title: 2023_MERSCOPE_Lung_nTMA

type: RNA

city: Cambridge

first: Samouil

middle: L

last: Farhi

state: MA

address: 75 Ames St

department: Spatial Technology Platform

institute: Broad Institute of MIT and Harvard

description: A normal TMA of 45 cores 1.2 mm in diameter representing a broad range of normal tissues. Samples were sourced from the same patient in either duplicate or triplicate. This TMA was chosen for the breadth of tissue lineages included and the relatively large core size.

hyb_protocol: MERSCOPE samples were imaged according to manufacturer protocol “9160001 MERSCOPE Instrument User Guide RevF”. Samples were processed in two batches, the first of four samples, two of each TMA and with each library prepped in parallel; and a follow up sample of each TMA re-run with the breast panel. Samples were first hybridized with anchoring probes overnight before being embedded in a polyacrylamide gel. Samples were incubated for two hours with a digestion solution at 37˚C and then overnight at 47˚C overnight in a detergent clearing solution and proteinase K to remove native proteins while the anchoring probes kept nucleic acids bound to the gel. After clearing, samples were additionally photobleached using Vizgen’s MERSCOPE Photobleacher for three hours at room temperature in the clearing solution. Samples were hybridized with encoding probes and a cell boundary stain (PN 10400118) and then imaged with imaging kits (PN 10400005). Samples were stored at 37˚C in clearing solution after hybridization and before final imaging. After an initial examination of the data, a second batch of both TMAs was run a second time with the human breast panel, increasing the set imaging capture thickness from 5 µm to 10 µm to capture more tissue from cores that had lifted during the gel embedding process. MERSCOPE data acquired with a 10 µm imaging depth, resulted in a median 3.0-fold increase in expression across all transcripts. We excluded the 5 µm MERSCOPE breast panel data from most comparisons have left references to the lung panel data in as an illustrative example of an unsuccessful run (indicated as such throughout the figures). Data was processed on premises through the standard Vizgen workflow to generate cell by gene and transcript by location matrices. We segmented the data with a built-in Cellpose method on the most accurate looking cell boundary stain.

scan_protocol: MERSCOPE samples were imaged according to manufacturer protocol “9160001 MERSCOPE Instrument User Guide RevF”. Samples were hybridized with encoding probes and a cell boundary stain (PN 10400118) and then imaged with imaging kits (PN 10400005). Samples were stored at 37˚C in clearing solution after hybridization and before final imaging.

data_processing:
Data was processed through the standard Vizgen workflow to generate cell by gene and transcript by location matrices. We segmented the data with a built-in Cellpose method on the most accurate looking cell boundary stain. After data acquisition, the resulting outputs were uploaded to a Google bucket associated with a terra.bio Workspace for distribution and follow on analysis.To facilitate standardized data formatting and subsequent analytical processes, we built a data ingestion pipeline with the following objectives: a) to grab cell-level and transcript-level data from diverse platforms and normalize the data structure; b) to tag each cell and transcript with essential metadata including tissue type, tumor status, PD-L1 status, among others to transform the data into various formats tailored to the requirements of particularized analyses. Specifically, to tag the data, core centers in the TMA were manually identified using DAPI images (Xenium) or cell metadata that contains global coordinates (MERSCOPE and CosMx) using QGIS(version:3.16.10-Hannover). Cells or transcripts within a specified radius were then labeled with core metadata via spatial joining (implemented by GeoPandas, version:0.13.0). In instances where cores are in close proximity or when a uniform radius cannot be applied effectively, we manually generated the core boundary masks.
*.zip contains cell_boundaries.parquet, cell_by_gene.csv, cell_metadata.csv, detected_transcripts.csv of all regions for this name MERSCOPE run.

source_name: A normal tissue TMA (nTMA) contained forty-five 1.2 mm diameter cores spanning sixteen normal tissue types isolated with each tissue type coming from one patient and represented in 2-3 cores.

growth_protocol: Three TMAs were constructed using FFPE clinical discards at Brigham and Women’s Hospital Pathology Core and were acquired with a waiver of consent for non-sequencing based readouts under IRB 2014P001026

treatment_protocol: Sequential sections were prepared according to manufacturer instructions ( “91600112 MERSCOPE User Guide Formalin-Fixed Paraffin-Embedded Tissue Sample Preparation RevB” for Vizgen) at the Brigham and Women’s Hospital Pathology Core. Prior to collecting samples, ~50 µm of each TMA were faced off to reach deeper into the sample where RNA integrity was likely higher. 5 µm sequential sections were then collected, floated in a 37˚C water bath, and adhered to Vizgen FFPE coverslips (Vizgen, PN 10500102). TMAs were sliced as close to the center of the active area as possible for each platform.  Samples were baked at 55 ˚C for 15 minutes for MERSCOPE. Sections were stored at -20˚C.

tag: gene panel

value: Lung panel

tag: year


title: Huh-7_DEAB1

status: Public on Oct 03 2025

type: SRA

city: Zhengzhou

first: Xuhua

last: Duan

address: No. 1 Longhu Middle Ring Road, Jinshui District

country: China

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: Huh-7_DEAB1

library_source: transcriptomic

data_processing:
Quality Control: Raw data in fastq format were processed using fastp software to remove reads containing adapters, ploy-N, and low-quality reads.
Reads Mapping: The reference genome index was built with Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Gene Expression Quantification: featureCounts v1.5.0-p3 was used to count reads , and FPKM was calculated based on gene length and read counts.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Huh-7 and Hep-G2 cells were treated under various conditions as described: a blank control; exposure to 8 μM Tan IIA for 48 hours; treatment with 8 μg/mL 4-diethylaminobenzaldehyde (DEAB) for 48 hours; shALDH7A1 infection for 48 hours; preheating at 44 °C (Huh-7) or 45 °C (Hep-G2) for 10 min; and 8 μM Tan IIA treatment for 48 hours following preheating at 44 °C for 10 min.

tag: cell line

tag: cell type

value: Hepatocellular carcinoma

tag: genotype

value: TP53 mutant

tag: treatment

value: Incubated with 8 μg/mL 4-diethylaminobenzaldehyde (DEAB) for 48 h.

tag: batch


title: 2023_MERSCOPE_Breast_tTMA1

country: USA

description: A tumor TMA of 170 cores, 0.6 mm in diameter, including a variety of cancer samples and healthy lymphoid tissue as a positive staining control. The TMA samples were selected from samples previously characterized by ImmunoProfile and were selected to encompass both high and low levels of the biomarkers in the ImmunoProfile panel [CD8, PD-1, PD-L1, Foxp3, tumor marker (Cytokeratin, Sox10, or PAX8)]. Annotations were performed by KF and SR based on H&E and immunofluorescence staining. Cores included both tumor and healthy control annotation, though for the purpose of this study, all were combined under their tumor label. Tumors were also chosen to be a mixture of PD-L1 high and PD-L1 low. This TMA had previously been studied by both H&E, and several highly multiplexed immunostaining approaches, and was known to be of high morphological integrity.

source_name: Tumor TMA 1 (tTMA1) consisted of one hundred and seventy 0.6 mm diameter cores (i.e. sampled regions) from seven different cancer types, with 3-6 patients per cancer type, and 3-6 cores per patient.

value: Breast panel


title: 2024_MERSCOPE_Breast_tTMA2

description: A tumor TMA of 48 cores, 1.2 mm in diameter, including a variety of cancer. This TMA was chosen for the breadth of tissue lineages included and the relatively large core size.

source_name: Tumor TMA 2 (tTMA2) consisted of forty-eight 1.2 mm diameter cores from nineteen different cancer types, with each tissue type coming from one or two patients and represented in 2-3 cores.


title: Huh-7_shALDH7A1_1

description: Library name: Huh-7_shALDH7A1_1

value: Infected with letivirus carrying shRNA trageting ALDH7A1


title: GBM10Periphery

city: Houston

first: Ailiang

last: Zeng

state: TX

address: 12515 stoney creek dr

department: Cancer Biology

institute: MD Anderson Cancer Center

description: Library name: GBM10Periphery

library_source: transcriptomic single cell

data_processing:
FastQ preparation: mkfastq (cellranger): https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq
Count Matrix Generation: count (cellranger): https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count
Data Normalization: scTransform (Satija): https://satijalab.org/seurat/v3.1/sctransform_vignette.html
https://satijalab.org/seurat/articles/integration_large_datasets.html
Assembly: mm10-3.0.0 (mouse), GRCh38-3.0.0 (human)
Supplementary files format and content: tsv.gz/barcodes
Supplementary files format and content: tsv.gz/genes
Supplementary files format and content: mtx.gz/counts

source_name: glioblastoma

extract_protocol:
Tumor samples were mechanically minced before enzymatic digestion, cells were then spun down at 800g with the brake off in a 0.9M sucrose solution to remove myelin. Cell pellets were then frozen. Upon bringing samples back up CD45+ FACs selection was performed before entering the 10x protocol
https://assets.ctfassets.net/an68im79xiti/4tjk4KvXzTWgTs8f3tvUjq/2259891d68c53693e753e1b45e42de2d/CG000183_ChromiumSingleCell3__v3_UG_Rev_C.pdf

tag: tissue

value: glioblastoma

tag: spatial sampling

value: Periphery

value: immune cells


title: GBM11Border

description: Library name: GBM11Border

value: Border


title: A.shNC+Vehicle rep1

status: Public on Oct 04 2025

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

description: Library name: Sample 1

data_processing:
Sequencing read quality was inspected using fastp v0.24.0. Adapter removal and read trimming were performed. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the hg38 (Subread v2.0.8) . FeatureCounts (Subread v2.0.8) was used to count the reads numbers mapped to each gene. And then FPKM/TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: text file include gene names, sample name, read-counts values for each Sample
/
Assembly: hg38
Supplementary files format and content: txt file includes read counts for each sample.

source_name: pancreatic ductal adenocarcinoma cell line

extract_protocol:
RNA was harvested using Trizol reagent(Life Technologies). Illumina NEB Ultra directional RNA library Prep Kit was used with 1 ug of total RNA for the construction sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: WT


title: Huh-7_DEAB3

description: Library name: Huh-7_DEAB3


title: GBM6Core

description: Library name: GBM6Core

value: Core


title: Sample12, asymptomatic

city: zhengzhou

first: Shen

last: Li

address: No. 1 East Jianshe Road

department: The Department of Neurology

institute: The Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China

description:
Library name: Sample12
SeekOne® MM

data_processing:
The scRNA-seq data were analyzed using R version 4.02 as follows: (1) Seurat R package was used to convert scRNA-seq data as a Seurat object and the “FindVariableFeatures” function was used to select the highly variable genes after quality control; (2) principal component analysis was performed based on the selected variable genes to analyze the scRNA-seq data; (3) Merge R package was used to integrate single-cell data, and the “Merge” function was applied in the Seurat object to integrated scRNA-seq data from 12 atherosclerotic plaques; (4) after integration, uniform manifold approximation and projection (UMAP) were applied to analyze the scRNA-seq data; (5) Cell types (e.g., endothelial cells, smooth muscle cells, macrophages) were annotated using CellMarker and PanglaoDB dataset, as well as previous studies. Gene expression was visualized using a violin plot, feature plot, dot plot, and heatmap, generated with the Seurat function. Markers for a specific cluster against all remaining cells were identified using the “FindAllMarkers” function (only.pos=TRUE, min.pct=0.25).
Assembly: HG38
Assembly: GRCm38
Supplementary files format and content: processed data files format and content
Supplementary files format and content: Tab-separated values files and matrix files

