title: L.HHS.43

description: Library name: 107081-001-028


title: L.HHS.42

status: Public on Aug 07 2026

type: SRA

city: Leiden

first: Eveline

last: Gart

state: Zuid Holland

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

description: Library name: 107081-001-027

library_source: transcriptomic

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html, DESeq2-method.32).

molecule: total RNA

organism: Mus musculus

source_name: Liver, dexter lobe

growth_protocol: Animals were bred and housed at an AAALAC-accredited SPF animal facility (TNO Metabolic Health Research, Leiden, the Netherlands). The Ldlr−/−.Leiden mouse model was chosen because these mice develop characteristics of the metabolic syndrome including obesity, insulin resistance, hyperlipidemia, MASLD with fibrosis and atherosclerosis when fed a high fat diet. Male mice were selected due to their higher susceptibility to obesity and inflammation compared to females. Mice (aged 14-19 weeks) were group-housed in a temperature-controlled room at 50-60% humidity and with a 12h light-dark cycle. Mice had access to food and water ad libitum. Body weight, food intake per cage and clinical signs were monitored regularly. One group of n=8 mice served as healthy control group and received the grain-based chow diet (Ssniff Spezialdiäten, Soest, Germany) and a total of 75 mice received an HFD containing 45 kCal% fat from lard, 35 kCal% carbohydrates and 20 kCal% casein (Research Diets, New Brunswick, NJ, USA) to induce MASH and atherosclerosis.

extract_protocol:
At the study endpoint at t=14 weeks (or at t=0 for the HFD reference group), mice were sacrificed by gradual fill CO2 asphyxiation. Liver tissue, hearts with aortic roots, ascending aortas, perigonadal (pgWAT) and subcutaneous white adipose tissue (scWAT) and brown adipose tissue (BAT) were collected. Left gastrocnemius and soleus muscles were isolated jointly and right gastrocnemius and quadriceps were isolated separately. Tissues were snap-frozen in liquid nitrogen for biochemical/transcriptome analyses. For transcriptomics analysis, snap-frozen tissue of the right liver lobe, right quadriceps femoris, perigonadal WAT and ascending aorta were used. RNA was extracted using the RNA-Stat60 total RNA isolation kit (Amsbio) for liver, muscle and aorta and using the Ambion RNAqueous total RNA isolation kit (ThermoFisher Scientific, Waltman, MA, USA) for WAT.
mRNA was isolated from total RNA with oligo-dT magnetic beads. Next, cDNA was synthesized and subsequently ligated with sequencing adapters and amplified by PCR and was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 v1.5 sequencer (Illumina, San Diego) with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-30 million read counts per sample. Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: At t=0, after a 20-week run-in period on the HFD, mice were matched based on body weight, age and glucose, cholesterol and triglyceride levels into equal groups of n=15 mice each. Group sizes were calculated by power analysis (GPower), using a minimal effect size of 30%, two-sided t-test with 95% confidence interval, 90% power and α of 0.05. One group served as HFD reference group and was sacrificed at t=0 to indicate the histological severity (in particular MASH and atherosclerosis) at the start of the intervention period and determine whether the interventions affected parameters beyond levels at the start of the intervention period or merely blocked further progression. Another group on HFD received daily subcutaneous saline injections (HFD vehicle control) for 14 weeks. The third group on HFD received daily subcutaneous semaglutide injections (100 µL; Ozempic®, Novo Nordisk, Bagsværd, Denmark). To acclimatize to the final semaglutide dosage (0.12 mg/kg body weight/day), the dose was escalated over the course of five days at a rate of 0.024 (20%) 0.048 (40%) 0.072 (60%), 0.096 (80%) mg/kg body weight/day until the final dose was reached that was maintained for 14 weeks. Doses were adjusted based on weekly individual body weights. For the fourth group of mice on HFD, a running wheel (Mouse Igloo+Fast Trac, Datesand, Bredbury, UK) was added into the cage, to which the mice had unlimited access and which has been shown to increase voluntary movement in these mice12. The last group on HFD received both subcutaneous semaglutide injections and a running wheel in the cage.

tag: tissue

value: Liver, dexter lobe

tag: genotype

tag: treatment

value: HHS

tag: treatmdescript

tag: animalnr


title: L.HHS.39

description: Library name: 107081-001-024


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A4). mRNA

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 450 Serra Mall

department: Genetics

country: USA

institute: Stanford University

description:
Library name: validation_moi1_1_rep01_a4_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_1_rep01_a4_filtered_feature_bc_matrix.h5

library_source: transcriptomic single cell

data_processing:
We aligned reads to transcripts and identified cells using the 10x Genomics Cell Ranger Count v9. For the guides, we input the guide FASTQ files as CRISPR Guide Capture libraries and the feature_reference file containing the guide sequences.
Assembly: human hg38
Supplementary files format and content: .h5 files from Cellranger

molecule: polyA RNA

organism: Homo sapiens

source_name: WTC11 (human iPSC line)

extract_protocol:
Cells were collected using centrifugation, washed with PBS+BSA and subjected to 10x Genomics 3' scRNA-seq
Libraries were constructed accroding to the protocol detailed in Ray et al 2025 (dx.doi.org/10.17504/protocols.io.3byl4z7drvo5/v1)

tag: cell type

value: WTC11 (human iPSC line)

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.1, replicate 1, channel A4


title: L.HHS.40

description: Library name: 107081-001-025


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A3). mRNA

description:
Library name: validation_moi1_1_rep01_a3_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_1_rep01_a3_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.1, replicate 1, channel A3


title: L.HH.37

description: Library name: 107081-001-022

value: HH


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A1). gRNA

description:
Library name: validation_moi1_1_rep01_a1_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_1_rep01_a1_filtered_feature_bc_matrix.h5

library_source: other

molecule: other

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.1, replicate 1, channel A1


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A2). mRNA

description:
Library name: validation_moi1_1_rep01_a2_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_1_rep01_a2_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.1, replicate 1, channel A2


title: L.HH.36

description: Library name: 107081-001-021


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A1). mRNA

description:
Library name: validation_moi1_1_rep01_a1_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_1_rep01_a1_filtered_feature_bc_matrix.h5


title: L.HH.38

description: Library name: 107081-001-023


title: Validation DC-TAP-seq for 203 genes at MOI 14.4 (replicate 2, channel B8). gRNA

description:
Library name: validation_moi14_4_rep02_b8_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi14_4_rep02_b8_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 14.4, replicate 2, channel B8


title: L.HH.34

description: Library name: 107081-001-019


title: Validation DC-TAP-seq for 203 genes at MOI 14.4 (replicate 2, channel B8). mRNA

description:
Library name: validation_moi14_4_rep02_b8_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi14_4_rep02_b8_filtered_feature_bc_matrix.h5


title: Validation DC-TAP-seq for 203 genes at MOI 14.4 (replicate 2, channel B7). mRNA

description:
Library name: validation_moi14_4_rep02_b7_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi14_4_rep02_b7_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 14.4, replicate 2, channel B7


title: L.HH.32

description: Library name: 107081-001-017


title: Validation DC-TAP-seq for 203 genes at MOI 14.4 (replicate 2, channel B7). gRNA

description:
Library name: validation_moi14_4_rep02_b7_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi14_4_rep02_b7_filtered_feature_bc_matrix.h5


title: L.HH.35

description: Library name: 107081-001-020


title: L.HH.33

description: Library name: 107081-001-018


title: L.HH.31

description: Library name: 107081-001-016


title: L.HH.30

description: Library name: 107081-001-015


title: Validation DC-TAP-seq for 203 genes at MOI 12.6 (replicate 1, channel A7). gRNA

description:
Library name: validation_moi12_6_rep01_a7_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi12_6_rep01_a7_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 12.6, replicate 1, channel A7


title: L.HH.29

description: Library name: 107081-001-014


title: Validation DC-TAP-seq for 203 genes at MOI 12.6 (replicate 1, channel A8). gRNA

description:
Library name: validation_moi12_6_rep01_a8_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi12_6_rep01_a8_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 12.6, replicate 1, channel A8


title: Validation DC-TAP-seq for 203 genes at MOI 12.6 (replicate 1, channel A8). mRNA

description:
Library name: validation_moi12_6_rep01_a8_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi12_6_rep01_a8_filtered_feature_bc_matrix.h5


title: L.HH.28

description: Library name: 107081-001-013


title: Validation DC-TAP-seq for 203 genes at MOI 12.6 (replicate 1, channel A7). mRNA

description:
Library name: validation_moi12_6_rep01_a7_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi12_6_rep01_a7_filtered_feature_bc_matrix.h5


title: L.HH.27

description: Library name: 107081-001-012


title: L.HH.24

description: Library name: 107081-001-009


title: L.CC.8

description: Library name: 107081-001-008

value: CC


title: RPE1_Digestion_control_TR3

city: New York

first: Viviana

middle: I

last: Risca

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: Library name: RPE1_Digestion_control_TR3

library_source: genomic

data_processing:
Paired-end BAMs were converted to RPGC-normalized bigWig coverage using deepTools bamCoverage (hg38, chrX excluded). Fragment coverage was calculated by extending read pairs, and insert size-stratified tracks were generated for nucleosomal (100–200 bp) and sub-nucleosomal (<100 bp) fragments. Metaprofiles were computed as the mean signal around feature centers, including occupied CTCF motifs (JASPAR MA0139.1; top 5% by ChIP-seq or Cut&Run signal), ENCODE DNase footprints, and TSS/TES regions. Fragment-length distributions were derived from properly paired autosomal reads (MAPQ ≥30), downsampled to equal depth across replicates, and quantified as |TLEN| histograms with counts per million normalization. GC-balanced fragment-end composition and genome-wide GC-coverage bias were assessed by stratifying 1 kb windows into GC quantiles, sampling equal numbers of fragments per stratum, and normalizing coverage to the mean of filtered bins. Pairwise concordance among coverage tracks was evaluated by tiling the genome into 5 kbp bins, extracting mean signal, excluding zero or extreme bins, and calculating Pearson, Spearman, and Kendall correlations after mean-normalization. All scripts recorded parameters, contig sets, and software versions to ensure reproducibility.
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

growth_protocol: hTERT-RPE1  cells were cultured in the media and conditions recommended by ATCC.

