title: Skin, depleted, rep2

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

description: 10x Genomics

data_processing:
CellRanger (v 6.0.1) was used to process raw sequencing data before subsequent analyses with parameter '--include-introns=false' and 'refdata-gex-mm10-2020-A' reference data.
Assembly: mm10
Supplementary files format and content: Tab-separated values file and count matrix

extract_protocol:
The excised skin from MAFIA mice was cut into small pieces and incubated in 5 mL of dissociation buffer (5 mL RPMI 1640 (no calcium or magnesium) with 232U DNAse I, 0.25 mg/mL Liberase stock (2.5 mg/mL), 23.2 mM HEPES, and 2.32mM sodium pyruvate) at 37°C for 60 minutes. The digestion was stopped by adding 10 µL of 0.5 M EDTA and 400 µL FBS, and the samples were transferred to GentleMacs tubes (Miltenyi Biotec, Cat#130-093-237) for dissociation (program: m_impTumor_01.01). The digested samples were filtered through a 70 µm filter, resuspended in 4 mL of FACS buffer (500 mL PBS, 2 mL of 0.5 M EDTA, 25 mL FBS, and 5 mL non-essential amino acids (100x stock)) and stained with viability dye (Propidium iodide). Live cells were sorted by DiVa cell sorter (BD Biosciences). 18K sorted PI- live cells were loaded for scRNA-seq library preparation.
The live cells were sorted and loaded on the 10x Genomics Chromium using the Chromium Single Cell 3’ Reagent V3 Kit and the sequencing libraries were constructed following the user guide.

value: Male

value: 5 months old

value: MaFIA


title: Skin, depleted, rep1

status: Public on Dec 22 2025

type: SRA

country: USA

description: 10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

source_name: Skin

tag: tissue

value: Skin

tag: Sex

tag: age

tag: genotype

tag: treatment


title: Skin, depleted, rep3

description: 10x Genomics

value: Female


title: Skin, control, rep3

description: 10x Genomics

value: Vehicle


title: Skin, control, rep1

description: 10x Genomics


title: DIPG10_H3K4me3

city: Kensington

first: Holly

last: Holliday

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute

description: Library name: DIPG10_H3K4me3

library_source: genomic

data_processing:
Quality control analysis of CUT&RUN reads was performed using fastQC (v0.11.9).
Adapter trimming was performed using cutadapt (v4.2) with parameters: --error-rate 0.1 --times 1 --overlap 3 --action trim --minimum-length 17 --pair-filter any. Reads were aligned using bowtie2 (v2.5.0) with -k 1 against the GRCh38 human reference genome.
BAM files were sorted, and optical duplicates marked using picard (v2.27.5) with parameters: --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --VALIDATION_STRINGENCY SILENT.
Marked duplicates were filtered and removed using samtools (v1.12).
Peak calling was performed using MACS2 (v2.2.7.1) using IgG as the control. Narrow peaks parameters: --keep-dup all -p 1e-5 and broad peak using parameters: --keep-dup all -q 0.05 --broad --broad-cutoff 0.05. BigWig coverage files were generated using deeptools bamCoverage (v3.5.1) with parameters: --binSize 10 --normalizeUsing BPM --effectiveGenomeSize 2913022398. Broad peak settings were used for H3K27M and H3K27me3, and narrow peaks for SPT16, BRD4, H3K27ac, H3K4me3.
Assembly: hg38
Supplementary files format and content: narrowPeak
Supplementary files format and content: BigWig
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

source_name: Diffuse Midline Glioma

growth_protocol: DMG cells were maintained as neurospheres in Tumour Stem Cell (TSM) media consisting of a 1:1 mixture of DMEM/F12 and Neurobasal medium (Invitrogen) supplemented with Glutamax, Pyruvate, non-essential amino acids, HEPES buffer, antibiotic/antimycotic, B-27 (Invitrogen), Heparin (0.0002%), EGF (20 ng/mL), bFGF (20 ng/mL), PDGF-AA (10 ng/mL) and PDGF-BB (10 ng/mL) (StemCell Technologies).

extract_protocol:
CUT&RUN was performed using the EpiCypher CUTANA CUT&RUN kit according to the manufacturer’s instructions. Briefly, 500,000 viable cells per reaction were washed and permeabilized with 0.01% Digitonin, which was determined to be the minimum concentration for effective permeabilization. Cells were incubated with 0.5 µg antibody, or a 1:50 dilution for SPT16, on a nutator overnight at 4°C. Following washing, pAG-MNase was added to the reactions and CaCl2 was used to activate antibody-bound MNase for targeted chromatin digestion and release of DNA fragments
The entire volume of purified DNA (ranging from 1-10 ng) was used as input for NGS library preparation, according to the EpiCypher CUTANA Library Prep Kit instructions.

value: Diffuse Midline Glioma

tag: cell line

tag: cell type

value: H3 WT

tag: antibody

value: EpiCypher 13-0041


title: DIPG10_H3K27M_rep2

description: Library name: DIPG10_H3K27M_rep2


title: DIPG10_BRD4_rep2

description: Library name: DIPG10_BRD4_rep2

value: EpiCypher 13-2003


title: RNAseq_D4_IFNy_LPS6H

city: Los Angeles

first: Aleksandr

last: Gorin

state: CA

address: 611 Charles E Young Dr E 570C Boyer Hall

institute: UCLA

description: Library name: RNAseq_D4_IFNy_LPS6H

library_source: transcriptomic

data_processing:
Low quality reads were trimmed (cutoff q=20) and adapter sequences were removed with cutadapt. Reads were aligned to the hg38 human genome using STAR with the following options: --outSAMunmapped Within, --outSAMtype BAM SortedByCoordinate, --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outFilterMismatchNoverLmax 0.04, --seedSearchStartLmax 30. Aligned reads were filtered based on mapping score (MAPQ ≥ 30) by Samtools. Aligned reads were filtered based on mapping score (MAPQ ≥ 30) by Samtools. Counts for each gene were generated using featureCounts. Counts were normalized by CPM. Analysis of gene expression was limited to protein coding gene. Pseudocount was set a 1.
Assembly: hg38
Supplementary files format and content: csv file of CPM of reads for each gene

source_name: MCSF differentiated monocyte-derived macrophages

growth_protocol: Human blood from deidentified donors was obtained from the UCLA CFAR Centralized Laboratory Support Core in accordance with UCLA IRB 11-000443. PBMC were isolated from blood by Ficoll (Cytiva 17-1440-03) density centrifugation and cryopreserved in 10%DMSO (Sigma-Aldrich, D2438) in Embryonic Stem cell FBS (Gibco, 11875-093). Monocytes were purified from PBMC using pan-monocyte isolation magnetic beads (Miltenyi 130-096-537). Monocytes were plated on 6-well tissue culture plates at a density of 1.2 x106 cells/well for 6 days in 3mL of RPMI (Gibco, 11875-093) supplemented with 10% ES fetal bovine serum (Gibco, 10439-024), penicillin-streptomycin (Corning, 30-002-CI), L-glutamine (2mM; Corning, 25-005-CI) and human M-CSF (20 ng/ml; R&D systems 216-MC-100). M-CSF was replenished to a concentration of 20ng/mL by adding 60ng M-CSF to each well (assuming that all M-CSF was depleted).

extract_protocol:
Qiagen RNEase miniprep kit
Libraries were constructed by BGI.

treatment_protocol: Macrophages were treated with human IFNy or PBS control for 8 hours. Cells were washed and subsequently cultured in either regular media or media with 1µM ruxolitinib for an additional 88 hours at which time they were restimulated with 100ng/mL LPS. Cells were collected for RNAseq on Day 0 after the 8 hour stimulation or on day 4 during (or immediately prior to) LPS restimulation.