source_name: carotid atherosclerosis plaque

extract_protocol:
After harvested, CAS plaques and mouse carotid arteries were washed in ice-cold RPMI1640 and dissociated using SeekOne® Multi-tissue dissociation kit 2 from Miltenyi Biotec as instructions. DNase treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Miltenyi 130-094-183) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albuminat.
scRNA-seq libraries were prepared using the SeekOne® MM Single Cell 3’ library preparation kit. Briefly, appropriate number of cells were loaded into the flow channel of the SeekOne® MM chip that has 170,000 microwells; the cells were allowed to settle in microwells by gravity. After removing the unsettled cells, sufficient cell-barcoded magnetic beads (CBBs) were pipetted into the flow channel and allowed to settle in the microwells under a magnetic field. Next, excess CBBs were rinsed out, and the cells in the MM chip were lysed to release RNA, which was captured by the CBB in the same microwell. Subsequently, all CBBs were collected, and reverse transcription was performed at 37 ℃ for 30 min to label the complementary DNA (cDNA) with cell barcode on the beads. Exonuclease I treatment was performed to remove unused primers from the CBBs. Subsequently, thebarcoded cDNA on the CBBs was hybridized with a random primer containing reads 2 SeqPrimer sequence on the 5’ end to generate second strand DNA with the cell barcode on the 3’ end. The resulting second-strand DNA was denatured from the CBBs, purified, and amplified using PCR. The amplified cDNA product was cleaned to remove unwanted fragments and added to a full-length sequencing adapter and sample index using indexed PCR. The indexed sequencing libraries were cleaned with solid phase reversible immobilization beads, quantified using quantitative PCR (KAPA Biosystems KK4824), and sequenced on an Illumina NovaSeq 6000 with a PE150 read length or a DNBSEQ-T7 platform with a PE100 read length

treatment_protocol: 12 CAS plaques obtained following carotid endarterectomy (CEA) and carotid arteries from mice

value: carotid atherosclerosis plaque

value: tissue


title: Sample10, asymptomatic

description:
Library name: Sample10
SeekOne® MM


title: ChIP-seq of pooled male and female Stra8-AVI hippocampus input

city: Kansas City

first: Ning

last: Wang

state: KS

address: 3901 Rainbow Boulevard, Kansas City, KS

department: Cell Biology and Physiology

institute: UNIVERSITY OF KANSAS MEDICAL CENT

description: Library name: ChIP input

library_source: genomic

data_processing:
In our ChIP-seq analysis, data preprocessing began with adapter and low-quality sequence trimming using Cutadapt, configured with specific parameters to ensure precision (--times 1, -e 0.1, -O 3, --quality-cutoff 25). Cleaned reads were then aligned to the mouse genome (Mus musculus GRCm39; Ensembl release 105) using Bowtie2, which excluded unaligned reads and limited insert sizes (--no-unal, --maxins 2000). Post-alignment, Samtools filtered the reads to retain only properly paired and primary alignments, enhancing processing speed with parallel threading (-f 3, -F 12, -F 256, -@ 10). Coverage visualization was performed by Deeptools, applying a scaling factor and setting high-resolution parameters (--scaleFactor 1, --binSize 1, -p 10). Peak calling was conducted using Macs2, which operated on BAM files and incorporated several features to refine the analysis (-f BAM, -g mm, --call-summits, -m 5 50, p-value cutoff of 0.05). Memory management during these operations was optimized by Picard, which adjusted Java heap sizes and parallel garbage collection parameters (Xms40g, Xmx40g, -XX=20). The software tools mentioned (Cutadapt, Bowtie2, Samtools, Deeptools, Macs2, and Picard) are run on Linux operating systems
Assembly: mm10
Supplementary files format and content: bigWig files

molecule: genomic DNA

organism: Mus musculus

source_name: hippocampus

extract_protocol:
For the Chromatin immunoprecipitation (ChIP) assay, fresh hippocampal tissue were cut in small pieces and fixed using 1% formaldehyde for 10 minutes. The fixed tissue was then quenched and homogenized, followed by two washes in phosphate-buffered saline (PBS). Cells were lysed using 1 ml of lysis buffer from the EZ-ChIP kit (Millipore, Cat. No. 17-371RF), and chromatin was sheared to approximately 1000 bp fragments using a Diagenode pico bioruptor. The sheared chromatin underwent a preclearing step with Protein G beads. A 10 µl aliquot of this precleared chromatin was set aside as the input sample. The remaining chromatin was incubated with either anti-AVI antibody or preimmune IgG overnight at 4°C, followed by a 2-hour incubation with Protein Agarose G beads to capture the antibody-chromatin complexes. Post-incubation, the complexes were washed and eluted from the beads using 1% SDS and 0.1M NaHCO3 (pH 9.0) at 65°C. Crosslinks were then reversed by overnight incubation at the same temperature. DNA was deproteinized at 45°C for 2 hours and subsequently purified.
Chromatin Immunoprecipitation sequencing (ChIP-Seq) was conducted at the University of Kansas Medical Center – Genomics Core using the Illumina NovaSeq 6000 Sequencing System. The procedure commenced with 5 ng of both fragmented input and immunoprecipitated chromatin, prepared using the TruSeq ChIP Sample Prep Kit (Illumina, Cat. No. IP-202-1012). The chromatin samples underwent end repair and 3’ adenylation, followed by ligation with Illumina indexed adapters. Amplification of the library was performed using PCR with Illumina adapter-specific primers. The amplified libraries were then purified using KAPA Pure magnetic bead purification system (KAPA, Cat. No. KK8002).  Quality control and sizing of the prepared libraries were assessed using the Agilent TapeStation 4200 HS D1000 ScreenTape. Quantification was carried out on the Roche LightCycler96 using the FastStart Essential DNA Green Master qPCR kit (Roche, Cat. No. 06402712001), adjusting the ChIP-Seq libraries to a concentration of 1.9nM for pooling. Prior to sequencing, the libraries were denatured with NaOH, neutralized with 400mM Tris-HCl (pH 8.0), and diluted to 380 pM for optimal clustering. Clustering and sequencing were performed on a NovaSeq 6000 S1 flow cell using the S1 Reagent Kit v1.5 – 200 cycle (Illumina, Cat. No. 20028318). Post-sequencing, data were converted from .bcl to .fastq format using bcl2fastq software, followed by de-multiplexing to yield sample-specific sequences for downstream analysis.

value: hippocampus

tag: Sex

value: pooled male and female

tag: chip antibody


title: Sample6, symptomatic

description:
Library name: Sample6
SeekOne® MM


title: Sample3, symptomatic

description:
Library name: Sample3
SeekOne® MM


title: Huh-7-Heated+Tan_IIA2

description: Library name: Huh-7-Heated+Tan_IIA2

value: Heated for 10 min, then reinoculated and incubated with 4 μM Tan IIA for 36 h.


title: Sample1, symptomatic

description:
Library name: Sample1
SeekOne® MM


title: Huh-7_Tan_IIA_3

description: Library name: Huh-7_Tan_IIA_3

value: Incubated with  8 μM Tan IIA for 48 h.


title: Sample2, symptomatic

description:
Library name: Sample2
SeekOne® MM


title: Huh-7-Heated+Tan_IIA1

description: Library name: Huh-7-Heated+Tan_IIA1

value: Hepatocellular carcinoma


title: Huh-7_Drug_3

description: Library name: Huh-7_Drug_3

value: TP53 mutant


title: Huh-7_Tan_IIA_2

description: Library name: Huh-7_Tan_IIA_2


title: Huh-7_Tan_IIA_1

description: Library name: Huh-7_Tan_IIA_1


title: Huh-7_DEAB2

description: Library name: Huh-7_DEAB2

value: Incubated with 8 μg/mL 4-diethylaminobenzaldehyde (DEAB) for 48 h.


title: Sample9, asymptomatic

description:
Library name: Sample9
SeekOne® MM


title: 2023_MERSCOPE_Breast_nTMA

value: Breast panel


title: Huh-7_shALDH7A1_3

description: Library name: Huh-7_shALDH7A1_3

value: Infected with letivirus carrying shRNA trageting ALDH7A1


title: 2023_MERSCOPE_Lung_tTMA1

value: Lung panel


title: Huh-7_shALDH7A1_2

description: Library name: Huh-7_shALDH7A1_2


title: ChIP-seq of male Stra8-AVI hippocampus

description: Library name: ChIP Stra8-AVI male

value: male

value: anti-AVI antibody (R&D systems, unconjugated)


title: Lung_bleomycin_Leptin antibody_2

city: Dallas

first: Xuenan

last: Sun

address: Internal Medicine/Touchstone diabetes Center,55235 Harry Hines BLVD L5.100

department: Internal Medicine Touch Stone Diabetes Center

institute: UT Southwestern Medical Center

description:
Library name: Sample14
column name in raw_counts_All_samples.txt:Kidney+bleomycin+LepAb
LL_2

data_processing:
The analysis involves normalizing raw read counts to adjust for sequencing depth, followed by statistical testing to calculate p-values, and concluding with multiple testing correction to determine adjusted p values (p adj).
Sequence reads were trimmed for adaptor sequence/ low-qualigy sequence/ N>10%
Trimmed sequence reads were mapped to GRCm39/mm39.
software is using DESeq2(Anders et al., 2014) to analyze.
Nomalized method is DESeq
Assembly: Mus musculus (GRCm39/mm39)
Supplementary files format and content: tab-limited text file incudes rqw counts for each sample
Supplementary files format and content: cvs fines include FPKM values for each sample

source_name: lung

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen). 1.5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA library preparation (Poly A enrichment+non-directional) following Novogene's protocols

value: lung

value: bleomycin+Ieptin antibody treatment


title: Lung_bleomycin_Leptin antibody_1

description:
Library name: Sample13
column name in raw_counts_All_samples.txt:Kidney+bleomycin+LepAb
LL_1

value: WT


title: Sample8, asymptomatic

description:
Library name: Sample8
SeekOne® MM

value: carotid atherosclerosis plaque


title: Huh-7_Heated2

description: Library name: Huh-7_Heated2

value: Heated for 10 min


title: Lung_bleomycin_IgG_3

description:
Library name: Sample12
column name in raw_counts_All_samples.txt:Kidney+bleomycin+LepAb
LI_3

value: bleomycin+IgG treatment


title: 2024_MERSCOPE_Breast_tTMA1


title: Huh-7_Blank_3

description: Library name: Huh-7_Blank_3

value: Non-treated


title: Huh-7_Heated1

description: Library name: Huh-7_Heated1


title: Huh-7_Blank_2

description: Library name: Huh-7_Blank_2


title: ChIP-seq of pooled male and female wild-type hippocampus

description: Library name: ChIP wild-type

value: hippocampus

value: pooled male and female


title: Huh-7_Drug_2

description: Library name: Huh-7_Drug_2

value: Hepatocellular carcinoma

value: Incubated with  8 μM Tan IIA for 48 h.


title: Huh-7-Heated+Tan_IIA3

description: Library name: Huh-7-Heated+Tan_IIA3

value: TP53 mutant

value: Heated for 10 min, then reinoculated and incubated with 4 μM Tan IIA for 36 h.


