title: Cerebral cortex, dMCAO, d28, rep4

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

description: single nucleus RNA seq

data_processing:
Reads were processed using 10x Genomics Cell Ranger analytical pipeline (v4.0) and mouse mm10 pre-mRNA reference (10x Genomics). Dataset aggregation was performed using the Cellranger aggr function. Downstream analysis was performed using the R software package Seurat (v3.2.2, http://satijalab.org/seurat/) 1. We removed nucleus doublets by Scrublet (v0.2.1) 2 and low-quality nuclei with less than 200 genes detected and removed genes expressed in fewer than 50 cells, leaving 107,020 cells and 20,785 genes for further analysis. The filtered raw gene expression matrix was cell-normalized over total number of counts, multiplied by 10,000 and log transformed.
Genome_build: mm10
Supplementary_files_format_and_content: expression_matrix.mtx.gz, genes.txt.gz, cellIDs.txt.gz, metadata.txt.gz

source_name: brain

extract_protocol:
[Nuclei isolation from frozen samples]  Frozen mouse brain tissue samples were homogenized and lysed with Triton X-100 in RNase-free water for nuclei isolation. The isolated nuclei were purified, centrifuged, and resuspended in PBS with BSA and RNAse Inhibitor. The nuclei were diluted to 700 nuclei/ul and loaded to 10x Genomics Chromium Controller to encapsulate single nuclei into droplet emulsions following the manufacturer’s recommendations (Pleasanton, CA, United States).
Library preparation was performed according to the instructions in the Chromium Next GEM 3’ Single Cell Reagent kits v3.1. Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay (Thermo Fisher Scientific, Wilmington, DE) and quality assessed by BioAnalyzer (Agilent Technologies, Santa Clara, CA). Libraries were sequenced on a NovaSeq 6000 instrument (Illumina, San Diego, CA, United States), and reads were subsequently processed using 10x Genomics Cell Ranger analytical pipeline (v4.0) and mouse mm10 pre-mRNA reference. Dataset aggregation was performed using the cellranger aggr function normalizing for the total number of confidently mapped reads across libraries.

treatment_protocol: [A model of focal cerebral ischemia]  A small craniotomy was made over the trunk of the left MCA and above the rhinal fissure. Distal MCAO was performed by placing a small piece of cellulose paper soaked with a 10% solution of FeCl3 in saline just before its bifurcation between the frontal and parietal branches. The paper remains placed on the artery for 5 minutes and after 20 minutes artery occlusion is completed. Complete interruption of blood flow was confirmed under an operating microscope. These experimental conditions led to moderately sized cortical infarcts. Rectal temperature was monitored and maintained at 37°C±0.5°C with a thermostatically controlled a heating pad during surgery and a heating lamp for 4 hours after surgery.

value: brain

value: whole cerebral cortex cells

value: dMCAO, d28


title: Cerebral cortex, dMCAO, d28, rep3

status: Public on Dec 24 2025

type: SRA

description: single nucleus RNA seq

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: strain

tag: treatment


title: Arm1,Pig#4,HOPE, 24h

city: Philadelphia

first: Ting

last: Peng

state: PA

address: CTRB 6200

department: Pathology and Laboratory Medicine

country: USA

institute: Children's hospital of Philadelphia

description:
Library name: Sample26
name for fastq files: GC23

data_processing:
Study Arm 1: Bulk RNA-seq raw fastq files were first subjected to quality control using FastQCa (v0.12.1) to identify potential issues such as contamination and adapter sequences. After trimming low-quality sequences, FastQC was rerun on the cleaned reads to ensure that all major quality issues were resolved. Study Arm 2: Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification. After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Study Arm 1: The sequencing reads were then aligned to the Sus scrofa reference genome (Sscrofa11.1) using HISAT2 (v2.2.1). Study Arm 2: The trimmed reads were mapped to the Sus Scrofa reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Study Arm 1: Gene expression levels were quantified with featureCounts (v2.0.6), and differential expression analysis was conducted using DESeq2. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison. Study Arm 2: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the geneid feature in the annotation file. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison.
Assembly: Study Arm 1: The sequencing reads were then aligned to the Sus scrofa reference genome (Sscrofa11.1) using HISAT2 (v2.2.1). Study Arm 2: The trimmed reads were mapped to the Sus Scrofa reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: csv file for normalized data for Arm1 and Arm2

organism: Sus scrofa

source_name: Myocardium

extract_protocol:
Total RNA was extracted using the Rneasy Mini Kit (Qiagen) as per manufacturer guidelines. RNA purity was assessed on a NanoDrop spectrophotometer. Study Arm 1: RNA concentration was measured on a Qubit 2.0 fluorometer (Invitrogen). RNA integrity was assessed on an Agilent Bioanalyzer 2100 using a Nano 6000 assay kit (Agilent Technologies); samples with RIN > 6 were used for library preparation. A total amount of > 600 ng RNA per sample was used as input material for the RNA sample preparations. Study Arm 2: RNA samples were quantified using Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA inputs were normalized to 100ng.
Study Arm 1: Sequencing libraries were generated using Illumina TruSeq Stranded mRNA kit and modified the protocol by replacing the Illumina TruSeq PCR reaction with KAPA HiFi HotStart Ready Mix for the final PCR step to ensure compatibility with the 2x75bp paired-end sequencing on the Aviti Element. Study Arm 2: ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software.

treatment_protocol: Myocardial biopsies were collected at the end of experiment, flash-frozen in liquid nitrogen and stored at -80°C.

value: Myocardium

value: Cardiomyocytes

tag: experimental treatment

value: HOPE

tag: experimental time


title: BC-TuX-4IC-MFAP2_OE_replcate 2

city: New Orleans

first: Elizabeth

middle: Carol

last: Martin

state: LA

address: 1430 Tulane Avenue

department: Medicine

institute: Tulane University

description: Library name: Sample 5

data_processing:
Kallisto was used to map short sequencing reads to the reference genome.
Assembly: Reads were aligned to the human genome with cDNA sequences corresponding to Ensembl genes, excluding ncRNA genes.
Supplementary files format and content: Data files represent relative gene abundance as TMPs. Format excel.

molecule: polyA RNA

organism: Homo sapiens

source_name: Cell line

growth_protocol: The metaplastic TNBC cell line TU-BcX-4IC and non-metaplastic TNBC cell line MDA-MB-231 (ATCC, Manassas, VA, USA) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, Waltham, MA, USA) supplemented with 10% HyClone Cosmic Calf Serum (Cytiva), 1% minimal essential amino acids (Gibco, Waltham, MA), 1% non-essential amino acids (Gibco, Waltham, MA, USA), 1% antibiotic/anti-mycotic (Gibco, Waltham, MA, USA) and insulin (Gibco, Waltham, MA, USA) under mycoplasma-free conditions at 37 °C and 5% v/v CO2. Cells were seeded in T25 flasks and collected at 80% confluence for RNA extraction.

extract_protocol:
Total RNA was extracted from the cell lines using Quick RNA Miniprep Kit from Zymo Research (Irvine, CA, USA) and sent to Azenta (TU-BcX-4IC) (Burlington, MA, USA)  for RNA sequencing.
The RNA sequencing workflow after RNA isolation included initial PolyA selection: based mRNA enrichment, mRNA fragmentation, and random priming with subsequent first- and second-strand complementary DMA (cDNA) synthesis. Afterward, end-repair 5’ phosphorylation and nucleotide (dA)-tailing were performed. Last, adaptor ligation, polymerase chain reaction (PCR), and Illumina NovaSeq technology-based sequencing with 2 150-base pair (bp) read length were carried out.

