diet 12 weeks


title: NMFH1

description: Library name: LR2022_38

source_name: cells

value: cells


title: male, perigonadal white adipose tissue, wildtype, high fat diet chronic, biological replicate 3

description: Library name: Sample 71


title: biological replicate-2 Cyc8 mutant Pol II ChIP (IP)

description: Library name: 2-Cyc8_IP

value: log Phase yeast cells


title: male, perigonadal white adipose tissue, wildtype, high fat diet chronic, biological replicate 2

description: Library name: Sample 70


title: biological replicate-2 Cyc8 mutant Pol II ChIP (Input)

description: Library name: 2-Cyc8_IN


title: Tim4- 10wpi [Gex]

description:
Library name: TIM4NEG10WPIGex
TIM4NEG10WPIGex
runharmonysubsettedres07.rds
tim4neg10wpi_barcodes.tsv.gz
tim4neg10wpi_features.tsv.gz
tim4neg10wpi_matrix.mtx.gz

value: liver

tag: bcg4 totalseq_hash_ab_biolegend

value: batch 2


title: male, perigonadal white adipose tissue, wildtype, high fat diet chronic, biological replicate 1

description: Library name: Sample 69


title: high 10wpi [Gex]

description:
Library name: HIGH10WPIGex
HIGH10WPIGex
runharmonysubsettedres07.rds
high10wpi_barcodes.tsv.gz
high10wpi_features.tsv.gz
high10wpi_matrix.mtx.gz

value: Kupffer cell

tag: bcg5 totalseq_hash_ab_biolegend


title: USZ-21_MFS2

description: Library name: LR2022_12


title: USZ-21_UPS1

description: Library name: LR2022_11

value: undifferentiated pleomorphic sarcoma


title: biological replicate-1 wild type Pol II ChIP (Input)

description: Library name: 1-wt_IN


title: MoMacs 10wpi [Gex]

description:
Library name: MOMACS10WPIGex
MOMACS10WPIGex
runharmonysubsettedres07.rds
momacs10wpi_barcodes.tsv.gz
momacs10wpi_features.tsv.gz
momacs10wpi_matrix.mtx.gz

value: Monocytes

tag: bcg6 totalseq_hash_ab_biolegend


title: biological replicate-1 Cyc8 mutant Pol II ChIP (Input)

description: Library name: 1-Cyc8_IN


title: USZ-21_LG1

description: Library name: LR2022_8

value: low grade undifferentiated sarcoma


title: Tim4- 4wpi [Gex]

description:
Library name: TIM4NEG4WPIGex
TIM4NEG4WPIGex
runharmonysubsettedres07.rds
tim4neg4wpi_barcodes.tsv.gz
tim4neg4wpi_features.tsv.gz
tim4neg4wpi_matrix.mtx.gz

value: 4 weeks post injection

value: contains 3 infected and two PBS samples

value: batch 1


title: male, perigonadal white adipose tissue, wildtype, high fat diet, acute, biological replicate 4

description: Library name: Sample 68

value: perigonadal white adipose tissue

value: high fat diet one week


title: USZ-20_REA1

description: Library name: LR2022_4

value: BCOR-rearranged sarcoma


title: low 4wpi [Gex]

description:
Library name: LOW4WPIGex
LOW4WPIGex
runharmonysubsettedres07.rds
low4wpi_barcodes.tsv.gz
low4wpi_features.tsv.gz
low4wpi_matrix.mtx.gz


title: biological replicate-3 Cyc8-Achor-away Snf2-HA (Input)

description: Library name: 3-Cyc8-AA-Snf2-HA-IN

data_processing:
NovaSeq 2x150 v2.0.0
Sequencing reads were first trimmed using TrimGalore (v0.6.10) with cutadapt (v2.6) and FastQC (v0.12.1), applying the parameters: '-q 25 --length 25 -e 0.1 --stringency 4 --paired -o trimmed/ "$R1" "$R2"'.
The resulting trimmed reads were aligned to the R64-1-1 reference genome using Bowtie2 with pari-end mode '-1 "$R1" -2 "$R2"' (v2.5.2). Alignment files in SAM format were converted to BAM format with SAMtools suite (v1.19.2).
3 replicates each of IP and Input BAM files were merged repectively using the samtools merge function. Both merged and non-merged BAM files were then transformed into bigWig format using BamCoverage function from the deepTools suite (v3.5.4) (parameter '--binSize 10'), for visualization in JBrowse2 (v2.10.2).
Peak calling was performed with MACS2(v 2.2.6) (using the parameters '-BAMPE -q 0.01`) using ChIP as test group and IP as control.
Assembly: R64-1-1
Supplementary files format and content: bigWig

extract_protocol:
Following ChIP protocol, input and IP chromatin samples had cross-links reversed at 65oC with high salt in the presence of Pronase to digest protein. Input and IP DNA was finally purified through a Quiagen QIAquick PCR purification kit.
The extracted DNA was sent to Azenta life sciences for library preparation and pair end sequecing using Illumina NovaSeq 6000 platform

treatment_protocol: Rapamycin (1μg/ ml, dissolved in DMSO) was added to the relevant samples at early exponential growth phase (OD600 = ~0.3) and samples for ChIP were taken after 1 hour and cross-linked with formaldehyde.