extract_protocol:
Fixed-chromatin CAD digestions were performed to validate TEVp-dependent activation on nuclei. K562, hTERT RPE-1 (ATCC CRL-4000), and GM12878 (Coriell) cells were cultured under standard conditions and harvested at defined densities, with hTERT RPE-1 cells induced into a quiescent (G0) state by contact inhibition. Cells were washed with pre-warmed DPBS and fixed either with 1% methanol-free formaldehyde (Thermo Fisher Scientific, 28908) alone or using dual crosslinking with 3 mM DSG (freshly prepared 300 mM stock in DMSO) for 35 min followed by 1% formaldehyde for 10 min. Fixation was quenched with Tris–HCl to a final concentration of 750 mM, and cells were pelleted, washed twice with ice-cold DPBS, resuspended to 4 × 10^6 cells/mL, and snap-frozen in liquid nitrogen for storage at −80 °C. Frozen pellets were lysed on ice in 1× WDB-10 buffer (10 mM HEPES–KOH pH 7.5, 10 mM KCl, 3 mM MgCl₂, 1 mM DTT) supplemented with 0.2% NP-40 to isolate nuclei, which were then treated with RNase (RNase A, Thermo Scientific EN0531, 0.36 µg/µL for hTERT RPE-1; RNase T1, Thermo Scientific EN0542, 10 U/µL for K562 and GM12878) at 30–37 °C for 15 min. CAD digestion was initiated by adding 20 µL Peak 1 TST–muGFP–SUMOEu1–CAD:ICAD2×TEV proenzyme and 5 µL TEV protease (NEB, P8112S, Lot 3) per reaction, incubated for 20 min at 30 °C followed by 1 h at 37 °C with shaking at 1000 rpm. Reactions were quenched with 1 mM ZnCl₂ and washed with 1× WDB-10 + 0.2% NP-40. For titration experiments, GM12878 nuclei (4 × 10^6 per replicate) were digested with CAD at 4–500 U in 1× WDB-10. DNA was deproteinated, crosslinks reversed with Proteinase K (NEB, P8107S, 20 µg/µL) in the presence of SDS and NaCl overnight at 65 °C, and purified using the Genomic DNA Clean & Concentrator-10 kit (Zymo, D4011) with a 1:5 sample-to-binding-buffer ratio to retain low-molecular-weight fragments.
Purified DNA (50–700 bp) was used to prepare libraries with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) using modifications to retain short fragments. Adapter ligation, USER enzyme treatment, and size selection with Ampure XP beads were performed according to the manufacturer’s instructions, and libraries were indexed (NEB, E6441A) with 4 PCR cycles, cleaned with 1.2× Ampure XP beads, and quantified by Qubit dsDNA HS and TapeStation analysis. CAD-seq libraries were sequenced on Illumina NextSeq 1000 (2×60 bp) or NovaSeq X/X Plus (2×150 bp) platforms.

tag: cell line

value: Retinal Pigment Epithelial cell

value: WT


title: K562_Digestion_control

description: Library name: K562_Digestion_control

value: myelogenous leukemia cell


title: RPE1_Digestion_control_TR4

description: Library name: RPE1_Digestion_control_TR4


title: L.HH.25

description: Library name: 107081-001-010


title: L.CC.7

description: Library name: 107081-001-007


title: RPE1_Digestion_control_TR1

description: Library name: RPE1_Digestion_control_TR1


title: L.CC.6

description: Library name: 107081-001-006


title: RPE1_CAD-seq_250U_TR1

description: Library name: RPE1_CAD-seq_250U_TR1


title: RPE1_Digestion_control_TR2

description: Library name: RPE1_Digestion_control_TR2


title: L.CC.5

description: Library name: 107081-001-005


title: L.CC.4

description: Library name: 107081-001-004


title: RPE1_CAD-seq_25U_NoRNase_TR2

description: Library name: RPE1_CAD-seq_25U_NoRNase_TR2


title: RPE1_CAD-seq_250U_TR2

description: Library name: RPE1_CAD-seq_250U_TR2


title: L.CC.3

description: Library name: 107081-001-003


title: L.CC.2

description: Library name: 107081-001-002


title: L.CC.1

description: Library name: 107081-001-001


title: RPE1_CAD-seq_25U_TR1

description: Library name: RPE1_CAD-seq_25U_TR1


title: RPE1_CAD-seq_25U_NoRNase_TR1

description: Library name: RPE1_CAD-seq_25U_NoRNase_TR1


title: RPE1_CAD-seq_25U_TR2

description: Library name: RPE1_CAD-seq_25U_TR2


title: RPE1_CAD-seq_2.5U_TR2

description: Library name: RPE1_CAD-seq_2.5U_TR2


title: hCG2

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

description: Library name: hCG2

data_processing:
library strategy: Micro-C
Genomic alignment using BWA-MEM against the mm10 genome build with the following parameters “-5SP -T0”
Valid ligation events were identified using pairtools with the following parameters “parse --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30”
Multi-dimensional contact matrices were generated using Juicertools
Assembly: mm10
Supplementary files format and content: contact matrix in hic format
Supplementary files format and content: chromatin loop in bedpe format

source_name: ovary

growth_protocol: 21 days old mice

extract_protocol:
Sample preparation follows protocol in Dovetail Micro-C kit (Cantata Bio)
Micro-C libraries were prepared using the Dovetail Micro-C kit, 2-3 technical replicates / sample

treatment_protocol: mice were injected with 5 IU eCG, after 44h mice were either humanely killed (0h post-hCG) or injected with 5 IU hCG (6h post-hCG). hCG-injected mice were humanely killed 6 h post-treatment. All mice were dissected and ovaries were punctured for granulosa cell collection.

value: ovary

value: granulosa cells

value: 5IU eCG per mouse for 46 hours, then 5IU hCG per mouse for 6 hours


title: RPE1_CAD-seq_2.5U_TR1

description: Library name: RPE1_CAD-seq_2.5U_TR1


title: PMSG2

description: Library name: PMSG2

value: 5IU eCG per mouse for 46 hours


title: hCG1

description: Library name: hCG1


title: GM12878_Digestion_control_TR3

description: Library name: GM12878_Digestion_control_TR3

value: B lymphoblastoid cell line


title: PMSG1

description: Library name: PMSG1


title: GM12878_Digestion_control_TR2

description: Library name: GM12878_Digestion_control_TR2


title: GM12878_Digestion_control_TR4

description: Library name: GM12878_Digestion_control_TR4


title: IFE basal cells male 1, male 2, female 1 and female 2

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

description:
Library name: GEMX-OCM_Male_Female
Proceeded by GEMX-OCM_ChIp

data_processing:
Quality control and downstream analysis were performed using the Seurat R package (v.5.1.0). For each sample, cells were filtered using the following criteria: showed expression of more than 2000 and less than 6000 unique genes and had less than 7.5% UMI counts belonging to mitochondrial sequences.
Doublets are detected with both DoubletFinder and scds, by default parameters. The cells with both doublet score on scds greater than or equal to 0.75 and labelled as doublet on DoubletFinder are filtered out.
Read counts were normalized using the NormalizeData() function of Seurat, with parameter ‘normalization.method = "LogNormalize" and scale.factor=10000’. A PCA for each sample was calculated using the scaled expression data of the 2000 most variable genes (identified as outliers on a mean/variability plot, implemented in the FindVariableGenes().
UMAP calculation and graph-based clustering were performed for each sample using Seurat (default parameters) with the first 40 respective PCA components as input.
On each dataset, to identify cell proliferation stages, the S-phase and G2/M-phase scores were computed by CellCycleScoring() function, implemented in the Seurat.
Assembly: mm10-2020-A
Supplementary files format and content: tsv.gz / barcode and expressed genes
Supplementary files format and content: mtx.gz / gene expression count

source_name: skin

extract_protocol:
To isolate skin epidermal cells, ears were dissected, opened in two along the cartilage with forceps. Fat tissue and cartilage were removed and skin was floated on 0.25% trypsin + EDTA 1mM (Gibco, Thermo Fisher Scientific) in DMEM (Gibco, Thermo Fisher Scientific) overnight at 4°C. The day after, the epidermis was carefully separated from the dermis by using forceps and then floated on a rocking plate (100 rpm) at 37°C for 10min on the trypsin mix. Tissue was cut into pieces, and epidermal cells were mechanically dissociated by pipetting with a 5ml pipette. Trypsin was neutralized by adding DMEM supplemented with 5% Chelex-treated fetal calf serum (CFCS), and samples were filtrated on a 70-μm filter then on a 40-μm filter and washed in PBS supplemented with 2% CFCS (FACS buffer). Single cells were incubated with a biotinylated anti-CD34 primary antibody (clone RAM34, BD Biosciences, 1:50) diluted in FACS buffer, incubated for 30 min on ice, and protected from light. Cells were washed with FACS buffer, incubated for 30 min on ice, with streptavidin–APC secondary antibody (BD Biosciences, 1:100) and CD49f (Integrin alpha 6) PE-Cyanine7 conjugated antibody (clone eBioGoH3 (GoH3), Thermo Fisher Scientific, 1:250). Then the cells were washed again and finally resuspended in a Hoechst (10 mg/ml) solution diluted at 1:4 000 in FACS buffer. Cell sorting was performed on a BD FACSAria III using the FACSDiva software (BD Bioscience) at the ULB Flow Cytometry Platform: living epidermal cells were gated by forward scatter, side scatter and negative for Hoechst. Bulge (hair follicle) cells were excluded by CD34 staining. Only basal cells (integrin alpha6 positive) cells were sorted.  A total of 100,000 cells were sorted for each sample (1 sample containing 2 different mice from the same litter).
Two independent male and two independent female single cells suspension were loaded and multiplexed on a GEM-X OCM 3’Chip Kit (v4 4-plex, PN-1000747, 10x Genomics) and barcoded with a Chromium X instrument according to the manufacturer’s recommendations (10x Genomics). The libraries were prepared using the GEM-X Universal 3’ Kit (v4 4-plex, PN-1000779, 10x Genomics).

