title: M2 + LCN2 d0 2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

hyb_protocol: Labeled fragments were hybridized to Applied Biosystems Clariom S Mouse Arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization Oven 645

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

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

label: Biotin

source_name: M2 macrophages, treated with LCN2 on d0 after start of differentiation

label_protocol: We used the Applied Biosystems GeneChipTM 3' IVT Pico Kit (catlog n.: 902789) for cDNA synthesis, amplification, cRNA synthesis, second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin according to manufacturer's instructions.

growth_protocol: BMDMs were grown from bone marrow from wildtype C57BL/6 mice (RPMI + 10 % FCS + 1 % PenStrep + 10 ng/ml recombinant murine mCSF) for seven days

extract_protocol: RNA was isolated using the Rneasy Mini Kit (Quiagen) according to the manufacturer's instructions.

treatment_protocol: BMDMs were stimulated towards anti-inflammatory (M2) phenotype with 20 ng/ml recombinant murine IL-4

value: IL4-stimulated macrophages

value: in vitro differentiated from bone marrow

value: wildtype


title: Mia PACA-2 CDAE67Q Pool 5

status: Public on Jan 24 2024

type: SRA

city: Toulouse

first: Pierre

last: Cordelier

address: 2, avenue Hubert Curien

country: France

institute: Cancer Research Center of Toulouse

library_source: transcriptomic

data_processing:
RNA-seq data was processed with standard approaches. we first converted from Illumina format to fastq using bcl2fastq.
Quality control was performed with FastQC and adaptor sequences were trimmed using Trimmomatic. Quality control with FastQC was run again after adaptor removal. Gene expression was quantified at the transcript level by Salmon. Import of Transcript-level abundances and counts from Salmon and name conversion to HUGO gene symbols was performed with the tximport R package
Assembly: GRCh38/hg38
Supplementary files format and content: Text file with raw counts

molecule: total RNA

organism: Homo sapiens

source_name: pancreatic cancer

growth_protocol: cancer cells were obtained from the ATCC and cultured in Dulbecco Modified Eagle Medium (DMEM) 4.5 g/L glucose containing 10% Fetal Bovine Serum (FBS), 100 IU/mL penicillin, 100 µg/mL streptomycin and 250 ng/mL fungizone (AB) and 100 µg/mL normocin (Invivogen) to avoid mycoplasma  contamination. Cells were incubated at 37°C with 5% CO2

extract_protocol:
Total RNA was extracted with RNeasy kit (Qiagen) according to the manufacturer’s instructions; quality and quantity were measured on a Nanodrop system (ThermoFisher Scientific)
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

treatment_protocol: Not applicable

tag: tissue

value: pancreatic cancer

tag: cell line

value: Mia PACA-2

tag: cell type

value: cancerous

tag: treatment


title: Mia PACA-2 CDAE67Q Pool 4


title: EAE_Spp1_Pos_3

city: Hangzhou

first: DANYANG

last: HE

state: Zhejiang

address: 600 Dunyu Road Sandun Town

department: School of Life Sciences

country: China

institute: Westlake Univeristy

data_processing:
For bulk RNA-Seq, FASTQ files were trimmed using cutadapt (v2.10) with ‘-q 30’ and aligned to the mouse genome/transcriptome (GENCODE GRCm38 vM25, mm10) using STAR (v2.7.5c) with ‘twopassModeBasic’. The expression abundances were estimated (expected counts and TPM values) using RSEM (v1.3.3). COMBAT was used to correct for batch effects. The count matrix was processed with the edgeR package (v3.32.0) in R to calculate DEGs with the default parameters. Principal component analysis (PCA) was run on the centered expression matrix  of the top 2000 variable genes. Gene set enrichment analyses (Broad, GSEA 4.2.3 build 10) and TopGO (v2.40.0) were used for pathway analysis with graphical rendering using clusterProfiler (v3.16.1). Heatmaps were plotted with Complexheatmap (v2.6.2).
For single cell RNA-Seq, Reads processing, alignment to the mm10 transcriptome and unique molecular identifier(UMI) counting/collapsing were performed using Cellranger toolkit (v7.0.0, 10x Genomics) with ‘—include-introns false’. Main downstream analysis like ‘Demultiplexing with hashtag oligos (HTOs)’, clustering and filtering were run with Seurat (v4.1.1) in R(v4.1.3)/Rstudio.
Assembly: mm10
Supplementary files format and content: csv file includes raw tpm for each sample (bulk RNA-Seq)
Supplementary files format and content: CellRanger output matrix files and HTO setting csv file packaged in format .zip (single cell RNA-Seq)
Supplementary files format and content: Final Seurat Object in format .rds (single cell RNA-Seq)

organism: Mus musculus

source_name: brain

extract_protocol:
"For bulk RNA-Seq,  2,000 freshly sorted microglia were lysed in 10μL TCL buffer (QIAGEN) supplemented with 1% 2-mercaptoethanol.   For single cell RNA-Seq, cell hashing was performed by incubating the single cell suspensions with antibody cocktails containing FACS antibodies and TotalSeq antibody (Biolegend) at 1:100 final dilution for each antibody, followed by incubation for 30min on ice. Next, cells were washed and CD45+CD11b+CX3CR1+ were sorted for single cell capturing and library preparations. Briefly, 70,000 cells pooled from 10 biological samples (with 1-8 mice pooled per sample) were partitioned into nanoliter Gel-bead-inEmulsions (GEMs) droplets using the Chromium Single Cell 3′ V3.1 Kits (10x Genomics).
For bulk RNA-Seq, full-length RNA-seq libraries were prepared following a modified SMART-Seq2 protocol. The cDNA libraries were generated using the TruePrep RNA Library Prep Kit for Illumina and pair-end sequenced (150 bp × 2) with Novaseq 6000 (Illumina).

treatment_protocol: Brains were homogenized in ice-cold HBSS supplemented with 15mM HEPES and 0.5% glucose by 5 gentle strokes in a 7 mL glass Dounce homogenizer. Myelin debris were removed by density gradient separation; pellet was resuspended in 40% Percoll and centrifuged in 800G for 20 min at 4°C. Isolated microglia were labeled with a combination of conjugated antibodies, and Flow-sorted for subsequent library construction.