value: YBL29; MAT a; tor1-1; fpr1::loxP-LEU2-loxP; RPL13A-2XFKBP12::loxP; CYC8-FRB::HIS3; SNF2::hphNT1-3HA

value: Grown for 1 hour after the addition of rapamycin (final concentration = 1μg/ ml)

value: HA antibody


title: high 4wpi [Gex]

description:
Library name: HIGH4WPIGex
HIGH4WPIGex
runharmonysubsettedres07.rds
high4wpi_barcodes.tsv.gz
high4wpi_features.tsv.gz
high4wpi_matrix.mtx.gz


title: male, perigonadal white adipose tissue, wildtype, high fat diet, acute, biological replicate 1

description: Library name: Sample 65

value: male

value: wildtype


title: biological replicate-1 Cyc8-Achor-away Snf2-HA (ChIP)

description: Library name: 1-Cyc8-AA-Snf2-HA-IP

value: log Phase yeast cells


title: male, perigonadal white adipose tissue, wildtype, low fat diet, biological replicate 4

description: Library name: Sample 64

value: low fat diet


title: MoMac 4wpi [Gex]

description:
Library name: MOMACS4WPIGex
MOMACS4WPIGex
runharmonysubsettedres07.rds
momacs4wpi_barcodes.tsv.gz
momacs4wpi_features.tsv.gz
momacs4wpi_matrix.mtx.gz

value: liver


title: HG_no_coculture_2

city: Luzhou

first: Xiaoqin

last: Shi

state: Sichuan

address: No. 1, Xianglin Road, Longmata District, Luzhou City,

institute: The Affiliated Hospital of Southwest Medical University

description:
Library name: Sample 8
Column name in gene_expression.txt and lncRNA_expression_anno.txt: HG-non-coculture-2_count, HG-non-coculture-2_FPKM
Column name in circRNA_expression.txt: HG-non-coculture-2_junc_reads, HG-non-coculture-2_SRPBM

data_processing:
mRNA/lncRNA: Adapters and low-quality reads were trimmed using Seqtk. Clean reads were mapped to the human reference genome (GRCh38) using HISAT2 (v2.0.4). Gene expression was quantified using StringTie (v1.3.0), with counts TMM-normalized and converted to FPKM.
circRNA: Adapters and low‐quality reads were trimmed using Seqtk. Clean reads were mapped to the human reference genome (GRCh38) using BWA-MEM. circRNAs were predicted from the aligned reads using CIRI; predicted loci were merged across samples and annotated against circBase, and junction reads were counted and normalized to SRPBM for expression quantification.
Assembly: GRCh38
Supplementary files format and content: Gene_expression.txt and lncRNA_expression_anno.txt include raw counts and FPKM values for each samples. CircRNA_expression.txt includes junction reads and SRPBM values for each samples.

source_name: HRMVPC-Immortalized

extract_protocol:
Total RNA was isolated using the MJzol Animal RNA Extraction Kit (MagBeads).
VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® was used for library construction.

tag: cell line

value: HRMVPC-Immortalized

value: pericyte

value: WT

value: without HRMEC-Immortalized co-culture, 25 mM glucose, 24 hours


title: HG_no_coculture_1

description:
Library name: Sample 7
Column name in gene_expression.txt and lncRNA_expression_anno.txt: HG-non-coculture-1_count, HG-non-coculture-1_FPKM
Column name in circRNA_expression.txt: HG-non-coculture-1_junc_reads, HG-non-coculture-1_SRPBM


title: biological replicate-1 Cyc8-Achor-away Snf2-HA (Input)

description: Library name: 1-Cyc8-AA-Snf2-HA-IN


title: Trans11  mouse muscle, after transplantation

city: Beijing

first: xupeng

last: liu

state: Beijing

address: No.3 Datun Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

data_processing:
CLC Genomics Workbench v11.0.1
Seguence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork (parameter- Quality limit. 0.05)
Trimmed sequence reads were maped to GrcM38/mm0 using CLc genomic benchwoank (parameters-mismath cost. 2 insertion cost: 3 deletion cost:3 engthfaction. .8 similanity faction. 0.8
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: quadriceps femoris muscle

growth_protocol: 10-week-old male 129 mice (n=10) were used and had free access to water and food. The lights were on from 08.00 to 20.00, the temperature was maintained at 21 to 24°C, and the humidity was maintained at 40–70%.

extract_protocol:
RNA is extracted from tissues or cells using standard extraction methods (Trizol), followed by rigorous quality control of RNA samples through Agilent 2100 bioanalyzer.
RNA libraryis for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to the manufacturer's instructions.

treatment_protocol: The muscle stem cells were obtained from the mice by biopsy, and after autologous muscle stem cell transplantation or sham surgery, the muscle stem cells or tissues of the mice were obtained for analysis.

value: quadriceps femoris muscle

value: after transplantation


title: HG_coculture_3

description:
Library name: Sample 6
Column name in gene_expression.txt and lncRNA_expression_anno.txt: HG-coculture-1_count, HG-coculture-3_FPKM
Column name in circRNA_expression.txt: HG-coculture-3_junc_reads, HG-coculture-3_SRPBM

value: co-cultured with HRMEC-Immortalized, 25 mM glucose, 24 hours


title: male, perigonadal white adipose tissue, wildtype, low fat diet, biological replicate 3

description: Library name: Sample 63

source_name: perigonadal white adipose tissue

value: perigonadal white adipose tissue


title: Sample4A HTO

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

data_processing:
Alignment to human reference and assembly of VDJ contigs using Cellranger (v6.0.2) multi pipeline
Assembly: GRCh38, GENCODE v32/Ensembl 98
Supplementary files format and content: h5 filtered matrices

source_name: PBMC

extract_protocol:
PCR cycle number for the cDNA amplification was set to 16 cycles for a target recovery of <2000 cells. cDNA QC and Quantification via Tapestation. 2uL cDNA was used as input for the V(D)J amplification. 50ng cDNA was used as input for the 5’ Gene Expression Library Construction. Remaining cDNA was stored at -20°C.
50ng amplified V(D)J products was used as input for the V(D)J Library Construction. For the GEX library sample 50ng cDNA was used and index PCR cycle number was set to 14 cycles with a cDNA input of 26-50 ng. For surface protein library construction 5uL cleaned up supernatant product was used.
Library QC and Quantification via Tapestation.

treatment_protocol: Cells were surface stained and sorted based on positive tetramer staining into 50% FBS/PBS. Cells were pelleted and resuspended ~30uL 0.04% BSA/PBS solution. GEMs were produced using the Chromium Next GEM Single Cell 5'v2 (Dual Index) kit with Feature Barcoding technology and a Chromium Controller from 10X Genomics (Model GCG-SR-1).