title: DIPG10_SPT16_rep2

description: Library name: DIPG10_SPT16_rep2


title: DIPG10_SPT16_rep1

description: Library name: DIPG10_SPT16_rep1


title: DIPG6_BRD4_rep1

description: Library name: DIPG6_BRD4_rep1

value: SU-DIPGVI


title: DIPG6_H3K4me3

description: Library name: DIPG6_H3K4me3


title: DIPG6_H3K27M_rep2

description: Library name: DIPG6_H3K27M_rep2


title: DIPG6_IgG_rep1

description: Library name: DIPG6_IgG_rep1

value: EpiCypher 13-0042


title: DIPG6_BRD4_rep2

description: Library name: DIPG6_BRD4_rep2


title: DIPG6_SPT16_rep2

description: Library name: DIPG6_SPT16_rep2


title: DIPG6_SPT16_rep1

description: Library name: DIPG6_SPT16_rep1


title: mESCs, DMSO, 15min, rep2

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description: Library name: 15min_rep2

data_processing:
The paired-end fastq files were mapped to the M. musculus genome (mm10) using Bowtie2. Duplicate reads with the same start and end coordinates were not included in the downstream analysis and discarded. Bam files were created using samtools, followed by bedpe generation using sam2bam command in bedtools. From the bedpe file, the extreme ends of the mates representing the ends of the sequenced fragments were extracted into a bed file, where each entry contained the chromosome, start and end coordinate of each unique sequenced fragment. Centers of fragments belonging to 142-152 bp fragments were used to make coverage files in the wiggle format with a step size of 1 bp. The coverage of fragment centers at each base-pair location was normalized by the factor N:   N = [genome size] / (Total number of mapped reads) Here, [genome size] refers to a number close to total mappable bases, which was 2.8x109 for mouse.
Assembly: mm10
Supplementary files format and content: Normalized coverage of 142-152 bp from MNase-seq data in bigWig format

source_name: E14 mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cell line E14 (mESCs; Gates Biomanufacturing Facility at University of Colorado Denver) were utilized for MNase-seq experiments. Cells were tested for mycoplasma contamination and confirmed to be negative before experimental work. mESCs were cultured under feeder-free conditions on 0.1% gelatin-coated T-25 flasks in knockout DMEM (Life Technologies), 20% embryonic stem cell-qualified fetal bovine serum (FBS; Life Technologies), 2 mM L-glutamine (Life Technologies), 0.1 mM non-essential amino acids (Life Technologies), 100UmL-1 penicllin/streptomycin (Life Technologies), 0.05 mM β-mercaptoethanol (Sigma), and 1000UmL-1 ESGRO mouse leukemia inhibitory factor medium supplement (LIF; Millipore). mESCs were cultured at 37°C with 5% CO2 and subcultured every 2 days. Cells were harvested for experiments by aspirating the growth media, applying 0.25% trypsin-EDTA (Gibco) for 2-3 minutes, and centrifuging at 2000 rpm for 5 minutes.

extract_protocol:
After harvesting serum-grown mESCs, cells were washed in cold 1x phosphate buffered saline solution (PBS). Cell number and viability were measured with CountessTM 3 Automated Cell Counter (Invitrogen). MNase-seq digestions proceeded with 1 x 10^6 mESCs. mESC samples were centrifuged at 2000 rpm for 5 minutes to remove 1x PBS. Cells were resuspended in 1 mL cold Nuclear Extraction Buffer (20 mM HEPES pH 8.0, 10 mM KCl, 0.1% Triton, 20% glycerol, 0.5 mM spermidine) and incubated on ice for 10 minutes to facilitate nuclei isolation. Nuclei were centrifuged at 2500 rpm for 10 min, then resuspended in 40 uL Reaction Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 2 mM EGTA, 10 mM CaCl2, 10 mM MgCl2). Samples were incubated at 37°C for 5 minutes prior to starting digestion to allow for reaction temperature equilibration. 0.07 U micrococcal nuclease (Sigma) was added to each sample along with nuclease-free water (Invitrogen) to adjust reaction volumes to 50 uL. Reactions proceeded at 37°C for time points of 3, 6, 7, 9, 11, 12, and 15 minutes. At each time point, 10 uL of reaction (0.2 x 106 mESC nuclei) was removed and quenched with 10 uL 2x Stop Buffer (500 mM NaCl, 10 mM EGTA, 0.1% digitonin, 1% SDS, 100 ug RNase A, 50 ug glycogen). Digested DNA was purified by phenol:chloroform:isoamyl alcohol extraction protocol. Purifed DNA concentration and sample quality was determined via Qubit 4 fluorometer and Agilent D1000 Tapestation respectively.
Sequencing libraries were prepared using the SRSLY PicoPlus NGS Library Prep Kit and protocol, described as follows. 10 ng of digested DNA was combined with SRSLY ssEnhancer and incubated on ice for 2 minutes, followed by heat shock at 98C for 3 minutes and another incubation on ice for 2 minutes. Phosphorylation and ligation reaction was achieved by mixing sample with SRSLY Adapter A, SRSLY Adapter B, and SRSLY Master Mix and then incubating samples at 37C for 1 hour. Samples were then purified in a final volume of 15 uL nuclease-free water via 0.54x AMPure bead clean to enrich for small fragments. To each sample, SRSLY PCR Master Mix and unique P5 and P7 barcoded primers were added. The following PCR protocol was used: 98C for 3 minutes, 98C for 20 seconds, 65C for 30 seconds, 72C for 30 seconds, 72C for 1 minute with steps 2-4 repeated for 10 cycles. Final library purification was achieved via 0.95x AMPure bead clean, after which library quality was assessed via Agilent TapeStation.

value: E14 mouse embryonic stem cells

value: mouse embryonic stem cells

value: DMSO


title: Skin, control, rep2

description: 10x Genomics


title: mESCs, DMSO, 6min, rep2

description: Library name: 6min_rep2


title: mESCs, Control, 9min, rep1

description: Library name: 9min_rep1


title: mESCs, DMSO, 7min, rep1

description: Library name: 7min_rep1


title: DIPG10_BRD4_rep1

description: Library name: DIPG10_BRD4_rep1


title: mESCs, Control, 15min, rep1

description: Library name: 15min_rep1


title: mESCs, Control, 12min, rep1

description: Library name: 12min_rep1


title: DIPG6_H3K27M_rep1

description: Library name: DIPG6_H3K27M_rep1


title: mESCs, DMSO, 11min, rep1

description: Library name: 11min_rep1


title: mESCs, DMSO, 9min, rep3

description: Library name: 9min_rep3


title: p95h PHZ 2

city: Seattle

first: Edie

middle: I

last: Crosse

state: Washington

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description: Library name: CFU-E.srsf2_p95h.phz.3184

data_processing:
Genome annotation: A genome annotation for the human UCSC hg19 (GRCh37) and mouse mm10 (GRCm38) genomes assembly was created by merging annotations from UCSC knownGene (Meyer et al., Nucleic Acids Res, 2013), Ensembl 71 (Flicek et al., Nucleic Acids Res, 2013), and MISO v2.0 (Katz et al., Nat Methods, 2010). Reads were mapped to the transcriptome using Bowtie (option “-v 2”) from the RSEM v1.2.4 package (Li et al., BMC Bioinformatics, 2011). Transcripts per million (TPM) were normalized with the trimmed mean of M values (TMM) methods (Robinson et al., Genome Biol, 2010). Unaligned reads were mapped to the genome with TopHat v2.0.8b (Trapnell et al., Bioinformatics, 2009), as well as to an expanded annotation created by computing all possible combinations of annotated 5′ and 3′ splice sites per gene.
Differential expression analysis: Differentially expressed genes were defined as those with an associated Bayes factor ≥ 100 (computed using Wagenmakers’s Bayesian framework (Wagenmakers et al., Cogn Psychol, 2010) and an associated fold-change ≥ 1.5. Gene set enrichment analysis (GSEA (Subramanian et al., Proc Natl Acad Sci U S A, 2005)) was carried out on ranked lists of differentially expressed genes (ranked by p.value) and were considered significant with a false discovery rate (FDR) of < 0.1. Principal component analyses were carried out using core R statistical packages and visualized with ggplot2. Genes that were significantly enriched according to the GSEA analyses were loaded into g:Profiler (https://biit.cs.ut.ee/gprofiler/gost) to determine which cellular processes were driving the GSEA result.
Differentiaion splicing analysis: Isoform expression was quantified with MISO v2.0 (Katz et al., Nat Methods, 2010), using the combined RSEM and TopHat alignments as input. Differential isoform expressions between sample groups were identified with two-sided t-tests. Differentially spliced events were defined as those with at least 20 isoform-identifying reads in each sample, a minimum delta psi of 0.1 and a p-value < 0.05. Visualizations of the data were created in the R programming environment, using the dplyr, ggplot2, tidyverse, and UpSetR (Conway et al., Bioinformatics, 2017) packages. BAM coverage sashimi plots were visualized using the Integrative Genomics Viewer (Robinson et al., Nature Biotechnol, 2011) and coverage plots were generated using the coverage() function from GenomicAlignments (Lawrence et al., PLoS Comput Biol, 2013) and visualized with ggplot2. Differentially spliced genes were categorized based on gene ontology terms for erythrocyte differentiation (GO:0030218), heme metabolism (GO:0042168), mitotic cell cycle (GO:0000278), cytoskeleton (GO:0005856), DNA repair (GO:0006281), transcriptional regulatory activity (GO:0140110) and epigenetic regulation (GO:0040029).
Assembly: The human UCSC hg19 (GRCh37) and mouse mm10 (GRCm38) genomes
Supplementary files format and content: File "Table S2_Normalized_Reads.xlsx". Normalized reads RNA-sequencing data CFU-E cells
Supplementary files format and content: File "Table_S3_Differentially_expresssed_genes_all_comparisons.xlsx". Differentially expressed genes all comparisons CFU-E cells
Supplementary files format and content: File "Table_S4_Differentially_spliced_all_comparisons_all_splice_types.xlsx". Differentially spliced genes all comparisons all splice types CFU-E cells