value: brain

tag: disease state

value: EAE recovered to clinical score 1-2

value: GFP+ microglia

tag: genotype

value: Spp1-GFP heterozygous

tag: development stage

value: 8-10 week


title: M2 + LCN2 d0 3

type: RNA

country: Germany

value: LCN2 on d0 after start of differentiation


title: CD4+ T cell from BCL6fl/fl 1 4x4

city: Columbia

first: Jerod

last: Skyberg

state: MO

address: Veterinary Pathobiology, 1500 Bouchelle

country: USA

institute: University of Missouri

data_processing:
OnestopRNASeq
FastQC and MultiQC were used for raw reads quality control and QoRTs for post-alignment quality control
Reads were aligned to the reference genome assembly mm10 with star_2.7.5a and annotated with gencode.vM25.
Aligned exon reads were counted toward gene expression with featureCounts_2.0.0 with default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM  values for each Sample

extract_protocol:
RNA was isolated via Rneasy kit.
Stranded mRNA libaries were constructed by the University of Missouri Genomics Core facility using a poly A enrichment method

value: vaccinated and infected

tag: time

value: 28 days after vaccination, 28 days after challenge


title: confined_A375_RNA_NC2

city: New York

first: Miranda

last: Hunter

state: NY

address: 418 E 68th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.
FASTQC was used for quality control of raw sequencing reads.
Trimmomatic was used to remove sequencing adapters.
Reads were aligned to GRCh38 using STAR and alignment checked using SeQC.
Assembly: GRCh38
Supplementary files format and content: Counts matrix for each sample in .tab format.

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Universal Mini kit following manufacturer’s instructions. RNA samples were quantified using Qubit 2.0 Fluorometer and RNA integrity was checked using Agilent TapeStation 4200.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation, and quantified by using Qubit 2.0 Fluorometer as well as by quantitative PCR).

value: Melanoma

value: unconfined


title: M2 + LCN2 d0 1


title: 4T1 tumor cells, uniSTING mRNA, Preparation 1

city: Chapel Hill

first: Ying

last: Wang

state: NC

address: 125 Mason Farm Road, 3118G Marsico Hall, Marsico Hall/3118G/3nd

institute: University of North Carolina at Chapel Hill

data_processing:
After removing reads with adapter or of low quality, clean reads were aligned to the mouse GRCm39 reference genome using hisat2 software, and only the uniquely mapped reads were retained for downstream analysis. The gene expression level was quantified using FeatureCounts function from Subread version 2.0.1.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: 4T1 tumor cells were cultured in RPMI1640 supplemented with 10% FBS at 37 °C and 5% CO2 in a humidified atmosphere.

extract_protocol:
Total RNA was extracted from 4T1 cells after different treatments by using RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. 1.0 µg of total RNA was used for the construction of sequencing libraries.
RNA library was generated by using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s recommendations

treatment_protocol: 4T1 tumor cells were treated with mRNAs (uniSTING mRNA or EGFP mRNA) either mixed with TransIT®-mRNA transfection agent (Mirus Bio) or encapsulated into SS-OP LNPs in DMEM culture medium supplemented with 10% FBS, according to the manufacturer’s instructions or conditions optimized in the Liu lab.

value: Breast cancer cells

value: WT

value: uniSTING mRNA


title: M2 + LCN2 d7 1

source_name: M2 macrophages, treated with LCN2 on d7 after start of differentiation

value: IL4-stimulated macrophages

value: in vitro differentiated from bone marrow

value: wildtype


title: M2 + LCN2 d7 2

value: LCN2 on d7 after start of differentiation


title: 4T1 tumor cells, Mock mRNA, Preparation 2

value: Mock (EGFP) mRNA


title: M2 vehicle 3

source_name: M2 macrophages, vehicle treated

value: vehicle


title: Mia PACA-2 CDA Pool 4

value: pancreatic cancer

value: Mia PACA-2

value: cancerous


title: 4T1 tumor cells, uniSTING mRNA, Preparation 2


title: CD4+ T cell from CD4-cre BCL6fl/fl 3 4x4

value: CD4-cre BCL6fl/fl


title: 4T1 tumor cells, Mock mRNA, Preparation 1


title: Mia PACA-2 Control Pool 4


title: M2 vehicle 2


title: Synovium+R805(10µg) mRNA-seq

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

data_processing:
Raw sequencing reads were processed using Partek Flow Analysis Software (build version 10.0.21.0210). Briefly, raw reads were checked for their quality, trimmed and reads with an average base quality score per position>30 were considered for alignment. Trimmed reads were aligned to the dog genome version canFam3-Ensembl_v102 using STAR -2.6.1d with default parameters. Reads with alignment percentage >75% were deduplicated based on their unique molecular identifiers (UMIs). Reads mapping to the same chromosomal location with duplicate UMIs were removed. Thereafter ‘Knee’ plot was constructed using the cumulative fraction of reads/UMIs for all barcodes. Barcodes below the cut-off defined by the location of the knee were assigned as true cell barcodes and quantified. Further noise filtration was done by removing cells having >5% mitochondrial counts and total read counts >24,000. Genes not expressed in any cell were also removed as an additional clean-up step. Cleaned-up reads were normalized using counts per million (CPM) method followed by log-transformation generating count matrices for each sample. Samples were batch-corrected on the basis of expressed genes and mitochondrial reads percent. Count matrices were used to visualize and explore the samples in further details by generating tSNE plots, a non-linear dimensional reduction technique. This algorithm learns the underlying manifold of the data and places similar cells together in a low-dimensional space.
Genome_build: canFam3-Ensembl_v102
Supplementary_files_format_and_content: Sparse matrix files with genes in columns and cells in rows

organism: Canis lupus familiaris

source_name: synovium treated with R805

extract_protocol:
Single cell samples were prepared using Next GEM Single Cell 5’ v2 (dual index) and Chip Kit (10x Genomics) according to the manufacturer’s protocol. Briefly samples were FACS sorted using DAPI to select live cells followed by resuspension in 0.04% BSA-PBS. Nearly 1200cells/µl were added to each well of the chip with a target cell recovery estimate of 10000 cells. Thereafter Gel bead-in Emulsions (GEMs) were generated using GemCode Single-Cell Instrument. GEMs were reverse transcribed, droplets were broken and single stranded cDNA was isolated. cDNAs were cleaned up with DynaBeads and amplified. Finally, cDNAs were ligated with adapters, post-ligation products were amplified, cleaned-up with SPRIselect and purified libraries were sequenced on Novaseq.
Chromium Next GEM Single Cell 5’ v2 (dual index)

value: synovium


title: CD4+ T cell from CD4-cre BCL6fl/fl 2 4x4

value: vaccinated and infected

value: 28 days after vaccination, 28 days after challenge


title: Synovium+Vehicle mRNA-seq

source_name: synovium


title: M2 + LCN2 d7 3


title: A375_RNAseq_HMGB2_OE1

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Universal Mini kit following manufacturer’s instructions. RNA samples were quantified using Qubit 2.0 Fluorometer and RNA integrity was checked using Agilent TapeStation 4200.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation, and quantified by using Qubit 2.0 Fluorometer as well as by quantitative PCR.