value: skin

value: keratinocytes


title: IFE basal cells castrated male 2

description: Library name: X2

data_processing:
Quality of each raw data was checked with FastQC (https://www. bioinformatics.babraham.ac.uk/projects/fastqc/).
The adaptor sequences and low-quality regions were trimmed by TrimmomaticPE.
Trimmed reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR aligner (v.2.7.5a) to generate read alignments for each sample.
Duplicate reads were removed by Picard MarkDuplicates module (http://broadinstitute.github.io/picard/).
After transcript assembling, gene-level counts were obtained using HTseq (v.0.11.1) and normalized to 20 million aligned reads per count.
Assembly: mm10/Grcm38.87
Supplementary files format and content: .txt / normalized gene expression

extract_protocol:
To isolate skin epidermal cells, ears were dissected, opened in two along the cartilage with forceps. Fat tissue and cartilage were removed and skin was floated on 0.25% trypsin + EDTA 1mM (Gibco, Thermo Fisher Scientific) in DMEM (Gibco, Thermo Fisher Scientific) overnight at 4°C. The day after, the epidermis was carefully separated from the dermis by using forceps and then floated on a rocking plate (100 rpm) at 37°C for 10min on the trypsin mix. Tissue was cut into pieces, and epidermal cells were mechanically dissociated by pipetting with a 5ml pipette. Trypsin was neutralized by adding DMEM supplemented with 5% Chelex-treated fetal calf serum (CFCS), and samples were filtrated on a 70-μm filter then on a 40-μm filter and washed in PBS supplemented with 2% CFCS (FACS buffer). Single cells were incubated with a biotinylated anti-CD34 primary antibody (clone RAM34, BD Biosciences, 1:50) diluted in FACS buffer, incubated for 30 min on ice, and protected from light. Cells were washed with FACS buffer, incubated for 30 min on ice, with streptavidin–APC secondary antibody (BD Biosciences, 1:100) and CD49f (Integrin alpha 6) PE-Cyanine7 conjugated antibody (clone eBioGoH3 (GoH3), Thermo Fisher Scientific, 1:250). Then the cells were washed again and finally resuspended in a Hoechst (10 mg/ml) solution diluted at 1:4 000 in FACS buffer. Cell sorting was performed on a BD FACSAria III using the FACSDiva software (BD Bioscience) at the ULB Flow Cytometry Platform: living epidermal cells were gated by forward scatter, side scatter and negative for Hoechst. Bulge (hair follicle) cells were excluded by CD34 staining. Only basal cells (integrin alpha6 positive) cells were sorted.  A total of 100,000 cells were sorted for each sample (1 sample containing 2 different mice from the same litter). FACS isolated cells were collected into 350 ml of lysis buffer (RLT buffer, RNeasy Microkit, Qiagen) supplemented with β-mercaptoethanol. RNA extraction was then carried out using RNeasy Micro kit (Qiagen) according to the manufacturer’s recommendations. Prior to sequencing, the quality of RNA was evaluated by Fragment Analyzer (Agilent).
Indexed cDNA libraries were obtained using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB E6420S) following manufacturer’s recommendations.


title: GM12878_Digestion_control_TR1

description: Library name: GM12878_Digestion_control_TR1


title: GM12878_CAD-seq_500U_TR2

description: Library name: GM12878_CAD-seq_500U_TR2


title: IFE basal cells female 2

description: Library name: Female2


title: IFE basal cells castrated male 1

description: Library name: X1


title: GM12878_CAD-seq_500U_TR1

description: Library name: GM12878_CAD-seq_500U_TR1


title: GM12878_CAD-seq_100U_TR2

description: Library name: GM12878_CAD-seq_100U_TR2


title: IFE basal cells female 1

description: Library name: Female1


title: IFE basal cells male 2

description: Library name: Male3


title: GM12878_CAD-seq_100U_TR1

description: Library name: GM12878_CAD-seq_100U_TR1


title: IFE basal cells male 1

description: Library name: Male1


title: GM12878_CAD-seq_20U_TR2

description: Library name: GM12878_CAD-seq_20U_TR2


title: GM12878_CAD-seq_20U_TR1

description: Library name: GM12878_CAD-seq_20U_TR1


title: C3KO_trained_4

city: Los Angeles

first: Hrishikesh

last: Kulkarni

state: California

address: 10833 Le Conte Ave 52-257 CHS

department: Pulmonary, Critical Care, Sleep Medicine

institute: University of California Los Angeles

description: Sample 2.4

data_processing:
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng 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 (Takara-Clontech) per manufacturer's protocol.
cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.
Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes TPM counts valued for each sample

source_name: Lung

extract_protocol:
RNA was extracted using RNeasy Plus kits (Qiagen, Cat #: 74134). Samples were sent for RNA-Sequencing
Alveolar macrophages from C3-deficient and wildtype mice were trained with HKCA, with subsequent restimulation by LPS and cytokine analysis of the supernatants with polyA selection.

value: Lung

value: Primary

value: Alveolar Macrophages

value: trained using heat-killed Candida albicans


title: GM12878_CAD-seq_4U_TR2

description: Library name: GM12878_CAD-seq_4U_TR2


title: C3KO_trained_1

description: Sample 2.1


title: RPE1_MC_R4T3

description: Library name: RPE1_MC_R4T3

data_processing:
Data processing includes alignment to the reference genome, removal of duplicates and low‑quality fragments, and generation of contact matrices to resolve local chromatin folding structures.
Assembly: hg38
Supplementary files format and content: cool

extract_protocol:
The Micro‑C extraction workflow crosslinks cells, performs precise MNase digestion to mononucleosomes, and carries out end‑repair to expose DNA ends from adjacent nucleosomes for subsequent proximity ligation.
Library construction involves adaptor ligation to the repaired DNA ends, dual‑end proximity ligation, reverse crosslinking, and purification, followed by direct library preparation and amplification to preserve short‑range nucleosome contact information.


title: GM12878_CAD-seq_4U_TR1

description: Library name: GM12878_CAD-seq_4U_TR1


title: WT_trained_4

description: Sample 1.4


title: RPE1_MC_R4T2

description: Library name: RPE1_MC_R4T2


title: WT_trained_3

description: Sample 1.3


title: WT_trained_2

description: Sample 1.2


title: RPE1_MC_R3T1

description: Library name: RPE1_MC_R3T1


title: RPE1_MC_R3T3

description: Library name: RPE1_MC_R3T3


title: 2-cell stage embryos, Control2

city: Wuhan

first: fan

last: chen

state: Hubei

address: Nanhu Av. 4

country: China

institute: Hubei Academy of Agricultural Sciences

data_processing:
The quantification of all libraries was done using the High DNA Sensitivity Bioanalyzer 2100 (Agilent) and real time QPCR. All libraries were sequenced using 150bp paired-end on the Illumina Novaseq platform.
Raw RNA was filtered by Trimmomatic, and the mus musculus reference genome (NCBI.GRCm39) was obtained.
Index of the reference genome was built using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome.
Htseq-count was used to count the reads numbers mapped to each gene.
Differential expression analysis of PNMC and Control groups were performed using the DESeq2 R package (1.16.1)
Assembly: NCBI.GRCm39
Supplementary files format and content: tab-delimited csv file includes FPKM values for each Sample

source_name: embryos

growth_protocol: 6～9 weeks female mice were superovulated by injecting of 10 IU PMSG (200 μL), followed by 10 IU of HCG (200 μL). After 12～14 h of HCG injection, female mouse was sacrificed, and ampullas were pierced in the M2 medium with the tip of the insulin needle to make the cumulus-oocytes complexes (COCs) flow out. Then COCs were cultured in the HTF fertilization drop in a 37 ℃, 5% CO2 incubator. Meanwhile, the epididymis of 12～16 weeks male mouse was collected and cut into pieces and capacitated in pre-balanced HIF medium for 1 h in a 37 ℃, 5% CO2 incubator. Finally, the capacitated sperms were added in the COCs fertilization drop for about 6 h in a 37 ℃, 5% CO2 incubator.The fertilized eggs (2-pronucleus, 2-PN) were randomly chosen and transferred to the control and PNMC drop, and cultured for  24 h, responding to 2-cell embryo.

extract_protocol:
The total RNA of each sample（2-cell embryos） was extracted using Invitrogen TRIzol® .
RNA libraries for RNA-seq were prepared using the  smart-seq2 system.

treatment_protocol: While the PNMC-treated groups were KSOM medium containing 25 nM PNMC, the control group was a KSOM medium containing the same volume of DMSO.

value: embryos

value: primary culture cell

tag: developmental stage

value: 2-cell stage embryos

value: control


title: RPE1_MC_R3T2

description: Library name: RPE1_MC_R3T2

value: Retinal Pigment Epithelial cell

value: WT


title: RPE1_MC_R2T3

description: Library name: RPE1_MC_R2T3


title: 2-cell stage embryos, PNMC3

value: 25 nM PNMC exposure


title: 2-cell stage embryos, Control1


title: RPE1_MC_R2T2

description: Library name: RPE1_MC_R2T2


title: RPE1_MC_R2T1

description: Library name: RPE1_MC_R2T1


title: 2-cell stage embryos, PNMC2


title: 2-cell stage embryos, PNMC1


title: PROCR+ cells, Cdh5+, Cd36-

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Pl

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
After the removal of adapter and trimming of low quality bases, the reads were used for expression quantification using Salmon (v0.9.1). Expression values were quantified by counts in gene level.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts and TPM

extract_protocol:
Total RNA was isolated using either RNeasy Micro Kit (Qiagen) or miRVana isolation kit (Ambion). RNA quality was checked at Bioanalyser before library preparation.
For samples with limited amount of RNA, we used NEBnext Single Cell/Low RNA Library prep Kit for Illumina to generate sequencing libraries. For samples with abundant RNA, stranded RNA libraries were prepared with 100ng total RNA using the KAPA RNA HyperPrep Kit with RiboErase
Libraries were sequenced on Illumina NextSeq 500 system (Illumina), and NovaSeq 6000 system (Illumina).

tag: type

value: EpCAM+, CD49fhigh, CD36-,PDPN-


title: RPE1_MC_R1T2

description: Library name: RPE1_MC_R1T2


title: RPE1_MC_R1T3

description: Library name: RPE1_MC_R1T3


title: PROCR+ cells, Cdh5-

value: EpCAM+, CD49fhigh, CD36-,PDPN+


title: RPE1_MC_R1T1

description: Library name: RPE1_MC_R1T1


title: Mcm8 WT MEF, No antibody

city: Jinan

first: Can

middle: xin

last: Wen

address: 44 West Wenhua Rd

department: Center for Reproductive Medicine

institute: Shandong University

data_processing:
The library preparations were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150bp paired-end reads were generated
The read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software, and all low-quality reads and PCR adapters were removed
High-quality mapped reads (MAPQ > 30) reads were aligned to the UCSC mm10 genome or hg19 genome using Bowtie2.
All peak calling was performed with MACS2 v2.1.2 using ‘macs2 -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dupall’.
bigWig files were generated using the genomicRanges R package. narrowPeak files were generated using MACS v2.1.2 with default settings.
Assembly: mm10；hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

source_name: MEF

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
The genomic DNA was extracted by the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903).
CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903). Libraries were amplified using TruePrep Index Kit V2 for Illumina (Vazyme Biotech, China; TD202) at 11 cycles on the thermocycler. Libraries were purified with the VAHTS DNA Clean Beads (Vazyme Biotech, China; N411) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: MEF

value: Mouse embryo fibroblasts

value: Mcm8 wildtype

value: no primary antibody used


title: BJAB-BAC16 AAA lytic 3

city: Nashville

first: John

last: Karijolich

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

description: Library name: 11246-YZ-18

data_processing:
trimed by fastp
aligned by STAR
count by featurecount
Assembly: GRCh38
Supplementary files format and content: txt file containing counts

source_name: BJAB

growth_protocol: BJAB-BAC16-WT/REV/AAA cells were maintained with 500 ug/ml Hygromycin B. All cells were maintained with 100 U of penicillin/ml and 100 ug of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2.