title: Kidney_Folicacid_Leptin antibody_3

description:
Library name: Sample9
column name in raw_counts_All_samples.txt:Kidney+bleomycin+LepAb
KL_3

source_name: kidney

value: kidney

value: folic acid+Leptin antibody treatment


title: ChIP-seq of female Stra8-AVI hippocampus

description: Library name: ChIP Stra8-AVI female

value: female


title: Huh-7_NC2

description: Library name: Huh-7_NC2


title: Huh-7_Blank_1

description: Library name: Huh-7_Blank_1


title: Stra8-cKO hippocampus female snRNA-seq

description:
Library name: Stra8-cKO hippocampus female
10x Genomics Chromium Single Nucleus Gene Expression data

data_processing:
Illumina base call files were demultiplexed and converted to FASTQ files using bcl2fastq (v2.20.0.422, Illumina). Reads were aligned to the mouse reference genome mm10 using the Cell Ranger pipeline (10x Genomics, v5.1.0), which also performed read deduplication, cell calling, and generation of cell-by-gene count matrices
Assembly: mm10
Supplementary files format and content: cellranger generated unfiltered feature-barcode matrix file

molecule: nuclear RNA

extract_protocol:
Hippocampal tissues from 3-month-old male and female mice were acutely dissected on ice and homogenized in 2 mL of chilled Nuclei EZ Lysis Buffer (Sigma, #N3408) using a Teflon pestle homogenizer with 10 gentle strokes. Homogenates were incubated on ice for 5 minutes to lyse cellular membranes and release nuclei. Nuclei were pelleted by centrifugation at 500 × g for 5 minutes at 4 °C, washed once with fresh lysis buffer, and resuspended in 200 μL of Nuclei EZ Storage Buffer (Sigma, #S8933) supplemented with 1 U/μL RNase inhibitor (Invitrogen, #10777019). To reduce clumping and ensure uniformity, the nuclei suspension was gently triturated using a pipette. Nuclei concentration and integrity were assessed using a Countess II FL Automated Cell Counter (Life Technologies), typically yielding >94% intact nuclei. Samples containing debris or aggregates were filtered through a 40 μm FLOWMI Cell Strainer (Thermo Fisher, #50-136-7555) to obtain a homogeneous, single-nucleus suspension suitable for downstream single-nucleus RNA sequencing.
Single-nucleus suspensions were prepared by adjusting nuclear concentrations to approximately 1,000 nuclei/μL using low-speed centrifugation at 4 °C and resuspending in calcium- and magnesium-free PBS (Thermo Fisher MT21040CV) containing 0.04% BSA. Emulsification was performed using the 10x Genomics Chromium X and the Chromium Next GEM Single Cell 3′ GEM Library & Gel Bead Kit v3.1, targeting 10,000 nuclei per sample. GEMs were generated on the Chromium Chip G and subjected to reverse transcription in an Eppendorf MasterCycler Pro thermal cycler. Post-GEM RT cleanup was conducted using 10x Recovery Agent and Dynabeads MyOne Silane beads to purify the cDNA. Amplification of second-strand cDNA was followed by library preparation, including fragmentation, end repair, A-tailing, adapter ligation, and sample index PCR using the Dual Index Kit TT Set A. Libraries were validated using the Agilent 4200 TapeStation and quantified with Roche LightCycler96 and KAPA Library Quant standards. Sequencing was carried out on the NovaSeq X Plus platform using a 100-cycle reagent kit with an asymmetric read structure (Read 1: 28 cycles; i7 index: 10 cycles; i5 index: 10 cycles; Read 2: 90 cycles). Demultiplexing and gene expression quantification were performed using the 10x Genomics Cell Ranger pipeline and visualized with Loupe Browser.

value: Stra8L/-; Nestin-Cre


title: Huh-7_NC1

description: Library name: Huh-7_NC1


title: Kidney_Folicacid_Leptin antibody_2

description:
Library name: Sample8
column name in raw_counts_All_samples.txt:Kidney+bleomycin+LepAb
KL_2


title: Stra8-cKO hippocampus male snRNA-seq

description:
Library name: Stra8-cKO hippocampus male
10x Genomics Chromium Single Nucleus Gene Expression data


title: Kidney_Folicacid_Leptin antibody_1

description:
Library name: Sample7
column name in raw_counts_All_samples.txt:Kidney+bleomycin+LepAb
KL_1


title: Lung_bleomycin_Leptin antibody_3

description:
Library name: Sample15
column name in raw_counts_All_samples.txt:Kidney+bleomycin+LepAb
LL_3

value: lung


title: Hep-G2-Heated+Tan_IIA3

description: Library name: Hep-G2-Heated+Tan_IIA3

value: TP53 wild type


title: Kidney_Folicaicd_IgG_3

description:
Library name: Sample6
column name in raw_counts_All_samples.txt:Kidney+bleomycin+LepAb
KI_3

value: WT

value: folic acid+IgG treatment


title: Huh-7_Heated3

description: Library name: Huh-7_Heated3

value: Heated for 10 min


title: Huh-7_Drug_1

description: Library name: Huh-7_Drug_1


title: Kidney_vehicle treatment_2

description:
Library name: Sample2
column name in raw_counts_All_samples.txt:Kidney+Folic acid+IgG
KC_2

value: vehicle


title: Hep-G2_Heated2

description: Library name: Hep-G2_Heated2


title: Hep-G2_Heated1

description: Library name: Hep-G2_Heated1


title: MouseMGTAM

description: Library name: MouseMGTAM

value: glioblastoma

value: immune cells

value: QPP

value: Mg-TAMs


title: Hep-G2-Heated+Tan_IIA2

description: Library name: Hep-G2-Heated+Tan_IIA2

value: Hepatocellular carcinoma


title: Hep-G2_NC2

description: Library name: Hep-G2_NC2

value: Non-treated


title: Hep-G2_NC1

description: Library name: Hep-G2_NC1


title: Lung_bleomycin_IgG_2

description:
Library name: Sample11
column name in raw_counts_All_samples.txt:Kidney+bleomycin+LepAb
LI_2

value: bleomycin+IgG treatment


title: Mouse7Core

description: Library name: Mouse7Core

value: Core


title: Huh-7_NC3

description: Library name: Huh-7_NC3

value: TP53 mutant


title: TCF3::HLF B-ALL patient scRNA-seq (TAS-seq; IkawaTag1)

city: Noda City

first: Aisa

last: Suzuki

state: Chiba

address: Yamasaki 2669

country: Japan

institute: Tokyo University of Science

description: Library name: Sample 2

data_processing:
Sequence reads were processed and analyzed using R studio. Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) of TAS-Seq and BD WTA kit data were processed as follows. After adapter removal and quality filtering by Cuadapt-2.10, gene expression libraries were aligned to human Ensemble RNA (GRCh38/hg38) by Bowtie2-2.3.4.1,  and count matrices were generated using the modified Python script of BD Rhapsody workflow. Cell barcodes were identified as valid if the inflection threshold of knee-plot read counts of each cell barcode was above the threshold identified by the DropletUtis package. Each sample’s origin and doublets were identified based on fold-change of the normalized read counts of Hashtag antibodies. To subtract the background read counts of each gene caused by RNA diffusion during the lysis step within the BD Rhapsody cartridge and reverse transcription, distribution-based error correction was performed. The resultant dataset was mainly analyzed using R software package Surat v4.0.4 in R 4.1.0. As quality control, doublets and cells with the mitochondrial gene proportion >20% were filtered out. The log-normalized gene counts were calculated using NormalizeData function (scale.factor=1,000,000) and highly variable genes were defined by the FindVariableFeatures function (selection.method=”vst”, nfeature=2000). Read counts were regressed out by the ScaleData function. Principal component analysis was performed on the variable genes, and principal components with p value < 0.05 were calculated by the Elbow. Differentially expressed genes were defined as those whose p value, as calculated by the Wilcoxon rank sum test and adjusted by the Bonferroni method is <0.05 and whose log2FoldChange is  > 0.5 or < -0.5.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
Cryopreserved bone marrow samples were thawed and incubated at 4°C for 10 min in Sulfo-NHS-LC-Biotin (10 μg/mL in PBS; EZ-Link™ Sulfo-NHS-LC-Biotin, Thermo Fisher Scientific, Cat# A39257) to biotinylate cell surface proteins. After three washes with Cell Staining Buffer (BioLegend, Cat# 420201), samples were incubated at 4°C for 15 min with TotalSeq™-A09xx PE-Streptavidin (corresponding to barcodes A0951: Patient1-Primary1, A0952:Patient1-Primary2, A0953:Patient1-Replase1, A0954:Patient1-Relapse2, A0955:Patient2-Primary1, A0961:Healthy donor1_Japan, A0962:Healthy donor2_Foreign country; final concentration 2.5 μg/mL; BioLegend) to label each sample with a unique DNA barcode. Cells were then stained with 1 μM Calcein AM at 37°C for 5 min to identify viable cells. Calcein(+) PE(+) 7-AAD(-) live cells were sorted using a FACS Aria III (BD Biosciences). Equal numbers of sorted cells from seven individual samples were pooled, and cells were loaded onto a BD Rhapsody cartridge (BD Biosciences, Cat# 665913) and processed using the BD Rhapsody Cartridge Reagent Kit (BD Biosciences), according to the manufacturer’s instructions.
Single cell suspensions were prepared from bone marrow samples and subjected to single-cell RNA preparation using BD Rhapsody. 10000 cells were loaded onto BD Rhapsody cartrige and captured cell number was asessed by BD Rhapsody scanner. Cell lysis, mRNA trap, cDNA synthesis, and primer digestion were performed according to the manufacture's instruction. cDNA amplification was performed by TAS-Seq protocol (Shichino et al. Commun Biol. 2022). Sequencing libraries from amplified cDNAs were produced by using NEB UltraII FS Kit for illumina (New England Biolabs) with some modifications. Sequencing was performed on an Illumina Novaseq 6000 sequencer at a depth of approximately 50000 reads per cell.

value: Bone marrow

value: BM MNC


title: Lung_bleomycin_IgG_1

description:
Library name: Sample10
column name in raw_counts_All_samples.txt:Kidney+bleomycin+LepAb
LI_1

value: lung


title: Hep-G2-Heated+Tan_IIA1

description: Library name: Hep-G2-Heated+Tan_IIA1

value: TP53 wild type

value: Heated for 10 min, then reinoculated and incubated with 4 μM Tan IIA for 36 h.


title: Kidney_Folicaicd_IgG_2

description:
Library name: Sample5
column name in raw_counts_All_samples.txt:Kidney+bleomycin+LepAb
KI_2

value: kidney

value: WT

value: folic acid+IgG treatment


title: Hep-G2_Tan_IIA3

description: Library name: Hep-G2_Tan_IIA3

value: Incubated with 4 μM Tan IIA for 36 h.


title: SMCs, 24hr coculture with MoS2-treated HMSCs (mito-Factory) rep2

city: Bryan

first: Irtisha

last: Singh

address: 8447 John Sharp Pkwy MREB II, Suite 4344

department: Cell Biology & Genetics

institute: Texas A&M University

description: Library name: TSMC_M2

data_processing:
Preprocessing, adapter and polyX trimming by Fastp - Bioconda v0.23.2
Trimmed outputs aligned to hg38 (STAR – Bioconda v2.7.10b)
Filtered for expressed genes only (RPKM > 1 in at least 50% of samples)
Unique reads counted to exon loci per gene, normalized in Fragments Per Kilobase per Million (FPKM)
Assembly: hg38 (UCSC)
Supplementary files format and content: csv file containing FPKM values for each sample

growth_protocol: Human mesenchymal stem cells (hMSCs) (ATCC) were cultured in alpha-MEM (Hyclone, GE Sciences) with 10% fetal bovine serum (Cytiva) and 1% penicillin/streptomycin (100 U/100 µg/mL, Life Technologies). Human Umbilical Artery Smooth Muscle Cells (HUASMCs) (PromoCell) were cultured in Endothelial Cell Medium (ScienCell) containing fetal bovine serum (FBS), Endothelial Cell Growth Supplement, and penicillin/streptomycin solution.

extract_protocol:
Zymogen Quick RNA Miniprep kit
Library construction and sequencing on Illumina NovaSeq 6000 were performed by Novogene (Sacramento, CA)

treatment_protocol: HUASMCs were sorted and RNA collected after 24-hour coculture with hMSCs or hMSCs pre-treated with MoS2 nanoflowers. Untreated HUASMCs are included as additional control.

