title: ABE OT 7C Rep 1

description:
Library name: CHTTABEOT7_1
Processed_GEO_Data_Sheet.xlsx


title: 5xFAD, hypothalamus, NR and fructose, rep1, batch 2019

status: Public on Apr 06 2026

type: SRA

city: Los Angeles

first: Xia

last: Yang

email: xyang123@ucla.edu, jading@ucla.edu

state: CA

address: 610 Charles E Young Dr S

country: USA

institute: University of California Los Angeles

description:
Library name: AD-NRF-1-19-Hyp
10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the mm10 genome and gene counts were calculated using CellRanger software (v 3.0.2) (10X Genomics).
CellBender remove-background was used on raw feature-barcode matrices to remove ambient RNA contamination.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: hypothalamus

extract_protocol:
Papain was used to digest freshly dissected hippocampus and hypothalamus tissues. The cells were suspended to a final concentration of 1000 cells/μl in 0.04% BSA-PBS.
Libraries were prepared according to the manufacturer's protocol (3' single cell RNAseq V3 kit, 10x Genomics).

treatment_protocol: High fructose (F), DHA, NR, DHA+F, NR+F

tag: tissue

value: hypothalamus

tag: genotype

tag: treatment

value: NR and fructose

tag: batch


title: BMDC E3 screen, Round 1, Ch9_hash

city: Palo Alto

first: Basak

last: Eraslan

address: 2360 Saint Francis Drive

institute: Genentech

description:
Library name: BMDC E3 screen, Round 1, Ch9_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

library_source: other

data_processing:
scRNA files were demultiplexed using Cellranger mkfastq
Assembly: mm10
Supplementary files format and content: H5AD file containing raw counts matrix

molecule: protein

source_name: Blood cells

extract_protocol:
BMDCs derived from mice. Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X controller with a Chromium Single Cell 3' GEM Library and Gel Bead kit.
Hashtag (HTO) and guide dial out (GDO) libraries were generated as described (Geiger-Schuller and Eraslan et al., 2020)

value: Blood cells

tag: cell type

value: BMDCs

tag: library type

value: HTO

tag: hto

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3, TotalSeq-A0304 anti-mouse Hashtag 4, TotalSeq-A0305 anti-mouse Hashtag 5, TotalSeq-A0306 anti-mouse Hashtag 6, TotalSeq-A0307 anti-mouse Hashtag 7, TotalSeq-A0308 anti-mouse Hashtag 8


title: 5xFAD, hypothalamus, NR and fructose, rep2, batch 2019

description:
Library name: AD-NRF-2-19-Hyp
10x Genomics


title: ABE OT 6C Rep 3

city: Urbana

first: Pablo

last: Perez-Pinera

state: il

address: 1406 West Green Street

institute: University of Illinois Urbana-Champaign

description:
Library name: CHTTABEOT6_3
Processed_GEO_Data_Sheet.xlsx

library_source: genomic

data_processing:
Crispresso2 utilized for base calling and base editing frequency quantification for all DNA NGS files. Sequences were filtered for 90% homology with a phred33 read qualitty of >30. Sequencecs were aligned to an inputted PCR amplicon with the gRNA region of interest
Assembly: chr38
Supplementary files format and content: Excel sheet containing editing rates and figure number

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
For mouse tissues only striatum extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency Samples for DNA editing were extracted using Qiagen's DNeasy DNA extraction kit
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits as per manufacturer's instructions Targeted genomic and exon high throughput sequencing with nextera indexing primers

tag: cell line

value: epitheleal

value: Lipofectamine 2000 transfected

tag: sample group

value: ABE OT 6C


title: ABE OT 6C Rep 2

description:
Library name: CHTTABEOT6_2
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch7_hash

description:
Library name: BMDC E3 screen, Round 1, Ch7_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch8_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch8_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

molecule: other

value: GDO


title: 5xFAD, hypothalamus, fructose, rep3, batch 2019

description:
Library name: AD-F-3-19-Hyp
10x Genomics

value: fructose


title: BMDC E3 screen, Round 1, Ch7_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch7_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: mRNA


title: BMDC E3 screen, Round 1, Ch6_hash

description:
Library name: BMDC E3 screen, Round 1, Ch6_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: ABE OT 6C Rep 1

description:
Library name: CHTTABEOT6_1
Processed_GEO_Data_Sheet.xlsx


title: Digit tip regenerates, 14 dpa, wildtype

city: Madison

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

institute: Morgridge Institute For Research

description:
Library name: WT
BGI Americas

library_source: transcriptomic

data_processing:
Analysis was conducted at the Duke Regeneromics Core. RNA-seq reads were trimmed by Trim Galore (v0.6.4) and mapped with STAR(51) v2.6.1d, with parameters --twopassMode Basic --runDirPerm All_RWX and supplying the Ensembl GRCm38 annotation) to the mouse genome (GRCm38). The mapped reads were counted using featureCounts (52) v1.6.4. Bioconductor package EdgeR(53) (v3.36.0) was employed to analyze differential expressions (DE) with litter and genotype information. Gene Ontology and KEGG enrichment tests were performed to analyze enriched biological processes by clusterProfiler(54) v3.16.1. The volcano plots were created by EnhancedVolcano (v1.6.0). The coverage depth was normalized by deeptools(55) v3.1.3 using RPKM for RNA-seq. TPM values were quantified from Salmon(56) v1.2.1 quantification and summarized via tximport v1.16.1(57). Differentially expressed genes were defined at p < 0.05 and log₂ fold change > 0.58. Gene ontology/pathway enrichment was performed with Metascape(58) . Statistically enriched terms (GO/KEGG, canonical pathways, Hallmark gene sets) were identified using cumulative hypergeometric testing; p values and enrichment factors were used for filtering. Significant terms were hierarchically clustered by Kappa similarity, and clusters were defined at a Kappa score threshold of 0.3.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes the raw count for each sample

source_name: Digit tip

extract_protocol:
Regenerating mouse digit tips were harvested and trimmed to exclude all tissue proximal to the distal interphalangeal joint. Digits were flash frozen in a mortar immersed in liquid nitrogen, then pulverized with a pestle. Powderized samples were then transferred to a Dounce homogenizer with Trizol (Invitrogen, CA) for an additional stage of homogenization. RNA was extracted from the Trizol mixture according to the manufacturer’s instructions, followed by clean up with an RNA Clean & Concentrator Kit (Zymo Research, CA).
Generation of RNA libraries and sequencing was performed by Innomics Inc (San Jose, CA). RNA samples were first enriched for mRNA containing poly-A tails using oligo(dT) beads, followed by fragmentation. Fragmented mRNA molecules were reverse transcribed into first-strand cDNA using random primers. Second-strand cDNA was synthesized using dUTP instead of dTTP to facilitate strand-specific sequencing. The resulting cDNA was end-repaired and 3' adenylated, followed by the ligation of adaptors to the ends of the 3' adenylated cDNA fragments. PCR amplification was then performed to enrich the cDNA library, which underwent quality control assessments. Libraries were circularized and amplified to form DNA nanoballs (DNBs). DNBs were loaded onto the DNBSEQ-T7 sequencing platform according to the manufacturer's protocol. High-throughput sequencing was performed, generating paired-end reads of 150 bp in length. The raw sequencing reads were QCed and filtered with SOPAnuke(50) to remove low quality reads. Final sequencing quality was assessed using FastQC.

treatment_protocol: For induction of conditional knockouts, mice were administered 75 mg/kg body weight of tamoxifen (Apex Bio) diluted in corn oil (Millipore Sigma) by intraperitoneal injection daily for 5 consecutive days, followed by 5 days of rest before digit amputation. For all mouse procedures, mice were anesthetized with isofluorane and oxygen in an induction chamber. Digit amputations were performed with a #10 scalpel and stereomicroscope. For distal phalangeal (P3) amputations, the distal 2/3 of P3 was removed with a transverse amputation, ensuring at least half of the nail matrix remained. For middle phalangeal (P2) amputations, a transverse cut was made at the midpoint of P2. Mice were given 5-10 mg/kg body weight of meloxicam subcutaneously twice daily for 48 hours post-procedure. Digits were harvested by sacrifice of the animal and processing of the tissue as described in subsequent sections.

value: Digit tip

value: Wildtype

value: Digit tip amputation


title: 5xFAD, hypothalamus, fructose, rep1, batch 2019

description:
Library name: AD-F-1-19-Hyp
10x Genomics


title: BMDC E3 screen, Round 1, Ch6_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch6_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch7_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch7_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: ABE OT 5C Rep 3

description:
Library name: CHTTABEOT5_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 5C


title: Digit tip regenerates, 14 dpa, Mmu.Sp6+Sp8 cKO

description:
Library name: K68
BGI Americas

value: Mmu.Sp6+Sp8 cKO


title: 5xFAD, hypothalamus, fructose, rep2, batch 2019

description:
Library name: AD-F-2-19-Hyp
10x Genomics

value: hypothalamus


title: Digit tip regenerates, 14 dpa, Mmu.Sp6 cKO

description:
Library name: K6
BGI Americas

value: Mmu.Sp6 cKO


title: BMDC E3 screen, Round 1, Ch5_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch5_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: Blood cells


title: ABE OT 5C Rep 1

description:
Library name: CHTTABEOT5_1
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch5_hash

description:
Library name: BMDC E3 screen, Round 1, Ch5_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

value: BMDCs


title: BMDC E3 screen, Round 1, Ch6_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch6_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: 5xFAD, hypothalamus, DHA and fructose, rep3, batch 2019

description:
Library name: AD-DHAF-3-19-Hyp
10x Genomics

value: DHA and fructose


title: BMDC E3 screen, Round 1, Ch5_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch5_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: ABE OT 4C Rep 2

description:
Library name: CHTTABEOT4_2
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 4C


title: ABE OT 4C Rep 3

description:
Library name: CHTTABEOT4_3
Processed_GEO_Data_Sheet.xlsx

value: epitheleal


title: ABE OT 4C Rep 1

description:
Library name: CHTTABEOT4_1
Processed_GEO_Data_Sheet.xlsx

value: Lipofectamine 2000 transfected


title: 5xFAD, hypothalamus, DHA and fructose, rep2, batch 2019

description:
Library name: AD-DHAF-2-19-Hyp
10x Genomics


title: ABE OT 5C Rep 2

description:
Library name: CHTTABEOT5_2
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch4_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch4_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch4_hash

description:
Library name: BMDC E3 screen, Round 1, Ch4_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

value: HTO

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3, TotalSeq-A0304 anti-mouse Hashtag 4, TotalSeq-A0305 anti-mouse Hashtag 5, TotalSeq-A0306 anti-mouse Hashtag 6, TotalSeq-A0307 anti-mouse Hashtag 7, TotalSeq-A0308 anti-mouse Hashtag 8


title: 5xFAD, hypothalamus, DHA and fructose, rep1, batch 2019

description:
Library name: AD-DHAF-1-19-Hyp
10x Genomics


title: Digit tip regenerates, 14 dpa, Mmu.Sp8 cKO

description:
Library name: K8
BGI Americas

value: Mmu.Sp8 cKO


title: 5xFAD, hypothalamus, rep1, batch 2020

description:
Library name: AD-1-20-Hyp
10x Genomics


title: 5xFAD, hypothalamus, rep3, batch 2020

description:
Library name: AD-3-20-Hyp
10x Genomics


title: BMDC E3 screen, Round 1, Ch4_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch4_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: GDO


title: BM Ldlr-/-Jak2V617FBM + Exercise

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description:
Library name: BMEX
BM_filtered_feature_bc_matrix.h5
BM_feature_reference.csv
BM_aggr_input.csv

data_processing:
Processed with Cell Ranger 5.0.1 and then aggregated with Cell Ranger 8.0.0 with normalization off
Assembly: mm10
Supplementary files format and content: Cell Ranger filtered gene and antibody expression per cell in h5 format
Supplementary files format and content: Gene and Antibody descriptions
Supplementary files format and content: Cell Ranger aggregate sample order

source_name: BM Progenitors

extract_protocol:
See publication for exact protocols
Single Cell 5' R2-only v3

value: BM Progenitors

value: Exercise


title: 5xFAD, hypothalamus, rep2, batch 2020

description:
Library name: AD-2-20-Hyp
10x Genomics


title: liver replicate 2

city: Rehovot

first: Roy

last: Novoselsky

address: Herzl 234

department: Molecular cell biology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: liver_rep2
FFPE samples stained with Atp1a1,Cd31,autofluorescence,DAPI. The FASTQ files correspond to the full capture areas A1, D1, while the processed data includes only the barcodes analyzed in the study.

