title: EVs  from plasma of Dicer cKO mice; 8 w old;2

description: Library name: cKO_2

data_processing:
The raw data were processed using an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexities, common RNA families (rRNA, tRNA, snRNA, snoRNA) (http://rfam.sanger.ac.uk/), repeats (http://www.girinst.org/repbase), and sequences <18 nt or >26 nt in length.
The unique sequences that aligned to the known miRNAs sequences in miRBase 22.0 were identified as known miRNA. Secondary structure of pre-miRNAs was presented as a hairpin, including 5p- and 3p- derived miRNA. The unique sequences mapping to the other arm of the pre-miRNAs sequences, which were not annotated in the miRBase 22.0, were considered to be 5p- or 3p- derived miRNA candidates.
The remaining unmapped sequences were matched to the Mus musculus genomic sequences in search of candidate novel miRNAs. To identify the results of putative miRNAs in Mus musculus, all the obtained miRNAs were used to predict the secondary structures using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi).
Known miRNAs were identified by comparison to the miRBase 20.0 database. Data analysis was performed by using ACGT101-miR (LC Sciences).
Assembly: Ensembl/v101
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: plasma

extract_protocol:
The purification of total exosome-derived RNA was carried out by the exoRNeasy Maxi Kit (Qiagen).
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing (1x50bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.

value: plasma

value: osteocyte-specific

value: Dicer cKO


title: Arabidopsis, hira-1,fas2-4_FAS2_3xFlag, 12DAG, Rep1

status: Public on Apr 12 2025

type: SRA

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

country: China

institute: Northwest A&F University

description: Library name: 12DAG_hira-1,fas2-4_FAS2_3xFlag_Rep1,ChIP

library_source: genomic

data_processing:
ChIP-seq reads were trimmed using the fastp tool (version 0.23.4)  with a quality score threshold of 20 for the final base.Reads shorter than 35 bp after trimming were discarded.
The clean reads were aligned to the TAIR 10 genome(https://www.arabidopsis.org/) using Bowtie2 with default parameters.
To create ChIP-Seq coverage plots,the locations of the mapped ChIP-Seq reads were extended to the ChIP length form Cross-Correlation analysis, RPGC (reads per genome coverage) normalized and reformatted in the BigWig file format.
Peaks were identified utilizing the 'callpeak' function of MACS2 (version 3.0.1).
Assembly: TAIR 10
Supplementary files format and content: BigWig files were generated by using the Deeptools  (version 3.5.2).The BigWig files for making plot were  assessed by merging results from 'bigwigcompare' of two independent biological replicates, employing the 'mean' operation.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 12DAG seedling

growth_protocol: Plants were grown on GM in a growth chamber under long-day conditions supplemented with 1% sucrose under long-day photoperiod and ~21°C. Seeds were stratified for 4 days at 4°C, and seedlings were harvested 12 days after germination.

extract_protocol:
Tissue was fixed with 1% formaldehyde for 12mins and stopped by adding glycine to a final concentration of 0.125M and incubating for 6 extra mins.After nuclear lysis,chromatin was sonicated using using Bioruptor® Pico with the following conditions: 14 cycles,10 sec ON/30 sec OFF at 4°C.
ChIP-Seq libraries were prepared using Ovation® Ultralow System V2 Library Preparation Kit (PART NO. 0344, 0344NB).

tag: tissue

value: 12DAG seedling

tag: chip antibody

value: Flag antibody (Sigma, F3165)

tag: genotype


title: EVs  from osteocyte-enriched subchondral bone; low stress area;2

city: Nanjing

last: Liu

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University

description: Library name: FEI_2

library_source: transcriptomic

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw dataswere calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
For the samples with biological replicates:Differential expression analysis of two conditions/groups was performed using the DESeq R package (3.0.3). The P-values was adjusted using the Benjamini& Hochberg method. Corrected P value of 0.05 was set as the threshold for significantly differential expression by default.
Assembly: homo_sapiens_Ensembl_97
Supplementary files format and content: tab-delimited file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: osteocyte-enriched subchondral bone

extract_protocol:
The purification of total exosome-derived RNA was carried out by the exoRNeasy Maxi Kit (Qiagen).
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: osteocyte-enriched subchondral bone

tag: cell line

tag: cell type

tag: treatment

value: low stress area


title: Arabidopsis, fas2-4_FAS2_3xFlag, 12DAG, Rep2

description: Library name: 12DAG_fas2-4_FAS2_3xFlag_Rep2,ChIP


title: Arabidopsis, Columbia-0, 12DAG, Group2, Rep3

description:
Library name: 12DAG_Columbia-0_Group2_R3
Control

data_processing:
Paired-end reads were subjected to filtering and trimming using the fastp tool (version 0.23.4).
The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using HISAT2 (VERSION 2.2.1).
Quantification was performed with Rsubread package (version 2.12.0) and normalized using TPM (Transcripts Per Kilobase of exon model per Million mapped reads).
Assembly: TAIR 10
Supplementary files format and content: Tab-delimited text includes raw counts for each sample.
Supplementary files format and content: Txt files include TPM values for each sample.

growth_protocol: Plants were grown on soil mixture in a growth chamber under long-day conditions at ~21°C.  seeds were stratified for 4 days at 4°C, and seedlings were harvested 12 days after germination.

extract_protocol:
total RNA was extracted by using RNA extraction  columns (Axygen, UE-MN-MS-RNA-250) following the manufacturer’s instructions.
RNA-Seq libraries  were constructed by BGI company.


title: sRNA-seq-colov2_for_rem8ov

city: Los Angeles

first: Steven

middle: E.

last: Jacobsen

state: CA

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

description: Library name: GSM102

data_processing:
Adaptor sequence (TGGAATTCTCGG) of small RNA-seq reads were trimmed with trim_galore, and trimmed reads were mapped to the reference genome TAIR10 using Bowtie2 with only one unique hit and zero mismatches. sRNA reads that mapped to chloroplast, mitochondrial DNA, tRNA, rRNA, small nucleolar RNAs (snoRNAs), and small nuclear RNAs (snRNAs) were removed using bedtools (v2.26.0). The deeptools version 3.1.3 was used to generate Bigwig tracks. The bamCoverage of deeptools version 3.1.3 was used to normalize the data with RPKM57.
Assembly: tair10
Supplementary files format and content: bigwig

source_name: unfertilized ovules (Ov)

extract_protocol:
Pistils and anther (stage 9 or younger) of each genotype were collected and ground into fine powder with liquid nitrogen. Total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo) according to the manufacturer’s instructions. Two micrograms of total RNA were mixed with equal volume of the 2x RNA loading dye, denatured at 65◦C for 10 min and immediately chilled on ice. Denatured total RNA was separated on 15% TBE urea gel (Invitrogen) and small RNAs from 15-30 nts were excised. The excised gel pieces were mashed by pestles. Small RNA was eluted with 400 uL nuclease-free water at 70◦C for 10 mins and then precipitated with ethanol.
Small RNA libraries were made using NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible) according to the manufacturer’s instructions

value: unfertilized ovules (Ov)

tag: ecotype

value: WT


title: EVs  from plasma of Dicer cKO mice; 8 w old;1

description: Library name: cKO_1

organism: Mus musculus


title: sRNA-seq-colov1_for_rem8ov

description: Library name: GSM101


title: DAPseq_VDD-VAL-GDE1

description: Library name: GSM100

source_name: floral tissue

value: floral tissue


title: Arabidopsis, Columbia-0, 12DAG, Group2, Rep2

description:
Library name: 12DAG_Columbia-0_Group2_R2
Control


title: EVs  from plasma of Dicer WT mice; 8 w old;2

description: Library name: WT_2


title: DAPseq_GUS

description: Library name: GSM99


title: Arabidopsis, Columbia-0, 12DAG, Group2, Rep1

description:
Library name: 12DAG_Columbia-0_Group2_R1
Control


title: EVs  from plasma of Dicer WT mice; 8 w old;1

description: Library name: WT_1


title: Arabidopsis, fas2-4_FAS2_3xFlag, 12DAG, Rep1

description: Library name: 12DAG_fas2-4_FAS2_3xFlag_Rep1,ChIP


title: purified CD8+T cells a4-1BB 4

status: Public on Apr 11 2025

city: CHICAGO

first: Bin

last: Zhang

state: IL

address: 300 E Superior St, Tarry 4-726

institute: Northwestern University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.7 and normalized by CPM
Assembly: mm10
Supplementary files format and content: peak score from every gene and every sample
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: CD8+ T cells

growth_protocol: Purified CD8+ T cells were cultured with the anti-CD3/28 for 4 days

extract_protocol:
Purified CD8+ T cells were stored in single cell suspension in Trizol and RNA was harvested using Direct-zol RNA kit Buffer and DNA was harvested using Active motif ATAC-seq kit.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: purified CD8+ T cells were treated with a4-1BB

value: CD8+ T cells


title: Human GBM 1B, Visium

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Rnger pipeline to generate FSATQ files
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barodes
Supplementary files format and content: features.tsv.gz: kist of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligend_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_potitions_list.csv.gz: list of spatial barcode and the coordinates specifying spots
Library strategy: Spatial Transcriptome

source_name: brain

extract_protocol:
Tissues were Formalin-Fixed Paraffin-Embedded, and 5µm sections were cut with microtome
Spatial transcriptome sequencing librarys were prepared with 10xGenomics Visium CytAssist Spatial Gene Expression Reagent Kits according to manufacture's construction

value: brain


title: purified CD8+T cells a4-1BB 1


title: Human GBM 1A, Visium

description: FFPE Spatial transcriptome sequencing


title: purified CD8+T cells control 3


title: purified CD8+T cells a4-1BB 3


title: purified CD8+T cells control 2


title: purified CD8+T cells control 4


title: Arabidopsis, fas2-4, 12DAG, Group2, Rep1

description:
Library name: 12DAG_fas2-4_Group2_R1
Treatment


title: purified CD8+T cells control 1


title: purified CD8+T cells a4-1BB 2


title: FL_NUP98-NSD1/WT1ko_edited CD34+HSPC scATAC

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: NUP98_NSD1_WT1ko_FL_ATAC

library_source: genomic single cell

data_processing:
The FASTQ files from chromatin accessibility data were processed to generate the cell-by-gene count matrix with CellRanger v.5.0.1 using default parameters, with GRCh38 as the human genome reference. The data were filtered to retain cells with at least 3,000 peaks detected, a minimum of 50% of reads in peaks, nucleosome signal below 4 and TSS enrichment score above 3
Dimensionality reduction was performed in Seurat (v.5.1.0) applying term frequency-inverse document frequency (TF-IDF) followed by single value decomposition for latent semantic indexing (LSI). For graphical representation, dimensions were further reduced via UMAP, removing the first LSI dimension which showed a high correlation (> 0.5) with sequencing depth.
Cell types were assigned based on gene activity scores as calculated by the GeneActivity function from Seurat (v.5.1.0) and concordance with the labels assigned via bridge dictionary mapping.
Transcription factor motif accessibility was calculated via chromVar
Genotyping FASTQ files were processed with the Gotcha R package (v.1.0), using wild-type and NUP98-NSD1 fusion sequences for perfect match.
Genotype calls were included in Seurat object metadata for downstream analysis
Differential analysis was performed via differential linear mixture models using the DiffLMM function from Gotcha (v.1.0)
Assembly: hg38 (GRCh38)
Supplementary files format and content: barcodes.tsv: a tab-delimited text files include list of cell-barcodes; peaks.bed: a tab-delimited text file include list of peaks and matrix.mtx: file in a sparse matrix format containing raw counts per peak per cell-barcode; fragments.tsv: A tab-delimited text file containing information about sequencing fragments, including chromosome, start and end positions, cell barcode, and read count

source_name: Human fetal liver derived CD34+ HSPC

growth_protocol: Cell were cultured in in X-VIVO 10 medium, supplemented with 1% BSA and FLT3L, G-CSF, SCF, TPO and IL-6.