treatment_protocol: No treatments were used in this study

value: Cell line

tag: cell line

value: breast cancer cell line

tag: genotype

value: WT


title: Cerebral cortex, dMCAO, d28, rep2

description: single nucleus RNA seq


title: Arm1,Pig#2,HOPE, 24h

description:
Library name: Sample25
name for fastq files: GC18


title: Arm1,Pig#6,HOPE, 12h

description:
Library name: Sample24
name for fastq files: GC27


title: VIC_tricuspid_calcified_3

type: RNA

city: Lille

first: Mickael

last: Rosa

address: Boulevard du professeur Jules Leclercq

country: France

institute: Université de Lille

description: Gene expression data from VIC isolated from calcified tricuspid aortic valves

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HuGene 2.0 chips.GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) using the Command Console software v4.1.2.

data_processing: The data were analyzed with GIANT (galaxy based tool, https://doi.org/10.1038/s41598-020-76769-w)

label: biotin

source_name: Calcified tricuspid aortic valve

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiagen Rneasy manufacturer's protocole

value: Aortic valve


title: E14 whole molar

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

country: Japan

institute: Tohoku University

library_source: transcriptomic single cell

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger pipeline v2.0 using default settings.
Secondary analysis was performed using Loupe Cell Browser v5 (10x Genomics, San Francisco, CA, USA). Clusters were defined by k-means clustering based on the PCA of the transcriptomic signature.
Assembly: Custom mm10 including common mouse transgenes
Supplementary files format and content: Cellranger filtered feature barcode matrix in HDF5 format
Supplementary files format and content: Cellranger raw feature barcode matrix in HDF5 format

source_name: Molar

extract_protocol:
Molars were dissected with sharp tweezers from seven littermates of P7 Krt14-RFP mice. Single cell dissociation was essentially performed as previously described (Li et al. 2015). Briefly, dissected incisors were incubated in 4 mg/ml Dispase II (Roche) for 14 min at 37°C. Then incisors were placed in cold DMEM/F12 and dental epithelium and mesenchyme were separated under microscope. The tissues are then placed in Accutase (Sigma) for 30min at 37°C. After pipetting up and down using 1000 μm tips, single cell suspension was further produced through a 70 μm sterile cell strainer. The cells were resuspended with 0.04% BSA containing cold PBS.
Single-cell suspensions were loaded onto a 10X Chromium Controller (10X Genomics) and library preparation was performed according to the manufacturer’s instructions for the 10X Chromium Next GEM Single Cell Library kit v2 (10X Genomics). Libraries were then pooled and sequenced on 4 lanes on a NextSeq500 sequencer (Illumina) using 10X Genomics recommended reads configuration.

value: Molar

tag: age


title: VIC_tricuspid_calcified_5


title: BC-TuX-4IC-vector_replcate 3

description: Library name: Sample 3


title: Arm1,Pig#4,HOPE, 12h

description:
Library name: Sample23
name for fastq files: GC22


title: Cerebral cortex, dMCAO, d28, rep1

description: single nucleus RNA seq


title: VIC_tricuspid_calcified_2


title: BC-TuX-4IC-vector_replcate 2

description: Library name: Sample 2


title: Arm1,Pig#2,HOPE, 12h

description:
Library name: Sample22
name for fastq files: GC17


title: Cerebral cortex, dMCAO, d14, rep3

description: single nucleus RNA seq

value: dMCAO, d14


title: BC-TuX-4IC-vector_replcate 1

description: Library name: Sample 1


title: Cerebral cortex, dMCAO, d14, rep2

description: single nucleus RNA seq


title: Cerebral cortex, dMCAO, d14, rep1

description: single nucleus RNA seq


title: Ischemic colon epithelium from patient #3

city: Baltimore

first: Maged

last: Zeineldin

state: MD

address: 1812 Ashland Ave

institute: Johns Hopkins University School of Medicine

description:
Library name: IS-3
RNA_Seq_Ischemic_Colitis_normalized_counts.csv: IS-3

data_processing:
FastQC software was used to exclude low-quality reads
Mapping HISAT2 software (version 2.0.5)
Counted and normalized as FPKM using featureCounts (version 1.5.0-p3)
Differentially expressed genes (DEG) were generated using DESeq2 (version 1.20.0) and edgeR (version 3.22.5)
Assembly: hg19
Supplementary files format and content: comma separated text file includeing raw counts for every sample

source_name: Colon

growth_protocol: These are archived FFPE samples

extract_protocol:
RNS extraction was done using Trizol Reagent manufacturer’s protocol, 500-ng were used for library prep
PolyA enrichment library prep was done by Novogene

treatment_protocol: No treatment: pathological ischemic and normal colon eoithelium were dissected from slides.

value: Colon

value: Epithelial cells

value: Hypoxia


title: Arm1,Pig#4,HOPE, 0h

description:
Library name: Sample17
name for fastq files: GC20


title: Arm1,Pig#6,HOPE, 0h

description:
Library name: Sample18
name for fastq files: GC25


title: BC-TuX-4IC-MFAP2_OE_replcate 1

description: Library name: Sample 4


title: Arm1,Pig#2,HOPE, 0h

description:
Library name: Sample16
name for fastq files: GC15


title: Ischemic colon epithelium from patient #1

description:
Library name: IS-1
RNA_Seq_Ischemic_Colitis_normalized_counts.csv: IS-1


title: VIC_tricuspid_calcified_4


title: VIC_control_4

description: Gene expression data from VIC isolated from control aortic valves

source_name: Control aortic valve


title: Arm1,Pig#5,SCS, 48h

description:
Library name: Sample15
name for fastq files: GC55

value: SCS


title: VIC_control_5


title: Cerebral cortex, dMCAO, d7, rep3

description: single nucleus RNA seq

value: dMCAO, d7


title: Normal colon epithelium from patient #2

description:
Library name: N-2
RNA_Seq_Ischemic_Colitis_normalized_counts.csv: N-2

value: Normal


title: VIC_control_3


title: Cerebral cortex, dMCAO, d7, rep2

description: single nucleus RNA seq

value: brain

value: whole cerebral cortex cells


title: VIC_tricuspid_calcified_1


title: Arm1,Pig#3,SCS, 48h

description:
Library name: Sample14
name for fastq files: GC50

value: Myocardium


title: Normal colon epithelium from patient #1

description:
Library name: N-1
RNA_Seq_Ischemic_Colitis_normalized_counts.csv: N-1


title: VIC_control_1


title: Arm1,Pig#1,SCS, 48h

description:
Library name: Sample13
name for fastq files: GC14

value: Cardiomyocytes


title: Cerebral cortex, dMCAO, d7, rep1

description: single nucleus RNA seq


title: LZG3

city: Nanjing

first: Yaxu

last: Liang

state: 江苏省

address: 江苏省南京市玄武区南京农业大学

country: China

institute: Nanjing agricultural university

description: Library name: sample12

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
we used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: GCF_000003025.6_Sscrofa11.1_genomic.fna
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: endometrium

extract_protocol:
Total RNA was extracted from endometrium samples using the Trizol method. Poly(A) + mRNA was isolated from total RNA using Dynabeads Oligo(dT)25
RNA was reverse transcribed into cDNA using random oligonucleotides, Super Script II, DNA Polymerase I, and RNase H. Adapters were ligated to both ends of cDNA fragments. Double-stranded cDNA of approximately 450 bp were selected using the AMPure XP bead-based purification system (Beckman Coulter, Beverly, CA, USA). Adapter-ligated libraries were enriched through polymerase chain reaction (PCR) amplification using the Illumina PCR Primer Cocktail for 15 cycles. The amplified libraries were purified using the AMPure XP system and quantified using the Agilent High Sensitivity DNA Assay on a Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Paired-end sequencing was performed on the NovaSeq X platform (Illumina, San Diego, CA, USA).