value: PBMC

value: T cell

value: Nivolumab

tag: library type

value: HTO


title: Trans6  mouse muscle, after transplantation


title: male, perigonadal white adipose tissue, wildtype, low fat diet, biological replicate 2

description: Library name: Sample 62

value: male


title: HG_coculture_2

description:
Library name: Sample 5
Column name in gene_expression.txt and lncRNA_expression_anno.txt: HG-coculture-1_count, HG-coculture-2_FPKM
Column name in circRNA_expression.txt: HG-coculture-2_junc_reads, HG-coculture-2_SRPBM


title: Sample3B HTO


title: Trans5  mouse muscle, after transplantation


title: HG_coculture_1

description:
Library name: Sample 4
Column name in gene_expression.txt and lncRNA_expression_anno.txt: HG-coculture-1_count, HG-coculture-1_FPKM
Column name in circRNA_expression.txt: HG-coculture-1_junc_reads, HG-coculture-1_SRPBM


title: Sample3A HTO


title: male, perigonadal white adipose tissue, wildtype, low fat diet, biological replicate 1

description: Library name: Sample 61

value: wildtype


title: female, perigonadal white adipose tissue, wildtype, high fat diet chronic, biological replicate 4

description: Library name: Sample 60

value: female

value: high fat diet 12 weeks


title: NG_coculture_3

description:
Library name: Sample 3
Column name in gene_expression.txt and lncRNA_expression_anno.txt: NG-coculture-3_count, NG-coculture-3_FPKM
Column name in circRNA_expression.txt: NG-coculture-3_junc_reads, NG-coculture-3_SRPBM

value: co-cultured with HRMEC-Immortalized, 5.5 mM glucose, 24 hours


title: Sample2B HTO


title: Sham192 mouse muscle, after transplantation


title: NG_coculture_2

description:
Library name: Sample 2
Column name in gene_expression.txt and lncRNA_expression_anno.txt: NG-coculture-2_count, NG-coculture-2_FPKM
Column name in circRNA_expression.txt: NG-coculture-2_junc_reads, NG-coculture-2_SRPBM

value: HRMVPC-Immortalized


title: Sham3  mouse muscle, after transplantation


title: female, perigonadal white adipose tissue, wildtype, high fat diet chronic, biological replicate 2

description: Library name: Sample 58


title: NG_coculture_1

description:
Library name: Sample 1
Column name in gene_expression.txt and lncRNA_expression_anno.txt: NG-coculture-1_count, NG-coculture-1_FPKM
Column name in circRNA_expression.txt: NG-coculture-1_junc_reads, NG-coculture-1_SRPBM

value: pericyte


title: Trans94  mouse muscle, after transplantation

value: WT


title: Sample1B HTO


title: female, perigonadal white adipose tissue, wildtype, high fat diet chronic, biological replicate 1

description: Library name: Sample 57


title: 72-year-old,T24-3

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

description: Library name: T243

data_processing:
The sequencing was analyzed using by Illumina NovaSeq 6000 platform PE150.  The quality of the sequencing data was assessed using FastQC (version 0.11.7;  available at http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc).
Assembly: hg38
Supplementary files format and content: bigWig (.bw) – processed signal file representing genome-wide chromatin accessibility.

source_name: brain

extract_protocol:
Cells were transferred into 1 ml cold homogenization buffer (HB) in a pre-chilled 2 ml Dounce (Sigma-Aldrich, USA), thawed on ice for 5 min, and homogenized with 10 strokes of loose ("A") and 20 strokes of tight ("B") pestles. The homogenate was filtered through a 70 μm strainer into a LoBind tube (Eppendorf). Nuclei were pelleted (350 × g, 5 min, 4 °C), resuspended in 400 μl HB, mixed with 400 μl of 50% iodixanol, and layered onto 30% and 40% iodixanol solutions. After centrifugation (3,000 × g, 20 min, 4 °C, brake off), the nuclei band was collected.Nuclei were washed with ATAC-RSB-Tween, stained with AO/PI, and counted. 50,000 nuclei were pelleted (500 × g, 10 min, 4 °C) and resuspended in 35 μl nuclease-free water for library preparation.
The ATAC-seq library was prepared using the TruePrep DNA Library Prep Kit V2. A 15 μl Tn5 reaction mix was added per instructions and incubated at 37 °C for 30 min. The product was purified with a MinElute column. PCR setup included fragmented DNA (24 μl), 5 × TAB (10 μl), PPM (5 μl), primers (N5** and N7**, 5 μl each), and TAE (1 μl). Amplification followed the manual, with 12 cycles determined via qPCR. Purification was repeated using a MinElute column. DNA sorting was performed using VAHTS DNA Clean Beads (0.55 × /1.0 × scheme), and fragmentation analysis used a Cartridge Kit. Libraries were sequenced with Illumina NovaSeq 6000.

value: brain

value: Female

value: Parieto-occipital contused cortex

value: occipitoparietal hemorrhage with scattered contusions

value: degraded 24h


title: Sample4A VDJ

value: PBMC

value: VDJ


title: Trans14  mouse muscle, after transplantation

value: quadriceps femoris muscle

value: after transplantation


title: 72-year-old,T0-3

description: Library name: T03

value: degraded 0h


title: Sample3B VDJ

value: T cell

value: Nivolumab


title: Trans4  mouse muscle, after transplantation


title: female, perigonadal white adipose tissue, wildtype, high fat diet, acute, biological replicate 4

description: Library name: Sample 56

value: perigonadal white adipose tissue

value: female

value: wildtype

value: high fat diet one week


title: female, perigonadal white adipose tissue, wildtype, high fat diet, acute, biological replicate 3

