title: BRI-1456

first: William

middle: V

last: Trim

address: 25 Shuttack Street

department: Systems Biology

institute: Harvard Medical School

description: 10X Genomics

data_processing:
Prior to upload to GEO FASTQ files were converted to BAM files and single nucleotide polymorphisms were removed using BAMboozle for de-identification purposes
Assembly: Hg38
Supplementary files format and content: barcodes.tsv.gz and features.tsc.gz

source_name: Omental Adipose tissue Stromal Cells - Obese no metabolic disease

extract_protocol:
Whole tissues were slowly frozen to -80ºC in CellSTOR reagent, and thawed on the day of A total of 10 patients were selected, split evenly into five per cohort, and their paired omental and subcutaneous adipose tissue samples were used for scRNA-seq. Adipose tissues were dissociated as detailed above. Following stromal cell isolation cell sorting was undertaken on a BD™FACSAria III cell sorter (BD) to separate CD45+/− events. Flow sorting was undertaken using the following fluorescently-labelled antibodies: CD45–BV785 (BioLegend™; CA, USA), CD235a–FITC (BioLegend™), Live-Dead Zombie Aqua™ (BioLegend™), and propidium iodide (PI) (Thermo-Fisher Scientific Inc.). Up to 5,000 cells (split 50:50 CD45+/−) per patient sample were put forward for scRNAseq. Flow cytometric cell sorting and scRNAseq were performed.  sequencing. Adipose explants were extensively mechanically minced and placed into 6mL pre-warmed (37ºC) adipose tissue media (referred to as adipose buffer hereon in) at pH 7.4 containing 5.5mM D-glucose, 140mM sodium chloride, 4.7mM potassium chloride, 1.25mM magnesium sulfoxide heptahydrate, 2.5mM calcium chloride dihydrate, 10mM N-(2-Hydroxyethyl)piperazine-N′-(2-ethanesulfonic acid) (HEPES), 2.5mM sodium phosphate monobasic dihydrate (all Sigma-Aldrich), and 2% bovine serum albumin (BSA) fraction V (Sigma-Aldrich), spiked with type-1 collagenase (250U/mL) (Worthington Biochemical; NJ, US). Samples were agitated at 180–200rpm on a orbital shaker at 37ºC for 45–60 minutes. Digestions were terminated with the addition of 2mM EDTA (final concentration) (Sigma-Aldrich). Following digestion, samples were passed through a 400μm gauze and centrifuged at 100 x g for 1 minute at RT, The remaining post-digestion solution was centrifuged at 300 x g for 7 minutes at RT, and was thereafter incubated with 9 volumes erythrocyte lysis buffer (155.1mM ammonium chloride, 9.9mM potassium bicarbonate, 0.1mM EDTA; all Sigma-Aldrich) for 10 minutes at RT. Post-lysis, samples were topped up with adipose buffer, centrifuged once more at 300 x g for 7 minutes at RT and the supernatant discarded before topping up with adipose buffer for filtering through 100μm gauze, and centrifuged once more at 300 x g for 7 minutes at RT before being resuspended in PBS containing 2mM EDTA and 2% FBS
The five patients from each cohort were combined and loaded onto a single lane (Chromium chip; 10x Genomics; CA, US) followed by encapsulation in a lipid droplet (Single cell 3’ kit; 10x Genomics), and subsequent cDNA and library generation according to manufacturers’ instructions. Cells were sequenced to an average of 25,726 reads per cell using Illumina Nextseq 500 (Illumina Inc.; CA, US). Reads were then processed using Cell Ranger v.3.1. (10x Genomics), to quantify transcript counts per putative cell. Quantification was performed using STAR aligner against the GRCh38-3.0.0. transcriptome.


title: RPE p53-/-, parental control, replicate 3

status: Public on Jun 26 2026

type: SRA

city: Boston

first: Huy

last: Nguyen

state: MA

address: 450 Brookline Ave

department: Radiation Oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: transcriptomic

data_processing:
Kallisto (version 0.48.0) was used to map the raw RNA-seq reads against the GENCODE human reference gene annotation (Release 44) and generate raw transcript abundance estimates.
The tximport Bioconductor R package was used to summarize the transcript abundance estimates to produce gene-level estimated counts.
Assembly: hg38
Supplementary files format and content: tab-delimited file with matrix table of raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Eye; Pigmented epithelium; Retina

growth_protocol: RPE p53-/-  parental and EWSR1 knockout cells were grown in DMEM/F12 containing GlutaMAX (Gibco) and supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich).

extract_protocol:
RNA samples were prepared using RNeasy Mini Kit and RNase-Free DNase Set (QIAGEN). RNA samples were quantified using Qubit 2.0 Fluorometer, and the RNA integrity was checked with 4200 TapeStation.
NEBNext Ultra II RNA Library Prep Kit for Illumina was used following the manufacturer’s recommendations (New England BioLabs). Briefly, mRNAs were initially enriched with Oligo d(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3´ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated using Agilent TapeStation and quantified using Qubit 2.0 Fluorometer as well as by quantitative PCR (KAPA Biosystems). The sequencing libraries were clustered on flowcell lanes. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions.

tag: tissue

value: Eye; Pigmented epithelium; Retina

tag: cell line

tag: cell type

value: epithelial cell

tag: genotype

value: EWSR1 wildtype


title: RPE p53-/-, parental control, replicate 2


title: BRI-1457

description: 10X Genomics

library_source: transcriptomic single cell

source_name: Omental Adipose tissue Stromal Cells - Obese  metabolic disease


title: RPE p53-/-, parental control, replicate 1


title: BRI-1458

description: 10X Genomics

source_name: Subcutaneous abdominal adipose stromal cells - Obese no metabolic disease


title: BRI-1459

description: 10X Genomics

source_name: Subcutaneous abdominal adipose stromal cells - Obese metabolic disease


title: RPE p53-/-, EWSR1 knockout, replicate 3

value: EWSR1 knockout


title: RPE p53-/-, EWSR1 knockout, replicate 2


title: RPE p53-/-, EWSR1 knockout, replicate 1


title: S1

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

description:
Library name: S1-CAR-T
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 with --expect-cells=5000 --nosecondary commands.
Assembly: GRCh38
Supplementary files format and content: Integrated Seurat .rds object
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
For spatial transcriptomic profiling, 7-10 μm rozen lung sections were mounted on Poly-L-Lysine-coated glass slides and for in situ polyadenylation, reverse transcription, and orthogonal microfluidic barcoding.
Barcoded cDNA was recovered, amplified, depleted of ribosomal and mitochondrial rRNA, and prepared for sequencing. Sequencing adapters were ligated using 7 PCR cycles (2× KAPA HiFi, P5/P7 primers), purified (0.8× SPRIselect), quality-checked, and sequenced on Illumina NovaSeq 6000 (paired-end 150 bp).

value: Lung

value: CD45+ cells

tag: treatment

value: CAR-T


title: S6

description:
Library name: S6-CAR-T-D-C
10x Genomics

value: CAR-T-D-C


title: 12-su

description:
Library name: 12-su
Bulk RNA-seq

data_processing:
FASTQ files were aligned to the mouse genome reference version gencode.vM32 by STAR 2.7.10b. Reads mapped to each gene were counted using --quantMode GeneCounts in STAR.
Assembly: gencode.v45
Supplementary files format and content: tab-delimited text files include read counts for each Sample

molecule: polyA RNA

source_name: Primary CD3 CAR-T cells

extract_protocol:
RNA was  extracted by TRIZOL. The RNA sequencing library was prepared using the NEBNext rRNA Depletion Kit v2 and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina
RNA-seq

value: Primary CD3 CAR-T cells

value: Ac4ManNAz 24h


title: 11-su

description:
Library name: 11-su
Bulk RNA-seq


title: 10-su

description:
Library name: 10-su
Bulk RNA-seq


title: 7-6h

description:
Library name: 7-6h
Bulk RNA-seq

value: MMAE 6h


title: 4-24h

description:
Library name: 4-24h
Bulk RNA-seq

value: MMAE 24h


title: 6-24h

description:
Library name: 6-24h
Bulk RNA-seq


title: 5-24h

description:
Library name: 5-24h
Bulk RNA-seq


title: RNA, Donor4, A38 (Cortex)-2

city: New York

first: Yang

last: Xie

state: NY

address: 101 6th Ave

institute: New York Genome Center

description:
Library name: LC695
scRNA-seq

data_processing:
Sequence alignment and processing: For hashing reactions, hashing indices were extracted from the DNA library barcode read and appended to the read name using in-house scripts. Barcode reads were then trimmed to 24 bp to meet Cell Ranger input requirements. DNA fastq files were aligned to the human reference genome (hg38) using ‘cellranger-atac count’ (Cell Ranger ATAC v2.0.0; 10x Genomics) with the ‘--chemistry=ARC-v1’ option. For hashing libraries, hashing indices were subsequently removed from the read names and added to the BAM barcode (CB) tag using in-house scripts to enable correct fragment generation and deduplication. Fragment files were generated from bam files using SnapATAC2 (v2.7.0) with the ‘.pp.make_fragment_file’ function162. Prior to quality control assessment, BAM files were deduplicated using Picard MarkDuplicates (v2.26.3) (http://broadinstitute.github.io/picard/). Standard quality control metrics were then calculated from the deduplicated BAM and fragment files. RNA fastq files were aligned to the custom GRCh38 reference genome using ‘cellranger count’ (Cell Ranger v6.1.2; 10x Genomics) with the options ‘--include-introns’ and ‘--chemistry=ARC-v1’. The resulting count matrices were used for all downstream transcriptomic analyses.
Preliminary quality control: Multiple complementary metrics were used to identify high-quality barcodes from both DNA and RNA modalities. For the DNA modality, histone modification data were first aggregated at the library level, and peak calling was performed using MACS2 (v2.1.2) to identify narrow peaks for H3K27ac and broad peaks for H3K27me3148. Per-cell fragment counts and the fraction of reads in peaks (FRiP) were then calculated for each barcode. DNA barcodes were retained based on thresholds applied to fragment number and FRiP. For hashing libraries, DNA bam files were first split by hashing indices prior to peak calling and FRiP calculation to ensure that quality metrics were computed separately for each hashed sample. For the RNA modality, barcodes were filtered based on the total number of unique molecular identifiers (UMIs) per cell, retaining barcodes with sufficient transcript coverage. High-quality cell barcodes were defined as those that passed quality control filters in both the DNA and RNA modalities and could be uniquely paired across modalities. For hashing libraries, RNA barcodes associated with more than two DNA barcodes were excluded to ensure unambiguous matching between modalities.
Assembly: GRCh38
Supplementary files format and content: Per-library AnnData (h5ad) containing filtered cells and cellranger output raw h5
Supplementary files format and content: Per-library AnnData (h5ad) containing filtered cells and cellranger-atac output fragments file

