title: ChIP_tbp_6h_rep4

city: MIAMI

first: Raghu

middle: Ram

last: Edupuganti

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

description: Library name: Sample 24

data_processing:
Raw FASTQ data were processed with Trimmomatic (v0.32) to remove low-quality reads and then aligned to the mouse genome (mm10) using STAR aligner v2.7.9a. We used deepTool2 to generate normalized bigwig (bamCoverage), and heatmaps (computeMatrix and plotHeatmap). Peaks were called using MACS2.1.2 with default parameters –shiftsize 75 –nomodel --extsize 200 –p 0.01 for all datasets. Whole cell extract input from the corresponding cell lines was used as a control. Peaks with fold change > 3 and a q-value < 0.01 were used for downstream analysis. Homer annotatePeaks v4.9.1-5 was used for peak annotation. BEDTools v2.28 function intersect was used to overlap common peaks. For TAF1 and TBP ChIP-seq experiments, spike-in normalization was performed using exogenous human chromatin. Trimmed reads were aligned to the mouse reference genome (mm10) using STAR aligner v2.7.9a79. To enable spike-in normalization, the same trimmed reads were also aligned separately to the human genome (hg19), and normalization factors were calculated based on the number of uniquely mapped human reads per sample. Subsequently, mouse-aligned BAM files were used to generate normalized coverage tracks. BigWig files were produced using bamCompare from the deepTools284, incorporating the --scaleFactorsMethod readCount option, and only uniquely mapped reads were retained for visualization and downstream analyses.
Assembly: mm10
Supplementary files format and content: The processed data files are in bigWig format.

source_name: Embryonic origin

growth_protocol: E14 ESCs were routinely grown on 0.1% gelatin coated plates in DMEM (high glucose, GlutaMAX Supplement) medium supplemented with 1 mM sodium pyruvate, 100 U/mL penicillin/100 U/mL streptomycin, 1X MEM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 15% Embryonic stem-cell FBS, and 1000 U/mL recombinant leukemia inhibitory factor (LIF). Cells were cultured at 37°C with 5% CO2. INTS11DEG cells were routinely maintained in ESC medium containing 10 µM trimethoprim.

extract_protocol:
ESCs were washed with PBS and fixed with ChIP cross-link GOLD reagent in PBS containing 1 mM MgCl2 for 30 minutes at room temperature. The cells were washed twice with PBS and fixed with 1% Formaldehyde for 10 minutes. Formaldehyde was quenched by the addition of Glycine to 125 mM. Fixed cells were scrapped and washed twice with chilled PBS, pelleted, and resuspended in NP Rinse 1 buffer (50 mM HEPES, pH 8.0, 140 mM NaCl, 1 mM EDTA, pH 8.0, 0.5 mM EGTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and incubated for 10 min on ice to isolate nuclei. The cells were pelleted at 1200g for 10 min and resuspended in NP1 Rince buffer 1 again and incubated for a further 10 min on ice and pelleted at 1200g.  The resulting nuclei were suspended in NP Rinse 2 buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 0.5 mM EGTA, pH 8.0, 200 mM NaCl) and incubated on ice for 10 min. The pellet was washed twice with shearing buffer (10 mM Tris-HCl, pH 8.0, 0.1% SDS, 1 mM EDTA, pH 8.0) without disturbing the pellet. Pellets were resuspended in shearing buffer with protease and phosphatase inhibitor cocktail and sonicated in a Covaris E220 sonicator for 20 min using settings 5% duty cycle, PIP 140 and 200 cycles burst, to generate DNA fragments between approximately 200 and 1,000 bp in length. Insoluble material was pelleted by centrifugation for 15 min at 16,000g. Chromatin was immunoprecipitated overnight at 4 °C with antibodies bound to ChIP-grade Protein A/G Magnetic beads in ChIP buffer (50 mM HEPES, pH 7.5, 300 mM NaCl, 1 mM EDTA, pH 8.0, 1% Triton X-100, 0.1% DOC, 0.1% SDS). After incubation, bead slurry was washed 5 times with ChIP buffer, once with DOC buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% DOC, 1 mM EDTA pH 8.0) and once with TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0). Chromatin was eluted with elution solution (0.1% NaHCO3, 1% SDS, and 1 mM EDTA) by incubating at 55 degrees for 15 min. After RNase A and Proteinase K digestion and de-crosslinking at 65 °C overnight, DNA was extracted with ChIP DNA Clean & Concentrator. In case of TAF1 and TBP ChIP-seq, human chromatin was used as a spike-in control. Experimental chromatin samples were mixed with a defined amount of HeLa cell chromatin, prepared using the same protocol as for the experimental ChIP-seq samples.
A minimum of 2 ng of DNA was used for library preparation according to the NEBNext Ultra II DNA Library Prep Kit for Illumina. Purity and size distribution were analyzed on Tapestation 2200. The constructed libraries were pooled and subjected to single-end sequencing with 75 base pairs read length on a NextSeq 500 platform.

treatment_protocol: To deplete INTS11DEG, cells were washed twice with PBS to remove Trimethoprim. After two washes, fresh ESC medium and DMSO (1µl/ ml) were added to the cells for 0, 3  or 6 hrs.

value: Embryonic origin

value: Mouse Embryonic Stem cells

value: INTS11 degron

value: 6 hr fresh media

tag: antibody

value: TBP


title: RNA_Prim_B92_IFNG_rep2

status: Public on Aug 08 2025

type: SRA

city: New York

first: Richard

last: Koche

state: New York

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: Library name: RNA_Prim_B92_IFNG_rep2

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Reads were aligned to mouse assembly mm9 with STAR v2.4 using default parameters
Assembly: mm9
Supplementary files format and content: Raw counts table

molecule: polyA RNA

organism: Mus musculus

source_name: thyroid

growth_protocol: Cells were grown in F12 Coons', 5% FBS, 1% PSG

extract_protocol:
For RNA-seq, RNA was extracted from cells utlizing TRIzol protocol according to the manufacturers instructions (Thermo Fisher Scientific).
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with either DMSO, 20ng/ml murine interferon gamma, 10nM trametinib or the combination of interferon gamma and trametinib for 96 hours.

tag: tissue

value: thyroid

tag: cell line

value: anaplastic thyroid cancer cell line Braf-CAV600E/p53

tag: cell type

value: primary tumor

tag: genotype

tag: treatment

value: IFNγ (20ng/ml)


title: ChIP_tbp_6h_rep3

state: FL

description: Library name: Sample 23

library_source: genomic

molecule: genomic DNA


title: RNA_Prim_B92_IFNG_rep1

description: Library name: RNA_Prim_B92_IFNG_rep1


title: ATAC_Prim_B92_IFNG_rep1

description: Library name: ATAC_Prim_B92_IFNG_rep1

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Version 2.3.4.1 of bowtie2 was employed to align reads to mouse assembly mm9 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0.
Enriched regions were discovered using MACS2 with a p-value setting of 0.001 and then filtered for blacklisted regions.
The BEDTools suite was used to create normalized bigwig files scaled to a sequencing depth of 10 million uniquely mapped fragments.
Assembly: mm9
Supplementary files format and content: normalized bigwigs

extract_protocol:
For ATAC-seq, cells were lysed and incubated with transposition reaction mix containing PBS, 1% Digitonin, Tween-20, and Transposase (llumina). Samples were incubated for 30 minutes at 37C in a thermomixer at 1000rpm. Prior to amplification, samples were concentrated with the DNA Clean and Concentrator Kit-5 (Zymo).
Libraries were prepared for sequencing using standard Illumina protocols


title: RNA_Prim_B92_Tram_rep2

description: Library name: RNA_Prim_B92_Tram_rep2

value: trametinib (10nM)


title: ChIP_tbp_6h_rep2

description: Library name: Sample 22


title: Spg Cells, H3K27me3, Dnmt3CKO/KO, rep2

city: Mainz

first: Joan

last: Barau

address: 4 Ackermannweg

country: Germany

institute: Institute of Molecular Biology IMB - Mainz

data_processing:
Paired-end reads were quality-trimmed using Trim Galore (v.0.6.10) with a minimum read length of 10 bp, and quality reports were generated using FastQC.
Reads were aligned to the mm10 reference genome using Bowtie2 (v.2.5.3) in local alignment mode  allowing a minimum fragment length of 10 bp and a maximum of 1000 bp, while excluding mixed and discordant alignments.
BAM files were first indexed using Samtools (v.1.10). Then, BigWig files were generated from the BAM files using bamCoverage (v. 2.27.1) , with normalization set to RPGC.
Peak calling was performed using MACS2 (v.2.1.2) on aligned BAM files, specifying the corresponding IgG file as control BAM. The analysis was conducted using broad peak calling mode, with genome size set to 'mm' (for mouse) and otherwise default settings.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak
Library strategy: CUT&Tag

source_name: testes

extract_protocol:
Chromatin profiling was performed using the CUT&Tag protocol as described by Kaya-Okur et al. (2020). Briefly, cells were immobilized on concanavalin A-coated beads and incubated with a primary antibody specific to the histone modification of interest. Following binding with a secondary antibody, protein A-Tn5 transposase was added 1:400 to introduce sequencing adapters at target sites.
DNA was extracted using Zymo DNA Clean & Concentrator (Cat. No.: D4014) and ibraries were amplified by PCR using 15 amplification cycles.

value: testes

value: germ cells

value: Spermatogonia


title: SVZ NSC lineage cell, OB rep1 [OB1_588405]

city: Heidelberg

first: Leo

middle: Carl

last: Förster

state: Deutschland

address: Im Neuenheimer Feld 581

institute: DKFZ

library_source: transcriptomic single cell

data_processing:
Read1 sequences were processed to extract and trim UMIs, storing them in the FASTQ identifier field. Processed paired-end reads were trimmed using trim-galore v0.5.0 and mapped to the mm10 genome reference with Ensembl96 gene annotations using STAR v2.5.3a setting "--bamRemoveDuplicatesType UniqueIdentical --outFilterMismatchNmax 9999 --outFilterScoreMinOverLread 0.2 --outFilterMatchNminOverLread 0.2 --alignSJoverhangMin 3 --alignSplicedMateMapLminOverLmate 0.2 --twopassMode Basic". UMI-containing readpairs were quantified with a custom script based on HTSeq to identify exonic and intronic UMIs and deduplicate them, reporting a merged UMI-counts matrix.  Cell transcriptomes were subset to 1:1 human-mouse orthologs reported in Ensembl102 to be consistent with our downstream human analyses. We excluded cells with fewer than 2000 UMIs or under 500 detected genes.
Assembly: mm10
Supplementary files format and content: counts: comma separated matrix of deduplicated UMI counts per cell (columns) per gene (rows). Metadata: comma separated matrix relating metdata (columns) per cell (rows)

source_name: Brain, olfactory bulb

extract_protocol:
RNA molecules were captured using an oligo dT(30) primer. mRNA was reverse-transcribed using a template switching oligonucleotide contianing an 8 bp unique molecular identifier to obtain cDNA which was subsequently amplified and purified using AMPureXP beads.
Purified cDNA was then used for Illumina Nextera XP library preparation according to Hagemann-Jensen et al. 2020 with modifications reported in Cerrizuela and Kaya et al. 2022.