description: Library name: Sample 55


title: 11F mouse MuSCs,before transplantation

source_name: Muscle stem cell

value: Muscle stem cell

value: WT

value: before transplantation


title: Sample3A VDJ


title: 62-year-old, T24-2

description: Library name: T242

value: brain

value: Female

value: Frontotemporal contused cortex

value: intracerebral hemorrhage with frontotemporal contusion


title: female, perigonadal white adipose tissue, wildtype, high fat diet chronic, biological replicate 3

description: Library name: Sample 59

value: high fat diet 12 weeks


title: 62-year-old, T0-2

description: Library name: T02


title: female, perigonadal white adipose tissue, wildtype, high fat diet, acute, biological replicate 2

description: Library name: Sample 54


title: Sample2B VDJ

value: PBMC

value: VDJ


title: 6F  mouse MuSCs, before transplantation


title: female, perigonadal white adipose tissue, wildtype, high fat diet, acute, biological replicate 1

description: Library name: Sample 53


title: 44-year-old, T24-1

description: Library name: T024

value: Frontal contused cortex

value: brain contusion due to traffic accident

value: degraded 24h


title: biological replicate-3 Cyc8-Achor-away Snf2-HA (ChIP)

description: Library name: 3-Cyc8-AA-Snf2-HA-IP

value: log Phase yeast cells

value: YBL29; MAT a; tor1-1; fpr1::loxP-LEU2-loxP; RPL13A-2XFKBP12::loxP; CYC8-FRB::HIS3; SNF2::hphNT1-3HA

value: Grown for 1 hour after the addition of rapamycin (final concentration = 1μg/ ml)


title: female, perigonadal white adipose tissue, wildtype, low fat diet, biological replicate 4

description: Library name: Sample 52

value: perigonadal white adipose tissue

value: female

value: wildtype

value: low fat diet


title: 5F mouse MuSCs, before transplantation

value: Muscle stem cell

value: WT

value: before transplantation


title: 44-year-old, T0-1

description: Library name: T0

value: brain

value: Female

value: degraded 0h


title: Sample2A VDJ

value: PBMC

value: T cell

value: Nivolumab

value: VDJ


title: Sample1B VDJ


title: biological replicate-1 Cyc8 mutant Pol II ChIP (IP)

description: Library name: 1-Cyc8_IP

value: log Phase yeast cells


title: 11F mouse MuSCs, after transplantation

value: after transplantation


title: female, perigonadal white adipose tissue, wildtype, low fat diet, biological replicate 3

description: Library name: Sample 51


title: Sample4A GEX

value: GEX


title: 67-year-old C24-3

description: Library name: C243

value: Frontoparietal cortex

value: degraded 24h


title: male, perigonadal white adipose tissue, wildtype, high fat diet, acute, biological replicate 3

description: Library name: Sample 67

value: perigonadal white adipose tissue

value: male

value: wildtype

value: high fat diet one week


title: female, perigonadal white adipose tissue, wildtype, low fat diet, biological replicate 2

description: Library name: Sample 50

value: female

value: low fat diet


title: 6F  mouse MuSCs, after transplantation

value: Muscle stem cell

value: WT


title: 67-year-old C0-3

description: Library name: C03

value: brain

value: Female

value: degraded 0h


title: male, perigonadal white adipose tissue, wildtype, high fat diet, acute, biological replicate 2

description: Library name: Sample 66


title: Sample3B GEX

value: PBMC

value: T cell

value: Nivolumab


title: HG_no_coculture_3

description:
Library name: Sample 9
Column name in gene_expression.txt and lncRNA_expression_anno.txt: HG-non-coculture-3_count, HG-non-coculture-3_FPKM
Column name in circRNA_expression.txt: HG-non-coculture-3_junc_reads HG-non-coculture-3_SRPBM

value: HRMVPC-Immortalized

value: pericyte

value: without HRMEC-Immortalized co-culture, 25 mM glucose, 24 hours


title: 5F  mouse MuSCs, after transplantation

value: after transplantation


title: 38-year-old C24-2

description: Library name: C242

value: Male

value: Frontotemporal cortex

value: degraded 24h


title: female, perigonadal white adipose tissue, wildtype, low fat diet, biological replicate 1

description: Library name: Sample 49

value: perigonadal white adipose tissue

value: female

value: wildtype


title: Sample3A GEX

value: GEX


title: male, intestinal epithelium, Tacr2null, high fat diet chronic, biological replicate 4

description: Library name: Sample 48

source_name: intestinal epithelium

value: intestinal epithelium

value: male

value: high fat diet 12 weeks


title: Primed EpiLC, Pcbp1, ChIP-seq

city: Haifa

first: Evgeny

last: Potapenko

address: Abba Khoushy Ave 199

department: Institute of Evolution

institute: University of Haifa

data_processing:
Firstly, reads were trimmed by fastp tool with default settings.
Trimmed reads were aligned to GRCm38/mm10 reference genome by Bowtie2 with default parameters.
Picard Markduplicates was used to mark duplicates.
Peak calling was performed using macs2 callpeak with such parameters: -g mm -q 0.01 –nomodel –SPMR. Input DNA for corresponding sample was used as controls.
BigWig files were generated with macs2 bdgcmp by subtracting bedgraph pileup of treatment from input sample.
Assembly: mm10
Supplementary files format and content: narrowPeak
Supplementary files format and content: BigWig

source_name: E14 Tg2a Bay Genomics

growth_protocol: Mouse ESCs were adapted for 3 passages in serum-free 2i-LIF-N2B27 medium (2i – MEK inhibitor PD0325901 (1uM, Axon) and GSK3β inhibitor CHIR99021 (3uM, Axon)) in tissue culture plastic preliminary treated with 0.01% poly-L-ornithine (Sigma). For EpiLC derivation, ESCs were trypsinized, washed with PBS and seeded in the amount of 250.000 cells to 6 well culture plate, pretreated with 15ug/ml of Fibronectin (Merck) in N2B27 medium supplemented with 12ng/ml bFGF (Peprotech), 20ng/ml Activin A (Peprotech) and 1% of KOSR (Gibco) for 48 hours.