value: endometrium


title: LZG2

address: 江苏省南京市玄武区南京农业大学

description: Library name: sample11


title: Arm1,Pig#5,SCS, 24h

description:
Library name: Sample12
name for fastq files: GC54


title: Cerebral cortex, dMCAO, d3, rep3

description: single nucleus RNA seq

value: dMCAO, d3


title: Ischemic colon epithelium from patient #2

description:
Library name: IS-2
RNA_Seq_Ischemic_Colitis_normalized_counts.csv: IS-2


title: Arm1,Pig#3,SCS, 24h

description:
Library name: Sample11
name for fastq files: GC49


title: LZG1

address: 江苏省南京市玄武区南京农业大学

description: Library name: sample10


title: Arm1,Pig#1,SCS, 24h

description:
Library name: Sample10
name for fastq files: GC13


title: LNZG3

address: 江苏省南京市玄武区南京农业大学

description: Library name: sample9


title: Arm1,Pig#5,SCS, 12h

description:
Library name: Sample9
name for fastq files: GC53


title: Cerebral cortex, sham, rep3

description: single nucleus RNA seq

value: Sham


title: LNZG2

address: 江苏省南京市玄武区南京农业大学

description: Library name: sample8


title: Cerebral cortex, sham, rep2

description: single nucleus RNA seq


title: Cerebral cortex, dMCAO, d7, rep4

description: single nucleus RNA seq


title: Cerebral cortex, dMCAO, d3, rep1

description: single nucleus RNA seq


title: VIC_control_2


title: LNZG1

address: 江苏省南京市玄武区南京农业大学

description: Library name: sample7


title: Arm1,Pig#3,SCS, 12h

description:
Library name: Sample8
name for fastq files: GC48


title: VIC under control medium for 24h_2

description: Gene expression data from VIC isolated from control aortic valves treated with control medium

tag: medium

value: Control medium

value: Vehicle supplementation


title: HZG3

address: 江苏省南京市玄武区南京农业大学

description: Library name: sample6


title: VIC under osteogenic medium for 24h_4

description: Gene expression data from VIC isolated from control aortic valves treated with osteogenic medium

value: Aortic valve

value: Osteogenic medium


title: Cerebral cortex, sham, rep1

description: single nucleus RNA seq


title: VIC under control medium for 24h_4


title: Cerebral cortex, dMCAO, d3, rep2

description: single nucleus RNA seq


title: VIC under osteogenic medium for 24h_5


title: VIC under osteogenic medium for 24h_2


title: VIC under osteogenic medium for 24h_3


title: VIC under control medium for 24h_5


title: VIC under control medium for 24h_1


title: Arm1,Pig#1,SCS, 12h

description:
Library name: Sample7
name for fastq files: GC12


title: Control HH3/3plus stage embryo with 0.5h additional incubation

city: Cambridge

first: Benjamin

middle: J

last: Steventon

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description: Library name: Sample 3

data_processing:
CellRanger (10X Genomics) filtered feature matrices were passed into Seurat (Satija et al., 2015) in R v4.2.3. Reads were mapped to the galGal6 reference genome from the Genome Reference Consortium. The following quality control steps were taken: checking the % of mitochondrial genes, filtering out cells with too low or high number of different genes expressed, normalising the data, and regressing for both sex effect and cell cycle. Principal Component Analysis (PCA) was then performed for dimensionality reduction, followed by Uniform Manifold Approximation and Projection (UMAP) using the first 12 principal components (dims = 1:12) and a clustering resolution of 0.30 for visualization of cellular transcriptomic profiles. Feature plots were generated to display the expression patterns of genes of interest across the UMAP space. Correlation analyses were conducted between the expression levels of genes of interest across individual cells to assess co-expression dynamics.
Assembly: galGal6 reference genome (see above)
Supplementary files format and content: CellRanger filtered matrices (barcodes, features, and matrix).

organism: Gallus gallus

source_name: Whole embryo

growth_protocol: HH3/3+ embryos were first placed in New culture (New et al., 1955). Control embryos used in this study were collected as part of a larger node ablation experiment. Embryos were incubated for 0.5h, 2.5h, or 5h following manipulation. Only unablated control embryos were used here; these were detached from the vitelline membrane using an eyelash knife and reattached, to match handling conditions with ablated samples.

extract_protocol:
Embryos were dissected in cold PBS+/+, and approximately half of the area opaca was trimmed to enrich for embryonic tissue. Each embryo was transferred to a 1.5mL Eppendorf tube, washed 3× with PBS+/+, and incubated in 1 mL 0.05% trypsin (Thermo Fisher Scientific) at 37C for 15min with gentle trituration every 5min. Trypsin was quenched with 100uL FBS, and cells were pelleted (450×g, 5min, 4C) and resuspended in PBS + 0.05% BSA (Sigma-Aldrich). Cell viability (85–95%) was assessed via haemocytometer.
Single-cell suspensions were submitted to the CRUK CI Genomics Core Facility for 10X Genomics library preparation and Illumina sequencing.

value: Whole embryo

value: WT


title: Arm1,Pig#5,SCS, 0h

description:
Library name: Sample3
name for fastq files: GC51


title: VIC under control medium for 24h_3


title: Arm1,Pig#3,SCS, 0h

description:
Library name: Sample2
name for fastq files: GC46


title: HNZG3

address: 江苏省南京市玄武区南京农业大学

description: Library name: sample3


title: Arm1,Pig#1,SCS, 0h

description:
Library name: Sample1
name for fastq files: GC10


title: Control HH3/3plus stage embryo with 5h additional incubation

description: Library name: Sample 1


title: HZG2

address: 江苏省南京市玄武区南京农业大学

description: Library name: sample5


title: HZG1

address: 江苏省南京市玄武区南京农业大学

description: Library name: sample4


title: day 11 chicken embryonic pituitary_CORT

city: College Park

first: Tom

last: Porter

state: Maryland

address: 8127 Regents Drive

department: Animal and Avian Sciences

institute: University of Maryland

description:
Library name: e11 CEP_CORT
10X Genomics

data_processing:
The demultiplexing, quality control, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.2.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Further quality control was done and projections were generated using the Rstudio computer program; specifically the Seurat package v4.2.0 (https://cran.r-project.org/web/packages/Seurat/index.html)
Data visualization and cell type identification were made using Loupe Browser v8.0.0 (https://www.10xgenomics.com/support/software/loupe-browser/latest)
Assembly: GRCg6a (Ensembl release 105)
Supplementary files format and content: CellRanger output files: Basal_filtered_feature_bc_matrix.h5, CORT_filtered_feature_bc_matrix.h5
Supplementary files format and content: Rstudio: Basal.h5Seurat, CORT.h5Seurat
Supplementary files format and content: Rstudio: Basal_projection_RStudio.csv, CORT_projection_Rstudio.csv
Supplementary files format and content: Loupe Browser: Basal_Cell Types_Loupe.csv, CORT_Cell Types_Loupe.csv

source_name: Pituitary

extract_protocol:
Pituitaries were dissected from e11 embryos (n=246), trypsin-dispersed, and pooled. Cells were counted, and the cell viability was assessed by the trypan blue dye-exclusion method. An individual e11 pituitary gland yielded around 300,000 cells and cell viability was > 95% in all experiments. Dispersed cells were plated at a density of 1,000,000 cells per well in poly-L-lysine-coated 24-well plates and were allowed to attach for 1 h at 37.5°C. Dulbecco's Modified Eagle Medium w/F12 modifications (DMEM/F12) medium supplemented with 0.1% bovine serum albumin (BSA), 100 U/mL penicillin, and 100 μg/mL streptomycin was added, and the cells were cultured for an additional 19 h. CORT (100 nM final concentration) was added to appropriate wells for an additional 6 h, and the cells were fixed following the methanol fixation and rehydration of the single cell suspension according to GENEWIZ protocol (10x Genomics). Methanol fixed cells were further processed by the Next-Generation Sequencing team at GENEWIZ from Azenta Life Sciences.
At GENEWIZ, cell viability was assessed and, if necessary, dead cell removal was performed. Cells were then processed by the 10x Genomics Chromium™ Controller to create single-cell libraries. Within the Chromium Controller, cells were loaded onto a microfluidic chip and encapsulated within droplets containing barcoded gel beads and reagents for reverse transcription. Following cell lysis, the beads captured the poly(A) tails of the mRNA molecules. Reverse transcription generated cDNA tagged with a 10x barcode to identify the cell and a unique molecular identifier (UMI) to label the mRNA transcript. The pooled cDNA was amplified in bulk, and Illumina adapters, including a sample index, were added to the fragments to generate sequencing libraries. The libraries were then pooled and sequenced on the Illumina® platform.