value: Brain, olfactory bulb


title: Spg Cells, H3K9me3, Dnmt3CKO/KO, rep2


title: ChIP_tbp_3h_rep3

description: Library name: Sample 19

value: 3 hr fresh media


title: Spg Cells, H3K4me3, Dnmt3CKO/KO, rep2


title: ChIP_tbp_6h_rep1

description: Library name: Sample 21


title: ChIP_tbp_3h_rep4

description: Library name: Sample 20


title: SVZ NSC lineage cell, OB rep1 [OB1_588399]


title: ChIP_tbp_3h_rep1

description: Library name: Sample 17


title: ChIP_tbp_0h_rep4

description: Library name: Sample 16

value: 0 hr fresh media


title: SVZ NSC lineage cell, OB rep1 [OB1_588401]


title: Spg Cells, IgG, Control, rep2

value: wild type


title: Spg Cells, H3K9me2, Dnmt3CKO/KO, rep2


title: ChIP_tbp_0h_rep3

description: Library name: Sample 15

value: Embryonic origin


title: SVZ NSC lineage cell, OB rep1 [OB1_588403]


title: ChIP_tbp_0h_rep2

description: Library name: Sample 14

value: Mouse Embryonic Stem cells


title: ChIP_tbp_0h_rep1

description: Library name: Sample 13

value: INTS11 degron


title: SVZ NSC lineage cell, OB rep1 [OB1_588393]


title: ChIP_tbp_3h_rep2

description: Library name: Sample 18


title: Spg Cells, H3K4me3, Control, rep2


title: SVZ NSC lineage cell, OB rep1 [OB1_588391]


title: ChIP_TAF1_6h_rep2

description: Library name: Sample 10

value: 6 hr fresh media


title: ChIP_TAF1_6h_rep1

description: Library name: Sample 9


title: SVZ NSC lineage cell, OB rep1 [OB1_588389]


title: ChIP_TAF1_6h_rep3

description: Library name: Sample 11


title: Spg Cells, H3K9me3, Control, rep2


title: ChIP_TAF1_3h_rep4

description: Library name: Sample 8


title: SVZ NSC lineage cell, OB rep1 [OB1_588387]


title: Spg Cells, H3K9me2, Control, rep2


title: ChIP_TAF1_3h_rep2

description: Library name: Sample 6


title: ChIP_TAF1_3h_rep1

description: Library name: Sample 5


title: Spg Cells, IgG, Dnmt3CKO/KO, rep1


title: ChIP_TAF1_3h_rep3

description: Library name: Sample 7


title: SVZ NSC lineage cell, OB rep1 [OB1_588383]


title: ChIP_TAF1_0h_rep3

description: Library name: Sample 3


title: Spg Cells, H3K27me3, Dnmt3CKO/KO, rep1


title: ChIP_TAF1_0h_rep4

description: Library name: Sample 4


title: Spg Cells, H3K4me3, Dnmt3CKO/KO, rep1


title: Spg Cells, H3K27me3, Control, rep2


title: SVZ NSC lineage cell, OB rep1 [OB1_588381]


title: ChIP_TAF1_0h_rep1

description: Library name: Sample 1


title: SVZ NSC lineage cell, OB rep1 [OB1_588395]


title: Spg Cells, H3K9me3, Dnmt3CKO/KO, rep1


title: SVZ NSC lineage cell, OB rep1 [OB1_588379]


title: ChIP_TAF1_6h_rep4

description: Library name: Sample 12


title: KO+CLP1

city: wuhan

first: Hong

last: Duo

address: No. 169 East Lake Road, Wuchang District

country: China

institute: Zhongnan Hospital of Wuhan University

description: Library name: D1

data_processing:
Raw reads were filtered using fastp to remove adapter sequences, low-quality reads, and reads with >10% N bases.
Clean reads were mapped to the Mus musculus reference genome (GRCm38/mm10) using HISAT2.
Transcript assembly and quantification were performed using StringTie.
Gene expression levels were normalized as FPKM (fragments per kilobase per million reads).
Differential expression analysis was conducted using the DESeq2 package in R. Genes with adjusted P-value < 0.05 were considered differentially expressed.
Assembly: GRCm38/mm10
Supplementary files format and content: A gene expression matrix in tab-delimited text format was provided. Rows represent genes, columns represent samples, and values are normalized expression levels (FPKM).

molecule: total RNA

source_name: Liver

growth_protocol: Mice were housed under specific pathogen-free (SPF) conditions with a 12-hour light/dark cycle and free access to food and water.

extract_protocol:
Total RNA was extracted from kidney tissue using TRIzol reagent (Invitrogen) following the manufacturer’s protocol. RNA purity and integrity were assessed using NanoDrop and Agilent 2100 Bioanalyzer.
Poly(A)+ RNA was enriched using oligo(dT) magnetic beads and fragmented. First- and second-strand cDNA synthesis was performed, followed by end repair, A-tailing, adapter ligation, and PCR amplification. Libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit (NEB) and sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Mice were randomly assigned to experimental groups and subjected to cecal ligation and puncture (CLP) or sham surgery. RP105 knockout mice were generated by CRISPR/Cas9. Liver tissues were collected 24 hours after surgery.

value: Liver

value: RP105 knockout

value: clp

tag: batch


title: ChIP_TAF1_0h_rep2

description: Library name: Sample 2


title: KO+CLP2

description: Library name: D2


title: Spg Cells, H3K4me3,Dnmt3CKO/KO, rep1


title: KO2

description: Library name: C2

value: sham


title: KO1

description: Library name: C1


title: CLP3

description: Library name: B3

value: WT


title: KO+CLP3

description: Library name: D3


title: SVZ NSC lineage cell, OB rep1 [OB1_588385]


title: SVZ NSC lineage cell, OB rep1 [OB1_588377]


title: CLP2

description: Library name: B2


title: SVZ NSC lineage cell, OB rep1 [OB1_588373]


title: Spg Cells, H3K27me3, Control, rep1


title: Spg Cells, H3K4me3, Control, rep1


title: Wild type1

description: Library name: A1


title: SVZ NSC lineage cell, OB rep1 [OB1_588369]


title: Spg Cells, H3K9me3, Control, rep1


title: TSP2KO mouse (3mos) dermal fibroblasts sample3

city: New Haven

first: Yaqing

last: Huang

state: CT

address: 10 Amistad Room 304A

department: Pathology

institute: Yale University

description: Library name: TK3

data_processing:
Sequencing data were aligned to the mouse genome (mm10) using Cell Ranger (10x Genomics). The raw matrix was then analyzed with the Seurat R package (version 5.0.3) [26]. Cells with low-quality reads (nFeatures < 300, or mitochondrial gene percentage < 0.1% or > 10%) were excluded during the QC process. A total of 18,193 and 20,134 cells remained for WT and KO samples (n=3), respectively, and these were merged and integrated using canonical correlation analysis (CCA) reduction (dims.use = 1:40). Graph-based clustering was performed using the FindClusters function in Seurat (resolution = 0.4, dims.use = 1:40), and markers for each cluster were identified using the FindAllMarkers function (min.pct = 0.5, log fold change > 0.25). Cluster visualization on a 2D map was done using uniform manifold approximation and projection (UMAP) via the RunUMAP function.
Given the uneven distribution of cell numbers across clusters, differential gene analysis between genotypes within individual clusters was performed to minimize confounding variance. Specifically, comparisons were made between individual KO and WT samples, resulting in the generation of nine gene lists. A scoring value was created to reflect the frequency of each gene across the nine gene lists. P-values were integrated using Fisher’s method. Genes were ranked based on Fisher p-value, average fold change (Avg Log2FC), ratio, power (Avg Log2FC × ratio), and score (frequency across datasets). Genes with a score of 6 or higher were selected for further analysis. Downstream GO pathway and network analysis were performed using the STRING database (https://string-db.org/).
For cell-cell communication analysis, cells were processed using the NICHES package [28]. Autocrine signaling in endothelial, epithelial, and immune cells were excluded to focus specifically on fibroblast interactions. The signaling archetypes were annotated based on the sending and receiving cell types, with most interactions being related to fibroblast autocrine pathways.  Cell-cell signaling edges were down-sampled to mitigate sample variation due to sample size and integrated with rpca (resolution = 0.2, dims.use = 29). Differential cell-cell signaling between genotypes was explored using the FindMarkers function.
For bulk RNA-seq data, FASTQ files from individual samples were inputted and analyzed using the Partek Flow platform. Specifically, reads were aligned to the mouse reference genome (mm10) using STAR within the platform [31]. The aligned reads were then mapped to known transcripts using RefSeq as the annotation model. Low-expression genes (features < 10) were filtered out, and the remaining counts were normalized based on the median ratio (DESeq2 only). Following normalization, principal component analysis (PCA) and differential analysis were performed. A list of 462 genes was generated using thresholds of FDR < 0.05 and fold change > 1.5 or < -1.5. Downstream pathway analysis, including GO pathways and GSEA, was conducted using the STRING database (https://string-db.org/) and the Web-based Gene Set Analysis Toolkit (https://www.webgestalt.org).
Assembly: mouse reference genome (mm10)
Supplementary files format and content: All_Annotated_V2.Robj - All isolated cells together, final cleaned/clustered/classed Seurat object (R object)
Supplementary files format and content: fibro.integrated.Robj - Cell-cell signaling between fibroblasts, final downsampled, integrated, and annotated

source_name: skin

extract_protocol:
Dermal fibroblasts (DFs) were isolated from 12-week-old WT and TSP2KO mouse dorsal skin according to the established protocol. Briefly, mouse dorsal skins were shaved, excised, treated with 5% antibiotic-antimycotic (Gibco), and incubated in 25 μg/ml Trypsin (Sigma) overnight at 4°C. After separation from the epidermis and adipose tissue, the dermis was physically disrupted and then digested using collagenase IV (Worthington Biochemical) for 3 hrs under 37 °C. After centrifuge, cell pellet was then resuspended in 25mM glucose Dulbecco’s Modified Eagle Medium (DMEM, Gibco) with 10% (v/v) fetal bovine serum (FBS, Peak Serum Inc) and 1% (v/v) penicillin-streptomycin (P/S, Gibco) and culture for 3-5 days to enrich the fibroblast population. For single-cell RNA sample preparation, after the enrichment assay, fibroblasts were lifted using trypsin (Sigma), suspended in PBS at a concentration of 1000 cells/µl, and passed through a 100 µm cell strainer (BD Bioscience). For bulk RNA sequencing, RNA was isolated from passage 1 fibroblasts using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
The single-cell suspension was sent to the Yale Microarray Center, where library preparation was performed using the Chromium Next GEM single-cell 3’ v3 reagent kit (10x Genomics). For bulk-RNA sequencing, approximately 2 µg of RNA per sample was sent to the Yale Genomics Core for sequencing using the Illumina TruSeq Stranded mRNA kit (Illumina).

value: skin

value: Primary dermal fibroblasts

value: Fibroblasts


title: SVZ NSC lineage cell, OB rep1 [OB1_588365]


title: Spg Cells, H3K9me2, Control, rep1

value: testes

value: germ cells

value: Spermatogonia


title: TSP2KO mouse (3mos) dermal fibroblasts sample1

description: Library name: TK1


title: WT mouse (3mos) dermal fibroblasts sample3

description: Library name: WT3


title: Spg Cells, IgG, Control, rep1


title: ID793

city: Hannover

first: Karen

middle: I.

last: Lopez-Cayuqueo

address: Carl-Neuberg-Str.1,30625 Hannover

department: Department of Nephrology and Hypertension

institute: Hannover Medical School (MHH)

description: Library name: Sample8

data_processing:
Provided FASTQ files were aligned using STAR and the mm9 genome, reads were counted using featureCounts with -p -t exon -O -g gene_id -s 0. Sequencing quality was assessed using FASTQC.
Assembly: mm9
Supplementary files format and content: Raw Counts

source_name: Kidney

extract_protocol:
Total RNA was extracted from whole kidney samples using the RNeasy Mini Kit (Qiagen #74104).
Library construction and sequencing was performed by Novogene (Cambridge, UK). Libraries were sequenced on Illumina NovaSeq 6000 flow cells (paired-end, 150bp).

