title: hMDM, sHDL-1

city: Nashville

first: Kasey

last: Vickers

address: 2220 Pierce Ave, PRB 312

institute: VUMC

description: Library name: CC-sHDL-1-1

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt (v4.5)
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.12.1)(www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to the Gencode GRCh38.p13 genome using STAR (v2.7.11a). Gencode v38 gene annotations were provided to STAR to improve the accuracy of mapping. featureCounts (v2.0.6)[3] was used to count the number of mapped reads to each gene. Only protein coding genes were used in the down-stream analysis
ComplexHeatmap was used for cluster analysis and visualization. Significantly differential expressed genes with absolute fold change >= 2 and FDR adjusted p value <= 0.05 were detected by DESeq2 (v1.42.1)
For each differential expression comparison, low expressed genes with less than 5 median read count in both conditions were excluded. Genome Ontology and KEGG pathway over-representation analysis was performed on differentially expressed genes using the WebGestaltR package (v1.0.0)
Gene set enrichment analysis was performed using GSEA package (v4.3.2) on database (v2022.1.Hs).
Assembly: human GRCh38.p13
Supplementary files format and content: tsv file contains fpkm for each sample

source_name: Human PBMCs

growth_protocol: Human monocyte derived macrophages (hMDM) were obtained by isolating peripheral blood mononuclear cells (PBMCs) from whole blood from healthy donors using the standard Ficoll density gradient procedure (Ficoll-Paque, GE Healthcare). Primary human CD14+ monocytes were isolated from PBMCs following CD14+ selection using magnetic-activated cell sorting, according to manufacturer’s instructions (Miltenyi Biotec), then seeded directly to tissue culture plates with GM-CSF (20 ng/mL, PeproTech) and maintained in DMEM supplemented with sodium pyruvate (110 mg/L), L-glutamine, 10% heat-inactivated FBS and 1% penicillin-streptomycin for 6 days

extract_protocol:
Total RNA was isolated using the Total RNA Purification kits (Norgen)
RNA-seq libraries were generated using the Universal Plus Total RNA Sequencing Kit with NuQuant (Tecan)

treatment_protocol: hMDM were treated with rHDL (1mg/mL) loaded with RNA oliogonucleotides (5ug) for 6h in serum free DMEM.

value: Human PBMCs

value: Human monocyte derived macrophages

value: sHDL


title: FFPE prostate cancer, Subject-13, pre_treat

status: Public on Dec 12 2025

type: RNA

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

country: USA

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.

tag: study subject id

tag: cohort

tag: treatment time-point


title: E2302014

type: SRA

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

description: Library name: E2302014

library_source: transcriptomic

data_processing:
Kallisto software (v0.50.0) was used for quantifying transcript abundance from RNA-seq data against the GRCh38 cDNA reference transcriptome from the Ensembl database (v101) (36).
Downstream analysis included only protein-coding genes and transcripts. Differential expression analysis was performed using the DESeq2 R package, and gene expressions were normalized through variance-stabilizing transformation
Assembly: GRCh38
Supplementary files format and content: Tab delimited text files containing TPM data for every sample

source_name: whole blood

extract_protocol:
Blood samples were collected in EDTA blood tubes immediately before the first durvalumab injection. The tubes were frozen at −80 °C within 4 hours of collection. Subsequently, all samples were transferred to the Centre Georges-François Leclerc for total RNA extraction and analysis via short-read RNA sequencing. Four mL of whole blood harvested in EDTA tubes were frozen at −80 °C until extraction. Total RNA was extracted with the Maxwell RSC simplyRNA Blood Kit (Promega, Madison, WI, USA), following the manufacturer’s instructions. RNA quantity and quality were assessed by spectrometry with absorbance at 230 nm, 260 nm, and 280 nm.
Eight hundred nanograms of total RNA were depleted of ribosomal and globin RNA using the NEBNext Globin and rRNA Depletion Kit (New England Biolabs, Ipswich, MA, USA). The depleted RNA was then used for library preparation with the NEBNext Ultra II RNA Directional Library Prep Kit for Illumina (New England Biolabs). RNA sequencing was performed on a NextSeq2000 device (Illumina, San Diego, CA, USA), using 2 × 100 bp paired-end reads and multiplexed to obtain 20 million reads per sample. For us, 20 million reads is a good balance between sensitivity and cost-efficiency. Indeed, such a read depth is consistent with easy implementation of RNA-seq in routine workflows.

treatment_protocol: The patients included in this study were participants in a multicentric, prospective clinical trial, the IOPREDI study, a French ancillary cohort of the STRONG study (NCT03084471). Participants were recruited from patients treated at 17 French sites. A total of 218 patients (IOPREDI) were recruited between July 2018 and August 2019, and 164 accepted blood withdrawal for the present study. Patients were considered eligible if they presented with a locally advanced or metastatic urothelial or non-urothelial carcinoma of the urinary tract. Detailed inclusion and exclusion criteria are available on ClinicalTrials.gov. All patients signed informed consent to participate in the trial. The trial protocol was approved by an institutional review committee and by the relevant French regional ethical committee (CPP SUD-OUEST and OUTRE-MER 4).

tag: tissue

value: whole blood

tag: age

tag: Sex

value: Female

tag: smoking history

value: Never

tag: patient activity

value: Restricted

tag: histology

value: Urothelial (transitional cell) carcinoma

tag: disease stage

value: III

tag: pdl1 staining

value: Missing

tag: clinical response_(recist)

value: PD

tag: pfs

tag: pfs events

tag: os

tag: os events

tag: irae

value: No


title: FFPE prostate cancer, Subject-12, post_treat

tag: study subject id


title: TAF2-V5 ab hepatocyte, replicate 3

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description: Library name: ChIP-V5-3

library_source: genomic

data_processing:
The data was processed using the Nextflow chipseq v.2.1.0 pipeline using the GRCh38 genome assembly.
Assembly: GRCh38
Supplementary files format and content: narrowPeak, text

molecule: genomic DNA

source_name: liver

extract_protocol:
ChIP was performed using IgG or V5 antibody and DNA was eluted from the immunoprecipitates.
Library was prepared using NEBNext Ultra II DNA library prepration kit

value: liver

tag: cell line

tag: cell type

value: HCC

tag: treatment

value: TAF2-V5 ab


title: FFPE prostate cancer, Subject-12, pre_treat

tag: cohort

tag: treatment time-point


title: Input DNA hepatocyte, replicate 3

description: Library name: ChIP-IgG-3

tag: tissue

value: input


title: hMDM, sHDL, WT tDR-2-4

description: Library name: wt tDR-2-4

value: WT tDR-2


title: FFPE prostate cancer, Subject-13, post_treat


title: FFPE prostate cancer, Subject-11, post_treat


title: FFPE prostate cancer, Subject-10, post_treat


title: FFPE prostate cancer, Subject-10, pre_treat


title: hMDM, sHDL, m1A tDR-1-2

description: Library name: m1A tDR-1-2

value: Human PBMCs

value: m1A tDR-1


title: TAF2-V5 ab hepatocyte, replicate 2

description: Library name: ChIP-V5-2


title: FFPE prostate cancer, Subject-9, pre_treat


title: FFPE prostate cancer, Subject-9, post_treat


title: hMDM, sHDL-4

description: Library name: CC-sHDL-1-4

value: Human monocyte derived macrophages

value: sHDL


title: E2302015

description: Library name: E2302015

value: whole blood

tag: age

tag: Sex

value: Female

tag: smoking history

tag: patient activity

value: In bed > 50% time

value: IV

value: Not evaluated


title: hMDM, sHDL-3

description: Library name: CC-sHDL-1-3


title: hMDM, sHDL-2

description: Library name: CC-sHDL-1-2


title: hMDM, sHDL, m1A tDR-2-4

description: Library name: m1A tDR-2-4

value: m1A tDR-2


title: hMDM, sHDL, m1A tDR-1-1

description: Library name: m1A tDR-1-1


title: E2302005

description: Library name: E2302005

value: Male

value: Former

value: Restricted

tag: histology

value: Urothelial (transitional cell) carcinoma

tag: disease stage

tag: pdl1 staining

value: Missing

tag: clinical response_(recist)

value: PD

value: Yes


title: hMDM, sHDL, m1A tDR-2-1

description: Library name: m1A tDR-2-1

value: Human PBMCs


title: E2302012

description: Library name: E2302012

value: Never

value: Normal

value: III

tag: pfs

tag: pfs events

tag: os

tag: os events

value: No


title: E2302013

description: Library name: E2302013

value: whole blood

value: Undetermined

tag: irae


title: hMDM, sHDL, WT tDR-2-1

description: Library name: wt tDR-2-1

tag: cell type

value: Human monocyte derived macrophages

tag: treatment

value: WT tDR-2


title: FFPE prostate cancer, Subject-8, pre_treat

tag: study subject id

tag: cohort

tag: treatment time-point


title: E2302019

description: Library name: E2302019

tag: tissue

tag: age

tag: Sex

value: IV


title: hMDM, sHDL, WT tDR-2-3

description: Library name: wt tDR-2-3


title: hMDM, sHDL, m1A tDR-2-3

description: Library name: m1A tDR-2-3

value: m1A tDR-2


title: hMDM, sHDL, m1A tDR-2-2

description: Library name: m1A tDR-2-2


title: hMDM, sHDL, WT tDR-2-2

description: Library name: wt tDR-2-2


title: hMDM, sHDL, m1A tDR-1-4

description: Library name: m1A tDR-1-4

value: m1A tDR-1


title: E2302010

description: Library name: E2302010

value: Female

tag: smoking history

tag: patient activity

tag: histology

value: PR


title: Human Nasal Epithelial Cells from a 2 year old; with IFN B  treatment

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

data_processing:
BCL files generated from sequencer were converted using bcl2fastq (Illumina) to fastq files, quality-checked using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapter and quality trimming was performed using trimgalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Summary QC files for before and after quality trimming was performed using MultiQC.
Alignment to was performed using STAR, followed by count estimation using RSEM.
For differential expression analysis, read counts were estimated using tximport, followed by normalization and differential expression analysis performed using Deseq2.
Assembly: hg38 reference
Supplementary files format and content: TPMCounts_IFN.txt

source_name: Human Nasal Epithelial

growth_protocol: We obtained AECs using 2.7 mm cytology brushes rotated in each nostril for nasal AECs. Immediately after collection, AECs were detached from the brushes by scrapping and agitation within the transport medium and subsequent centrifugation at 500g for 5 min at 4 °C. Conditionally reprogrammed cell (CRC) methods were used to optimize initial proliferation and survival of neonatal/infant AEC cultures.