source_name: Bone marrow

extract_protocol:
For RNA-sequencing, live, lineageneg, c-kithigh, Sca-1neg, CD41neg, CD16/32neg, CD150neg, CD105pos CFU-E cells were directly sorted into extraction buffer (EB) from the PicoPureTM RNA Isolation Kit (Applied Biosystems) and subsequently stored at -80oC. RNA was isolated as described before (Jutzi et al., Leukemia, 2023).
150 bp paired-end library prep and RNA-sequencing on an Illumina NovaSeq 6000 Sequencing System. Each sample was sequenced to a minimum depth of 100 million reads.

treatment_protocol: Mice were subcutaneously injected with either PBS or 30 mg/kg PHZ on days 0 and 1, followed by sorting and RNA-sequencing of bone marrow-derived CFU-E cells on day 4.

value: Bone marrow

value: CFU-E

value: Mx1-Cre Srsf2P95H/+

value: 30 mg/kg PHZ


title: p95h PHZ 1

description: Library name: CFU-E.srsf2_p95h.phz.3163


title: mESCs, Control, 6min, rep1

description: Library name: 6min_rep1


title: mESCs, DMSO, 3min, rep3

description: Library name: 3min_rep3


title: mESCs, DMSO, 5min, rep1

description: Library name: 5min_rep1


title: mESCs, DMSO, 3min, rep2

description: Library name: 3min_rep2


title: WT PHZ 2

description: Library name: CFU-E.srsf2_wt.phz.3172


title: p95h PHZ 4

description: Library name: CFU-E.srsf2_p95h.phz.3194


title: p95h PBS 1

description: Library name: CFU-E.srsf2_p95h.pbs.3176

value: PBS


title: mESCs, DMSO, 9min, rep2

description: Library name: 9min_rep2


title: p95h PHZ 5

description: Library name: CFU-E.srsf2_p95h.phz.3200


title: mESCs, Control, 3min, rep1

description: Library name: 3min_rep1


title: p95h PHZ 3

description: Library name: CFU-E.srsf2_p95h.phz.3193


title: p95h PBS 5

description: Library name: CFU-E.srsf2_p95h.pbs.3227


title: DIPG10_H3K27M_rep1

description: Library name: DIPG10_H3K27M_rep1


title: p95h PBS 4

description: Library name: CFU-E.srsf2_p95h.pbs.3220


title: p95h PBS 3

description: Library name: CFU-E.srsf2_p95h.pbs.3192


title: mESCs, DMSO, 12min, rep2

description: Library name: 12min_rep2


title: PPCL-68 EVs treated BMDM, Replicate 3

city: Washington

first: Amrita

last: Cheema

state: DC

address: 3900 Reservoir Road NW

department: Oncology

institute: Georgetown University Medical Centre

description: Library name: Sample9

data_processing:
The files were provided in BAM format containing mapping results. Alignment was performed using HISAT2 (v2.0.5) to the reference using default parameters. Gene expression quantification was performed using featureCounts (v1.5.0-p3). Differential gene expression analysis was performed using DESeq2 (v1.20.0) with |log2(FoldChange)| >= 1 & padj <=0.05. Enrichment analysis was performed using clusterProfiler (v3.8.1) with padj < 0.05.*
Assembly: mm10
Supplementary files format and content: comma-delimeted text file include raw counts for each sample

source_name: Bone marrow derived macrophage

extract_protocol:
The total RNA was extracted using Norgene total RNA extraction kit as per the manufactures protocol.
Libraries were prepared using NEBNext Ultra II non-directional RNA Library Prep kit (New England BioLabs, # E7770S).
RNA quality control (QC) was assessed using Qubit (Thermo Fisher) and Bioanalyzer (Agilent) analysis.

value: Bone marrow derived macrophage

value: WT

value: PPCL-68 Evs

tag: time


title: p95h PBS 2

description: Library name: CFU-E.srsf2_p95h.pbs.3190


title: WT PHZ 4

description: Library name: CFU-E.srsf2_wt.phz.3201


title: WT PHZ 5

description: Library name: CFU-E.srsf2_wt.phz.3222


title: WT PHZ 1

description: Library name: CFU-E.srsf2_wt.phz.3161


title: WT PHZ 3

description: Library name: CFU-E.srsf2_wt.phz.3182


title: WT PBS 5

description: Library name: CFU-E.srsf2_wt.pbs.3248


title: WT PBS 2

description: Library name: CFU-E.srsf2_wt.pbs.3187


title: WT PBS 4

description: Library name: CFU-E.srsf2_wt.pbs.3202


title: PPCL-68 EVs treated BMDM, Replicate 2

description: Library name: Sample8


title: PPCL-68 EVs treated BMDM, Replicate 1

description: Library name: Sample7


title: PANC-1 EVs treated BMDM, Replicate 2

description: Library name: Sample5

value: PANC-1 Evs


title: PANC-1 EVs treated BMDM, Replicate 3

description: Library name: Sample6


title: WT PBS 3

description: Library name: CFU-E.srsf2_wt.pbs.TT3165


title: hTERT HPNE EVs treated BMDM, Replicate 3

description: Library name: Sample3

value: hTERT HPNE Evs


title: PANC-1 EVs treated BMDM, Replicate 1

description: Library name: Sample4


title: hTERT HPNE EVs treated BMDM, Replicate 2

description: Library name: Sample2


title: F13

city: Shanghai

first: Nengzhuang

last: WANG

address: Changhai Road NO.168

country: China

institute: Changhai hospital

description: Library name: Sample5

data_processing:
Basecalls performed using CASAVA version 1.8
The demultiplexing,barcoded processing,gene counting and aggregationg were made using the Cell Ranger Software v7.1.0（https://www.10xgenomics.com/support/software/cell-ranger/latest）
Assembly: mm10
Supplementary files format and content: Table-separated values files and matrix files

source_name: testis

extract_protocol:
The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35 μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs 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). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: The 6-week-old healthy ICR male mouse were purchased from the SIPPR-BK Experiment Animal Ltd.(Shanghai, China),and kept in Individual Ventilated Cages (IVC) in the Naval Medical University's Animal house according to the ethical standards of the Naval Medical University Ethics Committee. We Ensured that the indoor feeding conditions are suitable for the growth of mouse, and the water was provided for mouse normally every day. After adaptive feeding in IVC system for 1 week, 14 mouse were divided into control group (Control) and Smoking group (Smoke) according to the random principle, with 7 mouse in each group. Mouse in the Smoke group were placed in the self-made poisoning chamber (80cm×60cm×80cm). These mice were exposed in the chamber at the same time every day, 30 minutes a day, 15 cigarettes at a time (Fig. 1A). The Taishan brand of cigarettes (Shandong Tobacco Group Co. Ltd., Shandong Province, China), with each cigarette containing 1.1 mg of nicotine and 11 mg of tar, was used in this study. The particle concentration of the smoke within the exposure chamber was monitored every two weeks through gravimetric determinations of the ultrafine glass fiber microporous membrane (0.45 μm pore size, Xingya Purification Material Factory, Shanghai, China), and the membrane was pasted to the smoke entrance of the exposure chamber, and the weight of the membrane was weighed before and after cigarette smoke exposure. The result of the assay was that the amount of smoke produced per exposure was 3.47 mg/ m3. At the same time, mouse in the control group were placed in a homemade poison chamber every day, but were not exposed to cigarette. The entire exposure period was 12 weeks.At the end of the exposure cycle, mouse were sacrificed by cervical dislocation, and both testes were weighed, the left testis of every mouse was placed in testicular protective solution for subsequent single-cell transcriptome sequencing, and the right testis was placed in fixative solution for more than 24 hours for subsequent pathology analysis.