value: Smooth muscle cells

value: Coculture with MoS2-treated HMSCs, 24hr


title: Kidney_Folicaicd_IgG_1

description:
Library name: Sample4
column name in raw_counts_All_samples.txt:Lung+bleomycin+IgG
KI_1


title: Sample13, carotid bifurcation

description:
Library name: Sample13
SeekOne® MM

source_name: carotid bifurcation

value: carotid bifurcation

value: tissue


title: Kidney_vehicle treatment_3

description:
Library name: Sample3
column name in raw_counts_All_samples.txt:Kidney+Folic acid+LepAb
KC_3

value: vehicle


title: Hep-G2_Tan_IIA2

description: Library name: Hep-G2_Tan_IIA2

value: Hepatocellular carcinoma


title: Hep-G2_Tan_IIA1

description: Library name: Hep-G2_Tan_IIA1


title: SMCs, 24hr coculture with HMSCs (mito-Transfer) rep3

description: Library name: TSMC_H3

source_name: Human Umbilical Artery Smooth Muscle Cells

value: Coculture with HMSCs, 24hr


title: Hep-G2_Heated3

description: Library name: Hep-G2_Heated3

value: Heated for 10 min


title: Kidney_vehicle treatment_1

description:
Library name: Sample1
column name in raw_counts_All_samples.txt:Kidney+vehicle
KC_1


title: SMCs, 24hr coculture with HMSCs (mito-Transfer) rep1

description: Library name: TSMC_H1

value: Human Umbilical Artery Smooth Muscle Cells


title: 4PM_run1

city: Milano MI

first: Aurora

last: Maurizio

state: Italy

address: Via Olgettina, 60

department: Center for Omics Sciences (COSR)

country: Italy

institute: IRCCS Ospedale San Raffaele

description: Library name: 4PM_run1

data_processing:
Single end reads (100bp) were generated on NovaSeq 6000 (Illumina) instrument following manufacturer recommendations.
Reads from multiple lanes were merged and trimmed with Trimmomatic.
Reads were aligned to GRCm38 reference genome using STAR aligner (v2.5.3a)
FeatureCounts (v1.6.4) was used to compute reads mapping on exons as annotated in GENCODE Mus musculus basic gene annotation (version v22) and obtain transcript quantification summarized at the gene level, excluding multimapping reads.
Only genes with at least 1 CPM (Counts per million) in at least 3 samples were retained.
Assembly: GRCm38  (GENCODE v22)
Supplementary files format and content: Tab separated file of raw counts. Gizipped.

extract_protocol:
mRNA was extracted with the RNeasy Mini Kit (Qiagen) from mouse BMDCs after treatment.
NGS libraries were constructed utilizing the TruSeq Stranded mRNA (Illumina) protocol.

treatment_protocol: Overnight stimulation of BMDCs with heat-inactivated bacteria (PM or PH).

value: Bone marrow

value: dendritic cells

tag: sample id

value: PM


title: MouseMOTAM

description: Library name: MouseMOTAM

value: glioblastoma

value: immune cells

value: QPP

value: Mo-TAMs


title: Hep-G2_NC3

description: Library name: Hep-G2_NC3

value: TP53 wild type

value: Non-treated


title: Mouse8Core

description: Library name: Mouse8Core

value: Core


title: SMCs, Untreated, Bio rep2

description: Library name: TSMC_2

value: Smooth muscle cells


title: Mouse8Border

description: Library name: Mouse8Border

value: Border


title: Mouse8Periphery

description: Library name: Mouse8Periphery

value: Periphery


title: SMCs, Untreated, Bio rep1

description: Library name: TSMC_1


title: 3PH_run1

description: Library name: 3PH_run1

value: PH


title: Mouse7Border

description: Library name: Mouse7Border


title: TCF3::HLF B-ALL patient scRNA-seq (TAS-seq; IkawaWTA1)

description: Library name: Sample 1

value: BM MNC


title: Mouse7Periphery

description: Library name: Mouse7Periphery


title: 1PM_run1

description: Library name: 1PM_run1


title: SMCs, 24hr coculture with MoS2-treated HMSCs (mito-Factory) rep3

description: Library name: TSMC_M3

value: Coculture with MoS2-treated HMSCs, 24hr


title: CD127n_ELPs_fetal_HP11.1

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Human reference transcriptome from the UCSC website (release hg38) using BWA version 0.7.4.4  was used to align the second reads
Assembly: hg38
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 28,307 genes detected.

extract_protocol:
no extraction_cell lysates
Cachiarelli et al. (Cell 162:412, 2015)

tag: developmental stage

value: fetal

tag: age

value: 20 PCW


title: Sample14, common carotid

description:
Library name: Sample14
SeekOne® MM

source_name: common carotid

value: common carotid

value: tissue


title: SMCs, 24hr coculture with MoS2-treated HMSCs (mito-Factory) rep1

description: Library name: TSMC_M1

value: Human Umbilical Artery Smooth Muscle Cells


title: 3PH_run2

description: Library name: 3PH_run2

value: Bone marrow

value: dendritic cells


title: Adipose-specific Cullin 3 knockout mice, 8-week WD, rep1

city: Oklahoma City

first: Tiangang

state: OK

address: 975 NE 10TH ST

institute: University of Oklahoma Health Sciences Center

description:
Library name: Cul3AKO-1
Cul3AKO1_fpkm

data_processing:
Raw FASTQ reads were cleaned using in-house Perl scripts by removing adapter sequences, poly-N reads, and low-quality reads. Quality metrics (Q20, Q30, GC content) were calculated, and only high-quality clean reads were used for further analysis.
Clean paired-end reads were aligned to the reference genome using Hisat2 v2.0.5, which supports splice junction mapping for more accurate alignment based on gene annotation files.
FeatureCounts was used to count reads mapped to each gene. Gene expression levels were calculated as FPKM, accounting for both sequencing depth and gene length.
Assembly: mm10
Supplementary files format and content: FPKM, Excel.

source_name: White adipose tissue

extract_protocol:
TRIzol Reagent
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: White adipose tissue

value: male

value: KO

value: fed Western diet for 8 weeks


title: Wild type mice, 8-week WD, rep4

description:
Library name: WT-4
WT4_fpkm

value: WT


title: CD127p_ELPs_young_FP12.2

value: young

value: 32 YPP


title: Wild type mice, 8-week WD, rep3

description:
Library name: WT-3
WT3_fpkm


title: 1PM_run2

description: Library name: 1PM_run2

value: PM


title: Wild type mice, 8-week WD, rep1

description:
Library name: WT-1
WT1_fpkm


title: 4PH_run1

description: Library name: 4PH_run1

value: PH


title: Adipose-specific Cullin 3 knockout mice, 8-week WD, rep4

description:
Library name: Cul3AKO-4
Cul3AKO4_fpkm


title: SMCs, Untreated, Bio rep3

description: Library name: TSMC_3

value: Smooth muscle cells


title: CD127p_ELPs_young_FP12.1


title: PSC Yoda1 bio rep3

city: Durham

first: Sandip

middle: Madhusudan

last: Swain

state: NC

address: 905 South Lasalle St, Room 1043

department: Medicine

institute: Duke University

description:
Library name: Sample 14
Stellate cells rawdata.txt
ST93_yoda-25-uM

data_processing:
liver library data processing step using Hisat2 v2.0.5. stellate cells data processing step: using TrimGalore toolkit
Assembly: Hisat2 v2.0.5 and GRCm38v73
Supplementary files format and content: text file incllude raw count for each sample

source_name: pancreatic stellate cells

extract_protocol:
RNA was harvested using Life Technologies Ribopure kit
liver library was constructed by Novogene using their standard protocol.Stellate cells library was constructed by The Sequnecing and Genomics Technologies Duke Core Facility

value: pancreatic stellate cells


title: CD127p_ELPs_young_GP9


title: CD127p_ELPs_fetal_HP12.2

value: fetal

value: 20 PCW


title: CD127n_ELPs_young_FP11.2


title: 3PM_run1

description: Library name: 3PM_run1


title: CD127n_ELPs_young_FP11.1


title: PSC DMSO bio rep1

description:
Library name: Sample 9
Stellate cells rawdata.txt
ST90_DMSO


title: CD127n_ELPs_fetal_HP11.2


title: CD127p_ELPs_old_EP9.2

value: old

value: 50 YPP


title: SMCs, 24hr coculture with HMSCs (mito-Transfer) rep2

description: Library name: TSMC_H2

value: Human Umbilical Artery Smooth Muscle Cells

value: Coculture with HMSCs, 24hr


title: Adipose-specific Cullin 3 knockout mice, 8-week WD, rep2

description:
Library name: Cul3AKO-2
Cul3AKO2_fpkm

value: White adipose tissue


title: CD127p_ELPs_old_EP9.1


title: Adipose-specific Cullin 3 knockout mice, 8-week WD, rep3

description:
Library name: Cul3AKO-3
Cul3AKO3_fpkm

value: male


title: CD127p_ELPs_old_CP9.1

value: 52 YPP


title: CD127p_ELPs_old_CP9.2


title: Wild type mice, 8-week WD, rep2

description:
Library name: WT-2
WT2_fpkm

value: fed Western diet for 8 weeks


title: 1PH_run1

description: Library name: 1PH_run1

value: Bone marrow

value: dendritic cells


title: PSC Yoda1 bio rep1

description:
Library name: Sample 12
Stellate cells rawdata.txt
ST90_yoda-25-uM


title: Liver TRPV4 KO bio rep2

description:
Library name: Sample 4
gene_count.txt
D2

source_name: liver

value: liver


title: CD7n10p_MLPs_old_EP13.2


title: CD127p_ELPs_fetal_HP12.1


title: PSC DMSO bio rep2

description:
Library name: Sample 10
Stellate cells rawdata.txt
ST92_DMSO


title: CD7n10p_MLPs_old_CP13.2


title: CD7n_MLPs_old_EP11.2


title: PSC DMSO bio rep3

description:
Library name: Sample 11
Stellate cells rawdata.txt
ST93_DMSO


title: CD7n10p_MLPs_old_CP13.1


title: CD7n10p_MLPs_young_GP13

value: young

value: 32 YPP


title: Liver WT + GSK219 bio rep2

description:
Library name: Sample 7
gene_count.txt
E2


title: Control_Rep1_H3K4me1

description: Library name: Sample 2

data_processing:
Sequence reads were processed and analyzed using the Galaxy platform (https://usegalaxy.org).
Raw sequencing data were downloaded using the SRA Toolkit (v3.1.1) and were assessed for quality using FastQC (Galaxy v0.74). Adapter sequences and low-quality bases were trimmed using Trimmomatic (Galaxy v0.39). Reads were aligned to the reference genome (hg19 or hg38) using Bowtie2 (Galaxy v2.5.3). Coverage tracks in bigWig format were generated using Bam Coverage (Galaxy v3.5.4). CUT&Tag peaks for H3K4me1 were identified using MACS2 call peak (Galaxy v2.2.9.1) and visualized in IGV (v2.18.4).
Assembly: GRCh38
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

growth_protocol: YCUB2 cells were maintained in RPMI supplemented with 10% fatal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
CUT&Tag assays were performed using the CUT&Tag Assay Kit (Cell Signaling Technology, #77552) according to the manufacturer’s instructions.
CUT&Tag assays were performed using the CUT&Tag Assay Kit (Cell Signaling Technology, #77552) according to the manufacturer’s instructions. 5×10^4 cells were immobilized on Concanavalin A-coated magnetic beads and sequentially incubated with primary antibodies specific to H3K4me1 and IgG followed by a secondary antibody provided in the kit. pA-Tn5 was then added to facilitate targeted tagmentation of chromatin. After tagmentation, DNA was extracted and purified using the spin columns included in the kit. Indexed libraries were generated by PCR amplification and subsequently purified for next-generation sequencing. Quality and concentration of the libraries were measured by Agilent 2200 Bioanalyzer and High Sensitivity D1000 Screen Tape (Agilent Technologies), respectively. Pooled libraries were sequenced by NovaSeq X Plus (Illumina).