extract_protocol:
AECs were collected for RNA studies using TRIzol (Thermo Fisher), and RNA was subsequently extracted using phase separation.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit from Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Three infant AECs were plated at  1.5 x 10^5 cells/well on collagen coated 6 well dishes (pureCol) for approximately 24 hours .  After 24hr of plating,  the cells were transitioned to serum free media. The cells were treated the next day with either IFN-λ/IL-29 (100ng/mL) or IFN β (1ng/mL) in serum free media.

value: Human Nasal Epithelial

tag: genotype

value: Euploid

value: 2 year old

value: IFN B


title: E2302009

description: Library name: E2302009

value: Male

value: Former

value: In bed < 50% time

value: Urothelial (transitional cell) carcinoma

tag: disease stage

tag: pdl1 staining

tag: clinical response_(recist)

value: Not evaluated

tag: pfs


title: FFPE prostate cancer, Subject-8, post_treat


title: FFPE prostate cancer, Subject-11, pre_treat


title: SCC-25, RARG KO, RARγ, biol rep 1

city: New York

first: Helen

last: Hoxie

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

description:
Library name: RARGKO_RARg_1
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization

data_processing:
Samples were sequenced using a NextSeq 2000 (PE50)
Sequencing reads were trimmed with Trim Galore and quality-checked with FastQC.
Reads were aligned to hg38 with Bowtie2, with parameters adjusted to allow dovetailing.
Sorted BAM files were filtered to remove mitochondrial alignments, sequences with MAPQ scores <30, PCR duplicates. 1 sample replicate (PAR_RARγ_1) was discarded for poor quality.
Separate alignments to E. coli M-12 were performed to calculate single-scaler normalization factors for each sample based on the fraction of uniquely mapped E. coli reads. Deeptools bamCoverage was used to generate spike-in normalized bigWig files for IGV visualization. For all track windows, replicates were overlayed and autoscaled by antibody target, with RARγ and IgG samples grouped together for scaling.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

growth_protocol: Human SCC-25 oral squamous carcinoma cells (CRL-1628 ATCC) were cultured in DMEM/F-12 (Thermo, Cat No. 11320033) supplemented with 100U/mL Pen Strep and hydrocortisone (400 ng/ml) and 10% FBS.

extract_protocol:
SCC-25 cells were fixed the next day for 2 minutes with 0.1% methanol-free formaldehyde directly in the dish before quenching with 20x Glycine for 2 minutes. Cells were trypsinized and collected, washed with 1% FCS in 1XPBS, and resuspended in Nuclei Extraction Buffer (Epicypher) for 10 minutes on ice.400,000 nuclei per sample were added to activated ConA beads and processed according to  Epicypher’s CUTANA Cross-linking Protocol (v1.9, 2022). ). SNAP-CUTANA™ K-MetStat Panel of d-nucleosomes was spiked into IgG, H3K4me3, and H3K27me3 samples. E. coli DNA was spiked into all samples for single scalar normalization.
IDT-xGen kit

tag: cell line

value: Head and Neck Cancer Sqamous Cells

value: RARG knockout

tag: chip antibody

value: RARγ1 (Cell Signaling Technology, #8965)


title: E2302007

description: Library name: E2302007

value: whole blood

value: Restricted

value: IV

tag: pfs events

tag: os

tag: os events

tag: irae

value: No


title: hMDM, sHDL, WT tDR-1-4

description: Library name: wt tDR-1-4

tag: tissue

value: Human PBMCs

tag: cell type

value: Human monocyte derived macrophages

tag: treatment

value: WT tDR-1


title: hMDM, sHDL, WT tDR-1-2

description: Library name: wt tDR-1-2


title: Human Nasal Epithelial Cells from a 1.25 year old; with IFN L treatment

value: Human Nasal Epithelial

value: Euploid

tag: age

value: 1.25 year old

value: IFN L


title: Human Nasal Epithelial Cells from a 2 year old; with IFN L treatment

value: 2 year old


title: hMDM, sHDL, m1A tDR-1-3

description: Library name: m1A tDR-1-3

value: m1A tDR-1


title: SCC-25, RARG KO, RARγ, biol rep 3

description:
Library name: RARGKO_RARg_3
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: FFPE prostate cancer, Subject-6, post_treat

tag: study subject id

tag: cohort

tag: treatment time-point


title: Human Nasal Epithelial Cells from a 1.25 year old; with IFN B treatment

tag: genotype

value: IFN B


title: SCC-25, PAR, RARγ, biol rep 3

description:
Library name: PAR_RARg_3
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization

value: Head and Neck Cancer Sqamous Cells

value: Parental


title: Human Nasal Epithelial Cells from a 1.8 year old; with IFN B treatment

value: 1.8 year old


title: Human Nasal Epithelial Cells from a 1.8 year old; with IFN L treatment


title: Human Nasal Epithelial Cells from a 1.25 year old; with no IFN treatment

value: NT


title: FFPE prostate cancer, Subject-7, pre_treat


title: FFPE prostate cancer, Subject-6, pre_treat


title: hMDM, sHDL, WT tDR-1-3

description: Library name: wt tDR-1-3


title: FFPE prostate cancer, Subject-7, post_treat


title: FFPE prostate cancer, Subject-4, post_treat


title: hMDM, sHDL, WT tDR-1-1

description: Library name: wt tDR-1-1


title: Human Nasal Epithelial Cells from a 2 year old; with no IFN treatment


title: SCC-25, PAR, RARγ, biol rep 2

description:
Library name: PAR_RARg_2
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization

value: RARγ1 (Cell Signaling Technology, #8965)


title: SCC-25, RARG KO, RARγ, biol rep 2

description:
Library name: RARGKO_RARg_2
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization

value: RARG knockout


title: FFPE prostate cancer, Subject-4, pre_treat


title: Human Nasal Epithelial Cells from a 1.8 year old; with no IFN treatment


title: Trisomy 21 sample RSV treated, Sample B

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Pre-processing of the single-cell FASTQ samples, including demultiplexing, alignment, count, and quality visualization, was performed using Cell Ranger (version 6; 10X Genomics).
For the reference, we used a concatenated genome file comprising the human genome reference (hg38) from Ensembl, RSV genome reference from GenBank, and R125-eGFP transcript sequences.
Next, we used the Seurat scRNA-seq pipeline for further downstream analysis on each sample individually. We filtered genes present in at least 10 cells, cells with low gene and transcript numbers (<200) and removed cells with greater than 15% mitochondrial content per sample.
Next, normalization was performed on each of the samples using SCTransform  with 2000 variable genes, followed by doublet removal using DoubletFinder43. Principal component analysis (PCA) was then performed, followed by KNN graph using the first 30 PCAs, clustering using a resolution of 0.1, and Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) for visualization.
All the samples were then integrated, followed by creation of PCA, KNN graph (first 30 PCs), clustering (using a resolution of 0.1) and UMAP. Individual pairwise integration of different conditions was performed in the same fashion for differential expression analysis. Pseudo bulk analysis, using Wilcox t-test was performed between each condition with a significance level of p-value < 0.05 and log fold change > 0.25 or <0.25. Gene ontology was performed using the Hallmark genes dataset using the fgsea package in R.
Assembly: hg38
Supplementary files format and content: Tab seperated value files and matrix files.

growth_protocol: We obtained airway epithelium Cells (AECs)  using 2.7 mm cytology brushes rotated in each nostril for nasal AECs. Immediately after collection, AECs were detached from the brushes by scrapping and agitation within the transport medium and subsequent centrifugation at 500g for 5 min at 4 °C. Conditionally reprogrammed cell (CRC) methods were used to optimize initial proliferation and survival of neonatal/infant AEC cultures.

extract_protocol:
AECs were collected for RNA studies using TRIzol (Thermo Fisher), and RNA was subsequently extracted using phase separation.
Single-cell RNA-seq libraries were generated using the Chromium Next GEM Single Cell v 3.1 (10x Genomics, US).

treatment_protocol: Human nasal AECs were seeded on PureCol coated plates at 150,000 cells/well in 2mL CRC media. Cells were allowed to rest for 18-24 hours before CRC media was replaced with serum-free airway epithelial growth media (referred to as Serum Free Media or SF media). SF media is composed of airway epithelial growth media (Promocell). Cells were serum starved for 18-24 hours before introduction of virus. Virus stocks were diluted in airway epithelial growth media containing only retinoic acid (RA only media) to facilitate minimum growth requirements in conditionally reprogrammed cells. Virus stocks were diluted to an MOI of 1 per well.

value: Trisomy 21

value: RSV treated


title: SCC-25, RARG KO, H3K27me3, biol rep 3

description:
Library name: RARGKO_H3K27me3_3
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization

value: H3K27me3 (ThermoFisher, #MA5-11198)


title: Trisomy 21 sample RSV treated, Sample A

description: 10X Genomics


title: FFPE prostate cancer, Subject-3, post_treat


title: SCC-25, RARG KO, H3K27me3, biol rep 2

description:
Library name: RARGKO_H3K27me3_2
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: SCC-25, PAR, H3K27me3, biol rep 3

description:
Library name: PAR_H3K27me3_3
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: SCC-25, RARG KO, H3K27me3, biol rep 1

description:
Library name: RARGKO_H3K27me3_1
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: Trisomy 21 sample Mock treated, Sample C

description: 10X Genomics

value: Mock treatment


title: FFPE prostate cancer, Subject-3, pre_treat


title: Trisomy 21 sample Mock treated, Sample D

description: 10X Genomics

value: Human Nasal Epithelial


title: Euploid RSV treated, Sample B

description: 10X Genomics

value: Euploid


title: Euploid Mock Treatment, Sample D

description: 10X Genomics


title: SCC-25, PAR, H3K27me3, biol rep 1

description:
Library name: PAR_H3K27me3_1
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: Euploid RSV treated, Sample A

description: 10X Genomics


title: Euploid Mock Treatment, Sample C

description: 10X Genomics


title: EW.iMP.4

city: Cambridge

first: Emile

last: Wogram

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

data_processing:
Reads were aligned to the human (GRCh38) genome using STAR v2.7.1a (indexed using Ensembl 96 transcript models).
Gene levels were determined with the methods used by Gosselin et al.
Briefly, SAM files were converted to HOMER tags, which were used (with Ensembl 96 transcript models) to generate raw counts with HOMER’s analyzeRepeats.pl.
Assembly: human (GRCh38/hg38)
Supplementary files format and content: tab-delimited text; gene symbol and HOMER counts

source_name: human induced pluripotent stem cells (hiPSC)

extract_protocol:
RNA was collected using the Qiagen MicroRNeasy+ kit according to the manufacturer’s protocol
3 ng of RNA was used as input using Takara’s SMART-Seq v4 Ultra Low Input RNA protocol per manufacturer’s guidelines

value: iPSCs were generated from human foreskin fibroblasts from Coriell Institute (AG07095).