value: testis

value: male

value: 8 weeks

value: smoking


title: F2

description: Library name: Sample2

value: control


title: F21

description: Library name: Sample6


title: F12

description: Library name: Sample4


title: WT PBS 1

description: Library name: CFU-E.srsf2_wt.pbs.3097


title: F1

description: Library name: Sample1


title: DIPG10_IgG_rep1

description: Library name: DIPG10_IgG_rep1

value: Diffuse Midline Glioma

value: H3 WT

value: EpiCypher 13-0042


title: BALBC mammary gland 3

city: Merelbeke

first: Robbe

last: Salembier

state: East-Flanders

address: Salisburylaan 133

department: Department of Veterinary and Biosciences

country: Belgium

institute: Ugent

description:
Library name: Sample 38
BALBCgland3.bam

data_processing:
Reads were mapped to the mouse reference genome (mm10) using HISAT2.
Read counts were generated using the summariseOverlaps function from BioConductor package GenomicAlignments.
DESeq2 was performed on counts of each model compared to their respective healthy mammary gland (4T1-hot, 4T1-cold, EMT6, D2A1 and 66CL4 tumors vs BALB/c, Py230 and AT3 tumors vs C57BL/6, MVT1 and MET1 tumors vs  FVB/N).
Hall marks of cancer were calculated for all models based on DESeq2 results. Log2-fold change values of all genes were exctracted from each model after DESeq2 and put into a dataframe, comparing each model to each other for different gene sets visualized in heatmaps.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  4T1-hot primary tumors vs BALB/c gland.
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  4T1-cold primary tumors vs BALB/c gland.
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  EMT6 primary tumors vs BALB/c gland.
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  D2A1 primary tumors vs BALB/c gland.
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  66CL4 primary tumors vs BALB/c gland.
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  PY230 primary tumors vs C57BL/6 gland.
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  AT3 primary tumors vs C57BL/6 gland.
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  MET1 primary tumors vs FVB/N gland.
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  MVT1 primary tumors vs FVB/N gland.
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  baseline healthy BALBC gland. (Intercept from results)
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  baseline healthy C57BL/6 gland. (Intercept from results)
Supplementary files format and content: tab-delimited text file including DESeq2 results for smaples from  baseline healthy FVB/N gland. (Intercept from results)
Supplementary files format and content: tab-delimited text file including RAW gene counts from all models. After function SummarizeOverlaps function, mode="IntersectionNotEmpty" .

source_name: BALBC mammary gland

growth_protocol: Female mice were individually caged and intraductally inoculated in the third mammary gland pair with 5×104 D2A1, 5×104 EMT6, 4×103 4T1-cold, 2×105 AT3, 5×104 4T1-hot, 2×105 66CL4, 2×105 PY230, 12.5×103 MET1 or 12.5×103 MVT1 cells suspended in a cold mixture of PBS and Matrigel® (1:10; Corning) or just Matrigel for healthy control mammary glands.

extract_protocol:
Primary tumors and healthy mammary glands were removed at 2 w p.i., flash frozen in liquid nitrogen and RNA was isolated using the Rneasy Mini Kit (QiAgen, Valencia, CA, USA) according to the manufacturer's instuctions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: BALBC mammary gland

value: WT female BALB/c


title: BALBC mammary gland 1

description:
Library name: Sample 36
BALBCgland1.bam


title: F9

description: Library name: Sample3


title: C57BL6 mammary gland 3

description:
Library name: Sample 35
C57BL6gland3.bam

source_name: C57BL6 mammary gland

value: C57BL6 mammary gland

value: WT female C57BL/6


title: C57BL6 mammary gland 2

description:
Library name: Sample 34
C57BL6gland2.bam


title: C57BL6 mammary gland 1

description:
Library name: Sample 33
C57BL6gland1.bam


title: FVBN mammary gland 3

description:
Library name: Sample 32
FVBNgland3.bam

source_name: FVBN mammary gland

value: FVBN mammary gland

value: WT female FVB/N


title: FVBN mammary gland 2

description:
Library name: Sample 31
FVBNgland2.bam


title: MVT1 priamry tumor 3

description:
Library name: Sample 29
MVT12.bam

source_name: MVT1 primary tumor

value: MVT1 primary tumor


title: FVBN mammary gland 1

description:
Library name: Sample 30
FVBNgland1.bam


title: MVT1 primary tumor 2

description:
Library name: Sample 28
MVT11.bam


title: MET1 primary tumor 3

description:
Library name: Sample 26
MET13.bam

source_name: MET1 primary tumor

value: MET1 primary tumor


title: MET1 primary tumor 2

description:
Library name: Sample 25
MET12.bam


title: MVT1 primary tumor 1

description:
Library name: Sample 27
MVT-1-4.bam


title: AT3 primary tumor 3

description:
Library name: Sample 22
AT33.bam

source_name: AT3 primary tumor

value: AT3 primary tumor


title: AT3 primary tumor 4

description:
Library name: Sample 23
AT34.bam


title: AT3 primary tumor 2

description:
Library name: Sample 21
AT32.bam


title: hTERT HPNE EVs treated BMDM, Replicate 1

description: Library name: Sample1

value: Bone marrow derived macrophage

value: WT

value: hTERT HPNE Evs


title: AT3 primary tumor 1

description:
Library name: Sample 20
AT31.bam


title: BALBC mammary gland 2

description:
Library name: Sample 37
BALBCgland2.bam


title: Py230 primary tumor 2

description:
Library name: Sample 17
Py230-5.bam

source_name: Py230 primary tumor

value: Py230 primary tumor


title: MET1 primary tumor 1

description:
Library name: Sample 24
MET11.bam


title: 66cl4 primary tumor 2

description:
Library name: Sample 14
66cl42.bam

source_name: 66cl4 primary tumor

value: 66cl4 primary tumor


title: 4T1-cold primarty tumor 3

description:
Library name: Sample 12
4T1-cold-6.bam

source_name: 4T1 primary tumor

value: 4T1 primary tumor


title: Py230 primary tumor 1

description:
Library name: Sample 16
Py230-4.bam


title: 66cl4 primary tumor 3

description:
Library name: Sample 15
66cl43.bam


title: D2A1 primary tumor 2

description:
Library name: Sample 8
D2A11.bam

source_name: D2A1 primary tumor

value: D2A1 primary tumor


title: Py230 primary tumor 4

description:
Library name: Sample 19
Py2303.bam


title: 4T1-cold primary tumor 2

description:
Library name: Sample 11
4T1-cold-4.bam


title: 4T1-cold primary tumor 1

description:
Library name: Sample 10
4T1cold2.bam


title: D2A1 primary tumor 1

description:
Library name: Sample 7
D2A1-4.bam


title: D2A1 primary tumor 3

description:
Library name: Sample 9
D2A13.bam


title: EMT6 primary tumor 2

description:
Library name: Sample 5
EMT62.bam

source_name: EMT6 priamry tumor

value: EMT6 priamry tumor


title: EMT6 primary tumor 3

description:
Library name: Sample 6
EMT63.bam


title: EMT6 priamry tumor 1

description:
Library name: Sample 4
EMT61.bam


title: 4T1-hot primary tumor 3

description:
Library name: Sample 3
4T1hot3.bam

source_name: 4T1-luc primary tumor

value: 4T1-luc primary tumor


title: 4T1-hot primary tumor 1

description:
Library name: Sample 1
4T1hot1.bam

value: WT female BALB/c


title: Multiplexed Cell lines 4T1WT, 66CL4WT, AT3, PY230 antibody info

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

institute: VIB

description:
Library name: RSA002_HTO
RSA002_raw_feature_bc_matrix.h5
Used antibodies added in feature_reference.csv