value: Melanoma


title: M2 vehicle 1


title: Mia PACA-2 CDAE67Q Pool 3


title: m6Apool2_IP_jc003_rep2

city: Rehovot

first: Ran

last: Shachar

address: 234 Herzl St.

department: Department of Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Synaptic Systems (Cat# 202003; RRID: AB_2279214)  + Cell Signaling D9D9W

data_processing:
alignment using STAR (V. 2.5.3a)
Read coverages were obtained using the R package txtools (https://github.com/AngelCampos/txtools)
Assembly: SK1-YPS138, hg19-mm9, CAST-HOUS
Supplementary files format and content: rds

organism:
Homo sapiens
Mus musculus

source_name: jc003_mice cell line, with human chromosome 3

growth_protocol: All yeast strains used in this work were grown in YPD (2% dextrose) at 30C. To induce synchronous sporulation, cells were grown for 24 h in 1% yeast extract, 2% peptone, 4% dextrose at 30C, diluted in BYTA (1% yeast extract, 2% tryptone, 1% potassium acetate, 50 mM potassium phthalate) to OD600 = 0.2 and grown for another 16 h at 30C, 250 rpm. Cells were then washed two times with water and re-suspended in Sporulation medium (0.3% potassium acetate) at OD600 = 2.0 and incubated at 30C at 190 rpm. Human monochromosome hybrid cells JCRB2201, JCRB2202 and JCRB2203 were purchased from the Japanese Collection of Research Bioresources (JCRB), and cultured in DMEM (GIBCO) supplemented with 10% fetal bovine serum (FBS) and 0.8mg/ml G418(Gibco,79N9555) 37. mESCs, BJ, and NIH 3T3 cells were cultured in DMEM (GIBCO) supplemented with 10% FBS and 1% Penicillin and Streptomycin.

extract_protocol:
Yeast total RNA samples were prepared by adjusting previously published protocols. After fast freezing the yeast cells in liquid nitrogen, yeast cells were resuspended in equal amounts of phenol:Chloroform:Isoamyl alcohol (Sigma Aldrich), buffer AE (50mM sodium acetate, 10mM EDTA 1% SDS), and glass beads in Eppendorf tube. The tube was vortexed for 15 minutes in a bullet blender, heated to 65 °C for 30 minutes, followed by another round of 5 minutes vortex and 30 minutes heating to 65 °C. Samples were placed on ice for 5 minutes and centrifuged for 10 minutes (12000g, 4 °C). The supernatant was isolated, re-extracted with phenol:Chloroform:Isoamyl alcohol, and precipitated with sodium acetate and isopropanol. For all types of mammalian cell lines, total RNA was extracted with BIO TRI RNA reagent (Bio-lab). Enrichment for mRNA was done by two rounds of poly-A selection using Oligo(dT) beads (Dynabeads mRNA DIRECT) in both total RNAs from yeast and mammals.
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)
m6A-seq2

tag: fraction

value: IP


title: AGED_CCR2_POSITIVE_3

city: Shanghai

first: Congfeng

last: Xu

address: NO. 600 Yishan road

institute: Shanghai Jiaotong University School of Medicine Affiliated Sixth People's Hospital

data_processing:
The read quality for raw reads were performed by FastQC and poor quality sequences and adaptors were trimmed with Cutadapt software.
Reads were mapped to reference mouse genome and transcriptome (Ver. 101) with HISAT2.
The assembly of mapped reads were conducted using StringTie.
Assembly: Reads were mapped to reference mouse genome and transcriptome (Ver. 101) with HISAT2.
Supplementary files format and content: gene_count_matrix.txt: Tab-delimited text file includes gene counts for each sample.

source_name: heart

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma Aldrich, US) from FACS-sorted CRMs.
Sequencing libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit from Clontech (Japan)

value: heart

tag: group

value: aged

value: macrophages


title: Mia PACA-2 CDA Pool 3


title: Mia PACA-2 Control Pool 3


title: AGED_CCR2_POSITIVE_2


title: AGED_CCR2_POSITIVE_1


title: m6Apool2_IP_jc003_rep1


title: CD4+ T cell from BCL6fl/fl 4 4x2

value: 28 days after vaccination, 14 days after challenge


title: m6Apool2_IP_jc002_rep2

source_name: jc002_mice cell line, with human chromosome 2


title: AGED_CCR2_NEGATIVE_2


title: Mia PACA-2 CDAE67Q Pool 2


title: AGED_CCR2_NEGATIVE_3


title: CD4+ T cell from BCL6fl/fl 3 4x2


title: AGED_CCR2_NEGATIVE_1


title: m6Apool2_IP_jc002_rep1


title: CD4+ T cell from CD4-cre BCL6fl/fl 1 4x4


title: Mia PACA-2 Control Pool 2


title: Mia PACA-2 CDA Pool 2


title: CD4+ T cell from BCL6fl/fl 2 4x2


title: A375_RNAseq_HMGB2_EV1

value: Empty vector


title: HFD_CCR2_POSITIVE_3

value: high-fat diet


title: CD4+ T cell from CD4-cre BCL6fl/fl 3 4x2


title: HFD_CCR2_POSITIVE_2


title: Mia PACA-2 CDA Pool 1


title: Mia PACA-2 CDAE67Q Pool 1


title: m6Apool2_IP_jc001_rep1

source_name: jc001_mice cell line, with human chromosome 1


title: Mia PACA-2 Control Pool 1


title: HFD_CCR2_POSITIVE_1


title: m6Apool1_IP_jc003_rep1


title: m6Apool1_IP_jc003_rep2


title: CD4+ T cell from CD4-cre BCL6fl/fl 2 4x2


title: HFD_CCR2_NEGATIVE_3


title: GBC-SD cells,oeHEGBC,no3

city: shanghai

first: Liang

last: Yang

address: No.2699,West Gaoke Road, Pudong New Area, Shanghai

institute: Shanghai First Maternity and Infant Hospital

description: LINC3:read count

data_processing:
After the samples were measured on the machine, the image files were obtained and converted by the software of the measurement platform to generate the FASTQ data.
The FASTAQ data was further trimmed for adapter sequence/low quality sequence using Cutadapt.
Trimmed sequence was mapped to a reference genome using HISAT2 v2.0.5.
Read count extraction was performed using Htseq(0.9.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: GBC-SD

extract_protocol:
RNA was harvested using Trizol method, ≥1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufaturer's protocol.