extract_protocol:
Nuclei isolation procedure is the same as scATAC-seq, and the isolated nuclei were processed according to the Chromium Next GEM Single Cell ATAC Solution User Guide (version CG000209 Rev F, 10x Genomics) with some modifications: During the GEM generation and barcoding reaction, GoT-Cha primer mix was added to the barcoding mixture. During the post-GEM incubation clean-up, 45.5 µl of Elution Solution I was used to elute material from SPRIselect beads. A total of 5 µl was used for GoT-ChA library construction, and the remaining 40 µl was used for ATAC library construction as per the standard protocol.
Two additional PCR reactions were performed for GoT-Cha library construction. The first PCR amplifies genotyping fragments before sample indexing. After a 1.2 x SPRIselect cleanup, biotinylated PCR products were bound using Dynabeads M-280 Streptavidin magnetic beads (Thermo Fisher) at room temperature for 15 minutes. The beads were washed twice with 1x SSPE buffer and once with 10 mM Tris-HCl (pH 8.0) before resuspending in water. The bead-bound fragments were amplified and indexed using P5 and P7 primers. The final libraries were quantified using a High-Sensitivity DNA Chip (Agilent Technologies) run on a Bioanalyzer 2100 system.

treatment_protocol: No treatment.

value: Human fetal liver derived CD34+ HSPC

value: NUP98-NSD1/WT1ko, Wild type


title: CB_NUP98-NSD1/WT1ko_edited CD34+HSPC scATAC

description: Library name: NUP98_NSD1_WT1ko_CB_ATAC

source_name: Human cord blood derived CD34+ HSPC

value: Human cord blood derived CD34+ HSPC


title: CB_NUP98-NSD1/WT1ko_edited CD34+HSPC GoT-ChA

description: Library name: NUP98_NSD1_WT1ko_CB_GOTCHA


title: FL_NUP98-NSD1/WT1ko_edited CD34+HSPC GoT-ChA

description: Library name: NUP98_NSD1_WT1ko_FL_GOTCHA


title: Human CD45+ sorted from FL_NUP98-NSD1/WT1ko_derived xenograft cells_rep3

description: Library name: NUP98_NSD1_WT1ko_FL_rep3

data_processing:
Sequenced FASTQ files were aligned, filtered, barcoded and UMI counted using Cell Ranger ARC version 2.0.0, by 10X Genomics, with the hg38 human genome reference. Peaks were called using ‘CallPeaks’, the MACS2 wrapper function, in Signac (v1.3.0).
Cells were filtered to retain only those with total number of fragments in peaks > 1000 and < 50000, percentage of reads aligned in peak regions > 20%, blacklist ratio < 0.002, nucleosome signal < 1.5 and the TSS enrichment score > 2.
Blacklist ratio is calculated as the number of reads aligned to blacklist region divided by the total number of reads, nucleosome signal was calculated by ‘NucleosomeSignal’ function in Signac and TSS enrichment score was calculated by ‘TSSEnrichment’.
Latent semantic indexing (LSI) was then applied to the top 95% of peaks in terms of their variability, which combines the term frequency-inverse document frequency (TFIDF) used for normalization and singular-value decomposition (SVD) used for dimensional reduction.
The first LSI component was excluded from all downstream analysis as it highly correlated with sequencing depth. De-novo clustering was performed by using ‘FindNeighbors’ and FindClusters functions in Signac. Motif position frequency matrices were retrieved from JASPAR 2020 database and was added to the scATAC data in Signac.
ChromVAR motif analysis was performed using the RunChromVAR function in Signac, and results of selected transcription factor were visualized on UMAP using FeaturePlot function.
Gene activity scores were computed using the GeneActivity function of Signac by aggregating the accessibility of genomic regions within a gene body and promoter (2 kb upstream of the transcription start site).
Assembly: hg38 (GRCh38)
Supplementary files format and content: barcodes.tsv: a tab-delimited text files include list of cell-barcodes; peaks.bed: a tab-delimited text file include list of peaks and matrix.mtx: file in a sparse matrix format containing raw counts per peak per cell-barcode; fragments.tsv: A tab-delimited text file containing information about sequencing fragments, including chromosome, start and end positions, cell barcode, and read count
Supplementary files format and content: scatac_integrated.rds: This file contains the integrated single-cell ATAC-seq dataset, stored as an RDS object.

growth_protocol: Cells were xenotransplanted in NSG mice for 10-16 weeks.

extract_protocol:
Xenografted cell were isolated from bone marrow. Human cells were enriched using mouse depletion kit (Miltenyi Biotec) and human CD45+ cells were sorted by flow cytometry (BD FACSMelody). On average, 3-5x10^5 cells per sample was submitted for scRNA-seq (10x Genomics Chromium Next GEM Single Cell ATAC Reagent Kit v1.1).
Viability of single cells was assessed using Acridine Orange/Propidium Iodide viability staining reagent (Nexcelom), and debris-free suspensions of >80% viability were deemed suitable for experiments. The 10x Genomics Chromium Next GEM Single Cell ATAC Reagent Kit v1.1 was used for scATAC-seq.

treatment_protocol: No treatment

value: Human CD45+ cells


title: Human CD45+ sorted from FL_OR2W5ko_derived xenograft cells_rep2

description: Library name: Primary_OR_FL_rep2

value: Control


title: Human CD45+ sorted from FL_NUP98-NSD1_derived xenograft cells_rep1

description: Library name: NUP98_NSD1_FL_rep1


title: Human CD45+ sorted from FL_NUP98-NSD1/WT1ko_derived xenograft cells_rep4

description: Library name: NUP98_NSD1_WT1ko_FL_rep4


title: Human CD45+ sorted from FL_NUP98-NSD1/WT1ko_derived xenograft cells_rep2

description: Library name: NUP98_NSD1_WT1ko_FL_rep2


title: Human CD45+ sorted from FL_NUP98-NSD1/WT1ko_derived xenograft cells_rep1

description: Library name: NUP98_NSD1_WT1ko_FL_rep1


title: Human CD45+ sorted from FL_OR2W5ko_derived xenograft cells_rep1

description: Library name: Primary_OR_FL_rep1


title: Human CD45+ sorted from Ara-C treated FL_NUP98-NSD1/WT1ko_derived xenograft cells

description:
Library name: AraC_treated
10X Genomics

library_source: transcriptomic single cell

data_processing:
Sequenced FASTQ files were aligned, filtered, barcoded, and UMI-counted using Cell Ranger Chromium Single Cell RNA-seq v7.1.0  and v5.0.1 (10X Genomics) with the hg38 human genome reference.
Cells were filtered to retain those with ≥1000 UMIs, ≥400 expressed genes, and <15% of reads mapping to the mitochondrial genome.
UMI counts were normalized to a total of 10,000 UMIs per cell and log-transformed with a pseudocount of 1 using the “LogNormalize” function in the Seurat package (v4.0.3)
The top 2000 highly variable genes were identified with the “vst” method in the “FindVariableFeatures” function, and the data were scaled using the “ScaleData” function.
Principal component analysis was performed using the top 2000 highly variable features (“RunPCA” function) and the top 30 principal components were used in the downstream analysis.
K-Nearest Neighbor graphs were obtained by using the “FindNeighbors” function whereas the UMAPs were obtained by the “RunUMAP” function. The Louvain algorithm was used to cluster cells based on expression similarity.
Differential markers for each cluster were identified using the Wilcox test (“FindAllMarkers” function) with adjusted p-value < 0.01, absolute log2 fold change > 0.25, and minimum 10% of cells expressing the gene in both comparison groups using 1000 random cells to represent each cluster. T
Assembly: hg38 (GRCh38)
Supplementary files format and content: barcodes.tsv: A tab-delimited text file containing a list of cell barcodes; genes.tsv: A tab-delimited text file containing gene annotations, including gene IDs and gene names; matrix.mtx: A file in sparse matrix format containing raw counts per gene per cell barcode
Supplementary files format and content: scrna_integrated.rds: This file contains the integrated single-cell RNA-seq dataset, stored as an RDS object.

extract_protocol:
Xenografted cell were isolated from bone marrow. Human cells were enriched using mouse depletion kit (Miltenyi Biotec) and human CD45+ cells were sorted by flow cytometry (BD FACSMelody). On average, 3-5x10^5 cells per sample was submitted for scRNA-seq (Chromium 10x Genomics 5' GEX v2).
Viability of single cells was assessed using Acridine Orange/Propidium Iodide viability staining reagent (Nexcelom), and debris-free suspensions of >80% viability were deemed suitable for experiments. The Chromium 10x Genomics 5' GEX v2 protocol was used for scRNA-seq

treatment_protocol: Select xenografts were treated with either PBS, cytarabine, revumenib or venetoclax.


title: Human CD45+ sorted from Revumenib treated FL_NUP98-NSD1/WT1ko_derived xenograft cells

description:
Library name: Revumenib_treated
10X Genomics


title: Human CD45+ sorted from FL_NUP98-NSD1/WT1ko with PRDM16ko_derived xenograft cells

description:
Library name: PRDM16ko
10X Genomics


title: Human CD45+ sorted from PDX2 xenograft cells

description:
Library name: PDX2
10X Genomics

source_name: Human PDX model

value: Human PDX model

value: NUP98-NSD1/FLT3-ITD/WT1 mutation


title: Human CD45+ sorted from CB_NUP98-NSD1/WT1ko_derived xenograft cells_rep2

description:
Library name: NUP98_NSD1_WT1ko_CB_rep2
10X Genomics


title: Human CD45+ sorted from PDX1 xenograft cells

description:
Library name: PDX1
10X Genomics


description:
Library name: Primary_OR_FL_rep2
10X Genomics


title: Human CD45+ sorted from CB_OR2W5_derived xenograft cells_rep2

description:
Library name: Primary_OR_CB_rep2
10X Genomics


title: Human CD45+ sorted from CB_NUP98-NSD1/WT1ko_derived xenograft cells_rep1

description:
Library name: NUP98_NSD1_WT1ko_CB_rep1
10X Genomics


description:
Library name: Primary_OR_FL_rep1
10X Genomics


title: Human CD45+ sorted from CB_OR2W5_derived xenograft cells_rep1

description:
Library name: Primary_OR_CB_rep1
10X Genomics


description:
Library name: NUP98_NSD1_WT1ko_FL_rep1
10X Genomics


description:
Library name: NUP98_NSD1_WT1ko_FL_rep2
10X Genomics


title: Human CD45+ sorted from FL_NUP98-NSD1_derived xenograft cells_rep4

description:
Library name: NUP98_NSD1_FL_rep4
10X Genomics


title: Human CD45+ sorted from FL_WT1ko_derived xenograft cells_rep1

description:
Library name: Primary_WT1_FL_rep1
10X Genomics


title: Human CD45+ sorted from Venetoclax treated FL_NUP98-NSD1/WT1ko_derived xenograft cells

description:
Library name: Venetoclax_treated
10X Genomics


title: Human CD45+ sorted from FL_NUP98-NSD1_derived xenograft cells_rep2

description:
Library name: NUP98_NSD1_FL_rep2
10X Genomics


title: Human CD45+ sorted from FL_NUP98-NSD1/WT1ko_derived xenograft cells_rep3

description:
Library name: NUP98_NSD1_WT1ko_FL_rep3
10X Genomics


title: Human CD45+ sorted from Control FL_NUP98-NSD1/WT1ko_derived xenograft cells

description:
Library name: Venetoclax_control
10X Genomics


title: Human CD45+ sorted from FL_NUP98-NSD1/WT1ko_derived xenograft cells

description:
Library name: NNW_control
10X Genomics


title: Human CD45+ sorted from FL_NUP98-NSD1_derived xenograft cells_rep1

description:
Library name: NUP98_NSD1_FL_rep1
10X Genomics


title: 3782-BW-98 ATAC-seq

city: Philadelphia

first: Brandon

last: Wenz

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
Consensus peak file was generated using the peak caller Genrich with parameters: "Genrich -t /path/to/all/bamFiles -j -o /path/to/outputFile -v -E /path/to/hg38/blacklistFile.bed -m 10 -g 50 -e MT,X,Y, …"
Assembly: GRCh38
Supplementary files format and content: The processed data file is the consensus peak call set generated when using all 189 samples as input.