source_name: Cortex

extract_protocol:
Ground frozen tissue was homogenized in 9 mL lysis buffer composed of 0.32 M sucrose, 0.1% Triton X-100, 5 mM MgCl₂, 25 mM KCl, 10 mM Tris-HCl (pH 8.0), 1 mM DTT, Roche cOmplete Mini Protease Inhibitor, 20 U/mL SUPERaseIN, and 20 μg/mL RNH1. Homogenization used glass Dounce homogenizers, followed by sequential filtration through 70 μm (Corning, 352350) and 30 μm (Sysmex, 04-004-2326) strainers. Myelin debris was removed by adding a sample-specific volume of myelin removal beads (Miltenyi Biotec, 130-096-433) to the homogenate, incubating on a rotating mixer at 4°C for 15 min, and passing the suspension through LS columns (Miltenyi Biotec, 130-042-401) on a QuadroMACS Separator (Miltenyi Biotec, 130-091-051). Bead volume was adjusted per sample based on tissue myelin content. Flow-through was collected and columns were washed with 2 mL wash buffer (0.1% Triton X-100, 5 mM MgCl₂, 25 mM KCl, 10 mM Tris-HCl pH 8.0, 1 mM DTT, Roche cOmplete Mini Protease Inhibitor, 20 U/mL SUPERaseIN, and 20 μg/mL RNH1). Samples were centrifuged at 1,000g for 10 min at 4°C in a Thermo Scientific Sorvall Legend RT+ benchtop centrifuge (Thermo, 75004377) with a swinging bucket rotor (Sorvall, 75006445). Supernatant was aspirated carefully and the pellet was resuspended in 1 mL sort buffer: DPBS, 1% BSA, 1 mM EDTA, 1 mM DTT, Roche cOmplete Mini Protease Inhibitor, 20 U/mL SUPERaseIN, and 20 μg/mL RNH1. For NeuN staining and FANS sorting, Mouse anti-NeuN conjugated to Alexa Fluor 488 (Millipore, MAB377X) and Hoechst 33342 (Invitrogen, H3570) were added at 1:1000. Nuclei were incubated on a rotating mixer at 4°C for 30 min and then diluted to 750,000 nuclei/mL using additional sort buffer prior to FANS. Sorting was performed on a BD Influx cell sorter (BD Biosciences, 646500) using “1-drop pure” mode with a 100 μm nozzle and sheath pressure of 20 PSI; 1× PBS served as sheath fluid, and the nuclei were kept at 4°C. Hoechst-positive nuclei with 2N DNA content were gated using SSC-Area × Hoechst-Area. Debris was excluded using FSC-Area × SSC-Area, and aggregates were excluded using FSC and SSC pulse Area- and Width-based parameters. Nuclei were then gated by NeuN (488), and NeuN-positive and NeuN-negative fractions were collected into separate 2 mL DNA LoBind tubes (Eppendorf, 022431048) containing 250 μL 5× collection buffer (DPBS, 5% BSA, Roche cOmplete Mini Protease Inhibitor, 100 U/μL SUPERaseIN, and 100 μg/mL RNH1). Collected nuclei were centrifuged at 300g for 5 min at 4°C, followed by 500g for 10 min, using an Eppendorf 5417R microcentrifuge with a swinging bucket rotor (Eppendorf A-8-11). Supernatant was removed to ~250 μL per tube. Nuclei from matching populations were pooled and quantified.
To assemble indexed pA-Tn5 complexes compatible with the Chromium Next GEM Single Cell Multiome kit (10x Genomics, 1000283), we synthesized all custom oligonucleotides at a concentration of 100 µM. Custom oligos were mixed in two separate PCR tubes (10 µL AdapterA + 10 µL pMENT-A, and 10 µL AdapterB + 10 µL pMENT-B) and annealed in a thermal cycler using the following program: 95 °C for 5 min, then slow cooling to 12 °C, at 0.1 °C/s. The 20 µL annealed oligos were mixed with 120 µL unloaded pA-Tn5 (0.5 mg/mL, MacroLab) in each tube and incubated at room temperature for 30 mins, followed by an additional 10 mins at 4 °C. Equal volumes of assembled pA-Tn5-AdapterA/pMENT-A and pA-Tn5-AdapterB/pMENT-B were then combined to form functional indexed pA-Tn5 complexes, which were stored at -20 °C. Sorted NeuN⁺ and NeuN⁻ nuclei were pelleted using a swinging-bucket centrifuge (5804R, Eppendorf) and counted using a cell counter (RWD C100-Pro) with DAPI staining. For nuclei extracted from the same tissue block, we aimed to obtain 0.5 million nuclei per histone mark. For cortical regions and pons, NeuN⁺ and NeuN⁻ nuclei were combined to achieve ~50% of NeuN⁺ nuclei. For cerebellum, NeuN⁺ and NeuN⁻ nuclei were combined to achieve ~50% of NeuN⁻ nuclei. In this study, we used antibodies against histone modification marks that performed well in prior studies: H3K27ac (Abcam, ab4729) and H3K27me3 (Abcam, ab192985). Indexed pA-Tn5-antibody conjugates were assembled by mixing 1 µg antibody with 1 µL assembled pA-Tn5 (0.4 mg/mL) in 30 µL MED#1 gently, rotating for 1 hr at room temperature, and then adding 45 µL MED#1. In parallel, 0.5 million nuclei per tube were permeabilized with OMNI buffer on ice for 4 min and washed once with high-salt MED#1 buffer. Permeabilized nuclei were resuspended in 75 µL of the conjugate-containing mixture and incubated at 4 °C overnight for epitope targeting. Indexed pA-Tn5 and antibodies were removed by washing twice with MED#2 buffer. Tagmentation was performed in 70 µL MED#2 buffer supplemented with 10 mM MgCl₂ (Invitrogen, AM9530G) at 37 °C for 1 h at 550 r.p.m. in a ThermoMixer (Eppendorf), and then the reaction was terminated by adding 2× stop solution. Nuclei were washed once with 1× nuclei buffer, concentrated within 20 µL 1× nuclei buffer, and counted again using DAPI. Nuclei tagmented with different indexed pA-Tn5 complexes were combined in equal proportions, and 25,000-30,000 nuclei were aliquoted and loaded for a single droplet-generation reaction using the Chromium Next GEM Single Cell Multiome kit. DNA and RNA library amplification was then performed according to the Chromium Next GEM Single Cell Multiome kit manual with increased amplification cycles for the DNA library. Final libraries were sequenced on a NovaSeq (Illumina) platform using standard Illumina primers. For DNA libraries, read lengths were 100 + 8 + 27 + 100 (Read 1 + Index 1 + Index 2 + Read 2). For RNA libraries, read lengths were 28 + 10 + 10 + 90 (Read 1 + Index 1 + Index 2 + Read 2)

value: Cortex

tag: batch


title: 1-untr

description:
Library name: 1-untr
Bulk RNA-seq

value: DMSO


title: 2-untr

description:
Library name: 2-untr
Bulk RNA-seq


title: H3K27me3, Donor4, A38 (Cortex)

description:
Library name: LC691
scCUT&Tag

library_source: genomic

molecule: genomic DNA


title: H3K27me3, Donor4, A5-A7 (Cortex)

description:
Library name: LC690
scCUT&Tag


title: RNA, Donor4, CBL (Cerebellum)-4

description:
Library name: BI280
scRNA-seq

source_name: Cerebellum

value: Cerebellum


title: RNA, Donor4, CBV (Cerebellum)

description:
Library name: BI278
scRNA-seq


title: H3K27me3, Donor4, CBL (Cerebellum)-2

description:
Library name: BI277
scCUT&Tag


title: H3K27ac, Donor4, CBL (Cerebellum)-2

description:
Library name: BI276
scCUT&Tag


title: H3K27ac, Donor4, CBV (Cerebellum)-2

description:
Library name: BI275
scCUT&Tag


title: RNA, Donor2, CBL (Cerebellum)-6

description:
Library name: BI274
scRNA-seq


title: H3K27ac, Donor2, CBL (Cerebellum)-2

description:
Library name: BI273
scCUT&Tag


title: RNA, Donor1, V1C (Cortex)-2

description:
Library name: BI269
scRNA-seq


title: RNA, Donor2, CBV (Cerebellum)-2

description:
Library name: BI268
scRNA-seq


title: RNAseq, HSEC Donor3, PCSK9-EE7000, 2

status: Public on Jun 28 2026

first: Jennifer

last: Marlowe

state: Massachusetts

address: 201 Brookline Avenue

institute: nChroma Bio

description: Library name: NGSRS3185

data_processing:
Sequencing reads were aligned to the human reference genome (GRCh38) and gene and transcript counts and normalized counts (TPM) were calculated using the nf-core RNA-seq pipeline using the STAR aligner and RSEM workflow for transcript quantification.
Assembly: GRCh38
Supplementary files format and content: genes.results file generated by RSEM containing the following columns: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

source_name: Spleen

growth_protocol: Primary human hepatocytes (PHH) from three different human donors isolated from mice with a chimeric humanized liver (PXB cells®) were obtained from Phoenix Bio. Pre-plated cells were kept in hepatocyte growth medium (dHCGM media [PhoenixBio], 10% FBS). Primary human splenic endothelial cells (HSECs) (Innoprot and Accegen) from three different human donors were cultured in media (endothelial cell medium (ScienCell) with 5% FBS, 1% Pen-Strep, and 1% endothelial cell growth supplement [ScienCell]) and incubated at 37˚C and in 5% CO2. Primary human adrenal cortical cells (HAdCCs) (Accegen) from three different human donors were cultured in media (Mesenchymal Stem Cell Medium (Innoprot) with 5% FBS, 1% Pen-Strep and 1% Mesenchymal Stem Cell Growth Serum (Innoprot) and incubated at 37˚C and in 5% CO2.

extract_protocol:
For RNA extraction of all donors and sample types, Beckman Coulter RNAdvance v2 Kit was used. For RNA extraction from each PHH donor, two 24-well replicate plates per donor containing 336 µL cell lysate were combined and 4 x 63 µL aliquots of lysate were processed . For RNA extraction from each HAdCC donor, all replicate wells of each condition from two replicate plates each containing 3 wells of 63 µL cell lysate were combined and 3 x 63 µL aliquots of lysate were processed. For RNA extraction from HSEC, all replicate wells of each condition from two replicate plates each containing 3 wells of 63 µL cell lysate were combined and 3 x 63 µL aliquots of lysate were processed. The remaining lysate from each cell type was used for DNA extraction. For all samples, lysate aliquots were transferred to separate technical replicate wells of a 0.5 mL deep well plate and mixed with Beckman Coulter-patented SPRI paramagnetic beads to bind total RNA from the cell lysate. Bound RNA was then pelleted with a plate magnet, removing the supernatant allowing DNA and other contaminants to be removed through DNase treatment and a series of buffer (Wash WBD) and 70% ethanol washes, respectively. Total RNA was then eluted from the magnetic beads in nuclease-free water (HAdCC and HSEC samples (96-well plate format) were eluted in 22 uL per sample combining the replicates for a total of 44 uL eluate. PHH samples (24-well format) were eluted in 26 uL.).
Total RNA sequencing libraries were generated using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus. Samples were normalized with nuclease-free water to 100 ng in 11 µL total volume. Concentrations of final libraries were determined by using either the Quant-iT High Sensitivity DNA kit on the VICTOR Nivo plate reader or the Qubit DNA High Sensitivity kit on the Qubit Flex Fluorometer. Library fragment size was also checked on a DNA D1000 or HSD1000 ScreenTape on the Agilent 4200 Tapestation instrument. To ensure proper quantification of sequenceable library molecules, a qPCR reaction was also performed using the NEBNext Library Quant Kit for Illumina.  Total RNA-seq libraries were shipped to SeqCenter for sequencing on a NovaSeq X. Sequencing used a 2 x 151 bp configuration and targeted sequencing depth was >100 M read-pairs per library. Note that PHH Donor 3 sequencing data had a high percentage of duplicates. Therefore, the library prep and sequencing were repeated, with RNA-seq libraries sequenced in the Sponsor’s laboratory on a NextSeq2000 with a 2 x 151 bp configuration and targeted sequencing depth >100 M read-pairs per library.

treatment_protocol: For PHH, on the day of treatment cells were treated with 500 µL culture media supplemented with 1 µg/mL of rhApoE3 and 0.5 or 1 µg/mL CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). For HSEC, one day before test or control article treatment, 10,000 cells per well were seeded into a 96-well tissue culture plate pre-coated with 150 µg/mL of human fibronectin and containing 200 µL culture media. On the day of treatment (Day 0), culture media was replaced with 100 µL of fresh media containing 1 µg/mL of rhApoE3 and CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). For HAdCCs, one day before test or control article treatment, 10,000 cells per well were seeded into a 96-well tissue culture plate pre-coated with 150 µg/mL of Poly-L-Lysine (Sigma-Aldrich) and containing 200 µL culture media. On the day of treatment (Day 0), culture media was replaced with 100 µL of media containing 1 µg/mL of rhApoE3 and CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). Plates were maintained, cells sub-cultured (cell trypsinization every 3-4 days, followed by transfer of ~10,000 cells to a new 96-well culture plate with fresh media). All cells were collected for extraction 14 days after treatment.

value: Spleen

value: HSEC cells

value: Human Splenic Endothelial Cells


title: H3K27me3, Donor2, CBL (Cerebellum)

description:
Library name: BI271
scCUT&Tag


title: H3K27ac, Donor1, V1C (Cortex)

description:
Library name: BI265
scCUT&Tag


title: RNA, Donor2, CBV (Cerebellum)-1

description:
Library name: BI267
scRNA-seq


title: H3K27ac, Donor2, CBV (Cerebellum)

description:
Library name: BI263
scCUT&Tag


title: H3K27ac, Donor2, A38 (Cortex)

description:
Library name: BI259
scCUT&Tag


title: RNA, Donor4, V1C (Cortex)-4

description:
Library name: BI258
scRNA-seq


title: RNA, Donor4, V1C (Cortex)-3

description:
Library name: BI257
scRNA-seq


title: RNA, Donor2, MTG (Cortex)-2

description:
Library name: BI256
scRNA-seq


title: H3K27me3, Donor4, V1C (Cortex)-2

description:
Library name: BI255
scCUT&Tag


title: RNA, Donor4, V1C (Cortex)-2

description:
Library name: BI246
scRNA-seq


title: H3K27ac, Donor2, MTG (Cortex)

description:
Library name: BI253
scCUT&Tag


title: H3K27me3, Donor4, V1C (Cortex)-1

description:
Library name: BI238
scCUT&Tag


title: H3K27ac, Donor4, V1C (Cortex)-1

description:
Library name: BI237
scCUT&Tag


title: H3K27ac, Donor4, V1C (Cortex)-2

description:
Library name: BI254
scCUT&Tag


title: RNA, Donor4, V1C (Cortex)-1

description:
Library name: BI245
scRNA-seq


title: RNA, Donor2, V1C (Cortex)-2

description:
Library name: BI232
scRNA-seq


title: RNA, Donor2, V1C (Cortex)-1

description:
Library name: BI231
scRNA-seq


title: RNA, Donor1, V1C (Cortex)-1

description:
Library name: BI230
scRNA-seq


title: H3K27me3, Donor2, V1C (Cortex)

description:
Library name: BI224
scCUT&Tag


title: H3K27ac, Donor2, V1C (Cortex)

description:
Library name: BI223
scCUT&Tag


title: H3K27me3, Donor1, V1C (Cortex)

description:
Library name: BI222
scCUT&Tag


title: RNA, Donor4, M1C (Cortex)

description:
Library name: BI220
scRNA-seq


title: RNA, Donor2, M1C (Cortex)-1

description:
Library name: BI218
scRNA-seq


title: RNA, Donor2, M1C (Cortex)-2

description:
Library name: BI219
scRNA-seq


title: RNA, Donor1, M1C (Cortex)-1

description:
Library name: BI216
scRNA-seq


title: RNAseq, HAdCC Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSRS3208

source_name: Adrenal

value: Adrenal

value: HAdCC cells

value: Human Adrenal Cortical Cells


title: H3K27me3, Donor4, M1C (Cortex)