extract_protocol:
Cells were fixed with 1% Formaldehyde for 10 minutes, then quenched with 0.125M Glycine. Chromatin was lysed in SDS-containing buffer with protease inhibitors cocktail (Roche) and sheared to fragments around 500 bp by sonicator FisherScientific CL-18. For precipitation chromatin of 1.5 million cells and 12ug of antibodies conjugated with MabSelect sure Sepharose (Cytiva) were taken. The precipitated chromatin was sequentially washed with SDS-containing buffer and with TE. Precipitated chromatin complexes were then eluted and subjected to cross-link reversal reaction. DNA was extracted with a phenol/chloroform, then precipitated with isopropanol and washed by ethanol. The precipitate was dissolved in TE buffer and subjected to library preparation. Each ChIP was validated using q-PCR against selected loci.
DNA libraries were prepared for sequencing using standard Illumina protocols.

value: E14 Tg2a Bay Genomics

value: Mouse embryonic stem cells

tag: condition

value: Primed EpiLC

tag: chip antibody

value: Pcbp1 (Abcam, ab74793)


title: 38-year-old C0-2

description: Library name: C02

value: brain

value: degraded 0h


title: Sample2B GEX

value: PBMC

value: T cell

value: Nivolumab


title: 318B-2_VDJ - HC - CITEseq

status: Public on Jun 05 2026

city: London

first: Jo

last: Spencer

state: Kent

address: Guy’s Hospital Campus

country: United Kingdom

institute: King's College London

description: Library name: 318B-2_VDJ

library_source: other

data_processing:
Raw reads were processed using CellRanger (pipeline version cellranger-arc-2.0.2)
Assembly: hg38
Supplementary files format and content: Tab separated files for gene IDs, cell barcodes and count matrix per sample
Library strategy: BCR-Seq

molecule: other

source_name: appendix

extract_protocol:
Live single CD19+ B cells were stained with ADT antibodies and anti-CD19 antibody used for FACS. Cells were sorted into 200ml 100% FBS, washed with ice-cold 1xPBS and then centrifuged at 500 g for 5 min at 4°C. They were resuspended in FACS buffer (2% FBS in DPBS).
Cells were loaded onto a 10X Genomics Chromium controller for library generation.

value: appendix

value: B cell


title: Naïve ESCs, Pcbp1, ChIP-seq

value: Naive


title: 53-year-old C24-1

description: Library name: C24

value: Male

value: Frontal cortex

value: degraded 24h


title: male, intestinal epithelium, Tacr2null, high fat diet chronic, biological replicate 3

description: Library name: Sample 47

extract_protocol:
NOTE for intestinal intestinal epithelium: the small intestine was cut longitudanally, and the intestinal epithelium was scraped using microscope slides from the middle of the length of the entire intestine (roughly 16-20 cm in a typical 34 cm small intestine). The tissues (isolated intestinal epithelium or perigonadal white adipose tissues) were processed via commercial RNeasy RNA purification kits using manufacturers protocols.
Total RNA samples were prepared into RNA-Seq libraries using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommended protocol. Briefly, for each sample, 200 ng total RNA was polyA selected, and converted to double-stranded cDNA followed by fragmentation and ligation of sequencing adapters. The libraries were then PCR amplified 12 cycles using barcoded PCR primers, purified, and size selected using AMPure XP Beads before loading onto an Illumina NextSeq 2000 for 100 base single-read sequencing.

value: intestinal epithelium

value: male


title: EpiLC cells, PCBP1 KO, rep 3

description:
12
EpiLC_KO_R3

data_processing:
Sequence reads were trimmed for adapter sequence/low-quality sequence using fastp software with default parameters, and quality control was assessed by FastQC.
Trimmed high quality sequences were mapped to GRCm38/mm10 genome using STAR tool in the two-pass mode.
Quality control of the RNA-seq experiment was analyzed with the ReadDistribution and the GeneBodyCoverage tools from the RseQC.
Read counts for each gene was estimated by featureCounts tool.
Differential expression analysis of two groups (KO samples and WT samples) was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: Bigwig file format of reads aligned to the genome.

extract_protocol:
RNAs from each biological replicate of ESC and of EpiLC was extracted with Trizol (Invitrogen) following the manufacturer's recommendations.
The libraries for NGS analyses were constructed using TruSeq Stranded mRNA kit (Illumina) following the manufacturer's recommendations. 1 μg of total RNA was taken as input material for the protocol.

value: E14 Tg2a Bay Genomics

value: PCBP1 knockout

value: 48h of Naive-to-EpiLC transition


title: Sample2A GEX

value: GEX


title: male, intestinal epithelium, Tacr2null, high fat diet chronic, biological replicate 2

description: Library name: Sample 46

data_processing:
Raw sequencing reads were quality-assessed using FastQC, and adapters were removed using Cutadapt.
Trimmed reads were aligned to the mouse reference genome (ENSEMBL GRCm38) using STAR aligner version 2.6.1d.
The distribution of mapped reads across genomic features was analyzed with RSeQC v3.0.1.
Differential gene expression analysis was performed using DESeq2 (v2.11.40.8) implemented in R (v4.2.2) via the Galaxy platform.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

value: high fat diet 12 weeks


title: 53-year-old C0-1

description: Library name: C0

value: brain

value: degraded 0h


title: Sample1B GEX

value: PBMC

value: T cell


title: male, intestinal epithelium, Tacr2null, high fat diet chronic, biological replicate 1

description: Library name: Sample 45


title: mPFC, Ketamine-3, Day15

city: Yokohama City

first: Waki

last: Nakajima

state: Kanazawa-Ku

address: 3-9, Fukuura

department: Physiology

institute: Yokohama City University

description: Library name: Sample 9

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to rn6 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: rn6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Brain (mPFC)

extract_protocol:
Total RNA was harvested using the RNeasy plus universal kits (Qiagen). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacture's protocols.