source_name: liver

extract_protocol:
Human liver wedge biopsies were supplied by the Penn Transplant Institute. Samples were derived from human livers deemed fit for transplantation, and were collected at the time of the surgery. Samples were flash frozen and stored at -80 C. Chromatin accessibility profiles were generated using a modified Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) called Omni-ATAC. Briefly, approximately 20 mg of tissue was dounce homogenized in a homogenization buffer. Tissue homogenate was layered over Iodixanol density gradient and spun. Nuclei were extracted post-centrifugation and quantified using a hemocytometer. Approximately 50,000 nuclei were rinsed and added to the Omni-ATAC reaction mix.
Transposition reactions were incubated at 37 C for thirty minutes. Reactions were cleaned with spin columns and eluted. Polymerase chain reaction (PCR) was initially performed for five cycles. At this point, a qPCR reaction was performed to determine the additional number of PCR cycles to use. The additional number of PCR cycles is determined by calculating the qPCR cycle at which the fluorescence intensity is equal to one-third the maximum fluorescent intensity of the reaction. Libraries were purified and profiles were measured using Bioanalyzer High-Sensitivity DNA Analysis Kit (Agilent). Libraries that pass visual quality control and concentration checks were frozen at -20 C.

value: liver


title: 3782-BW-96 ATAC-seq


title: 3782-BW-99 ATAC-seq


title: 3782-BW-9 ATAC-seq


title: 3782-BW-97 ATAC-seq


title: 3782-BW-93 ATAC-seq


title: 3782-BW-92 ATAC-seq


title: Human CD45+ sorted from FL_WT1ko_derived xenograft cells_rep2

description:
Library name: Primary_WT1_FL_rep2
10X Genomics


title: 3782-BW-90 ATAC-seq


title: 3782-BW-8 ATAC-seq


title: 3782-BW-89 ATAC-seq


title: 3782-BW-87 ATAC-seq


title: 3782-BW-88 ATAC-seq


description: Library name: NUP98_NSD1_FL_rep2


title: 3782-BW-85 ATAC-seq


title: 3782-BW-7 ATAC-seq


title: 3782-BW-80 ATAC-seq


title: 3782-BW-78 ATAC-seq


title: 3782-BW-84 ATAC-seq


title: 3782-BW-82 ATAC-seq


title: 3782-BW-83 ATAC-seq


title: 3782-BW-77 ATAC-seq


title: 3782-BW-95 ATAC-seq


title: 3782-BW-81 ATAC-seq


title: 3782-BW-94 ATAC-seq


title: 3782-BW-73 ATAC-seq


title: 3782-BW-91 ATAC-seq


title: 3782-BW-74 ATAC-seq


title: 3782-BW-71 ATAC-seq


title: 3782-BW-70 ATAC-seq


title: 3782-BW-6 ATAC-seq


title: 3782-BW-72 ATAC-seq


title: 3782-BW-75 ATAC-seq


title: 3782-BW-67 ATAC-seq


title: 3782-BW-68 ATAC-seq


title: 3782-BW-66 ATAC-seq


title: 3782-BW-86 ATAC-seq


title: 3782-BW-64 ATAC-seq


title: Human CD45+ sorted from FL_NUP98-NSD1_derived xenograft cells_rep3

description:
Library name: NUP98_NSD1_FL_rep3
10X Genomics


title: 3782-BW-62 ATAC-seq


title: 3782-BW-69 ATAC-seq


title: 3782-BW-61 ATAC-seq


title: 3782-BW-60 ATAC-seq


title: 3782-BW-59 ATAC-seq


title: 3782-BW-57 ATAC-seq


title: 3782-BW-58 ATAC-seq


title: 3782-BW-5 ATAC-seq


title: 3782-BW-55 ATAC-seq


title: 3782-BW-76 ATAC-seq


title: 3782-BW-53 ATAC-seq


title: 3782-BW-54 ATAC-seq


title: 3782-BW-56 ATAC-seq


title: 3782-BW-50 ATAC-seq


title: 3782-BW-48 ATAC-seq


title: 3782-BW-51 ATAC-seq


title: 3782-BW-49 ATAC-seq


title: 3782-BW-52 ATAC-seq


title: 3782-BW-65 ATAC-seq


title: 3782-BW-47 ATAC-seq


title: 3782-BW-46 ATAC-seq


title: 3782-BW-79 ATAC-seq


title: 3782-BW-43 ATAC-seq


title: 3782-BW-42 ATAC-seq


title: 3782-BW-44 ATAC-seq


title: 3782-BW-3 ATAC-seq


title: 3782-BW-63 ATAC-seq


title: 3782-BW-41 ATAC-seq


title: 3782-BW-38 ATAC-seq


title: 3782-BW-39 ATAC-seq


title: 3782-BW-40 ATAC-seq


title: 3782-BW-35 ATAC-seq


title: 3782-BW-33 ATAC-seq


title: 3782-BW-34 ATAC-seq


title: 3782-BW-32 ATAC-seq


title: 3782-BW-30 ATAC-seq


title: 3782-BW-2 ATAC-seq


title: 3782-BW-4 ATAC-seq


title: 3782-BW-31 ATAC-seq


title: 3782-BW-29 ATAC-seq


title: 3782-BW-45 ATAC-seq


title: 3782-BW-28 ATAC-seq


title: 3782-BW-27 ATAC-seq


title: 3782-BW-22 ATAC-seq


title: 3782-BW-25 ATAC-seq


title: 3782-BW-23 ATAC-seq


title: 3782-BW-21 ATAC-seq


title: 3782-BW-20 ATAC-seq


title: 3782-BW-1 ATAC-seq


title: 3782-BW-18 ATAC-seq


title: 3782-BW-188 ATAC-seq


title: 3782-BW-24 ATAC-seq


title: 3782-BW-187 ATAC-seq


title: 3782-BW-36 ATAC-seq


title: 3782-BW-185 ATAC-seq


title: 3782-BW-19 ATAC-seq


title: 3782-BW-184 ATAC-seq


title: 3782-BW-186 ATAC-seq


title: 3782-BW-180 ATAC-seq


title: 3782-BW-181 ATAC-seq


title: 3782-BW-17 ATAC-seq


title: 3782-BW-183 ATAC-seq


title: 3782-BW-179 ATAC-seq


title: 3782-BW-182 ATAC-seq


title: 3782-BW-177 ATAC-seq


title: 3782-BW-178 ATAC-seq


title: 3782-BW-176 ATAC-seq


title: 3782-BW-174 ATAC-seq


title: 3782-BW-173 ATAC-seq


title: 3782-BW-175 ATAC-seq


title: 3782-BW-37 ATAC-seq


title: 3782-BW-172 ATAC-seq


title: 3782-BW-170 ATAC-seq


title: 3782-BW-169 ATAC-seq


title: 3782-BW-171 ATAC-seq


title: 3782-BW-189 ATAC-seq


title: 3782-BW-16 ATAC-seq


title: 3782-BW-166 ATAC-seq


title: 3782-BW-26 ATAC-seq


title: 3782-BW-164 ATAC-seq


title: 3782-BW-167 ATAC-seq


title: 3782-BW-163 ATAC-seq


title: 3782-BW-162 ATAC-seq


title: 3782-BW-165 ATAC-seq


title: 3782-BW-159 ATAC-seq


title: 3782-BW-160 ATAC-seq


title: 3782-BW-161 ATAC-seq


title: 3782-BW-157 ATAC-seq


title: 3782-BW-15 ATAC-seq


title: 3782-BW-151 ATAC-seq


title: 3782-BW-150 ATAC-seq


title: 3782-BW-158 ATAC-seq


title: 3782-BW-156 ATAC-seq


title: 3782-BW-155 ATAC-seq


title: 3782-BW-148 ATAC-seq


title: 3782-BW-168 ATAC-seq


title: 3782-BW-147 ATAC-seq


title: 3782-BW-145 ATAC-seq


title: 3782-BW-149 ATAC-seq


title: 3782-BW-142 ATAC-seq


title: 3782-BW-146 ATAC-seq


title: 3782-BW-143 ATAC-seq


title: 3782-BW-141 ATAC-seq


title: 3782-BW-154 ATAC-seq


title: 3782-BW-153 ATAC-seq


title: 3782-BW-152 ATAC-seq


title: 3782-BW-140 ATAC-seq


title: 3782-BW-14 ATAC-seq


title: 3782-BW-138 ATAC-seq


title: 3782-BW-144 ATAC-seq


title: 3782-BW-139 ATAC-seq


title: 3782-BW-135 ATAC-seq


title: 3782-BW-137 ATAC-seq


title: 3782-BW-136 ATAC-seq


title: 3782-BW-133 ATAC-seq


title: 3782-BW-134 ATAC-seq


title: 3782-BW-130 ATAC-seq


title: 3782-BW-12 ATAC-seq


title: 3782-BW-132 ATAC-seq


title: 3782-BW-128 ATAC-seq


title: 3782-BW-127 ATAC-seq


title: 3782-BW-131 ATAC-seq


title: 3782-BW-129 ATAC-seq


title: 3782-BW-126 ATAC-seq


title: 3782-BW-122 ATAC-seq


title: 3782-BW-125 ATAC-seq


title: 3782-BW-120 ATAC-seq


title: 3782-BW-13 ATAC-seq


title: 3782-BW-121 ATAC-seq


title: 3782-BW-11 ATAC-seq


title: 3782-BW-119 ATAC-seq


title: 3782-BW-118 ATAC-seq


title: 3782-BW-116 ATAC-seq


title: 3782-BW-117 ATAC-seq


title: 3782-BW-115 ATAC-seq


title: 3782-BW-114 ATAC-seq


title: 3782-BW-113 ATAC-seq


title: 3782-BW-112 ATAC-seq


title: 3782-BW-110 ATAC-seq


title: 3782-BW-10 ATAC-seq


title: 3782-BW-108 ATAC-seq


title: 3782-BW-107 ATAC-seq


title: 3782-BW-124 ATAC-seq


title: 3782-BW-123 ATAC-seq


title: 3782-BW-105 ATAC-seq


title: 3782-BW-102 ATAC-seq


title: 3782-BW-100 ATAC-seq


title: 3782-BW-101 ATAC-seq


title: B60041052018 CD38neg

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

data_processing:
Cell Ranger software v6.0.1 was used for barcode demultiplexing and UMI quantification.
Souporcell was used to demultiplex donor in samples where they were pooled.
Assembly: hg19
Supplementary files format and content: anndata with UMI counts, basic metadata and cell annotations

source_name: bone marrow

extract_protocol:
Total CD34+ cells (gate: size/singlets/ Zombie-negative/CD34-positive cells) or phenotypic HSC/MPPs (gate: size/singlets/ Zombie-negative/CD34-positive/bottom 10-20% CD38-low cells, CD45RA-) were sorted using the BD FACSAria Fusion. After the sort, up to 20.000 CD34+ cells were pooled with up to 10.000 phenotypic HSC/MPPs from different donors. After centrifugation, cells were resuspended in 47 μl PBS + 0.04% BSA for library prep using the Chromium™ Single Cell 3’ reagents. Cells were immediately processed for single-cell sequencing using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the manufacturer’s protocols.
Libraries from multiple samples were combined prior sequencing and sequenced on the Illumina NovaSeq 6000 system, aiming for a minimum of 40,000 reads per cell for gene expression and 10,000 reads per cell for cell surface protein.