value: iPSC-derived

value: XY

value: differentiation to macrophage precursor cells

tag: replicate number


title: EW.iMP.6

value: human induced pluripotent stem cells (hiPSC)


title: EW.iMP.3


title: FFPE prostate cancer, Subject-2, post_treat


title: FFPE prostate cancer, Subject-2, pre_treat


title: SCC-25, RARG KO, H3K4me3, biol rep 3

description:
Library name: RARGKO_H3K4me3_3
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization

value: Head and Neck Cancer Sqamous Cells


title: EW.iMP.5


title: FFPE prostate cancer, Subject-1, post_treat


title: SCC-25, RARG KO, H3K4me3, biol rep 2

description:
Library name: RARGKO_H3K4me3_2
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: EW.iMP.2


title: MSC15 cell line, WT, H3K27ac (ChIP)

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

institute: Institut Curie

description: Library name: MSC15_H3K27ac

data_processing:
Reads were trimmed with TrimGalore tool (v0.6.2)
Sequencing data were processed using nextflow ChIP-seq pipeline (Servant et al., 2023) (https://zenodo.org/records/10357860).
Briefly, reads were mapped with bwa (version 2.19.0) (Li and Durbin, 2010) to the human genome (version hg19). Duplicates or low-quality reads were removed.  Peaks were called with MACS2 (version 2.2.6) (Zhang et al., 2008) using the "narrow" option for transcription factors and the "broad" option for the H3K27ac histone mark. The fragment size was estimated from the data by MACS for transcription factors, while a fixed fragment size of 200 bp was used for histones. ChIP-seq data were normalized according to their respective input DNA samples
Assembly: hg19
Supplementary files format and content: narrowPeak for TF and broadPeak for H3K27ac mark

source_name: mesenchymal stem cells

growth_protocol: EW-1, TC-71, MHH-ES-1, SK-N-MC, MSCVL were were cultured at 37°C in 5% CO2 using RPMI and supplemented with 10% fetal bovine serum (FBS) and antibiotics. For the CHLA-9, the cells were maintained with IMDM and 20% FBS, 4mM Glutamine, 1X insulin-transferrin-selenium (ITS) and antibiotics at 37°C in 5% CO2. MSC15 were cultured with alpha-MEM, 10% MSC FBS, 2ng/ml of FGF, 1% L-glutamine and antibiotics at 37°C in 5% CO2 and in hypoxic-like condition (1.5% O2).

extract_protocol:
Cells were fixed for 10 minutes with 1% methanol-free formaldehyde and the chromatin was sonicated for 20 cycles (30 seconds on, 30 seconds off) at the "high" setting. ChIP-Seq experiment was performed for IKZF2, POU3F2, SOX6, FLI1 and H3K27ac using Diagenod kit. Respective inputs were used as normalization controls for all models.
ChIP sequencing libraries were generated using the TruSeq ChIP library preparation kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 (single -end, 100 bp).

treatment_protocol: Some cells were transfected by siRNA (non-targeting control, siCT or targeting the EWS-FLI1 fusion transcript, siEF1) using Lipofectamine RNAiMAX without antibiotics and they were harvested after 96 hours post transfection. For the shRNAs against the EWRS1-FLI fusion oncogenes, the cells were induced by addition of 1 µg/ml doxycycline to the cell culture medium for 7 days before ChIP-Seq experiment.

value: mesenchymal stem cells

value: Mesenchymal Stem cell (normal)


title: FFPE prostate cancer, Subject-1, pre_treat


title: EW.iMP.1


title: A673/TR/shEF1 cell line, WT, FLI1 (ChIP)

description: Library name: A673/TR/shEF1_FLI1

source_name: cell line

value: cell line

value: Ewing sarcoma cell line


title: 60.DIV.iMG.5

value: differentiation to macrophage precursor cells, monoculture for 60 days


title: 60.DIV.iMG.6


title: 60.DIV.iMG.4


title: SCC-25, PAR, H3K27me3, biol rep 2

description:
Library name: PAR_H3K27me3_2
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization

value: Parental


title: SCC-25, RARG KO, H3K4me3, biol rep 1

description:
Library name: RARGKO_H3K4me3_1
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization

value: RARG knockout


title: 60.DIV.iMG.3


title: CHLA-9 cell line, WT, FLI1 (ChIP)

description: Library name: CHLA-9_FLI1


title: SCC-25, PAR, H3K4me3, biol rep 3

description:
Library name: PAR_H3K4me3_3
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: 60.DIV.iMG.1


title: 60.DIV.iMG.2


title: SCC-25, PAR, H3K4me3, biol rep 2

description:
Library name: PAR_H3K4me3_2
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: A673/TR/shEF1 cell line, KD, H3K27ac (ChIP)

description: Library name: A673/TR/shEF1_DOX_H3K27ac


title: 60.DIS.iMG.H1.4

source_name: human embryonic stem cells (hESC)

value: human embryonic stem cells (hESC)

value: hESC-derived

value: differentiation to macrophage precursor cells, integration in cerebral organoids and treated with PBS for 60 days


title: CHLA-9 cell line, WT (Input)

description: Library name: CHLA-9_input


title: CHLA-9 cell line, WT, H3K27ac (ChIP)

description: Library name: CHLA-9_H3K27ac


title: SCC-25, RARG KO, IgG, biol rep 3

description:
Library name: RARGKO_IgG_3
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization

value: IgG (Epicypher, #13-0042)


title: 60.DIS.iMG.7095.PBS.2

value: iPSCs were generated from human foreskin fibroblasts from Coriell Institute (AG07095).


title: SK-N-MC cell line, WT (Input)

description: Library name: SK-N-MC_input

value: SK-N-MC


title: 60.DIS.iMG.H1.2

value: XY


title: SCC-25, RARG KO, IgG, biol rep 2

description:
Library name: RARGKO_IgG_2
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: RHO757

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

data_processing:
Single-end FASTQ reads were aligned to human genome build GRCh38 using hisat2 with defaut parameters
SAM files were processed and sorted to BAM format using sambamba v 0.63
Transcript counts were generated with htseq-count (v0.5.4p3)
Genome_build: GRCh38
Supplementary_files_format_and_content: processed data are raw counts of transcripts as determined by htseq-count

growth_protocol: hESCs are differentiated into pancreatic β-cells using different cocktails of growth factors, over 35 days

extract_protocol:
Culture media was removed, cells were washed three times, before total RNA was extracted using a Macherey-Nagel RNA extraction kit
Libraries were prepared using the TruSEQ Stranded Total RNA Prep with  Ribo-Zero Human Cat. No. RS-122-2201 as per manufacturer's protocol. Libraries sequenced using 150bp paired-end on HiSeq 2500 Platform.

value: Pancreatic beta-like cells

value: STARD10 KO

tag: timepoint


title: SCC-25, RARG KO, IgG, biol rep 1

description:
Library name: RARGKO_IgG_1
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization

value: Head and Neck Cancer Sqamous Cells


title: 60.DIS.iMG.H1.3


title: 60.DIS.iMG.7095.PBS.3

value: human induced pluripotent stem cells (hiPSC)

value: iPSC-derived


title: 60.DIS.iMG.7095.LEV.2

value: differentiation to macrophage precursor cells, integration in cerebral organoids and treated with levetiracetam for 60 days


title: RHO756


title: 60.DIS.iMG.6

value: differentiation to macrophage precursor cells, integration in cerebral organoids for 60 days in vitro


title: SCC-25, PAR, IgG, biol rep 3

description:
Library name: PAR_IgG_3
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: SCC-25, PAR, H3K4me3, biol rep 1

description:
Library name: PAR_H3K4me3_1
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: 60.DIS.iMG.7095.LEV.1


title: RHO755


title: RHO754


title: SCC-25, PAR, IgG, biol rep 2

description:
Library name: PAR_IgG_2
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization


title: 60.DIS.iMG.3


title: 60.DIS.iMG.7095.PBS.1


title: 60.DIS.iMG.H1.1


title: 60.DIS.iMG.2


title: 60.DIS.iMG.1


title: 60.DIS.iMG.4


title: 60.DIS.iMG.5


title: 10.DIV.iMG.2

value: differentiation to macrophage precursor cells, monoculture for 10 days


title: 10.DIV.iMG.6


title: 10.DIV.iMG.5


title: SCC-25, PAR, IgG, biol rep 1

description:
Library name: PAR_IgG_1
bigWig (hg38) generated from bamCoverage with E.coli spike-in normalization

value: Parental


title: TdTomato+ retinal ganglion cells from human iPSC-derived organoids upon transplantation - Sample 1

city: Boston

first: Emil

last: Kriukov

address: 20 Staniford St

institute: Schepens Eye Research Institute

description: Library name: AMf3

data_processing:
Cell ranger v. 7.0.1
velocyto v. 0.17.17
Assembly: 2024-A Mouse GRCm39 for mouse samples, 2024-a Human GRCh38 for human sample
Supplementary files format and content: Cell ranger output matrix (.mtx), barcodes (.tsv) and features (.tsv)
Supplementary files format and content: Velocyto output spliced/unspliced data matrix (.loom)

source_name: Retinal organoids

growth_protocol: The H9-BRN3B:tdTomatoThy1.2-hESCs cells were cultured on six-well plates coated with 2% Matrigel in mTeSR1 cell culture medium in a low oxygen condition (3.5% O2, 5% CO2, 95% humidity, 37C). Cell culture medium was replaced daily. Human RGCs were differentiated in 3D retinal organoid cultures as previously described. Briefly, the colonies of hESCs were enzymatically dissociated for 12 minutes to make a single-cell suspension during cell passaging. To initiate the formation of embryoid bodies, 7,500 hESCs per well was seeded in an ultra-low attachment 96-well U-bottom plate in a low oxygen condition for 24 hours and plate with EBs transferred to 20% O2 the next day. The differentiation medium was replaced daily and changed from a 3:1 mix of mTeSR1 and BE6.2-NIM [B27 + E6 at 2X concentration – neural induction medium: 1x L-glutamine, 1x sodium pyruvate, 1x antibiotic-antimycotic, 1x B27 without Vitamin A, 0.88 mg/mL NaCl, 38.8 mg/L insulin, 128 mg/L L-ascorbic acid, 28 μg/L selenium, 21.4 mg/L transferrin, and 38.8 mg/L NaHCO3 in DMEM/F12 (3500 mg/L dextrose)] to primarily BE6.2-NIM by day 8. To promote early retinal development, the medium was supplemented with 20 μM Y-27632 on day 0, 1% Matrigel from days 2 to 6, 3μM IWR-1-endo from days 1 to 4, and 55 ng/mL BMP4 on day 6. Following 48 hours, organoids were chopped and then placed on tissue culture-treated plastic in Long-Term Retinal Differentiation Medium (LT-RDM) [1x L-glutamine, 1x sodium pyruvate, 1x antibiotic-antimycotic, 1x B27, 1x non-essential amino acids, and 10% FBS in 50:50 1x DMEM/F12 (3500 mg/L Dextrose):DMEM (4500 mg/mL dextrose)] to support attachment of organoids and growth of retinal epithelium. The medium was exchanged every two days and transitioned to a 1:1 mix of LT-RDM and Retinal Differentiation Media (RDM) [LT-RDM without FBS] by day 17, with added 100nM smoothened agonist (SAG) from days 12 to 16. On day 17, the clusters of retinal tissue were moved to a poly (2-hydroxyethyl methacrylate) -coated flask for suspension culture in RDM supplemented with 100nM SAG. Starting on day 18, the medium was replaced every other day, gradually transitioning to pure LT-RDM by day 24. From day 26, the medium was enriched with 1mM taurine, and from day 32, it was supplemented with 250nM all-trans-retinoic acid. The LT-RDM was exchanged every other day until the retinal organoids were dissociated using Gentle MACS protocol and RGCs sorted with CD90.2 Dynabeads.