treatment_protocol: CORT (100 nM) treatment

value: Pituitary

value: CORT


title: anti-IgG

city: Fuzhou

first: You

last: Li

state: Fujian

address: No.15 Shangxiadian Road

institute: Fujian Agriculture and Forestry University

description: Library name: CK

library_source: genomic

data_processing:
The NFAT sample yielded 20.63 million raw reads, with 3.08 million uniquely mapped pairs after deduplication. The Control (CK) sample yielded 16.48 million raw reads, with 6.12 million(37.168) uniquely mapped pairs after deduplication. Both samples showed high data quality with >99.99
Supplementary files format and content: fq

molecule: genomic DNA

organism: Diaphorina citri

source_name: whole body

growth_protocol: The CHIP-Seq exper iment included three biological replicates for each condition ( NFAT antibody and control IgG)

extract_protocol:
Each biological replicate was processed separately starting from chromatin crosslinking of 100 CLas-free psyllids.
The ChIP-seq data were generated using 150 bp paired-end reads on an illumina NovaSeq.

treatment_protocol: Anti-NFAT(1:100); Anti-Rabbit IgG (Control, Beyotime, CAT#A701, 1:100)

value: whole body

value: anti-IgG


title: VIC under osteogenic medium and AM80 for 24h_5

description: Gene expression data from VIC isolated from control aortic valves treated with osteogenic medium and Am80

value: AM80 supplementation


title: day 11 chicken embryonic pituitary_basal

description:
Library name: e11 CEP_basal
10X Genomics

value: basal, untreated


title: anti-NFAT

description: Library name: NFAT

value: anti-NFAT


title: HNZG2

address: 江苏省南京市玄武区南京农业大学

description: Library name: sample2


title: HNZG1

address: 江苏省南京市玄武区南京农业大学

description: Library name: sample1


title: Control HH3/3plus stage embryo with 2.5h additional incubation

description: Library name: Sample 2


title: Ovarian granulosa cells, CTX3

status: Public on Dec 23 2025

city: Nanchang

first: Haocheng

last: Gu

state: Jiangxi Province

address: Hongguantang Sub-district

institute: Nanchang University

description:
Library name: Sample6
Column name in raw_counts_All_Samples.txt:CTX3

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
Assembly: GRCm39
Supplementary files format and content: tab-delimited xls file includes text file includes raw counts for each Sample

source_name: Ovarian granular cells

growth_protocol: Ovarian granulosa cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvest using Agilent2100 bioanalyzer. 1.3 μg of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: The in vitro model of premature ovarian failure was induced by adding cyclophosphamide (MCE) to cells after two days of adherent culture.

value: Ovarian granular cells

value: granular cells

value: Intraperitoneal injection of cyclophosphamide


title: Ovarian granulosa cells, Normal1

description:
Library name: Sample1
Column name in raw_counts_All_Samples.txt:Normal1


title: Ovarian granulosa cells, Normal2

description:
Library name: Sample2
Column name in raw_counts_All_Samples.txt:Normal2


title: Ovarian granulosa cells, CTX2

description:
Library name: Sample5
Column name in raw_counts_All_Samples.txt:CTX2


title: Ovarian granulosa cells, Normal3

description:
Library name: Sample3
Column name in raw_counts_All_Samples.txt:Normal3


title: Ovarian granulosa cells, CTX1

description:
Library name: Sample4
Column name in raw_counts_All_Samples.txt:CTX1


title: VIC under osteogenic medium for 24h_1


title: Lymph node cells, remitter-rep4

city: New Haven

first: Ying

last: Wu

state: CT

address: 300 George St

institute: Yale University

description:
Library name: Remitter_NOD_4_pLN
10x Genomics

data_processing:
The demultiplexing, aligning reads, counting barcodes and UMIs, generating feature-barcode matrices, and performing clustering and gene expression analysis was performed using Cell Ranger software v7.1.0.
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
The isolated mouse islets were incubated in 2ml Accutase™ Cell Dissociation reagent at room temperature for 5 mins on a tube rotator. After incubation, islet cells were resuspened thoroughly by pipet up and down. Five-time volume of culture medium with 10% FBS was added to stop excessive dissociation reactions. Then dissociated islet cells were washed and resuspened in PBS with 0.04% BSA. Pancreatic draining lymph node cells were dispersed into single cells by grinding the samples using the blunt end of a syringe over a cell strainer. Alive cells were counted using trypan blue and hemacytometer.
Library was constructed according to the manufacturer's protocols (Chromium Next GEM Single Cell 5' v2, Dual Index, 10X Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). Gel bead primers contain an Illumina TruSeq Read 1 primer, a 10x Barcode, a unique molecular identifier (UMI), and template switch oligo (TSO). Then the poly-A mRNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which was amplified. The amplifiedd cDNA from poly-A mRNA and the amplified DNA from cell surface protein Feature Barcode are separated by size selection for generating V(D)J and/or 5' Gene Expression libraries and Cell Surface Protein (hashtag) libraries, respectively.

value: Lymph node

tag: Sex

value: female

value: Lymph node cells

value: NOD

value: anti-CD3 mAb


title: Lymph node cells, remitter-rep3

description:
Library name: Remitter_NOD_3_pLN
10x Genomics


title: Lymph node cells, remitter-rep2

description:
Library name: Remitter_NOD_2_pLN
10x Genomics


title: Lymph node cells, remitter-rep1

description:
Library name: Remitter_NOD_1_pLN
10x Genomics


title: Islet cells, remitter-rep2

description:
Library name: Remitter_NOD_2
10x Genomics

source_name: Islet

value: Islet

value: Islet cells


title: Islet cells, remitter-rep3

description:
Library name: Remitter_NOD_3
10x Genomics


title: VIC under osteogenic medium and AM80 for 24h_3

value: Aortic valve

value: Osteogenic medium


title: VIC under osteogenic medium and AM80 for 24h_2


title: Islet cells, remitter-rep1

description:
Library name: Remitter_NOD_1
10x Genomics


title: VIC under osteogenic medium and AM80 for 24h_4


title: Pancreatic islet cells, ß-Tfrc-KO (biol rep 1)

city: Jette

first: Annelore

last: Van Mulders

state: Brussels

address: Laarbeeklaan 103

department: Faculty Medicine & Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description:
Library name: None-Sample3-Case
10x Genomics

data_processing:
The binary base call (BCL) files were demultiplexed into individual samples using the Cell Ranger mkfastq pipeline (v.6.0.2). The Cre transgene sequence was integrated into the mouse reference genome.
Assembly: Mouse mm10
Supplementary files format and content: Processed data files are provided in 10x Genomics format and include three files per sample: (1) *_barcodes.tsv.gz — list of cell barcodes, (2) *_features.tsv.gz — gene annotations, (3) *_matrix.mtx.gz — sparse matrix of gene expression counts. These files represent the filtered gene-cell expression matrices generated by Cell Ranger. Rows = genes, columns = cells.