value: Kidney


title: SVZ NSC lineage cell, OB rep1 [OB1_588361]

value: Brain, olfactory bulb


title: WT mouse (3mos) dermal fibroblasts sample2

description: Library name: WT2


title: WT mouse (3mos) dermal fibroblasts sample1

description: Library name: WT1


title: ID761

description: Library name: Sample5


title: SVZ NSC lineage cell, OB rep1 [OB1_588355]


title: ID792

description: Library name: Sample7


title: mouse uterus, Dysplastic-125DPI, V16, Visium

city: Ithaca

first: Matalin

last: Pirtz

address: 147 Grandview Ct., #147LA

institute: Cornell University

description: Fresh frozen, 10X Genomics (Single Cell 3' v3)

data_processing:
The raw sequencing reads were aligned to the custom mm39 + tdTomato sequence reference genome and quantified using the cellranger (v7.1.0, 10x Genomics) or spaceranger (v2.1.1, 10x Genomics) count function. The outputs are barcode, feature, and matrix files for further analysis involving gene counts
Assembly: mm39 + tdTomato sequence
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

source_name: uterus

extract_protocol:
scRNA - Mice were sacrificed at various time points in the diestrus phase of the estrous cycle. Each mouse was collected and processed independently to generate single-cell suspensions. Both uterine horns of individual mice were collected and placed in sterile 1X PBS containing 100 IU ml-1 of penicillin and 100 μl ml-1 streptomycin (Corning, 30-002-Cl). A portion of one uterine horn per mouse was set aside in 4% paraformaldehyde at 4˚C for paraffin embedding. The remaining uterine horns were placed in a 200 μL drop of the same PBS solution, cut open lengthwise, and minced into 1.5-2.5 mm pieces with scalpels. Minced tissues were transferred with the help of a sterile, wide bore 200 μl pipette tip into a 15 ml centrifuge tube containing 2 ml of the same PBS solution and then centrifuged for 6 minutes at 400 rcf at 4˚C. Then, the minced tissues for individual mice were digested using a Papain Dissociation System (Worthington Biochemical Corporation, New Jersey). Tissue was digested in papain mixture from the kit at 37˚C for 1.5 hours with periodic mechanical perturbation. After papain digestion, the papain was inhibited with 3 ml of our stop solution, a DMEM/FBS solution (DMEM Ham’s F12, Corning 10-092-CV; 20% fetal bovine serum [FBS], Sigma-Aldrich F4135; and 0.1 mg ml-1 DNase I, Stem Cell Technologies 07900). Cell suspension was placed in a new tube. Cells were centrifuged as before, and the supernatant was removed. Next, 1.35 ml of the albumin-ovomucoid inhibitor provided by the kit was added to the suspended cells, and the cells were resuspended gently. The reaction was stopped using 3 ml of our stop solution, mixed, and then cells were spun down at the same rate as before. The supernatant was removed, and the pellet was resuspended in 2 ml of 0.25% TrypLE Express Enzyme solution (Invitrogen, 12604013) prewarmed to 37˚C. The tube was then incubated at 37˚C with a loose cap for 10 minutes in a 5% CO2 incubator. Cells were resuspended with a 1-ml pipette tip 40 times, and then digestion was inhibited with our stop solution. Cells were spun down and supernatant was removed before the addition of 1 ml Dispase-mUE (Dispase II [7 mg ml-1 DMEM Ham’s F12], Neutral Protease, Worthington NPRO2; and 10 μg μL-1 DNase). Cells were aspirated in the solution gently 40 times using a 1 ml pipette tip. Then suspensions were filtered through a 35 μm filter (Falcon 08-771-23) to remove debris, and remaining cells were spun down. Cells were resuspended in 100 μl A-scR-Medium (5% FBS in DMEM Ham’s F12 with 1 mM Y-27632 [Toris 1257], placed on ice and transferred to Cornell’s Genomics Core for single-cell RNA sequencing for library preparation.
Visium - Mouse uteri from Doxycyline induced Pax8-rtTA Tre-Cre Trp53loxP/loxPRb1loxP/loxP Ai9 experimental mice and control littermates were dissected and frozen in O.C.T. (Tissue Tek O.C.T. Compound, VWR, 25608-930) filled molds (Disposable Based Molds, 15 x 15 mm, VWR, 60872-488) on a metal block chilled in dry ice for 10 minutes. Molds were wrapped in aluminum foil, placed and sealed in zip lock plastic bags and stored at -80°C (10xGenomics, protocol CG000240RevD). Embedded samples, and all materials for cryosectioning were equilibrated in a cryostat (Leica CM1950) chamber temperature -21°C (object head, -16°C) for 30 minutes. Transverse uterus sections of 10µm thickness were placed on chilled Visium Tissue Optimization Slides (10xGenomics, 1000191 Slide Kit), and Visium Spatial Gene Expression Slides (10xGenomics, 1000187 Slide Kit). Tissues processed on the Visium Tissue Optimization Slides (10xGenomics, protocol CG000238RevD) indicated the optimal uterine tissue permeabilization time was 12 minutes. For tissue optimization experiments Tiff fluorescent images (Microscope Olympus EX51, Camera Olympus XM10) were captured with a TRITC filter cube, 2x objective, and 700-ms exposure time. Uterine tissues on Visium Spatial Gene Expression Slides were processed for Hematoxylin & Eosin (H&E) staining (10xGenomics, protocol CG000160RevC). Immediately after staining, digital brightfield histology images were taken at 40x (Leica BioSystems, Aperio ScanScope CS2). Without delay cDNA Synthesis, Second Strand Synthesis & Denaturation, and cDNA Amplification was performed (10xGenomics, protocol CG000239RevE). Samples were frozen at -20°C and transferred to Cornell Genomics Facility for Quality Control (QC), Gene Expression Library Construction and sequencing.
scRNA - To begin single-cell RNA sequencing library preparation, cell aliquots were stained with trypan blue for live and dead cell calculation. Live cell preparations with a target cell recovery of 5,000 cells were loaded on a Chromium Controller (10X Genomics, Single Cell 3’ v3 chemistry) to perform single-cell partitioning and barcoding using the microfluidic platform device. The NextSeq500 System was used to sequence the cDNA library samples after barcode preparation.
Visium - The Illumina Sequencing parameters for all Visium samples were as follows, visium library preparations were run 2 times, they were re-balanced and re-pooled in between the 2 runs. The estimated dPCR was 2.5 nMol. Samples were run on a NextSeq2K P2 100bp flowell instrument, sequencing Kit NextSeq 2K P2 100 bp, read length 28+10+10+90, sequencing primer type TruSeq Compatible DNA/RNA, barcode type Dual barcode i7 and i5.

value: uterus

tag: estrous stage

value: diestrus

tag: sec stage

value: Dysplastic

value: Doxycycline, 125 DPI


title: mouse uterus, Dysplastic-112DPI, V14, Visium

value: Doxycycline, 112 DPI


title: ID765

description: Library name: Sample4


title: Wild type2

description: Library name: A2

value: Liver


title: ID791

description: Library name: Sample6


title: mouse uterus, Pre-dysplastic-43DPI, V13, Visium

value: Pre-dysplastic

value: Doxycycline, 43 DPI


title: mouse uterus, Dysplastic-131DPI, V15, Visium

value: Doxycycline, 131 DPI


title: SVZ NSC lineage cell, OB rep1 [OB1_588367]


title: SVZ NSC lineage cell, OB rep1 [OB1_588351]


title: ID764

description: Library name: Sample3


title: SVZ NSC lineage cell, OB rep1 [OB1_588349]


title: ID760

description: Library name: Sample1


title: mouse uterus, Pre-dysplastic-34DPI, V12, Visium

value: Doxycycline, 34 DPI


title: TSP2KO mouse (3mos) dermal fibroblasts sample2

description: Library name: TK2

value: skin

value: Primary dermal fibroblasts


title: SVZ NSC lineage cell, OB rep1 [OB1_588363]


title: ID763

description: Library name: Sample2


title: CLP1

description: Library name: B1

value: WT

value: clp


title: SVZ NSC lineage cell, OB rep1 [OB1_588347]


title: Zbtb16_KO, IGF2BP3, RIP

city: Shanghai

first: Wuchan

last: Wang

address: Tongji University

institute: Tongji University

data_processing:
BCL files were converted to demultiplexed fastq files with bcl2fastq. The quality of fastq files was checked with fastqc. The fastq files were trimmed and aligned to mouse genome mm39 using GENCODE annotation with STAR allowing for the two mismatches. Gene counts were obtained using FeatureCounts function of the Subread package.
Assembly: GRCm39/mm39
Supplementary files format and content: bigWig, narrowPeak (except for lnput sample)

extract_protocol:
Cells generated from cardiac differentiation at day 5.3 were crosslinked by UV and harvested by trypsinization. Cells were lysed with RIP buffer (100 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 7.0, 0.5% NP-40, 1× protease inhibitor, and 1 mM dithiothreitol) supplemented with RNase inhibitor and sonicated. 3 μg of IGF2BP3 antibody, or control rabbit IgG antibody, was conjugated to protein A/G magnetic beads by incubation at 4°C overnight. Beads were washed three times, then incubated with cell lysates in RIP buffer at 4°C for 6 h. After three washes with RIP buffer, the beads were resuspended in 80 μl of 1× PBS, followed by DNA digestion at 37°C for 15 min and incubation with 50 μg of proteinase K at 55°C for 1 h.
Input and co-immunoprecipitated RNAs were extracted using RNAiso Plus reagent and analyzed by RNA-seq.

value: mouse embryonic stem cell line

value: Zbtb16 knockout

value: cardiomyocyte differentiation

tag: time

tag: rip antibody


title: mouse uterus, Pre-dysplastic-34DPI, V11, Visium

value: uterus


title: Ctrl, Input


title: Ctrl, IGF2BP3, RIP


title: 100 NaCl, 8794-JO-8

city: Nashville

first: Juan

middle: Pablo

last: Arroyo

state: TN

address: 1161 21st Ave South MCN C3111

department: Medicine

institute: Vanderbilt University Medical Center

data_processing:
Paired-end RNA sequencing reads were trimmed and filtered for quality using Trimgalore v0.6.7 (Krueger et al., 2023). Trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) (Dobin et al., 2013) v2.7.9a with the –quantMode GeneCounts parameter against the mm10 mouse genome and GENCODE comprehensive gene annotations (Release M23). ~37-60 million uniquely mapped reads were acquired per sample. DESeq2 package v1.34.0 (Love et al. 2014) was used to perform normalization.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing normalized counts for each sample

source_name: kidney

growth_protocol: Cells were cultured high-glucose and pyruvate-containing DMEM supplemented with 10% FBS and 100 IU/mL penicillin plus 100 (μg/mL) streptomycin and grown to confluency

extract_protocol:
Trizol (Sigma) extraction per manufacturer's protocol
SuperScript IV (Thermo Fisher) per manufacturer's protocol

treatment_protocol: 12 hrs of FBS free DMEM +/- 100 mmol NaCl

value: kidney

value: IMCD

value: duct cells

value: 100 NaCl


title: SVZ NSC lineage cell, OB rep1 [OB1_588335]

value: Brain, olfactory bulb


title: 100 NaCl, 8794-JO-7


title: mouse uterus, Dysplastic-80DPI, V08-left, Visium

value: diestrus

value: Dysplastic

value: Doxycycline, 80 DPI


title: 100 NaCl, 8794-JO-6


title: SVZ NSC lineage cell, OB rep1 [OB1_588357]


title: mouse uterus, Pre-dysplastic-34DPI, V09, Visium

value: Pre-dysplastic

value: Doxycycline, 34 DPI


title: Zbtb16_KO, Input


title: 100 NaCl, 8794-JO-5


title: Control, 8794-JO-4

value: Control


title: S6_naive_inf

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: 10x Genomics

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Cell Ranger v7 was used for barcode processing, abundance estimation and aggregation. (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
Assembly: mm10
Supplementary files format and content: aggregated h5 file with cell barcode suffix tags indicating sample/capture source

source_name: lung

extract_protocol:
Lungs from mice at day 3 p.i. were processed to single-cell suspensions as described above. Single-cell suspensions were subjected to magnetic sorting using MojoSort™ Mouse anti-PE Nanobeads (BioLegend, #480080) to remove IV-positive, PE-tagged cells. Suspensions were subjected to magnetic separation a total of four times before the negative fraction was resuspended in buffer and counted.
Cell suspensions were captured in emulsion droplets using the Chromium Next GEM Single Cell 5’ GEM and Gel Bead Kits (10x Genomics, #1000244 and #1000264) on a 10x Chromium Controller. Amplification of cDNA and 5’ GEX library preparation and indexing were performed according to the manufacturer’s instructions using the Library Construction Kit and Dual Index Kit TT Set A (10x Genomics, #1000190 and #1000215).

treatment_protocol: At eight weeks old, mice were administered a first dose of prefusion-stabilized protein subunit vaccine based on the Wuhan-1 SARS-CoV-2 isolate (S-2P) through s.c. injection of either 0.5 µg of protein formulated with AddaVax (Invivogen, #vac-adx-10). The second dose was administered four weeks later and was the same amount as the first dose for each mouse. At approximately 30 days following the second dose of vaccine, mice were transferred to an animal biosafety level 3 (ABSL-3) facility and infected with SARS-CoV-2. Briefly, stock MA-SARS-CoV-2 or B.1.351 virus was diluted in sterile saline (Medline Industries, #RDI30296) to a working concentration of 2×107 PFU per milliliter (mL). Mice were anesthetized with isoflurane and infected i.n. with 50 microliters (µL) of virus solution (1×106 PFU) per mouse.