extract_protocol:
Three days following RGC transplantation, mice were euthanized, eyes enucleated and retinal tissue isolated and transferred into a tube containing PBS with 0.04% BSA on ice. Eight mouse retinas were pooled for each sample. The tissue was dissociated by mechanical and enzymatic methods using Gentle MACS protocols. Briefly, retinas were allowed to settle to the bottom of the tube and excess PBS carefully removed. Tissues were then rinsed with HBSS and transferred to a MACS M-tube and let to settle to the bottom of the tube before again removing excess HBSS. Tissues were then resuspended in 2ml of dissociation solution containing DNAse 1 (1mg/ml). The mixture was incubated at 37°C for 5min in a heating bath. The M-tube was then inverted ensuring that all retina tissues remained in solution, and the tube placed into the MACS tissue dissociator and the brain 1 program run. At the end of brain 1 program, the M-tube was removed from the MACS dissociator and incubated at 37°C for 5mins in a heating bath. The tube was then inverted again and placed back into the MACS dissociator and program brain 2 initiated, after which 10mL of isolation buffer was added to the dissociate and the mixture triturated 7-10 times with a 1000µl pipette tip. Then 12ml of the homogenate was transferred into a 15ml tube and cells pelleted at 200g for 5 mins at 4°C. The cell pellet was resuspended in 500µl of isolation buffer and filtered using a 70um cell strainer into a FACS tube for sorting. All tubes for this procedure were pre-blocked with 2% BSA in HBSS. Separate single stain samples for TdTomato+ and GFP+ were prepared and used to set the gates. The harvested cells were sorted separately for TdTomato +ve, and GFP +ve, and collected into separate collection tubes each containing 200μl of PBS with 0.04% BSA. The sorted cells were taken for single cell RNA sequencing library preparation.
Of the sorted cells, up to 10,000 viable cells per sample were used for single cell RNA library preparation following the 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol. Briefly, the droplet-based encapsulation method was used to encapsulate single cells with gel beads, partitioning oil, and a reverse transcription master mix generating GEMs. The generated GEMs were cleaned, gene expression libraries constructed and sequenced at a sequencing depth of 20,000 read pairs per cell, paired-end dual indexing (See manufactures instructions for detail).

treatment_protocol: The mice were anesthetized intraperitoneally with 100 mg/kg ketamine hydrochloride and 20 mg/kg xylazine hydrochloride solution dilute with saline, and the animals were allowed to be fully sedated. Pupils were dilated with 1% tropicamide ophthalmic solution (Baush & Lomb Americas Inc., Bridgewater, NJ). One drop of 0.5% proparacaine hydrochloride ophthalmic solution (Bausch & Lomb Americas Inc., Bridgewater, NJ) was instilled onto the cornea surface 2 minutes before subretinal injection. Using a glass pipette, 20,000 viable tdTomato+ve  human ES-derived RGCs in 1ml was injected into one eye of each mouse. One drop of Neomycin and Polymyxin B Sulfates and Bacitracin Zinc Ophthalmic ointment (Bausch & Lomb Americas Inc., Bridgewater, NJ) was applied onto the surface of injected eye following the procedure.

value: Retinal organoids

tag: collection time

value: 3 days after RGC transplantation

value: Retinal ganglion cells

tag: Sex

value: missing

tag: developmental stage

value: 35 days

tag: batch

value: Batch 3


title: Spatial transcriptome sequencing of duck beaks (HH36)

city: Hangzhou

last: Project

address: YuhangTang

country: China

description:
Library name: Duck_HH36
Fresh frozen Spatial transcriptome sequencing

data_processing:
Data preprocessing through SAW-pipeline (v7.1) and stereopy (v1.6.0) included filtering low-quality spots, normalization, and spatial binning.
Assembly: GRCg6a; IASCAAS_PekinDuck_T2T
Supplementary files format and content: gef: Stores the gene expression matrix along with spatial coordinates of bins/cells, used for spatial visualization.
Supplementary files format and content: h5ad: Stores single-cell level gene expression matrices and associated analysis results (e.g., clustering, dimensionality reduction).
Supplementary files format and content: barcodeToPos.h5: Contains the mapping between sequencing barcodes and their physical spatial coordinates on the chip.
Supplementary files format and content: ipr: Defines polygon regions for manual tissue boundary adjustment and region-specific analysis.
Supplementary files format and content: tiff: High-resolution microscope images of the tissue section
Library strategy: Spatial Transcriptomics

organism: Anas platyrhynchos

source_name: Embryo beak

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
Spatial transcriptomics was performed on cryosectioned chicken and duck embryonic beaks at stages (HH29 and HH36) using Stereo-seq (BGI). Sections were mounted onto Stereo-seq chips, fixed, and permeabilized to capture poly(A)+ mRNAs on DNA nanoball arrays. cDNA synthesis and library preparation were carried out following manufacturer protocols, and libraries were sequenced on the DNBSEQ platform. Spatial barcodes and unique molecular identifiers (UMIs) were decoded to generate expression matrices with positional information.

value: Embryo beak


title: RHO753


title: 10.DIV.iMG.3

tag: cell line

value: iPSCs were generated from human foreskin fibroblasts from Coriell Institute (AG07095).

value: XY


title: RHO752

value: Pancreatic beta-like cells

value: STARD10 KO


title: RHO751

source_name: Parental D35

value: WT


title: RHO748


title: RHO750


title: 10.DIV.iMG.4

value: human induced pluripotent stem cells (hiPSC)

value: iPSC-derived


title: 10.DIS.iMG.1

value: differentiation to macrophage precursor cells, integration in cerebral organoids for 10 days in vitro


title: RHO749


title: 10.DIS.iMG.6


title: Plasmid DNA, ISOMPRA 3'UTR Mutated Control Library, TechRep4

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

institute: Washington University in St. Louis

description: Library name: 3UTR.control.DNA.4

data_processing:
Sequencing reads were aligned to reference libraries using custom scripts to identify exact matches, normalized with edgeR (TMM method) to CPM, filtered for low counts, and used to calculate log₂(RNA/DNA) expression or translational efficiency (TRAP), with variant pairs filtered to retain those with ≥4 measurements across conditions.
Assembly: hg38

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: In Vitro: HEK cells were maintained in EMEMsupplemented with 10%FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol Reagent and Zymo Clean and Concentrator Kit. 5ug of RNA per replicate were used for Library Preparation.
RNA libraries for RNA-seq were prepared using a targeted-RNA seq library preparation approach that followed similar paradigms to a Tru-Seq library construction for Illumina Sequencing.

treatment_protocol: In Vitro: Transfection was induced on 24 hours after plating and then cells were harvested 48hours after using Trizol. In Vivo: Mice were injected with AAV virus at PND1 and allowed to age until date of harvest; PND10 for Empra/eISOMPRA, PND21 for uISOMPRA

value: Escherichia coli

value: ISOMPRA Library DNA from Plasmid


title: Spatial transcriptome sequencing of duck beaks (HH29)

description:
Library name: Duck_HH29
Fresh frozen Spatial transcriptome sequencing


title: RHO747


title: 10.DIS.iMG.5


title: Plasmid DNA, ISOMPRA 3'UTR Mutated Control Library, TechRep3

description: Library name: 3UTR.control.DNA.3


title: 10.DIS.iMG.4


title: RHO746


title: 10.DIV.iMG.1

value: differentiation to macrophage precursor cells, monoculture for 10 days


title: 10.DIS.iMG.2


title: Plasmid DNA, ISOMPRA 3'UTR Mutated Control Library, TechRep2

description: Library name: 3UTR.control.DNA.2


title: 10.DIS.iMG.3


title: N2, Primed, timepoint2, rep2

city: Ithaca

first: Siu Sylvia

last: Lee

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

description:
Library name: N2_rna_r2_P2
N2_RNA_Raw.counts_matrix.txt

data_processing:
Adaptor sequences were trimmed, and low-quality reads filtered from raw fastq files using the trim_galore function in Cutadapt (version 4.6).
Trimmed sequencing reads from the FASTQ files were then aligned to the reference genome (ce11/WBcel235) using STAR aligner.
Assembly: ce11/WBcel235
Supplementary files format and content: tab-delimited text file (.txt) includes raw counts for each sample

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole worm

extract_protocol:
Extraction protocol: RNA was extracted using TRIzol-chloroform and treated with TURBO DNase(Ambion), followed by purification using an RNA Clean-up Kit (Zymo). For each sample, 70-100 ng of total RNA was used to construct sequencing libraries. Further details are provided in the Materials & Methods section
RNA-seq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen).

value: Whole worm

value: P


title: N2, Naïve, timepoint2, rep2

description:
Library name: N2_rna_r2_N2
N2_RNA_Raw.counts_matrix.txt

value: N


title: N2, Primed, timepoint3.3, rep2

description:
Library name: N2_rna_r2_P3.3
N2_RNA_Raw.counts_matrix.txt


title: N2, Primed, timepoint1, rep2

description:
Library name: N2_rna_r2_P1
N2_RNA_Raw.counts_matrix.txt


title: RHO744


title: Plasmid DNA, ISOMPRA (repdna)

description: Library name: repdna

treatment_protocol: In Vitro: Transfection was induced on 24 hours after plating and then cells were harvested 48hours after using Trizol. In Vivo: Mice were injected with AAV virus at PND1 and allowed to age until date of harvest; PND10 for Empra/eISOMPRA, PND21 for uISOMPRA, Tet Experiments: HEK cells were transfected 24 hours after plating and then cells were either treated with vehicle or 0.5mg.mL Doxycyline based on condition and then harvested another 24 hours after drug treatment.


