title: MOLM13_sgAAVS_4d_H3K4me3

description: Library name: Sample2

value: Setd1b SET wildtype


title: KY-1668_030822_papain

status: Public on Apr 28 2025

type: SRA

city: Boston

first: Natalie

middle: Y. R.

last: Agar

state: Massachusetts

address: Harvard Medical School

department: Neurosurgery

country: USA

institute: Brigham and Women's Hospital

description: Library name: KY-1668_030822_papain

library_source: transcriptomic single cell

data_processing:
Barcoded cDNA transcripts from patients were pooled and sequenced using the NovaSeq 6000 Sequencing System.
Raw single-cell RNA seq reads generated by Illumina sequencer were demultiplexed into FASTQ and aligned to GRCh38 reference genome to generate count matrices using Cell Ranger v6.0.0 analysis pipelines (10x Genomics). The preliminarily processed data was used for downstream analysis by Seurat v4.3.0 (96). Low-quality and dead cells which had <200 or >2,500 unique transcripts or >5% of mitochondrial transcripts were filtered out. Multiple datasets (with and without inhibitors) were combined, normalized, identified variable features, and applied principal component analysis (PCA) using Seurat.  Batch effect correction of combined data was performed using Harmony algorithm v0.1.1 (97). Following batch correction, FindClusters was applied with a resolution of 0.5 to identify cell clusters and uniform manifold approximation and projection (UMAP). For visualization, plots were generated using a combination of Seurat, ggplot2, and scCustomize v2.1.2 (98).
Assembly: GRCh38
Supplementary files format and content: Matrix in h5 format

molecule: total RNA

organism: Homo sapiens

source_name: Brain

extract_protocol:
Fresh tissue samples were directly placed in MACS tissue storage buffer (Miltenyi Biotec, Germany) on ice before transportation to the processing laboratory. Given the potential need to transport tissue from different institutions we also tested the performance of tissue storage buffer (results in Supplementary Table 4). Once received in the laboratory, tissue cores were morselized into small pieces under sterile conditions using sterile scalpels, triturated using pipettes then transferred to a 50ml falcon tube (Corning, USA), then incubated with papain (37°C, 25 min)(Worthington, USA) according to manufacturer instructions. After incubation HBSS without magnesium or calcium was then added to make up to 50ml and the sample centrifuged (300×g, 5 min, 4◦C), supernatant aspirated before being passed through a 70μm cell strainer (BD, USA). Erythrocytes were removed by resuspending and incubating the obtained pellet in 5 ml of ACK-lysis buffer (eBioscience, USA) for 10 min, followed by centrifugation (300×g, 5 min,4°C). Residual myelin and extracellular debris were eliminated using the Debris Removal Kit (Miltenyi Biotech, Germany). Cell counts were quantified using an automated cell counter (Nexcelom, USA) after resuspending the pellet in PBS. Cells were stored in Bambanker (Wako, Japan). Cell suspensions were immediately placed in a storage container (Mr. FrostyTM, Thermo Fisher Scientific, USA) and stored in LN2.
Freshly isolated cells were droplet-separated using the Chromium Single Cell 3′ v.3 Reagent Kit with the 10x Genomics microfluidic system creating cDNA library with individual barcodes for individual cells. scRNA-seq was performed using the 10x Genomics Chromium Single Cell Controller

tag: tissue

value: Brain

tag: cell type

value: Disassociate tumor cell


title: multiome4epcam_ATAC

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

description:
3' single-cell multiome ATAC. h5 file contains both modalities
multiomeC57Depcam_atac_fragments.tsv.gz
multiomeC57Depcam_atac_fragments.tsv.gz.tbi

library_source: genomic

data_processing:
CellRanger was used to align reads to the Mus musculus reference (GENCODE vM23/Ensembl 98) and the Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85) from Ensembl70. Gene counts were analyzed with Seurat v471 for clustering, integration and differential gene expression and Monocle version 372 for clustering and pseudotime. Filtering cutoffs were set as follows: minimum genes per cell = 500, maximum genes = 5000, minimum UMIs per cell was set on a per-sample basis after inspecting a rank plot of UMI/cell. Cells with over 20% mitochondrial reads were also excluded. Differentially-expressed genes were identified via Seurat’s FindMarker function with default parameters. Samples were integrated using Seurat’s integration anchors and the first 30 principle components were used for integration and UMAP creation. Clusters were found using monocle (cluster_cells, resolution = 5 10-5, k = 8, partition_qval = 0.05). Psudotime was generated using Monocle’s learn_graph (default parameters). For ATAC analysis, peaks were called using Signac with MACS2, and gene activity scores were calculated with Signac.
Assembly: Mus musculus reference (GENCODE vM23/Ensembl 98)
Supplementary files format and content: filtered_feature_bc_matrix.h5 files
Supplementary files format and content: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Supplementary files format and content: featurereference.csv
Assembly: Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85)
Supplementary files format and content: Contain mRNA+ADT or mRNA + ATAC counts as appropriate
Supplementary files format and content: ATAC fragment files
Supplementary files format and content: Contain ADT antibodies used & barcode sequences
Library strategy: single-cell multiome RNA + ATAC

molecule: genomic DNA

organism: Mus musculus

source_name: testis

extract_protocol:
Rat cells were isolated from the testes of 3- to 4-month-old Sprague Dawley rats transgenic for the LacZ gene under the metallothionine promoter67. Mouse cells were isolated from C57BL/6 inbred mice also 3-4 months old. Tissue was chopped into fine pieces and incubated in collagenase (Sigma) at a concentration of 1mg/ml in HBSS (Gibco) for 15 minutes at 37C. Cells were spun down for 1 minute at 600 rcf, then resuspended in warm Trypsin (Gibco, 0.25%) with 20% DNase solution (Sigma, 7mg/ml dissolved in HBSS). Tissue was pipetted for 2 minutes with a 10 ml pipette and incubated at 37C for 5 minutes. Then tissue was pipetted for another 2 minutes and incubated at 37C for 3 minutes. FBS (Sigma F2442) was added to stop the digestion. Additional DNase was added until no turbidity was visible. Cells were washed in PBS-S twice (PBS [Gibco] with 1% FBS, 10 mM HEPES [Sigma Aldrich], 1 mg/ml glucose [Sigma Aldrich], 1 mM pyruvate [Gibco], 50 units/ml penicillin [Gibco], 50 ug/ml streptomycin [Gibco] prepared as described in 68). All centrifugation steps were 5 minutes at 600 rcf.   Cells were processed both as unselected samples and enriched for EPCAM as described below. Each biological replicate was then used for either encapsulation of cells with antibody treatment or further processed as nuclei for GEX+ATAC assay.
Cells were encapsulated and libraries generated for GEX+CITE using a Chromium Next GEM Single Cells 3’ Kit v3.1 with Feature Barcoding (10X Genomics) per manufacturer’s protocol. Prepared nuclei were encapsulated with the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit following manufacturer’s instructions. Each biological replicate was encapsulated individually. Libraries were sequenced on a NextSeq2000 sequencer (Illumina) using a 100-cycle sequencing kits to a minimum depth of 30k reads per cell.

value: testis

tag: Stage

value: Adult

tag: selection

value: EpCAM+

tag: library type

value: ATAC DNA


title: multiome4epcam_RNA

description:
3' single-cell multiome RNA. h5 file contains both modalities
multiomeC57Depcam_filtered_feature_bc_matrix.h5

library_source: transcriptomic

value: mRNA


title: mRNA-seq analysis of NT control mESCs replicate 1

city: Geneva

first: Simon

last: Braun

address: rue Michel Servet 1

country: Switzerland

institute: University of Geneva

description: Input mRNA-seq

data_processing:
Sequencing reads were trimmed using cutadapt 3.5 (adapters -m 20 -O 4 -e 0.2 -p). Reads were aligned to the mm10 genome wiusing STAR v2.7.5 (--readFilesCommand zcat --runThreadN 6 --genomeDir GRCm38.102 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard). m6A peaks enriched relative to input mRNA were called using MACS272 v2.7.1 (callpeak --nomodel --keep-dup all -B -q 0.05 --extsize 100 --shift -50 -g mm -t m6A.bam -c input.bam, filtered for score > 200). Peaks from NT, KO and ΔRRM1 datasets within 100 bp were merged using bedtools v2.30 and the numbers of reads from each replicate overlapping with the peak set was counted using featureCounts v2.0.3 (-T 4 -O -p -a -t exon -g gene_id).
Differential m6A peak calls were determined using the R software DESeq2 after pre-filtering peaks with low counts (rowSums > 50), with significance cut-offs set at FDR < 0.05 and fold change > 1.5 in either direction.
Assembly: mm10
Supplementary files format and content: bed files with raw m6A peak counts and gene counts for all conditions

molecule: polyA RNA

source_name: Embryonic stem cells (mESC)

growth_protocol: mESCs were cultured in media containing DMEM media, supplemented with LIF, 15% FBS, 0.1 mM β-Mercapthoethanol, 1x non-essential amino acids, 100 mM Hepes buffer, 100 U/ml Penicillin-Streptomycin at 37°C and 5% CO2 on plates coated with 0.2% gelatin solution

extract_protocol:
RNA was isolated using the RNAeasy kit (Qiagen, 74106). Next, mRNA was isolated using the mRNA Isolation kit (NEB, S1550S). mRNA was fragmented using the NEBNext Magnesium RNA fragmentation module (NEB, E6150S) and purified using Monarch RNA Cleanup Kit (NEB, T2030S). 100 ng mRNA was aliquoted and stored as input at -80°C. For m6A-RIP, 50 µl of Dynabeads protein G (Invitrogen, 10004D) were aliquoted and placed on a magnet. Supernatant was removed and beads were washed in 500 µl of m6A-IP buffer (10 mM TrisHCl pH7.4, 150 mM NaCl, 0.1% NP-40). After the initial washing, beads were resuspended in 500 µl m6A-IP buffer and incubated for 45 min at RT on a rotating wheel. Next, supernatant was removed and beads were resuspended in 400 µl m6A-IP buffer. Samples were placed on ice and 5 µg of m6A-antibody (Supplementary table 6), 5 µl RiboLock RNase Inhibitor (Thermo Fisher Scientific, E00381), 20 µl fragmented mRNA, 100 µl 5X m6A-IP buffer (50 mM Tris-HCl pH7.4, 750 mM NaCl, 0.5% NP-40) and 370 µl H2O were added. Samples were incubated for 2 h, at 4°C on a rotating wheel. Next, samples were placed on a magnet and supernatant was removed. Samples were washed twice in 500 µl ice cold m6A-IP buffer for 30 sec. After washing samples were resuspended in 150 µl RNA cleanup binding buffer of the Monarch RNA Cleanup Kit (NEB, T2030S). Samples were incubated for 5 min at RT on a rotating wheel. The eluate was transferred to a new tube. m6A-RIP mRNA was purified using the Monarch RNA Cleanup Kit (NEB, T2030S). Samples were eluted in 8 µl elution buffer.
The sequencing libraries were made using the Illumina Stranded mRNA Prep Ligation kit and protocol starting from 100 ng of input mRNA and m6A-RIP mRNA. To start, 8.5 ul of RNA, 8.5 ulof Fragmentation master mix and 8 ul of First Strand Synthesis master mix were mixed for direct First strand cDNA synthesis. Then protocol instructions were followed as described.
Library molarity and quality were assessed by Qubit and Tapestation (DNA High sensitivity chip). Libraries were sequenced on a NovaSeq 6000 Illumina sequencerwith paired-end 50 settings.