value: Control

tag: antibody


title: CD7p_MLPs_fetal_HP14.2


title: Liver WT bio rep1

description:
Library name: Sample 1
gene_count.txt
B3


title: CD7n10p_MLPs_old_EP13.1


title: Liver WT + GSRK219 bio rep3

description:
Library name: Sample 8
gene_count.txt
E4


title: Liver WT + GSK219 bio rep1

description:
Library name: Sample 6
gene_count.txt
E1


title: PSC Yoda1 bio rep2

description:
Library name: Sample 13
Stellate cells rawdata.txt
ST92_yoda-25-uM

value: pancreatic stellate cells


title: Liver TRPV4 KO bio rep3

description:
Library name: Sample 5
gene_count.txt
D3


title: Control_Rep2_H3K4me1

description: Library name: Sample 6


title: CD7p_MLPs_fetal_HP14.1

value: fetal


title: KO_Rep2_IgG

description: Library name: Sample 7

value: HLF-deficient

value: IgG


title: KO_Rep2_H3K4me1

description: Library name: Sample 8


title: CD7n_MLPs_old_EP11.1

value: old

value: 50 YPP


title: Control_Rep2_IgG

description: Library name: Sample 5


title: Liver WT bio rep2

description:
Library name: Sample 2
gene_count.txt
B4


title: Therapy PA2 repeat2 (assembly pathway 1)

city: Chicago

first: NOZOMU

last: TAKATA

state: Illinois

address: 303 East Superior Street, 10-220

department: Center for Vascular and Developmental Biology

institute: Northwestern University Feinberg School of Medicine

description: Library name: inj_MG_Org_A2G2_IKVAV_4_S59

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: hg38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: spinal cord

growth_protocol: Based on U.S. Provisional Patent No. 63/506,521

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
Directional mRNA libraries were prepared using Illumina UDI Kits per the manufacturer’s instructions

value: spinal cord

value: healthy indivisual

value: Peptide amphiphile


title: CD7n_MLPs_old_CP11.2

value: 52 YPP


title: Therapy PA2 (assembly pathway 1)

description: Library name: inj_MG_Org_A2G2_IKVAV_3_S54

treatment_protocol: Based on U.S. Provisional Patent No. 63/506,521


title: KO_Rep1_IgG

description: Library name: Sample 3


title: CD7n_MLPs_old_CP11.1


title: Liver TRPV4 KO bio rep1

description:
Library name: Sample 3
gene_count.txt
D1


title: Cortex_WT_rep3

city: Hamburg

first: Jan Broder

last: Engler

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

description: Library name: Cortex_WT3

data_processing:
Alignment with STAR (v2.7.9a)
Counting with featureCounts (v1.5.1)
Analysis with DESeq2 (v1.40.2)
Assembly: ensemble.mouse.GRCm39r104
Supplementary files format and content: RNA_counts_raw.txt: Tab separated value file of raw RNA counts
Supplementary files format and content: RNA_counts_norm.txt: Tab separated value file of normalized RNA counts

source_name: Cerebral cortex

extract_protocol:
RNeasy microkit (Qiagen)
TruSeq Stranded mRNA (Illumina)

value: Cerebral cortex

value: WT


title: KO_Rep1_H3K4me1

description: Library name: Sample 4

value: Bone marrow


title: Therapy control repeat2 (assembly pathway 1)

description: Library name: inj_MG_Org_E2_4_S57


title: CD7n_MLPs_young_FP13.2


title: Cortex_WT_rep4

description: Library name: Cortex_WT4


title: Control_Rep1_IgG

description: Library name: Sample 1


title: CD7n_MLPs_young_FP13.1


title: P.involutus MMN-K negative control Cm3

city: Monterotondo (RM), Italy

first: Flavia

last: Pinzari

state: Rome

address: Area della Ricerca di Roma 1

department: Institute for Biological Systems (IBS)

institute: Council of National Research of Italy (CNR)

data_processing:
Illumina NovaSeq Control Software 1.6.0  used for basecalling.
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.19).
Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014). Quality trimming of the reads has not been performed.
Trimmed raw reads were aligned to Paxillus involutus (GCA_000827475.1) using STAR (version 2.5.2b) (Dobin et al. 2013).
A count table was created using the HTSeq package (Anders et al., 2014) implemented in OmicBox (version 1.2.4).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Paxillus involutus

source_name: mycelium

growth_protocol: The fungal cultures were prepared using round sterile polystyrene 100x20 mm Petri dishes (N. 430167 Corning). 30 ml of agar were poured in each Petri dish. The positive control consisted of microcosms made with full MMN modified medium while the negative control and the microcosms containing the minerals were prepared using K-depleted MMN agar, prepared without KH2PO4. Sterile cellophane membranes (Cellophane™ 325P, 80mmm DIA, SBC292529 AA Packaging Ltd, Lancashire, UK) were placed on top of the agar before adding fungi and minerals. The membrane was essential to harvest the fungal biomass without residual agar.

extract_protocol:
Total RNA was extracted from each sample using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions, except that β- mercaptoethanol (10 μl l−1) was added to the RLC buffer. Up to 200 mg of frozen biomass from each biological replicate was extracted. Total RNA was eluted in 50 µl of sterile, distilled and RNAse free H2O and stored at –80◦C. The concentrations and quality of purified nucleic acids were checked on a NanoDrop (ND-8000 NanoDrop Technologies), Qubit® (using the RNA HS Assay Kits), and Agilent TapeStation 2200 using the High Sensitivity RNA ScreenTape (Agilent). cDNA libraries were prepared for sequencing using standard Illumina protocols by CeGAT Company (Germany).
cDNA libraries were prepared for sequencing using standard Illumina protocols by CeGAT Company (Germany). TruSeq Stranded mRNA (Illumina) kit was used.

treatment_protocol: Mineral flakes were placed in the centre of the Petri dish, on the membrane, and the fungus was inoculated in three points, around them (Wei et al., 2012). The minerals used, with decreasing level of K weatherability, were: muscovite, phlogopite, and K-vermiculite. The minerals were cut as flakes of ~2cm2, cleaned ultrasonically in deionised water, and sterilised by autoclaving (121°C, 15 minutes). The inoculums consisted of 5 mm in diameter agar plugs of P. involutus, obtained from the edge of 7-day-old actively growing cultures. All cultures were kept in the dark at 25◦C throughout the experiment. The microcosms were incubated for 21 days. Five biological replicates from each experiment were used for RNA extraction and sequencing. Fungal biomass was removed from the cellophane membrane and ground into a powder in liquid nitrogen using a sterilised mortar and pestle.

tag: strain

value: grown on K-depleted MMN


title: Therapy control (assembly pathway 1)

description: Library name: inj_MG_Org_E2_3_S52


title: P.involutus MMN-K negative control Cm5


title: P.involutus MMN-K negative control Cm4


title: P.involutus MMN-K negative control Cm2


title: CD7n_MLPs_young_GP11

value: young


title: Cortex_WT_rep2

description: Library name: Cortex_WT2


title: Cortex_L192P_rep4

description: Library name: Cortex_L192P4


title: CD7n_MLPs_fetal_HP13.1

value: 20 PCW


title: P.involutus MMN+K positive control Cp5

value: grown on complete MMN


title: Cortex_L192P_rep3

description: Library name: Cortex_L192P3


title: Cortex_WT_rep1

description: Library name: Cortex_WT1


title: P.involutus MMN+K positive control Cp3


title: 117p_CD7n_MPPs_fetal_DP13.2

value: 19 PCW


title: 117p_CD7p_MPPs_fetal_DP14.2

value: fetal


title: Cortex_L192P_rep2

description: Library name: Cortex_L192P2


title: P.involutus Muscovite M4

value: grown with muscovite


title: CD7n_MLPs_fetal_HP13.2


title: P.involutus MMN-K negative control Cm1


title: Plp1_Old_3_sciatic_nerve

city: Freiburg im Breisgau

first: Luis

last: Hortells

address: Albertstraße 25

institute: University of Freiburg

data_processing:
RNAseq data were analyzed using a Galaxy platform (Afgan et al., 2016). Adapters were trimmed from reads using Trim Galore. Reads were mapped to the Mus musculus genome (mm39) using STAR (Dobin et al., 2013) and duplicate reads were removed. Transcript abundance was estimated as fragments per kilobase of transcript per million fragments mapped using featureCounts (Liao et al., 2014) and differential expression of Ensembl mm39 annotated genes was determined using DESeq2 (Love et al., 2014) with q < 0.05 considered to be significant. Volcano plots were generated using ggplot2 and enrichment of molecular pathways from Gene Ontology was analyzed using Enrichr (Kuleshov et al., 2016).
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw-counts for each sample

source_name: sciatic nerve

extract_protocol:
HEART: Hearts were dissected and immediately transferred to 2% Fetal Bovine Serum (VWR Life Science Seradigm) in Dulbecco's Modified Eagle Medium (DMEM, 11965-092 GIBCO, USA) at 4 oC. Then, the hearts were minced with sterile scissors and digested in digestion buffer (100IU) of collagenase type II/ml in DMEM at 37 oC for 15 minutes. After this the tissue was triturated by pipetting up and down with serological pipettes 15 times, letting it rest 2 min, so the remaining tissue settled at the bottom. The supernatant was collected and centrifuged at 1000rpm for 3 minutes while the remaining tissue was digested again with collagenase (for 15 minutes). After centrifuging the supernatant was discarded and the pellet resuspended in DMEM and kept on ice. This sequence was repeated for 90 minutes (5 times) merging the supernatant of every digestion and keeping it on ice. After this process the isolated cells were treated with Red Blood Cells lysis (R7757, Sigma, USA) for 1 minute and then 15 ml of DMEM was added before centrifuging for 5 minutes at 1200 rpm. The supernatant was discarded, and the pellet was resuspended in PBS with 2mM EDTA to release clumps. SCIATIC NERVES: Sciatic nerves were dissected and immediately transferred to 2% Fetal Bovine Serum (VWR Life Science Seradigm) in Dulbecco's Modified Eagle Medium (DMEM, 11965-092 GIBCO, USA) at 4 oC. Next, the nerves were minced with sterile scissors in digestion buffer: 0.125% Trypsin + 0.3% Collagenase II, and then digested in thermoshaker at 37 oC (750 rpm) for 10 minutes. Finally, the digested nerves were mechanically dissociated by pipetting up and down 20 times and the digestion buffer was blocked by adding 10% FCS for 1 minute, on ice.  The cells were pelleted and then resuspended in FACS media: 0.5% BSA + 5mM EDTA in PBS, passing the suspension through a 40 μm strainer. FACS: Before Fluorescence-Activated Cell Sorting (FACS) the tdt+ cells, DRAQ7 was added to eliminate the dying cells. Viable tdt+/DRAQ7- cells were FACS sorted using a S3 Fluorescence-activated cell sorter (Bio-Rad, Hercules, CA, USA). The sorted tdt+ cells were collected in RLT plus (Qiagen, Venlo, Netherlands) and frozen at -80 oC.
RNA-seq libraries were generated using the Ovation SoLo RNA-Seq kit (Tecan). Libraries were quantified using Qubit (Thermo Fisher) and qPCR (Quantabio) and size distribution was checked using a Tapestation 4150 (Agilent). Libraries were sequenced on a NovaSeq 6000 (Illumina).