value: bone marrow

value: CD34pos CD38neg

tag: disease

value: Bthal


title: B60041052018 CD34


title: B60166112019 CD34 1


title: B60133072019 CD34 + B60170112019 HSC

value: CD34pos and HSC/MPPs


title: B60133072019 HSC + B60170112019 CD34


title: HD1 CD34

value: Healthy


title: B10059062019 CD34 + B10060062019 HSC


title: CNR_Rest_H3K4me3_Rep1

first: Bikash

last: Mishra

state: NY

address: 515 E 71st ST

institute: Hospital for Special Surgery

description:
CUT&RUN
Merged_CNR_H3K4me3_peaks.bed

data_processing:
Raw data underwent adapter trimming with FastP.
Sequencing read alignments were performed against (GRCh38/hg38) reference human genome using Bowtie2.
Peak calling was performed using MACS2 with the following parameters: "macs2 callpeak -f BAMPE --nomodel --shift -37 --extsize 76 -g hs -q 0.05".
Assembly: hg38
Supplementary files format and content: NarrowPeak for each sample
Library strategy: CUT&RUN

source_name: CD14+ monocytes

growth_protocol: Monocytes were cultured overnight before treatment at 37°C, 5% CO2 in RPMI-1640 medium supplemented with 10% heat-inactivated defined FBS, penicillin-streptomycin, L-glutamine and 20 ng/ml human M-CSF.

extract_protocol:
For ChIPseq, cells were fixed with 1% formaldehyde for 5 minutes, after quencing and cell lysis, chromatin was sonicated using a bioruptor pico (Diagenode). Sonicated samples were incubated with 5-10ug antibody for overnight and then incubated with Dynabeads Protein G for 1 hour and washed twice with sonication buffer ((10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% N-lauroylsarcosine), once with sonication buffer with 500 mM NaCl, once with LiCl wash buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 250 mM LiCl and 1% NP-40) and once with TE with 50 mM NaCl. After washing, DNA was eluted in freshly prepared direct elution buffer (10 mM Tris-HCl (pH 8.0), 5 mM EDTA (pH 8.0), 300 mM NaCl and 0.5% SDS). Cross-links were reversed by overnight incubation at 65 °C. RNA and protein were digested using RNase A and proteinase K, respectively. For CUT&RUN, cells were centrifuged for 3 min at 600 g at room temperature and then resuspended in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche Complete Protease Inhibitor EDTA-free tablet per 50 mL). Up to 500,000 cells per condition were centrifuged again for 3 min at 600 g at room temperature and resuspended in wash buffer. Activated Concanavalin-A beads (Bangs Laboratories BP531) in binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) were added to each condition and incubated for 10 min on a rotator at room temperature. Beads with nuclei were kept on a magnetic stand and washed with Dig-wash buffer (0.05% digitonin in wash buffer). After discarding the liquid, beads were resuspended with primary antibody in antibody buffer (2 mM EDTA in Dig-wash buffer) and incubated overnight at 4 °C on a nutator. Then beads were washed with freshly prepared Dig-wash buffer and incubated with 1 mg/ml pAG-MNase (CUTANA) in Dig-wash buffer for 1 h at 4 °C on a nutator. After two washes with Dig-wash buffer, ice-cold incubation buffer (2 mM CaCl2 in Dig-wash buffer) was added to the beads which were subsequently placed in a metal block in an ice-water bath maintained at 0 °C for 30 min. Freshly prepared 2x Stop buffer (340 mM NaCl, 20 mM EGTA, 4 mM EGTA, 0.05% digitonin, 100 µg/mL RNase A, 50 µg/mL glycogen) was then added and incubated for 10 min at 37 °C. Beads were placed on a magnet stand and supernatant was collected. 2 µL of 10% (wt/vol) SDS and 1.5 µL of 20 mg/ml Proteinase K were added to the supernatant and incubated for 30 min at 50 °C. DNA from both ChIP and CUT&RUN samples were purified using UltraPure™ Phenol:Chloroform:Isoamyl Alcohol (Invitrogen) following the manufacturer’s instructions.
Library fragments were amplified using 1× NEB next PCR master mix and 1.25 M of custom Nextera PCR primers as previously described, sing the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ∼30 nM in 20 µl.

treatment_protocol: Human CD14+ monocytes were treated with IL-4 (30ng/ml), TNF (10ng/ml) or IL-4 + TNF co-stimulation for 6 or 24 hours.

value: CD14+ monocytes

value: Untreated (Resting)


title: HD1 HSC

value: HSC/MPPs


title: B10059062019 HSC + B10060062019 CD34


title: CNR_IL10_LPS_H3K4me3_Rep2

description:
CUT&RUN
Merged_CNR_H3K4me3_peaks.bed


title: 3782-BW-111 ATAC-seq


title: 3782-BW-106 ATAC-seq


title: CNR_LPS_H3K4me3_Rep2

description:
CUT&RUN
Merged_CNR_H3K4me3_peaks.bed

value: LPS


title: CNR_LPS_H3K4me3_Rep1

description:
CUT&RUN
Merged_CNR_H3K4me3_peaks.bed


title: 3782-BW-104 ATAC-seq


title: 3782-BW-109 ATAC-seq


title: CNR_IL10_LPS_H3K4me3_Rep1

description:
CUT&RUN
Merged_CNR_H3K4me3_peaks.bed


title: 3782-BW-103 ATAC-seq


title: CNR_Rest_H3k27ac_Rep2

description:
CUT&RUN
Merged_CNR_H3K27ac_peaks.bed
CNR_H3K27ac_Normalized_counts.txt


title: CNR_IL10_H3K4me3_Rep2

description:
CUT&RUN
Merged_CNR_H3K4me3_peaks.bed


title: CNR_Rest_H3K4me3_Rep2

description:
CUT&RUN
Merged_CNR_H3K4me3_peaks.bed


title: B60166112019 CD34 2


title: CNR_LPS_H3k27ac_Rep2


title: CNR_IL10_H3K4me3_Rep1

description:
CUT&RUN
Merged_CNR_H3K4me3_peaks.bed


title: CNR_IL10_LPS_H3k27ac_Rep2


title: CNR_Rest_H3k27ac_Rep1


title: CNR_IL10_H3k27ac_Rep1


title: CNR_IL10_LPS_H3k27ac_Rep1


title: CNR_Rest_IRF1_Rep3

description:
CUT&RUN
Merged_IRF1_peaks.bed
CNR_IRF1_Normalized_counts.txt


title: CNR_LPS_IRF1_Rep3


title: CNR_IL10_H3k27ac_Rep2


title: CNR_Rest_IRF1_Rep1


title: CNR_LPS_IRF1_Rep2


title: CNR_LPS_IRF1_Rep1


title: CNR_Rest_IRF1_Rep2


title: CNR_IL10_LPS_IRF1_Rep2


title: CNR_IL10_LPS_IRF1_Rep1


title: CNR_IL10_LPS_IRF1_Rep3


title: CNR_IL10_IRF1_Rep2


title: CNR_IL10_IRF1_Rep1


title: ATAC_TNF_Rep3

description:
Merged_ATAC_peaks.bed
ATAC_normalized_counts.txt

data_processing:
Raw data underwent adapter trimming with FastP.
Sequencing read alignments were performed against (GRCh38/hg38) reference human genome using Bowtie2.
Peak calling was performed using MACS2 with the following parameters: "macs2 callpeak -f BAMPE --nomodel --shift -37 --extsize 76 -g hs -q 0.05".
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text files include log2CPM values for each sample

extract_protocol:
Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 x g for 10 min in a refrigerated centrifuge. Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 µl 2× TD buffer, 2.5 µl transposase (Illumina) and 22.5 µl nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition, the sample was purified using a MinElute PCR Purification kit.
Library fragments were amplified using 1× NEB next PCR master mix and 1.25 M of custom Nextera PCR primers as previously described, sing the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ∼30 nM in 20 µl.

value: TNF


title: ATAC_TNF_Rep2


title: ATAC_TNF_Rep1


title: CNR_LPS_H3k27ac_Rep1


title: ATAC_Rest_Rep2


title: ATAC_LPS_Rep1


title: ATAC_LPS_Rep4


title: ATAC_IL10+TNF_Rep4


title: ATAC_LPS_Rep3


title: ATAC_Rest_Rep4


title: ATAC_LPS_Rep2


title: ATAC_Rest_Rep1


title: ATAC_IL10+TNF_Rep3


title: ATAC_IL10+TNF_Rep1


title: CNR_IL10_IRF1_Rep3


title: Z. mays shoot apex, homozygous N siblings from segregating population in W22 background, control treatment, replicate 2

city: Edinburgh

first: Annis

middle: Elizabeth

last: Richardson

address: Max Borne Crescent, Kings Buildings

department: Institute of Molecular Plant Sciences, School of Biological Sciences

institute: University of Edinburgh

description: Library name: N_C_2

data_processing:
Sequence data was downloaded via ftp from Novogene servers
read quality was checked and the reads trimmed using FASTPQ with default paired-end read settings.
Trimmed reads were aligned to the Zea mays NAM5.0 B73 genome using HiSAT2.0 (minumum intron length 20, maximum intron length 20000) and samtools was used to produce .bam and associated .bai files.
FeatureCounts was used to extract read counts per gene
featurecount files were combined and passed through DeSeq2 in R to carry out differential gene expression analysis.
Assembly: Zea mays B73 NAM5.0 (Zm-B73-REFERENCE-NAM-5.0)
Supplementary files format and content: featureCounts output files as .txt, containing all raw reads attributed to gene annotations

organism: Zea mays

source_name: vegetative shoot apex

growth_protocol: The Truffula seed was provided by Gerry Neuffer, and originally called Ts-2620, found in an EMS mutagenised Mo17 population. The phenotype of Trf was analyzed in backcrosses into W22 and Mo17 advanced to generation 10. Field grown plants were grown at UC Berkeley Gill Tract, UC Davis and UMass Amherst during summer field seasons. All plants used for molecular analysis were backcrossed into W22 10 times. Seedlings grown for RNA and DNA extractions were grown under greenhouse conditions in 30x45x2.5cm trays with peat free soils plus osmocote.

extract_protocol:
RNA for all experiments was extracted from each pool using TRIzol. (Invitrogen) as described in the manual. RNA was DNAse treated to remove gDNA contamination using Invitrogen DNaseI (#18068015) digestion. RNA quality was checked using gel electrophoresis (1x Agarose in 1x TBE) and quantified using Qubit before sending for library preparation and 150bp PE sequencing by Novogene.
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. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: A segregating population of 5-week-old heterozygous Trf and homozygous normal (N) siblings in the W22 backcross background was genotyped using primers AD_4 and AD_5. Plants were cut at the root-shoot node and submerged in either 100μm Indole-3-Acetic Acid (Sigma I5148) in 1% ethanol, or 1% ethanol only, ensuring that at least 10cm of the shoot base was completely submerged. Shoot apices were harvested (~1cm encompassing the base of the meristem and young leaf tissue, outer leaf removed), dried briefly, and flash frozen in liquid nitrogen 30 minutes. 2 replicate pools for each treatment and genotype group were collected, containing 3 individuals in each pool.