title: Plasmid DNA, ISOMPRA 3'UTR Mutated Control Library, TechRep1

description: Library name: 3UTR.control.DNA.1


title: N2, Naïve, timepoint3.3, rep2

description:
Library name: N2_rna_r2_N3.3
N2_RNA_Raw.counts_matrix.txt


title: N2, Primed, timepoint1, rep1

description:
Library name: N2_rna_r1_P1
N2_RNA_Raw.counts_matrix.txt


title: RHO745


title: N2, Naïve, timepointNC, rep2

description:
Library name: N2_rna_r2_NC
N2_RNA_Raw.counts_matrix.txt

value: N (NC)


title: N2, Naïve, timepoint1, rep2

description:
Library name: N2_rna_r2_N1
N2_RNA_Raw.counts_matrix.txt


title: N2, Primed, timepoint2, rep1

description:
Library name: N2_rna_r1_P2
N2_RNA_Raw.counts_matrix.txt


title: RHO741

source_name: Parental D20


title: N2, Primed, timepoint3.3, rep1

description:
Library name: N2_rna_r1_P3.3
N2_RNA_Raw.counts_matrix.txt


title: RHO743


title: Plasmid DNA, ISOMPRA 3'UTR Library, TechRep2.1

description: Library name: 3UTR.plasmid2.1

data_processing:
Sequencing reads were aligned to reference libraries using custom scripts to identify exact matches, normalized with edgeR (TMM method) to CPM, filtered for low counts, and used to calculate log₂(RNA/DNA) expression or translational efficiency (TRAP), with variant pairs filtered to retain those with ≥4 measurements across conditions.
Assembly: hg38
Supplementary files format and content: raw files = fastq.gz , processed files = .txt

tag: cre status


title: Plasmid DNA, ISOMPRA 3'UTR Library, TechRep7

description: Library name: 3UTR.plasmid7


title: N2, Naïve, timepoint3.3, rep1

description:
Library name: N2_rna_r1_N3.3
N2_RNA_Raw.counts_matrix.txt


title: Plasmid DNA, ISOMPRA 3'UTR Library, TechRep8

description: Library name: 3UTR.plasmid8


title: RHO740


title: Plasmid DNA, ISOMPRA 3'UTR Library, TechRep6

description: Library name: 3UTR.plasmid6


title: RHO742


title: N2, Naïve, timepointNC, rep1

description:
Library name: N2_rna_r1_NC
N2_RNA_Raw.counts_matrix.txt


title: Plasmid DNA, ISOMPRA 3'UTR Library, TechRep4

description: Library name: 3UTR.plasmid4


title: glp-1, Primed, timepoint3.3, rep5

description:
Library name: R_r5_P3.3
glp1_RNA_Raw.counts_matrix.txt

value: glp-1 (ts)


title: N2, Naïve, timepoint2, rep1

description:
Library name: N2_rna_r1_N2
N2_RNA_Raw.counts_matrix.txt


title: RNA from TSP2KO mouse (3mos) dermal fibroblasts sample2

city: New Haven

first: Yaqing

last: Huang

state: CT

address: 10 Amistad Room 304A

department: Pathology

institute: Yale University

description:
Library name: TK2 RNA
TSP2-2_S37

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

organism: Mus musculus

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: glp-1, Naïve, timepointNC, rep5

description:
Library name: R_r5_NC
glp1_RNA_Raw.counts_matrix.txt


title: RNA from TSP2KO mouse (3mos) dermal fibroblasts sample3

description:
Library name: TK3 RNA
TSP2-3_S38


title: glp-1, Primed, timepoint1, rep5

description:
Library name: R_r5_P1
glp1_RNA_Raw.counts_matrix.txt


title: Plasmid DNA, ISOMPRA 3'UTR Library, TechRep5

description: Library name: 3UTR.plasmid5


title: glp-1, Primed, timepoint2, rep5

description:
Library name: R_r5_P2
glp1_RNA_Raw.counts_matrix.txt


title: N2, Naïve, timepoint1, rep1

description:
Library name: N2_rna_r1_N1
N2_RNA_Raw.counts_matrix.txt


title: Plasmid DNA, ISOMPRA 3'UTR Library, TechRep3

description: Library name: 3UTR.plasmid3


title: glp-1, Naïve, timepoint2, rep5

description:
Library name: R_r5_N2
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Primed, timepoint2, rep4

description:
Library name: R_r4_P2
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Naïve, timepoint3.3, rep5

description:
Library name: R_r5_N3.3
glp1_RNA_Raw.counts_matrix.txt


title: Plasmid DNA, ISOMPRA 3'UTR Library, TechRep1

description: Library name: 3UTR.plasmid1


title: RNA from TSP2KO mouse (3mos) dermal fibroblasts sample1

description:
Library name: TK1 RNA
TSP2-1_S36


title: glp-1, Naïve, timepoint1, rep5

description:
Library name: R_r5_N1
glp1_RNA_Raw.counts_matrix.txt


title: RNA from WT mouse (3mos) dermal fibroblasts sample3

description:
Library name: WT3 RNA
WT-3_S35


title: Plasmid DNA, Empra

description: Library name: rep1.dna.fastq

value: Empra Library DNA from Plasmid


title: Plasmid DNA, ISOMPRA

description: Library name: rep.dna1


title: glp-1, Primed, timepoint3.3, rep4

description:
Library name: R_r4_P3.3
glp1_RNA_Raw.counts_matrix.txt


title: Plasmid DNA, ISOMPRA 3'UTR Library, TechRep2

description: Library name: 3UTR.plasmid2


title: glp-1, Primed, timepoint2, rep3

description:
Library name: R_r3_P2
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Primed, timepoint3.6, rep3

description:
Library name: R_r3_P3.6
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Naïve, timepoint1, rep4

description:
Library name: R_r4_N1
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Naïve, timepoint3.3, rep4

description:
Library name: R_r4_N3.3
glp1_RNA_Raw.counts_matrix.txt


title: SNU-387_treated_3

first: Alexander

last: Zheleznyak

address: 660 S. Euclid

institute: WUSM

description: Library name: Sample_51

data_processing:
Basecalling and demultiplexing with Illumina BCLconvert
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCh38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

growth_protocol: standard cell culture conditions

extract_protocol:
RNA extraction was performed using Qiagen Rneasy Mini kit
Library preparation was performed with 10 ng of total RNA with a Bioanalyzer RIN score greater than 8.0. Ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina sequencing.

treatment_protocol: Treatment with 20 MBq Y-90 Therasphere beads was maintained for 10 days


title: SNU-387_treated_2

description: Library name: Sample_50


title: RNA from WT mouse (3mos) dermal fibroblasts sample1

description:
Library name: WT1 RNA
WT-1_S33


title: Liver, Hyal1 KO, HFD, rep2

city: Houston

first: Hari

middle: Krishna

last: Yalamanchili

state: Texas

address: 1250 Moursund St

department: Pediatrics

institute: Children’s Nutrition Research Center

data_processing:
Raw reads were aligned to the Mus musculus genome GRCm38 release V23 using STAR 2.7.9a
Differential gene expression analysis using DESeq2 v1.34.0
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Liver

extract_protocol:
Total RNA was isolated using Trizol reagents (Thermo Fisher).
cDNA libraries were prepared using an Illumina TruSeq RNA sample prep kit. The average size of the library cDNAs was 150 bp (excluding adapters). The integrity and quality of cDNA libraries were assessed using an Agilent 2100 Bioanalyzer and an ABI StepOne Plus real-time PCR system.

value: Liver

value: Hyal1 KO

value: HFD


title: Liver, Hyal1 KO, HFD, rep3


title: SK-Hep1_treated_3

description: Library name: Sample_48


title: RNA from WT mouse (3mos) dermal fibroblasts sample2

description:
Library name: WT2 RNA
WT-2_S34

value: WT


title: glp-1, Naïve, timepoint2, rep4

description:
Library name: R_r4_N2
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Primed, timepoint1, rep3

description:
Library name: R_r3_P1
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Naïve, timepointNC, rep3

description:
Library name: R_r3_NC
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Naïve, timepointNC, rep4

description:
Library name: R_r4_NC
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Naïve, timepoint3.6, rep3

description:
Library name: R_r3_N3.6
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Primed, timepoint3.3, rep3

description:
Library name: R_r3_P3.3
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Naïve, timepoint3.3, rep3

description:
Library name: R_r3_N3.3
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Primed, timepoint3.6, rep2

description:
Library name: R_r2_P3.6
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Naïve, timepoint2, rep3

description:
Library name: R_r3_N2
glp1_RNA_Raw.counts_matrix.txt


title: Liver, Control, HFD, rep3

value: Wild-type Control


title: glp-1, Naïve, timepoint1, rep3

description:
Library name: R_r3_N1
glp1_RNA_Raw.counts_matrix.txt


title: Liver, Hyal1 KO, HFD, rep1


title: SK-Hep1_treated_2

description: Library name: Sample_47


title: SK-Hep1_treated_1

description: Library name: Sample_46


title: glp-1, Primed, timepoint3.3, rep2

description:
Library name: R_r2_P3.3
glp1_RNA_Raw.counts_matrix.txt


title: MHCC-97H_treated_3

description: Library name: Sample_45


title: Liver, Hyal1 KO, LFD, rep3

value: LFD


title: MHCC-97H_treated_2

description: Library name: Sample_44


title: Liver, Control, HFD, rep1


title: glp-1, Primed, timepoint1, rep2

description:
Library name: R_r2_P1
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Naïve, timepointNC, rep2

description:
Library name: R_r2_NC
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Primed, timepoint2, rep2

description:
Library name: R_r2_P2
glp1_RNA_Raw.counts_matrix.txt


title: SNU-387_treated_1

description: Library name: Sample_49


title: Liver, Hyal1 KO, LFD, rep1


title: glp-1, Naïve, timepoint3.3, rep2

description:
Library name: R_r2_N3.3
glp1_RNA_Raw.counts_matrix.txt


title: MHCC-97H_treated_1

description: Library name: Sample_43


title: PLC/PRF/5_treated_3

description: Library name: Sample_42


title: glp-1, Naïve, timepoint3.6, rep2

description:
Library name: R_r2_N3.6
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Naïve, timepoint2, rep2

description:
Library name: R_r2_N2
glp1_RNA_Raw.counts_matrix.txt


title: Liver, Hyal1 KO, LFD, rep2


title: glp-1, Naïve, timepoint1, rep2

description:
Library name: R_r2_N1
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Primed, timepoint3.6, rep1

description:
Library name: R_r1_P3.6
glp1_RNA_Raw.counts_matrix.txt


title: Liver, Control, LFD, rep2


title: glp-1, Primed, timepoint3.3, rep1

description:
Library name: R_r1_P3.3
glp1_RNA_Raw.counts_matrix.txt


title: Liver, Control, HFD, rep2


title: SNU-449_treated_3

description: Library name: Sample_39


title: glp-1, Naïve, timepoint3.6, rep1

description:
Library name: R_r1_N3.6
glp1_RNA_Raw.counts_matrix.txt


title: PLC/PRF/5_treated_1

description: Library name: Sample_40


title: SNU-449_treated_2

description: Library name: Sample_38


title: glp-1, Naïve, timepoint3.3, rep1

description:
Library name: R_r1_N3.3
glp1_RNA_Raw.counts_matrix.txt


title: shHRS-2, replicate 3

city: PHILADELPHIA

first: Wei

last: Guo

state: PENNSYLVANIA

address: 433 S. University Avenue

institute: University of Pennsylvania

description: Library name: C3

data_processing:
Quality control: raw reads of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Read alignment: reference genome and gene model annotation files were downloaded from Ensembl release 94. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end reads were aligned to the reference genome using Hisat2 v2.0.5.
Quantification of gene expression: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential analysis: differential expression analysis was performed using the DESeq2 R package (1.20.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: Gene count matrix in csv format. The rows are Ensembl gene IDs and the columns are sample IDs.