library_source: other

data_processing:
CellRanger multi (v7.1.0) was used to map reads to the reference genome
After filtering, standard Seurat pipeline was used to process the data. Seurat objects were merged together using merge() function. Singlet cells were selected based on “CMO_HTODemux_classification.global”. Standard Seurat pipeline was performed on the merged Seurat object. FindNeighbors() function was used to calculate nearest neighbors for each cell using the first 25 principal components (PCs). Cell clusters were identified based on a shared nearest neighbor (SNN) with a 0.1 resolution. According to CMO label, clusters were annotated as their respective cell line.
Assembly: mm10 Ensembl98
Supplementary files format and content: .h5 files containing raw count matrices
Supplementary files format and content: RDS format Seurat object, containing two merged Seurat objects from the 2 pools containing only singlets and doublet cells filtered out. With UMAP coordinates and clusters identfied as the respective cell lines based on CMO labeling
Library strategy: CITE-seq

molecule: protein

growth_protocol: Cell lines were maintained at 37°C and 5% CO2  in a T75 flask. The 4T1-hot, 4T1-cold, EMT6, D2A1, MET1 and MVT1 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Thermo Fisher Scientific) and 100U/ml penicillin, 100 µg/ml streptomycin (both from Sigma-Aldrich, Overijse, Belgium). The 66CL4 cell culture were additionally supplemented with 1% Gibco™ MEM Non-Essential Amino Acids Solution (Thermo Fisher Scientific). AT3 cells were cultrured in Dulbecco’s Modified Eagle’s Medium (DMEM, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% FBS (from Sigma-Aldrich, Overijse, Belgium), 2mM Non-Essential Amino Acids Solution (Thermo Fisher Scientific), 15mM HEPES (Thermo Fisher Scientific, Waltham, MA, USA), 1X β-mercapthoethanol (Sigma-Aldrich, Overijse, Belgium), 100 U/ml penicillin and 100 µg/ml streptomycin (both from Sigma-Aldrich, Overijse, Belgium). PY230 cells were cultured in Ham's F-12K (Kaighn's) Medium (Thermo Fisher Scientific) supplemented with 0.1% MITO+ Serum Extender (Corning), 5% heat-inactivated FBS, 100 U/ml penicillin and 100 μg/ml streptomycin (Thermo Fisher Scientific).

extract_protocol:
Harvesting of confluent cells was performed through incubation with 0.25% trypsin-ethylenediaminetetraacetic acid (EDTA) (Sigma-Aldrich) for 5 min and centrifugation at 400 × g for 5 min for subsequent counting with a Bürker chamber. A total of 2 x 106 cells from each mouse tumor cell line were incubated for 30 minutes at 4°C with a unique TotalSeq-A cell hashing antibody specific against mouse CD45 and MHC class I (1:250 diluted, HTO; TotalSeq-A0301 - TotalSeq-A0309 (BioLegend)). After incubation, cells were washed and centrifuged at 400 x g, 5 min, 4°C. The supernatant was discarded, the cell pellet was subsequently resuspended in 100 µl Cell Multiplexing Oligonucleotides (CMOs) and incubated at room temperature (RT) for 5 min (CMO01 – CMO09 (10X Genomics)). Samples were washed again (400 x g, 5 min, 4°C) and resuspended in PBS supplemented with 1% bovine serum albumin (BSA) for sorting. DAPI was added to the cells to sort out live cells, using a BD FACSAria II cell sorter (BD Biosciences). The tagged sorted cells were pooled (pool 1: D2A1 + MVT1 + EMT6 + MET1 + 4T1-hot; pool 2: 4T1-cold + 66CL4 + AT3 + PY230) and loaded on a Chromium GemCode Single Cell Instrument (10X Genomics) to generate single cell Gel beads-in-EMulsion (GEM). The single cell (sc)RNA-seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead and Library kit, version Next GEM v3.1 according to the manufacturer's instructions (10X Genomics, User Guide CG000388) with the addition of the amplification primer 5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGAT*C*T-3´ (3 nM) during cDNA amplification to enrich the TotalSeq-A hashing protein oligos. Size selection with SPRIselect Reagent Kit (Beckman Coulter, B23318) was used to separate amplified cDNA molecules for 3′ gene expression, hashing protein and hashing lipid construction.
TotalSeq-A protein library construction, including sample index PCR using Illumina’s Truseq Small RNA primer sets, and SPRIselect size selection was performed according to the manufacturer’s instructions. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 5200 Fragment Analyzer (Agilent). Sequencing libraries were loaded on an Illumina NovaSeq flow cell at VIB Nucleomics Core with sequencing settings according to the recommendations of 10X Genomics.

value: Mouse Mammary Carcinoma Cell Line (BALB/c +  C57BL/6 derived)

value: Epithelial

tag: mice strain

value: BALB/c + C57BL/6


title: Multiplexed Cell lines 4T1WT, 66CL4WT, AT3, PY230 cell multiplexing oligo info

description:
Library name: RSA002_CMO
RSA002_raw_feature_bc_matrix.h5
Used feature barcodes added in feature_reference.csv

data_processing:
CellRanger multi (v7.1.0) was used to map reads to the reference genome
After filtering, standard Seurat pipeline was used to process the data. Seurat objects were merged together using merge() function. Singlet cells were selected based on “CMO_HTODemux_classification.global”. Standard Seurat pipeline was performed on the merged Seurat object. FindNeighbors() function was used to calculate nearest neighbors for each cell using the first 25 principal components (PCs). Cell clusters were identified based on a shared nearest neighbor (SNN) with a 0.1 resolution. According to CMO label, clusters were annotated as their respective cell line.
Assembly: mm10 Ensembl98
Supplementary files format and content: .h5 files containing raw count matrices
Supplementary files format and content: RDS format Seurat object, containing two merged Seurat objects from the 2 pools containing only singlets and doublet cells filtered out. With UMAP coordinates and clusters identfied as the respective cell lines based on CMO labeling

molecule: other


title: Multiplexed Cell lines 4T1WT, 66CL4WT, AT3, PY230

description:
Library name: RSA002_cDNA
RSA002_raw_feature_bc_matrix.h5

molecule: polyA RNA


title: Multiplexed Cell lines D2A1, MVT1, EMT6, MET1, FT1-Luc antibody info

description:
Library name: RSA001_HTO
RSA001_raw_feature_bc_matrix.h5
Used antibodies added in feature_reference.csv

source_name: D2A1, MVT1, EMT6, MET1, FT1-Luc

value: Mouse Mammary Carcinoma Cell Line (BALB/c + FVB/N derived)

value: D2A1, MVT1, EMT6, MET1, FT1-Luc

value: WT + Luciferase

value: BALB/c + FVB/N


title: Multiplexed Cell lines D2A1, MVT1, EMT6, MET1, FT1-Luc

description:
Library name: RSA001_cDNA
RSA001_raw_feature_bc_matrix.h5


title: Py230 primary tumor 3

description:
Library name: Sample 18
Py2302.bam

value: WT female C57BL/6


title: 4T1-hot_anti-PD-L1_tumor3

description: Library name: Sample 14

data_processing:
Reads were mapped to the mouse reference genome (mm10) using HISAT2.
Read counts were generated using the summariseOverlaps function from BioConductor package GenomicAlignments.
Raw counts were VST-normalized.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including VST-normalized read counts for smaples from  4T1-hot primary tumors.
Supplementary files format and content: tab-delimited text file including VST-normalized read counts for smaples from  4T1-cold primary tumors.

extract_protocol:
Primary tumors were removed, flash frozen in liquid nitrogen and RNA was isolated using the Rneasy Mini Kit (QiAgen, Valencia, CA, USA) according to the manufacturer's instuctions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Individually-caged mice were assigned to a group and provided with treatment, single-blinded (up to end of the study) in a climate-controlled animal facility. Recombinant anti-mPD-L1-mIgG1 clone B7-H1(BioXCell) or isotype control mouse IgG1 clone MOPC-21 (BioXCell) was systemic administrated though intraperitoneal (i.p.) injection at 200 µg/mouse. Doses wer given weekly up to 2 times.