extract_protocol:
RNA were extracted from latent and lytic BJAB-BAC16 WT, vIRF1-AAA and vIRF1-REV cells using TRIzol and then treated with DNase I and phenol:chloroform:isoamyl alcohol [25:24:1 (vol/vol)] extraction.
RNA were submitted to the Vanderbilt Technologies for Advanced Genomics (VANTAGE) for paired-end RNA-sequencing libraries preparation

treatment_protocol: BJAB-Bac16-WT/REV/AAA cells were lytic reactivated with 20 ng/ml TPA and 0.1 mM NaB for 3 days

value: BJAB

value: B lymphocyte

value: KSHV vIRF1 AAA

value: KSHV lytic reactivation


title: PROCR+ cells, Cdh5+, Cd36+

value: EpCAM+, CD49fhigh, CD36+,PDPN-


title: BJAB-BAC16 AAA lytic 2

description: Library name: 11246-YZ-17


title: Mcm8 KO MEF, S9.6

value: Mcm8 knockout

value: S9.6 antibody used


title: BJAB-BAC16 AAA lytic 1

description: Library name: 11246-YZ-16


title: Mcm8 WT MEF, S9.6


title: BJAB-BAC16 REV lytic 3

description: Library name: 11246-YZ-15

value: KSHV vIRF1 REV


title: B

city: Guangzhou

first: Huagui

last: Gao

state: Guangdong

address: No. 483 Wushan Road, Tianhe District

institute: South China Agricultural University

description:
Library name: Sample 2
B_fpkm

data_processing:
Illumina Casava2.19 software used for basecalling.
Rawdata(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.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2(v2.3.4.3).
RNAintegrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).RBSfinder and TransTermH were used to predict SD sequence and terminator sequence respectively.HTSeq v0.9.1 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.
Differential expression analysis of two groups (two biological replicates per condition) was performed using the DESeq R package (1.20.0). Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. KOBAS software used to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: ASM2040184v1
Supplementary files format and content: xls files include FPKM values for each Sample
Supplementary files format and content: (file.fq/.fastq) are sequence files in FASTQ format, typically with read sequences.

organism: Pseudomonas sp. HS-18

source_name: Pseudomonas sp.

growth_protocol: The Pseudomonas HS-18 strain was cultured in MM medium under conditions of 28°C/200 rpm. When the bacteria reached the logarithmic phase (OD6000.5), the cells were collected. Group A was the control group, with no carbon source in the medium, and Group B was the experimental group, containing 3 mM 3-OH PAME.

extract_protocol:
RNA was extracted using the Eastep Super Kit (Promega). The extraction volume was 1.5 mL of culture medium, and total RNA was used to construct the sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Pseudomonas sp.

value: bacterial cells

value: WT-Signal

value: signal induction culture


title: BJAB-BAC16 REV lytic 2

description: Library name: 11246-YZ-14


title: A

description:
Library name: Sample 1
A_fpkm

value: WT


title: BJAB-BAC16 REV lytic 1

description: Library name: 11246-YZ-13


title: BJAB-BAC16 WT lytic 3

description: Library name: 11246-YZ-12

value: KSHV WT


title: NF84, HepG2, p6, IFN

city: Bochum

first: Leyla

last: Sirkinti

address: Universitätsstraße 150

department: Translational and Computational Infection Research

country: Germany

institute: Ruhr University

description: Library name: Sample 12

data_processing:
Raw FASTQ sequencing reads were checked for quality using FastQC (version 0.12.1; available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc), followed by quality trimming with Trimmomatic 84. Low-quality and overrepresented sequences were trimmed. The trimmed reads from PMH, MLT, and 56D cells were mapped to the Mus musculus (GRCm39) reference genome (GCF_000001635.27), while the trimmed reads from HepG2 cells were mapped to the Homo sapiens (GRCh38) reference genome (GCF_000001405.40), both obtained from National Center for Biotechnology Information (NCBI). Mapping was performed using HISAT2 version 2.2.1 85. Picard was used to remove optical duplicates (available online at: https://broadinstitute.github.io/picard/). FeatureCounts version 2.0.6. 86 was used to generate gene counts, determining how many reads mapped to each gene in the reference genome. Unmapped reads from HISAT2 were mapped to the viral genome using Burrows-Wheeler Aligner version 0.7.18 87, and were used to algin to the HEV strain Kernow-C1 (GenBank accession Nr. HQ709170.1). Samtools version 1.21 88 was used to sort, index, and calculate coverage. Viral coverage plots were visualized in R using the ggplot2 library.
Assembly: GRCm39, GRCh38 and GenBank accession Nr. HQ709170.1
Supplementary files format and content: .txt file and exon reads

extract_protocol:
RNA extraction was done using the NucleoSpin RNA kit (Macherey-Nagel)
Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit (New England Biolabs) and the recommended related reagents by following the manufacturer’s instructions.

value: hepatoma

value: Kernow-C1/p6 RNA transfected, interferon treated

tag: batch


title: NF84, HepG2, p6, Mock

description: Library name: Sample 11

value: Kernow-C1/p6 RNA transfected


title: NF84, HepG2, tRNA, IFN

description: Library name: Sample 10

value: tRNA transfected, interferon treated


title: BJAB-BAC16 WT lytic 1

description: Library name: 11246-YZ-10

value: BJAB

value: B lymphocyte


title: BJAB-BAC16 WT lytic 2

description: Library name: 11246-YZ-11

value: KSHV lytic reactivation


title: NF84, HepG2, tRNA, Mock

description: Library name: Sample 9

value: tRNA transfected


title: NF81, HepG2, p6, IFN

description: Library name: Sample 8


title: BJAB-BAC16 AAA latent 3

description: Library name: 11246-YZ-9

value: KSHV vIRF1 AAA

value: no treatment


title: NF81, HepG2, p6, Mock

description: Library name: Sample 7


title: BJAB-BAC16 AAA latent 1

description: Library name: 11246-YZ-7


title: NF81, HepG2, tRNA, IFN

description: Library name: Sample 6


title: BJAB-BAC16 AAA latent 2

description: Library name: 11246-YZ-8


title: BJAB-BAC16 REV latent 3

description: Library name: 11246-YZ-6

value: KSHV vIRF1 REV


title: C3KO_trained_3

description: Sample 2.3

value: Lung

value: Primary

value: Alveolar Macrophages

value: trained using heat-killed Candida albicans


title: BJAB-BAC16 REV latent 2

description: Library name: 11246-YZ-5


title: C3KO_trained_2

description: Sample 2.2


title: NF74, HepG2, p6, IFN

description: Library name: Sample 4


title: BJAB-BAC16 WT latent 3

description: Library name: 11246-YZ-3


title: RPE1_MC_R4T1

description: Library name: RPE1_MC_R4T1

value: Retinal Pigment Epithelial cell

value: WT


title: BJAB-BAC16 REV latent 1

description: Library name: 11246-YZ-4


title: NF81, HepG2, tRNA, Mock

description: Library name: Sample 5

value: hepatoma


title: NF74, HepG2, tRNA, IFN

description: Library name: Sample 2


title: BJAB-BAC16 WT latent 1

description: Library name: 11246-YZ-1

value: KSHV WT


title: WT_trained_1

description: Sample 1.1


title: BJAB-BAC16 WT latent 2

description: Library name: 11246-YZ-2


title: RPE1_Pol2ser5_R2T3

description: Library name: RPE1_Pol2ser5_R2T3

data_processing:
CUT&Tag reads were aligned to the reference genome using BWA-MEM, filtered, and deduplicated; peaks were called with SICER2, replicate peak sets from biological and technic replicates were merged to generate a master peak set, and normalized bigWig tracks were produced using deepTools bamCoverage with read extension and RPGC normalization.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag libraries were prepared following the standard protocol, with in-house–prepared Tn5 transposase.
CUT&Tag libraries targeting Pol II Ser5 and H3K4me1 in hTERT-RPE1 cells were generated following a standard workflow, including antibody binding, pA-Tn5–mediated tagmentation, library amplification, and Illumina-compatible sequencing library preparation.


title: NF74, HepG2, p6, Mock

description: Library name: Sample 3

value: Kernow-C1/p6 RNA transfected


title: NF74, HepG2, tRNA, Mock

description: Library name: Sample 1


title: SGEP - Day 17

city: Buffalo

first: Stelios

middle: T.

last: Andreadis

address: 908 Furnas Hall

department: Chemical and Biological Engineering

institute: University at Buffalo

description:
Library name: D17
10x Genomics

data_processing:
Following library generation and sequencing on an illumina SP NovaSeq flowcell, reads were demultiplexed using the 10x Genomics Cell Ranger mkfastq command with bcl2fastq2 (v2.20.0.422). Once demultiplexed, individual samples were analyzed using Cell Ranger (v7.2.0) count against the human genome GRCh38. The resulting counts matrix served as input for subsequent downstream analysis.
Further preprocessing and downstream analysis was performed using R (v4.5.1). First, ambient RNA removal was handled using the SoupX17 (v1.6.2) package and potential doublets were removed using scDblFinder18 (v1.16.0) package. The data was then processed using the standard Seurat19 (v5.4.0) workflow, i.e., SCTransform, RunPCA, FindNeighbors, FindClusters and RunUMAP. Appropriate per-cell cutoffs (feature_cutoff > 750, count_cutoff > 1000, Mitochondrial transcripts > 10%) were applied to the dataset pre normalization. Effect of Cell cycle was regressed out during SCTransform normalization. Cells were scored for various cell types using either AddModuleScore from the Seurat package or AUCell20 (v1.30.1). Cells that were assigned both Pro-Acinar and Pro-Ductal by AUCell were considered bipotent.
Assembly: GRCh38-2024-A
Supplementary files format and content: Gzipped list of cell barcodes for the Cell Ranger count matrix.
Supplementary files format and content: Gzipped table of feature IDs, gene symbols, and feature types.
Supplementary files format and content: Gzipped sparse matrix of Cell Ranger-filtered UMI counts.
Supplementary files format and content: Gzipped list of cell barcodes for the SoupX-corrected count matrix.
Supplementary files format and content: Gzipped table of feature IDs, gene symbols, and feature types for the SoupX-corrected matrix.
Supplementary files format and content: Gzipped sparse matrix of SoupX-corrected UMI counts
Supplementary files format and content: Gzipped table of cell-level metadata, QC metrics, annotations, and dimensional-reduction coordinates.

extract_protocol:
Cells and embedded organoids were dissociated via TryplE™ Express.
The cells isolated at D17 were processed at the University at Buffalo Genomics Core (UBGBC) for scRNA sequencing. After lysis treatment, the cells were counted on a Logos Biosystems LUNA II in bright field mode using 0.4% Trypan blue exclusion for viability. The cells were captured (~10,000 cells per capture) using the 10X Genomics Chromium Platform with reagents from the Single Cell GEMX v4 kit according to the manufacturer’s recommendations. After drop-seq capture, cDNA from captured transcripts was used as input to generate double stranded Illumina sequencing libraries. Following final cleanup, qPCR (QuantaBio library quantification kit) was used to determine final concentration of the libraries. The single cell RNA libraries were diluted and denatured to 250 pM for sequencing on the NovaSeq 6000 (28x91 paired end read length).