source_name: primary cells

growth_protocol: Enriched human monocytes were obtained from healthy volunteers by Human Immunology Core at the University of Pennsylvania, which were only used for experiments when the purity was > 90% (confirmed by FACS analysis). Human macrophages (Mφ) were generated by incubating human monocytes with GM-CSF (10 ng/mL) for 5 days. Tumor-associated macrophages (TAMs) were induced using conditioned media (CM), prepared with modifications from previous methods.

extract_protocol:
Cells were collected and total RNA was extracted using an invitrogen PureLink RNA Mini Kit.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: To produce CM, WM9 were seeded at 70-80% confluence in 15-cm plates and cultured in RPMI1640 medium supplemented with 2% FBS for 3 days. The supernatant was then collected and concentrated 40-fold using centricons (Millipore, Inc.). To make the final CM, concentrated media were diluted at a 1:80 ratio in complete RPMI 1640. TAMs were subsequently induced by incubating with CM for 48 hours with or without HRS knockdown.

value: primary cells

value: macrophage


title: Liver, Control, LFD, rep1


title: glp-1, Naïve, timepoint1, rep1

description:
Library name: R_r1_N1
glp1_RNA_Raw.counts_matrix.txt

value: Whole worm


title: PLC/PRF/5_treated_2

description: Library name: Sample_41


title: glp-1, Primed, timepoint1, rep1

description:
Library name: R_r1_P1
glp1_RNA_Raw.counts_matrix.txt

value: P


title: glp-1, Primed, timepoint2, rep1

description:
Library name: R_r1_P2
glp1_RNA_Raw.counts_matrix.txt


title: glp-1, Naïve, timepointNC, rep1

description:
Library name: R_r1_NC
glp1_RNA_Raw.counts_matrix.txt


title: CTL, replicate 3

description: Library name: A3

value: CTL


title: SNU-449_treated_1

description: Library name: Sample_37


title: N2, Primed, timepoint1, replicate2

description: Library name: N2_atac_r2_P1

data_processing:
Adapters were trimmed using Cutadapt (version 4.6) integrated with Trim Galore, applying the parameters --gzip-nextseq 20 --cores 8 --paired.
The trimmed, paired-end sequencing files were then aligned to the reference genome Caenorhabditis elegans WBcel235 (ce11) using BWA with settings-t 8-M. The resultant BAM files were purged of mitochondrial DNA, blacklist regions, and duplicates and indexed for downstream analysis.
BAM files were converted to BigWig format with bamCoverage, without scaling adjustments to preserve original read densities. TSS signal coverage was then calculated for regions spanning 1000 bp upstream and downstream of each TSS using computeMatrix.
Peak calling was performed using MACS2 (version 2.2.7.1-r9). The settings employed were -f BAMPE --bdg --SPMR --gsize ce-q 0.05 --call-summits, with the default local correction parameters set to --slocal 1000 --llocal 10000. For visualization of read coverages, the makeTagDirectory function from the Homer software suite was used to create tag.dir. Bedgraph files were then generated using the makeUCSfile function with the parameters.tag.dir-o auto-fsize 1e10-res 1-color 106,42,73-style chipseq.
Assembly: ce11/WBcel235
Supplementary files format and content: bedGraph files indicate chromosomal position and intensity of chromatin accessibility.

extract_protocol:
Frozen worm pellets were allowed to thaw on ice, then homogenized to release nuclei. Repeated centrifugation was performed to remove cellular debris from nuclei samples. Purified nuclei were immediately subjected to the ATAC-seq procedure. Nuclei were gently resuspended in 47.5 µl Omni-ATAC buffer (composed of 2X Illumina Tagment DNA (TD) buffer, 16.5 µl 1X PBS, 0.1% TWEEN20, and 0.01% Digitonin) and mixed with 2.5µl of Illumina Tagment DNA Enzyme (TDE1) (Cat#20034197). The mixture was incubated at 37°C on a thermomixer set to 500 rpm for 0.5-1 hour. Tagmented DNA was then purified using a MinElute PCR Purification Kit (Qiagen #28004) and eluted in 10µl. The purified DNA fragments were stored at -20°C until PCR amplification
Fragmented DNA was purified using a MinElute PCR Purification Kit (Qiagen #28004) and PCR amplified using NEBNext Ultra II Q5 Master Mix (M0544S) for 12 cycles. Each sample utilized a common Adapter 1 primer (Ad1) and a unique index Adapter 2 (Ad2*) primer. Libraries were size-selected to retain DNA fragments between 100bp-600bp using Blue Pippin service, quantified using a Qubit, and quality-checked using a Bioanalyzer.


title: shHRS-2, replicate 2

description: Library name: C2


title: SNU-398_treated_3

description: Library name: Sample_36


title: glp-1, Naïve, timepoint2, rep1

description:
Library name: R_r1_N2
glp1_RNA_Raw.counts_matrix.txt

value: N


title: shHRS-1, replicate 3

description: Library name: B3


title: N2, Naïve, timepoint1, replicate2

description: Library name: N2_atac_r2_N1


title: N2, Primed, timepoint2, replicate2

description: Library name: N2_atac_r2_P2


title: SNU-398_treated_2

description: Library name: Sample_35


title: N2, Primed, timepoint3.3, replicate2

description: Library name: N2_atac_r2_P3.3


title: N2, Naïve, timepoint2, replicate2

description: Library name: N2_atac_r2_N2


title: Liver, Control, LFD, rep3


title: SNU-398_treated_1

description: Library name: Sample_34


title: N2, Primed, timepoint2, replicate1

description: Library name: N2_atac_r1_P2


title: CTL, replicate 2

description: Library name: A2


title: Hep-G2_treated_2

description: Library name: Sample_32


title: N2, Primed, timepoint3.3, replicate1

description: Library name: N2_atac_r1_P3.3


title: shHRS-1, replicate 1

description: Library name: B1


title: N2, Naïve, timepoint3.3, replicate1

description: Library name: N2_atac_r1_N3.3


title: shHRS-2, replicate 1

description: Library name: C1


title: glp-1, Primed, timepoint2, replicate4

description: Library name: A_r4_P2

value: glp-1 (ts)


title: N2, Naïve, timepoint1, replicate1

description: Library name: N2_atac_r1_N1


title: N2, Primed, timepoint1, replicate1

description: Library name: N2_atac_r1_P1


title: PLC/PRF/5_baseline_3

description: Library name: Sample_30


title: CTL, replicate 1

description: Library name: A1


title: Hep-G2_treated_3

description: Library name: Sample_33


title: PLC/PRF/5_baseline_2

description: Library name: Sample_29


title: N2, Naïve, timepoint2, replicate1

description: Library name: N2_atac_r1_N2


title: glp-1, Primed, timepoint3.3, replicate4

description: Library name: A_r4_P3.3


title: N2, Naïve, timepoint3.3, replicate2

description: Library name: N2_atac_r2_N3.3


title: Hep-G2_treated_1

description: Library name: Sample_31


title: glp-1, Primed, timepoint1, rep4

description:
Library name: R_r4_P1
glp1_RNA_Raw.counts_matrix.txt


title: PLC/PRF/5_baseline_1

description: Library name: Sample_28


title: BJ mESC Delta-Meg3-C1 Replicate 1 (RNA-seq)

city: Gif-sur-Yvette

first: Benoit

last: Moindrot

address: 1, avenue de la terrasse

institute: Institute for Integrative Biology of the Cell

description:
Library name: RNA-seq BJ Delta-Meg3 C1   (replicate 1)
RNA-seq

data_processing:
Paired-end sequencing reads were trimmed with Trimmomatic (0.39) and aligned to the mouse reference genome (mm10) with HISAT2 (2.2.1). Aligned reads were sorted with samtools (1.6), and genome coverage tracks were generated with bedtools (2.31.0). For allele-specific analyses, trimmed reads were additionally aligned to the JF1/MsJ N-masked genome using HISAT2 (2.2.1), and allele assignment was performed with SNPsplit (0.3.4). BAM files were further processed with deepTools bamCoverage (3.5.1) to generate bigWig files, normalized as CPM in 100-bp bins.
Assembly: mm10 (N-masked GRCm38/mm10)
Supplementary files format and content: BigWig

source_name: BJ1 (C57BL/6J x JF1)

growth_protocol: ESGRO Complete PLUS Clonal Grade Medium (Merck)

extract_protocol:
Total RNAs were extracted with RNeasy-Plus Mini-Kit (Qiagen, #74136), quantified by Qubit, and quality-checked with the Bioanalyzer RNA 6000 Assay kit (Agilent, #5067-1513). 210 ng RNA per sample were used for DNase I digestion (Merck, #AMPD1) and ribodepletion with Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) (New England Biolabs, E7400S).
RNA was then processed with Next® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs, E7770) for library preparation, without prior fragmentation. Definitive libraries were obtained after 13 PCR cycles

value: BJ1 (C57BL/6J x JF1)

value: mouse embryonic stem cells

value: BJ1 Delta-Meg3 C1 (C57BL/6J x JF1)


title: glp-1, Primed, timepoint1, replicate4

description: Library name: A_r4_P1


title: glp-1, Primed, timepoint2, replicate3

description: Library name: A_r3_P2


title: glp-1, Naïve, timepointNC, replicate4

description: Library name: A_r4_NC


title: JB mESC Zfp57-/- Meg3pro-/- Replicate 1 (RNA-seq)

description:
Library name: RNA-seq JB mESC Zfp57-/- Meg3 pro-/-   (replicate 1)
RNA-seq

source_name: JB1 (JF1 x C57BL/J6)

value: JB1 (JF1 x C57BL/J6)

value: JB1 Zfp57-/- Meg3 pro-/-  (JF1 x C57BL/J6)