value: lung

tag: vaccination

value: naive

tag: infection

tag: cellbarcode suffix_tag


title: SVZ NSC lineage cell, OB rep1 [OB1_588327]


title: Control, 8794-JO-3


title: Control, 8794-JO-1


title: SVZ NSC lineage cell, OB rep1 [OB1_588325]


title: S4_mock

description: 10x Genomics

value: mock


title: S5_mock

description: 10x Genomics


title: mouse uterus, Normal-130DPI, V01, Visium

value: Normal

value: Doxycycline, 130 DPI


title: SR1815, 4h, Replicate 5

city: Jupiter

first: Cameron

middle: James

last: Douglas

address: 120 Scripps Way

department: Chemistry

description: Library name: 782_10

data_processing:
Raw FASTQ reads were processed using the hpg_preprocess pipeline executed on a SLURM high-performance computing cluster. Quality control was performed on raw reads including adapter trimming, low-quality base removal, and whole-read filtering. Reads were aligned to the mouse reference genome (ENSEMBL GRCm38.r91) using STAR aligner. Post-alignment QC was conducted including contamination screening for rRNA, tRNA, mitochondrial, and mycoplasma sequences. Gene abundance was estimated using HTSeq (v0.11.2) with Python (v3.7.3).
Assembly: GRCm38.r91
Supplementary files format and content: Raw gene counts reported in the RawGeneCounts.csv file.

source_name: Primary Cortical Neuron

growth_protocol: Forebrains containing cortex and hippocampal formation were dissected from postnatal day 0 (PND 0) mouse pups to isolate primary cortical neurons in dissection media (culture grade H2O (Fisher Scientific: SH3052902), 10% 10x HBSS without Ca2+ and Mg2+ (Invitrogen: 14185052), 2% HEPES (Invitrogen: 15630080), 1% pyruvate (Invitrogen: 11360070), 1% glucose solution (Thermo: A2494001), and 0.02% Gentamicin (Invitrogen: 15710064). The cortices were placed in a digestion solution containing dissection media and 20 active units/mL of papain (Worthington: LS003124) for 30 min at 37 °C. Tissues were washed and triturated in plating medium consisting of Neurobasal (Invitrogen: 21103049) containing 5% FBS, heat inactivated (Invitrogen: 10082139), 2% Glutamax-I, (Invitrogen: 35050061), and 0.02% Gentamicin (Invitrogen: 15710064). Cells were then centrifuged for 5 min at 800xg and resuspended in plating medium at 300 µL per brain. Cell suspension was then diluted into feeding medium consisting of Neurobasal-A (Invitrogen: 10888022), 2% Glutamax-I, and 0.02% Gentamicin, 2% B-27 supplement (Invitrogen: 17504044),

extract_protocol:
On DIV 14 media was removed and 20 µL of DNA/RNA Shield (Zymo: R1100-50) was added to each well. Sample was collected and RNA was extracted using Zymo Quick-RNA MicroPrep kit (Zymo: R1050) following manufacturer protocol.
Libraries were prepped by The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology Genomics Core using a NEBNext Ultra II Direct RNA kit.

treatment_protocol: Neurons were isolated from Syngap1 conditional rescue (Syngap1+/ls) mice and plated using a BioTek EL406 (Agilent Technologies) into 384-well plates pre-coated with poly-D-lysine (PDL) (Aurora ABE2-01200B-PDL) at 15,000 cells in 80 µL/ well and placed in 37 °C incubator (42). A solution of 1% agarose was placed in the evaporation border wells prior to plating to minimize edge effects. On DIV 3, 10 µM 5-fluoro-2′-deoxyuridine (+FUDR) was added cultures to suppress the proliferation of glia. For 4 h treatments, 50% of media was replaced with fresh feeding media on DIV 3, 7, and 10.  On DIV 14 cultures were supplied vehicle or SR-1815 at 4.4 µM for 4 h through 50% media exchange.

value: Primary Cortical Neuron


title: Control, 8794-JO-2

value: kidney


title: mouse uterus, (S05: Normal-92DPI, V05-left; S06: Normal-111DPI, V05-right), Visium

value: uterus

value: S05:53LORLOAi9H; S06:P8R53LORLOAi9H

value: Doxycycline, (S05:92 DPI; S06:111 DPI)


title: mouse uterus, Dysplastic-97DPI, V06-right, Visium

value: Doxycycline, 97 DPI


title: S3_vax_inf

description: 10x Genomics

value: vax


title: S2_vax_inf

description: 10x Genomics


title: SVZ NSC lineage cell, OB rep1 [OB1_588317]

value: Brain, olfactory bulb


title: SR1815, 4h, Replicate 3

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description: Library name: 782_8


title: SVZ NSC lineage cell, OB rep1 [OB1_588337]


title: SVZ NSC lineage cell, OB rep1 [OB1_588319]


title: ChIP_SOX2_rep2

data_processing:
Raw FASTQ data were processed with Trimmomatic (v0.32) to remove low-quality reads and then aligned to the mouse genome (mm10) using STAR aligner v2.7.9a. We used deepTool2 to generate normalized bigwig (bamCoverage), and heatmaps (computeMatrix and plotHeatmap). Peaks were called using MACS2.1.2 with default parameters –shiftsize 75 –nomodel --extsize 200 –p 0.01 for all datasets. Whole cell extract input from the corresponding cell lines was used as a control. Peaks with fold change > 3 and a q-value < 0.01 were used for downstream analysis. Homer annotatePeaks v4.9.1-5 was used for peak annotation. BEDTools v2.28 function intersect was used to overlap common peaks.
Assembly: mm10
Supplementary files format and content: The processed data files are in bigWig format.

growth_protocol: E14 ESCs were routinely grown on 0.1% gelatin coated plates in DMEM (high glucose, GlutaMAX Supplement) medium supplemented with 1 mM sodium pyruvate, 100 U/mL penicillin/100 U/mL streptomycin, 1X MEM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 15% Embryonic stem-cell FBS, and 1000 U/mL recombinant leukemia inhibitory factor (LIF). Cells were cultured at 37°C with 5% CO2.

extract_protocol:
ESCs were washed with PBS and fixed with ChIP cross-link GOLD reagent in PBS containing 1 mM MgCl2 for 30 minutes at room temperature. The cells were washed twice with PBS and fixed with 1% Formaldehyde for 10 minutes. Formaldehyde was quenched by the addition of Glycine to 125 mM. Fixed cells were scrapped and washed twice with chilled PBS, pelleted, and resuspended in NP Rinse 1 buffer (50 mM HEPES, pH 8.0, 140 mM NaCl, 1 mM EDTA, pH 8.0, 0.5 mM EGTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and incubated for 10 min on ice to isolate nuclei. The cells were pelleted at 1200g for 10 min and resuspended in NP1 Rince buffer 1 again and incubated for a further 10 min on ice and pelleted at 1200g.  The resulting nuclei were suspended in NP Rinse 2 buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 0.5 mM EGTA, pH 8.0, 200 mM NaCl) and incubated on ice for 10 min. The pellet was washed twice with shearing buffer (10 mM Tris-HCl, pH 8.0, 0.1% SDS, 1 mM EDTA, pH 8.0) without disturbing the pellet. Pellets were resuspended in shearing buffer with protease and phosphatase inhibitor cocktail and sonicated in a Covaris E220 sonicator for 20 min using settings 5% duty cycle, PIP 140 and 200 cycles burst, to generate DNA fragments between approximately 200 and 1,000 bp in length. Insoluble material was pelleted by centrifugation for 15 min at 16,000g. Chromatin was immunoprecipitated overnight at 4 °C with antibodies bound to ChIP-grade Protein A/G Magnetic beads in ChIP buffer (50 mM HEPES, pH 7.5, 300 mM NaCl, 1 mM EDTA, pH 8.0, 1% Triton X-100, 0.1% DOC, 0.1% SDS). After incubation, bead slurry was washed 5 times with ChIP buffer, once with DOC buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% DOC, 1 mM EDTA pH 8.0) and once with TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0). Chromatin was eluted with elution solution (0.1% NaHCO3, 1% SDS, and 1 mM EDTA) by incubating at 55 degrees for 15 min. After RNase A and Proteinase K digestion and de-crosslinking at 65 °C overnight, DNA was extracted with ChIP DNA Clean & Concentrator.
A minimum of 2 ng of DNA was used for library preparation according to the NEBNextUltra II DNA Library Prep Kit for Illumina. Purity and size distribution were analyzed on Tapestation 2200. The constructed libraries were pooled and subjected to single-end sequencing with 75 base pairs read length on a NextSeq 500 platform.

value: Embryonic origin

value: Mouse Embryonic Stem cells

tag: chip antibody


title: SR1815, 4h, Replicate 4

description: Library name: 782_9


title: S1_naive_inf

description: 10x Genomics


title: SVZ NSC lineage cell, OB rep1 [OB1_588315]


title: SVZ NSC lineage cell, OB rep1 [OB1_588323]


title: mouse uterus, Normal-56DPI, V07-right, Visium

value: diestrus

value: Doxycycline, 56 DPI


title: ChIP_SOX2_rep1


title: SR1815, 4h, Replicate 2

description: Library name: 782_7


title: SVZ NSC lineage cell, OB rep1 [OB1_588313]


title: ChIP_OCT4_rep2


title: SVZ NSC lineage cell, OB rep1 [OB1_588311]


title: ChIP_OCT4_rep1


title: SR1815, 4h, Replicate 1

description: Library name: 782_6


title: Inguinal white adipose tissue, PTRF knockout adipose tissue from KNOCKOUT1 mice, snRNAseq

city: cehngsu

first: zhang

last: songling

state: China

address: wenjianqu

institute: Sichuan Agricultural University, Chengdu 611130, China

data_processing:
Raw reads from snRNA-seq were processed to generate generating count matrixes using CeleScope(v 1.14.1) pipeline with default parameter. Briefly, gene expression data were corrected using SoupX(v 1.16.2) to removal of ambient RNA signatures. Filtering of low-quality cells. For each sample, we performed doublet removal us ing DoubletFinder(v 2.0.3). DoubletFinder was run for each sample using principal components 1–20. nExp was set to 0.08 × nCells2/10,000, pN to 0.25 and pK to 0.09. Cells classified as doublets were then removed before additional analysis.
After filtering ambient mRNA and doublet cells for each sample. All sample were merged into a Seurat(v4.3.0) object. Select Feature_RNA>300 &percent.mt<20 &percent. HB<1 &nCount_ RNA>1000 cells. 21460 nucleis (Ptrf-/-: 9497, WT: 11963) were retained for the downstream analyses. then, use the standard process of Seurat for processing.
Data from different sample were normalized using the NormalizeData function with default options, and the top 2,000 most variable genes of each sample were calculated by Find VariableFeatures with the vst method. run RunPCA relied on 2000 variable gene. Then use the R package harmony (v1.0.3) performs batch effect removal (RunHarmony function). Using Seurat FindNeighbors (reduction= "harmony") ,FindClusters (resolution =0.17) to cluster cell. Clusters were identified with the Seurat functions FindNeighbors and FindClusters. Cluster-specific marker genes were unbiasedly analyzed using the 'FindAllMarkers' function in Seurat. Use=Wilcox, min.pct=0.1, logfc.threshold=0.25 to find all markers for each cluster(Table S3). Next, cluster identities were annotated based on top ranked marker genes, as well as expression of canonical marker genes as described in the manuscript. The cell clusters were visualized using the UMAP plots.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: inguinal white adipose

extract_protocol:
snRNA-seq samples was extracted from iWAT of 6-month-old mice(n = 2).
iWAT were isolated immediately and stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice after the surgery within 30 mins. The samples were washed in pre-cooled PBSE for three times, minced into small pieces, and then dissociated into nuclear suspensions using GEXSCOPE® Nucleus Separation Solution (Singleron Biotechnologies, Nanjing, China) refer to the manufacturer's product manual. The mixture was then centrifuged at 300 × g 4 ℃ for 5 mins to remove supernatant and resuspended in PBSE to 10^6 nuclei per 400μl. The isolated nuclei suspension was collected and filtered through a 40-micron sterile strainer. Finally, cell number and cell viability were measured by trypan blue staining microscopically. Nuclei were counted in a Luna cell counter and a nuclear density of 3-4 × 10^5 nuclei/mL were loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies).
Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. Individual libraries were sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: inguinal white adipose