source_name: Pancreatic islets

extract_protocol:
Tthe main pancreatic duct was injected with 2 mL ice-cold 1x HBSS containing 0.140 mL CIzyme RI (PELOBiotech, VitaCyte, 005-1030). The pancreas was digested for 17 min. at 37°C in 1 mL HBSS supplemented with 7.5% (w/v) sodium bicarbonate, 0.25% (w/v) bovine serum albumin (BSA) (Sigma-Aldrich, A1470), and 0.1 mg/mL kanamycin (Sigma-Aldrich, 11815032). Afterward, the tube was shaken and 14 mL HBSS, supplemented as described above, was added. After centrifugation and resuspension, the digest was filtered over a 500-micron filter (pluriSelect Life Science, 43-50500-50). The pellet was resuspended in 14 mL Histopaque 1100, the latter prepared by mixing Histopaque 1077 (Sigma-Aldrich, 10771) with Histopaque 1119 (Sigma-Aldrich, 11191) and centrifuged for 20 min. at 328 g without brake. The supernatant containing the islets was transferred to a new tube containing 25 mL HBSS, supplemented as described above. After centrifugation, the islets were resuspended in islet culture medium and were allowed to recover at 37°C and 5% CO2 for at least 2 hours before handpicking and subsequent overnight culture. After overnight culture, mouse islets were collected in a 1.5 mL tube, centrifuged (3 min. at 124 g) and dissociated into single cells with NeuroCult Dissociation Solution (StemCell Technologies, 05715). For fluorescence-activated cell sorting (FACS), cells were washed with RPMI 1640 + 10% (v/v) FBS before filtering over a 5 mL filter cap tube (Corning, Falcon, 352235). For scRNA-seq, cells were washed with ice-cold PBS + 0.04% (w/v) BSA before filtering with a 40-micron Flowmi cell strainer (Sigma, BAH136800040) into a new 1.5 mL tube on ice. Cell number and viability were measured with a NucleoCounter NC-200 using a Via1 cassette (ChemoMetec, 941-0012).
For scRNA-seq of islet cells of 3-week-old CTRL and β-Tfrc-KO mice, GEMs and scRNA-seq libraries were prepared with the Chromium Next GEM Single Cell 3’ Kit v3.1, Chromium Next GEM Chip G Single Cell Kit, and the Dual Index Kit TT Set A according to the manufacturer’s instructions using the Chromium Controller (10x Genomics). GEM reverse transcription (GEM-RT) was carried out in a C1000 Touch Thermal Cycler (Bio-Rad) at 53°C for 45 min., followed by inactivation at 85°C for 5 min. Cleanup of the GEM-RT product was performed using Dynabeads MyOne SILANE reagent and the SPRIselect Reagent Kit (Beckman Coulter). cDNA amplification involved an initial denaturation at 98°C for 3 min., followed by 11 to 12 cycles at 98°C for 15 sec., 63°C for 20 sec., and 72°C for 1 min., with a final extension at 72°C for 1 min. Subsequent steps included enzymatic fragmentation, size selection, and the addition of adaptors and sample indices. Sequencing libraries were loaded onto a NovaSeq 6000 using the Novaseq S2 Reagent Kit (Illumina).

value: Pancreatic islets

value: Beta-Tfrc-KO

value: 3 weeks


title: Pancreatic islet cells, CTRL (biol rep 2)

description:
Library name: None-Sample2-Contol
10x Genomics

value: Control


title: Pancreatic islet cells, CTRL (biol rep 1)

description:
Library name: None-Sample1-Contol
10x Genomics


title: CC70HCPOS2

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

description: Library name: CC70HCPOS2

data_processing:
R1 reads were used to identify both cell barcodes and UMI using UMI-tools version 1.0.1 with the following settings: “--bc-pattern='(?P<cell_1>.{16})(?P<umi_1>.{12})' --extract-method=regex --knee-method=distance --method=umis --set-cell-number=15000 –ed-above-threshold=discard”
After read extraction and addition of cell barcodes and UMI to headers of R2 reads, fastq reads were mapped to the ENSEMBL reference genome using STAR version 2.7.1a with standard settings except that any reads mapping to more than one location in the genome (ambiguous reads) were discarded (m = 1)
All reads mapping in the proper orientation within exons and introns were reported using featureCounts version 1.6.4 UMI counts were calculated using UMI-tools with ‘--per gene --gene-tag=XT --assigned-status-tag=XS --per-cell’ arguments.
Assembly: GRCm38.96
Supplementary files format and content: Tab-separated table of gene counts per cell barcode

source_name: Brain, hippocampus

extract_protocol:
To perform single nuclear RNA-seq, we FAN-sorted neurons from Nutrap transgenic mice from control and at different time points after intravenous wtLCMV challenge. Each sample represents 10000  neuronal nuclei. sorted nuclei were adjusted to 5.5x105 cells/mL of PBS, 0.04% BSA before proceeding with droplet generation.
Library was performed according to the manufacter's instructions Chromium Next GEM Single Cell 3ʹ Kit v3.1 (CG000204)

value: Brain, hippocampus

value: C57BL/6J, NuTRAP transgenic

value: Neurons

tag: neuronal population

value: virus-exposed neurons

tag: disease stage_(days_post_challenge)

value: 15 weeks

tag: biological replicate


title: VIC under osteogenic medium and AM80 for 24h_1

description: Gene expression data from VIC isolated from control aortic valves treated with osteogenic medium and Am80

value: AM80 supplementation


title: CC70HCNEG2

description: Library name: CC70HCNEG2

value: bystander neurons


title: CC70HCPOS1

description: Library name: CC70HCPOS1


title: CC70HCNEG1

description: Library name: CC70HCNEG1


title: CNC70HCNEG

description: Library name: CNC70HCNEG


title: CC10HCPOS2

description: Library name: CC10HCPOS2

value: 6.4 weeks


title: CC10HCNEG2

description: Library name: CC10HCNEG2


title: CC10HCPOS1

description: Library name: CC10HCPOS1


title: CNCHCNEG1

description: Library name: CNCHCNEG1


title: CNCHCPOS2

description: Library name: CNCHCPOS2


title: CNCHCNEG2

description: Library name: CNCHCNEG2


title: CNCHCPOS1

description: Library name: CNCHCPOS1


title: CC10HCNEG1

description: Library name: CC10HCNEG1


title: NCCHC

description: Library name: NCCHC

value: hetergenous population of bystander and virus-exposed neurons

value: 16 weeks


title: CNCHC

description: Library name: CNCHC


title: CC80HC

description: Library name: CC80HC


title: Pancreatic islet cells, ß-Tfrc-KO (biol rep 2)

description:
Library name: None-Sample4-Case
10x Genomics


title: CC10HC

description: Library name: CC10HC


description:
Library name: Input_WT_CnC10_H3K27ac_rep2_H3K27me3_rep2_H3K4me3_rep2_HC
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input

data_processing:
Basecalls performed using CASAVA version 1.8.2
Adaptors were trimming using cutadapt 1.9.1
Reads were mapped to the reference genome using bowtie2 2.2.26
Duplicated reads were marked with picard-tools-1.126 and removed with samtools 1.2
Peaks were called using macs2 v2.1.2 with -p 0.01 –to-large –nomodel and shiftsize set to 75
Reproducible peaks were obtained following ENCODE guidelines (https://www.encodeproject.org/chip-seq/histone)
chromatin states were assessed with ChromHMM 1.24 with 6 states
Assembly: GRCm38.96
Supplementary files format and content: bigWig for all samples, called peaks for each condition in bed format
Supplementary files format and content: chromatin state segments in bed format

extract_protocol:
To perform ChIP-seq, we extracted  nuclei from hippocampus and brainstem of viral déjà vu mice at different time points after intravenous wtLCMV challenge, chromatin was fixed then we FAN-sorted neuronal nulclei.  Each biological replicate represents 200K  neuronal nuclei.fixed chromatin was incubated with proper ChIP-seq grade antibody, then DNA was extracted. non ChIPed genomic DNA was extracted to serve as input
Nuclei were pelleted and resuspended with 25 µl of complete lysis buffer (lysis buffer + 1% protease inhibitor cocktail 200X provided in kit) per 100K nuclei and incubated for 5 minutes to ensure lysis then 75 complete Hank’s balanced salt solution buffer (HBSS) (ThermoFisher Scientific, 14175095) (HBSS + 1% protease inhibitor cocktail 200X) was added per 100 K nuclei. Chromatin was sheared by sonication using a Picoruptor® (Diagenode) for 6 cycles. 20% of sample was set aside to serve as input and volume corresponding to 200K was subjected to magnetic immunoprecipitation using ChIP-seq grade antibodies: anti-H3K4me3 antibody (Diagenode, C15310003), anti-H3K27me3 antibody (Diagenode, C15410195-10), and anti-H3K27ac antibody (abcam, 4729). The ChIPmentation libraries were sequenced using 50 bp single-end reads on the HiSeq X (Illumina).