data_processing:
Space Ranger (v3.1.2, 10x Genomics) for allignment of image to spatial data, and for UMI counting.
Samples were cropped to areas containing the ROI of the experiment using HiVis v1.0.2
Assembly: mm10
Supplementary files format and content: HiVis.h5ad - AnnData object with 2x2um spatial bins
Supplementary files format and content: fullres.tif - full-resolution histology image alligned to the h5ad
Supplementary files format and content: highres.tif - high-resolution histology image alligned to the h5ad
Supplementary files format and content: lowres.tif - low-resolution histology image alligned to the h5ad
Supplementary files format and content: scalefactors_json.json - spatial scaling factors for mapping coordinates to images
Supplementary files format and content: tissue_positions.csv - spatial coordinates of 2x2um bins
Supplementary files format and content: single_cells.h5ad - single-cell level AnnData object (gene expression per segmented cell)
Supplementary files format and content: hepatocytes.h5ad - single-cell level AnnData subset (gene expression per segmented hepatocyte)
Supplementary files format and content: cells_masks.geojson - single-cell segmentation masks (polygon boundaries per cell)
Library strategy: Spatial Transcriptomics

source_name: liver

extract_protocol:
According to 10x Genomics VisiumHD fluorescence protocol
According to 10x Genomics protocol

value: liver


title: ABE OT 3C Rep 3

description:
Library name: CHTTABEOT3_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 3C


title: liver replicate 1

description:
Library name: liver_rep1
FFPE samples stained with Atp1a1,Cd31,autofluorescence,DAPI. The FASTQ files correspond to the full capture areas A1, D1, while the processed data includes only the barcodes analyzed in the study.


title: BM Ldlr-/-Jak2V617FBM + SF

description:
Library name: BMSF
BM_filtered_feature_bc_matrix.h5
BM_feature_reference.csv
BM_aggr_input.csv

value: SF


title: 5xFAD, hypothalamus, NR, rep3, batch 2020

description:
Library name: AD-NR-3-20-Hyp
10x Genomics

value: hypothalamus

value: NR


title: AC014

first: Carly

last: Tymm

state: New York

institute: Columbia University Medical Center

description: Library name: AC014

data_processing:
Raw sequencing data for  5′ mRNA and TCR libraries were processed using 10X Genomics Cell Ranger to generate gene expression matrices and per-cell TCR annotations.
Assembly: mm10
Supplementary files format and content: 10X Single Cell:   For each single-cell sample,  standard 10X Genomics output files: barcodes.tsv (cell barcodes), features.tsv (gene annotations), and matrix.mtx (sparse gene × cell count matrix), filtered_contig_annotations.csv (per-cell TCR contigs), and clonotypes.csv (TCR clonotype assignments).                                                                                SeuratHeartICIscRNA_AllLeukocytes.rds: A combined Seurat object containing all extravascular leukocytes from the heart treated with ICI, used for global analyses of cardiac leukocyte populations. SeuratHeartICIscRNA_TCellswithTCR.rds: A subset Seurat object containing only T cell clusters from the extravascular leukocytes of ICI-treated mice, including linked TCR data, used for T cell–specific analyses such as clonal expansion and clonotype mapping.

source_name: Heart

growth_protocol: 8–12-week-old AJ mice were housed under IACUC-approved standard conditions with ad libitum access to food and water

extract_protocol:
Extravascular and intravascular leukocytes from heart tissue were isolated via flow sorting following heart digestion by Liberase TM.
Single-cell RNA-seq and TCR libraries were generated using the 10X Genomics Chromium OCM platform with 5′ mRNA and TCR sequencing according to the manufacturer’s protocol. OCM samples were multiplexed and sequenced across two lanes for both gene expression (GEX) and TCR libraries. FASTQ files are lane-specific and contain pooled reads from multiple samples. Sample identity was determined using Illumina index reads and 10x Genomics cell barcodes, and FASTQ files from both lanes corresponding to each OCM sample were combined for downstream analysis with Cell Ranger with outputs per sample

treatment_protocol: ICI treatment: biweekly 400 µg aPD1 + 400 µg aCTLA4 for 2 weeks, endpoint 3 days after last injection.

value: Heart

value: Leukocytes

value: A/J

value: ICI


title: ABE OT 3C Rep 2

description:
Library name: CHTTABEOT3_2
Processed_GEO_Data_Sheet.xlsx

value: epitheleal


title: BM Ldlr-/-Jak2V617FBM

description:
Library name: BMSED
BM_filtered_feature_bc_matrix.h5
BM_feature_reference.csv
BM_aggr_input.csv

value: Sedentary


title: BMDC E3 screen, Round 1, Ch3_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch3_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad

value: Blood cells

value: BMDCs

value: mRNA


title: ABE OT 3C Rep 1

description:
Library name: CHTTABEOT3_1
Processed_GEO_Data_Sheet.xlsx

value: Lipofectamine 2000 transfected


title: Aorta Ldlr-/-Jak2V617FBM + Exercise

description:
Library name: EXCD45
AORTA_filtered_feature_bc_matrix.h5
AORTA_feature_reference.csv
AORTA_aggr_input.csv

source_name: Aorta CD45 cells

value: Aorta CD45 cells


title: BMDC E3 screen, Round 1, Ch3_hash

description:
Library name: BMDC E3 screen, Round 1, Ch3_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

value: HTO

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3, TotalSeq-A0304 anti-mouse Hashtag 4, TotalSeq-A0305 anti-mouse Hashtag 5, TotalSeq-A0306 anti-mouse Hashtag 6, TotalSeq-A0307 anti-mouse Hashtag 7, TotalSeq-A0308 anti-mouse Hashtag 8


title: ABE OT 23C Rep 2

description:
Library name: CHTTABEOT23_2
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 23C


title: BMDC E3 screen, Round 1, Ch2_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch2_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: BM Ldlr-/-WTBM

description:
Library name: BMCTL
BM_filtered_feature_bc_matrix.h5
BM_feature_reference.csv
BM_aggr_input.csv

value: BM Progenitors

value: Ldlr-/-WTBM


title: BMDC E3 screen, Round 1, Ch3_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch3_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: GDO


title: ABE OT 23C Rep 3

description:
Library name: CHTTABEOT23_3
Processed_GEO_Data_Sheet.xlsx


title: 5xFAD, hypothalamus, NR, rep2, batch 2020

description:
Library name: AD-NR-2-20-Hyp
10x Genomics

value: hypothalamus

value: NR


title: 5xFAD, hypothalamus, DHA, rep3, batch 2020

description:
Library name: AD-DHA-3-20-Hyp
10x Genomics

value: DHA


title: 5xFAD, hypothalamus, NR, rep1, batch 2020

description:
Library name: AD-NR-1-20-Hyp
10x Genomics


title: 5xFAD, hypothalamus, DHA, rep2, batch 2020

description:
Library name: AD-DHA-2-20-Hyp
10x Genomics


title: 5xFAD, hypothalamus, DHA, rep1, batch 2020

description:
Library name: AD-DHA-1-20-Hyp
10x Genomics


title: ABE OT 23C Rep 1

description:
Library name: CHTTABEOT23_1
Processed_GEO_Data_Sheet.xlsx


title: Aorta Ldlr-/-Jak2V617FBM + SF

description:
Library name: SFCD45
AORTA_filtered_feature_bc_matrix.h5
AORTA_feature_reference.csv
AORTA_aggr_input.csv

value: SF


title: BMDC E3 screen, Round 1, Ch2_hash

description:
Library name: BMDC E3 screen, Round 1, Ch2_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch2_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch2_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad


title: BMDC E3 screen, Round 1, Ch1_mRNA

description:
Library name: BMDC E3 screen, Round 1, Ch1_mRNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
BMDC_E3_screen_raw.h5ad


title: ABE OT 22C Rep 1

description:
Library name: CHTTABEOT22_1
Processed_GEO_Data_Sheet.xlsx

value: epitheleal

value: ABE OT 22C


title: Wild-type, hippocampus, rep3, batch 2019

description:
Library name: WT-3-19-Hip
10x Genomics

source_name: hippocampus

value: hippocampus

value: Wild-type


title: BMDC E3 screen, Round 1, Ch1_hash

description:
Library name: BMDC E3 screen, Round 1, Ch1_hash
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag
BMDC_E3_screen_raw.h5ad

value: Blood cells

value: BMDCs


title: Basal epidermal cells, 3 dpa

description:
Library name: Krt19_3dpa
10x Genomics

data_processing:
Libraries were sequenced with either the NextSeq 500 (Duke Center for Genomic and Computational Biology, NC) or DNBseq (BGI Americas Corporation, MA). CellRanger (v 7.0.0) was used to process raw sequencing data before subsequent analyses with danRer11 reference data. CellBender (v 0.3.0) was used to create the filtered count matrix with parameter '--total-droplets-included 10000 --fpr 0.05 --epochs 150' and expected cells 5000 for injured, 2 dpa, 3 dpa, 6000 for 1dpa and 4000 for uninjured samples. The Seurat objects for downstream analysis and visualizations were created from the output files of the pipeline by collecting the filtered count matrix, clusters and UMAP reductions. The doublets were removed by package DoubletFinder (v 2.0.6) and filtered by 'nFeature_RNA > 200 & nFeature_RNA < 4000 & percent.mt < 25'. Combined data were integrated by the anchors from top 20 PCAs (principal components).  The batch effects were removed by harmony package (v 1.2.3). The top 18 PCAs were used to define the cluster with resolution 0.3. The top 12 PCAs were used to re-cluster the Basal Epidermal Keratinocytes. Differential gene expression analysis was conducted by Seurat (v 5.3.0) “FindMarkers” function using “Wilcoxon rank-sum test” as the test method.  RNA velocity were analyzed by velocyto (v 0.17.17). The continuous gene expression topologies were visualized by SPRING-dev (commit efe6ab4). The distribution of pseudotime by samples were performed by URD R package(v 1.1.1).
Assembly: danRer11
Supplementary files format and content: filtered count matrix saved in hdf5

molecule: nuclear RNA

organism: Danio rerio

source_name: Caudal fin

extract_protocol:
Dissociated cells from zebrafish caudal fin were prepared by the method of Thompson et al. 2020(47). Regenerating caudal fin samples were collected at time points ranging from 1 to 4 dpa via excision of the distal most 2 mm with a razor blade. For uninjured controls (0 dpa), a 2 mm section of mid caudal fin was excised that corresponded to the sampled area in injured fish. Cells were dissociated with 1.18 U/ml Liberase DH (Roche) in Hank's Balanced Salt Solution (Gibco) with stirring at 37 °C for 2 h, collected in 15 min increments, then strained through a 40 μm nylon cell strainer (Corning). Cell suspensions were stained with SYTOX Blue (Invitrogen) and sorted for exclusion of the dye via FACS (Astrios Cell Sorter via Duke Cancer Institute Flow Cytometry Core Facility). In experiments examining basal epidermal cell populations, cells were further sorted by endogenous red fluorescence of the krt1‑19e:h2az2a‑mCherry transgene and exclusion of green fluorescence from the krt4:LY‑EGFP transgene, which mark basal epidermal and superficial epidermal populations, respectively. FACS-sorted suspensions were then resuspended in PBS with 400 μg/mL non-acetylated bovine serum albumin (Sigma). An aliquot of the suspension was counted by hemacytometer and checked for viability with 0.4% trypan blue (Sigma), which ranged from 60-98% between samples.
Cells were encapsulated in gel bead emulsions and barcoded using the Chromium Controller (10x Genomics) with target yields of 6,000-10,000 cells. Preparation of cDNA and Illumina sequencing libraries was carried out according to the Chromium Single Cell 3’ Reagents Kit v.2 (10x Genomics).