value: GBC-SD

value: Gallbladder cancer cell

value: overexpressed lncRNA HEGBC


title: m6Apool2_IP_jc001_rep2


title: CD4+ T cell from CD4-cre BCL6fl/fl 4 4x2


title: HFD_CCR2_NEGATIVE_2


title: m6Apool1_IP_jc002_rep1


title: HFD 1

city: Riverside

first: Djurdjica

last: Coss

address: 109 Picnic Hill Rd

department: Biomedical Sciences

institute: University of California Riverside

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing and gene counting were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). The Cell Ranger generated differential gene expression matricies were imported into R with the Seurat (v4.3) package using the Read10x function. All samples were aggregated into one with the Seurat merge function. Quality control analysis was carried out on the aggregated object to identify and filter low quality cells based on gene counts >= 1000, UMI counts per cell >= 1000, log10 genes per UMI >= 0.8 and percent mitochondrial genes <20%
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pituitary gland

extract_protocol:
C57BL/6J male mice were placed on control (CTRL) or high fat diet (HFD) for 12 weeks. Pituitary glands were dissected and rinsed in 1x ice cold PBS and were digested using an enzyme cocktail containing 0.25% collagenase in 0.25% trypsin EDTA in HBSS with 25nM HEPES pH 7.2 for 30 minutes at 37C. Enzymatic reaction was stopped with 10% FBS and suspensions were passed through a 70um strainer and centrifuged to pellet cells into single-cell suspensions. Cell suspension was resuspended in 1X PBS in 0.04% BSA and counted. Samples were ran using the 10x Genomics 3' Single Cell Gene Expression assay and protocol.
Libraries were prepared according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Illumina R1 primer sequence, Feature barcode for cell multiplexing oligo label, Unique Molecular Identifier (UMI) and the 10x Barcode. For the gene expression library construction, the barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added to ensure that no sample indices overlapped between different libraries.

value: Pituitary gland

value: All cell types in pituitary gland

value: Wildtype

value: High fat diet


title: CTRL 2

description: 10x Genomics

value: Control diet


title: HFD 2

description: 10x Genomics


title: GBC-SD cells,oeHEGBC,no1

description: LINC1:read count


title: m6Apool1_IP_jc002_rep2


title: m6Apool1_IP_jc001_rep2


title: GBC-SD cells,oeControl,no3

description: CON3:read count

value: control


title: Ctrl_CCR2_POSITIVE_3


title: m6Apool1_IP_jc001_rep1


title: CD4+ T cell from CD4-cre BCL6fl/fl 1 4x2

value: CD4-cre BCL6fl/fl

value: vaccinated and infected


title: HFD_CCR2_NEGATIVE_1

value: heart


title: CTRL 1

description: 10x Genomics


title: AML6606P_H0_40_VEH_DMSO_4

city: San Francisco

first: Benjamin

last: Huang

address: 1450 3rd Street

institute: University of California San Francisco

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using Bowtie v2.
Transcript quantification was performed with RNA-seq by Expectation Maximization (RSEM) protocol.
Gene set enrichment analysis was performed using the package provided by the Broad Institute.
Assembly: mm10
Supplementary files format and content: Tab-separated values files including count, FPKM, and TPM values for each gene.

source_name: Bone Marrow

extract_protocol:
Bone marrow cells were collected from moribund mice, subjected to RBC lysis, homogenized in Trizol. RNA was extracted using standard Trizol based techniques
Libraries were prepared using the TruSeq Stranded Total RNA kit. Libraries were sequenced on a HiSeq 400 using 100 bp single-end or paired-end chemistry.

treatment_protocol: Mice were transplanted with primary leukemias, treated daily, and observed daily.

value: Bone Marrow

value: Acute Myeloid Leukemia

value: Vehicle (in vivo), DMSO (ex vivo)


title: m6Apool2_Input_jc003_rep2

value: input


title: Ctrl_CCR2_POSITIVE_2

value: macrophages


title: GBC-SD cells,oeControl,no2

description: CON2:read count

value: GBC-SD


title: Scramble_ADP_3

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Sramble_ADPVSScramble_negative_Gene_differential_expression.xlsx

data_processing:
The bulk RNA-seq reads were trimmed to remove the adapter and segments of bad quality. The trimmed reads were then mapped to the mouse reference genome mm10 using HISAT236.
HTSeq-count were then used to quantify the raw gene expression count matrices for all samples. The raw gene expression count matrices were then normalized using the DESeq226, which also identify the differential genes between samples of different conditions.
Assembly: mm10
Supplementary files format and content: Files include FPKM values for each Sample.

growth_protocol: A murine osteocyte-like cell line (MLO-Y4 cells) was maintained in α-MEM supplemented with 10% fetal bovine serum (FBS, Gibco, Thermo Fisher Scientific) and 1% (P/S) (516106, Sigma‒Aldrich).

extract_protocol:
Nucleospin RNA II kits were used for total RNA extraction. Subsequent denaturation by magnetic oligo (dT) beads was performed before RNA sample purification. After the first-strand cDNA was obtained by reverse transcription of purified mRNA and a second cDNA was synthesized, fragmented DNA samples were blunt ended and adenylated at the 3’ ends. Adaptors were ligated to construct a library.
DNA sample quantification was performed by Qubit (Invitrogen), and the samples were then sequenced by an Illumina Nova-seq 6000 instrument from Genergy Bio (Shanghai) after cBot cluster generation. Then, the raw DNA sequencing data were converted into Fastq format.

treatment_protocol: P2Y2 and P2Y6 were knocked down in MLO-Y4 cells by shRNA-lentivirus infections. P2Y2/P2Y6 and scramble cells are respectively stimulated with ADP and AMP with the concentration of 2 μM. The stimulation lasts 2 hrs in a 37 °C and 5% CO2 humidified incubator. Then total RNA was isolated for further analysis.

tag: strain

value: Wild type (WT)

tag: shRNA

value: Scramble

value: Stimulated with ADP and AMP (2 uM)


title: patient,Ngn2,AMG,CMO312,Day 20

city: Planegg-Martinstied

first: Giacomo

last: Masserdotti

address: Groshaderner Strasse 9

department: ISF

institute: Helmholtz Zentrum

data_processing:
Raw data were processed using CellRanger 6.0, according to manifacturer's protocol (10XGenomics).
Assembly: hg28, ensembl98
Supplementary files format and content: tsv file format

source_name: cel line

growth_protocol: pAstros from different genotypes were transduced with the indicated retroviruses; 2 days post transduction, the medium was changed with differentiation medium.