value: vegetative shoot apex

value: Homozygous N sibling from segregating Trf population in W22 background

tag: batch


title: Z. mays shoot apex, homozygous N siblings from segregating population in W22 background, control treatment, replicate 1

description: Library name: N_C_1


title: ATAC_IL10_Rep3


title: ATAC_IL10_Rep2


title: Z. mays shoot apex, heterozygous Trf mutants in W22 background, control treatment, replicate 2

description: Library name: TRF_C_2

value: Heterozygous Truffula, backcrossed in to W22


title: Z. mays shoot apex, homozygous N siblings from segregating population in W22 background, IAA treatment, replicate 1

description: Library name: N_IAA_2

value: IAA


title: ATAC_IL10_Rep1


title: ATAC_TNF_Rep4


title: Z. mays shoot apex, heterozygous Trf mutants in W22 background, control treatment, replicate 1

description: Library name: TRF_C_1

value: Control


title: Z. mays shoot apex, heterozygous Trf mutants in W22 background, treated with IAA, replicate 1

description: Library name: TRF_IAA_1


title: ATAC_IL10+LPS_Rep4


title: Z. mays shoot apex, heterozygous Trf mutants in W22 background, treated with IAA, replicate 2

description: Library name: TRF_IAA_3


title: ATAC_Rest_Rep3


title: ATAC_IL10+LPS_Rep2


title: ATAC_IL10+LPS_Rep3


title: RNA_TNF_Donor2

description:
TNF_D2
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt

data_processing:
Read quality was assessed and adapters trimmed using FastQC and cutadapt.
Reads were then mapped to the human genome (hg38) and reads in exons were counted against Gencode v38 with STAR Aligner.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes filtered raw counts and log2 transformed counts for each sample

molecule: polyA RNA

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 20 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1Ug of total RNA was used for the construction of sequencing libraries.
The NEBNext® Poly(A) mRNA Magnetic Isolation Module was used to enrich Poly(A) mRNA (input for library prep) following the manufacturer's protocol. RNA libraries were prepared for sequencing utilizing the NEBNext® Ultra™ II Directional RNA Library Prep kit (E7765L) according to the manufacturer's instructions.

treatment_protocol: Human CD14+ monocytes were cultured in M-CSF (20ng/ml) with or without IL-10 (100 ng/ml) overnight and then stimulated with LPS (10 ng/ml, for 3 hours) or TNF (20ng/ml, for 6hours). HPRT or IRF1/5-edited Monocytes were treated with LPS for 3hours.


title: ATAC_IL10+LPS_Rep1


title: ATAC_IL10+TNF_Rep2


title: RNA_TNF_Donor1

description:
TNF_D1
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt


title: ATAC_IL10_Rep4


title: Z. mays shoot apex, homozygous N siblings from segregating population in W22 background, IAA treatment, replicate 2

description: Library name: N_IAA_3


title: RNA_Resting_control_Donor3

description:
Rest_D3
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt


title: Zea mays shoot apex from heterozygous Truffula mutants in W22 background, replicate 3

description: Library name: TRF_M3

data_processing:
Sequence data was downloaded via ftp from Novogene servers
read quality was checked and the reads trimmed using FASTPQ with default paired-end read settings.
Trimmed reads were aligned to the Zea mays NAM5.0 B73 genome using HiSAT2.0 (minumum intron length 20, maximum intron length 20000) and samtools was used to produce .bam and associated .bai files.
FeatureCounts was used to extract read counts per gene
featurecount files were combined and passed through DeSeq2 to carry out different gene expression analysis.
Assembly: Zea mays B73 NAM5.0 (Zm-B73-REFERENCE-NAM-5.0)
Supplementary files format and content: featurecounts output .txt files, containing all raw counts per gene

extract_protocol:
A W22-backcrossed segregating population of 3-week old maize seedlings were first genotyped for herterozygous Trf versus homozygous normal (N). The outer 2 leaves were removed and 0.5cm of the shoot apex was dissected and flash frozen in liquid nitrogen. Three replicate pools were created for Trf and N siblings, 10 individuals per pool. RNA for all experiments was extracted from each pool using TRIzol. (Invitrogen) as described in the manual. RNA was DNAse treated to remove gDNA contamination using Invitrogen DNaseI (#18068015) digestion. RNA quality was checked using gel electrophoresis (1x Agarose in 1x TBE) and quantified using Qubit before sending for library preparation and 150bp PE sequencing by Novogene.
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. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Heterozygous Truffula, backcrossed in to W24

tag: age

value: 3-week old seedlings


title: Zea mays shoot apex from homozygous Normal siblings from Trf segregating population in W22 background, replicate 1

description: Library name: TRF_N1


title: Zea mays shoot apex from heterozygous Truffula mutants in W22 background, replicate 2

description: Library name: TRF_M2

value: Heterozygous Truffula, backcrossed in to W23


title: Zea mays shoot apex from homozygous Normal siblings from Trf segregating population in W22 background, replicate 2

description: Library name: TRF_N2


title: Zea mays shoot apex from homozygous Normal siblings from Trf segregating population in W22 background, replicate 3

description: Library name: TRF_N3


title: C57，SP，Day14，TransAM3

city: Hangzhou，Zhejiang

first: Yushi

last: Yao

address: Yuhangtang Rd, Zijingang Rd

institute: Zhejiang University

description: Library name: D14TransAM3

data_processing:
Clustering of the index-coded samples was performed on a cBot cluster generation system using a TruSeq PE cluster kit v3-cBot-HS (Illumina), according to the manufacturer’s instructions. After cluster generation, library preparations were sequenced on an Illumina Novaseq platform (Illumina). Raw RNA-seq fastq format data were processed through in-house Perl scripts, and clean data were obtained by removing reads containing adapter or poly(N) and low-quality reads from raw data
Reads were then mapped to mm10 RefSeq genes downloaded from the University of California Santa Cruz Table Browser using HISATt2 (v2.0.5). FeatureCounts (v1.5.0-p3) was used to count the read numbers mapped to each gene. Fragments per kilobase per million base pairs sequenced values of each gene were calculated based on the length and read counts mapped to the gene. A principal-component analysis (PCA) plot was generated, and differential gene expression analysis was performed by using the DESeq2 (v1.34.0) package in R (v4.1.2).
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Lung

extract_protocol:
The purified AMs per replicate were pelleted and lysed in TRIzol reagent (Thermo Fisher) and cryopreserved at −80 °C, followed by RNA extraction. RNA sample were sent to Novogene, where RNA-seq was performed.
Sequencing libraries were prepared using an NEBNext Ultra RNA library prep kit (New England Biolabs) following manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

value: Lung

value: macrophages/monocytes

value: WT


title: Zea mays shoot apex from heterozygous Truffula mutants in W22 background, replicate 1

description: Library name: TRF_M1


title: C57，SP，Day14，TransAM1

description: Library name: D14TransAM1


title: RNA_Resting_control_Donor1

description:
Rest_D1
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt


title: C57，SP，Day14，TransAM2

description: Library name: D14TransAM2


title: RNA_IL-10+TNF_Donor3

description:
IL10.plus.TNF_D3
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt


title: C57，SP，Day14，TRAM3

description: Library name: D14TRAM3


title: RNA_Resting_control_Donor2

description:
Rest_D2
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt


title: C57，SP，Day14，TRAM2

description: Library name: D14TRAM2


title: RNA_IL-10+TNF_Donor1

description:
IL10.plus.TNF_D1
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt


title: C57，SP，Day7，TransAM4

description: Library name: D7TransMac4


title: C57，SP，Day14，TRAM1

description: Library name: D14TRAM1


title: RNA_IL-10+TNF_Donor2

description:
IL10.plus.TNF_D2
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt


title: RNA_IL-10_Donor2

description:
IL10_D2
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt


title: RNA_IL-10_Donor3

description:
IL10_D3
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt


title: RNA_TNF_Donor3

description:
TNF_D3
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt


title: RNA_IL-10_Donor1

description:
IL10_D1
Dataset for TNF model
RNAseq_TNF_filtered_raw_counts.txt


title: C57，SP，Day7，TransAM3

description: Library name: D7TransMac3


title: C57，SP，Day7，TransAM2

description: Library name: D7TransMac2


title: C57，SP，Day7，TRAM4

description: Library name: D7TRAM4


title: RNA_LPS_IRF1_5_DKO_Rep_3

description:
LPS_IRF1.5_D565
CRISPR-Cas9 Edited (48hours) followed by 3 hours LPS treatment
RNAseq_Cas9_LPS_filtered_raw_counts.txt


title: C57，SP，Day7，TRAM3

description: Library name: D7TRAM3


title: RNA_LPS_IRF1_5_DKO_Rep_1

description:
LPS_IRF1.5_D562
CRISPR-Cas9 Edited (48hours) followed by 3 hours LPS treatment
RNAseq_Cas9_LPS_filtered_raw_counts.txt


title: C57，SP，Day7，TRAM2

description: Library name: D7TRAM2


title: C57，SP，Day7，TRAM1

description: Library name: D7TRAM1


title: RNA_LPS_HPRT_Rep_2

description:
LPS_HPRT_D563
CRISPR-Cas9 Edited (48hours) followed by 3 hours LPS treatment
RNAseq_Cas9_LPS_filtered_raw_counts.txt

value: HPRT-KO

value: LPS-HPRT-edited


title: RNA_LPS_HPRT_Rep_1

description:
LPS_HPRT_D562
CRISPR-Cas9 Edited (48hours) followed by 3 hours LPS treatment
RNAseq_Cas9_LPS_filtered_raw_counts.txt

value: CD14+ monocytes


title: RNA_LPS_IRF1_5_DKO_Rep_2

description:
LPS_IRF1.5_D563
CRISPR-Cas9 Edited (48hours) followed by 3 hours LPS treatment
RNAseq_Cas9_LPS_filtered_raw_counts.txt


title: C57，SP，Day7，TransAM1

description: Library name: D7TransMac1


title: C57，Naive，control，TRAM1

description: Library name: NaiveAM1


title: RNA_Rest_Control_Rep_3

description:
Rest_None_D565
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt

value: Untreated (Resting)


title: C57，Naive，control，TRAM4

description: Library name: NaiveAM4


title: RNA_LPS_Rep_3

description:
LPS_D565
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt

value: LPS


title: RNA_Rest_Control_Rep_1

description:
Rest_None_D562
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt


title: RNA_LPS_HPRT_Rep_3

description:
LPS_HPRT_D565
CRISPR-Cas9 Edited (48hours) followed by 3 hours LPS treatment
RNAseq_Cas9_LPS_filtered_raw_counts.txt


title: C57，SP，Day28，2

description: Library name: SP_2


title: RNA_LPS_Rep_1

description:
LPS_D562
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt


title: RNA_IL10_LPS_Rep_3

description:
IL10.plus.LPS_D565
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt


title: C57，SP，Day28，1

description: Library name: SP_1


title: C57，PBS，Day28，2

description: Library name: PBS_2


title: RNA_IL10_LPS_Rep_1

description:
IL10.plus.LPS_D562
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt


title: C57，Naive，control，TRAM3

description: Library name: NaiveAM3


title: C57，Naive，control，TRAM2

description: Library name: NaiveAM2


title: RNA_IL10_LPS_Rep_2

description:
IL10.plus.LPS_D563
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt


title: RNA_Rest_Control_Rep_2

description:
Rest_None_D563
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt


title: C57，SP，Day28，3

description: Library name: SP_3


title: Sample62_mRNA_CD34

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

data_processing:
CITE-seq transcriptomic data was aligned to the genome and demultiplexed into feature- barcode matrices with the CellRanger Single Cell Software Suite (10x Genomics, v3.0.0 for CB, and v4.0.0 for the other tissues). Cell surface protein data quantified using CITE-seq-Count (v1.4.3)
CITE-seq cells from pooled samples were demultiplexed using Souporcell, using the singularity container provided by the authors of Souporcell on GitHub for reproducibility and with the human genome reference, GRCh38 (GENCODE v32/Ensembl 98).
Assembly: GRCh38 human reference genome (v3.0.0 for CB, and v2020-A for the other tissues)
Supplementary files format and content: .h5mu object containing all tissues, composed of two anndata objects (.h5ad), one for mRNA and one for cell-surface protein.
Library strategy: CITE-seq