value: sciatic nerve

value: Schwann cell

value: tamoxifen


title: P.involutus Phlogopite P4

value: grown with phlogopite


title: Plp1_Old_2_sciatic_nerve


title: 117hi_CD7n_MPPs_old_EP10.1

value: old

value: 50 YPP


title: Cortex_L192P_rep1

description: Library name: Cortex_L192P1


title: P.involutus Muscovite M3


title: P.involutus Muscovite M2


title: P.involutus MMN+K positive control Cp1


title: P.involutus MMN+K positive control Cp4


title: P.involutus Phlogopite P2


title: P.involutus Muscovite M1


title: P.involutus MMN+K positive control Cp2


title: 117p_CD7n_MPPs_fetal_DP13.1


title: P.involutus Phlogopite P5


title: P.involutus Phlogopite P3


title: Plp1_Old_1_sciatic_nerve


title: 117hi_CD7n_MPPs_old_EP10.2


title: P.involutus Phlogopite P1


title: 117p_CD7p_MPPs_fetal_DP14.1


title: 117hi_CD7n_MPPs_old_CP10.2

value: 52 YPP


title: P.involutus Muscovite M5


title: Plp1_Old_1_heart

source_name: heart

value: heart


title: P.involutus Vermiculite V5

value: grown with K-vermiculite


title: 117hi_CD7n_MPPs_old_CP10.1


title: P.involutus Vermiculite V2


title: Plp1_Old_2_heart


title: P.involutus Vermiculite V1


title: 117hi_CD7n_MPPs_young_FP8.2

value: 32 YPP


title: 117hi_CD7n_MPPs_young_FP8.1


title: Plp1_Young_3_sciatic_nerve


title: YCUB2 cells, sg_IL1B_Rep1

description:
Library name: Sample 13
Column name in YCUB2_FPKM_assembl.txt: YCUB2BKO32_Rep1

data_processing:
Sequence reads were processed and analyzed using the Galaxy platform (https://usegalaxy.org).
Quality control was performed using FastQC (Galaxy v0.72), and low-quality reads were filtered using Trimmomatic (Galaxy v0.36.5) with default parameters. Reads were aligned to the reference genome (NCBI build 37, mm9) using HISAT2 (Galaxy v2.1.0).
The alignments were assembled and quantified using StringTie (Galaxy v1.3.4), and differentially expressed genes (DEGs) were identified using DESeq2 (Galaxy v2.11.40.2) with a false discovery rate (FDR) < 0.05 as the threshold for significance. Identified DEGs were further analyzed and visualized using iDep (version 0.96).
Assembly: mm9 or GRCh38
Supplementary files format and content: txt files include FPKM values for each sample

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Poly(A)+ mRNA from total RNA of one million sorted pro-B cells of WT, TCF3::PBX1 positive-ALL and TCF3::HLF positive-ALL mice or IL1B-sufficient and deficient YCUB2 cells was isolated by NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The library was then prepared by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

value: Bone marrow

value: IL1B knockout


title: YCUB2 cells, sg_IL1B_Rep3

description:
Library name: Sample 15
Column name in YCUB2_FPKM_assembl.txt: YCUB2BKO32_Rep3


title: YCUB2 cells, sg_IL1B_Rep2

description:
Library name: Sample 14
Column name in YCUB2_FPKM_assembl.txt: YCUB2BKO32_Rep2


title: YCUB2 cells, sg_Control_Rep3

description:
Library name: Sample 12
Column name in YCUB2_FPKM_assembl.txt: YCUB2ctrl_Rep3

value: Wild type


title: Plp1_Young_2_sciatic_nerve


title: Plp1_Young_1_sciatic_nerve


title: 117hi_CD7n_MPPs_young_GP10

value: young


title: Plp1_Old_3_heart


title: YCUB2 cells, sg_Control_Rep2

description:
Library name: Sample 11
Column name in YCUB2_FPKM_assembl.txt: YCUB2ctrl_Rep2


title: 117hi_CD7n_MPPs_fetal_HP8.1

value: 20 PCW


title: YCUB2 cells, sg_Control_Rep1

description:
Library name: Sample 10
Column name in YCUB2_FPKM_assembl.txt: YCUB2ctrl_Rep1


title: Pool3: 40, 48, 60, and 72 hpf dissections for ear enrichment

city: Berkeley

first: Ian

last: Swinburne

state: CA

address: Weill Hall, Room 585

department: Molecular and Cell Biology

institute: UC Berkeley

description: Library name: Pool_3

data_processing:
Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi-seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. We provide 8 FASTQ files (2 lanes x 4 reads per lane). The read files from an inDrops run have the following content: *_R1_001.fastq.gz : contains the 3' UTR cDNA read *_R2_001.fastq.gz : contains the first half of the cell barcode *_R3_001.fastq.gz : contains the library index for demultiplexing libraries *_R4_001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis (github.com/indrops).
To obtain the final counts matrix used for data analysis, total count filters were applied as described in Kukreja et. al. 2024, method section "Single cell RNA-seq Data preprocessing"
Assembly: GRCz11 genome assembly (Assembly Accession: GCF_000002035.6)
Supplementary files format and content: Filtered barcodes (EarAtlas_FullProcessed.h5ad): cell barcode, and associated metadata for all cells

organism: Danio rerio

source_name: ear / head region

growth_protocol: Danio buffer

extract_protocol:
To minimize sticking of cells to plastic, 1.5 ml collection tubes were coated with 10% BSA for 10 minutes, rinsed in PBS, and left on ice. Dissections were performed in modified DMEM plus tricaine: 1x DMEM (11039-021 (LifeTech)), 10 mM HEPES, 1x non-essential amino acids (11140076 (LifeTech)), 1mM sodium pyruvate (11360070 (LifeTech), 100 um B-mercaptoethanol (M3148 Sigma), and 0.33 mg/ml Tricaine (E10521 (Sigma)). The morning of an inDrops experiment, a team of 3-4 researchers dissected otic vesicle enriched tissue as in Fig. 1D using two 22-gauge trabecular needles with syringes for handles. For each inDrops run, 40-50 embryos were dissected, and the tissue was collected in a coated collection tube. The DMEM was removed and 50 µl of Trypsin-EDTA was added. Avoiding air bubbles, the tissue was pipetted up and down several times with a 200 µl pipette tip. The tissue was left on ice to dissociate for 3 minutes for 36 hpf tissue, 5 minutes for 48 hpf tissue, or 7 minutes for 60 hpf tissue. We then added 100 µl of FACSMax, pipetted the sample up and down (avoiding air bubbles) and incubated on ice for 2 minutes.  While incubating, we rinsed out a BSA coated tube with PBS. We then added 850 µl of FACSmax to the dissociated cells and pipetted through a 40 µm cell filter into a rinsed BSA coated tube. The samples were spun for 3 minutes at 300g in a cooled swinging bucket centrifuge. Supernatant was removed and cells were resuspended in 1 ml of 0.5% BSA in chilled PBS. We then spun down the cells again for 3 minutes at 300g in a cooled swinging bucket centrifuge. Supernatant was removed and cells were resuspended in 200 µl of 1x prechilled PBS. Cells were counted using a hemocytometer, diluted to 800,000 cells/ml and then used to collect ~15,000 cells by inDrops. Dissection, dissociation, and cell collection was performed twice for each condition.
inDrops v3 scRNA-seq

value: ear / head region


title: Pool2: 40, 48, 60, and 72 hpf dissections for ear enrichment

description: Library name: Pool_2


title: P.involutus Vermiculite V3


title: CD7p_HSCs_fetal_DP8.2

value: fetal

value: 19 PCW


title: Pool1: 40, 48, 60, and 72 hpf dissections for ear enrichment

description: Library name: Pool_1


title: Plp1_Young_1_heart

value: Schwann cell


title: Plp1_Young_2_heart

value: tamoxifen


title: Sox10_Old_3_sciatic_nerve

value: sciatic nerve


title: 9637 (8, 1h Bic + 1h TTX)

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Base-calling was performed with bcl2fastq v2.20.0.422
Reads were aligned to the mouse reference genome (GRCm38 with the Ensembl genome annotation Release 94) using STAR 2.5.4b (parameters: --alignIntronMax 100000, --outSJfilterReads Unique, --outSAMmultNmax 1, --outFilterMismatchNoverLmax 0.04) (PMID: 23104886)
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 1.6.5 (multi-mapping or multi-overlapping reads were discarded, stranded mode was set to “–s 2”) (PMID: 24227677)
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file containing read counts per gene over all samples

source_name: Primary hippocampal neurons

growth_protocol: P0 primary hippocampal cultures in B27 and 1% rat serum. AraC was added on DIV3.

extract_protocol:
Quiagen Rneasy mini kit with on-column DNA digestion
The sequencing library was prepared with the NEBNext Ultra II directional RNA Library Preparation kit with NEBnext Multiplex oligos (New England Biolabs, Ipswich, USA, NEB #E7765). Samples were enriched for poly A RNA with the Poly A module. Sequencing was performed on the Illumina NextSeq 500 (Illumina, San Diego, USA) in single-end output (75 cycles)

treatment_protocol: Treatment on DIV10/11

value: 1h bicuculline [50µM] + 1h TTX [1µM]

tag: culture preparation


title: 9639 (8, 1h Bic + 1h TBOA)

value: 1h bicuculline [50µM] + 1h TBOA [50µM]


title: CD7p_HSCs_fetal_DP8.1


title: CD7p_HSCs_fetal_HP15.2


title: 117hi_CD7n_MPPs_fetal_HP8.2


title: 9635 (8, 0.5h Bic + 0.5h TTX)

value: 0.5h bicuculline [50µM] + 0.5h TTX [1µM]


title: CD7p_HSCs_fetal_HP15.1


title: 9636 (8, 0.5h Bic + 0.5h TTX & NMDA)

value: 0.5h bicuculline [50µM] + 0.5h TTX [1µM] and NMDA [30µM]


title: CD7n_HSCs_fetal_DP6.2


title: Sox10_Old_2_sciatic_nerve


title: Plp1_Young_3_heart

value: heart


title: 9633 (8, 1h Bic)

value: 1h bicuculline [50µM]


title: Sox10_Old_1_sciatic_nerve


title: 9632 (8, 0.5h Bic)

value: 0.5h bicuculline [50µM]


title: CD7n_HSCs_fetal_DP6.1


title: Sox10_Old_3_heart


title: 9630 (6, 1h Bic + 1h TBOA)


title: 9631 (8, Control)

value: no treatment


title: 9629 (6, 1h Bic + 1h TTX & NMDA)

value: 1h bicuculline [50µM] + 1h TTX [1µM] and NMDA [30µM]


title: 9628 (6, 1h Bic + 1h TTX)


title: Sox10_Old_2_heart


title: CD7n_HSCs_fetal_HP6.2


title: 9638 (8, 1h Bic + 1h TTX & NMDA)


title: P.involutus Vermiculite V4

value: grown with K-vermiculite


title: 9627 (6, 0.5h Bic + 0.5h TTX & NMDA)


title: 9626 (6, 0.5h Bic + 0.5h TTX)


title: Sox10_Old_1_heart


title: CD7n_HSCs_fetal_HP6.1

value: 20 PCW


title: 9625 (6, 2h Bic)

value: 2h bicuculline [50µM]


title: 9624 (6, 1h Bic)


title: Sox10_Young_3_sciatic_nerve


title: HSCs_old_EP12.2

source_name: HSCs

value: HSCs

value: old

value: 50 YPP


title: Sox10_Young_2_sciatic_nerve

value: Schwann cell

value: tamoxifen


title: 9621 (3, 1h Bic + 1h TBOA)


title: HSCs_old_EP12.1


title: 9619 (3, 1h Bic + 1h TTX)

value: 1h bicuculline [50µM] + 1h TTX [1µM]


title: Sox10_Young_1_sciatic_nerve

value: sciatic nerve


title: 9618 (3, 0.5h Bic + 0.5h TTX & NMDA)


title: 9623 (6, 0.5h Bic)


title: 9620 (3, 1h Bic + 1h TTX & NMDA)


title: 9617 (3, 0.5h Bic + 0.5h TTX)

value: 0.5h bicuculline [50µM] + 0.5h TTX [1µM]


title: 9622 (6, Control)


title: 9616 (3, 2h Bic)


title: Sox10_Young_3_heart


title: 9615 (3, 1h Bic)


title: 9634 (8, 2h Bic)


title: Sox10_Young_2_heart


title: Sox10_Young_1_heart


title: HSCs_old_CP12.2

value: 52 YPP


title: 9614 (3, 0.5h Bic)


title: HSCs_young_FP6.1

value: young

value: 32 YPP


title: Tau_NR4

city: Guangzhou

first: Lipeng

last: Mao

state: Guangdong

address: No.601, West Huangpu Avenue

department: Department of Microbiology and Immunology

institute: Jinan University

data_processing:
Accurately quantified the effective concentration of the library (finally, the effective concentration of the library should not be less than 2nM), and then performperformed on-machine sequencing. what to read the data
Use the software FastQC and trim galore to filter the raw data, remove adapters, remove N-containing reads, and remove low-quality reads (reads below Q20) to obtain clean data.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: brain tissue

growth_protocol: The hTau.P301S mouse strain was a generous gift from Michel Goedert’s laboratory (Cambridge, United Kingdom). The animal procedures were under the approval of the Jinan University Institutional Animal Care and Use Committee with standard maintenance and feed condition (IACUC-20190319-010).