value: Embryonic stem cells (mESC)

tag: genotype

value: WT

tag: treatment

value: none (input)


title: CD4_sgFpr1_3

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
The raw sequences from all the samples were aligned to the GRCm38 transcriptome and quantified using kallisto.
Assembly: GRCm38
Supplementary files format and content: TAR gzipped folders of kallisto output

source_name: CNS

growth_protocol: Inbred C57BL/6J mice (The Jackson Laboratory, 000664) were used as a genetic background for all in vivo experiments. Mice were housed under standard conditions in a pathogen-free facility at the Hale Building for Transformative Medicine at 20–23°C and 50% humidity with access to water and food ad libitum and under a 12h light/dark cycle, in accordance with guidelines for care and experimentation defined by the Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
Cell suspensions were stained extracellularly as described above with Live/dead stain  and Fc block, and finally with a mix of antibodies in FACS buffer for 30 min at 4°C. All antibodies were diluted 1:100 in FACS buffer. Prior to sorting, cell suspensions were filtered through tubes with 35µm cell strainer caps (Falcon, 352235). For RNA-seq analyses, cells were sorted directly into 100µL Picopure™ Extraction Buffer (Thermo Scientific, KIT0204), incubated 30 min at 42°C and then stored at -80°C until RNA isolation and sequencing was performed.
Library was constructed using  Smart-Seq 2 protocols

value: CNS


title: Th17, Lkb1+/-, A485, rep3

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
Adapter sequences and low-quality bases were trimmed using TrimGalore v0.6.10 (https://github.com/FelixKrueger/TrimGalore) using the parameters, ‘--paired -q 20’. The mm10 genome and gene annotations were downloaded from GENCODE release M24 (Frankish et al. 2021). Trimmed reads were aligned to the mm10 reference genome to obtain gene counts using STAR v2.7.10a (Dobin et al. 2013), with the parameters, ‘--twopassMode Basic --quantMode GeneCounts.’
Assembly: mm10
Supplementary files format and content: tab-delimited gene counts from STAR

source_name: Th17 cell

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using KAPA RNA HyperPrep with rRNA reduction using QiaSeq FastSelect.

value: Th17 cell


title: CD4_sgFpr1_2


title: BTC-NY-MSK-5-GEX

description: Library name: S1_L001


title: multiome5epcam_ATAC

description:
3' single-cell multiome ATAC. h5 file contains both modalities
multiomeC57Cepcam_atac_fragments.tsv.gz
multiomeC57Cepcam_atac_fragments.tsv.gz.tbi


title: CD4_sgFpr1_1


title: multiome5epcam_RNA

description:
3' single-cell multiome RNA. h5 file contains both modalities
multiomeC57Cepcam_filtered_feature_bc_matrix.h5


title: Th17, Lkb1+/-, A485, rep1


title: MDA_with_inhibitor

description: Library name: S28_L001


title: Th17, Lkb1+/-, A485, rep2


title: CD4_sgRandom_3


title: mRNA-seq analysis of NT control mESCs replicate 2

description: Input mRNA-seq


title: CD4_AAVsgRosa_1


title: MDA_without_inhibitor

description: Library name: S27_L001


title: CD4_sgRandom_2


title: MSK_with_inhibitor

description: Library name: S26_L001


title: multiome3unselected_RNA

description:
3' single-cell multiome RNA. h5 file contains both modalities
multiomeC57B_filtered_feature_bc_matrix.h5

value: unselected


title: Th17, Lkb1+/-/Crtc2-/-, ctrl, rep3

value: ctrl


title: CD4_sgRandom_1


title: multiome2unselected_ATAC

description:
3' single-cell multiome ATAC. h5 file contains both modalities
multiomeC57A_atac_fragments.tsv.gz
multiomeC57A_atac_fragments.tsv.gz.tbi


title: CD8_AAVsgAnxa1_4


title: Th17, Lkb1+/-/Crtc2-/-, ctrl, rep1


title: KY-1668_030822_mech

description: Library name: KY-1668_mech


title: multiome2unselected_RNA

description:
3' single-cell multiome RNA. h5 file contains both modalities
multiomeC57A_filtered_feature_bc_matrix.h5


title: CD8_AAVsgAnxa1_3


title: Protein A08 Biopsy 2

description: Library name: DSP-1002883220504-D-A08_Protein

library_source: other

data_processing:
Purified libraries were sequenced by Illumina NovaSeq6000. The FASTQ reads from sequenced DSP library were processed by the GeoMx NGS DnD Pipeline to convert sequencing reads into counts per ROI (NanoString, MAN-10133_03). After processing, counts were uploaded to the GeoMx DSP Data Analysis Suite (NanoString Technologies, USA).
Assembly: GRCh38
Supplementary files format and content: .WTA and Protein probe and read summary matrices. xlsx
Library strategy: Spatial Transcriptomics

molecule: protein

source_name: Disassociated tumor cells

extract_protocol:
This is a single subject experimental design where multi-modality measurements are taken from the tissue samples from the same subject.  Biopsy cores were collected immediately during operation and transported in MACS storage solution (Miltenyi, Germany). Samples were then sent to the primary processing institution (MDACC) on ice via courier.   Sample Distribution: Formalin fixed samples were processed locally at MSKCC (Core 1). Fresh tissue placed in tissue storage solution and was immediately shipped for central processing at MDA (Core 2 & 3). Snap frozen specimens (Cores 4-5) were shipped to BWH/DFCI and MIT respectively.  Low volume glioma tissue processing: At the receiving institution, tissue cores were processed within 24 hours of the operation. Fresh tissue samples were directly placed in MACS tissue storage buffer (Miltenyi Biotec, Germany) on ice before transportation to the processing laboratory. Given the potential need to transport tissue from different institutions we also tested the performance of tissue storage buffer (results in Supplementary Table 4). Once received in the laboratory, tissue cores were morselized into small pieces under sterile conditions using sterile scalpels, triturated using pipettes then transferred to a 50ml falcon tube (Corning, USA), then incubated with papain (37°C, 25 min)(Worthington, USA) according to manufacturer instructions. After incubation HBSS without magnesium or calcium was then added to make up to 50ml and the sample centrifuged (300×g, 5 min, 4◦C), supernatant aspirated before being passed through a 70μm cell strainer (BD, USA). Erythrocytes were removed by resuspending and incubating the obtained pellet in 5 ml of ACK-lysis buffer (eBioscience, USA) for 10 min, followed by centrifugation (300×g, 5 min,4°C). Residual myelin and extracellular debris were eliminated using the Debris Removal Kit (Miltenyi Biotech, Germany). Cell counts were quantified using an automated cell counter (Nexcelom, USA) after resuspending the pellet in PBS. Cells were stored in Bambanker (Wako, Japan). Cell suspensions were immediately placed in a storage container (Mr. FrostyTM, Thermo Fisher Scientific, USA) and stored in LN2.
Digital Spatial profiling (DSP, Nanostring) experiments were performed according to the manufacturer's protocol. Briefly, slides were stained and imaged to visualize morphology markers, GFAP-AF488, 53-9892-82, Clone GA5, diluted 1-100, Syto83, S11364, diluted 1:25, CD45-AF594, NBP1-44763AF594, clone EM05, diluted 1:100, Ki67-AF647, NBP2-22112AF647, clone 8D5, diluted 1:100. Images at ×20 magnification were assembled to yield high-resolution regions of interest. As previously described, ROIs were illuminated and released tags were collected into 96-well plates. Sequential sections were used for GeoMx Protein and RNA profiling. For protein detection GeoMx (v1.0) Human NGS Protein Core, (v1.0) Human NGS Cell Death Protein, (v1.0) Human NGS Glial Cell Subtyping Protein, (v1.0) Human NGS Immune Activation Status Protein, (v1.0) Human NGS Immune Cell Typing Protein, (v1.0) Human NGS IO Drug Target Protein, (v1.1) Human NGS MAPK Signaling Protein, (v1.0) Human NGS Myeloid, (v1.0) Human NGS Neural Cell Typing Protein, (v1.0) Human NGS Pan-Tumor Protein, (v1.0) Human NGS PI3K/AKT Signaling modules were used to identify cell types.  Detection of mRNA was performed for morphology marker–defined compartments according to the NanoString GeoMX RNA assay protocol described previously (99) using the Whole Transcriptome Atlas probe reagent. Library preparation was also performed according to the manufacturer's protocol. DSP collection sample plates were dried, resuspended in nuclease-free water, and amplified using PCR according to the manufacturer’s protocol.

value: Disassociated tumor cells


title: Protein A07 Biopsy 2

description: Library name: DSP-1002883220504-D-A07_Protein


title: mouse2_epcam.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_mouse2_epcam_filtered_feature_bc_matrix.h5
mouse_featurereference.csv

data_processing:
CellRanger was used to align reads to the Mus musculus reference (GENCODE vM23/Ensembl 98) and the Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85) from Ensembl70. Gene counts were analyzed with Seurat v471 for clustering, integration and differential gene expression and Monocle version 372 for clustering and pseudotime. Filtering cutoffs were set as follows: minimum genes per cell = 500, maximum genes = 5000, minimum UMIs per cell was set on a per-sample basis after inspecting a rank plot of UMI/cell. Cells with over 20% mitochondrial reads were also excluded. Differentially-expressed genes were identified via Seurat’s FindMarker function with default parameters. Samples were integrated using Seurat’s integration anchors and the first 30 principle components were used for integration and UMAP creation. Clusters were found using monocle (cluster_cells, resolution = 5 10-5, k = 8, partition_qval = 0.05). Psudotime was generated using Monocle’s learn_graph (default parameters). For ATAC analysis, peaks were called using Signac with MACS2, and gene activity scores were calculated with Signac.
Assembly: Mus musculus reference (GENCODE vM23/Ensembl 98)
Supplementary files format and content: filtered_feature_bc_matrix.h5 files
Supplementary files format and content: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Supplementary files format and content: featurereference.csv
Assembly: Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85)
Supplementary files format and content: Contain mRNA+ADT or mRNA + ATAC counts as appropriate
Supplementary files format and content: ATAC fragment files
Supplementary files format and content: Contain ADT antibodies used & barcode sequences
Library strategy: CITE-Seq

value: ADT


title: Th17, Lkb1+/-, ctrl, rep1


title: mouse2_epcam

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_mouse2_epcam_filtered_feature_bc_matrix.h5


title: CD8_AAVsgAnxa1_1


title: mouse1_epcam.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_mouse1_epcam_filtered_feature_bc_matrix.h5
mouse_featurereference.csv


title: Protein A06 Biopsy 2

description: Library name: DSP-1002883220504-D-A06_Protein


title: CD8_AAVsgAnxa1_2


title: Polyp, Lkb1+/-, rep12

source_name: Polyp

value: Polyp


title: Th17, Lkb1+/-/Crtc2-/-, ctrl, rep2


title: Th17, Lkb1+/-, ctrl, rep2


title: Protein A05 Biopsy 2

description: Library name: DSP-1002883220504-D-A05_Protein


title: multiome3unselected_ATAC

description:
3' single-cell multiome ATAC. h5 file contains both modalities
multiomeC57B_atac_fragments.tsv.gz
multiomeC57B_atac_fragments.tsv.gz.tbi


title: MSK_no_inhibitor

description: Library name: S25_L001

value: Brain


title: Polyp, Lkb1+/-, rep11


title: CD8_AAVsgRosa_4


title: mouse1_epcam

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_mouse1_epcam_filtered_feature_bc_matrix.h5


title: CD8_AAVsgRosa_2


title: CD8_AAVsgRosa_3


title: Brain-Hippocampus, P15, KO, F, pup2.