treatment_protocol: In control group, rats were recieved no treatment. In K4 group, rats were administered K4 intravenously through a cannula for 7 days. In ketamine group, rats were administered ketamine subcutaneously for 7days. After continuous treatment, withdrawal was done for 7 days.

value: Brain (mPFC)

value: Wistar Kyoto rats

value: Ketamine


title: EpiLC cells, PCBP1 KO, rep 1

description:
10
EpiLC_KO_R1

value: Mouse embryonic stem cells


title: male, intestinal epithelium, Tacr2null, high fat diet, acute, biological replicate 4

description: Library name: Sample 44

value: high fat diet one week


title: Panc1_ChIPmentation_DMSO

city: Göttingen

first: Adi

last: Mackay

address: Robert-Koch-Straße 40

department: Pathology

institute: University Medical Center Göttingen

description: Library name: Panc1_ChIPmentation_DMSO

data_processing:
Samples were aligned using the NGSeqBasic pipeline
Peaks were called using macs2 and the cut-off q-value of <= 0.001.
Bigwig files were generated using the deeptools (v3.5.6)71 bamCoverage function with RPGC normalization.
Assembly: hg38
Supplementary files format and content: Bigwig files (.bw): signal information
Supplementary files format and content: narrowPeak files: containing peak calling information from MACS2

source_name: Pancreas

extract_protocol:
Cells were fixed with 15 mM EGS, incubated on a roller for 30 min at RT followed by incubation with 1% formaldehyde for additional 10 min on the roller before the reaction was quenched with 125 mM Glycine.
Libraries including antibody binding, tagmentation and DNA extraction were performed as described in the methods section.

value: Pancreas

value: Cell line

value: DMSO


title: Panc1_ChIPmentation_ICM

description: Library name: Panc1_ChIPmentation_ICM

value: Inflachromene


title: male, intestinal epithelium, Tacr2null, high fat diet, acute, biological replicate 3

city: La Jolla

first: Supriya

last: Srinivasan

institute: The Scripps Research Institute

description: Library name: Sample 43

value: intestinal epithelium

value: male


title: EpiLC cells, wild type, rep 3

description:
9
EpiLC_WT_R3

value: E14 Tg2a Bay Genomics

value: WT

value: 48h of Naive-to-EpiLC transition


title: mPFC, Ketamine-1, Day15

description: Library name: Sample 7


title: ChIPmentation_PDO3T

description: Library name: ChIPmentation_PDO3T

value: Patient derived organoids


title: ChIPmentation_PDO3T_ICM

description: Library name: ChIPmentation_PDO3T_ICM


title: EpiLC cells, wild type, rep 2

description:
8
EpiLC_WT_R2


title: mPFC, K4-3, Day15

description: Library name: Sample 6


title: male, intestinal epithelium, Tacr2null, high fat diet, acute, biological replicate 1

description: Library name: Sample 41


title: EpiLC cells, wild type, rep 1

description:
7
EpiLC_WT_R1


title: ChIPmentation_PDO51T

description: Library name: ChIPmentation_PDO51T


title: Naive cells, PCBP1 KO, rep 3

description:
6
Naive_KO_R3

value: PCBP1 knockout

value: Naive culture conditions


title: scRNA_PDO84T_ICM

description: Library name: scRNA_PDO84T_ICM

data_processing:
cell_ranger/3.1.0 counts function
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: Xxx.barcodes.tsv.gz: text file with cellular barcodes of the sample.
Supplementary files format and content: xxx.features.tsv.gz: text file with the genes quantified in the sample.
Supplementary files format and content: xxx.matrix.mtx.gz: text file containing the counts matrix.

extract_protocol:
According to the 10x user guide “Chromium Next GEM Single Cell 3’ Reagent Kits v3.1” (CG000204 Rev D)
According to the 10x user guide “Chromium Next GEM Single Cell 3’ Reagent Kits v3.1” (CG000204 Rev D)


title: mPFC, K4-1, Day15

description: Library name: Sample 4

value: Brain (mPFC)


title: Naive cells, PCBP1 KO, rep 2

description:
5
Naive_KO_R2


title: scRNA_PDO84T

description: Library name: scRNA_PDO84T


title: mPFC, Control-3, Day15

description: Library name: Sample 3

value: Wistar Kyoto rats

value: Control


title: Naive cells, PCBP1 KO, rep 1

description:
4
Naive_KO_R1

value: Mouse embryonic stem cells


title: scRNA_PDO54T_ICM

description: Library name: scRNA_PDO54T_ICM


title: mPFC, Control-2, Day15

description: Library name: Sample 2


title: male, intestinal epithelium, Tacr2null, low fat diet, biological replicate 1

description: Library name: Sample 37

value: low fat diet


title: Naive cells, wild type, rep 3

description:
3
Naive_WT_R3


title: mPFC, Control-1, Day15

description: Library name: Sample 1


title: scRNA_PDO54T

description: Library name: scRNA_PDO54T

value: Pancreas


title: Naive cells, wild type, rep 2

description:
2
Naive_WT_R2


title: female, intestinal epithelium, Tacr2null, high fat diet chronic, biological replicate 4