title: glp-1, Naïve, timepoint3.3, replicate4

description: Library name: A_r4_N3.3


title: glp-1, Naïve, timepointNC, replicate3

description: Library name: A_r3_NC


title: glp-1, Naïve, timepoint2, replicate4

description: Library name: A_r4_N2


title: MHCC-97H_baseline_2

description: Library name: Sample_26


title: glp-1, Naïve, timepoint1, replicate4

description: Library name: A_r4_N1


title: glp-1, Naïve, timepoint3.3, replicate3

description: Library name: A_r3_N3.3


title: JB mESC Zfp57-/- Replicate 1 (RNA-seq)

description:
Library name: RNA-seq JB mESC Zfp57-/-   (replicate 1)
RNA-seq


title: MHCC-97H_baseline_3

description: Library name: Sample_27


title: glp-1, Naïve, timepoint2, replicate3

description: Library name: A_r3_N2


title: glp-1, Primed, timepoint3.3, replicate3

description: Library name: A_r3_P3.3


title: JB mESC Zfp57-/- Meg3pro-/- Replicate 2 (RNA-seq)

description:
Library name: RNA-seq JB mESC Zfp57-/- Meg3 pro-/-   (replicate 2)
RNA-seq


title: glp-1, Primed, timepoint3.6, replicate2

description: Library name: A_r2_P3.6


title: JB mESC Zfp57-/- Replicate 2 (RNA-seq)

description:
Library name: RNA-seq JB mESC Zfp57-/-   (replicate 2)
RNA-seq


title: SNU-398_baselime_2

description: Library name: Sample_23


title: BJ mESC Delta-Meg3-C1 Replicate 2 (RNA-seq)

description:
Library name: RNA-seq BJ Delta-Meg3 C1   (replicate 2)
RNA-seq


title: SNU-398_baselime_3

description: Library name: Sample_24


title: glp-1, Naïve, timepoint1, replicate3

description: Library name: A_r3_N1


title: glp-1, Primed, timepoint1, replicate3

description: Library name: A_r3_P1


title: glp-1, Naïve, timepoint1, replicate2

description: Library name: A_r2_N1


title: glp-1, Primed, timepoint3.3, replicate2

description: Library name: A_r2_P3.3


title: SK-Hep1_baseline_2

description: Library name: Sample_20


title: SNU-398_baselime_1

description: Library name: Sample_22


title: glp-1, Naïve, timepoint3.3, replicate2

description: Library name: A_r2_N3.3


title: BJ mESC WT Replicate 1 (RNA-seq)

description:
Library name: RNA-seq BJ mESC WT   (replicate 1)
RNA-seq

value: BJ1 WT (C57BL/6J x JF1)


title: glp-1, Naïve, timepoint3.6, replicate2

description: Library name: A_r2_N3.6


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 20

description: Library name: 3UTR.ms20.exn.pre

source_name: brain

value: brain

value: uISOMPRA Library AAV Infection

value: Homozygous

value: F


title: MHCC-97H_baseline_1

description: Library name: Sample_25


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 20

description: Library name: 3UTR.ms20.exn.post


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 20

description: Library name: 3UTR.ms20.cortex.pre


title: SK-Hep1_baseline_1

description: Library name: Sample_19


title: glp-1, Primed, timepoint3.3, replicate1

description: Library name: A_r1_P3.3


title: glp-1, Naïve, timepointNC, replicate1

description: Library name: A_r1_NC


title: glp-1, Naïve, timepoint2, replicate2

description: Library name: A_r2_N2


title: BJ mESC WT Replicate 2 (RNA-seq)

description:
Library name: RNA-seq BJ mESC WT   (replicate 2)
RNA-seq


title: glp-1, Naïve, timepoint3.3, replicate1

description: Library name: A_r1_N3.3


title: glp-1, Primed, timepoint1, replicate2

description: Library name: A_r2_P1


title: glp-1, Primed, timepoint2, replicate2

description: Library name: A_r2_P2


title: SNU-475_baseline_3

description: Library name: Sample_15


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 19

description: Library name: 3UTR.ms19.cortex.post


title: G4_evolved_Bub3

city: Hanover

first: Soni

last: Lacefield

state: New Hampshire

address: 74 College St

department: Biochemistry and Cell Biology

institute: Geisel School of medicine at Dartmouth

description: Library name: 174199_58

data_processing:
Raw reads were trimmed with Trimmomatic v0.39, with the following parameters, “ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36”.  Trimmed reads were aligned to the Yeast genome S288C, available at NCBI accession GCF_000146045.2, using BWA 0.7.17, with default parameters.  Duplicate reads were marked with “MarkDuplicates” from Picard tools v2.27.1, with default parameters.
SNPs and small indels were called with FreeBayes v1.3.4 and the following parameters “--min-coverage 5 --limit-coverage 200 --min-alternate-fraction .2 --min-mapping-quality 15 --min-alternate-count 2”.  SNPs were annotated using SNPEff v5.0e.
Copy number analysis was performed using the following commands from the Genome Analysis Tool Kit (GATK) v4.5.0.0. Genome intervals for calculating copy number were determined with the PreprocessIntervals command, with the following parameters, “--padding 0 -imr OVERLAPPING_ONLY”.  Reads counts for each sample and each interval were collected using the CollectReadCounts command, with default parameters.  Copy number per interval was standardized and denoised using the DenoiseReadCounts command, with the “--standardized-copy-ratios” and “--denoised-copy-ratios” parameters.  Genome-wide copy number graphs were created by plotting columns 2 (“START”) and 4 (“LOG2_COPY_RATIO”) of the denoised copy ratio output.
Assembly: GCF_000146045.2
Supplementary files format and content: The TSV files contain the processed data (log2 ratios) used for plotting the copy number variation graphs.
Library strategy:

organism: Saccharomyces cerevisiae

source_name: overnight grown culture of Saccharomyces cerevisiae

extract_protocol:
Genomic DNA was isolated from individual samples using the Phenol/Chloroform/Isoamyl alcohol method and washed with 70% ethanol to get good quality samples.
Input DNA was quantified by Qubit (Thermo Fisher) and 200ng was used as input into the Nextera DNA with tagmentation workflow (Illumina) to generate Illumina sequencing libraries according to the manufacturer’s protocol. Libraries were normalized and pooled for sequencing on a NextSeq2000 (Illumina), targeting 10 million, 150bp paired-end reads per sample.

tag: strain


title: SK-Hep1_baseline_3

description: Library name: Sample_21


title: glp-1, Primed, timepoint1, replicate1

description: Library name: A_r1_P1

tag: tissue


title: SNU-475_baseline_2

description: Library name: Sample_14


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 18

description: Library name: 3UTR.ms18.exn.post

tag: cell type


title: E3_evolved_Bub3

description: Library name: 174199_57

value: overnight grown culture of Saccharomyces cerevisiae


title: glp-1, Primed, timepoint3.6, replicate1

description: Library name: A_r1_P3.6

tag: treatment


title: glp-1, Naïve, timepointNC, replicate2

description: Library name: A_r2_NC


title: wildtype_LY1_evolved_Bub3

description: Library name: 174199_55


title: Hep-3B_baseline_3

description: Library name: Sample_18


title: G1_evolved

description: Library name: 174199_49


title: glp-1, Primed, timepoint2, replicate1

description: Library name: A_r1_P2


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 19

description: Library name: 3UTR.ms19.exn.post


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 20

description: Library name: 3UTR.ms20.cortex.post


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 18

description: Library name: 3UTR.ms18.cortex.pre


title: Hep-3B_baseline_2

description: Library name: Sample_17


title: Hep-3B_baseline_1

description: Library name: Sample_16


title: F3_evolved

description: Library name: 174199_47


title: glp-1, Naïve, timepoint2, replicate1

description: Library name: A_r1_N2


title: C2_evolved_Bub3

description: Library name: 174199_56


title: SNU-449_baseline_1

description: Library name: Sample_10


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 19

description: Library name: 3UTR.ms19.exn.pre


title: SNU-475_baseline_1

description: Library name: Sample_13


title: glp-1, Naïve, timepoint1, replicate1

description: Library name: A_r1_N1


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 19

description: Library name: 3UTR.ms19.cortex.pre


title: glp-1, Naïve, timepoint3.6, replicate1

description: Library name: A_r1_N3.6


title: SNU-449_baseline_3

description: Library name: Sample_12


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 18

description: Library name: 3UTR.ms18.exn.pre


title: F3_non-evolved

description: Library name: 174199_20


title: SNU-423_baseline_3

description: Library name: Sample_9


title: G4_evolved

description: Library name: 174199_50


title: G4_non-evolved

description: Library name: 174199_23


title: shHRS-1, replicate 2

description: Library name: B2

value: primary cells

value: macrophage

value: WT


title: G1_non-evolved

description: Library name: 174199_22


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 18

description: Library name: 3UTR.ms18.cortex.post


title: SNU-423_baseline_2

description: Library name: Sample_8


title: SNU-449_baseline_2

description: Library name: Sample_11


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 17

description: Library name: 3UTR.ms17.exn.post


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 17

description: Library name: 3UTR.ms17.exn.pre


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 17

description: Library name: 3UTR.ms17.cortex.post


title: F4_non-evolved

description: Library name: 174199_21


title: E3_non-evolved

description: Library name: 174199_18


title: E3_evolved

description: Library name: 174199_45


title: Hep-G2_baseline_2

description: Library name: Sample_5


title: D4_evolved

description: Library name: 174199_42


title: Hep-G2_baseline_1

description: Library name: Sample_4


title: E4_non-evolved

description: Library name: 174199_19


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 16

description: Library name: 3UTR.ms16.cortex.post


title: Epithelial organoid from Hmox1 KO mice, hemin treated, 3

city: Aurora

last: Onyiah

state: CO

institute: University of Colorado

description: Library name: KO_Hem_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw FPKM values for all samples

source_name: Organoid

extract_protocol:
RNA was harvested using the Rneasy mini kit (Qiagen).
Performed by Novogene USA: Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Organoids were maintained in L-WRN cell conditioned enteroid media (DMEM/F12 supplemented with 1% Pen/Strep, 1% glutamax, 10% FBS) in a humidified atmosphere with 5% CO2 at 37C.