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: UMCG Groningen

description: Libraries were sequenced twice to reach at least 30% saturation (i.e., there are 4 raw data files per sample)

data_processing:
Data processing was performed with Cellranger v7.0.0
Assembly: mm10-2020-A
Supplementary files format and content: Processed data files contain the filtered feature matrix returned by CellRanger v7.0.0
Supplementary files format and content: Each sample has one file, where columns are barcodes and rows are genes

source_name: Brain-Hippocampus

extract_protocol:
Nuclei were isolated from fresh frozen mouse hippocampal brain tissue using a sucrose gradient ultracentrifugation protocol. Nuclei were separated into 3 populations using FANS: NeuN+ nuclei, Olig2+ nuclei, and the double negative nuclei. Approximately 42000 nuclei per sample were loaded onto the Chromium single cell chips (10x Genomics), with each sample consisting of all double negative nuclei, supplemented with an equal amount of neuronal and oligodendrocyte-lineage nuclei up to 42000. This strategy has previously been used to enrich for less abundant CNS cell types (Gerrits et al., Acta Neuropathologica, 2021).
Single-nucleus cDNA libraries were constructed and dual-indexed using the Chromium Single Cell 3′ Reagents Kit v3 and corresponding user guide (10× Genomics).

value: Brain-Hippocampus

tag: age

value: postnatal day 15

value: SHIP1 knockout (KO)

tag: Sex

value: F


title: CD8_AAVsgRosa_1


title: Protein A03 Biopsy 2

description: Library name: DSP-1002883220504-D-A03_Protein


title: Polyp, Lkb1+/-, rep9


title: Brain-Hippocampus, P15, WT, F, pup2


title: Protein No template Control

description: Library name: DSP-1002883220504-D-A01_Protein


title: Th17, Lkb1+/-, ctrl, rep3


title: Polyp, Lkb1+/-, rep10


title: Polyp, Lkb1+/-, rep8


title: WTA A08 Biopsy 2

description: Library name: DSP-1002883220504-H-A08_WTA


title: CD8_sgFpr1_4


title: Polyp, Lkb1+/-, rep6


title: Brain-Hippocampus, P15, WT, F, pup1


title: CD8_sgFpr1_3


title: Protein A04 Biopsy 2

description: Library name: DSP-1002883220504-D-A04_Protein


title: Brain-Hippocampus, P15, KO, M, pup2

value: M


title: Polyp, Lkb1+/-, rep5


title: Protein A02 Biopsy 1

description: Library name: DSP-1002883220504-D-A02_Protein


title: CD8_sgFpr1_1


title: Brain-Hippocampus, P15, KO, M, pup1


title: WTA A07 Biopsy 2

description: Library name: DSP-1002883220504-H-A07_WTA


title: Brain-Hippocampus, P15, KO, F, pup1


title: WTA A06 Biopsy 2

description: Library name: DSP-1002883220504-H-A06_WTA


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #2). Replicate 2

city: Stanford

first: Luca

last: Ducoli

state: CA

address: 269 Campus Drive CCSR 2150

institute: Stanford University

description: Library name: S11_704_2_2

data_processing:
For analyzing differentially expressed genes compared to the control, raw reads were first quantified with Salmon (ver. 0.12.0) (Patro et al. 2017) using the gencode release v39 basic annotation with the following settings: -l A -p 8 --gcBias --numGibbsSamples 20 --validateMappings.
Assembly: hg38
Supplementary files format and content: Salmon count output files

growth_protocol: The human A431 cell line was cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C

extract_protocol:
After 48h of ASO transfection, cells were lysed in LRT plus lysis buffer (Qiagen), and RNA isolation was performed using an RNeasy mini kit (Qiagen) following the manufacturer’s instructions.
From each sample, 500ng of RNA was used for the library preparation using the kit (QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI, Lexogen), pooled together with an equal concentration, and then sequenced on a NovaSeq X+, paired-end, 150 bp length, with ~30 M reads for each sample.

treatment_protocol: For each ASO, we performed a reverse transfection using Lipofectamine RNAiMAX (Thermo Fisher Scientific). In 10cm dishes, 2mL Opti-MEM, 20nM of scrambled control ASO or two ASOs targeting LINC00704 and LINC01116, and 25µL Lipofectamine RNAiMAX (Thermo) were mixed and incubated for 20min. Then, 1x106 A431 cells per dish were seeded into each 10cm dish and cultured for 48h in a 5% CO2 incubator.

tag: cell line

value: LINC00704-ASO transfection with Lipofectamine reagents


title: WTA A02 Biopsy 1

description: Library name: DSP-1002883220504-H-A02_WTA


title: WTA A05 Biopsy 2

description: Library name: DSP-1002883220504-H-A05_WTA


title: CD8_sgRandom_3


title: Polyp, Lkb1+/-, rep4


title: Brain-Hippocampus, P15, WT, M, pup2


title: Polyp, Lkb1+/-, rep2


title: CD8_sgRandom_5


title: Brain-Hippocampus, P15, WT, M, pup1


title: CD8_sgFpr1_2


title: WTA A04 Biopsy 2

description: Library name: DSP-1002883220504-H-A04_WTA


title: Polyp, Lkb1+/-, rep1


title: CD8_sgRandom_2


title: Polyp, Lkb1+/-, rep3


title: WTA A03 Biopsy 2

description: Library name: DSP-1002883220504-H-A03_WTA


title: Polyp, Lkb1+/-, rep7


title: Stomach, Lkb1+/+, rep12

source_name: Stomach

value: Stomach


title: Endothelial cells, Veh-treated, JAK2-V617F, rep3

type: RNA

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

hyb_protocol: Following fragmentation, ss-cDNA was hybridized for 16 hr at 45°C on GeneChip WT cartridge arrays. Arrays were then washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Clariom S, input 100-500ng)

growth_protocol: not applicable (no cell lines)

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) or RNeasy Plus Micro Kit according to manufacturers instructions.

treatment_protocol: for stromal niche cell isolation, flushed femurs and tibias were crushed with mortar and pestle. Bone chips were washed several times in PBS until the chips were white. Endosteal stromal cells were released from the hematopoietic-depleted bone chips by digestion with 3 mg/mL collagenase type I, 0.5 mg/ml collagenase Type II, and 15 μg/mL DNAse dissolved in PBS for 1 hour at 37°C at 110 rpm. The stromal and the BM fraction were used in all subsequent analyses. For bone chips cells, we used CD45/ TER-119/ CD3/ Gr-1/ (lineage) – PE-Cy7, CD31-Pacific Blue (PECAM-1), Sca-1-APC-Cy7, CD166-PE (ALCAM). For the BM fraction we used CD45/ TER-119/ CD3/ Gr-1/ (lineage markers) – PE-Cy7 CD31-Pacific Blue, Sca-1-APC-Cy7, CD140-PE. The stained cells were analyzed by FACS Vantage (BD Biosciences).

tag: strain

value: Balb/c

value: Endothelial cells

value: Veh-treated


title: sw480_Nc3

city: Harbin

first: Binbin

last: Cui

state: Heilongjiang

address: Baojian Road

country: China

institute: Harbin Medicial University

description: Library name: sw480_Nc3

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp 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 ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. 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.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include  gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: human colorectal cancer cells

value: CNOT7 control

value: No


title: WTA No template Control

description: Library name: DSP-1002883220504-H-A01_WTA

value: Disassociated tumor cells


title: Stomach, Lkb1+/+, rep11


title: sw480_Nc2

description: Library name: sw480_Nc2


title: CD8_sgRandom_4

value: CNS


title: Glioma_AAVsgAnxa1_4

value: Glioma


title: Stomach, Lkb1+/+, rep10


title: Endothelial cells, Veh-treated, JAK2-V617F, rep2


title: sw480_sh3

description: Library name: sw480_sh3

value: CNOT7 knockdown


title: Glioma_AAVsgAnxa1_3


title: sw480_Nc1

description: Library name: sw480_Nc1


title: Glioma_AAVsgAnxa1_2


title: Stomach, Lkb1+/+, rep9


title: sw480_sh2

description: Library name: sw480_sh2


title: CD8_sgRandom_1


title: Glioma_AAVsgAnxa1_1


title: Glioma_AAVsgRosa_2


title: Stomach, Lkb1+/+, rep6


title: Endothelial cells, Ruxo-treated, JAK2-V617F, rep1

value: Ruxo-treated


title: Mesenchymal stromal cells Veh-treated, JAK2-V617F, rep2

value: Mesenchymal stromal cells


title: Stomach, Lkb1+/+, rep7


title: Mesenchymal stromal cells Veh-treated, JAK2-V617F, rep3


title: Mesenchymal stromal cells Ruxo-treated, JAK2-V617F, rep 3


title: Stomach, Lkb1+/+, rep2


title: Endothelial cells, Ruxo-treated, JAK2-V617F, rep2


title: Endothelial cells, Ruxo-treated, JAK2-V617F, rep3


title: eCLIP-seq, LS174T, mouse PXR, IP, replicate 2

city: Pittsburgh

first: Min

last: Zhang

address: Salk Hall, 3501 Terrace St

institute: University of Pittsburgh

description: Library name: eCLIP_LS174T_mPXR_IP_rep2

data_processing:
The data was processed using CLIP Tool Kit (CTK).
eCLIP-Seq data were firstly demultiplexed using fastx-toolkit. Then the adapters were trimmed using Cutadapt and the low-quality reads were dropped.
The exact PCR duplicates were collapsed. The trimmed read 2 sequences were mapped to the hg38 genome using bwa (Li and Durbin, 2009). Only uniquely mapped reads were retained. The two IP replicates were merged for futther analysis.
For IP sample, we separated the reads into plus and minus strand. Peaks were called using MACS2, and peaks from plus and minus strands were merged as the final peak list.
Bedgraph files were generated using CTK for visualization in the UCSC genome browser based on the bed files of processed reads.
Assembly: hg38
Supplementary files format and content: bedgraph and peak files from MACS2

source_name: Colon

growth_protocol: LS174T cells were maintained in EMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA fragments were extracted using acid phenol:chloroform:isoamyl alcohol (25:24:1, pH 6.6) (Invitrogen) and cleaned up RNA Clean & Concentrator-5 columns (Zymo). After reverse transcription, qPCR was performed to determine the Ct value of the cDNA with Power SYBR Green Master Mix (Applied Biosystems).
DNA fragments were amplified with primers containing Illumina adapter sequences using Q5 High-Fidelity 2× Master Mix (NEB) for 9 to 18 cycles based on the Ct values, and PCR products were purified with Agencourt AMPureXP beads (Beckman Coulter). The DNA fragments ranging from 175 - 300 bp were selected via agarose gel electrophoresis. Fragments was excised and extracted using the MinElute Gel Extraction Kit (Qiagen) and libraries were validated using the 1× High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: LS174T cells were transfected with HA-tagged mouse Pxr (HA-mPxr) for 24 h. 20 million cells for each reaction were washed twice with ice-cold PBS, UV-crosslinked on ice with 254 nm at 400 mJ/cm2 with a UV crosslinker (XL-1000, Spectrolinker), lysed with iCLIP lysis buffer for 15 min on ice and digested with RNase I (Ambion) and Turbo DNase (Ambion) at 37°C on a ThermoMixer C (Eppendorf), and incubated with anti-PXR, anti-HA or anti-IgG antibodies overnight.

value: Colon


title: Stomach, Lkb1+/+, rep8


title: Mesenchymal stromal cells Ruxo-treated, JAK2-V617F, rep2


title: Glioma_AAVsgRosa_1


title: Microglia_AAVsgRosa_2

value: Microglia


title: L902Q_Ida [141.2]

source_name: Spleen GFP+ cells

growth_protocol: not applicable (cell lines)

treatment_protocol: After isolation from mice, tissues were homogenized and sorted for EGFP+ or EGFP-CD11b/Gr1+ BM cells and  EGFP+ or EGFP-Thy1.2+ splenocytes.

tag: cellular origin

value: Spleen


title: L902Q_Ida [141.1]

source_name: Spleen GFP- T cells


title: L902Q_Ida [141.4]

source_name: BM GFP+ cells

value: Bone marrow


title: eCLIP-seq, LS174T, mouse PXR, IP, replicate 1

description: Library name: eCLIP_LS174T_mPXR_IP_rep1


title: Stomach, Lkb1+/+, rep4

value: Stomach


title: Microglia_AAVsgRosa_1


title: Microglia_AAVsgAnxa1_3


title: eCLIP-seq, LS174T, mouse PXR, input

description: Library name: eCLIP_LS174T_mPXR_input


title: L902Q_Ida [140.2]


title: week1_4

description: Single cell RNA-Seq samples generated using 10X 3' feature protocol.

data_processing:
The raw sequences from all the samples were aligned to the GRCm38 reference genome using STAR, and then the quantification of these samples was done using CellRanger.
Assembly: GRCm38
Supplementary files format and content: TAR gzipped folders of filtered_feature_matrix output from Cellranger.