value: neurons

value: 6 weeks


description:
Library name: Input_WT_CnC10_H3K27ac_rep1_H3K27me3_rep1_H3K4me3_rep1_HC
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


description:
Library name: Input_WT_CnC10_H3K27ac_rep2_H3K27me3_rep2_H3K4me3_rep2_BS
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input

source_name: Brain, brainstem

value: Brain, brainstem


description:
Library name: Input_WT_CnC10_H3K27ac_rep1_H3K27me3_rep1_H3K4me3_rep1_BS
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


description:
Library name: Input_WT_CC70_H3K27ac_rep2_H3K27me3_rep2_H3K4me3_rep2_HC
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


description:
Library name: Input_WT_CC70_H3K27ac_rep1_H3K27me3_rep1_H3K4me3_rep1_HC
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


description:
Library name: Input_WT_CC30_H3K27ac_rep2_H3K27me3_rep2_H3K4me3_rep2_HC
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input

value: 8.4 weeks


description:
Library name: Input_WT_CC30_H3K27ac_rep1_H3K27me3_rep1_H3K4me3_rep1_HC
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


description:
Library name: Input_WT_CC30_H3K27ac_rep1_H3K27me3_rep1_H3K4me3_rep1_BS
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


title: CNC70HCPOS

description: Library name: CNC70HCPOS


description:
Library name: Input_WT_CC30_H3K27ac_rep2_H3K27me3_rep2_H3K4me3_rep2_BS
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


description:
Library name: Input_WT_CC10_H3K27ac_rep2_H3K27me3_rep2_HC
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


description:
Library name: Input_WT_CC10_H3K27ac_rep2_H3K27me3_rep2_H3K4me3_rep2_BS
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


description:
Library name: Input_WT_CC10_H3K27ac_rep1_H3K27me3_rep1_H3K4me3_rep2_HC
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


title: WT_CnC10_H3K4me3_BS_rep2

description:
Library name: WT_CnC10_H3K4me3_BS_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted

tag: chip antibody

value: anti-H3K4me3  Diagenode Cat#C15310003


title: Input_WT_CC10_H3K4me3_HC_rep1

description:
Library name: Input_WT_CC10_H3K4me3_HC_rep1
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


description:
Library name: Input_WT_CC10_H3K27ac_rep1_H3K27me3_rep1_H3K4me3_rep1_BS
chromatin was extracted  from sorted  neuronal nuclei then DNA was purified and sequenced to serve as input


title: WT_CnC10_H3K27me3_BS_rep2

description:
Library name: WT_CnC10_H3K27me3_BS_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted

value: anti-H3K27me3  Diagenode Cat#C15410195-10


title: WT_CnC10_H3K27ac_BS_rep2

description:
Library name: WT_CnC10_H3K27ac_BS_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted

value: anti-H3K27ac Abcam Cat#ab 4729


title: WT_CC30_H3K4me3_BS_rep2

description:
Library name: WT_CC30_H3K4me3_BS_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC30_H3K27ac_BS_rep1

description:
Library name: WT_CC30_H3K27ac_BS_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC30_H3K27ac_BS_rep2

description:
Library name: WT_CC30_H3K27ac_BS_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CnC10_H3K4me3_BS_rep1

description:
Library name: WT_CnC10_H3K4me3_BS_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CnC10_H3K27ac_BS_rep1

description:
Library name: WT_CnC10_H3K27ac_BS_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC30_H3K4me3_BS_rep1

description:
Library name: WT_CC30_H3K4me3_BS_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CnC10_H3K27me3_BS_rep1

description:
Library name: WT_CnC10_H3K27me3_BS_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC30_H3K27me3_BS_rep2

description:
Library name: WT_CC30_H3K27me3_BS_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_H3K4me3_BS_rep2

description:
Library name: WT_CC10_H3K4me3_BS_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_H3K27me3_BS_rep1

description:
Library name: WT_CC10_H3K27me3_BS_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_H3K4me3_BS_rep1

description:
Library name: WT_CC10_H3K4me3_BS_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_H3K27me3_BS_rep2

description:
Library name: WT_CC10_H3K27me3_BS_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_H3K27ac_BS_rep1

description:
Library name: WT_CC10_H3K27ac_BS_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CnC10_H3K27me3_HC_rep2

description:
Library name: WT_CnC10_H3K27me3_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted

value: Brain, hippocampus


title: WT_CnC10_H3K4me3_HC_rep1

description:
Library name: WT_CnC10_H3K4me3_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted

value: C57BL/6J, NuTRAP transgenic


title: WT_CnC10_H3K27me3_HC_rep1

description:
Library name: WT_CnC10_H3K27me3_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CnC10_H3K27ac_HC_rep2

description:
Library name: WT_CnC10_H3K27ac_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC70_H3K4me3_HC_rep1

description:
Library name: WT_CC70_H3K4me3_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CnC10_H3K27ac_HC_rep1

description:
Library name: WT_CnC10_H3K27ac_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC70_H3K27me3_HC_rep2

description:
Library name: WT_CC70_H3K27me3_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC70_H3K27me3_HC_rep1

description:
Library name: WT_CC70_H3K27me3_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC70_H3K27ac_HC_rep1

description:
Library name: WT_CC70_H3K27ac_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC30_H3K27me3_HC_rep1

description:
Library name: WT_CC30_H3K27me3_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_H3K4me3_HC_rep2

description:
Library name: WT_CC10_H3K4me3_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CnC10_H3K4me3_HC_rep2

description:
Library name: WT_CnC10_H3K4me3_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC30_H3K4me3_HC_rep1

description:
Library name: WT_CC30_H3K4me3_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC30_H3K27me3_HC_rep2

description:
Library name: WT_CC30_H3K27me3_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC30_H3K27me3_BS_rep1

description:
Library name: WT_CC30_H3K27me3_BS_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_H3K27ac_HC_rep2

description:
Library name: WT_CC10_H3K27ac_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_H3K27ac_HC_rep1

description:
Library name: WT_CC10_H3K27ac_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_H3K27me3_HC_rep2

description:
Library name: WT_CC10_H3K27me3_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_H3K27me3_HC_rep1

description:
Library name: WT_CC10_H3K27me3_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC70_H3K4me3_HC_rep2

description:
Library name: WT_CC70_H3K4me3_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_H3K27ac_BS_rep2

description:
Library name: WT_CC10_H3K27ac_BS_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC70_H3K27ac_HC_rep2

description:
Library name: WT_CC70_H3K27ac_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC70_GFPneg_BS_rep2

description:
Library name: WT_CC70_GFPneg_BS_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei

data_processing:
Basecalls performed using CASAVA version 1.8.2
Adaptors were trimming using cutadapt 1.9.1
Reads were mapped to the reference genome using bowtie2 2.2.26
Duplicated reads were marked with picard-tools-1.126 and removed with samtools 1.2
Reads were shifted by +4bp on the forward strand and -5bp on the reverse strand
Peaks were called using macs2 v2.1.2 with -p 0.01 –to-large –nomodel and shiftsize set to 75
Reproducible peaks were obtained by IDR procedure with -p 0.01
Assembly: Reproducible peaks overlapping blacklist (https://www.nature.com/articles/s41598-019-45839-z) were removed
Supplementary files format and content: bigWig for each samples and peak files in bed format for each condition

extract_protocol:
To perform ATAC-seq, we FAN-sorted neuronal nuclei from viral déjà vu mice at different time points after intravenous wtLCMV challenge. Each biological replicate represents 50000  neuronal nuclei
Neuronal nuclei were spun down at 500 g for 20 min at 4 °C. Nuclei were isolated in 50 μl of lysing solution composed of 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630. The nuclear pellet was resuspended into 50 μl of tagmentation buffer containing the Tn5 transposase (Illumina) and incubated at 37 °C for 30 min. The tagmented DNA was purified using MiniElute PCR Purification Kit (Qiagen). Libraries were preamplified for 5 cycles using indexed primer from Nextera kit (Illumina) and NEBNext High Fidelity PCR master mix (New England Biolabs). Preamplified libraries served as input to determine the number of remaining cycles needed for the second round of PCR amplification. Libraries were cleaned by Ampure Beads (Agencourt) at a 1.5× ratio.