tag: strain background

tag: age

value: 6 months old

value: PTRF knockout


title: SVZ NSC lineage cell, OB rep1 [OB1_588309]


title: ChIP_IgG_rep1

value: IgG (Invitrogen, #31235)


title: SVZ NSC lineage cell, OB rep1 [OB1_588307]


title: SVZ NSC lineage cell, OB rep1 [OB1_588305]


title: Inguinal white adipose tissue, PTRF knockout adipose tissue from KNOCKOUT2 mice, snRNAseq


title: Bone marrow-derived macrophages, FGK45-treated, NF-κB2 ChIP-seq

city: Wuhan

first: Shi

last: Chen

state: Hubei

address: 1095 Jiefang Avenue, Qiaokou District, Wuhan

institute: Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow was flushed from the tibias and femurs and passed through a 70um cell filter to remove fibrous tissue. Then, red blood cells were lysed with red blood cell lysis buffer. After centrifugation, washing, and resuspension, the bone marrow cells were cultured in Dulbecco's Modified Eagle Medium containing 10% heat-inactivated fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin, supplemented with 20 ng/mL murine macrophage-colony stimulating factor at 37°C, 5% CO2.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min and neutralized with 0.125 M glycine for 5 min at room temperature, and cells were washed with cold PBS and lysed in cold lysis buffer on ice. The cell lysate was sonicated and then incubated with anti-NF-κB2 antibody pre-coated on Dynabeads protein G (Life Technologies) at 4°C overnight. Immunoprecipitated products were collected and washed with RIPA buffer twice and LiCl washing buffer three times. Then, the immunoprecipitated products were digested with Proteinase K, and the formaldehyde cross-links were reversed. The purified DNA fragments were sent for high-throughput sequencing.
The purified DNA fragments were sent for high-throughput sequencing. Reads were mapped to the mouse genome (hg19) using “bowtie” software. Results from the ChIP-seq were visualized in Integrative Genomics Viewer.

treatment_protocol: Cells were treated with anti-mouse CD40 mAb (FGK4.5/FGK45) for 24h to activate, and the control groups were treated with IgG (Ctrl).

tag: strain

value: Bone marrow-derived macrophages

value: NF-κB2 (CST, D9S3M)

value: anti-CD40 mAb (FGK45)


title: Bone marrow-derived macrophages, IgG treated, NF-κB2 ChIP-seq

description: Ctrl

value: IgG


title: DMSO, 4h, Replicate 3

description: Library name: 782_3

value: Primary Cortical Neuron

value: DMSO


title: DMSO, 4h, Replicate 1

description: Library name: 782_1


title: SVZ NSC lineage cell, OB rep1 [OB1_588299]

tag: tissue


title: DMSO, 4h, Replicate 5

description: Library name: 782_5


title: Bone marrow-derived macrophages, IgG treated, INPUT

description: Ctrl-Input


title: DMSO, 4h, Replicate 2

description: Library name: 782_2


title: SVZ NSC lineage cell, OB rep1 [OB1_588329]


title: ST2 D0 24h scRNA-seq biol rep1

city: Kuopio

first: Ana

last: Hernández de Sande

email: anah@uef.fi, ahdesande@gmail.com

state: North-Savo

address: Yliopistonranta 1E

country: Finland

institute: University of Eastern Finland

description: 10x Genomics 3' scRNA-Seq

data_processing:
Demultiplexing, barcode processing (cell calling) and gene counting were carried out using the Cell Ranger pipeline (cellranger count, version 3.0.2; 10x Genomics) and the 10x Genomics combined mm10,hg19 reference transcriptome package. Additionally, a custom quantification was performed including miRNA genes and this raw count matrix is provided as additional file for each sample (version 6.1.1; 10x Genomics, cellranger count --include-introns).
Samtools was used to extract mouse reads corresponding to the cell barcodes that were assigned as mouse cells.
Assembly: mm10
Supplementary files format and content: Tab-separated files and matrix files from the filtered_feature_bc_matrix folder of Cell Ranger count pipeline output. Custom gtf file was used that contains microRNA genes.
Supplementary files format and content: Counts combined for protein-coding and mIRNA genes are provided in .h5ad file.

growth_protocol: Cells were cultured in RPMI1640 (Lonza) supplemented with 10% FBS (Gibco, Thermo Fisher) and 1% L-glutamine (Gibco, Thermo Fisher).

extract_protocol:
ST2 cells were passed through the strainer (40 μm Flowmi Cell Strainer, H13680-0040). Human and mouse samples were mixed in equal ration and loaded to Chromium Controler.
The Chromium Single Cell 3’ Kit (v2 Chemistry; 10x Genomics) was used to prepare scRNA-Seq libraries.

tag: cell line

value: WT


title: panKla, 0.5mM, Trophs, rep2

city: Cambridge

first: Sida

last: Ye

state: Massachusetts

address: 48 CREIGHTON ST

department: Department of Mathematics

institute: UMass Boston

description: Library name: UNT_Kla_Trophs_BR2_S13

data_processing:
The reference genome and gene annotations for P. falciparum (3D7, release 63) were downloaded from https://plasmodb.org/plasmo/. Raw reads were processed by MultiQC v1.20 (PMID: 27312411) to assess quality metrics and trimmed by Cutadapt v.2.10 (DOI: https://doi.org/10.14806/ej.17.1.200) to remove residual adapter sequences and low quality reads(phred score < 20). Trimmed reads were aligned to the reference genome by using BWA-mem v.0.7.17 (PMID: 19451168). Then, SAMtools v.1.10 was used to sort and index the bam files. Narrow peaks and broad peaks were called separately by MACS2(PMID: 18798982) against corresponding IgG controls at different stages with settings: “-p 0.01 --nomodel --extsize 200” and “-q 0.2 --nomodel --broad --keep-dup auto --max-gap 500”, respectively. The consensus peaks between two replicates were defined as those peaks have at least 50% overlaps by using  the BEDtools (PMID: 20110278) with settings: “bedtools intersect  -a -b -f 0.5 -F 0.5  -e -wo”. Consensus peaks were assigned and annotated by the custom R script using the following criteria: for narrow peak assignment, the occupancy of the peaks have been classified into genic peaks and non-genic peaks, the proportion of spanning range of genic peaks occupied on promoter(<=1000bp upstream of TSS), 5’UTR, exon, intron, 3’UTR were calculated, unique location was assigned to the location with highest proportion of occupancy for each peak, non-genic peaks with <= 2000bp distance to the nearest annotated gene was assigned to the nearest gene while those non-genic peaks has > 2000bp distance to the closest gene have no assignment; for broad peak assignment, those genic peaks covered only 1 gene will be piped into narrow peak assignment pipeline described above, while those broad genic peaks covered more than 1 gene have no assignment, broad non-genic peaks with <= 2000bp distance to the nearest annotated gene or overlapped with the nearest genes promoter regions were assigned to the nearest gene while those non-genic peaks has > 2000bp distance to the closest gene have no assignment. Normalized fold enrichment tracks and BigWig files were generated and visualized following the steps as previously published(PMID: 36379668)
Assembly: P. falciparum (3D7, release 63) were downloaded from https://plasmodb.org/plasmo/
Supplementary files format and content: BigWig files fpr 4 epigenetic antibodies with ring, troph and schizont stage after substracting the signal of IgG, which can be visualized in IGV
Library strategy: CUT&Run

organism: Plasmodium falciparum

source_name: panKla antibody

extract_protocol:
Parasites were treated for 12 hours and then harvested at ring stage (12-16 hpi), trophozoite stage (28-32hpi) and schizont (40-44 hpi). Both panKla antibody and a site-specific H4K12la antibody were employed, alongside H3K4me3 and H4K12ac as positive controls and IgG as a negative control.
Library was constructed by follow the protocol of NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S, NEB)

value: panKla antibody

tag: cell type

value: Human red blood cell

tag: cell subtype

value: O type

value: Lactylation treatment


title: panKla, 0.5mM, Rings, rep2

description: Library name: UNT_Kla_Rings_BR2_S13

tag: treatment


title: SVZ NSC lineage cell, OB rep1 [OB1_588293]

value: Brain, olfactory bulb

tag: genotype


title: H4K12la, 0.5mM, Trophs, rep1

description: Library name: UNT_H4K12la_Trophs_BR1_S4

source_name: H4K12la antibody

value: H4K12la antibody


title: H4K12la, 0.5mM, Trophs, rep2

description: Library name: UNT_H4K12la_Trophs_BR2_S14


title: panKla, 0.5mM, Schizont, rep2

description: Library name: UNT_Kla_Schizont_BR2_S13


title: DMSO, 4h, Replicate 4

description: Library name: 782_4


title: SR1815, 2wk, Replicate 2

description: Library name: 736_7

treatment_protocol: Neurons were isolated from Syngap1 conditional rescue (Syngap1+/ls) mice and plated using a BioTek EL406 (Agilent Technologies) into 384-well plates pre-coated with poly-D-lysine (PDL) (Aurora ABE2-01200B-PDL) at 15,000 cells in 80 µL/ well and placed in 37 °C incubator (42). A solution of 1% agarose was placed in the evaporation border wells prior to plating to minimize edge effects. On DIV 3, 10 µM 5-fluoro-2′-deoxyuridine (+FUDR) was added cultures to suppress the proliferation of glia. For 2-week treatments of SR-1815, cultures were treated with vehicle (DMSO) or SR-1815 at 1.5 µM on DIV 0, 3, 7, and 10 by replacing 50% of the conditioned media with fresh feeding media (+FUDR).


title: SVZ NSC lineage cell, OB rep1 [OB1_588277]


title: Inguinal white adipose tissue, normal adipose tissue  from WT2 mice, snRNAseq

value: inguinal white adipose


title: SVZ NSC lineage cell, OB rep1 [OB1_588287]


title: panKla, 0.5mM, Schizont, rep1

description: Library name: UNT_Kla_Schizont_BR1_S3


title: H4K12la, 0.5mM, Rings, rep1

description: Library name: UNT_H4K12la_Rings_BR1_S4


title: panKla, 0.5mM, Trophs, rep1

description: Library name: UNT_Kla_Trophs_BR1_S3


title: SR1815, 2wk, Replicate 5

description: Library name: 736_10r


title: SVZ NSC lineage cell, OB rep1 [OB1_588283]


title: panKla, 0.5mM, Rings, rep1

description: Library name: UNT_Kla_Rings_BR1_S3


title: H4K12ac, 0.5mM, Trophs, rep2

description: Library name: UNT_H4K12ac_Trophs_BR2_S15

source_name: H4K12ac antibody

value: H4K12ac antibody


title: Bone marrow-derived macrophages, FGK45-treated, INPUT


title: SR1815, 2wk, Replicate 4

description: Library name: 736_9r


title: H4K12ac, 0.5mM, Trophs, rep1

description: Library name: UNT_H4K12ac_Trophs_BR1_S5


title: SR1815, 2wk, Replicate 3

description: Library name: 736_8


title: H4K12la, 0.5mM, Schizont, rep1

description: Library name: UNT_H4K12la_Schizont_BR1_S4


title: H4K12la, 0.5mM, Rings, rep2

description: Library name: UNT_H4K12la_Rings_BR2_S14


title: DMSO, 2wk, Replicate 5

description: Library name: 736_5


title: SVZ NSC lineage cell, OB rep1 [OB1_588271]


title: SVZ NSC lineage cell, OB rep1 [OB1_588279]


title: H4K12ac, 0.5mM, Rings, rep2

description: Library name: UNT_H4K12ac_Rings_BR2_S15


title: H4K12ac, 0.5mM, Rings, rep1

description: Library name: UNT_H4K12ac_Rings_BR1_S5


title: H4K12la, 0.5mM, Schizont, rep2

description: Library name: UNT_H4K12la_Schizont_BR2_S14


title: SVZ NSC lineage cell, OB rep1 [OB1_588269]


title: SVZ NSC lineage cell, OB rep1 [OB1_588267]


title: SVZ NSC lineage cell, OB rep1 [OB1_588275]


title: SVZ NSC lineage cell, OB rep1 [OB1_588265]


title: SVZ NSC lineage cell, OB rep1 [OB1_588273]


title: siNemp1_120kPA_R3

city: St. Louis

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

description:
Library name: siNemp1_120kPA_R3
Column name in McNeill_siNemp1_raw_gene_counts.txt: siNemp1_120kPA_R3

data_processing:
Quality control of reads was performed using FastQC v.0.11.9
Sequence reads were trimmed for adapter sequence/low-quality sequence using Trimmomatic v.0.33.
Trimmed sequence reads were mapped to GRCh38/hg38 using Salmon v.1.80 with default parameters
Read count extraction and normalization were performed using edgeR.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample

organism: Homo sapiens

source_name: hTERT RPE-1 - CRL-4000

growth_protocol: Tissue culture cells are grown

extract_protocol:
RNeasy Kits for RNA Purification, Qiagen
Library preparation for bulk RNA-seq was performed with 500 ng to 1 ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits. Messenger RNA was reverse-transcribed to yield complementary DNA (cDNA) using SuperScript III reverse transcriptase (Life Technologies) and random hexamers. A second-strand reaction was performed to yield ds-cDNA. cDNA was blunt-ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends.