extract_protocol:
C57BL/6J mice were implanted intracranially with 100,000 GL261-TVA/G cells into the right striatum. Seven or fourteen days after implantation, the tumor site was injected with EnvA-RABDG at a concentration of 10,000 infectious units per mL. Seven days after EnvA-RABDG injection, mice were sacrificed and CNS was isolated using methods identical to those of human GBM samples above, except that sorted mCherry+ cells underwent single cell droplet encapsulation using 3’ feature barcode kits from 10X genomics.
Library was constructed using 3' feature barcode kits from 10X genomics

value: Inbred C57BL/6J mice (The Jackson Laboratory, 000664)

value: female

value: Brain


title: Microglia_AAVsgAnxa1_2


title: L902Q_Ida [140.3]

source_name: BM GFP- myeloid cells


title: Monocytes_AAVsgAnxa1_2

value: Monocytes


title: L902Q_Ida [141.3]


title: Stomach, Lkb1+/+, rep3


title: Microglia_AAVsgAnxa1_1


title: sw480_sh1

description: Library name: sw480_sh1

value: human colorectal cancer cells


title: Monocytes_AAVsgAnxa1_3


title: week1_2


title: Stomach, Lkb1+/+, rep1


title: L902Q_Ida [140.1]


title: Monocytes_AAVsgAnxa1_1


title: week2_2


title: Microglia_AAVsgRosa_3


title: L902Q_Ida [139.4]


title: week2_1


title: week1_1


title: L902Q_Ida [140.4]


title: Monocytes_AAVsgRosa_1


title: week1_3


title: hnRNPA2B1_2h_RAW264.7

city: Hangzhou

first: Shihao

state: Zhejiang Province

address: 866 Yuhangtang Rd

institute: Zhejiang University School of Medicine

data_processing:
*library strategy: Cut&Tag-seq
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
Cut&Tag-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Fastx v0.0.13, discarding reads left with < 20 bp
Cut&Tag-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.2.6. Only uniquely mapping reads with at most two mismatches were retained.
To create ATAC-seq coverage plots, the locations of the mapped ChIP-seq reads were renormalized (to reads per million, rpkm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off p-value <=0.01
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
50000 cells were harvested through HyperactiveUniversalCUT&TagAssayKitfor Illumina (TD903, Vazyme).
Cut&Tag libraries were prepared by  the HyperactiveUniversalCUT&TagAssayKitfor Illumina (TD903, Vazyme), complemented with TruePrep Index Kit V2 for Illumina. 40 ng of DNA was  using as starting material. Libraries were amplified using 10 cycles on thermocycler. Post amplification libraries were sized selected at 250-450bp using VAHTS DNA Clean Beads. Libraries were valided using Agilent2100 Bioanalyzer.

tag: cut&tag kit

value: Monocyte/macrophage-like cells

value: WT

value: LPS 100 ng/ml

tag: time


title: Microglia_sgFpr1_5

source_name: Microglia from Fpr1 KO mouse

value: CNS


title: hnRNPA2B1_1h_RAW264.7

value: HyperactiveUniversalCUT&TagAssayKitfor Illumina (TD903, Vazyme)


title: Microglia_sgFpr1_4


title: Microglia_sgFpr1_3


title: Hnrnpa2b1-KO, RAW264.7, LPS-1h, bio rep 2

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Fastx v0.0.13, discarding reads left with < 20 bp
ATAC-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.2.6. Only uniquely mapping reads with at most two mismatches were retained.
To create ATAC-seq coverage plots, the locations of the mapped ChIP-seq reads were renormalized (to reads per million, rpkm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off p-value <=0.01
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
50000 cells were lysised in 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2. Cell nuclei were harvested.
ATAC-seq libraries were prepared by  the Hyperactive ATAC-Seq Library Prep Kit for Illumina (TD711, Vazyme), complemented with TruePrep Index Kit V2 for Illumina. 50 ng of DNA was  using as starting material. Libraries were amplified using 9 cycles on thermocycler. Post amplification libraries were sized selected at 250-450bp using VAHTS DNA Clean Beads. Libraries were valided using Agilent2100 Bioanalyzer.

tag: atac-seq kit

value: Hyperactive ATAC-Seq Library Prep Kit for Illumina, TD711, Vazyme

value: Hnrnpa2b1 KO

value: 1 h


title: NC(no antibody)_2h_RAW264.7


title: Monocytes_AAVsgRosa_2


title: Microglia_sgFpr1_1

value: Microglia


title: Stomach, Lkb1+/+, rep5


title: L902Q_Ida [139.3]


title: L902Q_Ida [139.2]

value: Spleen


title: L902Q_Ruxo [137.4]

value: Bone marrow


title: L902Q_Ida [139.1]


title: Microglia_Scramble_4

source_name: Microglia from wild type mouse

value: Scramble


title: hnRNPA2B1_0h_RAW264.7


title: miRNA, control skeletal muscle sample 29

city: Norwich

first: Maisie

last: Evans

address: Norwich Research Park

country: United Kingdom

institute: UEA

data_processing:
FASTQ files were converted to FASTA files. Reads containing unasinged nucleotides were excluded. Adapter sequences (3’: AGATCGGAAGAGCACACGTCT; 5’: GTTCAGAGTTCTACAGTCCGACGATC) were trimmed.
sRNAs were mapped full length to human genome (v38) and corrosponding annotations using PAtMaN. The latest set of human miRNAs were downloaded from miRBase (v22)
Normalisation and DE analysis was performed using DESeq2 (v1.2.10).
Independent filtering was used to remove low abundance transcripts in normalised counts.sRNAs were considered DE if they had a a p-value <0.05, false discovery rate (FDR) <5% according to the Benjamini–Hochberg procedure and a log2 offset fold change >1.
Assembly: human genome (v38)
Supplementary files format and content: Excel xlsx format containing DE siRNAs and selected DE siRNAs (selected based on parameters set), for ARMS and ERMS.

source_name: skeletal muscle

extract_protocol:
Total RNA extraction using miRNeasy Mini Kit (Qiagen). RNA stored at -80°C until use.
Libraries constructed using NEBNext multiplex small RNA library prep (New England Biolabs).

value: skeletal muscle


title: miRNA, ARMS sample 13

source_name: soft tissue tumour biopsy from right hand


title: L902Q_Ruxo [138.4]


title: L902Q_Ruxo [138.2]


title: L902Q_Ruxo [137.2]


title: Microglia_sgFpr1_2


title: L902Q_Ruxo [138.3]


title: miRNA, control skeletal muscle sample 28


title: Microglia_Scramble_2


title: Hnrnpa2b1-KO, RAW264.7, LPS-1h, bio rep 1


title: L902Q_Vehicle [136.4]


title: L902Q_Ruxo [138.1]


title: Wild-type, RAW264.7, 0h, bio rep 2

value: 0 h


title: miRNA, control skeletal muscle sample 27, WT counterpart to R02_TS


title: miRNA, ERMS sample 10

source_name: soft tissue tumour biopsy from right leg


title: Wild-type, RAW264.7, LPS-1h, bio rep 2


title: Microglia_Scramble_5


title: miRNA, control skeletal muscle sample 20


title: L902Q_Vehicle [136.3]


title: miRNA, ERMS sample 9

source_name: soft tissue tumour biopsy from right groin


title: Mo-Macrophage_sgFpr1_5

source_name: Macrophages from Fpr1 KO mouse

value: Mo-Macrophage


title: Mo-Macrophage_sgFpr1_4


title: L902Q_Ruxo [137.3]


title: Microglia_Scramble_3


title: Inulin_CB_3

city: Beijing

first: Xiaoyan

last: Wang

address: No.10, Xitoutiao, You 'an Gate

department: Department of Neurobiology

institute: School of Basic Medical Sciences, Capital Medical University

data_processing:
Demultiplexed fastq files were aligned to mouse reference genome mm10 using CellRanger version 7.1.0 with introns included
Background removal was performed with CellBender version 0.2.2.
Sequencing data were analyzed using Seurat package (version 4.3.0.1) in R (version 4.2.2).
Assembly: mm10
Supplementary files format and content: h5 file for each sample

molecule: nuclear RNA

source_name: cerebellum

extract_protocol:
The nuclei isolation protocol was followed 10x Genomics(CG000124). Frozen brain tissues were lyzed in Hibernate A®/B27®/GlutaMAX™ (HEB) medium (Gibco) plus lysis buffer containing 10mM Tris-HCL pH7.4, 10mM NaCl, 3mM MaCl2 and 0.1% NP-40 for 15 min on ice, before filtering with a 30 µm MACS® SmartStrainer (Miltenyi Biotec). Nuclei suspension was collected after serial centrifuges at 500 rcf at 4℃ and washes with Nuclei Wash and Resuspension Buffer containing 1% BSA and 0.2U/µl RNase inhibitor. Myelin was removed by incubating the nuclei suspensions with Myelin Removal Beads II and LS column (Miltenyi Biotec). Density gradient centrifugation with sucrose cushion buffer was performed to concentrate the isolated nuclei. Once the nuclei concentration reached 1000 nuclei/µl, the samples were immediately proceeded for library preparation.
RNA libraries for snRNA-seq were prepared using Chromium Single Cell 3’ v3 reagent kit (10x Genomics) according to manufacturer’s instruction.
snRNA-seq

treatment_protocol: 5xFAD mice fed with Ain-93G diet starting at 5~6 weeks old, then change to Ain-93M diet at 7~8 weeks old. Ain-93M diet was maintained for control group, or switched to inulin diet for inulin group at 8~9 weeks old.

value: cerebellum

value: 93M supplemented with long chain inulin


title: miRNA, control skeletal muscle sample 23,  WT counterpart to R12_TS


title: Hnrnpa2b1-KO, RAW264.7, 0h, bio rep 2

value: Monocyte/macrophage-like cells


title: L902Q_Ruxo [137.1]


title: miRNA, ARMS sample 8

source_name: soft tissue biopsy from right foot

value: soft tissue biopsy from right foot


title: L902Q_Vehicle [136.2]


title: Inulin_CB_2


title: Mo-Macrophage_sgFpr1_3


title: Hnrnpa2b1-KO, RAW264.7, 0h, bio rep 1

value: LPS 100 ng/ml


title: L902Q_Vehicle [136.1]


title: Wild-type, RAW264.7,LPS-1h, bio rep 1

value: WT


title: Inulin_CB_1


title: Mo-Macrophage_sgFpr1_2

value: CNS


title: miRNA, ERMS sample 12

source_name: soft tissue tumour biopsy from leg

value: soft tissue tumour biopsy from leg


title: L902Q_Vehicle [135.4]


title: Microglia_Scramble_1


title: Ctrl_CB_3


title: Wild-type, RAW264.7, 0h, bio rep 1

value: Hyperactive ATAC-Seq Library Prep Kit for Illumina, TD711, Vazyme


title: miRNA, ERMS sample 7

source_name: soft tissue tumour biopsy from right thigh


title: miRNA, ARMS sample 1

source_name: soft tissue tumour biopsy from right arm


title: Control Sample 30

data_processing:
FASTQ files converted to FASTA files. Reads containing unassinged nucleotides were excluded.
Trim Galore was used to remove adapter sequence reads <20 nt.
Trimmed reads aligned to human genome (v38) using HISAT2
Transcripts were download from GENCODE (v28) and Ensembl (v92). Count matrices for transcripts were created using Kallisto.
Differentially expressed (DE) transcripts were determined using the DESeq2 package in R (v1.2.10). DE mRNAs were selected according to log2 fold change ≥2, p≤0.05 and false discovery rate (FDR) <5%.
Assembly: human genome (v38)
Supplementary files format and content: Excel xlsx file format containg selected DE mRNAs (based on the parameters set) for ERMS/SCRMS/PRMS and ARMS.

source_name: Skeletal Muscle

extract_protocol:
Total RNA extraction using miRNeasy Mini Kit (Qiagen). RNA stored at -80 °C until use.
mRNA libraries constrcuted using NEBNext ultra II RNA library prep kit (New England Biolabs). Some samples (R09, R11, R12, R13, R14, R17, R18, R21, R22, R24, R25, R26) were resequenced due to quality of the samples.