title: IFNGR_CC30_GFPpos_HC_rep2

description:
Library name: IFNGR_CC30_GFPpos_HC_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei

value: C57BL/6J, NuTRAP transgenic IFNGR2 floxed


title: WT_CC70_GFPpos_BS_rep1

description:
Library name: WT_CC70_GFPpos_BS_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei

value: virus-exposed neurons


title: WT_CC70_GFPneg_BS_rep1

description:
Library name: WT_CC70_GFPneg_BS_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei

value: 15 weeks


title: IFNGR_CC30_GFPpos_HC_rep1

description:
Library name: IFNGR_CC30_GFPpos_HC_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC30_H3K4me3_HC_rep2

description:
Library name: WT_CC30_H3K4me3_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC30_GFPpos_BS_rep2

description:
Library name: WT_CC30_GFPpos_BS_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC30_H3K27ac_HC_rep2

description:
Library name: WT_CC30_H3K27ac_HC_rep2
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC30_H3K27ac_HC_rep1

description:
Library name: WT_CC30_H3K27ac_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CC10_GFPpos_BS_rep1

description:
Library name: WT_CC10_GFPpos_BS_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC30_GFPneg_BS_rep1

description:
Library name: WT_CC30_GFPneg_BS_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC10_GFPneg_BS_rep1

description:
Library name: WT_CC10_GFPneg_BS_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC10_GFPneg_BS_rep2

description:
Library name: WT_CC10_GFPneg_BS_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC10_H3K4me3_HC_rep1

description:
Library name: WT_CC10_H3K4me3_HC_rep1
extracted chromatin from sorted 200K neuronal nuclei was incubated with proper ChIP-seq grade antibody, then DNA was extracted


title: WT_CnC10_GFPpos_BS_rep1

description:
Library name: WT_CnC10_GFPpos_BS_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC30_GFPneg_BS_rep2

description:
Library name: WT_CC30_GFPneg_BS_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC70_GFPpos_BS_rep2

description:
Library name: WT_CC70_GFPpos_BS_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC70_GFPpos_HC_rep2

description:
Library name: WT_CC70_GFPpos_HC_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CnC10_GFPneg_BS_rep2

description:
Library name: WT_CnC10_GFPneg_BS_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CnC10_GFPneg_BS_rep1

description:
Library name: WT_CnC10_GFPneg_BS_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC70_GFPpos_HC_rep1

description:
Library name: WT_CC70_GFPpos_HC_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC70_GFPneg_HC_rep2

description:
Library name: WT_CC70_GFPneg_HC_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC70_GFPneg_HC_rep1

description:
Library name: WT_CC70_GFPneg_HC_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC30_GFPpos_HC_rep2

description:
Library name: WT_CC30_GFPpos_HC_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC30_GFPpos_HC_rep1

description:
Library name: WT_CC30_GFPpos_HC_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC30_GFPpos_BS_rep1

description:
Library name: WT_CC30_GFPpos_BS_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC10_GFPpos_BS_rep2

description:
Library name: WT_CC10_GFPpos_BS_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC30_GFPneg_HC_rep2

description:
Library name: WT_CC30_GFPneg_HC_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC30_GFPneg_HC_rep1

description:
Library name: WT_CC30_GFPneg_HC_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC10_GFPneg_HC_rep2

description:
Library name: WT_CC10_GFPneg_HC_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC10_GFPpos_HC_rep2

description:
Library name: WT_CC10_GFPpos_HC_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CC10_GFPneg_HC_rep1

description:
Library name: WT_CC10_GFPneg_HC_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CnC10_GFPpos_HC_rep1

description:
Library name: WT_CnC10_GFPpos_HC_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CnC10_GFPpos_HC_rep2

description:
Library name: WT_CnC10_GFPpos_HC_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CnC10_GFPpos_BS_rep2

description:
Library name: WT_CnC10_GFPpos_BS_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CnC10_GFPneg_HC_rep1

description:
Library name: WT_CnC10_GFPneg_HC_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: WT_CnC10_GFPneg_HC_rep2

description:
Library name: WT_CnC10_GFPneg_HC_rep2
extracted and tagmented chromatin from sorted 50K neuronal nuclei


title: Mettl3 KO-Mettl3

city: Ann Arbor

first: Zhaowei

last: Han

state: Michigan

address: 1000 Wall St

department: Gilbert S. Omenn Department of Computational Medicine & Bioinformatics

institute: University of Michigan

description:
Library name: 9022-JX-5
PE150 on a 300 cycle S4 flow cell

data_processing:
Reads are trimmed using Trimmomatic v0.39, and the cleaned reads are aligned to the mm10 reference genome using Bowtie2 v2.5.1. Duplicate reads are removed with Picard's MarkDuplicates, and BAM files are sorted with Samtools v1.18 before being converted to BED format using BEDTools v2.31.1. Peak calling is performed with MACS2 v2.2.7.1, with narrow peaks saved in the "macs2.narrow" directory and broad peaks in the "macs2.broad" directory.
Assembly: mm10
Supplementary files format and content: bigWig files
Library strategy: CUT&Run

source_name: organoids

growth_protocol: Rx:GFP and Mettl3 KO harboring Dox-inducible HA-METTL3 were differentiatied with GMEM supplemented with 5% KSR, 1% NEAA, 1% β-ME, 1% Sodium Pyruvate) and AGN (0.1µM) at 37°C.

extract_protocol:
Day 4 WT and Mettl3KO ROs were harvested and trypsinized to single cell suspension. 2×106 cells were subjected for CUT&RUN experiment per antibody as previously described, A CUT&RUN kit (EpiCypher, 14-1048) was used as manufacture’s protocol and the following antibodies were used: METTL3 antibody (Abcam, Ab195352), H3K4me3 antibody (Millipore, 07-473) and H3K27me3 antibody (ActiveMotif, 39155).
The CUT&RUN-DNA were sent to University of Michigan DNA Sequencing Core for quality control, library preparation, and sequencing using Illumina NovaSeq S4 Libraries platform.