source_name: Mixed

extract_protocol: Single cell 3’ v.3.1 (10x Genomics). Libraries were sequenced on the Illumina NovaSeq 6000 system

value: Mixed


title: RNA_IL10_Rep_1

description:
IL10_D562
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt


title: AngIIEXAortaADV

first: Tzung

last: Hsiai

state: California

address: 650 Charles E Young Dr S

institute: University of California Los Angeles

description: Library name: Sample 3

data_processing:
Three gene count matrices were generated from raw FASTQ files for each sequencing run using the 10X Genomics Cloud Analysis platform. This platform aligns and quantifies UMI counts using cell ranger count, a 10X Genomics Cell Ranger software pipeline. Mouse (mm10) 2020-A was used as the reference transcriptome.
Assembly: Mouse (mm10) 2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: aorta

extract_protocol:
After isolation of the aorta from the thoracic aorta to the abdominal aorta, aorta adventitia layers were rapidly peeled out using micro forceps under the microscope on cold HBSS. In brief, the aortic adventitia was minced with microdissection scissors and then incubated with the enzyme mixture: LiberaseTM TL (Sigma-Aldrich, #540102001, 13 units/ml) and Elastase (Worthington, #LS006363, 48.4 units/ml) in HBSS (ThermoFisher, #14025092,), in the 37°C water bath for 20 min, followed by 37°C rotator for 40 min. After pipetting to prevent clumps, the cells were passed through a 40 µm strainer. Next, the cells were incubated with red blood cell lysis buffer (Abcam, # ab286858) for 5 min. The cells were rinsed with PBS with 0.04% BSA.
10 K cells were used for 3’ mRNA library construction, and Single-cell RNA Sequencing was performed using the 10X Genomics Chromium platform at the UCLA Technology Center for Genomics and Bioinformatics. We performed paired-end sequencing to a read depth of 500 million, providing about 50,000 paired-end reads per cell.

value: aorta


title: Calvarial preosteoblasts, cKO, rep3

city: Tianjin

first: Hairui

last: Yuan

state: Tianjin

address: 6 Huan-Rui-Bei Road

department: Chu Hsien-I Memorial Hospital & Institute of Endocrinology

institute: Tianjin medical university

data_processing:
Reads from each library were mapped to mouse transcriptome and filtered using HISAT2 software, following Strand alignment and filtering pipelines. Reads were normalized using DESeq.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

source_name: Calvarial preosteoblasts

growth_protocol: Primary preosteoblasts were cultured in α-MEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using a total RNA isolation kit (Omega Bio-Tek, Norcross, GA, USA), and mRNA is enriched by oligo (dT)-attached magnetic beads.
Sequencing libraries were generated using Hieff NGS® MaxUpTM II Dual-model mRNA Library Prep Kit for Illumina (YEASEN, Shanghai, China). The sequencing library was then sequenced on a MGISEQ-2000 platform (BGI, Shenzhen, China) and 150 bp paired-end reads were generated.

value: Calvarial preosteoblasts

value: Col1-cre; NELL2 fx/fx


title: AngIIAortaADV

description: Library name: Sample 2


title: RNA_LPS_Rep_2

description:
LPS_D563
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt


title: Calvarial preosteoblasts, cKO, rep2


title: RNA_IL10_Rep_3

description:
IL10_D565
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt


title: Sample59_mRNA_CD34


title: Calvarial preosteoblasts, cKO, rep1


title: C57，PBS，Day28，3

description: Library name: PBS_3


title: RNA_IL10_Rep_2

description:
IL10_D563
Dataset for LPS model
RNAseq_LPS_filtered_raw_counts.txt


title: Calvarial preosteoblasts, control, rep1

value: NELL2 fx/fx


title: Sample56_Protein_CD34

library_source: other

molecule: protein


title: Calvarial preosteoblasts, control, rep2


title: Sample60_mRNA_CD34


title: Stromal ST2 cells, siFn1_Vector

growth_protocol: ST2 cells were maintained in DMEM containing 10% FBS.

treatment_protocol: For co-transfection studies, ST2 cells were transfected with NELL2 expression construct (or vector) and 30 nM Fn1 siRNAs (or control siRNA) using lipofectamine 3000 transfection reagent.

value: Stromal cells

value: Fn1 knockdown


title: Sample58_Protein_CD34


title: VehicleAortaADV

description: Library name: Sample 1


title: Sample54_mRNA_MNC

value: MNC


title: Stromal ST2 cells, NC_Nell2

value: Nell2 overexpression


title: Calvarial preosteoblasts, control, rep3


title: Sample52_mRNA_MNC


title: Asthmatic_fibroblasts_IL-5_stimulated_3

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

description: Library name: D3T

data_processing:
RNA-seq data analysis was performed using the Ion Torrent Software Suite version 5.4. The Torrent Mapping Alignment Program (TMAP) was used to align the raw sequencing reads generated by the Ion Torrent sequencing data against the reference sequence derived from the hg19 (GRCh37) assembly. The raw read counts of the targeted genes were normalized using the Fragments Per Kilobase Million (FPKM) normalization method. Principal component analysis (PCA) was performed using the indicated samples with R statistical software. Differentially expressed gene (DEG) analysis was performed using the DESeq2 R/Bioconductor package with raw read counts from the RNA sequencing data to identify the differentially expressed genes (DEGs) in each comparison of cells treated with IL-5  against untreated cell lines.
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Following 6 hours of treatment with IL-5, Treated and non-treated cells were collected by trypsinization. Cells were pelleted and RNA was extracted from the cell pellet using the Qiagen RNeasy kit according to the manufacturer’s instructions.  Genomic DNA removal from all RNA extractions was ensured by treating the RNA with TURBO DNA-free Kit.
From Turbo DNase-treated RNA, 100 ng was used for the library preparation. Whole transcriptome sequencing was performed using targeted RNA-Seq with Ion AmpliSeq whole transcriptome human gene expression kit for 20,000 specific human RNA transcripts. In brief, cDNA was synthesized using a SuperScript VILO cDNA Synthesis kit and amplified using Ion AmpliSeq gene expression core panel primers. The amplified products were subjected to enzymatic shearing to get amplicons of ~200 bp, then ligated with the adapter and the unique barcodes. Next, the constructed library was purified using Agencourt AMPure XP Beads, quantified using an Ion Library TaqMan Quantitation Kit, and further diluted to 100 pM, and pooled equally with 16 individual samples. The diluted library was amplified and enriched in Ion Chef System according to the manufacturer’s instructions. The prepared template libraries were sequenced on an Ion S5 XL Semiconductor sequencer using Ion 540 Chip.
Targeted RNA-Seq using Ion AmpliSeq whole transcriptome human gene expression kit

value: Lung

value: Primary fibroblasts

value: Lung fibroblasts


title: Stromal ST2 cells, NC_Vector

value: Control


title: Sample53_Protein_MNC


title: C57，PBS，Day28，1

description: Library name: PBS_1

value: macrophages/monocytes

value: WT


title: Sample61_mRNA_CD34


title: Asthmatic_fibroblasts_IL-5_stimulated_2

description: Library name: D2T


title: Sample50_mRNA_CD34


title: Sample51_mRNA_CD34-


title: Asthmatic_fibroblasts_Unstimulated_3

description: Library name: D3C

value: Nill


title: Sample49_mRNA_MNC


title: Asthmatic_fibroblasts_Unstimulated_2

description: Library name: D2C


title: Sample55_Protein_CD34


title: Asthmatic_fibroblasts_Unstimulated_1

description: Library name: D1C


title: Normal_fibroblasts_Unstimulated_3

description: Library name: N3C


title: Sample48_Protein_MNC


title: Sample47_Protein_CD34


title: Sample46_Protein_CD34


title: Normal_fibroblasts_Unstimulated_1

description: Library name: N1C


title: Sample44_mRNA_CD34


title: Normal_fibroblasts_Unstimulated_2

description: Library name: N2C


title: Sample45_mRNA_CD34-


title: Sample43_mRNA_CD34


title: Sample57_Protein_CD34


title: Normal_fibroblasts_IL-5_stimulated_1

description: Library name: N1T


title: Asthmatic_fibroblasts_IL-5_stimulated_1

description: Library name: D1T


title: Sample41_Protein_MNC


title: Sample39_Protein_CD34-


title: BMSCs,Grx2-/--3

first: muzhe

last: li

address: Qixia District

institute: Nanjing University of Chinese Medicine

description: Library name: Sample 6

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count . PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow mesenchymal stem cells

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to themanufacturer’s protocol.
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: bone marrow mesenchymal stem cells


title: Sample40_Protein_MNC

value: Mixed


title: BMSCs,Grx2-/--1

description: Library name: Sample 4


title: Sample38_mRNA_CD34-


title: Sample37_mRNA_CD34


title: Sample36_Protein_CD34


title: Sample35_Protein_CD34-


title: BMSCs,Grx2+/+-1

description: Library name: Sample 1


title: BMSCs,Grx2+/+-3

description: Library name: Sample 3


title: Sample34_Protein_CD34


title: Sample33_mRNA_MNC


title: Sample32_mRNA_CD34


title: Normal_fibroblasts_IL-5_stimulated_3

description: Library name: N3T


title: Sample30_Protein_CD34-


title: Normal_fibroblasts_IL-5_stimulated_2

description: Library name: N2T


title: Sample31_Protein_CD34


title: Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, No Treatment, Biol Rep 5

city: Atlanta

first: Mandy

middle: L

last: Ford

state: GA

address: 101 Woodruff Cir

department: Surgery

institute: Emory University School of Medicine

description:
Library name: NT.5
Column name in RawCounts.txt: NT.5

data_processing:
Sequence alignment was conducted using STAR version 2.9.7a and transcripts were mapped to GRCm38.102
Transcript abundance estimates were calculated internal to the STAR aligner using the htseq-count algorithm
Raw counts were extracted for downstream analysis in R
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Spleen

growth_protocol: WT C57BL/6 mice were infected intraperitoneally with 1x10^5 pfu MHV68-OVA and left untreated or treated with cM7 on days 0, 2, 4, and 6. Spleens were collected on Day 10 post-infection and processed to a single cell suspension. Live leukocytes were selected for using a Ficoll-paque 1.084 gradient and stained for cell sorting. Antigen-specific CD8 T cells were sorted on a FACS Aria II as defined as CD4- CD8+ Thy1.2+ p79/Kb+ into 100% FBS. Sorted cells were resuspended in RLT buffer and stored at -80.

extract_protocol:
RNA was extracted using the RNAeasy Micro kit (Qiagen). Quality was assessed using a Fragment Analyzer (Agilent). 1 ng of total RNA used as input
cDNA was synthesized using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to manufacturer's instructions. cDNA was fragmented and appended with dual-index barcodes using the Nextera XT DNA Library Preparation kit (Illumina).

treatment_protocol: CD154:CD11b-specific blockade was achieved using a peptide mimetic of the CD11b binding domain on CD154 (cM7). 100ug of cM7 in sterile PBS was administered to treated mice on days 0, 2, 4, and 6.