extract_protocol:
Cells were collected at 20 days post transduction and FACS sorted, each sample into a separate tube. Then, CMO solution was added to the sorted cells, according to manifacturer's protocol (10XGenomics).
Equal number of cells from each condition was added to have a correct cell concentration. Then, ~20000 cells were loaded per lane, and 2 lanes were loaded.
Libraries were prepared according to manifacturer's protocol (10XGenomics).

treatment_protocol: AMG was added to the medium, when needed

value: cel line

value: pAstro

value: patient

tag: transcription factor

value: AMG

tag: day

value: Day 20

tag: barcode (10x)


title: m6Apool2_Input_jc003_rep1


title: Scramble_ADP_2


title: GBC-SD cells,oeHEGBC,no2

description: LINC2:read count

value: Gallbladder cancer cell

value: overexpressed lncRNA HEGBC


title: Ctrl_CCR2_POSITIVE_1

value: heart

value: control


title: m6Apool2_Input_jc002_rep2


title: patient,Ngn2,no treatment,CMO311,Day 20

value: no treatment


title: GBC-SD cells,oeControl,no1

description: CON1:read count


title: m6Apool2_Input_jc002_rep1


title: Scramble_ADP_1


title: patient,DsRed,AMG,CMO310,Day 20

value: DsRed


title: Scramble_negative_3


title: m6Apool2_Input_jc001_rep1

value: input


title: Ctrl_CCR2_NEGATIVE_2

value: macrophages


title: Ctrl_CCR2_NEGATIVE_1


title: patient,DsRed,no treatment,CMO309,Day 20


title: Tumor, CONV-RT physioxia, 24 hr, biol rep 3

city: Epalinges

first: Marie-Catherine

last: Vozenin

address: Rue de la Corniche, 9A

department: Radiation Oncologie

country: Switzerland

institute: CHUV

data_processing:
Alignment - RNA-STAR version 2.7.8a, standard parameters with NM-tag added
Merging of BAMs - Samtools merge version 1.13, standard parameters
Filtering of Mouse Reads - XenofilteR version 1.6, MM-threshold = 8
Counting of annotated genes - featureCounts version 2.0.1, standard parameters, reverse stranded, hg38 built-in
Assembly: hg38
Supplementary files format and content: txt - gene counts matrix by ENTREZ ID

source_name: Tumor

growth_protocol: U-87 MG cells were grown and expanded in high-glucose DMEM with 10% FBS at 37°C and 5% CO2. Once sufficient cells were available, 10 million were injected subcutaneously into the right flank of female Swiss nude mice.

extract_protocol:
Tumors were sampled 24h after radiotherapy and were disrupted in cold RLT lysis buffer with automated homogenizer (TissueLyser II, Qiagen) and total RNA extracted using the RNEasy mini kit (Qiagen) according to manufacturer instructions.
RNA quality (RQN > 6.8) was assessed on a Fragment Analyzer (Agilent Technologies). RNA-seq libraries were prepared from 500 ng of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina) using a unique dual indexing strategy, and following the official protocol automated on a Sciclone liquid handling robot (PerkinElmer). Libraries were quantified by a fluorimetric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies). Cluster generation was performed with 2 nM of an equimolar pool from the resulting libraries using the Illumina HiSeq 3000/4000 SR Cluster Kit reagents and sequenced on the Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents for 150 cycles (single end).

treatment_protocol: Tumors were grown subcutaneously and once the volume measured 50 - 90 mm3, they were treated with 20 Gy electrons at CONV (~0.1 Gy/s) or FLASH (>100 Gy/s) dose rates using the Oriatron eRT6 (PMB-Alcen, FR) at CHUV. No-RT controls were left untreated.

value: Tumor

value: U-87 MG

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: CONV-RT physioxia, 24 hr


title: m6Apool2_Input_jc001_rep2


title: Scramble_negative_1

value: Wild type (WT)

value: Scramble

value: Stimulated with ADP and AMP (2 uM)


title: Tumor, No-RT physioxia, late, biol rep 5

value: No-RT physioxia, late


title: control,Ngn2,AMG,CMO308,Day 20

value: cel line

value: pAstro

value: AMG

value: Day 20


title: control,Ngn2,no treatment,CMO307,Day 20

value: control

value: no treatment


title: Ctrl_CCR2_NEGATIVE_3

value: heart


title: m6Apool1_Input_jc003_rep2

value: input


title: P2Y6_Negative_3

description: P2Y6_2_ADPVSP2Y6_2_Negative_Gene_differential_expression.xlsx


title: P2Y6_Negative_2


title: control,DsRed,AMG,CMO306,Day 20

value: DsRed


title: m6Apool1_Input_jc002_rep2


title: control,DsRed,no treatment,CMO305,Day 20


title: Tumor, No-RT physioxia, 24 hr, biol rep 4

value: Tumor

value: U-87 MG

value: No-RT physioxia, 24 hr


title: P2Y6_Negative_1


title: Tumor, CONV-RT hypoxia, 24 hr, biol rep 4

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: CONV-RT hypoxia, 24 hr


title: Scramble_negative_2

value: Wild type (WT)

value: Scramble

value: Stimulated with ADP and AMP (2 uM)


title: patient,Ngn2,AMG,CMO308,Day 5

description:
10XGenomics
Sample1.tar
Sample2.tar

growth_protocol: pAstros from different genotypes were transduced with the indicated retroviruses; 48 hours later, the medium was changed with differentiation medium.

extract_protocol:
Cells were collected and FACS sorted at 5 days post infection, each sample into a separate tube. Then, CMO solution was added to the cells, according to manifacturer's protocol (10XGenomics).
Equal number of cells from each condition was added to have a correct cell concentration. Then, ~20000 cells were loaded per lane, and 2 lanes were loaded.
Libraries were prepared according to manifacturer's protocol (10XGenomics).