description:
Library name: BI215
scCUT&Tag


title: H3K27me3, Donor2, M1C (Cortex)

description:
Library name: BI214
scCUT&Tag


title: H3K27me3, Donor1, M1C (Cortex)

description:
Library name: BI212
scCUT&Tag


title: H3K27ac, Donor2, M1C (Cortex)

description:
Library name: BI213
scCUT&Tag


title: H3K27ac, Donor1, M1C (Cortex)

description:
Library name: BI211
scCUT&Tag


title: RNA, Donor4, MTG (Cortex)-2

description:
Library name: BI210
scRNA-seq


title: RNA, Donor4, MTG (Cortex)-1

description:
Library name: BI209
scRNA-seq


title: RNA, Donor2, MTG (Cortex)-1

description:
Library name: BI208
scRNA-seq


title: RNA, Donor1, MTG (Cortex)-1

description:
Library name: BI206
scRNA-seq


title: RNA, Donor1, MTG (Cortex)-2

description:
Library name: BI207
scRNA-seq


title: RNAseq, HSEC Donor3, PCSK9-EE7000, 1

description: Library name: NGSRS3184


title: H3K27me3, Donor4, MTG (Cortex)

description:
Library name: BI205
scCUT&Tag


title: H3K27me3, Donor2, MTG (Cortex)

description:
Library name: BI203
scCUT&Tag


title: H3K27ac, Donor4, MTG (Cortex)

description:
Library name: BI204
scCUT&Tag


title: H3K27me3, Donor1, MTG (Cortex)

description:
Library name: BI202
scCUT&Tag


title: H3K27ac, Donor1, MTG (Cortex)

description:
Library name: BI201
scCUT&Tag


title: RNA, Donor4, A38 (Cortex)-1

description:
Library name: BI200
scRNA-seq


title: RNA, Donor4, A5-A7 (Cortex)-1

description:
Library name: BI199
scRNA-seq


title: H3K27ac, Donor4, A5-A7 (Cortex)

description:
Library name: BI197
scCUT&Tag


title: H3K27ac, Donor4, A38 (Cortex)

description:
Library name: BI198
scCUT&Tag


title: RNA, Donor1, Pro (Cortex)-1

description:
Library name: BI180
scRNA-seq


title: RNA, Donor2, Pro (Cortex)

description:
Library name: BI179
scRNA-seq


title: RNA, Donor1, Pro (Cortex)-2

description:
Library name: BI181
scRNA-seq


title: RNA, Donor4, A5-A7 (Cortex)-2

description:
Library name: LC694
scRNA-seq


title: H3K27ac / H3K27me3, Donor2, Pro (Cortex)-2

description:
Library name: BI174
scCUT&Tag


title: H3K27ac / H3K27me3, Donor2, Pro (Cortex)-1

description:
Library name: BI173
scCUT&Tag


title: RNA, Donor1, MEC (Cortex)-2

description:
Library name: BI172
scRNA-seq


title: RNA, Donor1, MEC (Cortex)-1

description:
Library name: BI171
scRNA-seq


title: RNA, Donor2, MEC (Cortex)-3

description:
Library name: BI170
scRNA-seq


title: RNA, Donor2, MEC (Cortex)-2

description:
Library name: BI169
scRNA-seq


title: RNAseq, HSEC Donor2, PCSK9-EE7000, 1

description: Library name: NGSRS3164


title: RNA, Donor2, MEC (Cortex)-1

description:
Library name: BI168
scRNA-seq


title: RNA, Donor1, A19 (Cortex)-1

description:
Library name: BI163
scRNA-seq


title: RNA, Donor2, A19 (Cortex)

description:
Library name: BI162
scRNA-seq


title: RNA, Donor1, A19 (Cortex)-2

description:
Library name: BI164
scRNA-seq


title: H3K27ac, Donor1, MEC (Cortex)

description:
Library name: BI160
scCUT&Tag


title: H3K27ac / H3K27me3, Donor2 / Donor4, MEC (Cortex)-3

description:
Library name: BI159
scCUT&Tag

value: Donor2 / Donor4


title: H3K27ac / H3K27me3, Donor2 / Donor4, MEC (Cortex)-2

description:
Library name: BI158
scCUT&Tag


title: H3K27ac / H3K27me3, Donor2 / Donor4, MEC (Cortex)-1

description:
Library name: BI157
scCUT&Tag


title: H3K27ac / H3K27me3, Donor2, A19 (Cortex)-2

description:
Library name: BI152
scCUT&Tag


title: RNAseq, HSEC Donor2, Untreated, 3

description: Library name: NGSRS3178


title: RNAseq, HSEC Donor2, Mock-treatment, 2

description: Library name: NGSRS3173


title: RNA, Donor1, ITG (Cortex)-2

description:
Library name: BI149
scRNA-seq


title: H3K27ac / H3K27me3, Donor2, A19 (Cortex)-1

description:
Library name: BI151
scCUT&Tag


title: RNA, Donor1, ITG (Cortex)-1

description:
Library name: BI148
scRNA-seq


title: RNA, Donor4, ITG (Cortex)

description:
Library name: BI147
scRNA-seq


title: RNA, Donor1, A46 (Cortex)

description:
Library name: BI145
scRNA-seq


title: RNA, Donor2, A46 (Cortex)-1

description:
Library name: BI144
scRNA-seq


title: RNA, Donor4, A46 (Cortex)-2

description:
Library name: BI143
scRNA-seq


title: RNA, Donor4, A46 (Cortex)-1

description:
Library name: BI142
scRNA-seq


title: RNA, Donor1, TH-TL (Cortex)-1

description:
Library name: BI140
scRNA-seq


title: RNA, Donor1, V2 (Cortex)-3

description:
Library name: BI139
scRNA-seq


title: RNA, Donor1, TH-TL (Cortex)-2

description:
Library name: BI141
scRNA-seq


title: H3K27ac / H3K27me3, Donor4, ITG (Cortex)-1

description:
Library name: BI133
scCUT&Tag


title: H3K27ac / H3K27me3, Donor4, ITG (Cortex)-3

description:
Library name: BI135
scCUT&Tag


title: H3K27ac / H3K27me3, Donor2, A46 (Cortex)-3

description:
Library name: BI132
scCUT&Tag


title: H3K27ac / H3K27me3, Donor2, A46 (Cortex)-2

description:
Library name: BI131
scCUT&Tag


title: H3K27ac / H3K27me3, Donor2, A46 (Cortex)-1

description:
Library name: BI130
scCUT&Tag


title: H3K27ac / H3K27me3, Donor4, A46 (Cortex)-3

description:
Library name: BI128
scCUT&Tag


title: H3K27me3, Donor4, A46 (Cortex)

description:
Library name: BI129
scCUT&Tag


title: H3K27ac / H3K27me3, Donor4, A46 (Cortex)-2

description:
Library name: BI127
scCUT&Tag


title: RAW 264.7 Cells, LPS+gamma-tocopherol, 24h, rep3

city: Shanghai

first: Yue

address: No.801 Heqing Rd. Minhang District

country: China

institute: Fudan University

description: Library name: GToco_3

data_processing:
Raw sequencing reads in FASTQ format were filtered to remove adapter sequences, low-quality reads, and reads containing excessive ambiguous bases using TrimGalore. The filtered clean reads were used for downstream analysis.
Clean reads were aligned to the Mus musculus reference genome GRCm39 using HISAT2.
Gene-level read counts were generated using featureCounts based on the corresponding genome annotation file. Reads mapped to annotated gene regions were counted to estimate gene expression abundance in each sample.
Assembly: GRCm39
Supplementary files format and content: Raw gene count matrix is provided. Rows represent genes, and columns represent individual RNA-seq samples. Gene symbols, and read count values for each sample are included.

organism: Mus musculus

growth_protocol: RAW264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from RAW264.7 cells. RNA integrity was assessed using a Qsep100 system, and RNA concentration was measured using a NanoDrop spectrophotometer. RNA samples that passed quality control were used for library construction.
RNA-seq libraries were prepared using an oligo(dT)-based mRNA-seq library construction protocol. Briefly, mRNA was enriched from total RNA, fragmented, reverse-transcribed into cDNA, end-repaired, A-tailed, adapter-ligated, PCR-amplified, and purified with magnetic beads. Library quality was assessed using Qubit and an Agilent Fragment Analyzer. Qualified libraries were sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 150 bp reads.

treatment_protocol: RAW264.7 cells were divided into three groups: control, vehicle, and γ-tocopherol-treated groups. The control group consisted of untreated RAW264.7 cells. The vehicle group consisted of RAW264.7 cells stimulated with LPS at 100 ng/mL for 24 h and treated with solvent control. The γ-tocopherol group consisted of RAW264.7 cells stimulated with LPS at 100 ng/mL for 24 h and treated with 500 μM γ-tocopherol.

value: macrophage

value: LPS+gamma-tocopherol


title: H3K27ac / H3K27me3, Donor4, A46 (Cortex)-1

description:
Library name: BI126
scCUT&Tag


title: H3K27ac / H3K27me3, Donor1, A38 (Cortex)-3

description:
Library name: BI125
scCUT&Tag


title: RAW 264.7 Cells, LPS+gamma-tocopherol, 24h, rep2

description: Library name: GToco_2


title: RNAseq, HSEC Donor1, Untreated, 2

description: Library name: NGSRS3157


title: RAW 264.7 Cells, LPS+gamma-tocopherol, 24h, rep1

description: Library name: GToco_1


title: RAW 264.7 Cells, LPS, 24h, rep3

description: Library name: VEH_3

value: LPS


title: H3K27ac / H3K27me3, Donor1, A38 (Cortex)-1

description:
Library name: BI123
scCUT&Tag


title: RNA, Donor2, A5-A7 (Cortex)-2

description: Library name: BI122


title: RAW 264.7 Cells, LPS, 24h, rep1

description: Library name: VEH_1


title: RNA, Donor2, A5-A7 (Cortex)-1

description: Library name: BI121


title: RAW 264.7 Cells, Control, 24h, rep3

description: Library name: CON_3

value: Control


title: RNA, Donor4, V2 (Cortex)-2

description: Library name: BI119


title: RNA, Donor4, TH-TL (Cortex)

description: Library name: BI120


title: RAW 264.7 Cells, Control, 24h, rep2

description: Library name: CON_2


title: RNA, Donor4, V2 (Cortex)-1

description: Library name: BI118


title: Cell_pool_16_samples

city: Aurora

first: Sarah

middle: E

last: Clark

state: CO

address: 12700 E 19th Ave, Mail Stop 8333

institute: University of Colorado School of Medicine

description:
Library name: Fixed_cell_pool
Pooled RNA seq of 16 samples

data_processing:
FASTQ files were quantified using the the Chromium Mouse Transcriptome Probe Set (v1.0.1 mm10-2020-A) as a part of Cell Ranger 'multi' pipeline.  'Config.csv' file matches sample barcodes to sample names.  Note that sample 16 was not from this study but had to be included with the run to complete the full 16 sample panel.  only 15 samples are relevant to this current study.
Assembly: Chromium Mouse Transcriptome Probe Set (v1.0.1 mm10-2020-A)
Supplementary files format and content: Archive of demultiplexed CellRanger multi outputs

growth_protocol: Cells isolated from lung tissue of C57BL/6 J (wildtype) mice

extract_protocol:
Cells were fixed and permeabilized using a 4% formaldehyde fixative solution and the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics).
Libaries were prepared using 10X Genomics Fixed RNA Profiling kit and following manufacturer's instructions

treatment_protocol: Mice were treated intratracheally with 50 uL of PBS, heat-killed Prevotella, or live Streptococcus pneumoniae

value: Lung

tag: strain

value: C57BL/6 J

value: WT


title: RNA, Donor2, V2 (Cortex)

description: Library name: BI117

value: Cortex


title: RNA, Donor2, Ig (Cortex)

description: Library name: BI115


title: Block 8, WT

city: South San Francisco

first: Anne

last: Biton

state: CA

address: 1 DNA way

institute: Genentech

description:
Library name: LIB6241489
FFPE Spatial transcriptome sequencing

data_processing:
SpaceRanger v3.0.1 was run on the raw sequencing data, then aligned to gene expression counts using the mm10-2020-A reference genome from 10x, and the Visium v2.0 mouse transcriptome probeset.
High resolution H&E images were aligned with the CytAssist image using the landmark-based alignment tool in Loupe browser
Aligned H&E images were integrated with expression data (at the 8um bin size) using custom scripts to generate a SpatialData ZARR.
Assembly: GRCm38/mm10-2020-A
Supplementary files format and content: LIB[#]_SAM[#].sd.zarr.tar.gz: Gzipped SpatialData object
Supplementary files format and content: [SLIDE_ID]-fiducials-image-registration.json: Manual registration file for Visium coordinates to high-resolution H&E
Supplementary files format and content: LIB[#]_SAM[#]_spaceranger.tar.gz: Gzipped raw SpaceRanger outputs
Supplementary files format and content: LIB[#]_[CAPTUREAREA]_[SLIDE_ID]_[CAPTUREAREA]_[SAMPLE].tiff: CytAssist image associated with registration file
Library strategy: Spatial Transcriptomics

extract_protocol:
Lungs were inflated with low-melting point agarose and then embedded in PFA.  5um sections were cut from embedded tissue.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium HD Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: Bleomycin


title: Ecig_3

city: Stanford

first: Chad

middle: S

last: Weldy

address: 870 Quarry Road, CVRC Falk

department: Medicine, Cardiovascular Medicine

institute: Stanford University

description:
Library name: Ecig_3
10X Genomics, scATACseq

library_source: genomic single cell

data_processing:
Demultiplexed Fastq files and matrix files were generated with Cellranger for RNA and Cellranger-atac for ATAC datasets.
Assembly: mm10 genome used for reference
Supplementary files format and content: filtered sequence read with matrix.h5 files are reported and ultimately used in Seurat and SIgnac for data analysis.