treatment_protocol: No treatment

value: organoids

value: Mettl3 KO

value: Mettl3 KO; Dox-inducilbe HA-METTL5

value: AGN treated

tag: antibody

value: METTL3 antibody (Abcam, Ab195352)


title: Forestomach, Big_lesions, Batch2, Rep3

city: CAMBRIDGE

first: Maria

middle: Pilar

last: Alcolea

state: Cambridgeshire

address: Jeffrey Cheah Biomedical centre, Puddicombe way

department: Cambridge Stem Cell Institute

description: 10x Genomics

data_processing:
The raw scRNA-Seq data was processed using CellRanger (version 3.0.2).
Assembly: Ensembl GRCm38/mm10; release 92
Supplementary files format and content: Tab-separated values (tsv) files and matrix (mtx) files

source_name: Forestomach, big lesions

extract_protocol:
For scRNA-Seq, Fucci2a male mice were sacrificed 8 months after DEN treatment (age-matched mice were used as controls). After dissection as described above, tissues were flattened with the epithelial side up and visible tumour lesions were marked by making a half-cut using a 1 mm diameter punch under the dissecting microscope. Then, oesophagi and forestomachs were cut in half and incubated in 50 mM EDTA in PBS containing 1 U/µl RNAse Inhibitor (Life Technologies; AM2696) at 37°C for 30 minutes. Following incubation, the epithelium was carefully peeled away from the stroma using fine forceps. Epithelium and stroma were each flattened individually and tumours labelled with the half incision described above were then fully excised using 0.5-2 mm punch biopsies. Pools of biopsies from two to four animals (details below) were further processed as follows. Stroma was thoroughly minced and incubated in 4 mg/ml collagenase type 4 (Thermo Fisher Scientific; 17104019) in DMEM with 1 U/ml RNAse inhibitor for 1 h at 37°C in a rotator. EDTA was added to the samples at a final concentration of 5 mM and the suspension was diluted 1:5 in collection buffer (2% heat-inactivated fetal bovine serum (Life Technologies, 26140079), 25 mM HEPES (Life Technologies, 15630056) in PBS to reduce the collagenase activity. Cell suspensions were filtered through a 100 µm cell strainer, centrifuged at 300 × g for 5 min at 4°C, and resuspended in collection buffer before an additional filtering step with a 40 µm FlowMi tip filter (Thermo Fisher Scientific, 15342931) was performed to obtain single-cell suspensions. Cells were then centrifuged at 300 × g for 5 min at 4°C and resuspended in collection buffer containing 1 U/µl RNAse. In parallel, the epithelium was thoroughly minced and incubated for 10 min at 37°C in 0.5 mg/ml dispase (Sigma; D4818) in PBS containing 1 U/µl RNAse to create an epithelial cell suspension. EDTA was then added to the samples at a final concentration of 5 mM and the suspension diluted 1:5 in collection buffer to reduce the dispase activity. A single-cell suspension was obtained by filtering the samples through a 30 µm cell strainer. Cells were then centrifuged at 300 × g for 10 min at 4°C and resuspended in collection buffer containing 1 U/µl RNAse. Epithelial and stromal cells were then pooled together by condition (Ctrl, DEN, Tumour) prior to proceeding to library production for scRNA-seq.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kit (v3) and sequenced at the Genomics Core Facility of Cancer Research UK (CRUK), Cambridge Institute following the manufacturer’s instructions

treatment_protocol: To generate lesions in the upper gastrointestinal tract, mice were treated with Di-ethyl-nitrosamine (DEN) (Sigma, Cat. Nr. N0756) at 40 mg per litre in Ribena-flavoured water for 24h on three alternate days a week (i.e., Monday, Wednesday and Friday) for eight weeks; all other days, animals received DEN-free Ribena-flavoured water. Control animals received DEN-free Ribena-flavoured water.

value: Forestomach, big lesions

value: epithelial and stromal cells

value: DEN (diethylnitrosamine)


title: Rx-GFP WT-H3K27me3

description:
Library name: 9022-JX-3
PE150 on a 300 cycle S4 flow cell

value: WT

value: H3K27me3 antibody (ActiveMotif, 39155)


title: Forestomach, Small_lesions, Batch2, Rep2

description: 10x Genomics

source_name: Forestomach, small lesions

value: Forestomach, small lesions


title: Mettl3 KO-H3K4me3

description:
Library name: 9022-JX-8
PE150 on a 300 cycle S4 flow cell, Configured as NovaSeq 6002

value: Mettl3 KO; Dox-inducilbe HA-METTL7

value: H3K4me3 antibody (Millipore, 07-473)


title: Rx-GFP WT-Mettl3

description:
Library name: 9022-JX-1
PE150 on a 300 cycle S4 flow cell


title: Rx-GFP WT-H3K4me3

description:
Library name: 9022-JX-4
PE150 on a 300 cycle S4 flow cell


title: Mettl3 KO-H3K27me3

description:
Library name: 9022-JX-7
PE150 on a 300 cycle S4 flow cell, Configured as NovaSeq 6001

value: Mettl3 KO; Dox-inducilbe HA-METTL6


title: Oesophagus, Small_lesions, Batch2, Rep2

description: 10x Genomics

source_name: Oesophagus, small lesions

value: Oesophagus, small lesions


title: Forestomach, DEN, Batch2, Rep1

description: 10x Genomics

source_name: Forestomach, lesion-free DEN-treated

value: Forestomach, lesion-free DEN-treated


title: Forestomach, DEN, Batch2, Rep2

description: 10x Genomics


title: Oesophagus, DEN, Batch2, Rep2

description: 10x Genomics

source_name: Oesophagus, lesion-free DEN-treated

value: Oesophagus, lesion-free DEN-treated


title: Forestomach, Control, Batch2, Rep2

description: 10x Genomics

source_name: Forestomach, control

value: Forestomach, control

value: Ctrl


title: Forestomach, Control, Batch2, Rep1

description: 10x Genomics


title: Oesophagus, DEN, Batch2, Rep3

description: 10x Genomics


title: Oesophagus, Control, Batch2, Rep3

description: 10x Genomics

source_name: Oesophagus, control

value: Oesophagus, control


title: WT_CC10_GFPpos_HC_rep1

description:
Library name: WT_CC10_GFPpos_HC_rep1
extracted and tagmented chromatin from sorted 50K neuronal nuclei

value: Brain, hippocampus

value: C57BL/6J, NuTRAP transgenic

value: neurons

value: virus-exposed neurons

value: 6.4 weeks


title: Oesophagus, Control, Batch2, Rep2

description: 10x Genomics

value: epithelial and stromal cells


title: Forestomach, Big_lesions, Batch2, Rep2

description: 10x Genomics

value: Forestomach, big lesions

value: DEN (diethylnitrosamine)


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-N12

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: 18 months

tag: brain region

value: FC

tag: gender

value: M


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-O24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-P11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-P12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-N11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-O12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-M12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-P23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-M23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-O23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-L24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-P24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-M24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-N24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-M11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-L23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-L12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-N23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-K23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-O11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-K12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-L11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-J23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-J12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-J24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-J11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-K11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-I24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-I23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-H24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-I11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-H12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-G11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-G12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-K24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-E11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-F12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-H23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-I12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-H11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-F24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-G24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-E12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-E23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-F23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-E24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-F11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-G23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-D24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-D23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-D12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-C24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-C12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-C11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-D11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-B23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-C23


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-B12


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-B11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-A24


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-A11


title: AMB_200702_18mo_2A_3A_2_P5-6-A6-A23


title: AMB_200702_18mo_2A_3A_2_P5-5-F19-P21


title: AMB_200702_18mo_2A_3A_2_P5-5-F19-P9


title: AMB_200702_18mo_2A_3A_2_P5-5-F19-P22


title: AMB_200702_18mo_2A_3A_2_P5-5-F19-M22


title: AMB_200702_18mo_2A_3A_2_P5-5-F19-O21


title: AMB_200702_18mo_2A_3A_2_P5-5-F19-N21


title: AMB_200702_18mo_2A_3A_2_P5-5-F19-O22


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-M2


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-K14


title: AMB_200702_18mo_2A_3A_2_P5-1-J18-L2


title: AMB_200702_18mo_2A_3A_2_P5-1-J18-K13


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-L14


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-J14


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-I13


title: AMB_200702_18mo_2A_3A_2_P5-1-J18-I1


title: AMB_200702_18mo_2A_3A_2_P5-1-J18-H14


title: AMB_200702_18mo_2A_3A_2_P5-1-J18-H2


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-G14


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-H13


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-F2


title: AMB_200702_18mo_2A_3A_2_P5-1-J18-F14


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-D14


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-D2


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-C2


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title: AMB_200702_18mo_2A_3A_2_P5-1-J18-C14


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