value: cel line

value: pAstro

value: patient

value: Day 5


title: P2Y6_ADP_3


title: m6Apool1_Input_jc001_rep1


title: Tumor, No-RT hypoxia, late, biol rep 4

value: No-RT hypoxia, late


title: control,Ngn2,AMG,CMO307,Day 5

description:
10XGenomics
Sample1.tar
Sample2.tar

value: control

value: AMG


title: P2Y6_ADP_2


title: control,Ngn2,no treatment,CMO306,Day 5

description:
10XGenomics
Sample1.tar
Sample2.tar

value: no treatment


title: m6Apool1_Input_jc001_rep2

value: input


title: P2Y6_ADP_1


title: P2Y2_Negative_3

description: P2Y2_1_ADPVSP2Y2_1_Negative_Gene_differential_expression.xlsx


title: ovaries

city: Hefei

first: Qiang

last: Hong

address: Hefei

institute: Anhui Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz10 whole genome using HISAT, mapped to genes using Bowtie2.
fragments per kilo bases per million fragments (FPKM) were calculated using RSEM.
Assembly: GRCz10
Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.

organism: Danio rerio

source_name: ovary

extract_protocol:
Testes and ovaries were isolated, frozen on dry ice, and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols.

value: ovary

value: WT


title: patient,Ngn2,no treatment,CMO305,Day 5

description:
10XGenomics
Sample1.tar
Sample2.tar


title: testes

source_name: testis

value: testis


title: m6Apool1_Input_jc003_rep1


title: Tumor, No-RT physioxia, late, biol rep 4

value: Tumor

value: U-87 MG

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: No-RT physioxia, late


title: P2Y2_Negative_2

value: Wild type (WT)

value: Stimulated with ADP and AMP (2 uM)


title: Tumor, No-RT hyperoxia, late, biol rep 4

value: No-RT hyperoxia, late


title: control,DsRed,AMG,CMO303,Day 5

description:
10XGenomics
Sample1.tar
Sample2.tar

value: cel line

value: pAstro

value: DsRed

value: Day 5


title: Tumor, CONV-RT hypoxia, late, biol rep 5

value: CONV-RT hypoxia, late


title: KPC1245_HA-mSpdef_HA_REP2

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
Sequencing reads were mapped to the mouse or human genome (mm10/hg19) using Bowtie2 (2.4.4)
Duplicate read removal and sorting was performed using SAMtools (1.14)
Peaks were called using MACS2 (2.2.7.1) with 5% FDR cut off and broad peak option for histone- or narrow peak option for TF- datasets
Big wig files were generated using deeptools
Assembly: mm10/hg19
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: FC1245 KPC 2D cell line

growth_protocol: Human pancreatic cancer cells HPAF-II were cultured in RPMI supplemented with 10% fetal bovine serum (FBS). KPC 2D FC1245 cells were cultured in DMEM with 5% FBS. Penicillin/streptomycin were added to all cell cultures.

extract_protocol:
CUT&RUN was performed according to manufacturer’s instructions (CUTANA ChIC/CUT&RUN Kit, EpiCypher 14-1048).
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina according to manufacturer’s instructions.

value: FC1245 KPC 2D cell line

value: pancreatic ductal adenocarcinoma (PDA) cell

tag: antibody

value: HA tag, EpiCypher 13-2010


title: KPC1245_HA-mSpdef_HA_REP3


title: Tumor, CONV-RT physioxia, late, biol rep 5

value: CONV-RT physioxia, late


title: patient,DsRed,AMG,CMO304,Day 5

description:
10XGenomics
Sample1.tar
Sample2.tar

value: patient

value: AMG


title: KPC1245_HA-mSpdef_IgG

value: IgG control, EpiCypher 13-0042


title: Tumor, No-RT physioxia, 24 hr, biol rep 3

value: Tumor

value: U-87 MG

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: No-RT physioxia, 24 hr


title: patient,DsRed,no treatment,CMO301,Day 5

description:
10XGenomics
Sample1.tar
Sample2.tar

value: cel line

value: no treatment


title: P2Y2_ADP_3

value: Wild type (WT)

value: Stimulated with ADP and AMP (2 uM)


title: m6Apool1_Input_jc002_rep1

value: input


title: Tumor, No-RT hypoxia, late, biol rep 3

value: No-RT hypoxia, late


title: Tumor, No-RT physioxia, late, biol rep 3

value: No-RT physioxia, late


title: control,DsRed,no treatment,CMO302,Day 5

description:
10XGenomics
Sample1.tar
Sample2.tar

value: pAstro

value: control

value: DsRed

value: Day 5


title: P2Y2_ADP_1


title: KPC1245_HA-mSpdef_HA_REP1

value: FC1245 KPC 2D cell line

value: pancreatic ductal adenocarcinoma (PDA) cell

value: HA tag, EpiCypher 13-2010


title: Caco-2 cells, nutrient-depleted, BafA1, rep 3

city: Cankaya

first: Sreeparna

last: Banerjee

state: Ankara

address: Universiteler Mah., Dumlupinar Bulvari No:1

department: Biological Sciences

country: Turkey

institute: Middle East Technical University

data_processing:
Data processing was carried out by SZAOMICS Laboratories (Istanbul, Turkiye) with Illumina DRAGEN Bio-IT Platform (v3.9.5).
Raw sequencing data (.bcl) is demultiplexed and converted to FASTQ format with DRAGEN software.
Raw sequencing reads were trimmed to remove adaptor content and low-quality reads, and alignment was carried out with DRAGEN software.
Gene expression quantification was also carried out by following the RNA pipeline of DRAGEN software.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file of raw counts for each sample.
Supplementary files format and content: The processed data files contain the calculated TPM, expression-weighted means of transcript lengths, and raw counts for the genes.

growth_protocol: Caco-2 cells were grown in 1 g/L glucose-containing Eagle’s minimum essential medium (EMEM) supplemented with 20% fetal bovine serum (FBS), 1mM sodium pyruvate and 0.1 mM non-essential amino acids (NEAA), 2 mM L-glutamine and 100 U/mL penicillin - 100 μg/mL streptomycin. The cells were cultured in an incubator with 95% air and 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated with NucleoSpin RNA Kit (Macherey-Nagel) according to the manufacturer’s protocol.
Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit was used for library preparation by following the manufacturer's instructions.

treatment_protocol: For nutrient depletion, the Caco-2 cells were incubated for 48h in glucose and glutamine free DMEM supplemented with 1% FBS, 0.1 g/L glucose and 0.2 mM L-glutamine, 1mM sodium pyruvate, 0.1 mM non-essential amino acids and 1% penicillin/streptomycin. Sub-confluent Caco-2 cells were treated with 100nM Bafilomycin A1 (Invivogen) for 48h in nutrient-rich (NR) or nutrient-depleted (ND) medium for 48h.