value: Spleen

value: p79/Kb+ CD8 T cells

value: No Treatment

tag: infection


title: Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, cM7 Treatment, Biol Rep 4

description:
Library name: cM7.4
Column name in RawCounts.txt: cM7.4


title: Sample42_mRNA_MNC


title: Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, cM7 Treatment, Biol Rep 3

description:
Library name: cM7.3
Column name in RawCounts.txt: cM7.3


title: Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, cM7 Treatment, Biol Rep 5

description:
Library name: cM7.5
Column name in RawCounts.txt: cM7.5


title: BMSCs,Grx2-/--2

description: Library name: Sample 5


title: Sample29_Protein_MNC


title: Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, No Treatment, Biol Rep 4

description:
Library name: NT.4
Column name in RawCounts.txt: NT.4


title: Sample28_mRNA_CD34


title: Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, No Treatment, Biol Rep 2

description:
Library name: NT.2
Column name in RawCounts.txt: NT.2


title: Sample27_mRNA_CD34


title: BMSCs,Grx2+/+-2

description: Library name: Sample 2


title: Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, No Treatment, Biol Rep 1

description:
Library name: NT.1
Column name in RawCounts.txt: NT.1


title: Sample25_Protein_CD34


title: Sample24_Protein_CD34


title: CD45+ tumor-infiltrating cells from mice treated with PLT012 antibody

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

country: Spain

institute: IDIBAPS

description: Library name: PLT012

data_processing:
The raw sequencing data were processed using Cell Ranger (V3.0.2, 10× Genomics). Reads were aligned to the reference genome, and gene expression matrices were generated, providing gene counts per cell for each sample. The processed data were used for downstream transcriptomic analyses.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5. Detected cell-associated barcodes in MEX format

source_name: Liver

extract_protocol:
Cell multiplexing was performed using CellPlex reagents (10× Genomics) to enable sample pooling.
Single-cell libraries were then prepared using the Single Cell 3' v3.1 kit (10× Genomics) following the manufacturer’s protocol. This included cell barcoding, cDNA synthesis, and amplification steps. The resulting libraries were sequenced on the Illumina NovaSeq 6000 platform using the NovaSeq 6000 S4 Reagent Kit (300 cycles).

value: Liver

value: CD45+ cells

value: PLT012 antibody


title: CD45+ tumor-infiltrating cells from mice treated with control antibody

description: Library name: PLT_CTL

value: Control antibody


title: Sample23_Protein_CD34


title: Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, cM7 Treatment, Biol Rep 2

description:
Library name: cM7.2
Column name in RawCounts.txt: cM7.2


title: Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, cM7 Treatment, Biol Rep 1

description:
Library name: cM7.1
Column name in RawCounts.txt: cM7.1


title: Sample22_mRNA_MNC

value: MNC


title: 20_IFNgRfl/fl Non Infected

city: Amsterdam

first: Elena

last: Camerini

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

description: Library name: 20.-FL-NI

data_processing:
Quality assessment with FASTQC; Trimming of adapters and low quality sequences with cutadapt 3.5; Second quality assessment with FASTQC; Allignment to the genome (STAR2.7.9a); Calculating gene expression levels (RSEM1.3.1)
Assembly: GRCm39 Mus Musculus
Supplementary files format and content: The processed file are gene expression quantification data that countain the read count estimates

source_name: VAT

extract_protocol:
RNA was isolated nucleoZOL
RNA quality was assessed using a Fragment Analyzer and libraries were generated by polyA enrichment using a specific low-input protocol.  Libraries were sequenced on a NovaSeq6000 platform, generating paired-end 150 bp reads.

value: VAT

value: adipocytes

value: IFNgRfl/fl

value: not infected


title: 17_IFNgRfl/fl Non Infected

description: Library name: 17.-FL-NI


title: 18_IFNgRfl/fl Non Infected

description: Library name: 18.-FL-NI


title: Sample20_mRNA_CD34


title: Sample21_mRNA_MNC


title: 16_IFNgRfl/fl Non Infected

description: Library name: 16.-FL-NI


title: 9_IFNgRfl/fl Infected

description: Library name: 9.-FL-INF

value: Infection


title: Sample15_mRNA_CD34-


title: 8_IFNgRfl/fl Infected

description: Library name: 8.-FL-INF


title: 6_IFNgRfl/fl Infected

description: Library name: 6.-FL-INF


title: Sample10_mRNA_CD34


title: 11_IFNgRfl/fl AdipoqCre/+ Non Infected

description: Library name: 11.-KO-NI

value: IFNgRfl/fl AdipoqCre/+


title: 12_IFNgRfl/fl AdipoqCre/+ Non Infected

description: Library name: 12.-KO-NI


title: Sample19_Protein_CD34


title: Sample17_Protein_MNC


title: Mm Spleen, p79/Kb CD8 T cells, Day 10-Post MHV68 Infection, No Treatment, Biol Rep 3

description:
Library name: NT.3
Column name in RawCounts.txt: NT.3

value: WT


title: 14_IFNgRfl/fl AdipoqCre/+ Non Infected

description: Library name: 14.-KO-NI


title: Sample14_mRNA_CD34-


title: 4_IFNgRfl/fl AdipoqCre/+ Infected

description: Library name: 4.-KO-INF


title: Sample13_Protein_MNC


title: Sample9_mRNA_CD34


title: Sample16_mRNA_CD34-


title: Sample11_Protein_CD34-


title: Sample8_mRNA_CD34


title: 5_IFNgRfl/fl AdipoqCre/+ Infected

description: Library name: 5.-KO-INF


title: Sample12_Protein_CD34


title: 1_IFNgRfl/fl AdipoqCre/+ Infected

description: Library name: 1.-KO-INF


title: 2_IFNgRfl/fl AdipoqCre/+ Infected

description: Library name: 2.-KO-INF


title: 10_IFNgRfl/fl Infected

description: Library name: 10.-FL-INF


title: Sample7_Protein_CD34-


title: Sample6_Protein_CD34-


title: mouse lung, CKO, P14, rep3

city: Indianapolis

first: Micheala

last: Aldred

state: IN

address: 980 W Walnut St

institute: Indiana University

description:
Library name: 1508
Column name in text files: 1508_CKO-P14

data_processing:
QC of the raw sequence data was performed with FASTQC. No trimming was required.
Sequence reads were mapped to the UCSC mm10 reference genome using STAR (Spliced Transcripts Alignment to a Reference) (Dobin et al. 2012).
Post-alignment QC was determined with bamUtils (Breese and Liu 2013).
Low quality mapped reads (including reads mapped to multiple positions) were excluded and featureCounts (Liao, Smyth, and Shi 2013) was used to quantify the gene level expression.
Differential gene expression analysis was performed with edgeR (Robinson, Mccarthy, and Smyth 2010). In this workflow, the statistical methodology applied uses negative binomial generalized linear models with likelihood ratio tests.
Assembly: mm10
Supplementary files format and content: tab-delimited text file ILMN-1619_STAR_featureCounts_raw-counts.txt contains raw read counts for all samples
Supplementary files format and content: tab-delimited text file ILMN-1619_STAR_featureCounts_edgeR_CPM.txt contains Log2 counts per million for all samples

source_name: lung

extract_protocol:
RNA was extracted using miRNeasy mini kit (Qiagen). 100ng total RNA was used for library construction.
RNAseq libraries were prepared using KAPA RNA HyperPrep Kit (Roche) according to the manufacturer's instructions.

value: lung

value: CKO


title: Sample3_mRNA_MNC

value: Mixed


title: Sample4_mRNA_CD34


title: mouse lung, CKO, P14, rep1

description:
Library name: 1505
Column name in text files: 1505_CKO-P14


title: Sample5_Protein_CD34


title: mouse lung, CKO, P14, rep2

description:
Library name: 1508b
Column name in text files: 1508b_CKO-P14


title: Sample1_Protein_MNC


title: Sample2_Protein_CD34


title: mouse lung, Control, P14, rep3

description:
Library name: 1507
Column name in text files: 1507_Control-P14

value: Control


title: mouse lung, Control, P14, rep2

description:
Library name: 1503
Column name in text files: 1503_Control-P14


title: mouse lung, Control, P36, rep3

description:
Library name: 1424
Column name in text files: 1424_Control-P36


title: mouse lung, CKO, P36, rep3

description:
Library name: 1422
Column name in text files: 1422_CKO-P36


title: wt_seedling_2

city: Sevilla

first: Fernando

last: Rodríguez-Marín

state: Sevilla

address: Avda. Américo Vespucio, 49

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

description: Library name: Sample5

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Subsequent data analysis and visualization was performed using the R bioconductor package ballgown (https://www.bioconductor.org/packages/release/bioc/html/ballgown.html)
Assembly: tair10
Supplementary files format and content: comma-delimited text files include FPKM values for each sample

source_name: Six-day-old seedlings

extract_protocol:
RNA extraction was performed using Sure Prep kit (Fisher), following the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols. TruSeq Stranded Total RNA with Ribo-Zero kit (Illumina) and Illumina Stranded mRNA prep ligation kit (Illumina) were used for the construction of cDNA libraries for adult and seedling samples, respectively.

value: Six-day-old seedlings

value: Six days in continuous light at 125 µE m−2 s−1 grown in MS


title: mouse lung, Control, P14, rep1

description:
Library name: 1501
Column name in text files: 1501_Control-P14


title: ntrc_seedling_3

description: Library name: Sample9

value: ntrc mutant


title: mouse lung, Control, P36, rep2

description:
Library name: 1421
Column name in text files: 1421_Control-P36


title: mouse lung, CKO, P36, rep1

description:
Library name: 1419
Column name in text files: 1419_CKO-P36


title: mouse lung, CKO, P36, rep2

description:
Library name: 1420
Column name in text files: 1420_CKO-P36


title: wt_seedling_3

description: Library name: Sample6


title: mouse lung, Control, P36, rep1

description:
Library name: 1424b
Column name in text files: 1424b_Control-P36


title: ntrc_seedling_1

description: Library name: Sample7


title: ntrc_seedling_2

description: Library name: Sample8


title: wt_seedling_1

description: Library name: Sample4


title: pancreatic cancer, sgADAR1, rep4

city: Shanghai

first: Botai

last: Li

address: No. 25/Ln 2200 Xie-Tu Road

institute: Shanghai Jiao Tong University

description:
Library name: Tissue sgADAR1 rep4
ADAR4

data_processing:
For RNA-seq data analysis, paired-end clean reads were aligned to the mouse reference genome (GRCm39) using Hisat2.
Aligned reads were quantified for mRNA expression using featureCounts.
Differential expression analysis and data normalization were performed with DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for cell line samples.txt
Supplementary files format and content: tab-delimited text file includes raw counts for tissues samples.txt

source_name: pancreatic cancer

extract_protocol:
RNA was extracted from cell pellets using Trizol (Takara). Poly(A) RNA was isolated from 1 μg of total RNA to generate cDNA libraries following the TruSeq™ RNA Sample Prep Kit protocol.
The libraries were then sequenced using the Illumina NovaSeq 6000 platform.

value: pancreatic cancer


title: pancreatic cancer, sgADAR1, rep2

description:
Library name: Tissue sgADAR1 rep2
ADAR2


title: pancreatic cancer, sgADAR1, rep3

description:
Library name: Tissue sgADAR1 rep3
ADAR3


title: M-CSFMac_LPS_R2

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps-Universität Marburg

description: Illumina TruSeq

data_processing:
CLC Genomics Workbench v 10.0.1
Sequence reads were trimmed using the CLC workbench with quality score limit set to 0.05 and 25 nt minimal read length
Trimmed sequences were mapped to the GRCh38 human reference genome using the CLC workbench with the following parameters: Mismatch cost: 2. Insertion cost: 3. Deletion cost: 3. Length fraction: 0.8. Similarity fraction: 0.8. Max. hits for a read: 10. Strand specific: both.
Normalized expression values (e.g. RPKM) were calculated based on the read counts obtained from the CLC genomics workbench analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file, including gene identifiers and coordinates, read counts and RPKM values for each sample.