value: Skeletal Muscle


title: Mo-Macrophage_Scramble_2

source_name: Macrophages from wild type mouse


title: Control Sample 28, WT counterpart to R_02T


title: miRNA, ARMS sample 5

source_name: soft tissue tumour biopsy from right foot


title: Inulin_BS_2

source_name: midbrain+hindbrain

value: midbrain+hindbrain


title: L902Q_Vehicle [135.3]

source_name: BM GFP- myeloid cells


title: L902Q_Vehicle [135.1]

source_name: Spleen GFP- T cells

value: Spleen


title: miRNA, ARMS sample 2

value: soft tissue tumour biopsy from right arm


title: Glioma_sgFpr1_3

source_name: Glioma cells from Fpr1 KO mouse

value: Glioma


title: Glioma_sgFpr1_4


title: Mo-Macrophage_sgFpr1_1


title: Control Sample 27, WT counterpart to R_02T


title: L902Q_Vehicle [134.4]

source_name: BM GFP+ cells

value: Bone marrow


title: L902Q_Vehicle [135.2]

source_name: Spleen GFP+ cells


title: Ctrl_CB_2


title: Ctrl_BS_2


title: Mo-Macrophage_Scramble_3

value: Scramble


title: L902Q_Ruxo [133.4]


title: Ctrl_CB_1


title: Inulin_BS_3


title: Ctrl_BS_1


title: Control sample 23


title: Mo-Macrophage_Scramble_1

value: Mo-Macrophage


title: Control sample 22, WT counterpart to R_10T


title: L902Q_Ruxo [133.3]


title: Inulin_MB_3

source_name: thalamus+hypothalamus

value: thalamus+hypothalamus


title: L902Q_Ruxo [133.2]


title: Inulin_MB_2

value: 93M supplemented with long chain inulin


title: Glioma_AAVsgRosa_3

source_name: CNS


title: Glioma_sgFpr1_2


title: Control sample 21, WT counterpart to R_11T


title: Ctrl_BS_3


title: L902Q_Vehicle [134.1]


title: Inulin_BS_1


title: L902Q_Ruxo [132.4]


title: Control Sample 25, WT counterpart to R_15T


title: L902Q_Vehicle [134.2]


title: L902Q_Vehicle [134.3]


title: Astrocytes_sgFpr1_3

source_name: Astrocytes from Fpr1 KO mouse

value: Astrocytes


title: Ctrl_MB_3


title: Glioma_sgFpr1_1


title: Ctrl_MB_2


title: Control sample 24, WT counterpart to R_12T


title: Glioma_Scramble_4

source_name: Glioma cells from wild type mouse


title: Ctrl_MB_1


title: Glioma_Scramble_3


title: Control Sample 26, WT counterpart to R_13T


title: Astrocytes_sgFpr1_1


title: Inulin_FB_3

source_name: forebrain

value: forebrain


title: Glioma_Scramble_2


title: Inulin_MB_1


title: Astrocytes_Scramble_3

source_name: Astrocytes from wild type mouse


title: SCRMS sample 15

source_name: soft ttisue tumour biopsy from left leg

value: soft ttisue tumour biopsy from left leg


title: SCRMS sample 14

source_name: soft tissue tumour biopsy from left thumb


title: L902Q_Ruxo [132.1]


title: L902Q_Ruxo [132.3]


title: Glioma_Scramble_1


title: Control sample 20

source_name: Skeletal Muscle


title: V617F_Ruxo [131.3]


title: Inulin_FB_1


title: Control sample 19, WT counterpart to R_05T


title: Astrocytes_Scramble_4


title: Astrocytes_Scramble_1


title: L902Q_Ruxo [133.1]


title: L902Q_Ruxo [132.2]


title: Astrocytes_sgFpr1_2


title: Control sample 18, WT counterpart to R_14T


title: Ctrl_FB_2


title: Ctrl_FB_1


title: control sample 17, WT counterpart to R_06T


title: ERMS sample 10

source_name: soft tissue tumour biopsy from right leg


title: snRNA-seq from seed nuclei, day after pollination 7, replicate 2

city: Cambridge

first: Caroline

middle: Anne

last: Martin

address: 455 Main St

institute: Whitehead Institute

description:
Library name: A.thaliana_7DAP_bio_rep2
The barcodes.tsv, matrix.tsv, and features.tsv are derived from the CellRanger filtered_feature_bc_matrix for this replicate. All libraries were analyzed and annotated within timepoints. All 7 DAP data are combined in the "DAP7_merged_annotated_all_mods.rds" processed file.
L224_1606_S44_L003

data_processing:
Cell Ranger v7.1.0 (10X Genomics)
Assembly: TAIR10
Supplementary files format and content: CellRanger filtered matrix (.tsv)
Supplementary files format and content: Seurat objects (.rds)

organism: Arabidopsis thaliana

source_name: seed

growth_protocol: All plants (Arabidopsis thaliana (L.) Heynh., Col-0) used in HCR and snRNA-seq experiments were grown at 22C in a glasshouse on soil under long-day conditions (16 h: 8 h, light: dark). For timed crosses, we emasculated flower buds and pollinated stigma with mature papillae 2 days after.

extract_protocol:
Two biological replicates, (different plants hand pollinated and processed for snRNA-seq on different days) each containing seeds dissected from 10-15 siliques (500-800 seeds), were collected for each timepoint, producing six replicates total. Timed seeds were dissected into 150uL cold extraction buffer on ice (1x Partec nuclei extraction buffer, 4% BSA, 1mM DTT, 1:100 protease inhibitor cocktail for plants, and 1:30 Protector RNase inhibitor). Seeds were mechanically dissociated in 1.5mL tubes by grinding with an Axygen pestle for 10 turns. The nuclei suspension was filtered through a 30um cell strainer prewet with Partec nuclei staining buffer into a 5mL tube for fluorescence activated nuclei sorting (FANS). The strainer was rinsed with Partec nuclei staining buffer into the 5mL tube to bring the final suspension volume to 1mL. 1uL of 1mg/mL DAPI was added to increase nuclear signal. Nuclei were purified and concentrated by FANS on a BD FACS ARIA Cell Sorter using a 70um chip. We gated on 2N, 3N, 4N, 6N, 8N, and 16N peaks (Suppmentary Fig. 6). Nuclei were sorted into 30-50uL collection buffer (PBS-4% BSA) in a 1.5mL tube, and concentration was assessed using the ARIA nuclei count and by manual counting on a Neubauer Improved hemocytometer. Each biological replicate was processed individually using one Chromium Next GEM Single Cell 3’ Kit (v3.1) reaction with a target nuclei recovery of 10k, except for one 3DAP biological replicate, which was split across two reactions. In total, 7 libraries were generated in this study.
Chromium Next GEM Single Cell 3’ Kit (v3.1), Illumina

value: seed

tag: time point

value: day after pollination 7

tag: batch

value: replicate 2


title: ERMS sample 9

source_name: soft tissue tumour biopsy from right groin

tag: tissue


title: snRNA-seq from seed nuclei, day after pollination 5, replicate 2

description:
Library name: A.thaliana_5DAP_bio_rep2
The barcodes.tsv, matrix.tsv, and features.tsv are derived from the CellRanger filtered_feature_bc_matrix for this replicate. All libraries were analyzed and annotated within timepoints. All 5 DAP data are combined in the "DAP5_merged_annotated_all_mods.rds" processed file.
L224_1602_S46_L004

value: day after pollination 5


title: V617F_Ruxo [130.3]

source_name: BM GFP- myeloid cells


title: V617F_Ruxo [131.4]


title: Inulin_FB_2


title: MA9_FLT3ITD_Setd1b_dSET_Myc_rep1

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values corrected by Spike-In for each Sample.

growth_protocol: mouse MLL-AF9 leukemia cells were grown in RPMI media supplemented with 10% FBS, penicillin/streptomycin, and 10 ng/ml rmIL-3.

extract_protocol:
Total RNA was collected using Rneasy Mini Kit with DNase (QIAGEN).
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

tag: cell type

value: leukemia

value: Setd4b SET knockout

value: After wash with PBS, the cells were incubated without cytokines for 24 hr.


title: ERMS sample 7

source_name: soft tissue tumour biopsy from right thigh


title: Astrocytes_Scramble_2

data_processing:
The raw sequences from all the samples were aligned to the GRCm38 transcriptome and quantified using kallisto.
Assembly: GRCm38
Supplementary files format and content: TAR gzipped folders of kallisto output

value: CNS


title: ARMS sample 13

source_name: soft tissue tumour biopsy from right hand


title: MA9_FLT3ITD_Setd1b_dSET_Empty_rep3

value: Setd3b SET knockout


title: V617F_Ruxo [131.1]

source_name: Spleen GFP- T cells

value: Spleen


title: SCRMS sample 6

value: soft tissue tumour biopsy from right thigh


title: V617F_Ida [129.3]

value: Bone marrow


title: Ctrl_FB_3


title: V617F_Ida [129.2]

source_name: Spleen GFP+ cells


title: ERMS sample 12

source_name: soft tissue tumour biopsy from leg

value: soft tissue tumour biopsy from leg


title: ARMS sample 5

source_name: soft tissue tumour biopsy from right foot


title: snRNA-seq from seed nuclei, day after pollination 3, replicate 1a

description:
Library name: A.thaliana_3DAP_bio_rep1a
This replicate was split across two 10x reactions that were sequenced as two separate libraries. The barcodes.tsv, matrix.tsv, and features.tsv are derived from the CellRanger filtered_feature_bc_matrix for this replicate. All libraries were analyzed and annotated within timepoints. All 3 DAP data are combined in the "DAP3_merged_annotated_all_mods.rds" processed file.
L224_1603_S47_L004

value: day after pollination 3

value: replicate 1a


title: V617F_Ruxo [130.4]

source_name: BM GFP+ cells


title: snRNA-seq from seed nuclei, day after pollination 7, replicate 1

description:
Library name: A.thaliana_7DAP_bio_rep1
The barcodes.tsv, matrix.tsv, and features.tsv are derived from the CellRanger filtered_feature_bc_matrix for this replicate. All libraries were analyzed and annotated within timepoints.  All 7 DAP data are combined in the "DAP7_merged_annotated_all_mods.rds" processed file.
L224_1605_S43_L003

value: replicate 1


title: V617F_Ruxo [131.2]


title: V617F_Ida [129.1]


title: epcam_rat_2_ATAC

description:
3' single-cell multiome ATAC. h5 file contains both modalities
Multiome4_atac_fragments.tsv.gz
Multiome4_atac_fragments.tsv.gz.tbi

data_processing:
CellRanger was used to align reads to the Mus musculus reference (GENCODE vM23/Ensembl 98) and the Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85) from Ensembl70. Gene counts were analyzed with Seurat v471 for clustering, integration and differential gene expression and Monocle version 372 for clustering and pseudotime. Filtering cutoffs were set as follows: minimum genes per cell = 500, maximum genes = 5000, minimum UMIs per cell was set on a per-sample basis after inspecting a rank plot of UMI/cell. Cells with over 20% mitochondrial reads were also excluded. Differentially-expressed genes were identified via Seurat’s FindMarker function with default parameters. Samples were integrated using Seurat’s integration anchors and the first 30 principle components were used for integration and UMAP creation. Clusters were found using monocle (cluster_cells, resolution = 5 10-5, k = 8, partition_qval = 0.05). Psudotime was generated using Monocle’s learn_graph (default parameters). For ATAC analysis, peaks were called using Signac with MACS2, and gene activity scores were calculated with Signac.
Assembly: Mus musculus reference (GENCODE vM23/Ensembl 98)
Supplementary files format and content: filtered_feature_bc_matrix.h5 files
Supplementary files format and content: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Supplementary files format and content: featurereference.csv
Assembly: Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85)
Supplementary files format and content: Contain mRNA+ADT or mRNA + ATAC counts as appropriate
Supplementary files format and content: ATAC fragment files
Supplementary files format and content: Contain ADT antibodies used & barcode sequences
Library strategy: single-cell multiome RNA + ATAC

organism: Rattus norvegicus

source_name: testis

extract_protocol:
Rat cells were isolated from the testes of 3- to 4-month-old Sprague Dawley rats transgenic for the LacZ gene under the metallothionine promoter67. Mouse cells were isolated from C57BL/6 inbred mice also 3-4 months old. Tissue was chopped into fine pieces and incubated in collagenase (Sigma) at a concentration of 1mg/ml in HBSS (Gibco) for 15 minutes at 37C. Cells were spun down for 1 minute at 600 rcf, then resuspended in warm Trypsin (Gibco, 0.25%) with 20% DNase solution (Sigma, 7mg/ml dissolved in HBSS). Tissue was pipetted for 2 minutes with a 10 ml pipette and incubated at 37C for 5 minutes. Then tissue was pipetted for another 2 minutes and incubated at 37C for 3 minutes. FBS (Sigma F2442) was added to stop the digestion. Additional DNase was added until no turbidity was visible. Cells were washed in PBS-S twice (PBS [Gibco] with 1% FBS, 10 mM HEPES [Sigma Aldrich], 1 mg/ml glucose [Sigma Aldrich], 1 mM pyruvate [Gibco], 50 units/ml penicillin [Gibco], 50 ug/ml streptomycin [Gibco] prepared as described in 68). All centrifugation steps were 5 minutes at 600 rcf.   Cells were processed both as unselected samples and enriched for EPCAM as described below. Each biological replicate was then used for either encapsulation of cells with antibody treatment or further processed as nuclei for GEX+ATAC assay.
Cells were encapsulated and libraries generated for GEX+CITE using a Chromium Next GEM Single Cells 3’ Kit v3.1 with Feature Barcoding (10X Genomics) per manufacturer’s protocol. Prepared nuclei were encapsulated with the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit following manufacturer’s instructions. Each biological replicate was encapsulated individually. Libraries were sequenced on a NextSeq2000 sequencer (Illumina) using a 100-cycle sequencing kits to a minimum depth of 30k reads per cell.