treatment_protocol: Caudal fin amputations were performed with a transverse amputation approximately 2/3 of the distance from the distal fin surface to the caudal peduncle, using razor blades. Fish were anesthetized for all procedures in 0.75% v/v 2-phenoxyethanol (Sigma-Aldrich) in fish water. At specified time points, 2 mm of the distal most tissue was collected from the fin regenerate for analysis. Because of our study focus on the RE, uninjured samples were collected from the distal most 2 mm of uninjured fin containing the terminal edge of the epithelium, as opposed to the uninjured fin regions corresponding to each time point of regeneration. All work with zebrafish was performed in accordance with Duke University IACUC guidelines.

value: Caudal fin

value: Basal epidermal cells

value: krt1-19e:h2az2a-mCherry, krt4:LY-EGFP


title: Aorta Ldlr-/-Jak2V617FBM

description:
Library name: SEDCD45
AORTA_filtered_feature_bc_matrix.h5
AORTA_feature_reference.csv
AORTA_aggr_input.csv

value: Aorta CD45 cells

value: Sedentary


title: ABE OT 21C Rep 3

description:
Library name: CHTTABEOT21_3
Processed_GEO_Data_Sheet.xlsx

value: Lipofectamine 2000 transfected

value: ABE OT 21C


title: ABE OT 22C Rep 3

description:
Library name: CHTTABEOT22_3
Processed_GEO_Data_Sheet.xlsx


title: Aorta Ldlr-/-WTBM

description:
Library name: CONCD45
AORTA_filtered_feature_bc_matrix.h5
AORTA_feature_reference.csv
AORTA_aggr_input.csv

value: Ldlr-/-WTBM


title: ABE OT 22C Rep 2

description:
Library name: CHTTABEOT22_2
Processed_GEO_Data_Sheet.xlsx


title: BMDC E3 screen, Round 1, Ch1_FeatBarc

description:
Library name: BMDC E3 screen, Round 1, Ch1_FeatBarc
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Oligo reads
BMDC_E3_screen_raw.h5ad

value: GDO


title: 5xFAD, hippocampus, rep3, batch 2019

description:
Library name: AD-6-19-Hip
10x Genomics


title: Wild-type, hippocampus, rep2, batch 2019

description:
Library name: WT-2-19-Hip
10x Genomics


title: Basal epidermal cells, 1 dpa

description:
Library name: Krt19_1dpa
10x Genomics


title: ABE OT 21C Rep 2

description:
Library name: CHTTABEOT21_2
Processed_GEO_Data_Sheet.xlsx


title: Basal epidermal cells, 2 dpa

description:
Library name: Krt19_2dpa
10x Genomics


title: Wild-type, hippocampus, rep1, batch 2019

description:
Library name: WT-1-19-Hip
10x Genomics


title: 5xFAD, hippocampus, rep2, batch 2019

description:
Library name: AD-5-19-Hip
10x Genomics


title: long-read RNAseq from IOSE397 cells

city: Brisbane

first: Juliet

last: French

address: 300 Herston Rd

country: Australia

institute: QIMRB

description:
Library name: long-read_IOSE397
long-read_IOSE397

data_processing:
Raw long-read RNAseq slow5 files were base-called using Guppy v.6.4.6+ae70e8f and MinKNOW v.22.12.5. Raw FASTQ RNAseq files were processed using the HyDRA pipeline up to correction and trimming of both short and long reads. Briefly, data were checked for quality (FastQC v0.12.1, MultiQC v1.14, NanoPlot/NanoComp v1.41.6 and Fasta_splitter.py v1.0.6); short-reads were trimmed of adapters (Trimmomatics v0.36) and corrected using Rcorrector v1 and FilterUncorrectablePEfastq.py v2016; long-read were first corrected using RopeBWT2 vr187 and FMLRC2 v0.1.7 and then trimmed of adapters (Porechop v0.2.4, Chopper v0.5.0 and Cutadapt v3.9.13). TPM counts from short-reads were obtained by aligning them to GENCODEv36 + HyDRA ovarian metatranscriptome lncRNAs (STAR v2.7.1a, SAMtools v1.3, NovoSort v3.05.01) and quantifying the reads (RSEM v1.2.30). TPM counts from long-reads were obtained from aligning them to GENCODEv36 + HyDRA ovarian metatranscriptome lncRNAs (Minimap2 v2.26) and quantifying the reads (Salmon v1.3.0). All TPM counts were merged into the same file.
Assembly: GRCh38 v36
Supplementary files format and content: tpm_counts.tsv

molecule: polyA RNA

source_name: Ovary

growth_protocol: Thaw and culture of primary and immortalized FTSECs and OSECs was conducted in specific growth media to each cell line. Cell lines were maintained under standard conditions (37C, 5% CO2)

extract_protocol:
RNA was extracted using QIAGEN RNeasy Plus Mini kit
Short-read library: One microgram of total RNA was rRNA depleted with the Ribo-Zero™ Plus kit according to the manufacturers’ instructions (Illumina). Short-read RNAseq libraries were prepared using the Truseq Stranded mRNA Library Prep Kit (Illumina). Long-read library: cDNA libraries were generated with polyadenylation enrichment and SQK-NBD114.24 native barcoding kit.

value: Ovary

value: Immortalized ovarian surface epithelial cells

value: polyadenylation enrichment

value: Oxford Nanopore PromethION P48


title: ABE OT 21C Rep 1

description:
Library name: CHTTABEOT21_1
Processed_GEO_Data_Sheet.xlsx

value: epitheleal


title: long-read RNAseq from FT194 cells

description:
Library name: long-read_FT194
long-read_FT194

source_name: Fallopian tube

value: Fallopian tube

value: Immortalized fallopian tube secretory epithelial cells


title: 5xFAD, hippocampus, rep1, batch 2019

description:
Library name: AD-3-19-Hip
10x Genomics

value: hippocampus


title: ABE OT 20C Rep 3

description:
Library name: CHTTABEOT20_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 20C


title: ABE OT 20C Rep 1

description:
Library name: CHTTABEOT20_1
Processed_GEO_Data_Sheet.xlsx


title: Unlabeled

city: Irvine

first: Annie

last: Trinh

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: Library name: Unlabeled

data_processing:
For BrdU-labeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114) and unlabeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M), basecalling and alignment to the hg19 human reference genome were performed using Dorado v0.6.2. Chimeric reads were removed using samtools v1.15.1. To identify BrdU-containing reads, DNAscent v4.1.1 was used to detect the nucleoside analog within individual reads. CpG methylation and hydroxymethylation were called using Dorado v0.6.2. Nanoplot v1.41.6 was used to assess and visualize read-level statistics such as the number of reads, read length N50, mean and median read length, and mean and median read quality.
Assembly: GRCh37 (hg19)
Supplementary files format and content: Processed data are available in bedMethyl files (.bed) and read-level calls (.tsv).

growth_protocol: HUES64 and HUES8 TKO hESCs were cultured on Geltrex (Thermo Fisher Scientific, A1413302) coated tissue culture plates with mTeSR (STEMCELL Technologies) media. Cells were incubated at 37°C with 5% CO2. Media was changed daily and cells were passaged upon reaching 80% confluency using ReleSR (STEMCELL Technologies). H9 hESCs (WiCell) were cultured on tissue culture plates coated with Cultrex Reduced Growth Factor Basement Membrane Extract (R&D Systems, 343301001) in StemFlex medium (Thermo Fisher Scientific, A3349401). Cells were maintained at 37°C with 5% CO2. Medium was changed daily or every other day, and cells were passaged at ~80% confluency using Accutase (Innovative Cell Technologies, AT104). Following passaging, 2µM Thiazovivin (Selleck Chemicals LLC, S1049) was added for 24 h only. MDA-MB-231 breast cancer cells were maintained in DMEM (Gibco) media supplemented with 10% Fetal Bovine Serum (FBS, Seradigm). Cells were incubated at 37°C with 5% CO2. Media was changed every other day and cells were passaged upon reaching 80% confluency using  TrypLE (Gibco).

extract_protocol:
Genomic DNA was isolated using the Puregene Cell Kit (Qiagen, 158043) according to the manufacturer’s instructions.
For samples labeled with 500 µM BrdU and samples not labeled with BrdU, libraries were prepared using a Ligation Sequencing Kit (Oxford Nanopore Technologies, SQK-LSK114) according to the manufacturer’s instructions. Libraries generated from labeled samples were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114) and sequenced using a MinION Mk1b device. Libraries for samples labeled with BrdU and samples not labeled with BrdU were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M) and sequenced on a PromethION P2 solo device (Oxford Nanopore Technologies) for 72 hours. Minimum read length was set to 1000 bp. All sequencing data was collected using MinKNOW v23.07.5.

treatment_protocol: For the nocodazole experiment, hESCs were arrested with 1 µg/ml nocodazole for 16h, stained with the Live/Dead Fixable Violet Dead Cell Stain Kit (Invitrogen, L34964), fixed in  75% ethanol, counterstained with Propidium Iodide (Invitrogen, P3566), and live G2/M cells were isolated by FACS before genomic DNA extraction. For the BrdU pulse-chase experiments, BrdU pulses are conducted by adding BrdU to the culture medium at the desired final concentration and incubating for the specified durations (10 minutes, 30 minutes, or 1 hour). Cells are then either collected immediately (0h chase) or washed three times with DPBS and incubated in fresh mTeSR medium for 16 hours (16h chase). For mock treatments, BrdU is replaced with an equivalent volume of Ultrapure H2O. Cells subjected to mock treatments undergo the same incubation times as their BrdU-treated counterparts, with samples collected at 0h or following a 16h incubation.

value: human embryonic stem cells

value: WT

value: Unlabeled (no BrdU)


title: p53/Brca1-null luminal mammary epithelial cells replicate #3

type: RNA

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: Gene expression data for YFP+ p53/Brca1-null mammary epithelial cells sorted from p53L/L;Brca1L/L;Rosa26-Stop-YFP female mouse #3, 10-14 days after intraductal injection of Ad-K8-Cre

hyb_protocol: The biotinylated cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C

scan_protocol: Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured

data_processing: The raw CEL files were imported and processed with genepattern AffySTExpressionFileCreator tool from Broad institiute

label: biotin

label_protocol: Labeling, hybridization and scan were performed by the Dana-Farber Cancer Institute Molecular Biology Core Facility. The NuGEN Ovation V2 Amplification System was used to amplify and label the samples, according to manufacturer's protocol.

growth_protocol: Female mice of the indicated genotypes at around 2 months of age were used.

extract_protocol: RNeasy kit (Qiagen, #73504) was used on sorted mammary epithelial cells according to manufacturer's protocol.

treatment_protocol: YFP-marked mammary epithelial cells were sorted from female mice of the indicated genotypes 10-14 days after intraductal injection of Ad-K8-Cre.