value: WT

value: ND+100nM Bafilomycin A1


title: Tumor, CONV-RT physioxia, late, biol rep 4

value: Tumor

value: U-87 MG

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: CONV-RT physioxia, late


title: 12_C575_ko

city: Lund

first: Lautaro Francisco

middle: Francisco

last: Belfiori Carrasco

state: Skåne

address: Sölvegatan 19, BMC A10

country: Sweden

institute: Lund University

data_processing:
After  demultiplexing,  the  qualityof the Illumina  readsstored  in  FASTQfiles  was assessed by  means  ofFastQC  (v0.11.4)
Transcript quantification was performed using the Salmonpackage(v0.8.2)
quasi-mapping: salmon  quant -i  transcripts_index -l  IU -1reads1.fq -2  reads2.fq --validateMappings -o Sample1 -gcBias
The transcript index was derived from the GENCODE mouse release M28 (GRCm39)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Substantia nigra

growth_protocol: Animals were kept 12 hour ligth:dark cycle with ad libitum access to chow diet and water

extract_protocol:
A total of six 14µm-thick sections containing early substantia nigra (approximately equivalent to Bregma -2.92 to -3.16 in adult mice) were collected from each experimental animal, accommodating three per slide. Slides were stored at -80°C until staining and Laser Capture Capture Microdissection (LCM), which were performed on the same day. A short staining procedure was conducted and ice-cold solutions were used to preserve the RNA integrity. Briefly, sections were fixed in 70% EtOH for 2min, followed by staining with 1% w/v cresyl violet acetate prepared in 50% EtOH. AdhesiveCap clear tubes (415190-9211-000, Zeiss) were used for collecting the nigral tissue from each animal separately: approximately 0.3mm2 of tissue was harvested. Total RNA purification was performed following the RNeasy Micro kit.
SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio, Inc.) was used for cDNA library preparation; the output was then processed with the Nextera® XT DNA Library Preparation Kit (Illumina, Inc.) for paired-end (2x75bp) sequencing on an Illumina NextSeq500 instrument

treatment_protocol: One week old mice were sacrificed by decapitation; brain dissections were performed on ice under 2 minutes

value: Substantia nigra

value: Engrailed-1 hemizygous

tag: Sex

value: Male

value: 1 week of age


title: CD4+ T cell from BCL6fl/fl 1 4x2

extract_protocol:
RNA was isolated via Rneasy kit.
Stranded mRNA libaries were constructed by the University of Missouri Genomics Core facility using a poly A enrichment method

value: vaccinated and infected

value: 28 days after vaccination, 14 days after challenge


title: transOligoY4_2

treatment_protocol: Oligomycin A (5 mg, S1478, Selleck) was dissolved in DMSO to make a 50 mM stock solution. Then, the stock solution (1:1000, 50 μM as the working concentration) or the same volume of DMSO (Vehicle) was added to fresh culture medium to stimulate the MLO-Y4 cells for 1 hour at 37 °C. The supernatants from previous culture (vehicle and oligomycin A) are collected to stimulate normal-cultured MLO-Y4 for another 2 hrs. All four groups of cells are collected for total RNA extraction for further analysis.

value: Wild type (WT)

value: Stimulated with Oligomycin A (50 mM)


title: Tumor, FLASH-RT hypoxia, 24 hr, biol rep 4

tag: tissue

value: FLASH-RT hypoxia, 24 hr


title: transOligoY4_3

tag: cell line


title: Tumor, CONV-RT physioxia, late, biol rep 3

tag: cell type


title: Caco-2 cells, nutrient-depleted, BafA1, rep 2

tag: treatment


title: 11_C572_ko


title: 10_C5713_ko


title: P2Y2_Negative_1

value: Stimulated with ADP and AMP (2 uM)


title: transOligoY4_1


title: 09_C5743_wt

value: Wild type


title: Tumor, No-RT hyperoxia, 24 hr, biol rep 4

value: No-RT hyperoxia, 24 hr


title: Tumor, No-RT hypoxia, 24 hr, biol rep 4

value: Tumor

value: No-RT hypoxia, 24 hr


title: Caco-2 cells, nutrient-depleted, BafA1, rep 1

value: WT

value: ND+100nM Bafilomycin A1


title: Tumor, No-RT hyperoxia, late, biol rep 3

value: U-87 MG

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: No-RT hyperoxia, late


title: transDMSOY4_3

value: Stimulated with Oligomycin A (50 mM) and DMSO


title: Caco-2 cells, nutrient-depleted, vehicle, rep 2

value: ND


title: transDMSOY4_1


title: P2Y2_ADP_2


title: Caco-2 cells, nutrient-depleted, vehicle, rep 1


title: Tumor, CONV-RT physioxia, 24 hr, biol rep 2

value: CONV-RT physioxia, 24 hr


title: 08_C572S_wt

value: Substantia nigra

value: Male

value: 1 week of age


title: Tumor, FLASH-RT physioxia, late, biol rep 6

value: FLASH-RT physioxia, late


title: Caco-2 cells, nutrient-depleted, vehicle, rep 3


title: transDMSOY4_2

value: Wild type (WT)


title: OligoY4_3

value: Stimulated with Oligomycin A (50 mM)


title: 06_SWB_ko

value: Engrailed-1 hemizygous


title: 07_C5710_wt

value: Wild type


title: Caco-2 cells, nutrient-rich, BafA1, rep 2

value: WT

value: NR+100nM Bafilomycin A1


title: Tumor, No-RT hypoxia, 24 hr, biol rep 3

value: Tumor

value: U-87 MG

value: No-RT hypoxia, 24 hr


title: 05_SW22_ko


title: OligoY4_2


title: Caco-2 cells, nutrient-rich, BafA1, rep 1


title: Tumor, No-RT hyperoxia, late, biol rep 2

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: No-RT hyperoxia, late


title: 04_SW21_ko


title: Tumor, No-RT hypoxia, 24 hr, biol rep 2


title: OligoY4_1


title: Caco-2 cells, nutrient-rich, vehicle, rep 3

value: NR


title: DMSOY4_3

value: Stimulated with Oligomycin A (50 mM) and DMSO


title: Caco-2 cells, nutrient-rich, BafA1, rep 3


title: Tumor, FLASH-RT hypoxia, 24 hr, biol rep 3

value: FLASH-RT hypoxia, 24 hr


title: 03_SWG_wt

value: Substantia nigra

value: Male

value: 1 week of age


title: DMSOY4_2

value: Wild type (WT)


title: Caco-2 cells, nutrient-rich, vehicle, rep 2


title: 02_SW7_wt


title: Tumor, No-RT hypoxia, late, biol rep 2

value: No-RT hypoxia, late


title: ADPpositive_3

treatment_protocol: MLO-Y4 cells are stimulated with 1 μM or 2 μM ADP. The stimulation lasts 2 hrs in a 37 °C and 5% CO2 humidified incubator. Then total RNA was isolated for further analysis.