value: Organoid

value: Epithelial

value: Hmox1 fl/fl /Vil1 Cre

value: Hemin


title: E4_evolved

description: Library name: 174199_46


title: F4_evolved

description: Library name: 174199_48


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 16

description: Library name: 3UTR.ms16.exn.post


title: SNU-387_baseline_3

description: Library name: Sample_3


title: SNU-423_baseline_1

description: Library name: Sample_7


title: Epithelial organoid from Hmox1 KO mice, vehicle treated, 3

description: Library name: KO_NTC_3

value: Hmox1 KO /Vil1 Cre

value: Vehicle


title: Hep-G2_baseline_3

description: Library name: Sample_6


title: D2_non-evolved

description: Library name: 174199_13


title: D4_non-evolved

description: Library name: 174199_15


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 17

description: Library name: 3UTR.ms17.cortex.pre


title: D3_non-evolved

description: Library name: 174199_14


title: Epithelial organoid from Hmox1 KO mice, vehicle treated, 2

description: Library name: KO_NTC_2


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 16

description: Library name: 3UTR.ms16.cortex.pre


title: D2_evolved

description: Library name: 174199_40


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 16

description: Library name: 3UTR.ms16.exn.pre


title: Epithelial organoid from Hmox1 KO mice, hemin treated, 1

description: Library name: KO_Hem_1


title: D681-LNG2

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description: Library name: D681_001_ATAC_ABFNY-0304

library_source: genomic single cell

data_processing:
Alignment to the GRCh38 reference and demultiplexing of cell-identifying barcodes was performed using Cell Ranger ATAC (v.2.0.0, 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: The processed files are gzip-compressed, tab-delimited files tabulating the alignment position (chromosome, start, end), cell-identifying barcode, and read count for each unique fragment sequenced in an snATAC-seq library.

source_name: lung

extract_protocol:
Mononuclear cell suspensions were prepared from dissociated human lung tissue using the detailed protocol "Preparation of Single Cell Suspension from Human Lung Tissue" on protocols.io (dx.doi.org/10.17504/protocols.io.bwr9pd96). After dissection of the epithelium and lamina propria, mononuclear cell suspensions were prepared from dissociated human jejunum tissue using the detailed protocol "Preparation of Single Cell Suspensions of the Intra-Epithelial Layer and Lamina Propria from Human Intestinal Tissue" on protocols.io (dx.doi.org/10.17504/protocols.io.bwq7pdzn). The resulting single-cell suspensions from both tissue sites were cryopreserved and stored in liquid nitrogen. For snATAC-seq, cryopreserved cells were thawed rapidly at 37°C until small ice crystals remained. Cells were transferred into pre-warmed culture medium and gradually diluted to minimize shock. Following centrifugation, pellets were gently resuspended and treated with Benzonase (Millipore Sigma) to reduce cell clumping. Cells were washed in DPBS containing FBS and EDTA, and viability was assessed by fluorescence microscopy-based cell counting (Chemometec NC-3000). Finally, dead cells and contaminating populations (e.g., CD66b+, CD235ab+, and EpCAM+ cells) were removed using magnetic bead–based depletion (Miltenyi Biotec; BioMag Plus Streptavidin). Nuclei were prepared following the 10x Genomics protocol for single-cell ATAC sequencing (CG000169 Rev D) with minor adjustments. Briefly, 1 × 106 cells per sample were pelleted and resuspended in chilled lysis buffer containing detergents (Tween-20, NP-40 substitute, and digitonin) and BSA. After a brief incubation on ice, lysates were diluted in wash buffer and centrifuged to pellet intact nuclei.
Nuclei were resuspended in diluted nuclei buffer, counted by hemocytometer, and adjusted to a concentration corresponding to ~8,000 nuclei for loading into the 10x Genomics Chromium Controller for encapsulation and barcoding. Sequencing libraries were prepared using Chromium Next GEM Single Cell ATAC Reagent Kits v2 (10x Genomics) and sequenced on an Illumina NovaSeq X Plus with 2x100 paried-end reads.

value: lung

tag: organ donor

value: Immune cells


title: D3_evolved

description: Library name: 174199_41


title: Epithelial organoid from Hmox1 KO mice, hemin treated, 2

description: Library name: KO_Hem_2


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 15

description: Library name: 3UTR.ms15.cortex.pre


title: D1_evolved

description: Library name: 174199_39


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 15

description: Library name: 3UTR.ms15.exn.post


title: SNU-387_baseline_2

description: Library name: Sample_2


title: SNU-387_baseline_1

description: Library name: Sample_1


title: D1_non-evolved

description: Library name: 174199_12


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 14

description: Library name: 3UTR.ms14.exn.post


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 15

description: Library name: 3UTR.ms15.cortex.post


title: C4_evolved

description: Library name: 174199_38


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 15

description: Library name: 3UTR.ms15.exn.pre


title: Epithelial organoid from Hmox1 fl/fl mice, hemin treated, 3

description: Library name: Ctrl_Hem_3

value: Hmox1 fl/fl


title: D681-JLP2

description: Library name: D681_001_ATAC_ABFNY-0302

source_name: jejunum lamina propria

value: jejunum lamina propria


title: C2_evolved

description: Library name: 174199_36


title: Epithelial organoid from Hmox1 fl/fl mice, vehicle treated, 2

description: Library name: Ctrl_NTC_2


title: C3_non-evolved

description: Library name: 174199_10


title: Epithelial organoid from Hmox1 fl/fl mice, hemin treated, 2

description: Library name: Ctrl_Hem_2


title: C4_non-evolved

description: Library name: 174199_11


title: Epithelial organoid from Hmox1 KO mice, vehicle treated, 1

description: Library name: KO_NTC_1


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 14

description: Library name: 3UTR.ms14.cortex.pre

value: brain

value: uISOMPRA Library AAV Infection


title: Epithelial organoid from Hmox1 fl/fl mice, hemin treated, 1

description: Library name: Ctrl_Hem_1


title: D679-JLP1

description: Library name: D679_001_ATAC_ABFNY-0293


title: C2_non-evolved

description: Library name: 174199_09


title: D679-LNG1

description: Library name: D679_001_ATAC_ABFNY-0295


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 13

description: Library name: 3UTR.ms13.exn.post

value: Homozygous

value: F


title: Epithelial organoid from Hmox1 fl/fl mice, vehicle treated, 3

description: Library name: Ctrl_NTC_3


title: D600-LNG2

description: Library name: D600_001_ATAC_ABFNY-0160


title: C1_non-evolved

description: Library name: 174199_08

value: overnight grown culture of Saccharomyces cerevisiae


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 14

description: Library name: 3UTR.ms14.exn.pre


title: D681-JLP1

description: Library name: D681_001_ATAC_ABFNY-0301


title: B3_evolved

description: Library name: 174199_34


title: C3_evolved

description: Library name: 174199_37


title: D679-LNG2

description: Library name: D679_001_ATAC_ABFNY-0296


title: D681-LNG1

description: Library name: D681_001_ATAC_ABFNY-0303


title: D600-JLP1

description: Library name: D600_001_ATAC_ABFNY-0158


title: BAT, HFD, rep 1

city: Chongqing

first: Xiujuan

last: Jiang

address: Tiansheng road

institute: Southwest University

description:
Library name: BAT_HFD_W_1
HFD_W_1

data_processing:
Raw paired-end sequencing reads were quality-controlled and adapter-trimmed using fastp (v0.23.4) with default parameters to obtain clean reads.
The clean reads were aligned to the mouse reference genome (GRCm39) in orientation mode using HISAT2 (v2.2.1).
Transcript assembly and quantification were performed using StringTie (v2.2.1) with a reference-based approach. Gene expression levels were quantified as TPM (Transcripts Per Million) using RSEM (v1.3.3).
Differential gene expression analysis was performed using DESeq2 (v1.34.0). Genes with |log2(fold change)| ≥ 1 and a false discovery rate (FDR) < 0.05 were considered significantly differentially expressed.
Assembly: GRCm39 (GCF_000001635.27)
Supplementary files format and content: File: Exp_G_RSEM_TPM.csv is a tab-delimited text file containing gene expression levels quantified as TPM (Transcripts Per Million) by the RSEM software. The file includes data for all 623 genes across all 8 samples.

source_name: brown adipose tissue

growth_protocol: Male C57BL/6J mice (6 weeks old) were fed a high-fat diet (60% kcal from fat) for 16 weeks to establish the obesity model. Mice were housed under specific pathogen-free conditions at 22±2°C with a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted from brown adipose tissue using TRIzol® Reagent according to the manufacturer’s instructions. RNA quality was assessed using an ND-2000 spectrophotometer (NanoDrop Technologies) and a 5300 Bioanalyzer (Agilent Technologies). Only high-quality RNA samples (OD260/280=1.8-2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S ratio≥1.0, total amount>1 μg) were used for subsequent library construction.
Sequencing libraries were constructed using the Illumina® Stranded mRNA Prep, Ligation kit. Briefly, mRNA was isolated by polyA selection using oligo(dT) beads, fragmented, and then used for double-stranded cDNA synthesis with random hexamer primers. The cDNA underwent end repair, phosphorylation, adapter ligation, size selection (targeting ~300 bp fragments), and PCR amplification (15 cycles). Library quantification was performed using Qubit 4.0.

treatment_protocol: The intervention group (HFD+PTE) received 0.25% (w/v) Pu-erh tea extract (PTE) ad libitum in drinking water for 16 weeks concurrently with high-fat diet feeding. PTE was prepared by hot-water extraction of ripened Pu-erh tea followed by lyophilization.

value: brown adipose tissue

value: high fat diet


title: B2_non-evolved

description: Library name: 174199_06


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 14

description: Library name: 3UTR.ms14.cortex.post


title: D600-LNG1

description: Library name: D600_001_ATAC_ABFNY-0159


title: BAT, HFD+PTE, rep 3

description:
Library name: BAT_HFD_T_3
HFD_T_3

value: high fat diet + Pu-erh tea extract


title: BAT, HFD, rep 4

description:
Library name: BAT_HFD_W_4
HFD_W_4


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 13

description: Library name: 3UTR.ms13.exn.pre


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 12

description: Library name: 3UTR.ms12.exn.pre


title: BAT, HFD+PTE, rep 2

description:
Library name: BAT_HFD_T_2
HFD_T_2


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 13

description: Library name: 3UTR.ms13.cortex.post


title: A4_non-evolved

description: Library name: 174199_05


title: BAT, HFD, rep 2

description:
Library name: BAT_HFD_W_2
HFD_W_2


title: A4_evolved

description: Library name: 174199_32


title: D679-JLP2

description: Library name: D679_001_ATAC_ABFNY-0294


title: B2_evolved

description: Library name: 174199_33


title: B3_non-evolved

description: Library name: 174199_07


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 12

description: Library name: 3UTR.ms12.exn.post


title: BAT, HFD+PTE, rep 4

description:
Library name: BAT_HFD_T_4
HFD_T_4


title: Epithelial organoid from Hmox1 fl/fl mice, vehicle treated, 1

description: Library name: Ctrl_NTC_1

value: Organoid

value: Epithelial


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 13

description: Library name: 3UTR.ms13.cortex.pre


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 12

description: Library name: 3UTR.ms12.cortex.post


title: BAT, HFD, rep 3

description:
Library name: BAT_HFD_W_3
HFD_W_3