value: mammary epithelial cells

tag: group

value: YFP+ p53/Brca1-null mammary epithelial cells sorted from Ad-K8-Cre-injected p53L/L;Brca1L/L;Rosa26-Stop-YFP female mouse 3


title: 5xFAD, hippocampus, NR and fructose, rep3, batch 2019

description:
Library name: AD-NRF-3-19-Hip
10x Genomics

value: NR and fructose


title: ABE OT 1C Rep 3

description:
Library name: CHTTABEOT1_3
Processed_GEO_Data_Sheet.xlsx

value: Lipofectamine 2000 transfected

value: ABE OT 1C


title: p53/Brca1-null luminal mammary epithelial cells replicate #2

description: Gene expression data for YFP+ p53/Brca1-null mammary epithelial cells sorted from p53L/L;Brca1L/L;Rosa26-Stop-YFP female mouse #2, 10-14 days after intraductal injection of Ad-K8-Cre

value: YFP+ p53/Brca1-null mammary epithelial cells sorted from Ad-K8-Cre-injected p53L/L;Brca1L/L;Rosa26-Stop-YFP female mouse 2


title: RNA-seq of motor cortex, Day 30, Female, sample F_S1_MC

city: West Lafayette

first: Chongli

last: Yuan

state: Indiana

address: 480 Stadium Mall Drive

institute: Purdue University

description: Library name: F-S1-MC

data_processing:
Differential expression analysis was performed at the Medical Genomics Core at Indiana University.
Briefly, all data were mapped and annotated with hisat2 and DAVID.
Differentially expressed genes (DEGs) were determined using EdgeR
Assembly: USSC rn6
Supplementary files format and content: No processed data files included

organism: Rattus norvegicus

source_name: motor cortex

extract_protocol:
Total RNA was extracted using a PureLink RNA Mini Kit (ThermoFisher, 12183018A) following the manufacturer's protocol
The library was constructed by Novogene LLC.

value: motor cortex


title: ABE OT 1C Rep 2

description:
Library name: CHTTABEOT1_2
Processed_GEO_Data_Sheet.xlsx


title: RNA-seq of motor cortex, Day 30, Female, sample F_ln3_MC

description: Library name: F-In3-MC


title: 5xFAD, hippocampus, fructose, rep3, batch 2019

description:
Library name: AD-F-3-19-Hip
10x Genomics

value: fructose


title: 5xFAD, hippocampus, NR and fructose, rep2, batch 2019

description:
Library name: AD-NRF-2-19-Hip
10x Genomics


title: RNA-seq of motor cortex, Day 30, Female, sample F_S2_MC

description: Library name: F-S2-MC


title: ABE OT 1C Rep 1

description:
Library name: CHTTABEOT1_1
Processed_GEO_Data_Sheet.xlsx


title: RNA-seq of motor cortex, Day 30, Female, sample F_ln2_MC

description: Library name: F-In2-MC


title: 5xFAD, hippocampus, fructose, rep2, batch 2019

description:
Library name: AD-F-2-19-Hip
10x Genomics


title: 5xFAD, hippocampus, NR and fructose, rep1, batch 2019

description:
Library name: AD-NRF-1-19-Hip
10x Genomics


title: p53-null luminal mammary epithelial cells replicate #3

description: Gene expression data for YFP+ p53-null mammary epithelial cells sorted from p53L/L;Rosa26-Stop-YFP female mouse #3, 10-14 days after intraductal injection of Ad-K8-Cre

value: YFP+ p53-null mammary epithelial cells sorted from Ad-K8-Cre-injected p53L/L;Rosa26-Stop-YFP female mouse 3


title: p53-null luminal mammary epithelial cells replicate #1

description: Gene expression data for YFP+ p53-null mammary epithelial cells sorted from p53L/L;Rosa26-Stop-YFP female mouse #1, 10-14 days after intraductal injection of Ad-K8-Cre

value: YFP+ p53-null mammary epithelial cells sorted from Ad-K8-Cre-injected p53L/L;Rosa26-Stop-YFP female mouse 1


title: RNA-seq of motor cortex, Day 30, Female, sample F_ln1_MC

description: Library name: F-In1-MC


title: p53/Brca1-null luminal mammary epithelial cells replicate #1

description: Gene expression data for YFP+ p53/Brca1-null mammary epithelial cells sorted from p53L/L;Brca1L/L;Rosa26-Stop-YFP female mouse #1, 10-14 days after intraductal injection of Ad-K8-Cre

value: YFP+ p53/Brca1-null mammary epithelial cells sorted from Ad-K8-Cre-injected p53L/L;Brca1L/L;Rosa26-Stop-YFP female mouse 1


title: 5xFAD, hippocampus, fructose, rep1, batch 2019

description:
Library name: AD-F-1-19-Hip
10x Genomics


title: ABE OT 19C Rep 2

description:
Library name: CHTTABEOT19_2
Processed_GEO_Data_Sheet.xlsx

value: epitheleal

value: ABE OT 19C


title: RNA-seq of motor cortex, Day 30, Female, sample F_S3_MC

description: Library name: F-S3-MC


title: KASH_ABE_Rosa_RH2

description:
Library name: KASH_ABE_Rosa_RH2
Processed_GEO_Data_Sheet.xlsx

source_name: striatum

value: striatum

value: neuron

value: AAV9 injection with GFP-KASH


title: 5xFAD, hippocampus, DHA and fructose, rep3, batch 2019

description:
Library name: AD-DHAF-3-19-Hip
10x Genomics

value: hippocampus

value: DHA and fructose


title: 5xFAD, hippocampus, DHA and fructose, rep2, batch 2019

description:
Library name: AD-DHAF-2-19-Hip
10x Genomics


title: ABE OT 19C Rep 3

description:
Library name: CHTTABEOT19_3
Processed_GEO_Data_Sheet.xlsx


title: ABE OT 18C Rep 3

description:
Library name: CHTTABEOT18_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 18C


title: ABE OT 19C Rep 1

description:
Library name: CHTTABEOT19_1
Processed_GEO_Data_Sheet.xlsx


title: p53-null luminal mammary epithelial cells replicate #2

description: Gene expression data for YFP+ p53-null mammary epithelial cells sorted from p53L/L;Rosa26-Stop-YFP female mouse #2, 10-14 days after intraductal injection of Ad-K8-Cre

value: mammary epithelial cells

value: YFP+ p53-null mammary epithelial cells sorted from Ad-K8-Cre-injected p53L/L;Rosa26-Stop-YFP female mouse 2


title: KASH_ABE_Rosa_RH1

description:
Library name: KASH_ABE_Rosa_RH1
Processed_GEO_Data_Sheet.xlsx


title: RNA-seq of motor cortex, Day 7, Male, sample Sham-3-MC

description: Library name: Sham-3-MC_2


title: RNA-seq of motor cortex, Day 7, Male, sample Sham-1-MC-RNA

description: Library name: Sham-1-MC-RNA_3


title: p53/Runx1-null luminal mammary epithelial cells replicate #1

description: Gene expression data for YFP+ p53/Runx1-null mammary epithelial cells sorted from p53L/L;Runx1L/L;Rosa26-Stop-YFP female mouse #1, 10-14 days after intraductal injection of Ad-K8-Cre

value: YFP+ p53/Runx1-null mammary epithelial cells sorted from Ad-K8-Cre-injected p53L/L;Runx1L/L;Rosa26-Stop-YFP female mouse 1


title: 5xFAD, hippocampus, DHA and fructose, rep1, batch 2019

description:
Library name: AD-DHAF-1-19-Hip
10x Genomics


title: 5xFAD, hippocampus, rep3, batch 2020

description:
Library name: AD-3-20-Hip
10x Genomics


title: p53/Runx1-null luminal mammary epithelial cells replicate #2

description: Gene expression data for YFP+ p53/Runx1-null mammary epithelial cells sorted from p53L/L;Runx1L/L;Rosa26-Stop-YFP female mouse #2, 10-14 days after intraductal injection of Ad-K8-Cre

value: YFP+ p53/Runx1-null mammary epithelial cells sorted from Ad-K8-Cre-injected p53L/L;Runx1L/L;Rosa26-Stop-YFP female mouse 2


title: KASH_ABE_Rosa_LH2

description:
Library name: KASH_ABE_Rosa_LH2
Processed_GEO_Data_Sheet.xlsx


title: p53/Runx1-null luminal mammary epithelial cells replicate #3

description: Gene expression data for YFP+ p53/Runx1-null mammary epithelial cells sorted from p53L/L;Runx1L/L;Rosa26-Stop-YFP female mouse #3, 10-14 days after intraductal injection of Ad-K8-Cre

value: YFP+ p53/Runx1-null mammary epithelial cells sorted from Ad-K8-Cre-injected p53L/L;Runx1L/L;Rosa26-Stop-YFP female mouse 3


title: RNA-seq of motor cortex, Day 7, Male, sample Sham-1-MC

description: Library name: Sham-1-MC_1

value: motor cortex


title: ABE OT 17C Rep 3

description:
Library name: CHTTABEOT17_3
Processed_GEO_Data_Sheet.xlsx

value: Lipofectamine 2000 transfected

value: ABE OT 17C


title: ABE OT 18C Rep 1

description:
Library name: CHTTABEOT18_1
Processed_GEO_Data_Sheet.xlsx


title: RNA-seq of motor cortex, Day 7, Male, sample 7-inj-4-MC

description: Library name: 7-inj-4-MC_6


title: ABE OT 17C Rep 2

description:
Library name: CHTTABEOT17_2
Processed_GEO_Data_Sheet.xlsx


title: RNA-seq of motor cortex, Day 7, Male, sample 7-inj-2-MC

description: Library name: 7-inj-2-MC_4


title: KASH_ABE_Rosa_LH1

description:
Library name: KASH_ABE_Rosa_LH1
Processed_GEO_Data_Sheet.xlsx


title: ABE OT 17C Rep 1

description:
Library name: CHTTABEOT17_1
Processed_GEO_Data_Sheet.xlsx


title: ABE OT 18C Rep 2

description:
Library name: CHTTABEOT18_2
Processed_GEO_Data_Sheet.xlsx


title: KASH_ABE_HTT_RH2

description:
Library name: KASH_ABE_HTT_RH2
Processed_GEO_Data_Sheet.xlsx


title: KASH_ABE_HTT_LH2

description:
Library name: KASH_ABE_HTT_LH2
Processed_GEO_Data_Sheet.xlsx


title: RNA-seq of motor cortex, Day 7, Male, sample 7-inj-3-MC

description: Library name: 7-inj-3-MC_5


title: 5xFAD, hippocampus, rep2, batch 2020

description:
Library name: AD-2-20-Hip
10x Genomics


title: 5xFAD, hippocampus, rep1, batch 2020

description:
Library name: AD-1-20-Hip
10x Genomics


title: KASH_ABE_HTT_RH1

description:
Library name: KASH_ABE_HTT_RH1
Processed_GEO_Data_Sheet.xlsx


title: RNA-seq of motor cortex, Day 30, Male, sample S4

description: Library name: S4-MC


title: 5xFAD, hippocampus, NR, rep3, batch 2020

description:
Library name: AD-NR-3-20-Hip
10x Genomics

value: NR


title: KASH_ABE_HTT_LH1

description:
Library name: KASH_ABE_HTT_LH1
Processed_GEO_Data_Sheet.xlsx


title: ABE OT 16C Rep 3

description:
Library name: CHTTABEOT16_3
Processed_GEO_Data_Sheet.xlsx

value: epitheleal

value: ABE OT 16C


title: 5xFAD, hippocampus, NR, rep1, batch 2020

description:
Library name: AD-NR-1-20-Hip
10x Genomics


title: ABE OT 16C Rep 2

description:
Library name: CHTTABEOT16_2
Processed_GEO_Data_Sheet.xlsx


title: 5xFAD, hippocampus, NR, rep2, batch 2020

description:
Library name: AD-NR-2-20-Hip
10x Genomics


title: Basal epidermal cells, 4 dpa

description:
Library name: Krt19_4dpa
10x Genomics

value: Caudal fin

value: Basal epidermal cells

value: krt1-19e:h2az2a-mCherry, krt4:LY-EGFP


title: ABE OT 16C Rep 1

description:
Library name: CHTTABEOT16_1
Processed_GEO_Data_Sheet.xlsx


title: 5xFAD, hippocampus, DHA, rep2, batch 2020

description:
Library name: AD-DHA-2-20-Hip
10x Genomics

value: hippocampus

value: DHA


title: RNA-seq of motor cortex, Day 30, Male, sample S1

description: Library name: S1-MC


title: Basal epidermal cells, uninjured

description:
Library name: uninjured
10x Genomics


title: RNA-seq of motor cortex, Day 30, Male, sample S2

description: Library name: S2-MC


title: RNA-seq of motor cortex, Day 30, Male, sample Ln3

description: Library name: In3-MC


title: 5xFAD, hippocampus, DHA, rep1, batch 2020

description:
Library name: AD-DHA-1-20-Hip
10x Genomics


title: mandibular periosteal progenitors, M_3d_3

city: Shanghai

first: Jiahui

last: Du

address: Zhizaoju Road 639

country: China

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were trimmed using Cutadapt.
Trimmed reads were aligned with the GRCm39 genome using HISAT2
Read count extraction and normalization were performed using htseq-count.
Assembly: Mus_musculus.GRCm39.
Supplementary files format and content: Excel files include read count and fpkm values for each sample