value: testis

tag: Stage

value: Adult

value: EpCAM+

value: ATAC DNA


title: ARMS samples 2

source_name: soft tissue tumour biopsy from right arm


title: V617F_Ida [128.4]


title: MA9_FLT3ITD_Setd1b_dSET_Myc_rep3

value: Setd6b SET knockout


title: MA9_FLT3ITD_Setd1b_WT_Empty_rep3

value: leukemia

value: Setd1b SET wildtype


title: V617F_Ruxo [130.2]


title: ARMS sample 1

value: soft tissue tumour biopsy from right arm


title: MA9_FLT3ITD_Setd1b_dSET_Myc_rep2

value: Setd5b SET knockout

value: After wash with PBS, the cells were incubated without cytokines for 24 hr.


title: MA9_FLT3ITD_Setd1b_WT_Empty_rep2


title: snRNA-seq from seed nuclei, day after pollination 5, replicate 1

description:
Library name: A.thaliana_5DAP_bio_rep1
The barcodes.tsv, matrix.tsv, and features.tsv are derived from the CellRanger filtered_feature_bc_matrix for this replicate. All libraries were analyzed and annotated within timepoints.  All 5 DAP data are combined in the "DAP5_merged_annotated_all_mods.rds" processed file.
L224_1409_S1_L001

value: seed

value: day after pollination 5


title: ARMS sample 8

source_name: soft tissue biopsy from right foot

value: soft tissue biopsy from right foot


title: V617F_Ruxo [130.1]

value: Spleen


title: V617F_Ida [129.4]

value: Bone marrow


title: PRMS sample 11

source_name: soft tissue tumour biopsy from left thigh


title: V617F_Ida [128.2]


title: snRNA-seq from seed nuclei, day after pollination 3, replicate 2

description:
Library name: A.thaliana_3DAP_bio_rep2
The barcodes.tsv, matrix.tsv, and features.tsv are derived from the CellRanger filtered_feature_bc_matrix for this replicate. All libraries were analyzed and annotated within timepoints.  All 3 DAP data are combined in the "DAP3_merged_annotated_all_mods.rds" processed file.
L224_1607_S45_L003

value: day after pollination 3

value: replicate 2


title: 1243_0060_IPF - Fibroblast - TGFb1_PGE2_1nM

city: Biberach an der Riss

first: Christoph

middle: H

last: Mayr

address: Birkendorfer Str. 65

department: Immunology & Respiratory Diseases Research

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

data_processing:
Demultiplexing was performed using bcl2fastq2 v2.20.0.422 from Illumina
Sequencing reads from the RNA-sequencing experiment (FASTQ files) were processed with a pipeline building upon the implementation of the ENCODE “Long RNA-seq” pipeline (also described in Schlager et al. (4)): filtered reads were mapped against the Homo sapiens genome (hg38) using the STAR (v2.5.2b) aligner (5) allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Gene expression levels were quantified with the above annotations, using RSEM (v1.3.0) (6) and featureCounts (v1.5.1) (7). Quality controls were implemented using FastQC (v0.11.5) (8), picardmetrics (v0.2.4) (9), and dupRadar (v1.0.0) (10) at the respective steps.
Ddifferential expression analysis was performed on the mapped counts derived from featureCount using limma/voom (11, 12). If not otherwise stated, we used an absolute log2-fold change cut-off of 1 and a false discovery rate of <0.05.
Assembly: Homo sapiens genome (hg38)
Supplementary files format and content: tab-delimited text file inlcueds TPM for each sample

source_name: lung

growth_protocol: IPF-HLF at passage 6 were seeded in 6-well plates at a density of 300,000 cells/well in 2 mL FGM-2 for RNA or protein analysis.

extract_protocol:
Cells were washed with ice-cold PBS, before RNA lysates were generated using 350 µL/well RLT buffer (Qiagen, Cat.No. 1053393). Generated RNA lysates  were homogenized using QIAshredder homogenizers (QIAGEN, Cat.No. 79656), and further processed for RNA extraction using MagMAX™ total RNA isolation kit (Thermo Fisher Scientific, Cat.No. AM1830) including a DNA digestion step on a KingFisher™ Flex Purification System (Thermo Fisher Scientific) according to manufacturer’s instructions.
An input of 250 ng was employed for bulk mRNA-seq library preparation with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Cat. No. E7760), together with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Cat. No. E7490) and NEBNext Multiplex Oligos for Illumina (New England Biolabs, Cat. No. E7600) as per the manufacturer’s instructions. Ampure XP beads (Beckman Coulter, Cat. No. A63880) for double-stranded cDNA purification were used instead of the recommended SPRIselect Beads. Libraries were amplified with 13 PCR cycles. The final mRNA-seq libraries were eluted in 40 µL EB Buffer (Qiagen, Cat. No. 19086) and were quantified by the High Sensitivity dsDNA Quant-iT Assay Kit (Thermo Fisher Scientific, Cat. No. Q33120) on a Synergy HTX Multimode Reader (BioTek). Libraries were assessed for size distribution and adapter dimer presence (<0.5 %) by the High Sensitivity Small Fragment Kit on a 96-channel Fragment Analyzer (Agilent, Cat. No. DNF-477-0500). Libraries were normalized on the MicroLab STAR (Hamilton) and pooled.
Libraries were sequenced on a NovaSeq 6000 (Illumina) with dual index, paired-end reads (Read Parameter: Rd1:101, Rd2:10, Rd3:10, Rd4:101) with an average sequencing depth of ~>30 million Pass-Filter reads per sample.

treatment_protocol: After 24h incubation (37°C and 5% CO2), cells were serum starved with FBM for additional 24h. To induce myofibroblast differentiation, cells were stimulated with 2 ng/mL rhTGF-beta 1 in FBM for 48h. Afterwards cells were treated with nerandomilast plus 1 nM PGE2 or PGE2 only in FBM in the presence of 2 ng/mL rhTGF-beta 1 for 24h or 96h for RNA or protein analysis respectively.

value: lung

value: IPF-HLF

value: fibroblast


title: MA9_FLT3ITD_Setd1b_dSET_Empty_rep1

value: Setd1b SET knockout


title: MA9_FLT3ITD_Setd1b_dSET_Empty_rep2

value: Setd2b SET knockout


title: V617F_Ida [128.3]


title: V617F_Ida [128.1]


title: epcam_rat_1_ATAC

description:
3' single-cell multiome ATAC. h5 file contains both modalities
Multiome2_atac_fragments.tsv.gz
Multiome2_atac_fragments.tsv.gz.tbi

value: testis

value: Adult

tag: selection

value: EpCAM+

value: ATAC DNA


title: 1243_0059_IPF - Fibroblast - no_TGFb1_PGE2_1nM


title: snRNA-seq from seed nuclei, day after pollination 3, replicate 1b

description:
Library name: A.thaliana_3DAP_bio_rep1b
This replicate was split across two 10x reactions that were sequenced as two separate libraries. The barcodes.tsv, matrix.tsv, and features.tsv are derived from the CellRanger filtered_feature_bc_matrix for this replicate. All libraries were analyzed and annotated within timepoints. All 3 DAP data are combined in the "DAP3_merged_annotated_all_mods.rds" processed file.
L224_1604_S48_L004

value: replicate 1b


title: epcam_rat_2_RNA

description:
3' single-cell multiome RNA. h5 file contains both modalities
Multiome4_filtered_feature_bc_matrix.h5

tag: library type

value: mRNA


title: unselected_rat_1_ATAC

description:
3' single-cell multiome ATAC. h5 file contains both modalities
Multiome1_atac_fragments.tsv.gz
Multiome1_atac_fragments.tsv.gz.tbi

value: unselected


title: 1243_0057_IPF - Fibroblast - TGFb1


title: unselected_rat_2_ATAC

description:
3' single-cell multiome ATAC. h5 file contains both modalities
Multiome3_atac_fragments.tsv.gz
Multiome3_atac_fragments.tsv.gz.tbi


title: unselected_rat_2_RNA

description:
3' single-cell multiome RNA. h5 file contains both modalities
Multiome3_filtered_feature_bc_matrix.h5


title: MA9_FLT3ITD_Setd1b_WT_Empty_rep1

value: leukemia

tag: genotype

value: Setd1b SET wildtype

value: After wash with PBS, the cells were incubated without cytokines for 24 hr.


title: MA9_FLT3ITD_Setd1b_dSET_Myc_RNA_pol2_Total

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.1.0.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-1.56.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated. For histone modifications, DSG treatment was skipped.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.

tag: treatment

tag: chip antibody

value: RNA_pol2_Total (abcam Cat#ab8580)


title: V617F_Ida [127.4]

value: Bone marrow


title: V617F_Ida [127.2]

value: Spleen


title: MA9_FLT3ITD_Setd1b_dSET_Myc_RNA_pol2_S2P

value: RNA_pol2_S2P (abcam Cat#ab8580)


title: 1243_0062_IPF - Fibroblast - TGFb1_PGE2_1nM_BI1015550_1uM

value: lung

value: IPF-HLF

value: fibroblast


title: epcam_rat_1_RNA

description:
3' single-cell multiome RNA. h5 file contains both modalities
Multiome2_filtered_feature_bc_matrix.h5

value: testis


title: 1243_0058_IPF - Fibroblast - TGFb1_PGE2_1uM


title: MA9_FLT3ITD_Setd1b_WT_Empty_RNA_pol2_S2P


title: EpCAM.rat.4.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat13_epcam_filtered_feature_bc_matrix.h5
rat13_featurereference2.csv

data_processing:
CellRanger was used to align reads to the Mus musculus reference (GENCODE vM23/Ensembl 98) and the Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85) from Ensembl70. Gene counts were analyzed with Seurat v471 for clustering, integration and differential gene expression and Monocle version 372 for clustering and pseudotime. Filtering cutoffs were set as follows: minimum genes per cell = 500, maximum genes = 5000, minimum UMIs per cell was set on a per-sample basis after inspecting a rank plot of UMI/cell. Cells with over 20% mitochondrial reads were also excluded. Differentially-expressed genes were identified via Seurat’s FindMarker function with default parameters. Samples were integrated using Seurat’s integration anchors and the first 30 principle components were used for integration and UMAP creation. Clusters were found using monocle (cluster_cells, resolution = 5 10-5, k = 8, partition_qval = 0.05). Psudotime was generated using Monocle’s learn_graph (default parameters). For ATAC analysis, peaks were called using Signac with MACS2, and gene activity scores were calculated with Signac.
Assembly: Mus musculus reference (GENCODE vM23/Ensembl 98)
Supplementary files format and content: filtered_feature_bc_matrix.h5 files
Supplementary files format and content: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Supplementary files format and content: featurereference.csv
Assembly: Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85)
Supplementary files format and content: Contain mRNA+ADT or mRNA + ATAC counts as appropriate
Supplementary files format and content: ATAC fragment files
Supplementary files format and content: Contain ADT antibodies used & barcode sequences
Library strategy: CITE-Seq

value: Adult

value: ADT


title: unselected_rat_1_RNA

description:
3' single-cell multiome RNA. h5 file contains both modalities
Multiome1_filtered_feature_bc_matrix.h5


title: MA9_FLT3ITD_Setd1b_dSET_Empty_RNA_pol2_S2P

value: Setd1b SET knockout


title: 1243_0053_IPF - Fibroblast - TGFb1_PGE2_1nM_BI1015550_1uM


title: 1243_0055_IPF - Fibroblast - no_TGFb1


title: EpCAM.rat.3.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat12_epcam_filtered_feature_bc_matrix.h5
rat12_featurereference.csv