title: Multiplexed Cell lines D2A1, MVT1, EMT6, MET1, FT1-Luc cell multiplexing oligo info

description:
Library name: RSA001_CMO
RSA001_raw_feature_bc_matrix.h5
Used feature barcodes added in feature_reference.csv


title: 4T1-hot_anti-PD-L1_tumor2

description: Library name: Sample 13


title: 4T1-hot_anti-PD-L1_tumor1

description: Library name: Sample 12


title: 4T1-hot_IgG_tumor3

description: Library name: Sample 11

value: anti-IgG control


title: 4T1-hot_IgG_tumor1

description: Library name: Sample 9


title: 4T1-cold_anti-PD-L1_tumor 3

description: Library name: Sample 7


title: 4T1-cold_anti-PD-L1_tumor 2

description: Library name: Sample 6


title: 4T1-cold_anti-PD-L1_tumor 1

description: Library name: Sample 5


title: 4T1-cold_IgG_tumor4

description: Library name: Sample 4


title: 4T1-cold_anti-PD-L1_tumor 4

description: Library name: Sample 8


title: 66cl4 primary tumor 1

description:
Library name: Sample 13
66cl4-4.bam


title: 4T1-cold_IgG_tumor1

description: Library name: Sample 1


title: 4T1-cold_IgG_tumor2

description: Library name: Sample 2


title: Adult testis, Wild-type 4

city: Madrid

first: Alfonso

last: Gutiérrez-Adán

address: Av. Puerta de Hierro 28

department: Animal Reproduction

country: Spain

institute: INIA

data_processing:
Raw reads were evaluated usign FastQC and trimmed using Trimmomatic
Mapping was performed using STAR
Genes were quantified by featureCounts and differential expression was evaluated with DESeq2
Assembly: Mus musculus mm39
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Adult testis

extract_protocol:
Total RNA was isolated using TRIzol reagent and treated with Dnase for 1 h.
RNA libraries were prepared using the TruSeq RNA kit from Illumina (NEB, USA) according to the manufacturer's recommendations.

value: Adult testis

value: WT


title: Adult testis, Wild-type 3


title: ECM1 WT and KO

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: ECM1 WT and KO

data_processing:
Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina).
For each tissue section and corresponding library, the whole slide brightfield image and CytAssist image were aligned manually using the Loupe Browser (v6.4.1) via landmark registration. Each whole slide image was uploaded to a local OMERO server where a rectangular region of interest (ROI) containing just the tissue was drawn via OMERO.web and OMETIFF images of each ROI were programmatically generated using the OMERO Python API.
FASTQ files, the image registration JSON file, and associated OMETIFF corresponding to high resolution bright field image were used for further processing, including alignment to the GRCm38-specific filtered probe set (10x Genomics Mouse Probeset v1.0.0) using the version 2.1.0 Space Ranger count pipeline (10x Genomics).
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv.gz: cell barcode
Supplementary files format and content: features.tsv.gz: gene list
Supplementary files format and content: matrix.mtx.gz: gene by cell expression matrix file
Supplementary files format and content: tissue_hires_image.png: imaging files with high resolution
Supplementary files format and content: tissue_lowres_image.png: imaging files with low resolution
Library strategy: Spatial Transcriptomics by 10X Visium CytAssist

source_name: kidney

extract_protocol:
Col1α2-Ecm1+/+ and Col1α2-Ecm1-/- mice ischemic kidneys were quickly collected and embed in OCT. Then, immersing the OCT-embedded block in isopentane precooled with liquid nitrogen.  Four 25um sections from each tissue block were used for total RNA extraction (Qiagen), and the percentage of RNA fragments larger than 200bp as determined by Agilent TapeStation 4200 High Sensitivity DNA ScreenTape (DV200 score) was used as a measure of RNA quality.  Tissue blocks with DV200 scores above 30% were used for downstream processing; selected tissues had DV200 scores above 97%.
Briefly, 10um sections from each tissue block were placed on microscopy slides (ColorFrost Plus, Fisher) fixed with MeOH, H&E stained, then imaged in brightfield using a NanoZoomer SQ (Hamamatsu) slide scanner at 40x equivalent magnification (Protocol CG000614, 10x Genomics).  Each slide was incubated with mouse-specific probe sets provided by the manufacturer for subsequent mRNA labeling, probe transfer using the CytAssist (10x Genomics) onto one capture area of a 6.5mm x 6.5mm Visium CytAssist Slide, and subsequent library generation per the manufacturer's protocol (10x Genomics, CG000495, Rev C).  Library concentration was quantified using a Tapestation High Sensitivity DNA ScreenTape (Agilent) and fluorometry (Thermofisher Qubit) and verified via KAPA qPCR.  Libraries were pooled for sequencing on an Illumina NovaSeq X Plus 100 cycle 10B flow cell using a 28-10-10-90 read configuration, targeting 100,000 read pairs per spot covered by tissue (approximately 300M per tissue).

value: kidney

value: WT and KO

value: ECM1 WT and KO


title: 4T1-hot primary tumor 2

description:
Library name: Sample 2
4T1hot2.bam


title: Adult testis, Wild-type 1


title: Adult testis, Ssty2 knockout 4


title: Adult testis, Ssty2 knockout 3


title: Adult testis, Ssty2 knockout 2


title: choroid plexus CD45+ cells, tomato-2

city: Saint Louis

first: Alina

last: Ulezko Antonova

state: MO

address: 660 S. Euclid Ave

department: Path/Immuno

institute: WUSM

description: 10X Genomics

data_processing:
The GRCm39 mouse reference genome was customized to include Eyfp and tdTomato sequences (including the 3’UTR).
CellRanger version 7.0.0 from 10x Genomics was employed for alignment, sample demultiplexing, barcode processing, single cell counting, and the generation of the gene expression matrix.
Raw sequencing data were aligned using CellRanger v.7.0.0 with the cellranger count function and default parameters.
Assembly: GRCm39
Supplementary files format and content: .tsv.gz and .mtx.gz files are the CellRanger output.

source_name: Choroid plexus

growth_protocol: Flt3-Cre mice : Rosa26-LSL-Eyfp mice and Ms4a3-Cre : Rosa26-LSL-tdTomato mice bred in house

extract_protocol:
Choroid plexus CD45+ live cells were sorted and resuspended in 40 μl of PBS + 0.04% nuclease-free BSA (Sigma). The entire volume was loaded into the 10x Chromium chip. 3 to 5 mice from the same experimental group were pooled for each individual sample.
Single-cell gene expression libraries and sequencing were generated using the Next GEM Single Cell 3’ Reagents Kit from 10x Genomics. The Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used. Single cells partitioned into Gel-bead-in-Emulsions (GEMs) droplets underwent retro-transcriptase reaction, and cDNA received a unique 12-nucleotide barcode and unique molecular identifier (UMI). cDNA was amplified for 11 cycles before being purified using SPRIselect beads. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche). Normalized cDNA libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 28x10x10x150 sequencing recipe according to the manufacturer's protocol (Illumina). A median sequencing depth of 50,000 reads/cell was targeted for each gene expression library.

value: Choroid plexus

value: Choroid plexus immune cells

value: Ms4a3-Cre :Rosa26-LSL-tdTomato

tag: strain

value: 2-3 months old


title: choroid plexus CD45+ cells, tomato-1

description: 10X Genomics


title: 4T1-hot_IgG_tumor2

description: Library name: Sample 10

value: 4T1-luc primary tumor

value: WT female BALB/c


title: Lateral ventricle sample-2

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR (v2.7.9a).
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount (v2.0.3). Isoform expression of known Ensembl transcripts were quantified with Salmon (v1.5.2).
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC (v4.0).
Aligned gene counts were processed using the DESeq2 package with R (v4.3.0).
Assembly: mm10
Supplementary files format and content: all.gene_counts.tsv is a tab-delimited file that contains the raw counts of all bulk RNA-seq samples listed here.

growth_protocol: Bl6 female mice purchased from Jackson Laboratory

extract_protocol:
RNA was extracted and purified from the whole tissue using the RNeasy Micro Kit (Qiagen) and stored at -80°C until analysis. Total RNA integrity was determined using Agilent Bioanalyzer. Sequenced samples had an RNA integrity number (RIN) between 9.4 and 10.
Library preparation was performed with 10ng of total RNA per sample using the low-input Takara-Clontech SMARTer kit (Takarabio) according to manufacturer’s protocol. Libraries were pooled and sequenced on an Illumina NovaSeq-6000 S4 flow cell (2x150 sequencing recipe), targeting 50M reads per sample.