extract_protocol:
Hippocampus tissue from Thy1-hTau.P301S mice was resuspended in Trizol and dispersed by shaking. Aliquots were separated by agarose gel electrophoresis to ascertain RNA integrity and purity. NanoPhotometer spectrophotometry and the Agligent 2100 bioanalyzer were also used to confirm purity and integrity of RNA samples, respectively.
RNA libraries for RNA-seq were prepared using Illumina's NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols

treatment_protocol: In this study, we treated 12-month-old WT and Tau P301S mice with either 6 mM NR in drinking water or vehicle water for three months. At the end of the treatment, the 15-month-old mice went through behavioral tests, including the Morris water maze, Y maze, novel object location (NOL), and novel object recognition (NOR). After completing the experiments, the mice were sacrificed under anesthesia, and tissue samples were collected for further analysis.

value: brain tissue

value: primary cell

value: hippocampus cell

value: Tau P301S

value: Tau P301S with 6mM NR in drinking water (3 months) hippocampus


title: 9613 (3, Control)

value: no treatment


title: HSCs_young_GP12

value: HSCs


title: 9612 (7, 1h Bic + 1h TBOA)

value: 1h bicuculline [50µM] + 1h TBOA [50µM]


title: CD127p_ELPs_rep11


title: Tau_NR3


title: 9611 (7, 1h Bic + 1h TTX & NMDA)

value: 1h bicuculline [50µM] + 1h TTX [1µM] and NMDA [30µM]


title: HSCs_young_FP6.2


title: 9609 (7, 0.5h Bic + 0.5h TTX & NMDA)

value: 0.5h bicuculline [50µM] + 0.5h TTX [1µM] and NMDA [30µM]


title: Tau4

value: Tau P301S hippocampus


title: 9607 (7, 2h Bic)

value: 2h bicuculline [50µM]


title: CD127p_ELPs_rep10


title: HSCs_old_CP12.1

value: old


title: Tau_NR2


title: CD127p_ELPs_rep6


title: 9606 (7, 1h Bic)

value: 1h bicuculline [50µM]


title: CD127p_ELPs_rep7


title: H9C2_HPLM_1_3

city: Salt Lake City

first: Jordan

middle: A

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

description: 150 x 150 cycle paired end sequencesequence

data_processing:
NovaSeq 150x150 bp Sequencing:  Sequencing libraries were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP workflow (20043131).  Following transfer of the flowcell to an Illumina NovaSeq 6000 instrument, a 150 x 150 cycle paired end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5 (20028312).
Single base mismatch
XPRESSpipe v0.6.3 was used to process sequence files, with the following command: xpresspipe peRNAseq ... -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --sjdbOverhang 150 --quantification_method htseq --remove_rrna. See supplementary files for XPRESSpipe dependencies and settings used.
Assembly: Ensembl rattus_norvegicus release-104
Supplementary files format and content: Tab-delimited text file - sample counts

organism: Rattus norvegicus

growth_protocol: DMEM or HPLM in 10% FBS and 1% Penicillin-Streptavidin.

extract_protocol:
Total RNA samples (5-500 ng) were hybridized with NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat) (E7400) to substantially diminish rRNA from the samples.
Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 5 nM in preparation for Illumina sequence analysis.

treatment_protocol: Grown for 1 hour in the presence or absence of lactate.

value: Cardiomyoblast

value: HPLM


title: H9C2_HPLM_1_2


title: H9C2_HPLM_lac_1_3

value: HPLM -lactate


title: H9C2_HPLM_lac_1_1


title: Tau3

value: brain tissue


title: Tau2

value: primary cell


title: Tau1

value: hippocampus cell


title: H9C2_HPLM_1_1


title: H9C2_HPLM_lac_1_2


title: 9605 (7, 0.5h Bic)

value: 0.5h bicuculline [50µM]


title: CD127p_ELPs_rep4


title: 9610 (7, 1h Bic + 1h TTX)

value: 1h bicuculline [50µM] + 1h TTX [1µM]


title: CD127p_ELPs_rep5


title: CD127p_ELPs_rep8


title: H9C2_DMEM_lac_1_2

value: DMEM +lactate


title: 9604 (7, Control)

value: no treatment


title: WT_NR4

value: WT

value: WT with 6mM NR in drinking water (3 months) hippocampus


title: WT_NR3


title: CD127p_ELPs_rep9


title: Tau_NR1

value: Tau P301S

value: Tau P301S with 6mM NR in drinking water (3 months) hippocampus


title: CD127p_ELPs_rep2


title: WT_NR2


title: 9603 (1, 1h Bic + 1h TBOA)

value: 1h bicuculline [50µM] + 1h TBOA [50µM]


title: CD127p_ELPs_rep1


title: 9608 (7, 0.5h Bic + 0.5h TTX)

value: 0.5h bicuculline [50µM] + 0.5h TTX [1µM]


title: H9C2_DMEM_lac_1_1


title: H9C2_DMEM_1_3

value: DMEM


title: 9602 (1, 1h Bic + 1h TTX & NMDA)

value: 1h bicuculline [50µM] + 1h TTX [1µM] and NMDA [30µM]


title: CD7p10p_MLPs_rep8


title: 9601 (1, 1h Bic + 1h TTX)


title: H9C2_DMEM_1_1

value: Cardiomyoblast


title: H9C2_DMEM_lac_1_3


title: WT_NR1


title: 14 weeks, three biological replicate pool, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Single cell data was further processed with Seurat, version 2.3.4
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: the spinal cord organoid

growth_protocol: A new method to create a human spinal cord organoid.

extract_protocol:
Dissociated single organoid cells were encapsulated into oil droplet that contained barcoded beads, single cell, primers and enzymes by Chromium controller. Barcoded mRNAs from each cell were reverse transcribed and isolated
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).  Chromium Single Cell v2 Reagent Kit and Controller (10X Genomics, Pleasanton, CA, USA)

value: the spinal cord organoid

value: Human iPSCs 18a

value: Spinal cord organoid cells

value: Healthy control [PMID:21293464]


title: WT4

value: brain tissue

value: primary cell

value: hippocampus cell

value: WT hippocampus


title: CD7p10p_MLPs_rep9


title: WT2

value: WT


title: 9600 (1, 0.5h Bic + 0.5h TTX & NMDA)

value: 0.5h bicuculline [50µM] + 0.5h TTX [1µM] and NMDA [30µM]


title: 9598 (1, 2h Bic)

value: 2h bicuculline [50µM]


title: CD7p10p_MLPs_rep7


title: 9599 (1, 0.5h Bic + 0.5h TTX)


title: 5 weeks, three biological replicate pool, scRNAseq

description: 10x Genomics


title: 28 weeks, three biological replicate pool, scRNAseq

description: 10x Genomics


title: WT3


title: CD7p10p_MLPs_rep6


title: WT1


title: CD127p_ELPs_rep3


title: 20 weeks, three biological replicate pool, scRNAseq

description: 10x Genomics


title: 9597 (1, 1h Bic)

value: 1h bicuculline [50µM]


title: H9C2_DMEM_1_2


title: 9596 (1, 0.5h Bic)

value: 0.5h bicuculline [50µM]


title: CD7p10p_MLPs_rep5


title: Primary Culture Pericytes , TGFB-1 Treated, 8

city: Badalona

first: ANE

middle: MARTINEZ

last: LARRINAGA

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

department: Genesis of Cancer

country: Spain

institute: Institut de Recerca contra la Leucèmia Josep Carreras

data_processing:
For the RNA-seq data processing, reads were aligned to the mouse reference genome (mm10) using STAR (version_2.7.5c) in two-pass mode following STAR best practices and recommendations (46). The quality of the data was evaluated using STAR (v 2.7.5c) and samtools (version 1.15) . PCR duplicates were removed from aligned bam files using samtools (version 1.15) . Read counts were extracted from the aligned bam files using subread’s FeatureCounts (v 2.0.3) .
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Brain

extract_protocol:
RNA was extracted using Maxwell® RSC simplyRNA cell kit (Promega, AS1390).
Illumina-stranded-total-rna-prep-reference-guide-1000000124514-02

value: Brain

value: Primary culture

value: Pericytes cells


title: LPS3

city: Ann Arbor

first: Vinitha

last: Jacob

state: MI

address: 8200 Medical Science Research Building III,  III, 1153 West Medical Center Drive

institute: University of Michigan

data_processing:
FASTQ quality checks and reference genome alignment (HISAT2 software / GRCz11 - danRer11 genome assembly) steps were performed by Novogene Co. Ltd
featureCounts package was utilized for the unstranded data with a gene-based GFF feature type filter to obtain raw hit counts from the alignment files (bam) in the Galaxy platform (Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W345–W351, doi:10.1093/nar/gkac247)
Deseq2 analyses were performed in processing the count data and performing statistical analyses between the groups
Assembly: GRCz11 - danRer11
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: xlsx file contains processed count data and statistical analyses for each Sample

source_name: Whole organism

growth_protocol: 3 days post fertilization (dpf) zebrafish embryos were used.

extract_protocol: RNAseq library preparation (NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB,USA)) was performed by Novogene Co. Ltd

treatment_protocol: 3 dpf zebrafish embryos were incubated with either 40 ug/mL LPS or untreated (controls).  3 hours post treatment, 15-45 embryos per condition were collected for RNA-seq.

value: Whole organism

value: 3 dpf

value: ABTL

value: LPS


title: Primary Culture Pericytes , TGFB-1 Treated, 7


title: CD7p10p_MLPs_rep4


title: LPS2


title: Primary Culture Pericytes , TGFB-1 Treated, 6


title: WT-individual-4

city: nanjing

first: Juanhan

last: Liu

state: jiangsu

address: Medical School of Nanjing University

institute: nanjing university

description:
Library name: WT4
paired-end 250bp

data_processing:
CLC Genomics Workbench v 11.0.1Sequence reads were trimmed for adaptor sequences and low-quality sequences using CLC Genomics Workbench (parameter: Quality limit: 0.05)Trimmed sequence reads were mapped to the GRCm38/mm10 reference genome using CLC Genomics Workbench (parameters: mismatch cost: 2; insertion cost: 3; deletion cost: 3; length fraction: 0.8; similarity fraction: 0.8)Read count extraction and normalization were performed using CLC Genomics Workbenchmm10
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sampleCSV files include ASV_table for each sample

source_name: colon

growth_protocol: Wild-type (WT) and MERTK knockout (MERTK⁻/⁻) mice with C57BL/6J background were housed in a specific pathogen-free (SPF) animal facility under controlled conditions: temperature 22±2℃, humidity 50±10%, 12-hour light/dark cycle (7:00-19:00 light), with free access to standard rodent chow and sterile water. Mice were used for experiments at 8-10 weeks of age (body weight 20-25g).