value: EpCAM+


title: V617F_Ida [127.3]


title: V617F_Ruxo [126.3]


title: 1243_0050_IPF - Fibroblast - no_TGFb1_PGE2_1nM


title: V617F_Ida [127.1]


title: MA9_FLT3ITD_Setd1b_WT_Empty_RNA_pol2_Total


title: V617F_Ruxo [126.4]


title: EpCAM.rat.3

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat12_epcam_filtered_feature_bc_matrix.h5

value: mRNA


title: 1243_0049_IPF - Fibroblast - TGFb1_PGE2_1uM


title: MA9_FLT3ITD_Setd1b_WT_Empty_H3K4me3

value: H3K4me3 (abcam Cat#ab8580)


title: MA9_FLT3ITD_Setd1b_dSET_Myc_H3K4me3

value: leukemia


title: MA9_FLT3ITD_Setd1b_dSET_Empty_RNA_pol2_Total


title: MA9_FLT3ITD_Setd1b_dSET_Empty_H3K4me3


title: 1243_0048_IPF - Fibroblast - TGFb1


title: EpCAM.rat.2

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat11_epcam_curated_filtered_feature_bc_matrix.h5


title: 1243_0051_IPF - Fibroblast - TGFb1_PGE2_1nM


title: EpCAM.rat.4

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat13_epcam_filtered_feature_bc_matrix.h5


title: EpCAM.rat.2.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat11_epcam_curated_filtered_feature_bc_matrix.h5
rat11_featurereference.csv


title: V617F_Ruxo [126.1]


title: V617F_Ruxo [126.2]


title: MA9_FLT3ITD_Setd1b_WT_Emp_MYC_CT

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Reads were aligned to mm10 reference mouse genome, using bowtie2.3.3.1.
Duplication reads were removed from aligned file by using picard-tools-2.18.2
Tagcounts from either reference genome were compared and calculated the factor for normalization.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command with the normalization factor calculated above applied, and then converted to bigwig using UCSC BedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

growth_protocol: Mouse MLL-AF9 leukemia cells were grown in RPMI media supplemented with 10% FBS, penicillin/streptomycin, and 10 ng/ml rmIL-3.

extract_protocol:
Mouse MLL-AF9 FLT3-ITD leukemia cells were mixed with 1/10 number of 293T cells for spike-in control, and fixed with 0.1% formaldehyde. Cells were mixed with conA beads, and then incubated with MYC antibody.
Tagmentation was performed using pA-Tn5 with adaptor complex.

value: Setd1b SET wildtype

value: MYC (Cell signaling #13987)


title: V617F_Ruxo [125.4]

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.


title: 1243_0044_IPF - Fibroblast - TGFb1_PGE2_1nM_BI1015550_1uM


title: MA9_FLT3ITD_Setd1b_dSET_Myc_H3K4me3

value: After wash with PBS, the cells were incubated without cytokines for 24 hr.


title: EpCAM.rat.1

description:
3' single-cell RNAseq
Count_output_rat10_EpCAM_curated_filtered_feature_bc_matrix.h5

data_processing:
CellRanger was used to align reads to the Mus musculus reference (GENCODE vM23/Ensembl 98) and the Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85) from Ensembl70. Gene counts were analyzed with Seurat v471 for clustering, integration and differential gene expression and Monocle version 372 for clustering and pseudotime. Filtering cutoffs were set as follows: minimum genes per cell = 500, maximum genes = 5000, minimum UMIs per cell was set on a per-sample basis after inspecting a rank plot of UMI/cell. Cells with over 20% mitochondrial reads were also excluded. Differentially-expressed genes were identified via Seurat’s FindMarker function with default parameters. Samples were integrated using Seurat’s integration anchors and the first 30 principle components were used for integration and UMAP creation. Clusters were found using monocle (cluster_cells, resolution = 5 10-5, k = 8, partition_qval = 0.05). Psudotime was generated using Monocle’s learn_graph (default parameters). For ATAC analysis, peaks were called using Signac with MACS2, and gene activity scores were calculated with Signac.
Assembly: Mus musculus reference (GENCODE vM23/Ensembl 98)
Supplementary files format and content: filtered_feature_bc_matrix.h5 files
Supplementary files format and content: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Supplementary files format and content: featurereference.csv
Assembly: Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85)
Supplementary files format and content: Contain mRNA+ADT or mRNA + ATAC counts as appropriate
Supplementary files format and content: ATAC fragment files
Supplementary files format and content: Contain ADT antibodies used & barcode sequences


title: unselected.rat.4

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat13_unselected_filtered_feature_bc_matrix.h5

value: unselected


title: Bmpr1a_distal_3

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
Sequencing was performed on the Illumina platform, employing a paired-end 150-base strategy, under the supervision of Novogene Bioinformatics Technology Co., Ltd (Beijing, China).
The obtained sequencing reads were aligned to the mouse genome reference (mm10) using STAR (Spliced Transcripts Alignment to a Reference) with default parameters.
Differential expression analysis was conducted using DESeq2 software (version 1.28.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all the sample

source_name: small intestine

extract_protocol:
The process of RNA-seq library construction began with RNA extraction, using Trizol reagent (Catalog No: 15596026, Thermo Fisher Scientific)
cDNA libraries were generated using the Ovation RNA-Seq System V2 kit (NuGEN).

value: small intestine

value: Bmpr1a cKO


title: MA9_FLT3ITD_Setd1b_dSET_Emp_H3K4me3


title: unselected.rat.4.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat13_unselected_filtered_feature_bc_matrix.h5
rat13_featurereference2.csv


title: unselected.rat.3.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat12_unselected_filtered_feature_bc_matrix.h5
rat12_featurereference.csv


title: 1243_0046_IPF - Fibroblast - no_TGFb1

value: lung


title: 1243_0040_IPF - Fibroblast - TGFb1_PGE2_1uM

value: IPF-HLF


title: 1243_0042_IPF - Fibroblast - TGFb1_PGE2_1nM

value: fibroblast


title: Bmpr1a_distal_1


title: 1243_0041_IPF - Fibroblast - no_TGFb1_PGE2_1nM


title: unselected.rat.3

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat12_unselected_filtered_feature_bc_matrix.h5

value: testis


title: Bmpr1a_proximal_3


title: V617F_Ruxo [125.2]

value: Spleen


title: V617F_Ruxo [125.1]


title: Bmpr1a_distal_2


title: 1243_0039_IPF - Fibroblast - TGFb1


title: unselected.rat.2.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_rat11_unselected_curated_filtered_feature_bc_matrix.h5
rat11_featurereference.csv

value: Adult

value: ADT


title: Bmpr1a_proximal_2


title: 1243_0035_IPF - Fibroblast - TGFb1_PGE2_1nM_BI1015550_1uM


title: Bmpr1a_proximal_1


title: V617F_Vehicle [124.1]


title: V617F_Vehicle [124.3]

value: Bone marrow


title: V617F_Vehicle [123.4]


title: 1243_0033_IPF - Fibroblast - TGFb1_PGE2_1nM


title: V617F_Vehicle [124.2]


title: V617F_Vehicle [124.4]


title: 1243_0037_IPF - Fibroblast - no_TGFb1


title: WT_distal_3

value: WT


title: 1243_0032_IPF - Fibroblast - no_TGFb1_PGE2_1nM


title: unselected.rat.2

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_rat11_unselected_curated_filtered_feature_bc_matrix.h5

value: mRNA


title: WT_distal_1


title: 1243_0030_IPF - Fibroblast - TGFb1


title: WT_distal_2


title: 1243_0028_IPF - Fibroblast - no_TGFb1


title: WT_proximal_3


title: WT_proximal_2


title: V617F_Vehicle [123.2]


title: unselected.rat.1

description:
3' single-cell RNAseq
Count_output_rat10_unselected_curated_filtered_feature_bc_matrix.h5


title: V617F_Vehicle [123.1]


title: 1243_0026_IPF - Fibroblast - TGFb1_PGE2_1nM_BI1015550_1uM


title: V617F_Vehicle [123.3]


title: WT_proximal_1


title: V617F_Vehicle [122.2]


title: 1243_0024_IPF - Fibroblast - TGFb1_PGE2_1nM


title: V617F_Vehicle [122.3]


title: V617F_Vehicle [122.4]


title: 1243_0023_IPF - Fibroblast - no_TGFb1_PGE2_1nM


title: Dhx58hep-/-, I/R, scRNAseq

city: Shanghai

first: Jia

middle: Kai

last: W

address: 800 Xiangyin Road

institute: National Key Laboratory of Medical Immunology and Institute of Immunology

description: 10X Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v6.1.1) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 40%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. log2FC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: mm10Ensembl100
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: liver

growth_protocol: To generate hepatocyte-specific DHX58 deficiency, Dhx58f/f mouse was designed and constructed by ViewSolid Biotech using CRISPR/Cas9 techniques as previously described, and then hybridized with Alb-Cre transgenic mouse, purchased from The Jackson Laboratory

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: Dhx58f/f  and Dhx58hep-/- mice were treated with Sham or I/R

value: liver

value: I/R


title: 1243_0031_IPF - Fibroblast - TGFb1_PGE2_1uM


title: 1243_0022_IPF - Fibroblast - TGFb1_PGE2_1uM


title: V617F_Vehicle [122.1]

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) or RNeasy Plus Micro Kit according to manufacturers instructions.


title: Dhx58hep-/-, Sham, scRNAseq

description: 10X Genomics

value: Sham


title: Dhx58f/f, I/R, scRNAseq

description: 10X Genomics


title: 1243_0021_IPF - Fibroblast - TGFb1


title: Dhx58f/f, Sham, scRNAseq

description: 10X Genomics


title: empty_Ruxo [121.4]


title: 1243_0017_IPF - Fibroblast - TGFb1_PGE2_1nM_BI1015550_1uM


title: primed HSCs [primed-52_L2_Y0000708D87]

city: Guangzhou

first: chen

last: minqi

state: Guangdong

address: No.74, 2nd Zhongshan Road

institute: Sun Yat-sen University

data_processing:
RNA seq reads were aligned to mouse genome GRCm38 and gene annotation from the Ensembl database. For read alignment and expression quantification, low quality reads were removed and the adaptor sequences were trimmed by Trim Galore (v0.5.0, Babraham Bioinformatics). The remaining pair-end reads were mapped to the reference genome by Salmon (v0.03.1, COMBINE-lab) with ENCODE options. The uniquely mapped reads were counted and transformed to transcripts per kilobase millionreads (TPM)
Assembly: GRCm38
Supplementary files format and content: merge.count.csv with raw counts matrices

source_name: bone marrow

extract_protocol:
In brief, intact bone marrows from mice at the age of 6-8 weeks were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
smart-seq2

value: bone marrow

tag: age

value: 6-8 weeks

value: Cd4-cre;R26Tdtomato mice

value: primed HSCs


title: 1243_0019_IPF - Fibroblast - no_TGFb1

value: lung

tag: cell line


title: 1243_0015_IPF - Fibroblast - TGFb1_PGE2_1nM

value: IPF-HLF


title: empty_Ruxo [121.2]


title: 1243_0014_IPF - Fibroblast - no_TGFb1_PGE2_1nM

value: fibroblast


title: 1243_0013_IPF - Fibroblast - TGFb1_PGE2_1uM


title: primed HSCs [primed-49_L2_Y0002393D87]

tag: strain


title: empty_Ruxo [120.3]

tag: cellular origin


title: primed HSCs [primed-51_L2_Y0001889D87]


title: 1243_0012_IPF - Fibroblast - TGFb1


title: primed HSCs [primed-48_L2_Y0000669D87]


title: empty_Ruxo [120.2]


title: empty_Ruxo [121.1]


title: primed HSCs [primed-47_L2_Y0001489D87]


title: 1243_0010_IPF - Fibroblast - no_TGFb1


title: primed HSCs [primed-46_L2_Y0000650D87]


title: primed HSCs [primed-44_L2_Y0000709D87]


title: primed HSCs [primed-50_L2_Y0000727D87]


title: 1243_0006_IPF - Fibroblast - TGFb1_PGE2_1nM


title: empty_Ruxo [120.1]


title: 1243_0005_IPF - Fibroblast - no_TGFb1_PGE2_1nM


title: empty_Ruxo [120.4]


title: empty_Ida [119.3]


title: empty_Ida [119.2]


title: 1243_0004_IPF - Fibroblast - TGFb1_PGE2_1uM


title: empty_Ida [119.1]


title: empty_Ida [118.4]


title: 1243_0003_IPF - Fibroblast - TGFb1


title: 1243_0008_IPF - Fibroblast - TGFb1_PGE2_1nM_BI1015550_1uM


title: primed HSCs [primed-40_L2_Y0002391D87]


title: PDAML10, ADT

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

description:
Patient 10 baseline Single-cell
PDAML10_barcodes.tsv.gz
PDAML10_features.tsv.gz
PDAML10_matrix.mtx.gz

data_processing:
Reads were aligned to human genome assembly GRCh37/hg19 by HISAT2 (version 2.1.0) with default setting for paired-end reads. The aligned reads were converted to BAM files and sorted by SAMtools 1.9 with index files created. The sorted BAM files were processed in R (version 3.5; R Foundation for Statistical Computing, Vienna, Austria) with Bioconductor packages. The count matrix on gene level was generated by featureCounts in Rsubread function.
Assembly: GRCh37/hg19 for bulk RNAseq; Single-cell cellranger used the pre-built GRCh38 in the pipeline.
Supplementary files format and content: Gene raw count matrix in csv for bulk RNAseq; single-cell processed data contain the gene and protein expression matrices with cell barcodes.