source_name: aortic root, ascending aorta to brachiocephalic artery take off

extract_protocol:
Aortic tissue was dissected from the aortic root to the brachiocephalic artery (Ascending), from the brachiocephalic artery up including the carotid artery (carotid), and descending thoracic aorta from subclavian artery to renal arter (descending). Protocol follows as such:1) Prepare the Enzyme Solution (on ice):     Final (working) concentration of Liberase is 2 units/mL    Final (working) concentration of Elastase is 2 units/mL     For 1mL of enzyme solution:     Liberase TM (26 units/mL)  77  uL     Elastase (125 units/mL)   16  uL     HBSS      907 uL     Total      1   mL  2) Place enzyme mixture on ice while aorta is being harvested  3) Perfuse mouse with ~10mL PBS via LV puncture  4) Harvest aortic root and open longitudinally. Wash with PBS x3 in 12-well dish. Keep on ice while collecting from multiple mice.  5) Move root to 12-well dish with 1mL of enzyme mixture.  6) Incubate in 37C incubator for ~30-45 minutes (adjust time based on age and extent of calcification e.g. if Apoe w/ 16wk HFD incubate for 45 minutes). At the end of the incubation, mince thoroughly with scissors for a few minutes (<5min) until tissue is mostly dissolved.  7) Pipet up and down ~20-30 times to thoroughly disrupt tissue. Confirm full digestion under the microscope (single cells w/o clumps). If the tissue is not fully digested after pipetting incubate at 37C for an additional 10-15 minutes (may lead to increased cell lysis).   8) Transfer cell suspension into 1.5mL Eppendorf and centrifuge at 500xg for 5 minutes.  9) Carefully remove supernatant (confirm that the cell pellet is still present).  10) Resuspend the cells in 200uL HBSS (adjust volume as needed). Cell solution was then sorted for live cells on FACS and then proceeded to 10X capture following 10X protocol.  11) Immediately prior to FACS and/or staining, pass cells through a 35um strainer. Note: Coating collection tubes in BSA solution may improve cell survival. 1) Coat the 1.5mL eppendorf tubes used to store the cells prior to FACS, and the FACS collection eppendorf tubes, with 10% BSA in PBS (i.e. fill up tube, and pipette out all volume - then wait a few minutes and then pipet out the rest that gradually slid to the bottom).  2) Wash Buffer: 10mM Tris pH 7.4 (CATALOGUE NUMBER) 10mM NaCl (CATALOGUE NUMBER) 3mM MgCl2 (CATALOGUE NUMBER) 1% BSA (1:10 dilution from 10% BSA stock (CATALOGUE NUMBER)) 0.1% Tween-20 (1:100 dilution from 10% stock (CATALOGUE NUMBER))  NOTE: Wash buffer can be prepared ahead of time and kept at 4C without adding BSA. Add all reagents, except for BSA, to a new 500mL bottle of ultra-pure water and keep at 4C until needed.  3) 0.1X lysis buffer: 196uL wash buffer + 2uL 1X Promega digitonin and 2uL NP-40, followed by 1:10 (200uL + 1800uL) dilution with wash buffer.   After FACS (all centrifugation steps at 4C):  4) Spin cells at 500g x 10 min, gently pipet off all supernatant (with P1000 and P100).  5) Add 45uL 0.1X lysis buffer, mix x3, and incubate for 15 minutes on ice.  6) Add 50uL chilled wash buffer WITHOUT mixing.  7) Spin at 500g x10 min, remove 95uL supernatant with P100.  8) Add 45uL 1X diluted nuclei buffer (diluted 1:20 with H2O), WITHOUT mixing.  9) Spin at 500g x10 min. Remove supernatant with P100 (set to 40uL) and P10 (set to 10uL).  10) Resuspend in 7uL 1X diluted nuclei buffer.  11) Mix 25uL nuclei buffer and 25uL Trypan blue. Mix 1 uL nuclei suspension with 9uL od Trypan blue dilution (1:10 dilution). Load into hemacytometer and examine with Zeiss in microscope room (not TC scope). Count the average number of nuclei in the large boxes and calculate nuclei/uL. Remember to account for 10x dilution factor.  12) Dilute nuclei with more nuclei buffer, if desired.  13) Aim for 8000-9000 nuclei per capture
scRNA and scATAC libraries were prepared following 10X protocol.

value: aorta/arterial tissue

value: cells of the vessel wall

value: Myh11 CreERT2, ApoE-/-. ROSA tdTomato

value: Ecig 12 weeks

value: ATAC Batch 2


title: Block 16, WT

description:
Library name: LIB6241492
FFPE Spatial transcriptome sequencing


title: RNA, Donor1, Ig (Cortex)-2

description: Library name: BI116


title: RNA, Donor1, A5-A7 (Cortex)-2

description: Library name: BI113


title: Ecig_2

description:
Library name: Ecig_2
10X Genomics, scATACseq

value: aortic root, ascending aorta to brachiocephalic artery take off


title: RNA, Donor1, A5-A7 (Cortex)-1

description: Library name: BI112


title: RNA, Donor4, Ig (Cortex)-3

description: Library name: BI111


title: Ecig_1

description:
Library name: Ecig_1
10X Genomics, scATACseq


title: RNA, Donor4, Ig (Cortex)-2

description: Library name: BI110


title: Filtered_Air_2

description:
Library name: Filtered_Air_2
10X Genomics, scATACseq

value: Filtered Air

value: ATAC Batch 1


title: RNA, Donor4, Ig (Cortex)-1

description: Library name: BI109


title: Filtered_Air_1

description:
Library name: Filtered_Air_1
10X Genomics, scATACseq


title: RNA, Donor4, Pro (Cortex)-2

description: Library name: BI108


title: V_C3_NT

description:
Library name: V_C3_NT
10X Genomics, scRNAseq

value: RNA Batch 2


title: V_C3_T

description:
Library name: V_C3_T
10X Genomics, scRNAseq


title: V_C2_T

description:
Library name: V_C2_T
10X Genomics, scRNAseq


title: H3K27ac / H3K27me3, Donor4, TH-TL (Cortex)-2

description: Library name: BI105


title: H3K27ac / H3K27me3, Donor4, TH-TL (Cortex)-1

description: Library name: BI104


title: V_C1_T

description:
Library name: V_C1_T
10X Genomics, scRNAseq


title: H3K27ac / H3K27me3, Donor4, V2 (Cortex)-3

description: Library name: BI103


title: CAF#1, ATRA treatment (input)

city: Beijing

first: Xianglin

last: Yin

state: Other (Non U.S.)

address: No.1 Shuaifu garden, Dongcheng District

institute: Peking Union Medical College Hospital

description: Library name: 1-ATRA-input

data_processing:
The quality of raw sequencing data was assessed using FastQC (version 0.11.3).
Data preprocessing was performed with Trimmomatic (version 0.36) to remove adapter sequences, trim low-quality bases (quality <3) from the start and end of reads, and discard reads shorter than 50 bases.
High-quality paired-end reads passing the quality control steps were aligned to the human reference genome (build 38) using Hisat2 (version 2.1.0).
Only uniquely mapped reads with mapping quality score >20 were retained for downstream analysis. The aligned reads were further filtered and sorted using Samtools (version 1.9), and gene-level read counts were quantified with the featureCounts from Subread R package (version1.32.4).
To identify m6A peaks, we employed the exomePeak R package (version 2.16.0), using a window width of 150 bp and a fragment length of 100 bp.
Assembly: hg38
Supplementary files format and content: BED12 files represent m6A peaks information generated by exomePeak from MeRIP-seq data, including genomic coordinates, scores, strand orientation, and exon block structures.
Library strategy: MeRIP-seq

source_name: pancreas

extract_protocol:
RNA was harvested using TRIzol (Ambion).
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit v2 (Takara, #634413) following manufacturer's protocols. At least 10 ng of total RNA was used for the construction of sequencing libraries.

value: pancreas

value: pancreatic stellate cells

value: ATRA


title: H3K27me3, Donor1, MEC (Cortex)

description:
Library name: BI161
scCUT&Tag


title: H3K27ac / H3K27me3, Donor2, A19 (Cortex)-3

description:
Library name: BI153
scCUT&Tag


title: V_C1_NT

description:
Library name: V_C1_NT
10X Genomics, scRNAseq


title: RNA, Donor2, A46 (Cortex)-2

description:
Library name: BI146
scRNA-seq


title: NE_C3_T

description:
Library name: NE_C3_T
10X Genomics, scRNAseq

value: RNA Batch 1


title: H3K27ac / H3K27me3, Donor4, V2 (Cortex)-1

description: Library name: BI101


title: NE_C2_NT

description:
Library name: NE_C2_NT
10X Genomics, scRNAseq


title: H3K27ac / H3K27me3, Donor2, Ig (Cortex)-3

description: Library name: BI100


title: RNA, Donor1, V2 (Cortex)-1

description:
Library name: BI137
scRNA-seq


title: NE_C2_T

description:
Library name: NE_C2_T
10X Genomics, scRNAseq


title: H3K27ac / H3K27me3, Donor2, Ig (Cortex)-2

description: Library name: BI099


title: NE_C1_T

description:
Library name: NE_C1_T
10X Genomics, scRNAseq


title: H3K27ac / H3K27me3, Donor1, A5-A7 (Cortex)-2

description: Library name: BI097


title: H3K27ac / H3K27me3, Donor2, Ig (Cortex)-1

description: Library name: BI098


title: B16F10_siTet3-2_RiboZero_rep2

first: Lu

last: Liu

address: 131 Dongan Road

description: Library name: B16F10siTet3-2_RiboZero_rep2

data_processing:
Raw reads were trimmed using Trim_galore (v0.0.6), then the reads were aligned to the hg19 or mm10 reference genomes using Tophat (v2.1.1) with default parameters. Genes FPKM (fragment per million mapped reads per kilobase exon) were calculated by FPKM_count.py (v2.6.4).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values of each Sample

source_name: skin

growth_protocol: MCF7 and B16F10 cells were cultured in DMEM high glucose medium (Hyclone) containing 1% penicillin/streptomycin (Hyclone) and 10% fetal bovine serum FBS (ExCell Bio).

extract_protocol:
Total RNAs were extracted from cancer cells using the TRIzol reagent (Invitrogen, #15596018).
The sequencing libraries for RNA-seq were prepared using the VAHTS® Universal V6 RNA-seq Library Prep Kit (Vazyme) according to the manufacturer’s instructions.

value: skin

value: Melanoma

value: Tet3 KD


title: H3K27ac / H3K27me3, Donor1, A5-A7 (Cortex)-1

description: Library name: BI096

value: Cortex


title: H3K27ac / H3K27me3, Donor1, A25 (Cortex)-3

description: Library name: BI095


title: B16F10_siTet3-1_RiboZero_rep2

description: Library name: B16F10siTet3-1_RiboZero_rep2


title: B16F10_siNC_RiboZero_rep2

description: Library name: B16F10siNC_RiboZero_rep2

value: Control


title: H3K27ac / H3K27me3, Donor1, A25 (Cortex)-1

description: Library name: BI093


title: H3K27ac / H3K27me3, Donor4, Pro (Cortex)-2

description: Library name: BI092


title: H3K27ac / H3K27me3, Donor4, Pro (Cortex)-1

description: Library name: BI091


title: B16F10_Tet3KO_mRNAseq_rep2

description: Library name: B16F10Tet3KO_mRNAseq_rep2

value: Tet3 KO


title: B16F10_siTet3-2_RiboZero_rep1

description: Library name: B16F10siTet3-2_RiboZero_rep1


title: RNA, Donor1, CBL (Cerebellum)-2

description: Library name: BI090

value: Cerebellum


title: H3K27ac / H3K27me3, Donor1, A25 (Cortex)-2

description: Library name: BI094


title: B16F10_siTet3-1_RiboZero_rep1

description: Library name: B16F10siTet3-1_RiboZero_rep1


title: RNA, Donor4, Pro (Cortex)-1

description: Library name: BI107


title: H3K27ac / H3K27me3, Donor4, TH-TL (Cortex)-3

description: Library name: BI106


title: B16F10_Tet3KO_mRNAseq_rep1

description: Library name: B16F10Tet3KO_mRNAseq_rep1


title: RNA, Donor1, CBL (Cerebellum)-1

description: Library name: BI089


title: B16F10_WT_mRNAseq_rep2

description: Library name: B16F10WT_mRNAseq_rep2

value: WT


title: RNA, Donor1, CBV (Cerebellum)-2

description: Library name: BI088


title: B16F10_WT_mRNAseq_rep1

description: Library name: B16F10WT_mRNAseq_rep1


title: RNA, Donor1, CBV (Cerebellum)-1

description: Library name: BI087


title: RNA, Donor4, A19 (Cortex)

description: Library name: BI085


title: B16F10_siNC_RiboZero_rep1

description: Library name: B16F10siNC_RiboZero_rep1


title: RNA, Donor2, Idg (Cortex)-2

description: Library name: BI084


title: RNA, Donor4, A25 (Cortex)-2

description: Library name: BI082


title: RNA, Donor4, A25 (Cortex)-1

description: Library name: BI081


title: RNA, Donor2, A38 (Cortex)

description: Library name: BI083


title: RNA, Donor2, TH-TL (Cortex)-2

description: Library name: BI080


title: RNA, Donor2, TH-TL (Cortex)-1

description: Library name: BI079


title: H3K27ac / H3K27me3, Donor1, CBL (Cerebellum)-2

description: Library name: BI078


title: H3K27ac / H3K27me3, Donor1, CBL (Cerebellum)-1

description: Library name: BI077


title: NE_C3_NT

description:
Library name: NE_C3_NT
10X Genomics, scRNAseq

value: aorta/arterial tissue

value: cells of the vessel wall

value: Myh11 CreERT2, ApoE-/-. ROSA tdTomato


title: H3K27ac / H3K27me3, Donor1, CBV (Cerebellum)-1

description: Library name: BI075


title: H3K27ac, Donor4, A19 (Cortex)

description: Library name: BI073


title: 9_post_AMG510PD1_CD45_TCR

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

state: California

address: 1120 VETERANS BLVD.