source_name: mandibular periosteal progenitors

growth_protocol: mandibular periosteal progenitors were harvested from murine mandible of Plagl1 fl/fl mice and CTSK-iCre;Plagl1 fl/fl mice cultured in α-minimum essential medium containing 10% FBS and 1% penicillin-streptomycin overnight.

extract_protocol:
Periosteal progenitors was collected for RNA isolation using TRIzol.
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: For osteoblast induction, periosteal progenitors were cultured into complete media with  b-glycerophosphate (b-GP) (Sigma G9422, 5 mM), ascorbic acid (Sigma A4403, 50 ug/ml), and dexamethasone (Sigma D4902, 100 nM) .  OR control (without b-glycerophosphate (b-GP) (5 mM), ascorbic acid (50 ug/ml), and dexamethasone (100 nM)).

value: mandibular periosteal progenitors

value: CTSK-iCre;Plagl1 fl/fl

tag: osteoblast induction


title: OVA/Citra replicate2

city: Suzhou

first: Ziyi

last: Luo

address: suzhou

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: sample8

data_processing:
Raw reads were trimmed using Trim Galore (v0.5.0) with default parameters and quantified using Salmon
Assembly: GRcm39
Supplementary files format and content: Raw_FPKM_All_Samples.txt

source_name: CD8+ T cell

extract_protocol:
Total RNA was extracted from PAS-T cells treated with or without citraconate using RNeasy Mini Kit (Qiagen) and frozen in liquid nitrogen.
RNA integrity was assessed using an Agilent 2100 Bioanalyzer. Libraries were sequenced on an Illumina NextSeq 500 platform.

value: CD8+ T cell

value: with OVA peptide and citraconate


title: mandibular periosteal progenitors, M_3d_2

value: b-glycerophosphate (b-GP) (5 mM), ascorbic acid (50 ug/ml), and dexamethasone (100 nM)


title: ABE OT 15C Rep 2

description:
Library name: CHTTABEOT15_2
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 15C


title: 5xFAD, hippocampus, DHA, rep3, batch 2020

description:
Library name: AD-DHA-3-20-Hip
10x Genomics


city: Stanford

first: Lay Teng

last: Ang

address: Institute for Stem Cell Biology & Regenerative Medicine, Lokey Stem Cell Bldg, 265 Campus Drive

department: Urology

institute: Stanford University

description:
Library name: day 4 hPSC-derived vein endothelial cells (unsorted) scrnaseq
10x Genomics

data_processing:
For scRNA-seq, the demultiplexing, barcoded processing and gene counting were made using the CellRanger Count v9.0.1 Cloud Analysis software (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Human reference genome Hg38 (GRCh38)
Supplementary files format and content: Processed data files are Cell Ranger output files in HDF5 (.h5) format containing filtered gene-by-cell UMI count matrices for each sample.

source_name: H1 hPSC-derived

growth_protocol: hPSCs were maintained in mTesR Plus media before differentiation.

extract_protocol:
Cells were collected in papain and centrifuged at 300rcf for 5 min in DNA LoBind tubes. Cell pellets were resuspended in PBS containing 0.01% BSA and passed through a 40 µm cell strainer prior to counting. Cell concentration was adjusted as needed to approximately 1,000 cells/µL, followed by a second centrifugation and repeat cell count/viability assessment. Cell suspensions were maintained on ice until loading onto the Chromium Controller.
Library was prepared according to the manufacturer’s instructions for the Chromium Single Cell 3'GEM Library and Gel Bead kit v3 (PN-1000075), Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index, PN-1000121)) workflow (10x Genomics). Briefly, single cells were loaded with gel beads and partitioning oil to generate gel bead-in-emulsions (GEMs). Poly(A) RNA from lysed single cells in each GEM was reverse transcribed to barcoded cDNA containing a cell barcode and unique molecular identifier (UMI). After GEM-RT, GEMs were broken, barcoded cDNA was purified and amplified by PCR, and amplified cDNA was subjected to fragmentation, end repair and A-tailing, adaptor ligation, sample index PCR, and SPRI bead-based cleanup/size selection to generate dual-indexed gene expression libraries for paired-end Illumina sequencing. Libraries were indexed using the 10x Genomics Dual Index Plate TT Set A.

treatment_protocol: Differentiation of hPSCs into artery and vein ECs. All differentiation was conducted in defined, serum-free CDM2 basal media. Detailed instructions to how to prepare CDM2 are available.  Seeding hPSCs for differentiation (Step 0).   Step 1: Mid primitive streak induction, 24 hours.   Step 2: Lateral mesoderm induction, 24 hours.   Step 3A: Artery EC induction, 24 hours.   Step 3B: Primed EC induction, 24 hours.   Step 4B: Vein EC induction, 24 hours.

value: H1 hPSC-derived

value: vein EC

value: XY, wild-type

value: Unsorted


title: ABE OT 14C Rep 3

description:
Library name: CHTTABEOT14_3
Processed_GEO_Data_Sheet.xlsx

value: epitheleal

value: Lipofectamine 2000 transfected

value: ABE OT 14C


title: OVA replicate2

description: Library name: sample5

value: with OVA peptide


title: ABE OT 14C Rep 2

description:
Library name: CHTTABEOT14_2
Processed_GEO_Data_Sheet.xlsx


title: OVA/Citra replicate3

description: Library name: sample9


title: RNA-seq of motor cortex, Day 30, Male, sample Ln2

description: Library name: In2-MC

value: motor cortex


title: RNA-seq of motor cortex, Day 30, Male, sample Ln1

description: Library name: In1-MC


title: OVA replicate3

description: Library name: sample6


title: OVA/Citra replicate1

description: Library name: sample7

data_processing:
Raw reads were trimmed using Trim Galore (v0.5.0) with default parameters and quantified using Salmon
Assembly: GRcm39
Supplementary files format and content: 1 txt file

extract_protocol:
Total RNA was extracted from OVA-stimulated T cells treated with or without citraconate using RNeasy Mini Kit (Qiagen) and frozen in liquid nitrogen.
RNA integrity was assessed using an Agilent 2100 Bioanalyzer. Libraries were sequenced on an Illumina NextSeq 500 platform.


title: ABE OT 15C Rep 1

description:
Library name: CHTTABEOT15_1
Processed_GEO_Data_Sheet.xlsx


description:
Library name: day 4 hPSC-derived vein endothelial cells (sorted CD144+) scrnaseq
10x Genomics

value: CD144+ FACS sorted


title: mandibular tissue

description: 10x Genomics

data_processing:
Quality control, alignment, quantification and aggregation of sample count matrices were performed using the 10x Genomics Cell Ranger pipeline according to the manufacturer’s protocol.
Assembly: Mus_musculus.GRCm39.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mandibular tissue

extract_protocol:
Tissue was collected for digestion with Collagenase II (Sigma C6885), DNase (Applichem A3778) and Liberase TL(Roche 5401020001), washed with ice-cold DPBS.
Barcoding, cDNA amplification and library construction were performed using the Chromium Single Cell 3’ Reagent Kits V3 exactly according to the manufacturer’s instructions. Libraries were sequenced using an Illumina NovaSeq  and the paired-end 150 bp sequencing flow cell and produced about 100G base-pairs.

treatment_protocol: mandibular tissue were harvested from murine mandible at 7 days post mandibular defect.

value: mandibular tissue

value: CONTROL

value: 7 days post mandibular defect


title: ABE OT 15C Rep 3

description:
Library name: CHTTABEOT15_3
Processed_GEO_Data_Sheet.xlsx


title: mandibular periosteal progenitors, M_3d_1

value: mandibular periosteal progenitors

value: CTSK-iCre;Plagl1 fl/fl


description:
Library name: day 3 hPSC-derived primed endothelial cells (unsorted) scrnaseq
10x Genomics

value: primed EC


title: ABE OT 14C Rep 1

description:
Library name: CHTTABEOT14_1
Processed_GEO_Data_Sheet.xlsx


title: mandibular periosteal progenitors, C_3d_3

value: Plagl1 fl/fl

value: b-glycerophosphate (b-GP) (5 mM), ascorbic acid (50 ug/ml), and dexamethasone (100 nM)


title: OVA replicate1

description: Library name: sample4

value: CD8+ T cell


title: ABE OT 13C Rep 3

description:
Library name: CHTTABEOT13_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 13C


description:
Library name: day 3 hPSC-derived primed endothelial cells (sorted CD144+) scrnaseq
10x Genomics

value: H1 hPSC-derived

value: XY, wild-type


title: mandibular periosteal progenitors, C_3d_2


title: CTRL replicate1

description: Library name: sample1

value: without OVA peptide


description:
Library name: day 2 hPSC-derived lateral mesoderm scrnaseq
10x Genomics

value: lateral mesoderm

value: Unsorted


title: Patient 9 pre-GNOS-PV01 Tumor Region 1

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description:
Library name: Patient_9_pre_GNOS_PV01_tumor_region_1
Bulk TCR-seq from gDNA

data_processing:
The immunoSEQ Analyzer from Adaptive Biotechnologies was used to analyze resolved TCR sequences.
Assembly: hg18 (NCBI 36)
Supplementary files format and content: Processed data are presented in .tsv files containing the CDR3B sequences, counts and frequencies, VDJ gene usage, etc.
Library strategy: TCR-seq

source_name: glioblastoma tumor

extract_protocol:
gDNA was extracted from PBMCs or frozen tumor samples using the Qiagen AllPrep DNA/RNA Kit
gDNA was submitted to Adpative Biotechnologies for immunoSEQ. In brief, multiplex PCR amplification was used to target the CDR3 region of the T cell receptor genes. The amplified DNA was then sequenced.