tag: tissue region

value: Lateral ventricle

value: Choroid plexus total cells


title: Lateral ventricle sample-3


title: Lateral ventricle sample-1


title: Fourth ventricle sample-3

value: Fourth ventricle


title: choroid plexus CD45+ cells, YFP-1a

description: 10X Genomics

value: Flt3-Cre :Rosa26-LSL-Eyfp


title: choroid plexus CD45+ cells, YFP-2b

description: 10X Genomics


title: choroid plexus CD45+ cells, YFP-3

description: 10X Genomics


title: Fourth ventricle sample-1


title: Fourth ventricle sample-2


title: choroid plexus CD45+ cells, LCMV-1

description: 10X Genomics

data_processing:
CellRanger version 7.0.0 from 10x Genomics was employed for alignment, sample demultiplexing, barcode processing, single cell counting, and the generation of the gene expression matrix.
Raw sequencing data were aligned using CellRanger v.7.0.0 with the cellranger count function and default parameters.
SoupX was run according to the R tutorial to minimize the ambient RNA contamination from T cells and plasma cells. The following genes were used to manually determine the contaminating fraction in each sample: "Ccl5, Tox, S100a6, S100a4, Nkg7, Cd3g, Cd3e, Ms4a4b, Trbc2, Igkc, Ighm, Igha, Ighg1, Ighg2b, Ighg2c, Iglc1, Iglv1, Jchain". A SoupX-corrected gene count matrix was used to generate the Seurat object.
Assembly: GRCm39
Supplementary files format and content: .tsv.gz and .mtx.gz files are the CellRanger output.

extract_protocol:
Choroid plexus CD45+ live cells were sorted and resuspended in 40 μl of PBS + 0.04% nuclease-free BSA (Sigma). The entire volume was loaded into the 10x Chromium chip. 5 mice from the same experimental group were pooled for each individual sample.
Single-cell gene expression libraries and sequencing were generated using the Next GEM Single Cell 3’ Reagents Kit from 10x Genomics. The Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used. Single cells partitioned into Gel-bead-in-Emulsions (GEMs) droplets underwent retro-transcriptase reaction, and cDNA received a unique 12-nucleotide barcode and unique molecular identifier (UMI). cDNA was amplified for 11 cycles before being purified using SPRIselect beads. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche). Normalized cDNA libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 28x10x10x150 sequencing recipe according to the manufacturer's protocol (Illumina). A median sequencing depth of 50,000 reads/cell was targeted for each gene expression library.

treatment_protocol: LCMV clone 13, produced in-house, or an equal volume of PBS, was intravenously injected into 7-8-week-old C57BL/6J female mice at a titer of approximately 2.5x106. Mice receiving LCMV or PBS were randomized prior to injection to normalize the microbiota. Throughout the infection period, mice were housed in a BSL3 infection room and monitored daily.

value: Wild-Type

value: 10-11 weeks old

value: LCMV


title: 4T1-cold_IgG_tumor3

description: Library name: Sample 3

value: 4T1 primary tumor

value: anti-IgG control


title: choroid plexus CD45+ cells, PBS-1

description: 10X Genomics

value: PBS


title: choroid plexus CD45+ cells, PBS-2

description: 10X Genomics


title: cFGF23-Hyp_4

city: Zurich

first: Ganesh

last: Pathare

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

data_processing:
In brief, amplified cDNA samples were subjected to different quality control standards. RNA sample was used for library preparation using NEB Next® Ultra RNA Library Prep Kit for Illumina®.
Indices were included to multiplex multiple samples. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.
The library was ready after end repair, A-tailing, adapter ligation, and size selection. After amplification and purification, the insert size of the library was validated on an Agilent 2100 and quantified using quantitative qPCR.
. Libraries were then sequenced on Illumina NovaSeq 6000 S4 flow cell with PE150 according to results from library quality control and expected data volume.
Assembly: mm10
Supplementary files format and content: .xls files included raw counts for each sample

source_name: Kidney

growth_protocol: For details related to animal study please refer to -Zhukouskaya, 2021, Sci Adv

extract_protocol:
RNA was isolated from total kidney
RNA sample was used for library preparation using NEB Next® Ultra RNA Library Prep Kit for Illumina®.

treatment_protocol: The treatment consisted of intravenous injection of AAV-cFGF23 administered at the dose of 1 × 1012 vg per mouse at 4 weeks of age. Mice were sacrificed after 3 months when they were at 4 months of age.

value: Kidney


title: cFGF23-Hyp_3


title: cFGF23-Hyp_2


title: Hyp_3

value: Hyp


title: Adult testis, Ssty2 knockout 1

value: Adult testis


title: Hyp_5


title: cFGF23-Hyp_1


title: Hyp_2


title: cFGF23-Hyp_5


title: Adult testis, Wild-type 2

value: WT


title: WT_5


title: WT_4


title: WT_3


title: Hyp_4


title: WT_2


title: WT_1


title: E14_H3K36me2_KDM2A_2B_jmjcMUT_rep2

city: Beijing

first: Falong

last: Lu

address: 1 West Beichen Road Chaoyang District

institute: Institute of Genetics and Developmental Biology

data_processing:
Base-calling were perform with Illumina sequencing system running RTA v1.18.54.
Reads were trimmed to remove the adapter sequences and low quality bases using Trim Galore.
Clean reads were aligned to the mouse reference genome (mm10) using Bowtie2 with default parameters.
Unmapped reads, multiple mapped reads and PCR duplicates were removed by samtools and sambamba.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage(v3.3.1); Scores represent RPKM.

growth_protocol: WT, Kdm2a/Kdm2b DKO, Kdm2a/Kdm2b JmjC double mutation E14Tg2a mESCs were cultured on 0.2% gelatin-coated plates in DMEM supplemented with 15% fetal bovine serum, 1% penicillin/streptomycin, 1% nonessential amino acid, 1% sodium pyruvate, β-mercaptoethanol and 1000 U/mL LIF (ESGRO, Millipore).

extract_protocol:
Approximately 4 × 10^6 cells were crosslinked with 1% formaldehyde for 5 min. After quenching with 125 mM glycine, the cells were harvested and digested by MNase (NEB, M0247S, 2 U/ml) at 37°C for 20 min to produce soluble chromatin with DNA fragments. The lysates were then centrifuged at 10800 rpm for 10 min at 4°C. The supernatants were collected and pre-cleared for 1 hour with Protein A and protein G Dynabeads. Meanwhile, protein A and protein G Dynabeads were pre-linked with antibody against H3K36me2. The pre-cleared supernatant was then transferred to antibody-beads complex and incubated overnight at 4°C whilst rocking. Bound chromatin was washed extensively with low salt buffer, high salt buffer, LiCl buffer and two washes with TE buffer. ChIP DNA was then eluted and reverse-crosslinked at 65°C for 16 h using elution buffer. After being treated by RNase A and proteinase K, ChIP DNA was extracted by phenol: chloroform and ready for constructing library.
The sequence libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB), following the manufacturer’s guidelines. The H3K36me2 library was subjected to pair-end (150 bp) sequencing on a Novaseq (Illumina).

tag: chip antibody


title: E14_H3K36me2_KDM2A_2B_DKO_rep2


title: Control, DMGMOUSE1, scRNASeq

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Murine DMG Cell Line (DIPG4423) injected in mice