institute: AMGEN, INC.

description: Library name: 9_post_TCR

data_processing:
Cell Ranger v 3.1.0
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expression UMI count data in Market Exchange Format (MEX)
Supplementary files format and content: all_contig_annotations.csv:  list of TCR contigs

source_name: Implanted CT26-KRAS-G12C tumors into Balb/C mice

growth_protocol: Mice were implanted subcutaneously with CT26-KRAS-G12C tumors, and tumors were allowed to develop for 14 days.

extract_protocol:
Tumors were harvested, dissected, and placed in Liberase TL (0.2 mg/ml). Tumors solutions were homogenized using a gentleMACS Dissociator, treated with 0.002% EDTA and 10% FBS, and passed through a 70-micrometer filter to remove clumps. Cells were then stained and sorted, gating on CD45+ live cells for single-cell RNA-seq.
Chromium NextGEM Single Cell 5' v1.1 (10x Genomics)

treatment_protocol: Tumors were treated for 4 days.

value: CD45+ cells

value: Balb/c

value: AMG 510 + anti-PD-1

tag: library type

value: TCR


title: H3K27ac, Donor2, Idg (Cortex)

description: Library name: BI072


title: H3K27ac / H3K27me3, Donor1, CBV (Cerebellum)-2

description: Library name: BI076


title: 8_post_AMG510PD1_CD45_TCR

description: Library name: 8_post_TCR

value: Implanted CT26-KRAS-G12C tumors into Balb/C mice


title: H3K27ac / H3K27me3, Donor4, V2 (Cortex)-2

description: Library name: BI102


title: H3K27me3, Donor2, A38 (Cortex)

description: Library name: BI071


title: 7_post_AMG510PD1_CD45_TCR

description: Library name: 7_post_TCR


title: 6b_post_AMG510_CD45_TCR

description: Library name: 6_post_TCR

value: AMG 510


title: H3K27me3, Donor4, A25 (Cortex)

description: Library name: BI070


title: H3K27ac, Donor4, A25 (Cortex)

description: Library name: BI069


title: 6a_post_AMG510_CD45_TCR

description: Library name: 5b_post_TCR


title: 5_post_AMG510_CD45_TCR

description: Library name: 5a_post_TCR


title: H3K27me3, Donor2, TH-TL (Cortex)

description: Library name: BI068


title: H3K27ac, Donor2, TH-TL (Cortex)

description: Library name: BI067


title: 4_post_AMG510_CD45_TCR

description: Library name: 4_post_TCR


title: RNA, Donor4, CBV (Cerebellum)-5

description: Library name: BI064


title: RNA, Donor4, CBL (Cerebellum)-3

description:
Library name: BI279
scRNA-seq


title: 3_post_Vehicle_CD45_TCR

description: Library name: 3_post_TCR

value: Vehicle


title: RNA, Donor4, CBV (Cerebellum)-4

description: Library name: BI063


title: RNA, Donor4, CBV (Cerebellum)-3

description: Library name: BI062


title: 2_post_Vehicle_CD45_TCR

description: Library name: 2_post_TCR


title: 1_post_Vehicle_CD45_TCR

description: Library name: 1_post_TCR


title: RNA, Donor4, CBV (Cerebellum)-2

description: Library name: BI061


title: RNA, Donor4, CBV (Cerebellum)-1

description: Library name: BI060


title: 15_post_MEKi_CD45_TCR

description: Library name: 15_post_TCR

value: MEK inhibitor


title: 14_post_MEKi_CD45_TCR

description: Library name: 14_post_TCR


title: H3K27me3, Donor4, CBV (Cerebellum)-4

description: Library name: BI055


title: 13_post_MEKi_CD45_TCR

description: Library name: 13_post_TCR


title: H3K27me3, Donor4, CBV (Cerebellum)-3

description: Library name: BI054


title: H3K27me3, Donor4, CBV (Cerebellum)-2

description: Library name: BI053


title: 12_post_PD1_CD45_TCR

description: Library name: 12_post_TCR


title: 11_post_PD1_CD45_TCR

description: Library name: 11_post_TCR


title: H3K27me3, Donor4, CBV (Cerebellum)-1

description: Library name: BI052


title: 10_post_PD1_CD45_TCR

description: Library name: 10_post_TCR


title: 9_pre_AMG510PD1_CD45_TCR

description: Library name: 9_pre_TCR


title: H3K27ac, Donor4, CBV (Cerebellum)

description: Library name: BI051


title: RNA, Donor4, Idg (Cortex)-3

description: Library name: BI048


title: 8_pre_AMG510PD1_CD45_TCR

description: Library name: 8_pre_TCR


title: RNA, Donor2, Idg (Cortex)-1

description: Library name: BI047


title: RNA, Donor4, CBL (Cerebellum)-2

description: Library name: BI046


title: 7_pre_AMG510PD1_CD45_TCR

description: Library name: 7_pre_TCR


title: 6b_pre_AMG510_CD45_TCR

description: Library name: 6b_pre_TCR


title: RNA, Donor4, CBL (Cerebellum)-1

description: Library name: BI045


title: 6a_pre_AMG510_CD45_TCR

description: Library name: 6a_pre_TCR


title: 5_pre_AMG510_CD45_TCR

description: Library name: 5_pre_TCR


title: RNA, Donor1, Idg (Cortex)-1

description: Library name: BI042


title: RNA, Donor1, Idg (Cortex)-2

description: Library name: BI043


title: NE_C1_NT

description:
Library name: NE_C1_NT
10X Genomics, scRNAseq

value: aortic root, ascending aorta to brachiocephalic artery take off

value: Filtered Air

value: RNA Batch 1


title: 4_pre_AMG510_CD45_TCR

description: Library name: 4_pre_TCR


title: RNA, Donor4, Idg (Cortex)-2

description: Library name: BI039

value: Cortex


title: 2_pre_Vehicle_CD45_TCR

description: Library name: 2_pre_TCR


title: 3_pre_Vehicle_CD45_TCR

description: Library name: 3_pre_TCR


title: RNA, Donor2, ITG (Cortex)-3

description: Library name: BI037


title: RNA, Donor4, Idg (Cortex)-1

description: Library name: BI038


title: RNA, Donor2, ITG (Cortex)-2

description: Library name: BI036


title: 15_pre_MEKi_CD45_TCR

description: Library name: 15_pre_TCR


title: RNA, Donor2, ITG (Cortex)-1

description: Library name: BI035


title: 1_pre_Vehicle_CD45_TCR

description: Library name: 1_pre_TCR


title: 14_pre_MEKi_CD45_TCR

description: Library name: 14_pre_TCR


title: H3K27me3, Donor4, Idg (Cortex)-2

description: Library name: BI034


title: 13_pre_MEKi_CD45_TCR

description: Library name: 13_pre_TCR


title: H3K27me3, Donor2, Idg (Cortex)

description: Library name: BI033


title: H3K27ac, Donor4, CBL (Cerebellum)

description: Library name: BI032

value: Cerebellum


title: 12_pre_PD1_CD45_TCR

description: Library name: 12_pre_TCR


title: 11_pre_PD1_CD45_TCR

description: Library name: 11_pre_TCR


title: 9_post_AMG510PD1_CD45

description: Library name: 9_post

value: GEX


title: H3K27me3, Donor1, Idg (Cortex)

description: Library name: BI029


title: H3K27me3, Donor4, CBL (Cerebellum)

description: Library name: BI031


title: 10_pre_PD1_CD45_TCR

description: Library name: 10_pre_TCR


title: H3K27ac, Donor1, Idg (Cortex)

description: Library name: BI028


title: 8_post_AMG510PD1_CD45

description: Library name: 8_post


title: H3K27me3, Donor4, Idg (Cortex)-1

description: Library name: BI025


title: 7_post_AMG510PD1_CD45

description: Library name: 7_post


title: H3K27ac, Donor4, Idg (Cortex)

description: Library name: BI024


title: 6b_post_AMG510_CD45

description: Library name: 6_post


title: H3K27ac, Donor2, ITG (Cortex)

description: Library name: BI023


title: 6a_post_AMG510_CD45

description: Library name: 5b_post


title: H3K27me3, Donor2, ITG (Cortex)-2

description: Library name: BI022


title: 5_post_AMG510_CD45

description: Library name: 5a_post


title: H3K27me3, Donor2, ITG (Cortex)-1

description: Library name: BI021


title: 4_post_AMG510_CD45

description: Library name: 4_post


title: RNA, Donor2, A25 (Cortex)-2

description: Library name: BI018


title: 3_post_Vehicle_CD45

description: Library name: 3_post


title: 1_post_Vehicle_CD45

description: Library name: 1_post


title: RNA, Donor2, CBL (Cerebellum)-4

description: Library name: BI016


title: RNA, Donor2, A25 (Cortex)-1

description: Library name: BI017


title: 2_post_Vehicle_CD45

description: Library name: 2_post


title: 15_post_MEKi_CD45

description: Library name: 15_post


title: RNA, Donor2, CBL (Cerebellum)-3

description: Library name: BI015


title: RNA, Donor2, CBL (Cerebellum)-2

description: Library name: BI014


title: RNA, Donor1, V2 (Cortex)-2

description:
Library name: BI138
scRNA-seq


title: 14_post_MEKi_CD45

description: Library name: 14_post


title: RNA, Donor2, CBL (Cerebellum)-1

description: Library name: BI013


title: 13_post_MEKi_CD45

description: Library name: 13_post


title: H3K27me3, Donor2, A25 (Cortex)

description: Library name: BI010


title: H3K27ac, Donor2, A25 (Cortex)

description: Library name: BI009


title: H3K27me3, Donor2, CBL (Cerebellum)-3

description: Library name: BI008


title: 11_post_PD1_CD45

description: Library name: 11_post


title: 12_post_PD1_CD45

description: Library name: 12_post


title: 10_post_PD1_CD45

description: Library name: 10_post


title: H3K27ac, Donor2, CBL (Cerebellum)

description: Library name: BI007


title: 9_pre_AMG510PD1_CD45

description: Library name: 9_pre


title: 8_pre_AMG510PD1_CD45

description: Library name: 8_pre


title: H3K27me3, Donor2, CBL (Cerebellum)-2

description: Library name: BI006


title: H3K27me3, Donor2, CBL (Cerebellum)-1

description: Library name: BI005


title: 7_pre_AMG510PD1_CD45

description: Library name: 7_pre


title: RNA, Donor2, PN (Pons)-2

description: Library name: BC866

source_name: Pons

value: Pons


title: H3K27ac / H3K27me3, Donor1, A38 (Cortex)-2

description:
Library name: BI124
scCUT&Tag


title: 6b_pre_AMG510_CD45

description: Library name: 6b_pre


title: RNA, Donor2, PN (Pons)-1

description: Library name: BC865


title: 6a_pre_AMG510_CD45

description: Library name: 6a_pre


title: H3K27me3, Donor2, PN (Pons)

description: Library name: BC858


title: H3K27ac, Donor2, PN (Pons)

description: Library name: BC857


title: 5_pre_AMG510_CD45

description: Library name: 5_pre


title: 3_pre_Vehicle_CD45

description: Library name: 3_pre


title: RNA, Donor4, PN (Pons)-2

description: Library name: BC856


title: 4_pre_AMG510_CD45

description: Library name: 4_pre


title: RNA, Donor4, PN (Pons)-1

description: Library name: BC855


title: 2_pre_Vehicle_CD45

description: Library name: 2_pre


title: RAW 264.7 Cells, Control, 24h, rep1

description: Library name: CON_1

value: macrophage

value: Control


title: 1_pre_Vehicle_CD45

description: Library name: 1_pre

value: CD45+ cells


title: H3K27ac, Donor4, PN (Pons)

description: Library name: BC842


title: RNA, Donor1, PN (Pons)-2

description: Library name: BC828


title: 14_pre_MEKi_CD45

description: Library name: 14_pre

value: Balb/c


title: RNA, Donor1, PN (Pons)-1

description: Library name: BC827


title: 15_pre_MEKi_CD45

description: Library name: 15_pre


title: 13_pre_MEKi_CD45

description: Library name: 13_pre


title: H3K27me3, Donor4, PN (Pons)

description: Library name: BC843


title: 11_pre_PD1_CD45

description: Library name: 11_pre


title: H3K27me3, Donor1, PN (Pons)

description: Library name: BC814


title: H3K27ac, Donor1, PN (Pons)

description: Library name: BC813


title: breast cancer_CA18_C

type: RNA

city: Houston

middle: Fraser

last: Symmans

state: TX

address: 2130 W Holcombe Blvd #11.4000

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX.

data_processing:
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 600 breast cancer specific genes.

label: biotin

source_name: breast cancer sample

label_protocol: A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization. At least 1 ug of RNA is required for cRNA synthesis.