value: Human iPSC


title: RPE1_Pol2ser5_R2T2

description: Library name: RPE1_Pol2ser5_R2T2


title: WA09 - Day 46

description: Library name: H46

data_processing:
Sequenced reads were processed using nf-core/rnaseq (v3.14.0) pipeline. Quality of the reads was assessed using FastQC (v0.12.1). Sequencing reads were trimmed using Trim Galore (v0.6.7) to eliminate the remains of Ilumina adaptors and filtering reads that were shorter than 20 bp. The filtered reads were then mapped to the mouse genome (GRCm39, Ensembl) using STAR (v2.7.9a) and quantified using Salmon (v1.10.1). The abundance estimates were imported into R using tximport (v1.26.1) package.
Further preprocessing and downstream analysis was performed using R (v4.5.1). The resulting gene-level counts were used for differential gene expression and PCA analysis  using the DESeq2 (v1.38.3) package. Genes that had at least 10 counts in minimum of 2 samples were considered for differential expression analysis and were considered to be differentially expressed if adjusted P < 0.05. Heatmaps were plotted using the pheatmap package and the volcano plots using the EnhancedVolcano package.
Assembly: GRCm39, Ensembl
Supplementary files format and content: Tab-delimited gzipped table mapping sample_id to experimental factors used in the DESeq2 design
Supplementary files format and content: Tab-delimited gzipped matrix of unfiltered TPM values (Salmon abundance, gene-level via tximport)
Supplementary files format and content: Tab-delimited gzipped matrix of unfiltered raw counts (Salmon NumReads, gene-level via tximport with countsFromAbundance="no")
Supplementary files format and content: Tab-delimited gzipped matrix of DESeq2 size-factor-normalized counts, pre-filtered to genes with rowSums(counts ≥ 10) ≥ 2 samples.
Supplementary files format and content: Tab-delimited gzipped matrix of unfiltered length-scaled counts (tximport with countsFromAbundance="lengthScaledTPM"); used as input to DESeq2.

extract_protocol:
Total RNA was isolated for all conditions using RNeasy Mini Kit and quality control analysis was performed by RNA gel and Agilent Fragment Analyzer.
Sequencing libraries were prepared as per standard Illumina protocols (Illumina Stranded Total RNA Prep with Ribo-Zero Plus), quality checked and quantified by Kapa Biosystems qPCR. The multiplexed libraries were sequenced in pair-end (2 X 50 bp) on the NovaSeq 6000 at 300 pM with 1% loading control.

value: Human ESCs


title: RPE1_Pol2ser5_R1T3

description: Library name: RPE1_Pol2ser5_R1T3


title: RPE1_Pol2ser5_R2T1

description: Library name: RPE1_Pol2ser5_R2T1


title: WA09 - Day 25

description: Library name: H25


title: WA09 - Day 32

description: Library name: H32


title: Non4-1

status: Public on Aug 08 2026

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

description: Library name: Non4-1

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: mm10
Supplementary files format and content: txt files include FPKM values for each Sample

source_name: Embryo

growth_protocol: After in vitro fertilization, embryos were cultured in potassium simplex optimized medium (KSOM) at 37°C under 5% CO2 until the 2-cell stage (28 hours post insemination: 28 hpi).

extract_protocol:
For RNA-seq analyses, after the removal of zona pellucida in acid Tyrode, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
For RNA-seq analyses, SMART-seq library preparation was performed using SMART-Seq® mRNA HT (634795, Takara). The produced cDNA was amplified by PCR. The amplified cDNA was purified using KAPA HyperPure Beads (KK8011, KAPA Biosystems). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit dsDNA HS Assay kit (Q32854, Thermo Scientific).

treatment_protocol: After insemination, fertilized embryos were collected at 12-14 hpi for mRNA injection. mRNAs were injected using a piezo manipulator (Prime Tech, Tsukuba, Japan).

value: Embryo

value: 2-cell embryo

value: Non injection control


title: WA09 - Day 17

description: Library name: H17


title: WA09 - Day 10

description: Library name: H10


title: ABMR-2

type: RNA

first: Ziyang

last: Li

address: Albinusdreef

department: Pathology

institute: Leiden University Medical Center

description: profile 770 genes across 37 pathways

hyb_protocol: Hybridization of RNA samples with the probes occurred at 65°C for 17 hours, followed by loading onto the nCounter Prep Station in accordance with the manufacturer’s instructions.

scan_protocol: Data collection was performed by the nCounter MAX Digital Analyzer.

data_processing: Data analysis was conducted using the nSolver 4.0 Analysis Software System, including quality control (QC) based on Imaging QC, Binding Density QC, Positive Control QC, and   Limit of Detection QC. Samples that passed QC were subjected to a two-step data transformation   process (positive control normalization and housekeeping gene normalization), and normalized counts   were exported for subsequent differential gene expression (DGE) analysis.

label: not applicable

source_name: renal biopsy transport medium

label_protocol: not applicable

growth_protocol: not applicable

extract_protocol: We harvested BTM from the pathology ward. Samples were centrifuged and the sediments were lysed with 500 μl TRIzol™ Reagent (Ambion, Foster City, CA, USA) or 350 μl buffered RLT (included in RNeasy Micro Kit, QIAGEN, Hilden, Germany) + 3.5 μl 2-Mercaptoethanol (Merck Schuchardt OHG, Hohenbrunn, Germany) and homogenized.

treatment_protocol: not applicable

tag: diagnosis

value: rejection


title: RPE1_Pol2ser5_R1T1

description: Library name: RPE1_Pol2ser5_R1T1


title: WA09 - Day 13

description: Library name: H13


title: RPE1_H3K4me1_R2T2

description: Library name: RPE1_H3K4me1_R2T2


title: RPE1_Pol2ser5_R1T2

description: Library name: RPE1_Pol2ser5_R1T2


title: RPE1_H3K4me1_R1T2

description: Library name: RPE1_H3K4me1_R1T2


title: RPE1_H3K4me1_R2T1

description: Library name: RPE1_H3K4me1_R2T1


title: WA09 - Day 0

description: Library name: H0


title: WA09 - Day 3

description: Library name: H3


title: RPE1_H3K4me1_R1T1

description: Library name: RPE1_H3K4me1_R1T1


title: RPE1_ATAC_R2T3

description: Library name: RPE1_ATAC_R2T3

data_processing:
Reads were aligned to the reference genome, filtered and deduplicated, peaks were called to identify accessible chromatin regions, and normalized signal tracks were generated for downstream analysis.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
ATAC-seq libraries were generated by isolating nuclei followed by Tn5 transposase–mediated tagmentation to simultaneously fragment chromatin and insert sequencing adapters.
Tagmented DNA was PCR-amplified, size-selected, and purified to produce Illumina-compatible sequencing libraries.


title: RPE1_ATAC_R2T2

description: Library name: RPE1_ATAC_R2T2


title: BXS0114 - Day 46

description: Library name: B46


title: BXS0114 - Day 32

description: Library name: B32


title: BXS0114 - Day 25

description: Library name: B25


title: RPE1_ATAC_R2T1

description: Library name: RPE1_ATAC_R2T1


title: BXS0114 - Day 17

description: Library name: B17


title: BXS0114 - Day 13

description: Library name: B13


title: RPE1_ATAC_R1T3

description: Library name: RPE1_ATAC_R1T3


title: RPE1_ATAC_R1T2

description: Library name: RPE1_ATAC_R1T2


title: NETseq_InactiveRelA_purF-_site1_Rep2

city: Madison

first: Michael

last: Wolfe

state: WI

address: 1300 University Ave

institute: University of Wisconsin-Madison

description: Library name: RL3942_NETseq_Rep2

data_processing:
NET-seq data were processed using standard tools and scaled for quantitative comparison across samples based on the number of B. subtilis spike-in reads that mapped uniquely to B. subtilis genome. Adapters, linker, and control oligos potentially contaminating each sample were trimmed from raw reads using cutadapt (v3.4) (10.14806/ej.17.1.200). Reads with a minimum length of 15 nt were mapped to the MG1655 genome (NC_000913.3) using Bowtie (v1.3.0) allowing one mismatch and allowing random assignment of reads mapping to multiple loci based on alignment stratum (Bowtie options --best -a -M 1 -v 1) (10.1038/nmeth.1923). Alignments for all samples, except those derived from E. coli RL3938, were converted to BAM and BED files using samtools (v1.16.1) and bedtools (v2.30.0) (10.1093/bioinformatics/btp352 (PMID: 19505943); 10.1093/bioinformatics/btq033 (PMID: 20110278)) . To bring mapped reads from RL3938 into parity with those of the other strains, alignments were randomly down-sampled to 30% of mapped reads using samtools (option -s 10.3) prior to conversion to BED files. The specific 3′-end counts for each genome position were determined using bedtools (options -d -strand - -5 [plus strand] or -d -strand + -5 [minus strand]). To scale read count between samples, the 3′-end counts mapped to each genome position were scaled to total read counts per ten million and multiplied by the B. subtilis-unique scaling factor.
NET-seq scaling factors: To determine the scaling factor for each sample, we first identified specific regions in the B. subtilis genome (Accession: NC_000964.3) to which E. coli reads did not map (Bsu-unique regions) using an E. coli-only NET-seq dataset (10.1093/nar/gkae209). We mapped reads from the E. coli-only NET-seq library to a combined E. coli MG1655 and B. subtilis strain 168 genome file using Bowtie with options to suppress reads that map to multiple loci and allowing no mismatches (options –best -a -m 1 -v 0). After conversion to BAM and BED files, total locus coverage (read coverage not 3′-end coverage) was determined for the B. subtilis str 168 genome. We then generated a BED table of regions with zero coverage (i.e., regions of the B. subtilis genome to which E. coli-only reads did not map) to detect B. subtilis-unique reads present in E. coli NET-seq samples containing a B. subtilis spike-in. To determine the number of B. subtilis-unique reads in each sample with B. subtilis spike-ins, we followed the same NET-seq processing pipeline used to generate the table of B. subtilis unique loci above but used Bedtools to count 3′-end coverage for both B. subtilis unique reads and reads mapping to both B. subtilis and E. coli (i.e., not mapping to the B. subtilis unique loci). To determine the B. subtilis-unique scaling factor for each sample, the fraction of B. subtilis-unique reads was calculated as the B. subtilis-unique counts divided by the total number of reads mapping to E. coli and B. subtilis loci (Table Sa). The smallest B. subtilis-unique fraction was identified among the set of samples to be compared, and this number was divided by the B. subtilis-unique fraction for each sample to obtain the B. subtilis-unique scaling fraction. The scaling fraction was converted to a scaling factor by multiplying it by 107 divided by the total reads mapped to E. coli. The scaling factor was then used to generate scaled reads per 107 reads for each sample. For most analyses, the average of the two scaled reads per genome position was used.
Assembly: U00096.3 and AL009126.3
Supplementary files format and content: Spike-in scaled NETseq wig coverage files