description: Library name: Sample 36

value: female

value: high fat diet 12 weeks


title: scRNA_PDO51T_ICM

description: Library name: scRNA_PDO51T_ICM

value: Inflachromene


title: Naive cells, wild type, rep 1

description:
1
Naive_WT_R1


title: alx3 alx4a Mutant 48hpf CNCCs

city: Aurora

middle: T

last: Nichols

institute: University of Colorado Anschutz Medical Campus

description:
Library name: alx3_alx4a_Mutant
10x genomics

data_processing:
Recovered sequencing reads were mapped to a custom Cell Ranger reference based on the GRCz11/danRer11 genome assembly using the Cell Ranger pipeline (10X Genomics). This Cell Ranger reference contained the alx3 transcript from Ensembl release 91 (GRCz10) mapped to the GCRz11 genome in place of the release 101 (GRCZ11) version due to inaccurate truncation of the 3’ UTR in the most recent version7. The 10X Genomics Cell Ranger pipeline was used to identify cell-associate barcodes.
Assembly: GRCz11/danRer11 genome assembly with the alx3 transcript from Ensembl release 91 (GRCz10) mapped to the GCRz11 genome in place of the release 101 (GRCZ11) version due to inaccurate truncation of the 3’ UTR in the most recent version7.
Supplementary files format and content: wt.barcodes.tsv.gz : barcodes for WT dataset in tsv file
Supplementary files format and content: alx3M.barcodes.tsv.gz : barcodes for alx3M dataset in tsv file
Supplementary files format and content: alx3Malx4aM.barcodes.tsv.gz : barcodes for alx3Malx4aM dataset in tsv file
Supplementary files format and content: wt.features.tsv.gz : features for WT dataset in tsv file
Supplementary files format and content: alx3M.features.tsv.gz : features for alx3M dataset in tsv file
Supplementary files format and content: alx3Malx4aM.features.tsv.gz : features for alx3Malx4aM dataset in tsv file
Supplementary files format and content: wt.matrix.mtx.gz : matrix for WT dataset in mtx file
Supplementary files format and content: alx3M.matrix.mtx.gz : matrix for alx3M dataset in mtx file
Supplementary files format and content: alx3Malx4aM.matrix.mtx.gz : matrix for alx3Malc4aM dataset in mtx file
Supplementary files format and content: 230724_A00405_0714_BH55GNDSX7_L3_Nichols_demux.csv : csv of all data files

organism: Danio rerio

source_name: 48hpf zebrafish embryo

growth_protocol: Zebrafish were grown to 48hpf in E2 embryo media

extract_protocol:
33 double transgenic fli1:EGFP;sox10:mRFP embryos per genotype were dissociated into single-cell suspension using cold-active protease from Bacillus licheniformis, DNase, EDTA, and trituration.
Sorted cells (at 3.27 x 105 cells/ml in wild type, at 2.72 x 105 cells/ml in alx3-/-, and at 2.86 x 105 cells/ml in alx3-/-;alx4a-/- with ~85% viability) were loaded into the 10X Chromium Controller aiming to capture > 10,000 cells per sample. 2x150 paired-end sequencing Chromium 10X Genomics libraries were sequenced using the NovaSEQ6000.

value: 48hpf zebrafish embryo

value: Cranial neural crest

value: alx3;alx4a mutant


title: scRNA_PDO51T

description: Library name: scRNA_PDO51T


title: female, intestinal epithelium, Tacr2null, high fat diet chronic, biological replicate 3

description: Library name: Sample 35

value: intestinal epithelium


title: 2581, Cre+, AngII

city: Los Angeles

first: Jonathan

middle: William

last: Nelson

address: 1333 San Pablo St.

department: Medicine

institute: University of Southern California

description:
10x Genomics
NUC230517SG_8

data_processing:
Fastq files were prepared using bcl2fastq (Illumina) and then aligned to a reference genome using Cellranger v. 7.1.0 (10x Genomics). Reads were mapped to both exonic and intronic regions to include the pre-mRNA transcriptome.
Ambient RNA contamination was estimated and removed using SoupX v. 1.6.2
Cells with cleaned-up reads were then subjected to doublet removal using DoubletFinder v. 2.0
Mitochondrial features were manually removed by excluding all features starting with mt-
The normalized count matrix integration, batch effect correctiong, and cell clustering were performed using Seurat v. 4.3.0
Assembly: mm10
Supplementary files format and content: Raw and filtered feature-barcode matrices from each replicate
Supplementary files format and content: Integrated seurat objects containing multiple replicates

source_name: Whole Kidney

extract_protocol:
Kidney cortex was dissected out after PBS washout via aortic perfusion and snap-frozen in liquid nitrogen immediately after dissection. Frozen tissue was stored at -80 °C until subsequent tissue processing. Prepare the nuclei isolation buffer (NIB, includes 146 mM NaCl, 10 mM Tris-HCl, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween-20, 0.01% BSA, pH 7.5), and add 1 tablet of cOmplete ULTRA per 10 ml NIB. The samples were ground for 30 times in 2ml NIB1 (4mL NIB + 20µl RNasin Plus + 20µl SUPERaseIN) with a 2ml Dounce grinder and a loose pestle, then homogenate was passed through a 200 µm strainer. The homogenate was ground for 15 times with a tight pestle, then 2 ml NIB1 was added and the homogenate was incubated for 5 min on ice. The homogenate was passed through a 40 µm strainer, then centrifuged at 500g for 5 min at 4°C. The pellet was resuspended in 4 ml NIB2 (4mL NIB + 4µl RNasin Plus + 4µl SUPERaseIN) and the suspension was incubated on ice for 5 min, then centrifuged at 500g for 5 min at 4°C. The pellet was resuspended in 1.5 ml of nuclei resuspension buffer (NSB, 10mL DPBS + 10µl RNasin Plus), then centrifuged at 500g for 5 min at 4°C. Repeat this step, then the suspension was passed through a 5 µm strainer. The suspension was centrifuged at 500g for 5 min at 4°C, and the pellet was resuspended in 10 ml NSB. The nuclei suspension was mixed with 5µl Vybrant Ruby stain and incubated on ice for 15 min. The nuclei were sorted in 500 µl final resuspension buffer (FSB, 1ml DPBS with 1% BSA + 5 µl Protector RNase inhibitor) with a low flow rate and pressure to ensure high viability.A 561+683 emission gate was used to select for ruby stained nulcei. Low trigger pulse width was used as singlet discriminator. One hundred thousand nuclei were collected and centrifuged at 500g for 5 min at 4°C. The top supernatant was carefully removed, and 50 µl volume was left to resuspend the nuclei pellet.
Single nucleus RNA-seq was performed using a Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 (10x Genomics). Single nuclei were partitioned in droplets with single Gel Beads, which contained primers with cell-tagging indexes. Single nucleus suspensions with concentration of at least 300/µl were loaded targeting 10,000 nuclei per sample. The resulting cDNA was profiled on a Bioanalyzer NanoChip (Agilent), then used as a template for library preparation according to the reagent kit protocol. ( https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry )

tag: strain

value: Male

value: Cre+

value: Whole Kidney

value: All Kidney Cells

value: AngII

tag: age


title: scRNA_PDO3T_ICM

description: Library name: scRNA_PDO3T_ICM

tag: tissue

value: Patient derived organoids


title: female, intestinal epithelium, Tacr2null, high fat diet chronic, biological replicate 2

address: 10550 North Torrey Pines Road

description: Library name: Sample 34

tag: genotype


title: 2744, Cre-, Saline

description:
10x Genomics
NUC230517SG_7

value: Cre-

tag: treatment

value: Saline


title: female, intestinal epithelium, Tacr2null, high fat diet chronic, biological replicate 1

description: Library name: Sample 33


title: scRNA_PDO3T

description: Library name: scRNA_PDO3T

tag: cell type


title: scRNA_PDO3N

description: Library name: scRNA_PDO3N


title: WT3

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: Library name: WT3

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.99 mouse transcriptome, with RSEM, to obtain expression estimates at gene level.
Assembly: GRCm38.99
Supplementary files format and content: Estimated raw counts for each gene in each sample, as calculated by RSEM

growth_protocol: !0T1/2 cells were maintained in DMEM supplemented with 10% FBS and 1% Pen/Strep, and growth in humidified atmosphere at 5% CO2 and 37C.

extract_protocol:
RNA was extracted using Qiagen miniRNeasy kit (74004, Qiagen, Germany) following manufacturer’s instructions.
mRNA was captured and libraries were prepared using the KAPA mRNA HyperPrep kit (08098115702, Roche, Switzerland) following manufacturer’s instructions. Pooled libraries were sequenced using illumina NextSeq500 at Children’s Research Institute Sequencing Facility.

treatment_protocol: No treatments were applied to the biological material prior to extraction.

value: Embryonic fibroblast

value: WT


title: 2701, Cre-, AngII

description:
10x Genomics
NUC230517SG_6

tag: Sex


title: WT2

description: Library name: WT2


title: female, intestinal epithelium, Tacr2null, high fat diet, acute, biological replicate 3

description: Library name: Sample 31

value: female

value: high fat diet one week


title: scRNA_MicePanc1_AndCellCulturePanc1

description: Library name: scRNA_MicePanc1_AndCellCulturePanc1

data_processing:
Demultiplexing was performed using CogentAP (Takara Bio).
Assembly: GRCh38
Supplementary files format and content: Count Matrices for the respective samples

extract_protocol:
Cell suspensions were dispensed into the Takara ICELL8 nano-well chips.
full-length SMART-Seq ICELL8 Reagent Kit was used to generate libraries according to the manufecturer protocol. In brief cDNA was synthesized, illumina libraries were generated with P5, P7 and Tn5 mixture. Following chip extraction and library pooling they were size selected using Agencourt AMPure XP magnetic beads (Beckman Coulter).

value: Pancreas

value: Cell line

value: Carrier/DMSO and Inflachromene


title: 2743, Cre-, AngII

description:
10x Genomics
NUC230517SG_4


title: female, intestinal epithelium, Tacr2null, high fat diet, acute, biological replicate 2

description: Library name: Sample 30


title: scATAC_ICM_Mouse35

description: Library name: scATAC_ICM_Mouse35

library_source: genomic single cell

data_processing:
cellranger-atac-2.1.0
Assembly: refdata-cellranger-arc-GRCh38-2020-A-2.0.0
Supplementary files format and content: XXX.barcodes.tsv: text file containing cellular barcodes of the sample.
Supplementary files format and content: XXX.matrix.mtx: accessibility matrix per cell
Supplementary files format and content: xxx.peaks.bed: peak file with chromosome, start and end positions for each detected peak

extract_protocol:
according to the 10x “Nuclei isolation for Single Cell ATAC Sequencing” demonstrated protocol (Document CG000169 Rev E) with shortened lysis time of 1min
according to the respective 10x user guide “Chromium Next GEM Single Cell ATAC Reagent Kits V2” (document CG000496 Rev B)

value: Inflachromene


title: RKO3

description: Library name: RKO3

value: Ranbp2 KO


title: 2583, Cre+, Saline

description:
10x Genomics
NUC230517SG_3

value: Male


title: female, intestinal epithelium, Tacr2null, high fat diet, acute, biological replicate 1

description: Library name: Sample 29

value: intestinal epithelium


title: RKO2

description: Library name: RKO2


title: scATAC_ICM_Mouse11

description: Library name: scATAC_ICM_Mouse11


title: female, intestinal epithelium, Tacr2null, low fat diet, biological replicate 4

description: Library name: Sample 28

value: low fat diet


title: 2580, Cre+, AngII

description:
10x Genomics
NUC230517SG_2

value: Cre+

value: Whole Kidney

value: All Kidney Cells


title: scATAC_Control_Mouse31

description: Library name: scATAC_Control_Mouse31

value: Carrier


title: RKO1

description: Library name: RKO1


title: 2584, Cre-, Saline

description:
10x Genomics
NUC230517SG_1

value: Cre-

value: Saline


title: scATAC_Control_Mouse12

description: Library name: scATAC_Control_Mouse12


title: female, intestinal epithelium, Tacr2null, low fat diet, biological replicate 3

description: Library name: Sample 27


title: Primed EpiLC, Input, ChIP-seq

value: E14 Tg2a Bay Genomics

value: Mouse embryonic stem cells

value: Primed EpiLC