source_name: Bone marrow

growth_protocol: Bone marrow aspirate was collected from enrolled patients at different time points and healthy donors.

extract_protocol:
Bulk RNAseq: RNA was isolated from PAXgeneTM BM RNA tubes using the PAXgene BM RNA kit (PreAnalytiX). RNA quantity was measured using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA) and RNA quality was assessed using the TapeStation system (Agilent Technologies, Santa Clara, CA). All samples had RNA Integrity Numbers (RIN) of seven or higher. Single-cell: BM mononuclear cells (BMMCs) were purified from BM aspirate using density centrifugation, cryopreserved, and stored in liquid nitrogen.
Bulk RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina Inc., San Diego, CA) using 1 μg of total RNA input and paired-end 75-bp sequencing on a HiSeq 3000 (Illumina, San Diego, CA). The 10x Genomics 3’v3 Single Cell Immune profiling platform was used for scRNA-seq of BMMCs. cDNA amplification was performed according to manufacturer’s instructions with the addition of 1 ul 0.2 uM ADT additive primer per sample to amply ADT tags.

treatment_protocol: No treatment

tag: gender

value: Male


title: primed HSCs [primed-45_L2_R07D87]


title: empty_Ida [118.2]

value: Spleen


title: 1243_0001_IPF - Fibroblast - no_TGFb1


title: primed HSCs [primed-39_L2_Y0000661D87]


title: empty_Ida [118.3]

source_name: BM GFP- myeloid cells


title: empty_Ida [119.4]


title: empty_Ida [118.1]


title: PDAML9, ADT

description:
Patient 9 baseline Single-cell
PDAML9_barcodes.tsv.gz
PDAML9_features.tsv.gz
PDAML9_matrix.mtx.gz

value: Female


title: PDAML8, ADT

description:
Patient 8 baseline Single-cell
PDAML8_barcodes.tsv.gz
PDAML8_features.tsv.gz
PDAML8_matrix.mtx.gz


title: primed HSCs [primed-43_L2_Y0000526D87]


title: primed HSCs [primed-38_L2_Y0000649D87]


title: empty_Ida [117.4]


title: primed HSCs [primed-37_L2_Y0002909D87]


title: primed HSCs [primed-42_L2_Y0000726D87]


title: empty_Ida [117.3]


title: primed HSCs [primed-41_L2_Y0000752D87]


title: PDAML7, ADT

description:
Patient 7 baseline Single-cell
PDAML7_barcodes.tsv.gz
PDAML7_features.tsv.gz
PDAML7_matrix.mtx.gz


title: primed HSCs [primed-35_L2_Y0000725D87]


title: PDAML6, ADT

description:
Patient 6 baseline Single-cell
PDAML6_barcodes.tsv.gz
PDAML6_features.tsv.gz
PDAML6_matrix.mtx.gz


title: empty_Ida [117.1]


title: empty_Ida [117.2]


title: PDAML5_EOC2, ADT

description:
Patient 5 end of cycle 2 Single-cell
PDAML5_EOC2_barcodes.tsv.gz
PDAML5_EOC2_features.tsv.gz
PDAML5_EOC2_matrix.mtx.gz


title: empty_Ruxo [116.4]


title: empty_Ruxo [121.3]


title: PDAML10, GEX


title: empty_Ruxo [116.3]


title: primed HSCs [primed-33_L2_Y0000668D87]


title: primed HSCs [primed-34_L2_Y0000751D87]


title: PDAML9, GEX


title: PDAML8, GEX


title: primed HSCs [primed-32_L2_Y0000806D87]


title: primed HSCs [primed-31_L2_Y0000648D87]


title: primed HSCs [primed-36_L2_Y0000525D87]


title: primed HSCs [primed-30_L2_Y0000085D87]


title: PDAML6, GEX


title: primed HSCs [primed-29_L2_Y0000706D87]


title: V617F_Ruxo [125.3]


title: empty_Ruxo [116.2]


title: primed HSCs [primed-28_L2_Y0000524D87]


title: PDAML3, ADT

description:
Patient 3 baseline Single-cell
PDAML3_barcodes.tsv.gz
PDAML3_features.tsv.gz
PDAML3_matrix.mtx.gz


title: empty_Ruxo [115.4]


title: empty_Ruxo [116.1]


title: PDAML4, ADT

description:
Patient 4 baseline Single-cell
PDAML4_barcodes.tsv.gz
PDAML4_features.tsv.gz
PDAML4_matrix.mtx.gz


title: empty_Ruxo [115.2]


title: primed HSCs [primed-26_L2_Y0000750D87]


title: empty_Ruxo [115.3]


title: PDAML2, ADT

description:
Patient 2 baseline Single-cell
PDAML2_barcodes.tsv.gz
PDAML2_features.tsv.gz
PDAML2_matrix.mtx.gz


title: PDAML1_EOC2, ADT

description:
Patient 1 end of cycle 2 Single-cell
PDAML1_EOC2_barcodes.tsv.gz
PDAML1_EOC2_features.tsv.gz
PDAML1_EOC2_matrix.mtx.gz


title: primed HSCs [primed-25_L2_Y0000660D87]


title: empty_Ruxo [115.1]


title: PDAML7, GEX


title: primed HSCs [primed-24_L2_Y0000647D87]


title: PDAML4, GEX


title: empty_Vehicle [114.4]


title: PDAML5_EOC2, GEX


title: empty_Vehicle [114.3]


title: empty_Vehicle [114.2]


title: empty_Vehicle [114.1]


title: PDAML2, GEX


title: primed HSCs [primed-23_L2_Y0000083D87]


title: empty_Vehicle [113.4]


title: PDAML3, GEX


title: primed HSCs [primed-22_L2_Y0000705D87]


title: empty_Vehicle [113.3]


title: primed HSCs [primed-21_L2_Y0000523D87]


title: PDAML1_EOC2, GEX


title: primed HSCs [primed-20_L2_Y0000724D87]


title: empty_Vehicle [113.2]


title: HD2, ADT

description: Healthy Donor 2 Single-cell


title: primed HSCs [primed-19_L2_Y0000741D87]


title: primed HSCs [primed-18_L2_Y0000667D87]


title: primed HSCs [primed-17_L2_Y0001066D87]


title: empty_Vehicle [112.4]


title: HD3, ADT

description: Healthy Donor 3 Single-cell


title: 13LGS_Otx2_Atlas_Biological_Rep2_technical_Rep2

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

description:
Library name: 13LGS_Otx2_Atlas_B2_T2
13LGS_Otx2_peaks.narrowPeak

data_processing:
Sequence reads were trimmed of low quality bases and adapters using cutadapt v3.5 76and Trim Galore v0.6.4_dev 77, using arguments ---paired --length 20 -e 0.1 --illumina -q 20 --stringency 3. Trimmed reads were aligned to mouse genome GRCm38 and 13LGS genome Itri_07Aug2017 using Bowtie2 78 with arguments -X 1000 --very-sensitive-local --no-mixed --no-discordant --no-dovetail. Unmapped reads with a MAPQ score of 30 or below were filtered from the analysis with SAMtools v1.12 79. Aligned reads were deduplicated using UMI-tools 80 dedup with parameters -chimeric-pairs="discard" --unpaired-reads="discard" --paired --ignore-umi. Technical replicates were collapsed into single biological replicates using samtools merge. For visualization, normalization was applied using deepTools bamCoverage v3.5.1 81 using arguments --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2311060300 (13LGS) or --effectiveGenomeSize 2651675564 (mouse). For each protein target, peaks were called jointly across replicates against IgG control using macs2 82 using arguments -f BAMPE --keep-dup all -q 0.05 -g 2311060300 (13LGS) or -g 2651675564 (mouse). For mouse samples, peaks on mitochondrial reads and blacklisted ENCODE regions 83 were filtered from analysis.
Assembly: GRCm38
Supplementary files format and content: txt for called peaks
Library strategy: CUT&Run

organism: Ictidomys tridecemlineatus

source_name: P5 retina

extract_protocol:
Nuclei were isolated according to the described protocol 75, using a lysis buffer modified to contain 0.01% Tween-20 and 0.01% Nonidet P40, as well as 1X protease inhibitor cocktail (Roche, 11873580001) in all solutions. Samples were lysed for 5 minutes in the lysis buffer with gentle trituration throughout, as described. CUT&RUN was performed using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher, 14-1048). For each reaction, either 500,000 13LGS nuclei or 385,000 mouse nuclei were used. The CUTANA protocol v4.0 protocol was followed with minor modifications. In brief, isolated nuclei were resuspended in CUT&RUN wash buffer and added directly to Concanavalin A beads. Then 0.5 µg of the following antibodies were added to each respective reaction: IgG control (EpiCypher, 13-0042), H3K4me1 (EpiCypher, 13-0057), H3K4me3 (EpiCypher, 13-0041), H3K27ac (EpiCypher, 13-0059), H3K27me3 (EpiCypher, 13-0055), NeuroD1 (Cell Signaling, 62953), Otx2 (R&D Systems, BAF1979), or Otx2 (Atlas Antibodies, HPA000633).  H3K9me3 (Abcam, ab8898) was used at 0.41 µg of antibody per reaction.
The total CUT&RUN DNA yield, up to 5 ng of total purified DNA, was used for library preparation, using reagents from CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, 14-1001) or NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S). The EpiCypher CUTANA Library Prep Kit User Manual v1.3 was followed and indexing performed using NEBNext® Multiplex Oligos for Illumina® (NEB, E7395S) or Dual Index Kit TT Set A (10X Genomics, PN-1000215). Final libraries were sequenced at the Novogene sequencing core (Sacramento, CA, USA) on the NovaSeq X Plus (Illumina) to generate paired-end 150 base pair reads.

value: P5 retina


title: HD3, GEX

description: Healthy Donor 3 Single-cell

value: Bone marrow


title: primed HSCs [primed-16_L2_Y0000646D87]


title: empty_Vehicle [113.1]


title: 13LGS_Otx2_Atlas_Biological_Rep2_technical_Rep1

description:
Library name: 13LGS_Otx2_Atlas_B2_T1
13LGS_Otx2_peaks.narrowPeak


title: primed HSCs [primed-15_L2_Y0000704D87]


title: HD1, GEX

description: Healthy Donor 1 Single-cell


title: primed HSCs [primed-27_L2_F0000343D87]


title: HD2, GEX

description: Healthy Donor 2 Single-cell


title: 13LGS_Otx2_RD_Biological_Rep2_technical_Rep2

description:
Library name: 13LGS_Otx2_RD_B2_T2
13LGS_Otx2_peaks.narrowPeak


title: empty_Vehicle [112.2]


title: empty_Vehicle [112.3]


title: primed HSCs [primed-13_L2_F0000342D87]


title: primed HSCs [primed-14_L2_Y0000522D87]


title: empty_Vehicle [112.1]


title: 13LGS_Otx2_RD_Biological_Rep2_technical_Rep1

description:
Library name: 13LGS_Otx2_RD_B2_T1
13LGS_Otx2_peaks.narrowPeak