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns

treatment_protocol: Patients consented to future tissue-based research sample collections from either prospective biopsy or surgical resection.

tag: er status

value: P

tag: pr status

tag: her2 status

value: N

tag: ajcc stage

value: III

tag: sample collection type

value: Cytology

tag: setting of sample collection

value: Surgical Tissue Sample


title: 12_pre_PD1_CD45

description: Library name: 12_pre

value: Implanted CT26-KRAS-G12C tumors into Balb/C mice


title: 10_pre_PD1_CD45

description: Library name: 10_pre


title: breast cancer_CA18_S

value: Tissue


title: breast cancer_MD85_C

value: IIB


title: breast cancer_MD85_S


title: 2_4b_AMG510

description: Library name: 2_4b

data_processing:
Space Ranger 2.0.0
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expression UMI count data in Market Exchange Format (MEX)
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: image of tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and position coordinates
Library strategy: Spatial Transcriptomics

extract_protocol:
Tissue was embedded in OCT and flash frozen in isopentane/liquid nitrogen. 10 micrometer sections were sliced from OCT-embedded blocks for placement onto Visium slides.
Visium Spatial Gene Expression v1 (PN-1000187)

value: AMG 510


title: 2_4a_AMG510

description: Library name: 2_4a


title: 1_4b_Vehicle

description: Library name: 1_4b

value: Vehicle


title: 1_4a_Vehicle

description: Library name: 1_4a


title: breast cancer_SK41_C


title: breast cancer_SK37_C


title: breast cancer_SK41_S


title: 4_3b_PD1

description: Library name: 4_3b


title: breast cancer_SK37_S


title: 4_3a_PD1

description: Library name: 4_3a


title: 3_3b_AMG510PD1

description: Library name: 3_3b

value: AMG 510 + anti-PD-1


title: breast cancer_SK35_C


title: breast cancer_SK35_S


title: 4_2b_PD1

description: Library name: 4_2b


title: breast cancer_SK14_C


title: 3_3a_AMG510PD1

description: Library name: 3_3a


title: breast cancer_AN39_C

value: IIA


title: 3_1a_AMG510PD1

description: Library name: 3_1a


title: breast cancer_SK14_S


title: 4_2a_PD1

description: Library name: 4_2a


title: breast cancer_AN39_S


title: 3_1b_AMG510PD1

description: Library name: 3_1b


title: breast cancer_MD70_C

value: I


title: 2_2b_AMG510

description: Library name: 2_2b


title: 2_2a_AMG510

description: Library name: 2_2a


title: breast cancer_MD70_S


title: breast cancer_MD62_C


title: breast cancer_MD62_S


title: CT26_KRAS-G12C, baseline

description: Library name: CT26_invitro

data_processing:
Cell Ranger v6.0.0
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expression UMI count data in Market Exchange Format (MEX)

source_name: in-vitro CT26-KRAS-G12C tumor cells

extract_protocol:
Tumors were harvested, dissected, and placed in Liberase TL (0.2 mg/ml). Tumors solutions were homogenized using a gentleMACS Dissociator, treated with 0.002% EDTA and 10% FBS, and passed through a 70-micrometer filter to remove clumps. Cells were then frozen in media with 10% DMSO until encapsulation.
Chromium NextGEM Single Cell 3' v3.1 (10x Genomics)

value: in-vitro CT26-KRAS-G12C tumor cells

value: CT26-KRAS-G12C neoplastic cells


title: breast cancer_CA12_S


title: breast cancer_CA12_C


title: breast cancer_AN36_C


title: Total tumor, MEK inhibitor, 2

description: Library name: 3_2

value: Total cells from tumor

value: MEK inhibitor


title: Total tumor, MEK inhibitor, 1

description: Library name: 3_1

value: Balb/c


title: Total tumor, MEK inhibitor, 3

description: Library name: 3_3


title: 1_1a_Vehicle

description: Library name: 1_1a


title: breast cancer_AN36_S

value: P

value: N


title: 1_1b_Vehicle

description: Library name: 1_1b


title: Total tumor, KRAS inhibitor, 3

description: Library name: 2_5


title: breast cancer_AN31_C

value: Cytology


title: Total tumor, KRAS inhibitor, 2

description: Library name: 2_3


title: breast cancer_AN31_S

value: Surgical Tissue Sample


title: breast cancer_AN18_C


title: Total tumor, KRAS inhibitor, 1

description: Library name: 2_2

value: Implanted CT26-KRAS-G12C tumors into Balb/C mice


title: breast cancer_AN18_S

value: Tissue


title: breast cancer_AN17_S


title: breast cancer_AN17_C


title: Total tumor, Vehicle, 1

description: Library name: 1_1


title: Total tumor, Vehicle, 3

description: Library name: 1_5


title: Total tumor, Vehicle, 2

description: Library name: 1_4


title: E9.25-bulk-T37KO-PGC-18

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

description: Library name: E9.25-bulk-T37KO-PGC-18

data_processing:
For scRNA-seq, quality control of the raw FASTQ data was conducted using Trim Galore (v0.6.4), followed by read alignment to the mm10 genome with STAR (v2.7.3a) under default settings. Only uniquely mapped reads were retained and filtered with Sambamba (v1.0.0). Mapping quality was assessed using RSeQC (v3.0.0). Raw counts were obtained with featureCounts (v2.0.6), while TPM and FPKM values were computed using StringTie (v2.0). For bulk RNA-seq, the raw RNA-seq data were first trimmed with TrimGalore (v0.6.10) to remove low-quality sequences and adapter contamination. Clean reads were then aligned to the mm10 reference genome using HISAT2 (v2.2.1). Gene-level counts were obtained with featureCounts (v2.0.1) based on UCSC GTF annotation, and FPKM values were calculated using Cufflinks (v2.2.1).
Assembly: mm10
Supplementary files format and content: Txt file includes raw counts for each smaple.

source_name: E9.25 embryo

extract_protocol:
For scRNA-seq, the E8.5 Nanog-EGFP transgenic embryos and E9.5 Oct4-EGFP transgenic embryos were dissected from recipient mice and digested with 0.25% Trypsin-EDTA (Thermo Fisher, Cat#25200072) at 37 °C. After digestion, the embryos were gently pipetted and resuspended in the H-CZB medium. The single PGC from wild-type and Trim37ko embryos were picked by a Piezo-drill micromanipulator and transferred into a 200 µL tube containing 3.5 µL lysis buffer. For bulk RNA-seq, E9.25 control and Trim37ko embryos carrying Nanog-EGFP transgene were dissected from recipient mice and digested with 0.25% Trypsin-EDTA (Thermo Fisher Scientific, Cat#25200072) at 37 °C. Following digestion, Nanog-EGFP positive PGCs were isolated from the suspension via FACS. Approximately 80 PGCs per sample were transferred into a 200 µL tube containing 3.5 µL of lysis buffer.
The lysate was then subjected to cDNA amplification using the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat#N712).
Libraries of RNA-seq subjected to deep sequencing on Illumina NovaSeq6000 platform following the manufacturer’s instructions (Illumina) to produce 150bp paired-end reads by Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: E9.25 embryo