treatment_protocol: siRNA Treatment to cell

value: hTERT RPE-1 - CRL-4000

value: Epithelial Cells


title: DMSO, 2wk, Replicate 1

description: Library name: 736_1


title: siNemp1_120kPA_R2

description:
Library name: siNemp1_120kPA_R2
Column name in McNeill_siNemp1_raw_gene_counts.txt: siNemp1_120kPA_R2


title: H3K4me3, 0.5mM, Schizont, rep1

description: Library name: UNT_H3K4me3_Schizont_BR1_S2

source_name: H3K4me3 antibody

value: H3K4me3 antibody


title: H4K12ac, 0.5mM, Schizont, rep2

description: Library name: UNT_H4K12ac_Schizont_BR2_S15


title: Treg.VAT.DT.8

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Library name: Treg.VAT.DT.8

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: VAT

extract_protocol:
For population-level RNA-seq, samples were double-sorted, and 1,000 MmSCs were collected into 5 microliters of TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich) in DNA LoBind tubes (Eppendorf). For whole-tissue RNA-seq, muscles were dissected and immediately frozen in liquid nitrogen until all samples were collected. Fresh-frozen muscles were homogenized in TRIzol followed by RNA isolation according to the manufacturer's protocol. 2 ng RNA were resuspended in 5 microliters of TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich).
Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf).

value: VAT

value: Treg

tag: Sex

value: male

value: week 20


title: SR1815, 2wk, Replicate 1

description: Library name: 736_6

value: Primary Cortical Neuron


title: DMSO, 2wk, Replicate 3

description: Library name: 736_3

value: DMSO


title: H3K4me3, 0.5mM, Schizont, rep2

description: Library name: UNT_H3K4me3_Schizont_BR2_S12


title: DMSO, 2wk, Replicate 2

description: Library name: 736_2


title: H3K4me3, 0.5mM, Trophs, rep2

description: Library name: UNT_H3K4me3_Trophs_BR2_S12


title: H4K12ac, 0.5mM, Schizont, rep1

description: Library name: UNT_H4K12ac_Schizont_BR1_S5


title: H3K4me3, 0.5mM, Trophs, rep1

description: Library name: UNT_H3K4me3_Trophs_BR1_S2


title: Inguinal white adipose tissue, normal adipose tissue from WT1 mice, snRNAseq

value: 6 months old

value: WT


title: H3K4me3, 0.5mM, Rings, rep2

description: Library name: UNT_H3K4me3_Rings_BR2_S12

value: Human red blood cell

value: O type


title: Treg.VAT.DT.7

description: Library name: Treg.VAT.DT.7


title: siNemp1_120kPA_R1

description:
Library name: siNemp1_120kPA_R1
Column name in McNeill_siNemp1_raw_gene_counts.txt: siNemp1_120kPA_R1


title: SVZ NSC lineage cell, OB rep1 [OB1_588261]

value: Brain, olfactory bulb


title: H3K4me3, 0.5mM, Rings, rep1

description: Library name: UNT_H3K4me3_Rings_BR1_S2

value: Lactylation treatment


title: SVZ NSC lineage cell, OB rep1 [OB1_588259]


title: Treg.VAT.DT.6

description: Library name: Treg.VAT.DT.6


title: panKla, 8mM, Trophs, rep2

description: Library name: 8mM_Kla_Trophs_BR2_S18

value: panKla antibody


title: Control_120kPA_R3

description:
Library name: Control_120kPA_R3
Column name in McNeill_siNemp1_raw_gene_counts.txt: Control_120kPA_R3

value: Control


title: Treg.VAT.DT.5

description: Library name: Treg.VAT.DT.5


title: Control_120kPA_R2

description:
Library name: Control_120kPA_R2
Column name in McNeill_siNemp1_raw_gene_counts.txt: Control_120kPA_R2

value: hTERT RPE-1 - CRL-4000


title: DMSO, 2wk, Replicate 4

description: Library name: 736_4


title: siNemp1_10kPA_R2

description:
Library name: siNemp1_10kPA_R2
Column name in McNeill_siNemp1_raw_gene_counts.txt: siNemp1_10kPA_R2

value: Epithelial Cells


title: Treg.VAT.PBS.4

description: Library name: Treg.VAT.PBS.4


title: Control_120kPA_R1

description:
Library name: Control_120kPA_R1
Column name in McNeill_siNemp1_raw_gene_counts.txt: Control_120kPA_R1


title: panKla, 8mM, Trophs, rep1

description: Library name: 8mM_Kla_Trophs_BR1_S8


title: SVZ NSC lineage cell, OB rep1 [OB1_588249]


title: SVZ NSC lineage cell, OB rep1 [OB1_588255]


title: panKla, 8mM, Schizont, rep1

description: Library name: 8mM_Kla_Schizont_BR1_S8


title: panKla, 8mM, Schizont, rep2

description: Library name: 8mM_Kla_Schizont_BR2_S18


title: Treg.VAT.PBS.2

description: Library name: Treg.VAT.PBS.2


title: siNemp1_10kPA_R1

description:
Library name: siNemp1_10kPA_R1
Column name in McNeill_siNemp1_raw_gene_counts.txt: siNemp1_10kPA_R1


title: SVZ NSC lineage cell, OB rep1 [OB1_588247]


title: SVZ NSC lineage cell, OB rep1 [OB1_588245]


title: SVZ NSC lineage cell, OB rep1 [OB1_588243]


title: panKla, 8mM, Rings, rep1

description: Library name: 8mM_Kla_Rings_BR1_S8


title: panKla, 8mM, Rings, rep2

description: Library name: 8mM_Kla_Rings_BR2_S18


title: Treg.EarSkin.DT.6

description: Library name: Treg.EarSkin.DT.6

source_name: Ear Skin

value: Ear Skin


title: Treg.VAT.PBS.1

description: Library name: Treg.VAT.PBS.1

value: VAT


title: Control_10kPA_R2

description:
Library name: Control_10kPA_R2
Column name in McNeill_siNemp1_raw_gene_counts.txt: Control_10kPA_R2


title: Control_10kPA_R1

description:
Library name: Control_10kPA_R1
Column name in McNeill_siNemp1_raw_gene_counts.txt: Control_10kPA_R1


title: SVZ NSC lineage cell, OB rep1 [OB1_588263]

source_name: Brain, olfactory bulb


title: SVZ NSC lineage cell, OB rep1 [OB1_588239]


title: Treg.VAT.PBS.3

description: Library name: Treg.VAT.PBS.3

value: Treg


title: SVZ NSC lineage cell, OB rep1 [OB1_588235]


title: Treg.EarSkin.DT.5

description: Library name: Treg.EarSkin.DT.5

value: male


title: ZANO

first: Hongrui

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

institute: Shanghai ninth people's hospital

description: Library name: FIL-ASPCs-3 + NAC

data_processing:
ATAC-seq reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)

source_name: adipose stem and progenitor cells

extract_protocol:
The ATAC experiments were performed as described (Buenrostro et al., 2013).
Cells were  vehicle treated and then collected and treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina). DNA was purified using MinElute PCR Purification Kit (Qiagen). All samples were then amplified by PCR using NEBNextHigh-Fidelity 2× PCR Master Mix (New Englands Labs) with primers containing a barcode to generate libraries. DNA was again purified using AMPure Beads.DNA libraries for ATAC-seq were prepared using NextEra Library Prep Kit following manufacturer's protocols.

value: adipose stem and progenitor cells

tag: group

value: FIL-ASPCs-3 + NAC


title: Treg.EarSkin.DT.4

description: Library name: Treg.EarSkin.DT.4

value: week 20


title: SVZ NSC lineage cell, OB rep1 [OB1_588229]

data_processing:
Read1 sequences were processed to extract and trim UMIs, storing them in the FASTQ identifier field. Processed paired-end reads were trimmed using trim-galore v0.5.0 and mapped to the mm10 genome reference with Ensembl96 gene annotations using STAR v2.5.3a setting "--bamRemoveDuplicatesType UniqueIdentical --outFilterMismatchNmax 9999 --outFilterScoreMinOverLread 0.2 --outFilterMatchNminOverLread 0.2 --alignSJoverhangMin 3 --alignSplicedMateMapLminOverLmate 0.2 --twopassMode Basic". UMI-containing readpairs were quantified with a custom script based on HTSeq to identify exonic and intronic UMIs and deduplicate them, reporting a merged UMI-counts matrix.  Cell transcriptomes were subset to 1:1 human-mouse orthologs reported in Ensembl102 to be consistent with our downstream human analyses. We excluded cells with fewer than 2000 UMIs or under 500 detected genes.
Assembly: mm10
Supplementary files format and content: counts: comma separated matrix of deduplicated UMI counts per cell (columns) per gene (rows). Metadata: comma separated matrix relating metdata (columns) per cell (rows)

extract_protocol:
RNA molecules were captured using an oligo dT(30) primer. mRNA was reverse-transcribed using a template switching oligonucleotide contianing an 8 bp unique molecular identifier to obtain cDNA which was subsequently amplified and purified using AMPureXP beads.
Purified cDNA was then used for Illumina Nextera XP library preparation according to Hagemann-Jensen et al. 2020 with modifications reported in Cerrizuela and Kaya et al. 2022.


title: Treg.EarSkin.PBS.3

description: Library name: Treg.EarSkin.PBS.3


title: H4K12la, 8mM, Schizont, rep1

description: Library name: 8mM_H4K12la_Schizont_BR1_S9

value: H4K12la antibody


title: SVZ NSC lineage cell, OB rep1 [OB1_588231]


title: LXRO

description: Library name: FIL-ASPCs-2 + NAC

value: FIL-ASPCs-2 + NAC


title: Treg.EarSkin.PBS.2

description: Library name: Treg.EarSkin.PBS.2

value: WT


title: H4K12la, 8mM, Rings, rep2

description: Library name: 8mM_H4K12la_Rings_BR2_S19

value: Human red blood cell

value: O type


title: H4K12la, 8mM, Schizont, rep2

description: Library name: 8mM_H4K12la_Schizont_BR2_S19

value: Lactylation treatment


title: LQWO

description: Library name: FIL-ASPCs-1 + NAC

value: FIL-ASPCs-1 + NAC


title: LQWA

description: Library name: FIL-ASPCs-1


title: Treg.EarSkin.PBS.1

description: Library name: Treg.EarSkin.PBS.1


title: H4K12la, 8mM, Rings, rep1

description: Library name: 8mM_H4K12la_Rings_BR1_S9


title: LXRA

description: Library name: FIL-ASPCs-2


title: Treg.liver.DT.5

description: Library name: Treg.liver.DT.5

source_name: Liver

value: Liver


title: FIL-ASPCs-3,IP

description: Library name: FIL-ASPCs-3_IP

data_processing:
MeRIP-seq reads were aligned to the hg38 reference genome using hisat2(2.1.0)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

extract_protocol:
Total RNA was extracted from the cerebral cortex of mice using TRIzol reagent. After cell lysis, chloroform was added and centrifuged to separate the layers. The upper aqueous phase was collected, and isopropanol was added to precipitate RNA, followed by a wash with 70% ethanol.
RNA libraries were constructed using an Illumina library preparation kit, synthesizing cDNA from m6A-modified RNA in the samples, followed by adapter ligation and PCR amplification to obtain the library.