organism: Escherichia coli

growth_protocol: A single colony was inoculated into MOPS EZ rich defined medium with 0.2% (w/v) glucose (RDM, Teknova) for overnight growth at 37 °C. A 2.5-mL portion of the overnight culture was inoculated into 0.85 L RDM supplemented with ampicillin (100 µg/mL) to maintain plasmids pALS13 or pALS14. The cultures were grown in Fernbach flasks on an orbital shaker at 200 rpm and 37 °C until cell density reached early log-phase (apparent OD600 ~0.39 +/– 0.02). RelA expression was then induced by addition of IPTG to 1 mM with continued shaking at 37 °C. After 5 minutes of induction, cells for GTP quantitation were removed and rapidly filtered (described in detail below). FLAG-tagged RNAP B. subtilis cells (strain RL3116) were then added as spike-in, 50 mL samples were removed for ChIP, and the remaining culture for NET-Seq analysis was rapidly filtered through a 0.45 µ cellulose filter, quickly scraped from the filter with a spatula, and plunged into liquid nitrogen before storage at –80 °C as described previously (Churchman et al. 2012). Cells for ChIP were immediately mixed with sodium phosphate (pH 7.6, 10 mM final) and formaldehyde (1% final) and incubated at 37 °C for crosslinking as described previously, (Hustmyer et al. 2022) followed by quenching with glycine (100 mM final) for 30 min at 4 °C. The crosslinked cells were then centrifuged, washed multiple times with phosphate-buffered saline (PBS; 137 mM NaCl, 2.7 KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4), and stored at –80 °C. Biological triplicate samples were collected for each strain or experimental condition. B. subtilis cells were added from pre-measured and stored aliquots to E. coli cultures immediately before harvest at a ratio of 3.3% B. subtilis-to-E. coli cells as calculated from a pre-determined relationship between apparent OD600 and colony-forming units for each E. coli strain grown in RDM. Aliquots of B. subtilis RL3116 cells at measured cell densities were prepared from late log–phase cultures that were cooled on ice, mixed with cold glycerol to a final concentration of 15% glycerol, flash-frozen in liquid nitrogen, and stored at –80°C. Prior to adding B. subtilis cells to the E. coli cultures, aliquots were thawed in ice water and stored on ice.

extract_protocol:
Nascent RNA was purified as described previously (Larson et al. 2014) with slight modifications. Frozen cells harvested from 0.5 L cell culture were combined with frozen lysis buffer (20 mM Tris-HCl, pH 8.0, 0.4% Triton-X 100, 0.1% NP-40), 100 mM NH4Cl, 10 mM MnCl2, 1x EDTA-free cOmplete Mini protease inhibitor cocktail (Roche)), and 50U/mL RNasin [Promega, N211B]). The mixture was subjected to six rounds of milling at 15 Hz for 3 min in a Retsch MM400 Mixer Mill using 50 ml canisters pre-cooled in liquid nitrogen and 25 mm stainless steel balls. The lysate volume was adjusted to 5.5 mL of lysis buffer by gentle addition of cold lysis buffer and RQ1 DNase I (Promega, 0.054 U/mL) was added followed by incubation for 20 min on ice. The reaction was quenched with EDTA (25 mM final) to release ribosomes from the transcripts and chelate Mg2+ to inactivate RNAP. The lysate was then clarified at 4 °C by centrifugation at 25,000 xg for 10 min and incubated with 0.5 mL anti-FLAG M2 affinity resin (Sigma-Aldrich) for 3 h at 4 °C to isolate RNAP-nascent transcript complexes. The resin was washed four times with lysis buffer with 100 mM NH4Cl, 300 mM KCl, 1 mM EDTA, and 50 U/mL RNasin. ECs were eluted with 600 µL lysis buffer with 2 mg/mL FLAG peptide (Sigma-Aldrich), 100mM NH4Cl, 1mM EDTA, and 50U/mL RNasin. Nascent RNA was extracted from the eluate with miRNeasy Mini Kit (Qiagen) following manufacturer’s instructions. The nascent RNA sample was further purified by an additional overnight isopropanol-GlycoBlue precipitation at -20 °C, dissolved in DEPC-treated water, and stored at –80°C.
NET-seq library preparation was performed as described previously (Larson et al. 2014) with minor changes to use custom adaptors compatible with sequencing using Illumina NovaSeq 6000. An adaptor oligo (14047) was adenylated using a NEB 5´ DNA Adenylation kit (by incubating 6 µM of the oligo with 80 µM ATP, 6 µM Mth RNA ligase (NEB), and 25% (v/v) PEG 8000 in 1X NEB Buffer 1 at 65 °C for 4 hours, inactivated at 85 °C for 5 min, and then and precipitated overnight at -20°C with isopropanol. Precipitated nascent RNA (1 µg per sample) was then ligated to the 5 adenylated adaptor oligo in triplicate reactions using a T4 RNA Ligase 2, truncated (T4 Rnl2tr) kit (NEB) with 10% DMSO, 22% PEG8000, 3 µM adenylated DNA linker, T4 Rnl2tr [14.7U/µL], RNasin [2U/µL], and 1x T4 RNA Ligase Reaction Buffer). These ligation reactions were incubated for 4 hrs at 37°C and the RNA ligase was inactivated with Proteinase K (0.04U/µL) (NEB, P8107).  The ligated material was then subjected to cDNA synthesis (1 h) and cDNA circularization reactions (3 h) using CircLigase (Lucigen) as described previously (Larson et al. 2014; Bao et al. 2024). Circularized cDNA libraries were PCR amplified as previously described 10 with Q5 DNA polymerase (NEB) using PCR conditions recommended by the manufacturer and dual-indexed primers for the NovaSeq6000 (Illumina) sequencing platform. Library concentration and size distribution were determined using an Agilent TapeStation 4150 before 150-nt paired-end sequencing on an Illumina NovaSeq 6000 instrument (sequencing performed by the University of Wisconsin-Madison Biotechnology Center).

value: RL3000 delrpoZ[del2-5] rpoC[R362A, R417A, K615A]::3XFLAG yja::cat pALS14 purF[R45A]


title: BXS0114 - Day 0

description: Library name: B0


title: RPE1_ATAC_R1T1

description: Library name: RPE1_ATAC_R1T1


title: BXS0114 - Day 3

description: Library name: B3


title: BXS0114 - Day 10

description: Library name: B10


title: Milk fat globule_day 5_low insulin resistance_biol rep 7

city: Oxford

first: Fadil

middle: M

last: Hannan

state: Oxfordshire

address: Level 3, Women's Centre, John Radcliffe Hospital

department: Nuffield Department of Women's and Reproductive Health

country: United Kingdom

institute: University of Oxford

description:
Library name: MFG106
MFG106

data_processing:
The sequencing libraries were multiplexed and loaded on an Illumina NovaSeq 6000 instrument. Samples were sequenced using a 2x150 paired-end (PE) configuration. Image analysis and base calling were conducted on instrument, and raw sequence data were converted into FASTQ files and demultiplexed using Illumina bcl2fastq program version 2.20.
Assembly: HC11: mm9, NCBI Build 37. MCF-12A and MFG: human (hg19, GRCh37).
Supplementary files format and content: CSV files containing raw counts data for each sample; one counts file per dataset.

source_name: Breastmilk-derived milk fat globules

extract_protocol:
HC11 and MCF-12A RNA was extracted using the RNeasy mini plus kit (Qiagen). MFG RNA was extracted using the RNeasy plus universal kit (Qiagen).
HC11 and MCF-12A RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). MFG RNA libraries were prepared using rRNA depletion followed by NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer’s recommendations.

value: Breastmilk-derived milk fat globules

value: Low


title: NETseq_InactiveRelA_purF-_site1_Rep1

description: Library name: RL3942_NETseq_Rep1


title: NETseq_RelA*_purF-_site1_Rep2

description: Library name: RL3941_NETseq_Rep2

value: RL3000 delrpoZ[del2-5] rpoC[R362A, R417A, K615A]::3XFLAG yja::cat pALS13 purF[R45A]


title: Milk fat globule_day 5_low insulin resistance_biol rep 6

description:
Library name: MFG105
MFG105


title: Milk fat globule_day 5_low insulin resistance_biol rep 5

description:
Library name: MFG104
MFG104


title: NETseq_InactiveRelA_purF-_Rep2

description: Library name: RL3940_NETseq_Rep2

value: RL3000 rpoC::3XFLAG yja::cat pALS14 purF[R45A]


title: NETseq_InactiveRelA_purF-_Rep1

description: Library name: RL3940_NETseq_Rep1


title: Milk fat globule_day 5_low insulin resistance_biol rep 3

description:
Library name: MFG102
MFG102


title: NETseq_RelA*_purF-_site1_Rep1

description: Library name: RL3941_NETseq_Rep1


title: Milk fat globule_day 5_low insulin resistance_biol rep 2

description:
Library name: MFG101
MFG101


title: NETseq_RelA*_purF-_Rep2

description: Library name: RL3939_NETseq_Rep2

value: RL3000 rpoC::3XFLAG yja::cat pALS13 purF[R45A]


title: Milk fat globule_day 5_low insulin resistance_biol rep 4

description:
Library name: MFG103
MFG103


title: Milk fat globule_day 5_low insulin resistance_biol rep 1

description:
Library name: MFG100
MFG100


title: NETseq_RelA*_purF-_Rep1

description: Library name: RL3939_NETseq_Rep1


title: BTM_3

description: profile 770 genes across 37 pathways

source_name: Tumor-free tissue from nephrectomy

extract_protocol: We harvested tumor-free tissues from a tumor nephrectomy. These tissues were cut into slices of 1.5x1.5x20 mm. Pairs of tissue pieces were then placed in 15 ml phosphate-buffered saline (PBS). In addition, two larger pieces of the adjacent   tissue from the same nephrectomy were processed either as FFPE or fresh-frozen samples which were stored at -80 ℃. Before centrifuging BTM, biopsies were removed, and the resulting sediments were lysed with 500 μl TRIzol™ Reagent (Ambion, Foster City, CA, USA) or 350 μl buffered RLT (included in RNeasy Micro Kit, QIAGEN, Hilden, Germany) + 3.5 μl 2-Mercaptoethanol (Merck Schuchardt OHG, Hohenbrunn, Germany) and homogenized.