value: glioblastoma tumor

tag: Sex

value: Male


title: ABE OT 13C Rep 2

description:
Library name: CHTTABEOT13_2
Processed_GEO_Data_Sheet.xlsx

value: epitheleal

value: Lipofectamine 2000 transfected


title: Clone 596-7 derived R1 resistant Replicate 3 with Dox

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description: Library name: Sample_R1-3

data_processing:
Six RNA samples were pooled and sequenced in one lanes on HiSeq4000 with Illumina HiSeq3000/4000 chemistry.
All the samples have yields above 108 million reads. Pass filtered reads have Q30 or above values about 93%.
Both reads of each sample was trimmed for adapters and low quality bases using Trimmomatic software and aligned with reference human hg19 genome and Ensembl v70 transcripts using star software.
Quantification was carried out using the transcriptome bam file created by star and Ensembl v70 transcriptome as the index for RSEM.
Assembly: hg19 & Ensembl v70
Supplementary files format and content: Tab-delimited text file containing CPM TMM normalized counts and associated averages, t-tests, and fold changes.

source_name: HT-29 colon adenocarcinoma

growth_protocol: Cells (596-7; R1+Dox) were seeded onto a 6-well plate and maintained for 44 hours. Subsequently, total RNA was extracted using the Qiagen RNeasy Mini Kit.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit. DNAI was treated while preparing total RNA.
RNA libraries for RNA-seq were prepared using TrusSeq Stranded Total RNA Kit following manufacturer's protocols.

treatment_protocol: R1 cells were treated with doxycycline (1 μg/ml) for 44 hours, while 596-7 cells were not treated with doxycycline.

value: HT-29 colon adenocarcinoma

value: HT-29-derived clone 596-7 cell

value: Res


title: CTRL replicate3

description: Library name: sample3


title: CTRL replicate2

description: Library name: sample2


title: Clone 596-7 derived R1 resistant Replicate 2 with Dox

description: Library name: Sample_R1-2


title: mandibular periosteal progenitors, C_3d_1

value: mandibular periosteal progenitors


title: mandibular periosteal progenitors, C_0d_1

value: Plagl1 fl/fl

value: control


title: H1_hPSC scrnaseq, replicate 1

description:
Library name: H1_hPSC scrnaseq, replicate 1
10x Genomics
H1_old_filtered_feature_bc_matrix.h5

source_name: H1 hPSC

value: H1 hPSC

value: hPSC


title: Patient 9 pre-GNOS-PV01 Tumor Region 2

description:
Library name: Patient_9_pre_GNOS_PV01_tumor_region_2
Bulk TCR-seq from gDNA


title: Patient 9 pre-GNOS-PV01 Tumor Region 3

description:
Library name: Patient_9_pre_GNOS_PV01_tumor_region_3
Bulk TCR-seq from gDNA


title: ABE OT 11C Rep 3

description:
Library name: CHTTABEOT11_3
Processed_GEO_Data_Sheet.xlsx

data_processing:
Crispresso2 utilized for base calling and base editing frequency quantification for all DNA NGS files. Sequences were filtered for 90% homology with a phred33 read qualitty of >30. Sequencecs were aligned to an inputted PCR amplicon with the gRNA region of interest
Assembly: chr38
Supplementary files format and content: Excel sheet containing editing rates and figure number

extract_protocol:
For mouse tissues only striatum extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency Samples for DNA editing were extracted using Qiagen's DNeasy DNA extraction kit
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits as per manufacturer's instructions Targeted genomic and exon high throughput sequencing with nextera indexing primers

value: ABE OT 11C


description:
Library name: day 1 hPSC-derived primitive streak scrnaseq
10x Genomics

value: H1 hPSC-derived

value: primitive streak

value: XY, wild-type


title: ABE OT 13C Rep 1

description:
Library name: CHTTABEOT13_1
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 13C


title: mandibular periosteal progenitors, C_0d_3


title: mandibular periosteal progenitors, C_0d_2


title: ABE OT 12C Rep 3

description:
Library name: CHTTABEOT12_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 12C


title: ABE OT 12C Rep 2

description:
Library name: CHTTABEOT12_2
Processed_GEO_Data_Sheet.xlsx


title: Clone 596-7 derived R1 resistant Replicate 1 with Dox

description: Library name: Sample_R1-1


title: WT mice;scWAT;C99

city: HeFei

first: zhao

last: li

address: Daoxiangcun

institute: ustc

data_processing:
IIIlumina Casava1.7 software used for basecalling
Sequenced reads were trimed for adaptor sequence
Reads Per Kilobase of exon per Megabase of library size (RPKM ) were calculated
Assembly: mm9
Supplementary files format and content: tab-delimited text files include raw counts for every sample
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Subcutaneous adipose tissue

extract_protocol:
Trizol extraction
RNA libraries were prepared for sequencing using standard IIIumina protocols

value: Subcutaneous adipose tissue

value: WT


title: Patient 9 post-GNOS-PV01 Tumor

description:
Library name: Patient_9_post_GNOS_PV01_tumor
Bulk TCR-seq from gDNA

value: glioblastoma tumor

value: Male


title: ABE OT 11C Rep 2

description:
Library name: CHTTABEOT11_2
Processed_GEO_Data_Sheet.xlsx

value: epitheleal

value: Lipofectamine 2000 transfected


title: WT mice;scWAT;C85


title: Patient 9 Pembro C1D1 PBMC

description:
Library name: Patient_9_Pembro_C1D1_PBMC
Bulk TCR-seq from gDNA

source_name: PBMC

value: PBMC


title: WT mice;scWAT;C75


title: ABE OT 11C Rep 1

description:
Library name: CHTTABEOT11_1
Processed_GEO_Data_Sheet.xlsx


title: Patient 9 Pembro C2D1 PBMC

description:
Library name: Patient_9_Pembro_C2D1_PBMC
Bulk TCR-seq from gDNA


title: Clone 596-7 Replicate 2 No Dox

description: Library name: Sample_596-7-2

value: HT-29 colon adenocarcinoma

value: HT-29-derived clone 596-7 cell

value: Control


title: Patient 9 C1D1 PBMC

description:
Library name: Patient_9_C1D1_PBMC
Bulk TCR-seq from gDNA


title: ABE OT 10C Rep 3

description:
Library name: CHTTABEOT10_3
Processed_GEO_Data_Sheet.xlsx

value: ABE OT 10C


title: CO5-1-SPG4-36 d100-R2

city: Daejeon

first: Mi-Ok

last: Lee

address: 125, Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
day 100
ESC, cortical organoids, SPAST ex17 KO

data_processing:
The sequence data were evaluated using the NGSQCToolkit v.2.3.3
The adapters were removed using Cutadapt v.3.7 with default settings
Low-quality sequences were trimmed using Sickle v.1.33
the clean reads were mapped to the reference genome using HISAT2 v.2.2.1 with default parameter settings and applying StringTie v.2.2.0 using the reference annotation file for estimating the expression levels of all genes and transcripts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: H9 ESCs were maintained in mTeSR in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cortical organoids were induced by 4-steps, 1) Embryonic body (10uM SB431642, 2.5uM Dorsomorphine, Sigma): change media everyday for 5 days,2) Neural induction (20ng/ml EGF and 20ng/ml bFGF (R&D) in 2% B27 contained Neurobasal-A) change media everyday for 10 day and everyotherday for 25day, 3) Neural Maturation for day 25~day42  (20ng/ml NT3 and 20ng/ml BDNF (Peprotech) in 2% B27 contained Neurobasal-A) change media every other day) 4 after Nueral Maturation, media were changed every 4 days until harvest the COs
RNA was harvested manually (Chroloform, isopropanol, 70% Ethanol). 5ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using Illumina TruSeq library preparation according to manufacturer specifications.

treatment_protocol: Cortical organoids were induced by 4-steps, 1) Embryonic body (1X10^6 cells/well)  for  6days,2) Neural induction , 3) Neural Maturation for day 25~day42, 4) after Nueral Maturation, media were changed every 4 days until harvest the COs

value: embryonic stem cells

value: SPAST ex17 KO

value: Brain organoids


title: Patient 8 Pseudoprogression Tumor

description:
Library name: Patient_8_pseudoprogression
Bulk TCR-seq from gDNA

value: Female


title: ABE OT 10C Rep 2

description:
Library name: CHTTABEOT10_2
Processed_GEO_Data_Sheet.xlsx


title: C2orf74 KO mice,scWAT;C34

value: C2orf74 KO


title: C2orf74 KO mice,scWAT;C695


title: Clone 596-7 Replicate 3 No Dox

description: Library name: Sample_596-7-3


title: CO5-1-SPG4-36 d100-R1


title: C2orf74 KO mice,scWAT;C7


title: CBE OT 8 Rep 02

description:
Library name: CBEOT8_01_02
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 8


title: Patient 8 pre-GNOS-PV01 Tumor Regions 1-3

description:
Library name: Patient_8_pre_GNOS_PV01_tumor_regions_1-3
Bulk TCR-seq from gDNA


title: CBE OT 8 Rep 03

description:
Library name: CBEOT8_01_03
Processed_GEO_Data_Sheet.xlsx


title: Clone 596-7 Replicate 1 No Dox

description: Library name: Sample_596-7-1


title: CO5-1-SPG4-33 d100-R2


title: WT mice;epWAT;C99

source_name: Epididymal adipose tissue

value: Epididymal adipose tissue


title: ABE OT 10C Rep 1

description:
Library name: CHTTABEOT10_1
Processed_GEO_Data_Sheet.xlsx


title: WT mice;epWAT;C85

value: WT


title: Patient 8 post-GNOS-PV01 Tumor

description:
Library name: Patient_8_post_GNOS_PV01_tumor
Bulk TCR-seq from gDNA

value: glioblastoma tumor


title: CO5-1-SPG4-33 d100-R1


title: CBE OT 8 Rep 01

description:
Library name: CBEOT8_01_01
Processed_GEO_Data_Sheet.xlsx


title: WT mice;epWAT;C75


title: Patient 8 C1D1 PBMC

description:
Library name: Patient_8_C1D1_PBMC
Bulk TCR-seq from gDNA


title: Patient 8 C5D1 PBMC

description:
Library name: Patient_8_C5D1_PBMC
Bulk TCR-seq from gDNA


title: CBE OT 3 Rep 03

description:
Library name: CBEOT3_01_03
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 3


title: CO5-H9-d100-R2

description:
day 100
ESC, cortical organoids,  WT


title: CO5-H9-d100-R1

description:
day 100
ESC, cortical organoids,  WT


title: CBE OT 3 Rep 02

description:
Library name: CBEOT3_01_02
Processed_GEO_Data_Sheet.xlsx

value: epitheleal


title: C2orf74 KO mice,epWAT;C695


title: C2orf74 KO mice,epWAT;C34


title: CBE OT 2 Rep 03

description:
Library name: CBEOT2_01_03
Processed_GEO_Data_Sheet.xlsx

value: Lipofectamine 2000 transfected

value: CBE OT 2


title: Patient 2 pre-GNOS-PV01 Tumor Region 4

description:
Library name: Patient_2_pre_GNOS_PV01_tumor_region_4
Bulk TCR-seq from gDNA


title: CO3-H9

description:
day 100
ESC, cortical organoids,  WT


title: Patient 2 pre-GNOS-PV01 Tumor Region 3

description:
Library name: Patient_2_pre_GNOS_PV01_tumor_region_3
Bulk TCR-seq from gDNA


title: CBE OT 3 Rep 01

description:
Library name: CBEOT3_01_01
Processed_GEO_Data_Sheet.xlsx


title: Patient 2 pre-GNOS-PV01 Tumor Region 2

description:
Library name: Patient_2_pre_GNOS_PV01_tumor_region_2
Bulk TCR-seq from gDNA