source_name: blood

growth_protocol: AEC II cells were cultured on ThinCert™ transwells in SAGM medium (Lonza), supplemented with 2% FCS. Primary macrophages were cultured in X-Vivo-15 medium (Lonza), supplemented with 5 % FCS.  THP1 cells were cultivated in RPMI Glutamax medium, supplemented with 5 % FCS. All cells were cultured at 37 °C with humidified 5% CO2 atmosphere.

extract_protocol:
RNA was extracted with Trizol reagent and DNaseI-treated, using established protocols. PolyA RNA was selected using magnetic beads.
Libraries were generated using the TruSeq Stranded mRNA Kit (Illumina) or the QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen), as indicated.

treatment_protocol:
Blood-derived monocytes (CD14 MACS purification) were differentiated into macrophages using 15 ng / ml recombinant GM-CSF or M-CSF for 7 days. THP1 cells were differentiated with PMA (20 nM) for two days.
Upon differentiation / attachment, cells were treated with different immune-stimuli at the following concentrations: Flagellin: 1 µg / ml. LPS: 100 ng / ml. Pam3csk4: 200 ng / ml. IFNalpha: 100 ng / ml.
For inhibitor experiments, cells were pre-treated with for 2 hours as follows, prior to further stimulations: - (DMSO only as solvent control). BAY 11-7082: 5 or 10 µM. Ruxolitinib: 1 or 5 µM, BX795: 1 or 5 µM

value: blood

value: blood-derivedmacrophage

tag: source

value: buffy coat, CD14+ monocytes, M-CFS-differentiation for 7 days

value: LPS

tag: time

value: 4 h


title: 15_IFNgRfl/fl AdipoqCre/+ Non Infected

description: Library name: 15.-KO-NI

value: VAT

value: adipocytes

value: not infected


title: M-CSFMac_Ctrl_R2

description: Illumina TruSeq

value: WT

value: control


title: pancreatic cancer, sgControl, rep4

description:
Library name: Tissue sgControl rep4
CON4


title: M-CSFMac_Ctrl_R1

description: Illumina TruSeq


title: M-CSFMac_LPS_R1

description: Illumina TruSeq


title: GM-CSFMac_LPS_R2

description: Illumina TruSeq

value: buffy coat, CD14+ monocytes, GM-CFS-differentiation for 7 days


title: pancreatic cancer, sgADAR1, rep1

description:
Library name: Tissue sgADAR1 rep1
ADAR1


title: GM-CSFMac_Ctrl_R2

description: Illumina TruSeq


title: pancreatic cancer, sgControl, rep3

description:
Library name: Tissue sgControl rep3
CON3


title: GM-CSFMac_LPS_R1

description: Illumina TruSeq


title: FC1199, sgADAR1+IFNγ, rep3

description:
Library name: FC1199 sgADAR1+IFNγ rep3
FA8-3

value: Pancreatic cancer cell line


title: aMac_Ctrl_R2

description: Illumina TruSeq

value: lung

value: alveolar macrophage

value: bronchoalveolar lavage


title: aMac_LPS_R2

description: Illumina TruSeq


title: FC1199, sgADAR1+IFNγ, rep2

description:
Library name: FC1199 sgADAR1+IFNγ rep2
FA8-2


title: aMac_LPS_R1

description: Illumina TruSeq


title: FC1199, sgControl+IFNγ, rep2

description:
Library name: FC1199 sgControl+IFNγ rep2
FCON-2


title: aMac_Ctrl_R1

description: Illumina TruSeq


title: pancreatic cancer, sgControl, rep2

description:
Library name: Tissue sgControl rep2
CON2


title: GM-CSFMac_Ctrl_R1

description: Illumina TruSeq


title: FC1199, sgControl+IFNγ, rep1

description:
Library name: FC1199 sgControl+IFNγ rep1
FCON-1


title: AECII_FLA_R2

description: Illumina TruSeq

value: type II pneumocyte

value: lung tissue resection

value: flagellin


title: pancreatic cancer, sgControl, rep1

description:
Library name: Tissue sgControl rep1
CON1

value: pancreatic cancer


title: BaF3 cells, NRAS G12D, ETV6 I209S P214L 3

city: Dallas

first: Glen

last: Liszczak

state: TX

address: 5323 Harry Hines Blvd, Building L3.104

institute: University of Texas Southwestern Medical Center

description: Library name: D3

data_processing:
Data processing was performed by Novogene Co. as follows: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm39
Supplementary files format and content: csv file includes gene counts, gene fpkm, and between group statistics for each sample

source_name: Lymphocyte

growth_protocol: BaF3 cells were maintaned in DMEM supplemented with 10% FBS and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Zymogen Direct-zol RNA Miniprep Kit.
Library's were constructed by Novogene Co. using the following methods: 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 using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: BaF3 cells were sorted into IL-3 deficient media on Day 0. Media was refreshed on Day 2. Cells were harvested on Day 3.

value: Lymphocyte

value: Pro B cells

value: ETV6 I209S P214L-IRES-ZsGreen

value: IL-3 deprivation


title: AECII_FLA_R1

description: Illumina TruSeq

value: 4 h


title: BaF3 cells, NRAS G12D, ETV6 I209S P214L 2

description: Library name: D2


title: AECII_Ctrl_R2

description: Illumina TruSeq


title: FC1199, sgADAR1+IFNγ, rep1

description:
Library name: FC1199 sgADAR1+IFNγ rep1
FA8-1


title: FC1199, sgControl+IFNγ, rep3

description:
Library name: FC1199 sgControl+IFNγ rep3
FCON-3


title: BaF3 cells, NRAS G12D, ETV6 I209S P214L 1

description: Library name: D1


title: BaF3 cells, NRAS G12D, ETV6 P214L 3

description: Library name: C3

value: ETV6 P214L-IRES-ZsGreen


title: BaF3 cells, NRAS G12D, ETV6 P214L 2

description: Library name: C2


title: Brain_PFC_DNA [BBN_9346]

type: genomic

city: Exeter

first: Katie

last: Lunnon

address: RILD Level 4, Barrack Road

department: Medical Research

institute: University of Exeter Medical School

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using the BeadArray Scanner (iScan) under standard settings

data_processing:
wateRmelon package in R environment (3.5.2)
Beta value

label: Bisulfite conversion

source_name: Prefrontal Cortex

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from PFC tissue using the All-prep universal kit (Qiagen)

value: Prefrontal Cortex

tag: brain bank

value: Bristol

tag: post-mortem delay

tag: braak stage

tag: Sex

value: F

tag: ad diagnosis

value: AD


title: Brain_PFC_DNA [BBN003.32243]

tag: tissue

value: Newcastle

value: Ctl


title: Brain_PFC_DNA [BBN_7413]

value: M


title: BaF3 cells, NRAS G12D, ETV6 P214L 1

description: Library name: C1

tag: genotype


title: AECII_Ctrl_R1

description: Illumina TruSeq

value: lung

tag: cell line

value: type II pneumocyte

value: WT

value: control


title: BaF3 cells, NRAS G12D, ETV6 3

description: Library name: B3

value: Lymphocyte

tag: cell type

value: wild-type ETV6-IRES-ZsGreen


title: Brain_PFC_DNA [BBN_7477]


title: BaF3 cells, NRAS G12D, ETV6 2

description: Library name: B2

value: Pro B cells

tag: treatment


title: Brain_PFC_DNA [BBN006.29544]


title: Brain_PFC_DNA [BBN_13401]


title: Brain_PFC_DNA [BBN003.28775]


title: BaF3 cells, NRAS G12D, ZsGreen 2

description: Library name: A2

value: ZsGreen control

value: IL-3 deprivation


title: Brain_PFC_DNA [BBN_4232]


title: BaF3 cells, NRAS G12D, ZsGreen 3

description: Library name: A3


title: Brain_PFC_DNA [BBN_9401]


title: BaF3 cells, NRAS G12D, ETV6 1

description: Library name: B1


title: Brain_PFC_DNA [BBN_24279]


title: Brain_PFC_DNA [BBN_26009]


title: BaF3 cells, NRAS G12D, ZsGreen 1

description: Library name: A1


title: Brain_PFC_DNA [BBN_9420]


title: Brain_PFC_DNA [BBN003.32200]


title: Brain_PFC_DNA [BBN_24337]


title: Brain_PFC_DNA [BBN_8918]


title: ER-Hoxb8 M-MDSC PAO1 dFliC 3

city: Paris

first: Maelys

last: BORN-BONY

address: 16 rue Henri Huchard

country: France

institute: INSERM

description: Library name: D1765T74

data_processing:
Sequencing was performed on the NovaSeq 6000 (Illumina), targeting between 15 and 20 M reads per sample and using paired-end 2 x 100 bp.  Analysis of the raw data was performed using R script and subsequent analysis and visualization were done using the Phantasus online tool
Assembly: Mm10
Supplementary files format and content: tab delimited text files which includes annotaion and raw counts for each sample

source_name: ER-Hoxb8 M-MDSC

extract_protocol:
SINGLE CELL RNA PURIFICATION KIT Norgen 51800
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech/Takara)

value: ER-Hoxb8 M-MDSC

value: PAO1 dFliC


title: ER-Hoxb8 M-MDSC PAO1 WT 3

description: Library name: D1765T68

value: PAO1 WT


title: ER-Hoxb8 M-MDSC PAO1 dFliC 2

description: Library name: D1765T72


title: ER-Hoxb8 M-MDSC PAO1 dFliC 1

description: Library name: D1765T70


title: ER-Hoxb8 M-MDSC PAO1 WT 2

description: Library name: D1765T66


title: Brain_PFC_DNA [BBN_8910]

value: Prefrontal Cortex

value: Bristol


title: ER-Hoxb8 M-MDSC PAO1 WT 1

description: Library name: D1765T64


title: Brain_PFC_DNA [BBN_9125]

value: F

value: AD


title: ER-Hoxb8 M-MDSC NT 3

description: Library name: D1765T62

value: NT


title: ER-Hoxb8 M-MDSC NT 1

description: Library name: D1765T58


title: ER-Hoxb8 M-MDSC NT 2

description: Library name: D1765T60


title: Sample18_Protein_CD34-

value: Mixed


title: Sample26_mRNA_CD34-


title: Brain_PFC_DNA [BBN006.35906]

value: M


title: ER-Hoxb8 PMN-MDSC PAO1 dFliC 2

description: Library name: D1765T73

source_name: ER-Hoxb8 PMN-MDSC

value: ER-Hoxb8 PMN-MDSC


title: Brain_PFC_DNA [BBN_3378]

value: Manchester

value: Ctl


title: ER-Hoxb8 PMN-MDSC PAO1 dFliC 1

description: Library name: D1765T71


title: Brain_PFC_DNA [BBN_9329]


title: ER-Hoxb8 PMN-MDSC PAO1 dFliC 3

description: Library name: D1765T75


title: Brain_PFC_DNA [BBN001.26493]

value: Edinburgh


title: Brain_PFC_DNA [BBN_9111]


title: Brain_PFC_DNA [BBN_25058]


title: ER-Hoxb8 PMN-MDSC PAO1 WT 1

description: Library name: D1765T65


title: Brain_PFC_DNA [BBN001.28793]


title: Brain_PFC_DNA [BBN_9323]


title: ER-Hoxb8 PMN-MDSC NT 3

description: Library name: D1765T63


title: ER-Hoxb8 PMN-MDSC NT 1

description: Library name: D1765T59


title: Brain_PFC_DNA [BBN007.29872]

value: Queen Sqaure


title: Brain_PFC_DNA [BBN001.28416]


title: Brain_PFC_DNA [BBN_8833]


title: ER-Hoxb8 PMN-MDSC NT 2

description: Library name: D1765T61


title: Brain_PFC_DNA [BBN_11663]


title: Brain_PFC_DNA [BBN005.30812]


title: Brain_PFC_DNA [BBN_5761]