value: Tumor-free tissue from nephrectomy


title: NETseq_InactiveRelA_purF_Rep2

description: Library name: RL3938_NETseq_Rep2

value: RL3000 rpoC::3XFLAG yja::kan pALS14


title: Milk fat globule_day 5_medium insulin resistance_biol rep 4

description:
Library name: MFG099
MFG099

value: WT

value: Medium


title: flLB1(5A)-2

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample.

extract_protocol:
After the removal of zona pellucida in acid Tyrode, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
SMART-seq library preparation was performed using SMART-Seq® HT Kit (Z4438N, Takara). The produced cDNA was amplified by PCR with 13 cycles. The amplified cDNA was purified using KAPA HyperPure Beads (KK8011, KAPA Biosystems). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit dsDNA HS Assay kit (Q32854, Thermo Scientific).

value: flLB1(5A) mRNA injection


title: Non2-2


title: NETseq_RelA*_purF_Rep2

description: Library name: RL3937_NETseq_Rep2

value: RL3000 rpoC::3XFLAG yja::kan pALS13


title: BMM IFNγ 3

city: Berkeley

first: Stefan

middle: A

last: Fattinger

address: 415 Weill Hall

institute: UC Berkeley

description: Library name: Sample 9

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36. Trimmed reads were mapped to the Mus musculus GRCm38 reference genome with STAR aligner v.2.5.2b. Analysis of raw counts was performed with DESeq2
Assembly: mm10
Supplementary files format and content: csv file including raw counts of each sample

source_name: Bone marrow derived macrphage (BMMs)

growth_protocol: Bone marrow-derived macrophages (BMMs) were differentiated from bone marrow and maintained in DMEM supplemented with 10% FBS, PenStrep, Glutamin, HEPES, and M-CSF in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysed with TRK lysis buffer (Omega Bio-Tek) and 2-mercaptoethanol followed by total RNA isolation using the E.Z.N.A Total RNA Kit I (Omega Bio-Tek)
RNA libraries for RNA-seq were prepared using an Illumina Poly(A) selection kit following manufacturer's protocols.

treatment_protocol: BMMs were left untreated, stimulated with 10ng/ml of IFNβ, IFNγ, TNF, or TGFβ for 6 hours or preexposed to 10ng/ml IFNβ for 24h before adding 10ng/ml IFNγ for 6h.

value: Bone marrow derived macrphage (BMMs)

value: B6 WT

value: IFNγ


title: NETseq_InactiveRelA_purF_Rep1

description: Library name: RL3938_NETseq_Rep1


title: Milk fat globule_day 5_medium insulin resistance_biol rep 3

description:
Library name: MFG098
MFG098


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A2). gRNA

first: Jesse

last: Engreitz

address: 450 Serra Mall

institute: Stanford University

description:
Library name: validation_moi1_1_rep01_a2_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_1_rep01_a2_filtered_feature_bc_matrix.h5

data_processing:
We aligned reads to transcripts and identified cells using the 10x Genomics Cell Ranger Count v9. For the guides, we input the guide FASTQ files as CRISPR Guide Capture libraries and the feature_reference file containing the guide sequences.
Assembly: human hg38
Supplementary files format and content: .h5 files from Cellranger

extract_protocol:
Cells were collected using centrifugation, washed with PBS+BSA and subjected to 10x Genomics 3' scRNA-seq
Libraries were constructed accroding to the protocol detailed in Ray et al 2025 (dx.doi.org/10.17504/protocols.io.3byl4z7drvo5/v1)

value: WTC11 (human iPSC line)

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.1, replicate 1, channel A2


title: Milk fat globule_day 5_medium insulin resistance_biol rep 2

description:
Library name: MFG097
MFG097


title: Milk fat globule_day 5_high insulin resistance_biol rep 10

description:
Library name: MFG095
MFG095

value: High


title: ChIPseqInput_InactiveRelA_purF-_site1_Rep2

description: Library name: RL3942_ChIPInput_Rep2

data_processing:
ChIP-seq data was processed as described previously Hustmyer et al. mBio (2022) and reproduced and modified here. Read quality control was performed using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (10.1093/bioinformatics/btw354). All ChIP-seq analysis were performed using an open-source-software-based ChIP-seq pipeline (https://github.com/mikewolfe/ChIPseq_pipeline). The pipeline manages computational jobs using Snakemake (https://doi.org/10.12688/f1000research.29032.2) and maintains the relationship between samples and their metadata using peppy (https://doi.org/10.1093/gigascience/giab077). Paired- and single-end reads were trimmed of adapter sequences using CutAdapt (10.14806/ej.17.1.200) with parameters ‘-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT’. Quality trimming was performed using trimmomatic (10.1093/bioinformatics/btu170) with parameters "LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15". The reads were aligned to the E. coli (Genbank accession: U00096.3) and B. sub (Genbank accession: AL009126.3) chromosomes using bowtie2 (10.1038/nmeth.1923) with parameters "-- end-to-end --very-sensitive --phred33". Raw read coverage was calculated using deepTools (10.1093/nar/gkw257) with the parameters "--binSize 5 --samFlagInclude 67 --extendReads". The raw coverage counts were first scaled by multiplying the raw coverage by a spike-in based scaling factor determined as described in Bonhoure et al. Genome Research 2014 (10.1101/gr.168260.113). Briefly, a background subtracted fragment count is determined in the spike-in fragments by taking the raw fragment counts across the B. sub chromosome AL009126.3 for paired extracted and input samples, dividing the read fragments by the total number of B. sub read fragments per million for each sample and then determining a background subtracted fragment count as follows: w_i = max(0,z_i-βx_i) Where, w_i is the background subtracted fragment count per position i, z_i is the fragment counts in the extracted sample, x_i is the fragment counts in the paired input sample, and β is a regression-based scale factor determined by linear regression with regions outside the full coding region of all genes plus an additional 300 bp upstream of each gene. The average enrichment for a given sample, k, is then calculated using the background subtracted fragment count per position j in each coding region plus an additional 300 bp upstream for each gene as follows: η_k=mean(w_j)  Finally, the spike-in based scaling factor for each sample k is determined as follows: S_k=η_k-(∑_(i=1)^n η_i )/n Where n is the total number of samples to be scaled together. This spike-in factor is then applied to the non-spike in fragments mapping to the E. coli genome by taking the raw fragment counts and first scaling by the total number of fragments per million that mapped to the E. coli genome per sample and then scaling by the spike-in scale factor S_k described above.  After initial scaling, all ChIP traces were copy-number corrected to account for changes in DNA content between the two genotypes as described in the input correction section below.
NET-seq scaling factors: To determine the scaling factor for each sample, we first identified specific regions in the B. subtilis genome (Accession: NC_000964.3) to which E. coli reads did not map (Bsu-unique regions) using an E. coli-only NET-seq dataset (10.1093/nar/gkae209). We mapped reads from the E. coli-only NET-seq library to a combined E. coli MG1655 and B. subtilis strain 168 genome file using Bowtie with options to suppress reads that map to multiple loci and allowing no mismatches (options –best -a -m 1 -v 0). After conversion to BAM and BED files, total locus coverage (read coverage not 3′-end coverage) was determined for the B. subtilis str 168 genome. We then generated a BED table of regions with zero coverage (i.e., regions of the B. subtilis genome to which E. coli-only reads did not map) to detect B. subtilis-unique reads present in E. coli NET-seq samples containing a B. subtilis spike-in. To determine the number of B. subtilis-unique reads in each sample with B. subtilis spike-ins, we followed the same NET-seq processing pipeline used to generate the table of B. subtilis unique loci above but used Bedtools to count 3′-end coverage for both B. subtilis unique reads and reads mapping to both B. subtilis and E. coli (i.e., not mapping to the B. subtilis unique loci). To determine the B. subtilis-unique scaling factor for each sample, the fraction of B. subtilis-unique reads was calculated as the B. subtilis-unique counts divided by the total number of reads mapping to E. coli and B. subtilis loci (Table Sa). The smallest B. subtilis-unique fraction was identified among the set of samples to be compared, and this number was divided by the B. subtilis-unique fraction for each sample to obtain the B. subtilis-unique scaling fraction. The scaling fraction was converted to a scaling factor by multiplying it by 107 divided by the total reads mapped to E. coli. The scaling factor was then used to generate scaled reads per 107 reads for each sample. For most analyses, the average of the two scaled reads per genome position was used.
Assembly: U00096.3 and AL009126.3
Supplementary files format and content: Spike-in scaled NETseq and ChIP-seq coverage wig files

extract_protocol:
ChIP-seq was performed as previously described (Hustmyer et al. 2022; Mooney et al. 2009). A cell pellet corresponding to 50 mL of crosslinked E. coli culture was mixed with separately formaldehyde-crosslinked B. subtilis RL3116 cells (using a volume of B. subtilis cells equivalent to 1% of the E. coli cells) and used for each IP reaction. Immunoprecipitation was performed as described (Hustmyer et al. 2022) using an antibody against the beta subunit of RNAP or the FLAG tag on the C-terminal end of the beta prime subunit.
Paired-end libraries were prepared using NEBNext Ultra II DNA library reagents according to the manufacturer’s protocols and sequenced on Illumina NovaSeq 6000.


title: ChIPseqInput_RelA*_purF-_site1_Rep2

description: Library name: RL3941_ChIPInput_Rep2


title: Milk fat globule_day 5_high insulin resistance_biol rep 9

description:
Library name: MFG094
MFG094

value: Breastmilk-derived milk fat globules


title: ChIPseqInput_InactiveRelA_purF-_site1_Rep1

description: Library name: RL3942_ChIPInput_Rep1


title: Milk fat globule_day 5_high insulin resistance_biol rep 6

description:
Library name: MFG091
MFG091


title: ChIPseqInput_InactiveRelA_purF-_Rep2

description: Library name: RL3940_ChIPInput_Rep2


title: ChIPseqInput_InactiveRelA_purF-_Rep1

description: Library name: RL3940_ChIPInput_Rep1


title: Milk fat globule_day 5_high insulin resistance_biol rep 5

description:
Library name: MFG090
MFG090


title: ChIPseq_InactiveRelA_purF-_site1_Rep2

description: Library name: RL3942_ChIP_Rep2


title: Milk fat globule_day 5_high insulin resistance_biol rep 3

description:
Library name: MFG088
MFG088


title: Milk fat globule_day 5_high insulin resistance_biol rep 2

description:
Library name: MFG087
MFG087


title: ChIPseq_InactiveRelA_purF-_site1_Rep1

description: Library name: RL3942_ChIP_Rep1


title: Milk fat globule_day 5_high insulin resistance_biol rep 1

description:
Library name: MFG086
MFG086


title: Milk fat globule_day 4_low insulin resistance_biol rep 11

description:
Library name: MFG085
MFG085

value: Low


title: ChIPseq_InactiveRelA_purF-_Rep1

description: Library name: RL3940_ChIP_Rep1


title: Milk fat globule_day 4_low insulin resistance_biol rep 10

description:
Library name: MFG084
MFG084


title: Milk fat globule_day 4_low insulin resistance_biol rep 8

description:
Library name: MFG082
MFG082


title: dgD-aPDL1, replicate 2, scRNAseq

city: Xiamen

first: Chaolong

last: Lin

address: 4221-117 Xiang Annan Road, Xiang 'an District, Xiamen City, Fujian Province