extract_protocol:
Colonic tissue samples were rinsed with RNase-free PBS to remove fecal residues, minced, and homogenized in TRIzol reagent , followed by 5 minutes of incubation at room temperature. Chloroform was added for extraction according to the reagent instructions, and the upper aqueous phase was collected after centrifugation. Total RNA was purified using the RNeasy Mini Plus Kit, including a gDNA elimination step.
1 μg of high-quality total RNA was used for library construction, following the manufacturer's protocol of the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB): mRNA was enriched using Oligo(dT) magnetic beads, fragmented (200-300 bp), reverse-transcribed into cDNA, subjected to end repair, A-tailing, and adapter ligation, followed by PCR amplification (12 cycles).

treatment_protocol: Control group: WT and MERTK⁻/⁻ mice were given sterile drinking water ad libitum for 7 days. DSS-induced group: WT and MERTK⁻/⁻ mice were given sterile drinking water containing 2.5% (w/v) dextran sulfate sodium (DSS, molecular weight 36-50 kDa) ad libitum for 7 days to induce colonic inflammation. Mice were monitored daily for general status (body weight, diarrhea, and bloody stool) during the experiment. On day 8, mice were euthanized, and distal colon tissues (2-3 cm from the anus) were collected for RNA extraction.

value: colon

value: Day 8


title: CD7p10p_MLPs_rep2

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Human reference transcriptome from the UCSC website (release hg38) using BWA version 0.7.4.4  was used to align the second reads
Assembly: hg38
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 28,307 genes detected.

extract_protocol:
no extraction_cell lysates
Cachiarelli et al. (Cell 162:412, 2015)


title: CD7p10p_MLPs_rep3


title: Control3


title: Control2


title: Primary Culture Pericytes , TGFB-1 Treated, 5


title: WT-individual-2

description:
Library name: WT2
paired-end 250bp


title: LPS1


title: CD7p10p_MLPs_rep1


title: CD7n10p_MLPs_rep9


title: Control1


title: Primary Culture Pericytes , Vehicle, 3


title: WT-individual-3

description:
Library name: WT3
paired-end 250bp


title: Primary Culture Pericytes , Vehicle, 2


title: WT+DSS-individual-4

description:
Library name: WD4
paired-end 250bp


title: AGO2-WT_IP_rep5

description: Library name: WtP5

data_processing:
OASIS 2.0 miRNA pipline (Rahman et al., 2018)
Assembly: miRBase v21
Supplementary files format and content: miRNA_counts_raw.txt: Tab separated value file of raw miRNA counts
Supplementary files format and content: miRNA_counts_norm.txt: Tab separated value file of normalized miRNA counts

source_name: Primary mouse cortical neurons

extract_protocol:
miRNeasy Micro Kit (Qiagen)
TruSeq Small RNA Library Prep Kit (Illumina)

value: Primary mouse cortical neurons

value: AAV EGFP-AGO2-WT

tag: sample type

value: EGFP-IP


title: WT-individual-1

description:
Library name: WT1
paired-end 250bp


title: CD7n10p_MLPs_rep7


title: CD7n10p_MLPs_rep8


title: Primary Culture Pericytes , Vehicle, 1

value: WT


title: Sample_KO2

city: Kansas City

first: Ning

last: Wang

address: 3901 Rainbow Boulevard, Kansas City, KS

institute: UNIVERSITY OF KANSAS MEDICAL CENT

data_processing:
The read quality was assessed with FastQC software.
The reads were mapped to the mouse genome (Mus musculus GRCm39; Ensembl release 105) by using STAR software, version 2.6.1c.
Transcript abundance estimates were calculated using the featureCounts software.
Expression normalization and differential gene expression calculations were performed in DESeq2 software.
Assembly: GRCm39.
Supplementary files format and content: tab delimited text file containing raw read counts

source_name: brain

extract_protocol:
RNA isolation was performed using the TRIzol-chloroform method (Thermo Fisher Scientific, Cat. No. 15596018).
Bulk mRNA sequencing was conducted at the University of Kansas Medical Center – Genomics Core, utilizing the Illumina NovaSeq 6000 Sequencing System. The process began with a quality control step, where RNA samples were assessed using the TapeStation 4200 equipped with RNA ScreenTape from Agilent Technologies. Library preparation involved 500 ng of total RNA, which was processed to isolate mRNA through oligo dT bead capture. This mRNA was then fragmented and reverse transcribed into cDNA. The cDNA underwent end repair, ligation with Unique Dual Index (UDI) adaptors, strand-specific selection, and PCR amplification using the Universal Plus mRNA-seq with UDI preparation kit from Tecan Genomics.
Following the preparation, library validation was conducted using DNA 1000 ScreenTape on the TapeStation 4200 to assess the  quality and size of the libraries. The concentration of each library was quantified using the NuQuant method on a Qubit 4 Fluorometer, and libraries were normalized and pooled to a concentration of 6nM. This pool was further validated and adjusted to a final concentration of 1.9nM for sequencing, using the Roche LightCycler96 with FastStart Essential DNA Green Master and KAPA Library Quant DNA Standards. For sequencing, pooled libraries were denatured, neutralized, and diluted before being loaded onto the NovaSeq 6000. A sequencing cycle of 2x101, with additional cycles for indexing, was performed using the S1 Reagent Kit. Post-sequencing, data were converted to fastq format using bcl2fastq, de-multiplexed, and made available for downstream analysis via secure FTP or Illumina BaseSpace.

value: brain


title: WT+DSS-individual-3

description:
Library name: WD3
paired-end 250bp


title: CD7n10p_MLPs_rep6


title: AGO2-WT_IP_rep4

description: Library name: WtP4


title: 9595 (1, Control)

value: no treatment


title: WT+DSS-individual-2

description:
Library name: WD2
paired-end 250bp


title: AGO2-WT_IP_rep3

description: Library name: WtP3


title: Sample_KO1


title: Primary Culture Pericytes , Vehicle, 4


title: WT+DSS-individual-1

description:
Library name: WD1
paired-end 250bp


title: AGO2-WT_IP_rep2

description: Library name: WtP2


title: Sample_WT2

value: Wild-type


title: CD7n10p_MLPs_rep5


title: MERTK-KO+DSS-individual-4

description:
Library name: MKD4
paired-end 250bp


title: CD7n10p_MLPs_rep4


title: CD7n10p_MLPs_rep3


title: MERTK-KO+DSS-individual-3

description:
Library name: MKD3
paired-end 250bp


title: AGO2-WT_IP_rep1

description: Library name: WtP1


title: MERTK-KO+DSS-individual-2

description:
Library name: MKD2
paired-end 250bp


title: Sample_WT1


title: AGO2-WT_input_rep3

description: Library name: WtN3

value: input


title: CD7n10p_MLPs_rep2


title: CD7n10p_MLPs_rep1


title: Pdgfbret/ret, replicate 4, scRNAseq

city: Lund

first: Kristian

last: Pietras

address: Sheelevägen 2

department: Division of Translational Cancer Research

country: Sweden

institute: Lund University

data_processing:
The raw reads were processed, mapped, and quantified using Cell Ranger count (v6.1.2) with default settings, with an initial expected cell count of 10,000.
We used DoubletFinder (v2.0.3) to filter out "doublets" assuming a doublet formation rate of 7.5%. pN=0.25 and pK were adjusted for each sample using pN-pK parameter sweeps and meanvariance- normalized bimodality coefficient (BCmvn) using paramSweep_v3.
We used DecontX to filter out barcodes that had more than 25% of reads identified as ambient RNA contamination.
Further quality control was perfored using Seurat (v4.0.3). The seurat (rds) object provided contains only cells that had a total number of transcripts lower than 50,000, number of features larger than 250 and lower than 8000, and percentage of mitochondrial and ribosomal genes lower than 10% and 25%, respectively.  We filtered out mitochondrial and hemoglobin genes, as well as features with less than 20 counts across cells.
Assembly: mm10 modified mouse reference genome that contained the RCAS-PDGFB longest possible sequence following Cell Ranger instructions.
Supplementary files format and content: barcodes.tsv.gz:  Cell Ranger's filtered tab-separated barcodes file
Supplementary files format and content: features.tsv.gz:  Cell Ranger's filtered tab-separated gene IDs file
Supplementary files format and content: matrix.mtx.gz:  Cell Ranger's filtered counts matrix
Supplementary files format and content: Braun_2024_scRNAseq_seurat.rds: seurat object containing all samples including only cells and features that passed filtering criteria and were used in downstream analyses.

source_name: brain tumor

extract_protocol:
Whole tumors were minced into smaller slices with a scalpel and incubated for 30 min with the supplier’s enzyme mixes, while being heated at 37°C and mechanically grinded in the gentle MACS Octo Dissociater with Heaters (Miltenyi). Samples were resuspended and applied to a 70 μm MACS SmartStrainer (Miltenyi), after which the single cell suspension underwent subsequent steps for debris removal and lysis of erythrocytes. For library preparation, 18,000 cells / 45 μl in 0.04% BSA.
Singlecell 3´ RNA-seq libraries were prepared using 10x Chromium system (v3.1). Samples were run using Read 1 28 cycles, i7 index 5 cycles, i5 index 0 cycles, Read 2 91 cycles on the Illumina NovaSeq 6000 to a depth of 50,000 reads/cell. This was performed in two different batches (time points). The first batch (batch1) included 3 samples, while the second batch (batch2) included 8 samples.

value: brain tumor

value: Ntv-a, Pdgfbrret/ret

value: batch 2


title: Pdgfbret/+, replicate 7, scRNAseq

value: Ntv-a, Pdgfbrret/+


title: Pdgfbret/ret, replicate 3, scRNAseq


title: AGO2-WT_input_rep4

description: Library name: WtN4


title: AGO2-WT_input_rep2

description: Library name: WtN2


title: MERTK-KO-individual-3

description:
Library name: MK3
paired-end 250bp


title: CD7p_MLPs_rep8


title: MERTK-KO-individual-4

description:
Library name: MK4
paired-end 250bp


title: MERTK-KO+DSS-individual-1

description:
Library name: MKD1
paired-end 250bp


title: CD7p_MLPs_rep9


title: AGO2-WT_input_rep5

description: Library name: WtN5


title: AGO2-WT_input_rep1

description: Library name: WtN1


title: Pdgfbret/ret, replicate 2, scRNAseq


title: MERTK-KO-individual-2

description:
Library name: MK2
paired-end 250bp


title: Pdgfbret/+, replicate 6, scRNAseq


title: CD7p_MLPs_rep7


title: AGO2-L192P_IP_rep4

description: Library name: MutP4

value: AAV EGFP-AGO2-L192P


title: CD7p_MLPs_rep6


title: MERTK-KO-individual-1

description:
Library name: MK1
paired-end 250bp


title: AGO2-L192P_IP_rep3

description: Library name: MutP3


title: Pdgfbret/+, replicate 4, scRNAseq


title: CD7p_MLPs_rep5


title: AGO2-L192P_IP_rep2

description: Library name: MutP2