tag: genetic modification

value: Trim37 kncokout

tag: time


title: breast cancer_MD46_C


title: E9.25-bulk-T37KO-PGC-17

description: Library name: E9.25-bulk-T37KO-PGC-17


title: breast cancer_MD46_S


title: E9.25-bulk-T37KO-PGC-16

description: Library name: E9.25-bulk-T37KO-PGC-16


title: breast cancer_SK03_C


title: E9.25-bulk-T37KO-PGC-14

description: Library name: E9.25-bulk-T37KO-PGC-14


title: breast cancer_SK03_S


title: E9.25-bulk-T37KO-PGC-15

description: Library name: E9.25-bulk-T37KO-PGC-15


title: breast cancer_UO34_S

value: III


title: E9.25-bulk-T37KO-PGC-12

description: Library name: E9.25-bulk-T37KO-PGC-12


title: breast cancer_UO27_S

value: IIB


title: E9.25-bulk-T37KO-PGC-13

description: Library name: E9.25-bulk-T37KO-PGC-13


title: breast cancer_UO34_C


title: breast cancer_UO27_C


title: E9.25-bulk-T37KO-PGC-11

description: Library name: E9.25-bulk-T37KO-PGC-11


title: E9.25-bulk-T37KO-PGC-10

description: Library name: E9.25-bulk-T37KO-PGC-10


title: breast cancer_UO26_C


title: breast cancer_UO26_S


title: E9.25-bulk-T37KO-PGC-9

description: Library name: E9.25-bulk-T37KO-PGC-9


title: breast cancer_UO21_C

value: IIA


title: E9.25-bulk-T37KO-PGC-8

description: Library name: E9.25-bulk-T37KO-PGC-8


title: E9.25-bulk-T37KO-PGC-7

description: Library name: E9.25-bulk-T37KO-PGC-7


title: breast cancer_UO21_S


title: breast cancer_AN08_C


title: E9.25-bulk-T37KO-PGC-4

description: Library name: E9.25-bulk-T37KO-PGC-4


title: breast cancer_MD26_C


title: E9.25-bulk-T37KO-PGC-5

description: Library name: E9.25-bulk-T37KO-PGC-5


title: breast cancer_AN08_S


title: E9.25-bulk-T37KO-PGC-6

description: Library name: E9.25-bulk-T37KO-PGC-6


title: E9.25-bulk-T37KO-PGC-3

description: Library name: E9.25-bulk-T37KO-PGC-3


title: breast cancer_MD26_S


title: E9.25-bulk-T37KO-PGC-2

description: Library name: E9.25-bulk-T37KO-PGC-2


title: breast cancer_UO18_S

value: I


title: E9.25-bulk-T37KO-PGC-1

description: Library name: E9.25-bulk-T37KO-PGC-1


title: breast cancer_UO18_C


title: E9.25-bulk-control-PGC-13

description: Library name: E9.25-bulk-control-PGC-13

value: Control


title: breast cancer_UO15_S


title: E9.25-bulk-control-PGC-11

description: Library name: E9.25-bulk-control-PGC-11


title: breast cancer_UO15_C


title: breast cancer_AN06_C


title: E9.25-bulk-control-PGC-12

description: Library name: E9.25-bulk-control-PGC-12


title: E9.25-bulk-control-PGC-10

description: Library name: E9.25-bulk-control-PGC-10


title: breast cancer_AN06_S


title: E9.25-bulk-control-PGC-9

description: Library name: E9.25-bulk-control-PGC-9


title: breast cancer_SK31_C


title: breast cancer_SK31_S


title: E9.25-bulk-control-PGC-8

description: Library name: E9.25-bulk-control-PGC-8


title: breast cancer_SK27_C


title: E9.25-bulk-control-PGC-7

description: Library name: E9.25-bulk-control-PGC-7


title: E9.25-bulk-control-PGC-6

description: Library name: E9.25-bulk-control-PGC-6


title: breast cancer_SK27_S


title: breast cancer_SK26_C


title: breast cancer_SK18_C


title: E9.25-bulk-control-PGC-5

description: Library name: E9.25-bulk-control-PGC-5


title: E9.25-bulk-control-PGC-3

description: Library name: E9.25-bulk-control-PGC-3


title: E9.25-bulk-control-PGC-4

description: Library name: E9.25-bulk-control-PGC-4


title: breast cancer_SK26_S


title: breast cancer_SK18_S


title: E9.25-bulk-control-PGC-2

description: Library name: E9.25-bulk-control-PGC-2


title: breast cancer_SK13_C


title: E9.25-bulk-control-PGC-1

description: Library name: E9.25-bulk-control-PGC-1


title: E9.5-scRNA-T37KO-PGC-30

description: Library name: E9.5-scRNA-T37KO-PGC-30

source_name: E9.5 embryo

value: E9.5 embryo


title: breast cancer_SK13_S


title: breast cancer_CA10_C


title: E9.5-scRNA-T37KO-PGC-29

description: Library name: E9.5-scRNA-T37KO-PGC-29


title: E9.5-scRNA-T37KO-PGC-28

description: Library name: E9.5-scRNA-T37KO-PGC-28


title: breast cancer_CA15_S


title: E9.5-scRNA-T37KO-PGC-26

description: Library name: E9.5-scRNA-T37KO-PGC-26


title: breast cancer_CA10_S


title: E9.5-scRNA-T37KO-PGC-27

description: Library name: E9.5-scRNA-T37KO-PGC-27


title: breast cancer_CA15_C


title: breast cancer_AMC03_C


title: E9.5-scRNA-T37KO-PGC-25

description: Library name: E9.5-scRNA-T37KO-PGC-25


title: E9.5-scRNA-T37KO-PGC-24

description: Library name: E9.5-scRNA-T37KO-PGC-24


title: breast cancer_AMC03_S


title: breast cancer_AMC01_C


title: E9.5-scRNA-T37KO-PGC-22

description: Library name: E9.5-scRNA-T37KO-PGC-22


title: breast cancer_AMC01_S


title: breast cancer_AN29_C


title: E9.5-scRNA-T37KO-PGC-21

description: Library name: E9.5-scRNA-T37KO-PGC-21


title: E9.5-scRNA-T37KO-PGC-20

description: Library name: E9.5-scRNA-T37KO-PGC-20


title: breast cancer_AN29_S


title: E9.5-scRNA-T37KO-PGC-19

description: Library name: E9.5-scRNA-T37KO-PGC-19


title: breast cancer_AN23_C


title: E9.5-scRNA-T37KO-PGC-18

description: Library name: E9.5-scRNA-T37KO-PGC-18


title: breast cancer_AN23_S


title: E9.5-scRNA-T37KO-PGC-23

description: Library name: E9.5-scRNA-T37KO-PGC-23


title: breast cancer_AN21_C


title: E9.5-scRNA-T37KO-PGC-17

description: Library name: E9.5-scRNA-T37KO-PGC-17


title: E9.5-scRNA-T37KO-PGC-16

description: Library name: E9.5-scRNA-T37KO-PGC-16


title: breast cancer_AN09_C


title: breast cancer_AN21_S


title: E9.5-scRNA-T37KO-PGC-15

description: Library name: E9.5-scRNA-T37KO-PGC-15


title: E9.5-scRNA-T37KO-PGC-14

description: Library name: E9.5-scRNA-T37KO-PGC-14


title: E9.5-scRNA-T37KO-PGC-13

description: Library name: E9.5-scRNA-T37KO-PGC-13


title: breast cancer_UO20_C


title: breast cancer_AN09_S


title: E9.5-scRNA-T37KO-PGC-12

description: Library name: E9.5-scRNA-T37KO-PGC-12


title: breast cancer_UO20_S


title: breast cancer_UO19_S


title: E9.5-scRNA-T37KO-PGC-11

description: Library name: E9.5-scRNA-T37KO-PGC-11


title: breast cancer_UO13_C


title: E9.5-scRNA-T37KO-PGC-10

description: Library name: E9.5-scRNA-T37KO-PGC-10


title: breast cancer_UO09_C


title: E9.5-scRNA-T37KO-PGC-8

description: Library name: E9.5-scRNA-T37KO-PGC-8


title: E9.5-scRNA-T37KO-PGC-9

description: Library name: E9.5-scRNA-T37KO-PGC-9


title: E9.5-scRNA-T37KO-PGC-7

description: Library name: E9.5-scRNA-T37KO-PGC-7


title: E9.5-scRNA-T37KO-PGC-6

description: Library name: E9.5-scRNA-T37KO-PGC-6


title: breast cancer_UO13_S


title: breast cancer_UO09_S


title: breast cancer_UO06_C


title: E9.5-scRNA-T37KO-PGC-5

description: Library name: E9.5-scRNA-T37KO-PGC-5


title: breast cancer_UO06_S


title: breast cancer_MD120_C


title: E9.5-scRNA-T37KO-PGC-4

description: Library name: E9.5-scRNA-T37KO-PGC-4


title: breast cancer_MD112_C


title: breast cancer_MD127_C

value: L


title: E9.5-scRNA-T37KO-PGC-1

description: Library name: E9.5-scRNA-T37KO-PGC-1


title: E9.5-scRNA-con-PGC-15

description: Library name: E9.5-scRNA-con-PGC-15


title: E9.5-scRNA-T37KO-PGC-3

description: Library name: E9.5-scRNA-T37KO-PGC-3


title: breast cancer_MD115_C


title: breast cancer_MD110_C


title: E9.5-scRNA-con-PGC-14

description: Library name: E9.5-scRNA-con-PGC-14


title: breast cancer_MD108_C


title: breast cancer_MD105_C


title: breast cancer_MD104_C


title: E9.5-scRNA-T37KO-PGC-2

description: Library name: E9.5-scRNA-T37KO-PGC-2


title: E9.5-scRNA-con-PGC-13

description: Library name: E9.5-scRNA-con-PGC-13


title: breast cancer_MD96_S


title: E9.5-scRNA-con-PGC-11

description: Library name: E9.5-scRNA-con-PGC-11


title: breast cancer_MD96_C


title: E9.5-scRNA-con-PGC-10

description: Library name: E9.5-scRNA-con-PGC-10


title: E9.5-scRNA-con-PGC-9

description: Library name: E9.5-scRNA-con-PGC-9


title: E9.5-scRNA-con-PGC-12

description: Library name: E9.5-scRNA-con-PGC-12


title: breast cancer_MD87_C


title: breast cancer_MD93_C


title: E9.5-scRNA-con-PGC-7

description: Library name: E9.5-scRNA-con-PGC-7


title: E9.5-scRNA-con-PGC-8

description: Library name: E9.5-scRNA-con-PGC-8


title: breast cancer_MD82_C


title: breast cancer_MD83_C


title: E9.5-scRNA-con-PGC-6

description: Library name: E9.5-scRNA-con-PGC-6


title: CAF#1, Control (MeRIP)

description: Library name: 1-con-IP

value: pancreas

value: pancreatic stellate cells

value: con


title: CAF#2, Control (MeRIP)

description: Library name: 2-con-IP


title: breast cancer_MD59_C

value: P

value: N


title: breast cancer_MD72_C

value: Cytology

value: Surgical Tissue Sample


title: E9.5-scRNA-con-PGC-4

description: Library name: E9.5-scRNA-con-PGC-4


title: E9.5-scRNA-con-PGC-3

description: Library name: E9.5-scRNA-con-PGC-3


title: E9.5-scRNA-con-PGC-5

description: Library name: E9.5-scRNA-con-PGC-5


title: breast cancer_MD44_C


title: E9.5-scRNA-con-PGC-2

description: Library name: E9.5-scRNA-con-PGC-2


title: breast cancer_MD41_C


title: breast cancer_MD43_C


title: E9.5-scRNA-con-PGC-1

description: Library name: E9.5-scRNA-con-PGC-1


title: E9.5-scRNA-T37KO-SC-9

description: Library name: E9.5-scRNA-T37KO-SC-9


title: breast cancer_MD36_C


title: breast cancer_MD33_C


title: E9.5-scRNA-T37KO-SC-8

description: Library name: E9.5-scRNA-T37KO-SC-8


title: E9.5-scRNA-T37KO-SC-7

description: Library name: E9.5-scRNA-T37KO-SC-7


title: breast cancer_MD31_C


title: breast cancer_MD30_C


title: breast cancer_MD91_C


title: E9.5-scRNA-T37KO-SC-5

description: Library name: E9.5-scRNA-T37KO-SC-5


title: E9.5-scRNA-T37KO-SC-6

description: Library name: E9.5-scRNA-T37KO-SC-6


title: breast cancer_MD27_C


title: E9.5-scRNA-T37KO-SC-4

description: Library name: E9.5-scRNA-T37KO-SC-4


title: breast cancer_MD90_C


title: breast cancer_MD74_C


title: E9.5-scRNA-T37KO-SC-1

description: Library name: E9.5-scRNA-T37KO-SC-1


title: E9.5-scRNA-T37KO-SC-2

description: Library name: E9.5-scRNA-T37KO-SC-2


title: breast cancer_MD78_C


title: E9.5-scRNA-con-SC-10

description: Library name: E9.5-scRNA-con-SC-10


title: breast cancer_MD71_C


title: E9.5-scRNA-con-SC-9

description: Library name: E9.5-scRNA-con-SC-9


title: breast cancer_MD69_C


title: breast cancer_MD67_C


title: E9.5-scRNA-con-SC-8

description: Library name: E9.5-scRNA-con-SC-8


title: CAF#1, Control (input)

description: Library name: 1-con-input


title: E9.5-scRNA-con-SC-6

description: Library name: E9.5-scRNA-con-SC-6


title: breast cancer_MD50_C


title: breast cancer_MD66_C


title: breast cancer_V-054

value: Tissue


title: E9.5-scRNA-con-SC-5

description: Library name: E9.5-scRNA-con-SC-5


title: E9.5-scRNA-con-SC-7

description: Library name: E9.5-scRNA-con-SC-7


title: E9.5-scRNA-con-SC-3

description: Library name: E9.5-scRNA-con-SC-3


title: breast cancer_V-029


title: breast cancer_MD49_C


title: E9.5-scRNA-con-SC-4

description: Library name: E9.5-scRNA-con-SC-4


title: E9.5-scRNA-con-SC-2

description: Library name: E9.5-scRNA-con-SC-2


title: E9.5-scRNA-con-SC-1

description: Library name: E9.5-scRNA-con-SC-1


title: breast cancer_V-094


title: breast cancer_V-080


title: E8.5-scRNA-T37KO-PGC-18

description: Library name: E8.5-scRNA-T37KO-PGC-18

source_name: E8.5 embryo

value: E8.5 embryo

value: Trim37 knockout


title: breast cancer_V-081


title: breast cancer_V-071


title: E8.5-scRNA-T37KO-PGC-16

description: Library name: E8.5-scRNA-T37KO-PGC-16


title: E8.5-scRNA-T37KO-PGC-15

description: Library name: E8.5-scRNA-T37KO-PGC-15


title: breast cancer_V-116

value: III


title: breast cancer_V-036


title: E8.5-scRNA-T37KO-PGC-17

description: Library name: E8.5-scRNA-T37KO-PGC-17


title: breast cancer_V-117


title: E8.5-scRNA-T37KO-PGC-14

description: Library name: E8.5-scRNA-T37KO-PGC-14


title: breast cancer_V-104


title: E8.5-scRNA-T37KO-PGC-13

description: Library name: E8.5-scRNA-T37KO-PGC-13


title: E8.5-scRNA-T37KO-PGC-12

description: Library name: E8.5-scRNA-T37KO-PGC-12


title: breast cancer_V-102

value: IIB


title: E8.5-scRNA-T37KO-PGC-11

description: Library name: E8.5-scRNA-T37KO-PGC-11


title: breast cancer_V-042

value: IIA


title: E8.5-scRNA-T37KO-PGC-10

description: Library name: E8.5-scRNA-T37KO-PGC-10


title: breast cancer_V-111


title: E8.5-scRNA-T37KO-PGC-9

description: Library name: E8.5-scRNA-T37KO-PGC-9


title: breast cancer_V-065


title: E8.5-scRNA-T37KO-PGC-7

description: Library name: E8.5-scRNA-T37KO-PGC-7


title: breast cancer_V-053

value: I


title: E8.5-scRNA-T37KO-PGC-8

description: Library name: E8.5-scRNA-T37KO-PGC-8


title: breast cancer_V-066


title: E8.5-scRNA-T37KO-PGC-6

description: Library name: E8.5-scRNA-T37KO-PGC-6


title: breast cancer_V-064


title: breast cancer_V-083


title: breast cancer_V-103


title: E8.5-scRNA-T37KO-PGC-3

description: Library name: E8.5-scRNA-T37KO-PGC-3


title: E8.5-scRNA-T37KO-PGC-5

description: Library name: E8.5-scRNA-T37KO-PGC-5


title: E8.5-scRNA-T37KO-PGC-4

description: Library name: E8.5-scRNA-T37KO-PGC-4


title: breast cancer_V-115


title: breast cancer_V-043


title: E8.5-scRNA-T37KO-PGC-2

description: Library name: E8.5-scRNA-T37KO-PGC-2


title: breast cancer_V-110


title: E8.5-scRNA-con-PGC-10

description: Library name: E8.5-scRNA-con-PGC-10

value: Control


title: E8.5-scRNA-con-PGC-12

description: Library name: E8.5-scRNA-con-PGC-12


title: breast cancer_V-047


title: E8.5-scRNA-T37KO-PGC-1

description: Library name: E8.5-scRNA-T37KO-PGC-1


title: breast cancer_V-021


title: E8.5-scRNA-con-PGC-9

description: Library name: E8.5-scRNA-con-PGC-9


title: E8.5-scRNA-con-PGC-11

description: Library name: E8.5-scRNA-con-PGC-11


title: breast cancer_ANON 18T


title: breast cancer_ANON 18S


title: breast cancer_ANON 18R


title: E8.5-scRNA-con-PGC-7

description: Library name: E8.5-scRNA-con-PGC-7


title: E8.5-scRNA-con-PGC-8

description: Library name: E8.5-scRNA-con-PGC-8


title: breast cancer_ANON 18Q


title: breast cancer_ANON 18P


title: E8.5-scRNA-con-PGC-6

description: Library name: E8.5-scRNA-con-PGC-6


title: breast cancer_ANON 18O


title: E8.5-scRNA-con-PGC-3

description: Library name: E8.5-scRNA-con-PGC-3


title: E8.5-scRNA-con-PGC-5

description: Library name: E8.5-scRNA-con-PGC-5


title: E8.5-scRNA-con-PGC-4

description: Library name: E8.5-scRNA-con-PGC-4


title: E8.5-scRNA-con-PGC-1

description: Library name: E8.5-scRNA-con-PGC-1


title: breast cancer_ANON 18N


title: E8.5-scRNA-con-PGC-2

description: Library name: E8.5-scRNA-con-PGC-2


title: breast cancer_ANON 18M


title: breast cancer_ANON 18L


title: breast cancer_ANON 18K


title: breast cancer_ANON 18J


title: E8.5-scRNA-con-SC-2

description: Library name: E8.5-scRNA-con-SC-2


title: E8.5-scRNA-con-SC-1

description: Library name: E8.5-scRNA-con-SC-1


title: breast cancer_ANON 18I


title: H3K9me3-T37KO-2

description: Library name: H3K9me3-T37KO-2

data_processing:
Raw sequencing reads were trimmed with Trim Galore (version 0.6.10) to remove adapter sequences and low-quality bases. The cleaned reads were then aligned to the mm10 reference genome using Bowtie2 (version 2.5.1) with the following parameters: -N 1 -X 1000 --no-mixed --no-discordant. Unmapped reads, multiple mapped reads, and PCR duplicates were subsequently filtered out using Sambamba (version 0.8.2). Peaks were called using MACS2 (version 2.2.6) with  -q 0.05 --nomodel --nolambda.To normalize read counts, RPKM (Reads Per Kilobase of transcript per Million mapped reads) was calculated in 100 bp bins using bamCoverage from deepTools (version 3.5.1).
Assembly: mm10
Supplementary files format and content: Bw files include the raw counts for each sample.
Library strategy: CUT&Tag