institute: Xiamen University

description: 10x Genomics

data_processing:
The demultiplexing，barcoded processing,gene counting and aggregation were made using the Cell Ranger software v5.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor-infiltrating lymphocytes

extract_protocol:
The tumors were excised and homogenized using a gentleMACS tissue dissociator with a Tumor Dissociation Kit for mice. The resulting cell mixture was filtered through a 70-µm cell strainer to obtain a single-cell suspension. Following centrifugation, the supernatant was discarded, and the pellet was resuspended in 1 ml of cold PBS supplemented with 2% FBS. The cell suspensions were stained with 7AAD and APC/Cyanine7-labeled anti-mouse CD45 antibodies. Subsequently, fluorescence-activated cell sorting (FACS) was employed to isolate CD45+ cells, ensuring a cell viability exceeded 90%. These sorted cells were then prepared for single-cell RNA sequencing (scRNA-seq) using the Chromium Next GEM Single Cell 3ʹ Kit v3.1, following the manufacturer’s protocols.
Library was performed according to the manufacter's (single cell3' v2 protocol,10x Genomics)

value: Tumor-infiltrating lymphocytes

value: immune cells


title: Milk fat globule_day 4_low insulin resistance_biol rep 7

description:
Library name: MFG081
MFG081


title: Intact_brc1-2_rep3

city: Beijing

first: Hao

last: Zhu

address: No. 37 Xueyuan Road, Haidian District, Beijing, China

institute: Beihang University

description:
Library name: Intact_brc1-2_rep3
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026). RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775) and sequenced on the Illumina NovaSeq 6000 platform to produce paired-end 150 bp reads.

data_processing:
RNA-seq: Raw reads were trimmed to remove adapters and low-quality reads using Cutadapt (v.3.5).
RNA-seq: High-quality reads were aligned to the Arabidopsis TAIR10 genome using HISAT2 (v.2.0.5) with default parameters; BAM files were sorted with SAMtools (v.1.13).
RNA-seq: Gene expression was quantified with FeatureCounts (v.2.0.1); differentially expressed genes were identified with DESeq2 (v.1.32.0).
CUT&Tag: Raw reads were processed with fastp (v.0.23.1); clean reads were aligned to TAIR10 using Bowtie2 (v.2.3.5.1), filtered with SAMtools (-F 1804 -f 2 -q 30), and deduplicated with Picard (v.2.23.3).
CUT&Tag: Deduplicated replicate BAMs were merged and converted to RPKM-normalized bigWig with deepTools (v.3.5.0); H3K27me3 peaks were called with MACS2 (v.2.2.7.1, --broad --broad-cutoff 0.05) and annotated with ChIPseeker (v.1.24.0).
Assembly: TAIR10
Supplementary files format and content: Tab-delimited file of raw gene-level read counts for each RNA-seq sample.
Supplementary files format and content: bigWig files of RPKM-normalized H3K27me3 CUT&Tag signal for each sample.

organism: Arabidopsis thaliana

source_name: axillary tissues

growth_protocol: Arabidopsis thaliana Col-0 seeds were surface-sterilized, sown on 1/2 MS agar plates (1/2 MS powder, 0.7% agar, 1% sucrose, pH 5.8), stratified at 4 °C for 3 days, and grown in a chamber at 22 °C under long-day conditions (16 h light/8 h dark).

extract_protocol:
Total RNA was extracted from seedlings or axillary tissues using TRIzol reagent (Invitrogen, 15596026) following the manufacturer's protocol. For CUT&Tag, nuclei were isolated from 0.2 g of axillary tissue and processed with the CUT&Tag Assay Kit (CST, 77552).
RNA-seq libraries were prepared with the RNA Library Prep Kit for Illumina (NEB, E7775). CUT&Tag libraries were prepared by immobilizing nuclei on Concanavalin A-coated beads, incubating with anti-H3K27me3 antibody (CST, 9733) or normal rabbit IgG (negative control), followed by anti-rabbit IgG, pAG-Tn5 tagmentation, and 16 cycles of amplification with DNA/RNA UD Indexes (Illumina, 20026121).

treatment_protocol: For rac-GR24 treatment, seedlings were grown on 1/2 MS plates containing 2.5 µM rac-GR24 (PhytoTech Labs, G3324) or DMSO (mock) for 7 days. For decapitation, the main shoot below the lowest cauline node was excised when the main inflorescence reached ~1 cm; axillary tissues (axillary buds and subtending rosette leaf axil tissues) were harvested after treatment.

value: axillary tissues


title: d0-GFP, replicate 2, scRNAseq

description: 10x Genomics


title: Milk fat globule_day 4_low insulin resistance_biol rep 6

description:
Library name: MFG080
MFG080


title: d0-GFP, replicate 1, scRNAseq

description: 10x Genomics


title: Milk fat globule_day 4_low insulin resistance_biol rep 4

description:
Library name: MFG078
MFG078


title: Vehicle, replicate 2, scRNAseq

description: 10x Genomics

value: Vehicle


title: Milk fat globule_day 4_low insulin resistance_biol rep 3

description:
Library name: MFG077
MFG077


title: Milk fat globule_day 4_low insulin resistance_biol rep 2

description:
Library name: MFG076
MFG076


title: F3 Subfertile,1

city: Genève

first: François-Xavier

last: Stubbe

state: Genève

address: 30, quai Ernest-Ansermet

department: MOCEL

country: Switzerland

institute: University of Geneva

description: Library name: Subfertile_1

data_processing:
Basecalls were performed using bcl2fastq for NovaSeq output
Single-end sequencing reads were quasi-mapped to the C. elegans transcriptome (WBcel235) using Salmon v1.10.3 with GC bias correction and mapping validation
Transcript-level quantifications were imported into R and summarized to gene level using tximport v1.34.0
DGE analysis was performed usig DESEQ2
Assembly: WBCel235
Supplementary files format and content: Gene level count matrix

organism: Caenorhabditis elegans

source_name: FAS158 F3 Subfertile worms

growth_protocol: Worms were on NGM petri dishes, seeded with OP50, at 25C

extract_protocol:
RNA was harvested using TriZol reagent. DNA was removed Ambion Turbo DNAse and cleaned by phenol/cloroform extraction
RNA-seq libraries were made following the Illumina TRUESeq protocol

treatment_protocol: P-1 animals were selected based on presence or absence of H3.3K27Mtet array. Animals carrying the array were placed on tetracylcin, these are P0. We then selected subfertile that we grew in absence of tretracyclin.

value: YA Dissected Germline


title: F3 Subfertile,3

description: Library name: Subfertile_3


title: Milk fat globule_day 4_medium insulin resistance_biol rep 13

description:
Library name: MFG074
MFG074

value: WT


title: P0 Array,3

description: Library name: P0_3

source_name: FAS158 P0 on tet


title: Milk fat globule_day 4_medium insulin resistance_biol rep 12

description:
Library name: MFG073
MFG073

value: Medium


title: P0 Array,2

description: Library name: P0_2


title: P0 wt,3

description: Library name: N2_3

source_name: FAS158 that has lost the array


title: Milk fat globule_day 4_medium insulin resistance_biol rep 11

description:
Library name: MFG072
MFG072


title: Milk fat globule_day 4_medium insulin resistance_biol rep 10

description:
Library name: MFG071
MFG071


title: P0 wt,2

description: Library name: N2_2


title: Milk fat globule_day 4_medium insulin resistance_biol rep 9

description:
Library name: MFG070
MFG070


title: Milk fat globule_day 4_medium insulin resistance_biol rep 8

description:
Library name: MFG069
MFG069


title: Milk fat globule_day 4_medium insulin resistance_biol rep 7

description:
Library name: MFG068
MFG068


title: F3 Fertile,1

description: Library name: Fertile_1

source_name: FAS158 F3 Fertile worms


title: Milk fat globule_day 4_medium insulin resistance_biol rep 6

description:
Library name: MFG067
MFG067


title: WhiteFat_DMSOforDex_KO_rep5

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

description:
Library name: WhiteFat_DMSOforDex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 or hg38 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

source_name: WhiteFat

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2–3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at −80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: WhiteFat

value: Mecp2 KO

tag: strain

tag: Sex

value: Male

tag: age

value: 1.5 months

tag: mouse id


title: Milk fat globule_day 4_medium insulin resistance_biol rep 5

description:
Library name: MFG066
MFG066


title: WhiteFat_DMSOforDex_KO_rep4

description:
Library name: WhiteFat_DMSOforDex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: ChIPseq_RelA*_purF-_site1_Rep1

description: Library name: RL3941_ChIP_Rep1

value: RL3000 delrpoZ[del2-5] rpoC[R362A, R417A, K615A]::3XFLAG yja::cat pALS13 purF[R45A]


title: WhiteFat_DMSOforDex_KO_rep3

description:
Library name: WhiteFat_DMSOforDex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 4_low insulin resistance_biol rep 9

description:
Library name: MFG083
MFG083


title: Milk fat globule_day 4_medium insulin resistance_biol rep 3

description:
Library name: MFG064
MFG064


title: WhiteFat_DMSOforDex_KO_rep2

description:
Library name: WhiteFat_DMSOforDex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 4_medium insulin resistance_biol rep 2

description:
Library name: MFG063
MFG063


title: WhiteFat_DMSOforDex_KO_rep1

description:
Library name: WhiteFat_DMSOforDex_KO_rep1_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: WhiteFat_Dex_KO_rep5

description:
Library name: WhiteFat_Dex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 4_medium insulin resistance_biol rep 1

description:
Library name: MFG062
MFG062


title: Milk fat globule_day 4_high insulin resistance_biol rep 13

description:
Library name: MFG061
MFG061


title: Vehicle, replicate 1, scRNAseq

description: 10x Genomics


title: Milk fat globule_day 4_low insulin resistance_biol rep 1

description:
Library name: MFG075
MFG075


title: WhiteFat_Dex_KO_rep3

description:
Library name: WhiteFat_Dex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 4_high insulin resistance_biol rep 11

description:
Library name: MFG059
MFG059


title: Milk fat globule_day 4_high insulin resistance_biol rep 10

description:
Library name: MFG058
MFG058


title: Thymus_DMSOforDex_KO_rep5

description:
Library name: Thymus_DMSOforDex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

source_name: Thymus

value: Thymus


title: Milk fat globule_day 4_high insulin resistance_biol rep 9

description:
Library name: MFG057
MFG057