value: DMSO


title: SVZ NSC lineage cell, OB rep1 [OB1_588219]

value: Brain, olfactory bulb


title: Treg.liver.DT.6

description: Library name: Treg.liver.DT.6


title: SVZ NSC lineage cell, OB rep1 [OB1_588221]


title: H4K12ac, 8mM, Trophs, rep2

description: Library name: 8mM_H4K12ac_Trophs_BR2_S20

value: H4K12ac antibody


title: H4K12la, 8mM, Trophs, rep1

description: Library name: 8mM_H4K12la_Trophs_BR1_S9


title: SVZ NSC lineage cell, OB rep1 [OB1_588215]


title: FIL-ASPCs-3,Input

description: Library name: FIL-ASPCs-3_Input


title: Treg.liver.DT.4

description: Library name: Treg.liver.DT.4


title: SVZ NSC lineage cell, OB rep1 [OB1_588225]


title: H4K12ac, 8mM, Schizont, rep2

description: Library name: 8mM_H4K12ac_Schizont_BR2_S20


title: SVZ NSC lineage cell, OB rep1 [OB1_588213]


title: Treg.liver.PBS.3

description: Library name: Treg.liver.PBS.3


title: FIL-ASPCs-3_FN,Input

description: Library name: FIL-ASPCs-3_FN_Input


title: FIL-ASPCs-3_FN,IP

description: Library name: FIL-ASPCs-3_FN_IP


title: Treg.liver.PBS.2

description: Library name: Treg.liver.PBS.2


title: H4K12la, 8mM, Trophs, rep2

description: Library name: 8mM_H4K12la_Trophs_BR2_S19


title: SVZ NSC lineage cell, OB rep1 [OB1_588223]


title: H4K12ac, 8mM, Trophs, rep1

description: Library name: 8mM_H4K12ac_Trophs_BR1_S10


title: FIL-ASPCs-2,IP

description: Library name: FIL-ASPCs-2_IP


title: H4K12ac, 8mM, Schizont, rep1

description: Library name: 8mM_H4K12ac_Schizont_BR1_S10


title: SVZ NSC lineage cell, OB rep1 [OB1_588211]


title: Treg.liver.PBS.1

description: Library name: Treg.liver.PBS.1


title: SVZ NSC lineage cell, OB rep1 [OB1_588207]


title: Treg.lung.DT.6

description: Library name: Treg.lung.DT.6

source_name: Lung

value: Lung


title: H4K12ac, 8mM, Rings, rep1

description: Library name: 8mM_H4K12ac_Rings_BR1_S10


title: H3K4me3, 8mM, Trophs, rep2

description: Library name: 8mM_H3K4me3_Trophs_BR2_S17

value: H3K4me3 antibody


title: FIL-ASPCs-2,Input

description: Library name: FIL-ASPCs-2_Input


title: H3K4me3, 8mM, Trophs, rep1

description: Library name: 8mM_H3K4me3_Trophs_BR1_S7


title: SVZ NSC lineage cell, OB rep1 [OB1_588199]


title: Treg.lung.DT.4

description: Library name: Treg.lung.DT.4

value: Treg

value: male


title: Treg.lung.DT.5

description: Library name: Treg.lung.DT.5


title: SVZ NSC lineage cell, OB rep1 [OB1_588197]


title: FIL-ASPCs-2_FN,IP

description: Library name: FIL-ASPCs-2_FN_IP

value: adipose stem and progenitor cells


title: FIL-ASPCs-2_FN,Input

description: Library name: FIL-ASPCs-2_FN_Input


title: H3K4me3, 8mM, Schizont, rep2

description: Library name: 8mM_H3K4me3_Schizont_BR2_S17


title: SVZ NSC lineage cell, OB rep1 [OB1_588191]


title: FIL-ASPCs-1,IP

description: Library name: FIL-ASPCs-1_IP


title: SVZ NSC lineage cell, OB rep1 [OB1_588187]


title: H3K4me3, 8mM, Schizont, rep1

description: Library name: 8mM_H3K4me3_Schizont_BR1_S7


title: Treg.lung.PBS.3

description: Library name: Treg.lung.PBS.3

value: week 20


title: Treg.lung.PBS.2

description: Library name: Treg.lung.PBS.2


title: H3K4me3, 8mM, Rings, rep1

description: Library name: 8mM_H3K4me3_Rings_BR1_S7


title: SVZ NSC lineage cell, OB rep1 [OB1_588185]


title: Treg.lung.PBS.1

description: Library name: Treg.lung.PBS.1


title: FIL-ASPCs-1,Input

description: Library name: FIL-ASPCs-1_Input


title: FIL-ASPCs-1_FN,IP

description: Library name: FIL-ASPCs-1_FN_IP


title: SVZ NSC lineage cell, OB rep1 [OB1_588171]


title: RNAseq, MuSCs, siRNA MyoD, replicate 2

city: La jolla

first: Chiara

last: Nicoletti

state: CA

address: 10901 North Torrey Pines Road

department: Development, Aging and Regeneration Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Library name: RNAseq_MuSCs_siMyoD_rep2

data_processing:
For RNA-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), and aligned to the hg19 Ensembl (November 2015) version of the human genome or to the mm10 Ensembl (November 2019) version of the mouse genome with STAR (v 2.7.3a), using a custom genome and index to simultaneously map and quantify ERCC92 spike-in-derived reads (parameters: --runMode alignReads --runThreadN 12 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts). Counts data (from STAR output in column 4, based on library preparation strandedness: second-strand) from all conditions were filtered based on their raw count, keeping genes where the sum of the counts for all samples was higher than 10. Size factors were calculated using the R environment (v4.1.3) package DESeq2 (v1.34.0) estimateSizeFactors function - using the counts related to the spike-in transcripts as control genes, then normalized and logged with the rlog function. DESeq2 was also used to perform Principal Component Analysis (PCA) and differential gene expression analysis (significance threshold: BH FDR<0.05). Differential expression analysis results were visualized with the heatplot function (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)) from the made4 (v1.68.0) package, after expression values from the DESeq2 object were turned into a matrix of Z-scores. Gene Ontology was performed on down- and up-regulated genes separately, using the gene symbols as input in EnrichR, and gene sets repositories GO Biological Processes 2023 and Descartes Cell Types and Tissue 2021. Top10 gene ontology terms shown in figure panels were ordered by pvalue. Gene Ontology bubble plots to summarize top50 gene ontology terms, were generated with the Python (v.3.8.1) GO-Figure script (parameters: -j standard -c log10-pval -e 100 -si 0.5 -s members -g single -n bpo --font_size small -q svg). For ATAC-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (v2.3.5.1) (parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --dovetail --phred33), sorted and converted into BAM format with the SAMtools sort function. Peak calling was performed with the Macs2 (v2.2.6) callpeak function (parameters: -f BAMPE -g hs -B -q 0.05 --nomodel --shift -100 --extsize 200) and filtered for black-list regions with the BEDtools suite (v2.29.2) intersect (parameters: -v), and sorted with the sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (v2.0.3) (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. Differential chromatin accessibility analysis was carried out in R, with the DESeq2 package. The R package ChIPQC (v1.30.0), (GetGRanges function was used to import peak lists from each biological replicate, a consensus peak list was calculated for all conditions using the IRanges (v2.28.0),function reduce, keeping peaks that were called in at least two samples. Counts for each peak in each biological replicate were quantified with the Rsubread (v2.8.2) featureCounts function (parameters: isPairedEnd= T, countMultiMappingReads= F, maxFragLength= 100). Counts were normalised and logged with the DESeq2 function rlog; DESeq2 was also used to perform Principal Component Analysis (PCA), and differential chromatin accessibility analysis (significance threshold: BH FDR<0.05). Differentially Accessible Regions (DARs) at gene promoter regions were retrieved with the IRanges function promoters (parameters: TxDb.Hsapiens.UCSC.hg19.knownGene, 1000, 200; mouse genome version was: TxDb.Mmusculus.UCSC.mm10.knownGene). Promoter DARs were visualized with the made4 function heatplot (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)), after expression values from the DESeq2 object were turned into a matrix of Z-scores. Due to R visualization limits, only promoters with |log2FC|>1.5 were plotted. Motif analysis was carried out with the HOMER (v4.11), findMotifsGenome function (parameters: hg19 -size given -nomotif). For ChIP-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9) and aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (parameters: --very-sensitive-local). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs -B --nomodel --SPMR -q 0.05), using input chromatin as control. For CUT&RUN: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned either to the hg19 UCSC (January 2016) version of the human genome (for the CUT&RUN for histone marks in IMR90 and IMR90/MyoD), or to the mm10 Ensembl (November 2019) version of the mouse genome (for the CUT&RUN of AcMe and MyoD in muSC), with Bowtie2 (parameters: --phred33 --end-to-end --no-unal --local --very-sensitive-local --no-mixed --no-discordant -I 10 -X 700 –dovetail) and converted to BAM format with the SAMtools (v1.10) function view (parameters: -bS). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs --nomodel --SPMR --call-summits -p 0.05) using input chromatin as control, and filtered for black-list regions with BEDtools intersect (parameters: -v), and sorted with the Unix sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. ChromHMM (v1.24) BinarizeBed function (parameters: -b 200 -peaks) was used to bin the genome in 200bp windows according to each IDR peak list. The BinarizeBed output was used as input to ChromHMM LearnModel (parameters: -b 200 12 hg19), to build a 12 chromatin states model based on the histone marks IDR peaks. Chromatin state numbers were converted to chromatin states names in R, based on the combination of histone marks they were enriched for. For HiChIP: Quality control of the raw data has been performed with FASTQC (v0.11.9). Alignment, filtering, normalization, and loop calling were performed with the Arima version of MAPS (v2.0) bash script (parameters: -C 0 -F 1 -M 1 -H 1 -o hg19 -f 1 -s 5000 -r 2000000 -d 2 -Q 30 -l 1000). Irreproducible Discovery Rate (IDR) was calculated with IDR2D parameters: value transformation= log additive inverse (-log(x)), ambiguity resolution method= overlap, remove non-standard chromosome, max gap= 1000, max factor= 1.5, jitter factor= 0.0001, mu= 0.1, sigma=1, rho=0.2, p=0.5, epsilon=0.001). Differential HiChIP analysis was performed with the DiffAnalysisHiChIP.r script within FitHiChIP (v7.1), and significance threshold was set to p-value<0.05.
Assembly: hg19, mm10
Supplementary files format and content: TXT raw counts files (RNA-seq)
Supplementary files format and content: BEDGRAPH pileup signal tracks, with TBI index (RNA-seq)
Supplementary files format and content: BIGWIG signal tracks (ATAC-seq data, CUT&RUN), also biological replicates average signal tracks
Supplementary files format and content: ARCPLOTS of looping interactions, with TBI index (HiChIP)