title: H9-p40-SPG4-36

description:
passage 40
ESC, SPAST ex17 KO


title: C2orf74 KO mice,epWAT;C7


title: H9-p40-SPG4-33

description:
passage 40
ESC, SPAST ex17 KO


title: C2orf74 KO mice,leydig cell;2-2

source_name: testis

value: testis

value: Leydig cell


title: Patient 2 post-GNOS-PV01 Tumor

description:
Library name: Patient_2_post_GNOS_PV01_tumor
Bulk TCR-seq from gDNA


title: CBE OT 2 Rep 01

description:
Library name: CBEOT2_01_01
Processed_GEO_Data_Sheet.xlsx


title: CBE OT 1 Rep 03

description:
Library name: CBEOT1_01_03
Processed_GEO_Data_Sheet.xlsx

value: CBE OT 1


title: C2orf74 KO mice,leydig cell;1


title: H9-p52-R1

description:
passage 52
ESC, WT


title: Patient 2 pre-GNOS-PV01 Tumor Region 1

description:
Library name: Patient_2_pre_GNOS_PV01_tumor_region_1
Bulk TCR-seq from gDNA


title: Patient 2 C1D1 PBMC

description:
Library name: Patient_2_C1D1_PBMC
Bulk TCR-seq from gDNA

value: PBMC


title: Patient 2 PD2 PBMC

description:
Library name: Patient_2_PD2_PBMC
Bulk TCR-seq from gDNA


title: WT mice,leydig cell;D-2


title: CBE OT 1 Rep 02

description:
Library name: CBEOT1_01_02
Processed_GEO_Data_Sheet.xlsx


title: FLOX2

status: Public on Apr 05 2026

city: shanghai

first: Xiaorui

last: Lyu

state: shanghai

address: 600 Yishan Road

department: Shanghai Diabetes Institute

institute: Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: SAT-FLOX2
10x Genomics

data_processing:
Raw sequencing data were processed using the Cell Ranger (version 7.1) to align reads to the reference genome (GRCh38) and generate a gene expression matrix.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: Animals were housed in groups of 3-5 per cage under specific pathogen-free (SPF) conditions, maintained at 22-24°C with 50–60% relative humidity and a 12-hour light-dark cycle, with unrestricted access to food and water.

extract_protocol:
Single nuclei were isolated from scWAT of GPSM1f/f (n = 3) and GPSM1ΔTreg (n = 3) mice using a sucrose gradient-based nuclei isolation protocol. Nuclei were stained with DAPI and sorted by fluorescence-activated cell sorting (FACS) to ensure high purity.
Single-nucleus RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3’ Library, following the manufacturer’s instructions. Briefly, GCs were resuspended in the master mikx andloaded together with partitioning oil and gel beads into the chip to generate the gelbead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every singleGEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence.Unigue Molecular ldentifier (UMl) and the 10x Barcode. The pooled barcoded cDNAwas then cleaned up with Silane DynaBeads, amplified by PCR and the apropiatedsized fragments were selected with SPRlselect reagent for subsequent libraryconstruction. During the library construction llumina R2 primer sequence, paired-endconstructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Seven-week-old mice were fed an NCD for 20-24 weeks or an HFD for 5-12 weeks for diet-induced obesity, and monitored on a daily basis and weighted every week.

value: Subcutaneous adipose tissue


title: WT mice,leydig cell;C


title: H9-p40-SPG4-22

description:
passage 40
ESC, SPAST ex17 KO

value: embryonic stem cells

value: SPAST ex17 KO


title: FLOX3

description:
Library name: SAT-FLOX3
10x Genomics


title: FLOX1

description:
Library name: SAT-FLOX1
10x Genomics


title: CBE OT 1 Rep 01

first: Pablo

last: Perez-Pinera

institute: University of Illinois Urbana-Champaign

description:
Library name: CBEOT1_01_01
Processed_GEO_Data_Sheet.xlsx


title: CKO2

description:
Library name: SAT-CKO2
10x Genomics


title: AEAA high-dose lung biol rep 5

city: ALAR

first: 海宏

last: 焦

address: Tarim University

institute: Tarim University

description: Library name: LPS+AEAAH-5

data_processing:
Raw reads were quality-assessed and filtered to remove adaptor sequences, low-quality reads, reads containing excessive Ns, and reads shorter than 20 bp.
Clean reads were aligned to the mouse reference genome (GRCm39) using HISAT2.
Mapped reads were assembled in a reference-based manner using StringTie. Gene and transcript abundances were quantified using RSEM and normalized as TPM (transcripts per million).
Differential expression analysis was performed using DESeq2. Genes with |log2FoldChange| >= 1 and FDR <= 0.05 were considered significantly differentially expressed.
Functional enrichment analyses of differentially expressed genes were performed using GO and KEGG databases.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files containing gene-level expression matrices for all samples, including raw read counts and TPM values, together with differential expression analysis results for pairwise comparisons.

source_name: Lung

growth_protocol: Seven-week-old male C57BL/6 mice were housed under specific pathogen-free conditions in top-filtered cages with a 12 h light/dark cycle and had ad libitum access to an AIN-76A diet and filtered drinking water.

extract_protocol:
Total RNA was extracted from lung tissues using TRIzol reagent according to the manufacturer’s instructions. RNA integrity and quality were assessed using an Agilent 5300 Fragment Analyzer, and RNA concentration was measured using a NanoDrop ND-2000 spectrophotometer.
Total RNA was extracted from frozen lung tissues using TRIzol reagent. RNA quantity and purity were assessed using a NanoDrop 2000 spectrophotometer, and RNA integrity was evaluated using an Agilent 5300 Fragment Analyzer. Samples with RIN ≥ 7.0 and OD260/280 ratios between 1.8 and 2.1 were used for library preparation. mRNA was enriched by removing rRNA, followed by fragmentation, first-strand and second-strand cDNA synthesis, adapter ligation, and PCR amplification. After library quality control, the libraries were sequenced on an Illumina NovaSeq 6000 platform in paired-end 150 bp mode (PE150).

treatment_protocol: Mice were randomly assigned to five groups. AEAA was administered in drinking water for 28 consecutive days at 0.5, 1, or 1.5 mg/mL as indicated. On day 29, acute lung injury was induced by intratracheal instillation of LPS (5 mg/kg) in the LPS and AEAA groups, while control mice received sterile saline. Lung tissues were collected 8 h after challenge.

tag: strain

value: male

tag: age

value: 7 weeks

value: Lung

value: wild type

value: AEAA 1.5 mg/mL for 28 days + LPS 5 mg/kg

tag: challenge

value: LPS 5 mg/kg

tag: time point

value: 8 h


title: AEAA high-dose lung biol rep 4

description: Library name: LPS+AEAAH-4


title: H9-p40-R1

description:
passage 40
ESC, WT

value: WT


title: AEAA mid-dose lung biol rep 5

description: Library name: LPS+AEAAM-5

value: AEAA 1.0 mg/mL for 28 days + LPS 5 mg/kg


title: AEAA mid-dose lung biol rep 4

description: Library name: LPS+AEAAM-4


title: AEAA low-dose lung biol rep 5

description: Library name: LPS+AEAAL-5

value: AEAA 0.5 mg/mL for 28 days + LPS 5 mg/kg


title: CKO3

description:
Library name: SAT-CKO3
10x Genomics


title: AEAA high-dose lung biol rep 2

description: Library name: LPS+AEAAH-2


title: AEAA high-dose lung biol rep 1

description: Library name: LPS+AEAAH-1


title: AEAA mid-dose lung biol rep 3

description: Library name: LPS+AEAAM-3


title: AEAA low-dose lung biol rep 3

description: Library name: LPS+AEAAL-3


title: AEAA low-dose lung biol rep 4

description: Library name: LPS+AEAAL-4


title: CKO1

description:
Library name: SAT-CKO1
10x Genomics


title: AEAA mid-dose lung biol rep 2

description: Library name: LPS+AEAAM-2


title: LPS lung biol rep 3

description: Library name: LPS-3


title: AEAA low-dose lung biol rep 1

description: Library name: LPS+AEAAL-1


title: LPS lung biol rep 2

description: Library name: LPS-2


title: AEAA low-dose lung biol rep 2

description: Library name: LPS+AEAAL-2


title: AEAA high-dose lung biol rep 3

description: Library name: LPS+AEAAH-3


title: Control lung biol rep 1

description: Library name: Ctrl-1


title: Control lung biol rep 4

description: Library name: Ctrl-4


title: LPS lung biol rep 5

description: Library name: LPS-5


title: Control lung biol rep 3

description: Library name: Ctrl-3


title: Control lung biol rep 2

description: Library name: Ctrl-2


title: AEAA mid-dose lung biol rep 1

description: Library name: LPS+AEAAM-1


title: LPS lung biol rep 1

description: Library name: LPS-1


title: LPS lung biol rep 4

description: Library name: LPS-4


title: ScLZ_wt_rep4

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description:
Library name: RNA_sample_37
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to mm10 using STAR
Duplicated reads were removed using SAMtools
Read count extraction and normalization were performed using QuasR/limma
Assembly: mm10
Supplementary files format and content: BigWig files created using the function qExportWig from the QuasR package for 100bp  tiles in the mm10 genome.

source_name: Testis

extract_protocol:
FACS-isolated populations of ScLZ, ScPD, rSt and elSt cells were pelleted at 2000g for 10 min at 4°C. Total RNA was extracted from cell pellets using the RNeasy Mini Kit (Qiagen 74104) according to manufacturer’s instructions. DNA removal was performed using on-column the RNase-Free DNase Set (Qiagen, 79254). RNA concentration was determined with Qubit RNA HS Assay Kit (Q32852). Quality of RNA was determined using Fragment Analyzer system
Libraries were prepared with the Illumina Stranded total RNA-seq protocol according to manufacturer’s instructions. Quality control of libraries was performed with Agilent 2100 Bioanalyzer System.  After passing the QC, sequencing was performed on Illumina NovaSeq platform (50 bp, paired end).

treatment_protocol: ScLZ, ScPD, rSt and elSt cells used for RNA-seq, we used a previously published protocol based on dual staining of DNA (Gill et al. 2024) on BD FACSAria II

value: Testis

value: Leptotene/zygotene spermatocytes

value: wt/wt

tag: replicate


title: rSt_wt_rep4

description:
Library name: RNA_sample_39
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)

tag: tissue

value: Round spermatids


title: elSt_MYC_rep4

description:
Library name: RNA_sample_48
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)

value: Elongating spermatids

tag: genotype

value: MYC/wt


title: ScLZ_MYC_rep4

description:
Library name: RNA_sample_45
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: elSt_H3.1_rep4

description:
Library name: RNA_sample_44
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: rSt_H3.1_rep4

description:
Library name: RNA_sample_43
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_wt_rep3

description:
Library name: RNA_sample_26
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)

value: Pachytene/diplotene spermatocytes


title: rSt_wt_rep3

description:
Library name: RNA_sample_27
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: elSt_wt_rep4

description:
Library name: RNA_sample_40
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_wt_rep4

description:
Library name: RNA_sample_38
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: rSt_MYC_rep4

description:
Library name: RNA_sample_47
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: elSt_H3.1_rep3

description:
Library name: RNA_sample_32
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: rSt_MYC_rep3

description:
Library name: RNA_sample_35
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_H3.1_rep4

description:
Library name: RNA_sample_42
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: rSt_H3.1_rep3

description:
Library name: RNA_sample_31
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_MYC_rep3

description:
Library name: RNA_sample_34
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScLZ_MYC_rep3

description:
Library name: RNA_sample_33
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: elSt_MYC_rep3

description:
Library name: RNA_sample_36
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_H3.1_rep3

description:
Library name: RNA_sample_30
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: elSt_MYC_rep2

description:
Library name: RNA_sample_24
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: elSt_wt_rep3

description:
Library name: RNA_sample_28
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScLZ_wt_rep3

description:
Library name: RNA_sample_25
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScLZ_H3.1_rep3

description:
Library name: RNA_sample_29
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_MYC_rep4

description:
Library name: RNA_sample_46
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_MYC_rep2