extract_protocol:
E9.25 control and Trim37ko embryos carrying Nanog-EGFP transgene were dissected from recipient mice and digested with 0.25% Trypsin-EDTA (Thermo Fisher Scientific, Cat#25200072) at 37 °C. Following digestion, Nanog-EGFP positive PGCs were isolated from the suspension via FACS.
Cleavage Under Targets and Tagmentation (CUT&Tag) was performed to detect  H3K27ac (anti-H3K27ac antibody, Abcam, Cat#ab4729) modification in the genomes of E9.0 control and Trim37ko PGCs. Approximately 1000 PGCs per sample were transferred into a 1.5 mL tube containing 500 µL of wash buffer. The samples were then processed and libraries constructed according to the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, Cat#TD904). All libraries were sequenced on the Illumina NovaSeq 6000 platform at Genergy Biotechnology Co. Ltd. (Shanghai, China).
For CUT&Tag, all libraries were sequenced on the Illumina NovaSeq 6000 platform at Genergy Biotechnology Co. Ltd. (Shanghai, China). For CUT&RUN, after ligation and USER enzyme treatment, samples were purified with AMPure beads, PCR amplified, and sequenced on an Illumina NovaSeq X Plus.

value: E9.25 embryo

tag: antibody


title: breast cancer_ANON 18G

value: Needle Biopsy Sample


title: H3K9me3-T37KO-3

description: Library name: H3K9me3-T37KO-3

tag: tissue


title: breast cancer_ANON 18F


title: breast cancer_ANON 18H


title: H3K9me3-T37KO-1

description: Library name: H3K9me3-T37KO-1


title: breast cancer_ANON 18E


title: breast cancer_ANON 17U


title: breast cancer_ANON 17Y


title: H3K9me3-control-3

description: Library name: H3K9me3-control-3


title: H3K9me3-control-2

description: Library name: H3K9me3-control-2


title: H3K27ac-T37KO-3

description: Library name: H3K27ac-T37KO-3


title: breast cancer_ANON 17T


title: H3K27ac-T37KO-2

description: Library name: H3K27ac-T37KO-2


title: H3K9me3-control-1

description: Library name: H3K9me3-control-1


title: breast cancer_ANON 17R


title: H3K27ac-control-3

description: Library name: H3K27ac-control-3


title: H3K27ac-control-2

description: Library name: H3K27ac-control-2


title: breast cancer_ANON 15I


title: breast cancer_ANON 15F


title: H3K27ac-T37KO-1

description: Library name: H3K27ac-T37KO-1


title: breast cancer_ANON 15E


title: breast cancer_ANON 15D


title: breast cancer_ANON 15C


title: H3K27ac-control-1

description: Library name: H3K27ac-control-1


title: E9.25-T37KO-ATAC-2

description: Library name: E9.25-T37KO-ATAC-2

data_processing:
Raw sequencing reads were trimmed with Trim Galore (version 0.6.10) to remove adapter sequences and low-quality bases. The cleaned reads were then aligned to the mm10 reference genome using Bowtie2 (version 2.5.1) with the following parameters: -N 1 -X 1000 --no-mixed --no-discordant. Unmapped reads, multiple mapped reads, and PCR duplicates were subsequently filtered out using Sambamba (version 0.8.2). Peaks were called using MACS2 (version 2.2.6) with  -q 0.05 --nomodel --nolambda.To normalize read counts, RPKM (Reads Per Kilobase of transcript per Million mapped reads) was calculated in 100 bp bins using bamCoverage from deepTools (version 3.5.1).
Assembly: mm10
Supplementary files format and content: Bw files include the raw counts for each sample.

extract_protocol:
E9.25 control and Trim37ko embryos carrying Nanog-EGFP transgene were dissected from recipient mice and digested with 0.25% Trypsin-EDTA (Thermo Fisher Scientific, Cat#25200072) at 37 °C. Following digestion, Nanog-EGFP positive PGCs were isolated from the suspension via FACS.
Approximately 1500 PGCs per sample were used for miniATAC-seq. Briefly, cells were transferred into 6 μL of lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, and 0.02% digitonin, 0.1% NP-40) on ice for 10 min. The ATAC reaction was performed by adding 4 μL ddH2O, 4 μL 5×TTBL, and 5 μL TTE mix V5 (Vazyme Biotech Co. Ltd, TD502) at 37 °C for 30 min and then stopped by adding 5 μL of 5× TS stop buffer at room temperature for 5 min. DNA was extracted by phenol-chloroform and ethanol purification after adding 40 ng of carrier RNA and 103 μL of Tris-EDTA.
DNA was dissolved in 29 μL ddH2O and PCR-amplified with 10 μL of index (Vazyme Biotech Co. Ltd, TD202), 10 μL 5× TAB, and 1 μL TAE (Vazyme Biotech Co. Ltd, TD502) with the program of 72 °C for 3 min, 98 °C for 30 s, (98 °C for 15 s, 60 °C for 30 s, and 72 °C for 3 min) with 16 cycles, and 72 °C for 5 min. The amplified DNA was size-selected using AMPure Beads for 200–800-bp DNA fragments. Libraries of RNA-seq subjected to deep sequencing on Illumina NovaSeq6000 platform following the manufacturer’s instructions (Illumina) to produce 150bp paired-end reads by Genergy Biotechnology Co. Ltd. (Shanghai, China).


title: breast cancer_ANON 15A


title: breast cancer_ANON 14Z


title: E9.25-T37KO-ATAC-1

description: Library name: E9.25-T37KO-ATAC-1


title: E9.25-control-ATAC-3

description: Library name: E9.25-control-ATAC-3


title: E9.25-T37KO-ATAC-3

description: Library name: E9.25-T37KO-ATAC-3


title: breast cancer_ANON 14V


title: breast cancer_ANON 14U


title: E9.25-control-ATAC-1

description: Library name: E9.25-control-ATAC-1


title: breast cancer_ANON 14O


title: E9.25-control-ATAC-2

description: Library name: E9.25-control-ATAC-2


title: Body, exposed to pathogen and caffeinated ant food, 05

city: Graz

first: Danae

last: Nyckees

address: Universitätsplatz 2

country: Austria

institute: University of Graz

description: Library name: sample50

data_processing:
The raw paired-end sequencing reads from the released RNA-Seq library was subject to processing. First, sequencing adaptors and low-quality nucleotides (Phred score threshold 30, stringency 2) were trimmed using Trim Galore (v. 0.6.0). Reads shorter than 70 bp were discarded and only intact pairs were retained for further processing. Secondly, the genome of F. fusca was retrieved from the GAGA project (Vizueta et al., 2025) and used to generate a genome index with STAR (v. 2.7.10b). Read mapping to the indexed reference genome for each sample was performed with the same software. Thirdly, PCR duplicate removal was performed using Picard (v. 2.18.7). Finally, the total reads from exon were transformed into counts using featureCounts (v. 2.0.6).
Assembly: GCA_048541905.1
Supplementary files format and content: each processed data file contains the gene name and the respective number of reads

organism: Formica fusca

source_name: thorax and abdomen

extract_protocol:
RNA was isolated from each sample with a phenol-chlorophorm extraction method. First, samples were homogenized with 500 µl TRI Reagent (T9424, Sigma-Aldrich, Missouri, United States) with a TissueLyser II (Qiagen, Venlo, Netherlands) for 1min at 30/s. Then, the volume was adjusted to 1 ml with TRI Reagent and the samples were vortexed. A volume of 150 µl of chloroform (C2432, Sigma-Aldrich, Missouri, United States) was added and the samples were vortexed vigorously. The samples were incubated at room temperature for 2 min and then on ice for 5 min. The samples are then centrifuged for 10 min at 14,000 rpm and at 4 °C. The supernatant was then carefully transferred to a new clean tube and 500 µl of isopropanol (190764, Sigma-Aldrich, Missouri, United States) was added. The samples are then vortexed vigorously and stored at -20 °C for approx. 24 h. The samples were centrifuged for 30 min at 14,000 rpm and at 4 °C. The isopropanol was removed and 500 µl of 80 % ethanol was added. The samples were centrifuged for 10 min at 14,000 rpm and at 4 °C. The ethanol was removed, and the samples were spined down to allow a second removal of the remaining solution. The RNA pellets were allowed to air dry for approx. 10 min with open cap. Finally, 40 µl of miliQ H2O were added and the RNA concentration and purity were measured with the Nanodrop Onec (Thermo Fisher Scientific, Massachusetts, United States). RNA extracts that were under 1.8 from the 260/280 ratio were subjected to a clean-up with GeneJET RNA Cleanup and Concentration Micro Kit (K0842, Thermo Fisher Scientific, Massachusetts, United States). Twenty microliters of RNA extracts were used and adjusted with nuclease-free water to reach a volume of 200 µl. Then, the manufacturer protocol was followed. As the amount of RNA was large, 20 µl of nuclease-free water was added instead of 10 for the final elution volume. RNA concentration and purity were measured with a Nanodrop and the RNA extracts with low purity levels were subjected to another round of clean-up.
Library construction was performed by Novogen using Illumina NovaSeq™ X Plus instruments and a paired-end 150 bp sequencing strategy.

treatment_protocol: Ten ants per experimental box were collected on day 4. Each ant was decapitated. Heads and bodies (thorax + abdomen) from each experimental colony and day were pooled respectively and conserved in RNAlater (R0901, Sigma-Aldrich, Missouri, United States). They were first stored at -20 °C for one night to allow the ants to sink and then at -80 °C until further analysis.

value: thorax and abdomen

value: exposed to Beauveria bassiana + ant food spiked with 100 ppm caffeine


title: breast cancer_ANON 14N


title: Head, exposed to pathogen and caffeinated ant food, 05

description: Library name: sample49

source_name: head

value: head


title: breast cancer_ANON 14M

value: P


title: Body, exposed to pathogen and caffeinated ant food, 04

description: Library name: sample48


title: breast cancer_ANON 14C

value: N


title: breast cancer_ANON 14E

value: U


title: Body, exposed to pathogen and caffeinated ant food, 03

description: Library name: sample46


title: Head, exposed to pathogen and caffeinated ant food, 03

description: Library name: sample45


title: breast cancer_ANON 14B

value: Surgical Tissue Sample


title: Body, exposed to pathogen and caffeinated ant food, 02

description: Library name: sample44


title: breast cancer_ANON 13U

value: Tissue


title: Head, exposed to pathogen and caffeinated ant food, 02

description: Library name: sample43


title: Body, exposed to pathogen and caffeinated ant food, 01

description: Library name: sample42


title: breast cancer_ANON 13Q


title: breast cancer_ANON 13G


title: breast cancer_ANON 13D


title: Head, sham and caffeinated ant food, 05

description: Library name: sample39

value: sham + ant food spiked with 100 ppm caffeine


title: Body, sham and caffeinated ant food, 05

description: Library name: sample40


title: Body, sham and caffeinated ant food, 04

description: Library name: sample38


title: breast cancer_ANON 13C


title: Body, sham and caffeinated ant food, 03

description: Library name: sample36


title: Head, sham and caffeinated ant food, 03

description: Library name: sample35


title: Body, sham and caffeinated ant food, 01

description: Library name: sample32


title: Head, sham and caffeinated ant food, 02

description: Library name: sample33


title: breast cancer_ANON 12Y


title: Head, sham and caffeinated ant food, 01

description: Library name: sample31


title: breast cancer_ANON 12W


title: breast cancer_ANON 12S


title: breast cancer_ANON 12T


title: Head, exposed to pathogen and ant food, 04

description: Library name: sample27

value: exposed to Beauveria bassiana + ant food


title: Body, exposed to pathogen and ant food, 03

description: Library name: sample26


title: breast cancer_ANON 12Q


title: breast cancer_ANON 12P


title: Body, exposed to pathogen and ant food, 02

description: Library name: sample24


title: breast cancer_ANON 12O


title: 3-untr

description:
Library name: 3-untr
Bulk RNA-seq

data_processing:
FASTQ files were aligned to the mouse genome reference version gencode.vM32 by STAR 2.7.10b. Reads mapped to each gene were counted using --quantMode GeneCounts in STAR.
Assembly: gencode.v45
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: Primary CD3 CAR-T cells

extract_protocol:
RNA was  extracted by TRIZOL. The RNA sequencing library was prepared using the NEBNext rRNA Depletion Kit v2 and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina
RNA-seq

value: Primary CD3 CAR-T cells

value: DMSO