source_name: Muscle Stem Cells

growth_protocol: IMR90 cells were cultured in EMEM supplemented with 10% FBS

extract_protocol:
For RNA-seq: IMR90 or IMR90/MyoD cells total RNA was extracted using Quick-RNA Microprep KIT (Zymo Research, R1051) following the manufacturer’s recommendation. RNA concentration was measured on Qubit (Invitrogen). For ATAC-seq: IMR90 or IMR90/MyoD cells were freshly collected directly processed for the library preparation. For ChIP-seq: IMR90 or IMR90/MyoD cells were fixed with 1% FA for 10 minutes at RT followed by quenching with glycine (final concentration 200 mM) for 15 minutes on ice. Nuclei were then extracted in hypotonic buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.05% NP-40, 1 mM PMSF and 1x protease inhibitor) and lysed in lysis buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM EDTA, pH 8.0, 0.5% SDS, 0.5% NP-40, 1 mM PMSF and 1x protease inhibitor and lysed in lysis buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM EDTA, pH 8.0, 0.5% SDS, 0.5% NP-40, 1 mM PMSF and 1x protease inhibitor). Chromatin was sheared with sonicator (S2 Covaris) to an average DNA fragment length of 200-500bp. 15µg of sonicated chromatin were diluted in 500µl RIPA Dilution Buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, pH 8.0, 0.1% Sodium Deoxycholate, 0.7% NP-40, 1 mM PMSF and 1x protease inhibitor), and precleared for 3 hours at 4°C with Protein A/G dinabeads. In parallel, 10µl of CTCF antibody (CST Cat#3418S), or 1µg of rabbit IgG (Santa Cruz #sc-2027) were prebound to Protein A/G dynabeads in 500µl of PBS containing 5 µg/ml BSA, for 3 hours at 4°C. Beads bound antibody were mixed with precleared chromatin and incubated overnight at 4°C on a rotator. Chromatin bound fraction was washed with RIPA washing buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, pH 8.0, 0.5% Sodium Deoxycholate, 1% NP-40) for 4 times, followed by LiCl washing buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, pH 8.0, 1% Sodium Deoxycholate, 1% NP-40), and TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA), each wash for 10 minutes at 4°C. Chromatin was then eluted in elution buffer (1% SDS in TE buffer) at 65°C for 6 hours 600 RPM rotation. For CUT&RUN: IMR90 or IMR90/MyoD cells or Muscle Stem Cells (MuSCs) were used as input. CUT&RUN experiments were performed using the CUT&RUN Assay Kit (CST #86652) with the following modification: cells were briefly fixed with 0.1% FA for 2 minutes at RT followed by quenching with glycine; antibody binding was performed O/N at 4C. Antibodies used: anti-MYOD (BD Bioscience, #554130), anti-H4K5/K12AcMe, anti-panAcMe, anti-H3K27ac (Active Motif #91193), anti-H3K4me3 (CST #9751), anti-H3K4me1 (Active Motif #39635), anti-H3K27me3 (Active Motif #39155), anti-H3K9me3 (Active Motif #39161). For HiChIP: IMR90 or IMR90/MyoD cells were fixed with 2%FA for 10 minutes at RT followed by quenching with STOP solution1 according to ARIMA HiC+ protocol. Digestion was performed overnight at 37C. Biotinylated enriched fragments were pulled down with anti-H3K27ac (Active Motif #91193) or anti-CTCF (Active Motif #91285). Experiments were performed using the ARIMA HiC+ kit according to manufacturer’s protocol.
For RNA-seq: Equal inputs of total RNA (10-100 ng) were used to generate stranded total RNA libraries for sequencing using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina #20040525). ERCC RNA Spike-in mix was added at the start of the protocol according to manufacturer’s instruction (Thermo Fisher Scientific #4456740). Libraries were sequenced at a depth of ~50M per library on NOVASeqS4 PE 2x100. For ATAC-seq: Freshly collected cells were subjected to ATAC-seq library preparation using the ATAC-seq Kit (Active Motif #53150) according to manufacturer’s protocol. For ChIP-seq: Precipitated chromatin and 10ng of input were used for library preparation using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21096) according to manufacturer’s protocol. Obtained libraries were sequenced at a depth of ~100M per library on NOVASeqS4 PE 2x100. For CUT&RUN: Libraries have been generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB #E7645S) according to manufacturer’s protocol. Libraries were sequenced at a depth of ~20M per library on NOVASeqS4 PE 2x100. For HiChIP: H3K27ac or CTCF enriched material was then used as input for library preparation using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21096) according to ARIMA HiChIP library preparation protocol. Obtained libraries were sequenced at a depth of ~300M per library on NOVASeqS4 PE 2x100.

treatment_protocol: IMR90 cells were transfected with vector containing TET-inducible MYOD (WT or domain-deleted mutant) or EMPTY vector control, cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and collected for GM time point. Primary mouse MuSCs 48h post-FACS sorting in 6-wells plates were transfected with 6.75 pmol of siScramble (DharmaconTM, Cat #D-001210601605) or siMyod1 (DharmaconTM, Cat #L-041113-00-0005) per well using Lipofectamine RNAiMAX (Invitrogen, Cat #13778150) using the manufacturer’s instructions. MuSCs have been collected 48h post-transfection for RNA isolation.

value: Muscle Stem Cells

value: siMyoD


title: SVZ NSC lineage cell, OB rep1 [OB1_588181]

first: Leo

address: Im Neuenheimer Feld 581

institute: DKFZ


title: Treg.Sp.DT.4

description: Library name: Treg.Sp.DT.4

source_name: Spleen

value: Spleen

value: WT


title: Treg.Sp.DT.6

description: Library name: Treg.Sp.DT.6


title: Treg.Sp.PBS.3

description: Library name: Treg.Sp.PBS.3


title: FIL-ASPCs-1_FN,Input

description: Library name: FIL-ASPCs-1_FN_Input


title: SVZ NSC lineage cell, OB rep1 [OB1_588169]


title: C-PJI04

city: Fuzhou

first: Xinyu

last: Fang

address: Chazhong road

institute: The First Affiliated Hospital of Fujian Medical University

data_processing:
Pass filter data of fastq format were processed by Cutadapt[1](version 1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1)
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Bowtie2 (v2.2.6) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Bowtie2(v2.2.6).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1p1) estimated gene expression levels from the pair-end clean data.
Assembly: Staphylococcus aureus (ID 154) - genome - NCBI (NIH. Gov)

organism: Staphylococcus aureus

source_name: MSSA

extract_protocol:
RNA was harvested using TRIzol.
RNA libraries for RNA-seq were prepared using VAHTS Total RNA-seq (Bacteria) Library Prep Kit for Illumina following manufacturer's protocols.

value: MSSA

tag: condition

value: chronic periprosthetic joint infection


title: RNAseq, MuSCs, siRNA MyoD, replicate 1

description: Library name: RNAseq_MuSCs_siMyoD_rep1


title: Jurkat, 12h, rep3

city: Berkeley

first: Thyago

middle: Leal

last: Calvo

state: California

address: 2151 Berkeley Way

department: IGI

institute: UC Berkeley

description: Library name: mRNA_J12h3

data_processing:
Adapters were trimmed with cutadapt, followed by trimming the first 5'-> 7 nucleotides in each read. Then, reads were also filtered with a quality score (-q 10) and by length (> 25 nt).
Reads were mapped in a sequential fashion against rRNA references, tRNA reference by tRAX, mtDNA, and ncRNAs before mapped against the Gencode v.37 GRCh38.p13 protein coding reference, resulting in only high quality mappings against mRNA sequences.
Gene counts were filtered out if any sampled had a zero count, and,then normalized with DESEq2.
Assembly: GRCh38.p13
Supplementary files format and content: CSV containing raw gene counts from RSEM
Supplementary files format and content: log2 normalized (DESeq2's median ratio method) gene expression

source_name: Human Jurkat Clone E6-1 (ATCC TIB-152)

growth_protocol: Cells were maintained in RPMI 1640 Medium (ATCC modification) with 10% FBS (VWR Seradigm Life Science), 0.01% Penicillin-Streptomycin (10,000 U/mL) (ThermoFisher),  density 1 x 10^5 cells ml^–1 to 1 × 10^6 cells ml^–1

extract_protocol:
RNA samples were extracted using the Direct-zol RNA Miniprep kit (Zymo Research)
mRNA-seq libraries were prepared from total RNA using the RealSeq RNA sequencing kits (Somagenics)

treatment_protocol: Jurkat cells were activated using anti-CD3/anti-CD28 antibodies (Tonbo). Flat bottom plates were coated with anti-CD3 antibody at a 10 μg/mL concentration at 4C for at least 12h. Then, anti-CD28 antibody was added to the cell culture media at a concentration of 5 µg/mL and, cells were incubated for the required timepoints.

value: Human Jurkat Clone E6-1 (ATCC TIB-152)

value: T lymphoblast

value: 12h post-activation


title: Treg.Sp.DT.5

description: Library name: Treg.Sp.DT.5


title: Jurkat, 5h, rep2

description: Library name: mRNA_J5h2

value: 5h post-activation


title: RNAseq, MuSCs, Control, replicate 1

description: Library name: RNAseq_MuSCs_Ctrl_rep1

value: siScrumble


title: SVZ NSC lineage cell, OB rep1 [OB1_588165]

city: Heidelberg

last: Förster

value: Brain, olfactory bulb


title: RNAseq, MuSCs, Control, replicate 2

description: Library name: RNAseq_MuSCs_Ctrl_rep2


title: Jurkat, 5h, rep1

description: Library name: mRNA_J5h1


title: C-PJI01


title: Jurkat, 5h, rep3

description: Library name: mRNA_J5h3


title: H3K4me3, 8mM, Rings, rep2

description: Library name: 8mM_H3K4me3_Rings_BR2_S17

value: H3K4me3 antibody

value: Human red blood cell

value: O type

value: Lactylation treatment


title: C-PJI03


title: Treg.Sp.PBS.2

description: Library name: Treg.Sp.PBS.2

value: Treg

value: male

value: week 20


title: D49.P2.2

description: Library name: 7weeksCD25nFoxp3p.2

source_name: Thymus

value: Thymus

value: Treg Progenitor

value: CD25- Foxp3+ Treg Progenitor

value: day 49


title: Treg.Sp.PBS.1

description: Library name: Treg.Sp.PBS.1

value: Spleen

value: WT


title: Jurkat, 12h, rep2

description: Library name: mRNA_J12h2

value: Human Jurkat Clone E6-1 (ATCC TIB-152)

value: T lymphoblast

value: 12h post-activation


title: Jurkat, 0h, rep3

description: Library name: mRNA_J0h3

value: control


title: C-PJI02

value: MSSA

value: chronic periprosthetic joint infection


title: ZANA

description: Library name: FIL-ASPCs-3

value: adipose stem and progenitor cells


title: D49.P2.3

description: Library name: 7weeksCD25nFoxp3p.3


title: Enterobacter cloacae, ST78, blaNDM eliminated, asmA knocked out 3

city: Guangzhou

first: Xu

last: Yang

address: Postal address, 151 Yanjiang Rd, Yuexiu District,

institute: the First Affiliated Hospital of Guangzhou Medical University

description: Library name: CY-9-A-3

data_processing:
The data generated from Illumina platform were used for bioinformatics analysis. All of the analyses were performed using the free online platform of Majorbio Cloud Platform (www.majorbio.com) from Shanghai Majorbio Bio-pharm Technology Co.,Ltd. The major software and parameters are as follows.
Assembly: High quality reads in each sample were mapped to the reference genome provided by the customer.
Supplementary files format and content: fastq file includes raw data for each Sample

organism: Enterobacter cloacae

source_name: bacteria

extract_protocol:
RNA was harvested using CTAB about 25 ug of total RNA was used for theconstruction of sequencing libraries.
Ribosomal RNA (rRNA) depletion instead of poly(A) purification is performed by RiboCop rRNA Depletion Kit for Mixed Bacterial Samples（lexogen，USA）and then all mRNAs were broken into short (200nt) fragments by adding fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized with random hexamer primers (Illumina). When the second strand cDNA was synthesized, dUTP was incorporated in place of dTTP. Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. RNA-seq transcriptome library was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using of total RNA. paired-end RNA-seq library was sequenced with the Illumina Novaseq 6000 (or other new sequenator) (Illumina Inc., San Diego, CA, USA) .

value: bacteria


title: Enterobacter cloacae, ST78, blaNDM eliminated, asmA knocked out 2

description: Library name: CY-9-A-2


title: Enterobacter cloacae, ST78, eliminates blaNDM 2

description: Library name: CY-9-2


title: A-PJI02

value: acute periprosthetic joint infection


title: A-PJI03


title: D49.P2.1

description: Library name: 7weeksCD25nFoxp3p.1

value: male


title: Jurkat, 0h, rep1

description: Library name: mRNA_J0h1


title: Enterobacter cloacae, ST78, blaNDM eliminated, asmA knocked out 1

description: Library name: CY-9-A-1


title: Enterobacter cloacae, ST78, eliminates blaNDM 3

description: Library name: CY-9-3


title: A-PJI04


title: D49.P1.3

description: Library name: 7weeksCD25pFoxp3n.3

value: CD25+ Foxp3- Treg Progenitor