growth_protocol: All B6 mice were maintained under barrier conditions and experiments were conducted under the protocol approved by the Columbia University Institute of Comparative Medicine (ICM) and the Institutional Animal Care and Use Committee (IACUC) under protocol AC-AABL655. First, cells were detached using ACCUTASETM and centrifuged at 250g for 6 minutes. The pellet was then resuspended in 1 ml of room temperature ACCUTASETM for 3 minutes and pipetted up and down approximately 20 times. Then 3 ml of fresh media was added, and cells were resuspended and centrifuged again at 250g for 6 minutes. Cells were filtered through a 70μm cell strainer to remove any clumps. Cells were resuspended in a volume of 100,000 cells/μl and cell viability was assessed using the Countess 3FL Automated Cell Counter. All intracranial injections were conducted under sterile conditions. Before intracranial implantation, 6-week-old B6(Cg)-Tyrc-2J/J mice from Jackson laboratories were anesthetized with 1-2% isoflurane anesthesia in oxygen delivered at 0.75 L/min and were immobilized in a mouse stereotactic instrument (Stoelting). A 1-cm incision was made at the midline of the scalp to expose the sagittal suture and lambda of the skull. A burr hole 1 mm in diameter was made in the skull at a position 1.5 mm posterior to the lambda and 1.5 mm lateral to the sagittal suture. A Hamilton syringe containing 100,000 cells suspended in 1 μl NeuroCult™ Basal Medium (STEMCELL Technologies) was inserted 5 mm below the skull surface and injected at a rate of 0.1 mL/min over 10 minutes. Two minutes following implantation, the syringe was slowly removed from the mouse brain in 1 mm increments spaced 30 seconds apart. Then, the burr whole was covered with bone wax (Fisher) and the incision was closed with three to four sutures (Fisher). After suturing, triple antibiotic ointment was applied to the wound and animals were injected (IP) with 0.05mg/kg of buprenorphine (Covetrus, approved by DOH/DEA). Mice were put on a heating pad until they woke up from anesthesia and then were placed back in the cage. Wounds and sutures were thoroughly monitored every day for 7 consecutive days to ensure complete recovery. Tumor presence and location were confirmed 12 days post-injection with MRI.were maintained under barrier conditions and experiments were conducted under the protocol approved by the Columbia University Institute of Comparative Medicine (ICM) and the Institutional Animal Care and Use Committee (IACUC) under protocol AC-AABL655. Juvenile male and female NOD.Cg Prkdcscid/J (NSGTM) mice were inoculated with 500,000 SU-DIPG-17-luciferase tagged cells in 1:1 suspension (200 μl total) with full media (Knockout DMEM/F12, Stempro neural supplement, Human FGF2, Human EGF2, Glutamine and Penicillin/Streptomycin) and Matrigel (BD Bioscience) via subcutaneous injection in the left flanks. Two weeks post-injection, animals were injected intraperitoneally with luciferin and scanned with PerkinElmer IVIS Optical Imagingto monitor tumor growth.

extract_protocol:
Three weeks after injection, untreated mice were euthanized for brainstem tumor single-cell isolation and Next-generation sequencing. Before euthanasia, mice were anesthetized with 2% isofluorane and perfused for 8 minutes with cold saline (1X PBS) and/or until the liver turned pale. Upon dissection of the brainstem, the tissue was placed in isolation media consisting of RPMI 1640 with GlutaMAX Supplement and HEPES (Gibco) with 0.01% 50X B27 supplement (Gibco). The tissue was then homogenized in a 15ml glass tissue grinder, filtered through a 70μm filter and spun down at 300g for 10 minutes at 4 degrees. The pellet was resuspended in 1ml of isolation media (per brainstem), 100ul of myelin removal beads were added (Miltenyi Biotec) and the mixture was incubated for 15 minutes. After one wash, the solution was then passed through LS+ positive separation columns (Miltenyi Biotec) to deplete the myelin. After another wash with single-cell buffer (HBBS + 0.04% BSA), the pellet was resuspended in 400 ul of RBC lysis buffer and incubated on ice for 2 minutes. Then, 1ml of single-cell buffer was added and sample was spun down at 250g for 5 minutes. Three more washes with single-cell buffer were performed and the final pellet was resuspended in the appropriate volume of single-cell buffer to have an approximate concentration of 1x106 cells/mL. Cell counting and viability was assessed with Countess 3FL Automated Cell Counter.
Dissociated cells were processed for single-cell gene expression capture (scRNA-seq) using the 10X Chromium 3’ Library and Gel Bead Kit (10x Genomics), following the manufacturer’s user guide. After Gel bead-in-EMulsion Reverse Transcription (GEM-RT) reaction, 12-15 cycles of polymerase chain reaction (PCR) amplification were performed to obtain cDNAs used for RNA seq library generation
Libraries were prepared following the manufacturer’s user guide and sequenced on the Illumina NovaSeq 6000 Sequencing System at the Columbia University Single Cell Analysis Core

treatment_protocol: Untreated for 3 weeks

value: Untreated


title: E14_H3K36me2_KDM2A_2B_jmjcMUT_rep1


title: Control,  DMGMOUSE2, scRNASeq

description: 10x Genomics

value: Murine DMG Cell Line (DIPG4423) injected in mice


title: choroid plexus CD45+ cells, LCMV-2

description: 10X Genomics

value: Choroid plexus

value: Choroid plexus immune cells


title: Normal, DMGMOUSEWT, scRNASeq

description: 10x Genomics

source_name: Murine Normal Brainstem

value: Murine Normal Brainstem


title: E14_H3K36me2_KDM2A_2B_DKO_rep1


title: E14_H3K36me2_input_ChIP_seq

value: none (input)


title: E14_H3K36me2_WT_ChIP_seq


title: E14_RRBS_KDM2A_2B_jmjcMUT_rep1

data_processing:
Base-calling were perform with Illumina sequencing system running RTA v1.18.54.
Reads were trimmed to remove the adapter sequences and low quality bases using Trim Galore.
Bismark v0.19.0 was used to align reads to mm10 and extract the coverage depth and methylation level of each cytosine.
Genome_build: mm10
Supplementary_files_format_and_content: Coverage files (using 1-based genomic genomic coordinates) that feature methylated and unmethylated counts.

growth_protocol: WT, Kdm2a KO, Kdm2b KO, Kdm2a/Kdm2b DKO, Kdm2a/Kdm2b JmjC double mutation E14Tg2a mESCs were cultured on 0.2% gelatin-coated plates in DMEM supplemented with 15% fetal bovine serum, 1% penicillin/streptomycin, 1% nonessential amino acid, 1% sodium pyruvate, β-mercaptoethanol and 1000 U/mL LIF (ESGRO, Millipore).

extract_protocol:
Genomic DNA (20 ng) with 1% nonmethylated lambda DNA spike-in was digested by Msp I enzyme.
DNA was then end-repaired, dA-tailed and ligated with methylated adaptors. Bisulfite conversion was carried out using a bisulfite conversion kit (Zymo Research) according to the manufacturer’s instructions. 3.5 h were used in both conversion steps. Bisulfite-converted DNA was then amplified by PCR to obtain the final library. The RRBS libraries were subjected to pair-end (150 bp) sequencing on a Novaseq.


title: E14_RRBS_KDM2A_2B_DKO_rep2


title: Hyp_1


title: E14_RRBS_KDM2A_2B_DKO_rep1


title: E14_RRBS_KDM2A_2B_jmjcMUT_rep2


title: E14_RRBS_KDM2A_KO_rep2


title: E14_RRBS_KDM2A_KO_rep1


title: E14_RRBS_KDM2B_KO_rep2


title: E14_RRBS_WT


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-P11

city: La Jolla

first: Joseph

middle: R

last: Ecker

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: hg38-donor-snp-substituted
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: DHC

tag: gender

value: M


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-P23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-O24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-P12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-O23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-O12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-N24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-O11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-P24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-N23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-M24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-N11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-N12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-M12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-M23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-M11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-L23


title: E14_RRBS_KDM2B_KO_rep1


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-L11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-L12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-K24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-K23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-K12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-K11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-J24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-J23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-J11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-J12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-I24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-I23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-I11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-H23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-I12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-H12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-G24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-H11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-H24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-G23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-L24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-F23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-F24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-G11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-F12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-G12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-E24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-F11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-E12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-D24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-E11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-C24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-D11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-C23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-D12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-C12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-C11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-B24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-B23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-B12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-B11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-A23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-A11


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-P9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-P22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-E23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-A12


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-P10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-P21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-O9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-N9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-O21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-N10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-O22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-M9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-D23


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-N21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-L22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-L21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-M10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-L9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-M22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-N22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-L10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-K9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-M21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-K10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-K22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-6-L2-A24


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-J9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-K21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-J22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-J21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-J10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-I9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-I22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-I10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-I21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-O10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-H9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-H22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-H21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-H10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-G21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-G10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-F9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-F21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-F10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-F22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-E22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-E21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-E10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-D9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-C10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-C21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-D21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-D10


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-C22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-B9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-B22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-A9


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-D22


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-A21


title: AMB_200303_18mo_8E_9H_8J_9J_2_P5-5-L6-B10


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title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-D8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-D20


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-D19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-C7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-D7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-C8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-C20


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-H7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-B8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-B19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-G19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-A19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-A20


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-P5


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-P18


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-B7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-A8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-O6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-O5


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-O17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-A7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-O18


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-P17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-N5


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-N17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-M5


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-N18


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-M17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-M18


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-L6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-3-J21-M6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P6-4-D14-C19