description:
Library name: RNA_sample_22
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScLZ_MYC_rep2

description:
Library name: RNA_sample_21
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: rSt_H3.1_rep2

description:
Library name: RNA_sample_19
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: rSt_wt_rep2

description:
Library name: RNA_sample_15
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScLZ_H3.1_rep2

description:
Library name: RNA_sample_17
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_wt_rep2

description:
Library name: RNA_sample_14
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScLZ_wt_rep1

description:
Library name: RNA_sample_9
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_H3.1_rep2

description:
Library name: RNA_sample_18
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: rSt_MYC_rep2

description:
Library name: RNA_sample_23
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: rSt_MYC_rep1

description:
Library name: RNA_sample_7
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_MYC_rep1

description:
Library name: RNA_sample_6
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScLZ_MYC_rep1

description:
Library name: RNA_sample_5
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: rSt_wt_rep1

description:
Library name: RNA_sample_11
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: elSt_wt_rep2

description:
Library name: RNA_sample_16
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: elSt_H3.1_rep1

description:
Library name: RNA_sample_4
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: elSt_H3.1_rep2

description:
Library name: RNA_sample_20
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: elSt_wt_rep1

description:
Library name: RNA_sample_12
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScLZ_wt_rep2

description:
Library name: RNA_sample_13
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_wt_rep1

description:
Library name: RNA_sample_10
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScLZ_H3.1_rep4

description:
Library name: RNA_sample_41
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: elSt_MYC_rep1

description:
Library name: RNA_sample_8
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScLZ_H3.1_rep1

description:
Library name: RNA_sample_1
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: ScPD_H3.1_rep1

description:
Library name: RNA_sample_2
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: rSt_H3.1_rep1

description:
Library name: RNA_sample_3
RNA-seq experiment to estimate the effects of H3.1/H3.1 and MYC/wt (relative to wt/wt control)


title: GPR35 positive, rep1

first: Ning

state: Shanghai

address: Fenglin Road 180

institute: Zhongshan Hospital, Fudan University

description: Library name: P1

data_processing:
1. Raw data quality control: Adapter-trimming and quality filtering were performed using fastp (v0.22.0) with parameters:removal of 3'-end adapters and discarding reads with mean quality scores < Q20
2. Alignment: HISAT2 (v2.1.0) was used to build the reference genome index and align paired-end clean reads to the reference genome.
3. Quantification: Read counts per gene were generated using HTSeq (v0.9.1) in union mode.
4. Normalization: Gene expression levels were normalized as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) to enable cross-sample/gene comparability.
5. Differential expression analysis: DESeq (v1.38.3) was applied to identify differentially expressed genes between comparative groups.
Assembly: GRCh38
Supplementary files format and content: csv files include FPKM values for each sample

source_name: neutrophil

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific).
RNA libraries for RNA-seq was prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols

value: neutrophil


title: GPR35 negative, rep2

description: Library name: N2


title: Apc_KO_Kras_WT_rep4

city: South San Francisco

first: Sandra

last: Melo

address: 1 DNA Way

institute: Genentech, Inc.

description: Library name: Apc_KO_Kras_WT_rep4

data_processing:
All snRNAseq data were pre-processed with 10X Cell Ranger ARC pipeline v.2.0.2, while all snRNAseq datasets were pre-processed with 10X Cell Ranger pipeline v.7.1.0. The genome was set to mm10-2020-A mouse genome reference, default parameters, and the platform set to 10x Genomics v3.1 3’ scRNAseq kit. The 10X Cell Ranger pipeline performs read de-multiplexing, alignment, and unique molecular identifiers (UMI) and cell barcode correction, producing a preliminary count matrix of cells by unique transcripts.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5

source_name: Small intestine

extract_protocol:
Nuclei from cryo-preserved intestinal tissue was isolated using the Nuclei Isolation Kit (10x Genomics, 1000494). Briefly, tissue was cut on ice in lysis buffer supplemented with RNase inhibitor, transferred to a 1.5ml tube, further dissociated using a pestle, and lysed for 10 min. The remainder of the nuclei isolation was performed according to manufacturing instructions.
cDNA yield was quantified using High Sensitivity D5000 ScreenTape on a TapeStation (Agilent Technologies), library preparation was performed using Dual Index Plate TT (10x Genomics), followed by quantification on TapeStation (Agilent Technologies) and a Qubit fluorometer (Thermo Fisher Scientific). The libraries were multiplexed and then sequenced on Illumina NovaSeq (Illumina) to generate at least 96M  paired-end reads.

value: Small intestine


title: Apc_KO_Kras_WT_rep2

description: Library name: Apc_KO_Kras_WT_rep2


title: GPR35 negative, rep3

description: Library name: N3


title: Apc_KO_Kras_WT_rep3

description: Library name: Apc_KO_Kras_WT_rep3


title: GPR35 positive, rep3

description: Library name: P3


title: Apc_KO_Kras_WT_rep1

description: Library name: Apc_KO_Kras_WT_rep1


title: Apc_KO_Kras_Q61R_rep2

description: Library name: Apc_KO_Kras_Q61R_rep2


title: GPR35 positive, rep2

description: Library name: P2


title: Apc_KO_Kras_G12D_rep3

description: Library name: Apc_KO_Kras_G12D_rep3


title: Apc_KO_Kras_Q61R_rep3

description: Library name: Apc_KO_Kras_Q61R_rep3


title: Apc_KO_Kras_G12D_rep4

description: Library name: Apc_KO_Kras_G12D_rep4


title: Apc_KO_Kras_G12D_rep2

description: Library name: Apc_KO_Kras_G12D_rep2


title: Apc_KO_Kras_G12D_rep1

description: Library name: Apc_KO_Kras_G12D_rep1


title: Apc_KO_Kras_Q61R_rep4

description: Library name: Apc_KO_Kras_Q61R_rep4


title: GPR35 negative, rep1

description: Library name: N1


title: Kras_WT-d10_rep4_gex

description: Library name: Kras_WT-d10_rep4_gex

data_processing:
. All snRNAseq and scATACseq datasets were pre-processed with 10X Cell Ranger ARC pipeline v.2.0.2, while all snRNAseq datasets were pre-processed with 10X Cell Ranger pipeline v.7.1.0. The genome was set to mm10-2020-A mouse genome reference, default parameters, and the platform set to 10x to Chromium Single Cell Multiome ATAC + Gene Expression kit or 10x Genomics v3.1 3’ scRNAseq kit. The 10X Cell Ranger pipeline performs read de-multiplexing, alignment, and unique molecular identifiers (UMI) and cell barcode correction, producing a preliminary count matrix of cells by unique transcripts in the case of RNAseq, and cells by unique fragments in the case of ATACseq.
Assembly: mm10
Supplementary files format and content: atac_fragments.tsv.gz

extract_protocol:
Nuclei from cryo-preserved intestinal tissue was isolated using the Nuclei Isolation Kit (10x Genomics, 1000494). Briefly, tissue was cut on ice in lysis buffer supplemented with RNase inhibitor, transferred to a 1.5ml tube, further dissociated using a pestle, and lysed for 10 min. The remainder of the nuclei isolation was performed according to manufacturing instructions.
cDNA yield was quantified using High Sensitivity D5000 ScreenTape on a TapeStation (Agilent Technologies), library preparation was performed using Dual Index Plate TT (10x Genomics), followed by quantification on TapeStation (Agilent Technologies) and a Qubit fluorometer (Thermo Fisher Scientific). ATAC libraries were performed using Sample Index Plate N, Set A (10x Genomics, 3000427) by quantification on TapeStation (Agilent Technologies) and a Qubit fluorometer (Thermo Fisher Scientific) before submission for sequencing. The libraries were multiplexed and then sequenced on Illumina NovaSeq (Illumina) to generate at least 96M (expression) or 112M (ATAC) paired-end reads.


title: Kras_WT-d10_rep2_gex

description: Library name: Kras_WT-d10_rep2_gex


title: Kras_Q61R-d10_rep3_gex

description: Library name: Kras_Q61R-d10_rep3_gex


title: Kras_WT-d10_rep4_atac

description: Library name: Kras_WT-d10_rep4_atac

library_source: genomic single cell


title: Kras_WT-d10_rep1_gex

description: Library name: Kras_WT-d10_rep1_gex


title: Kras_WT-d10_rep1_atac

description: Library name: Kras_WT-d10_rep1_atac


title: Kras_WT-d10_rep3_gex

description: Library name: Kras_WT-d10_rep3_gex


title: Kras_WT-d10_rep3_atac

description: Library name: Kras_WT-d10_rep3_atac


title: Kras_WT-d10_rep2_atac

description: Library name: Kras_WT-d10_rep2_atac


title: Kras_Q61R-d10_rep3_atac

description: Library name: Kras_Q61R-d10_rep3_atac


title: Kras_Q61R-d10_rep2_atac

description: Library name: Kras_Q61R-d10_rep2_atac


title: Kras_G12D-d10_rep3_atac

description: Library name: Kras_G12D-d10_rep3_atac


title: Kras_Q61R-d10_rep1_gex

description: Library name: Kras_Q61R-d10_rep1_gex


title: Kras_G12D-d10_rep1_gex

description: Library name: Kras_G12D-d10_rep1_gex


title: Kras_G12D-d10_rep2_atac

description: Library name: Kras_G12D-d10_rep2_atac


title: Kras_G12D-d10_rep2_gex

description: Library name: Kras_G12D-d10_rep2_gex


title: Kras_G12D-d10_rep3_gex

description: Library name: Kras_G12D-d10_rep3_gex


title: Kras_G12D-d10_rep1_atac

description: Library name: Kras_G12D-d10_rep1_atac


title: Apc_KO_Kras_G12D_rep2_gex

description: Library name: Apc_KO_Kras_G12D_rep2_gex

data_processing:
All snRNAseq and scATACseq datasets were pre-processed with 10X Cell Ranger ARC pipeline v.2.0.2, while all snRNAseq datasets were pre-processed with 10X Cell Ranger pipeline v.7.1.0. The genome was set to mm10-2020-A mouse genome reference, default parameters, and the platform set to 10x to Chromium Single Cell Multiome ATAC + Gene Expression kit or 10x Genomics v3.1 3’ scRNAseq kit. The 10X Cell Ranger pipeline performs read de-multiplexing, alignment, and unique molecular identifiers (UMI) and cell barcode correction, producing a preliminary count matrix of cells by unique transcripts in the case of RNAseq, and cells by unique fragments in the case of ATACseq.
Assembly: mm10
Supplementary files format and content: atac_fragments.tsv.gz, bam files, filtered_feature_bc_matrix.h5


title: Apc_KO_Kras_WT_rep1_atac

description: Library name: Apc_KO_Kras_WT_rep1_atac


title: Kras_Q61R-d10_rep2_gex

description: Library name: Kras_Q61R-d10_rep2_gex


title: Apc_KO_Kras_WT_rep2_gex

description: Library name: Apc_KO_Kras_WT_rep2_gex


title: Apc_KO_Kras_G12D_rep2_atac

description: Library name: Apc_KO_Kras_G12D_rep2_atac


title: Apc_KO_Kras_G12D_rep1_gex

description: Library name: Apc_KO_Kras_G12D_rep1_gex


title: Apc_KO_Kras_WT_rep3_gex

description: Library name: Apc_KO_Kras_WT_rep3_gex


title: Apc_KO_Kras_WT_rep3_atac

description: Library name: Apc_KO_Kras_WT_rep3_atac


title: Apc_KO_Kras_Q61R_rep1_gex

description: Library name: Apc_KO_Kras_Q61R_rep1_gex


title: Apc_KO_Kras_WT_rep1_gex

description: Library name: Apc_KO_Kras_WT_rep1_gex