value: Stimulated with 2 uM ADP


title: 01_SW31_wt

value: Wild type


title: bladder cancer-NMIBC-6

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

description: bladder cancer-NMIBC-6. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer

data_processing:
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4). The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization. Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software.
Supplementary files format and content: fastq and bam for each Sample

source_name: bladder cancer tissues

extract_protocol: Total RNA was extracted from FFPE tissues followed by library preparation according to Illumina standard instruction (SMARTer Stranded Total RNA-Seq Kit v2). Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina NovaSeq6000. The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina).

value: bladder cancer tissues

tag: type

value: NMIBC


title: Tumor, FLASH-RT physioxia, late, biol rep 5

value: Tumor

value: U-87 MG

value: FLASH-RT physioxia, late


title: ADPpositive_2

tag: genotype


title: Tumor, CONV-RT physioxia, late, biol rep 2

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: CONV-RT physioxia, late


title: stimulated, anti-LAIR-1, mouse 3

city: Utrecht

first: Akashdip

last: Singh

address: Lundlaan 6

country: Netherlands

institute: UMC Utrecht

data_processing:
Read 1 was used to identify the Illumina library index and CEL-seq sample barcode.
Read 2 was aligned to the mouse mm10 reference transcriptome using BWA MEM
Reads that mapped equally well to multiple locations were discarded.
Mapping and generation of count tables was done using the MapAndGo script.
Assembly: mm10
Supplementary files format and content: tsv file with count tables for genes per sample

source_name: naive CD8 T cells

extract_protocol:
Total RNA was extracted using the standard TRIzol (Invitrogen) protocol
Sequencing libraries were prepared with Illumina Truseq small RNA primers

treatment_protocol: For stimulation, 2.5 μg/ml anti-CD3ε (145-2C11, BD Biosciences), and 2.5 µg/ml anti-LAIR-1 (2C7, in-house) or 2.5 µg/ml isotype control (in-house) were immobilized overnight at 4 °C on U-bottom 96-wells plates in 50 µl PBS. Spleens from wild type mice were then isolated and splenocytes were isolated using manual dissociation. Afterwards, cells were washed twice with FB. Cells were then stained for surface markers under constant agitation at 4 °C, after which cells were washed and resuspended in FB. Approximately 1 million naïve CD8+ T cells (TCRβ+CD8+CD62L+CD44-) per mouse were then sorted and resuspended at a density of 500,000 cells/ml. 100,000 naïve CD8+ T cells were then added to previously coated U-bottom 96-wells plates and cultured for 6 hours at 37 °C with 5% CO2.

value: naive CD8 T cells

value: wild type

value: anti-CD3 + anti-LAIR-1


title: Tumor, FLASH-RT hypoxia, late, biol rep 3

value: FLASH-RT hypoxia, late


title: bladder cancer-NMIBC-5

description: bladder cancer-NMIBC-5. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer


title: Caco-2 cells, nutrient-rich, vehicle, rep 1

value: WT

value: NR


title: Tumor, CONV-RT hyperoxia, late, biol rep 4

value: CONV-RT hyperoxia, late


title: ADPpositive_1

value: Wild type (WT)

value: Stimulated with 2 uM ADP


title: bladder cancer-MIBC-6

description: bladder cancer-MIBC-6. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer

value: bladder cancer tissues

value: MIBC


title: stimulated, isotype, mouse 3

value: anti-CD3 + isotype


title: Tumor, FLASH-RT physioxia, late, biol rep 4

value: Tumor

value: U-87 MG


title: stimulated, anti-LAIR-1, mouse 1


title: ADPnegative_3

value: No treatment


title: ADPnegative_2


title: bladder cancer-NMIBC-4

description: bladder cancer-NMIBC-4. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer

value: NMIBC


title: stimulated, isotype, mouse 2


title: bladder cancer-MIBC-5

description: bladder cancer-MIBC-5. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer


title: ADPnegative_1


title: stimulated, anti-LAIR-1, mouse 2


title: ADP_1_100_3

description: genes_expression_FPKM_count_ADP_1_100.xlsx

value: Stimulated with 1 uM ADP


title: bladder cancer-MIBC-4

description: bladder cancer-MIBC-4. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer


title: bladder cancer-NMIBC-3

description: bladder cancer-NMIBC-3. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer


title: ADP_1_100_2


title: DMSOY4_1

value: Stimulated with Oligomycin A (50 mM) and DMSO


title: bladder cancer-MIBC-3

description: bladder cancer-MIBC-3. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer


title: unstimulated, anti-LAIR-1, mouse 1

value: naive CD8 T cells

value: wild type

value: isotype + anti-LAIR-1


title: unstimulated, anti-LAIR-1, mouse 3


title: bladder cancer-NMIBC-2

description: bladder cancer-NMIBC-2. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer


title: stimulated, isotype, mouse 1


title: bladder cancer-MIBC-2

description: bladder cancer-MIBC-2. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer


title: unstimulated, isotype, mouse 2

value: isotype + isotype


title: unstimulated, isotype, mouse 1


title: bladder cancer-NMIBC1

description: bladder cancer-NMIBC1. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer


title: unstimulated, anti-LAIR-1, mouse 2


title: bladder cancer-MIBC-1

description: bladder cancer-MIBC-1. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer


title: Tumor, No-RT hyperoxia, late, biol rep 1

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: No-RT hyperoxia, late


title: Tumor, FLASH-RT hypoxia, 24 hr, biol rep 2

value: FLASH-RT hypoxia, 24 hr


title: Tumor, No-RT physioxia, 24 hr, biol rep 2

value: No-RT physioxia, 24 hr


title: Tumor, FLASH-RT hypoxia, late, biol rep 2

value: FLASH-RT hypoxia, late


title: Tumor, FLASH-RT hyperoxia, 24 hr, biol rep 4

value: FLASH-RT hyperoxia, 24 hr


title: m6Apool2_IP_humanBJ_rep2

description: Synaptic Systems (Cat# 202003; RRID: AB_2279214)  + Cell Signaling D9D9W

source_name: human cell line BJ

value: BJ

value: IP


title: Tumor, CONV-RT hypoxia, 24 hr, biol rep 3

value: Tumor

value: U-87 MG

value: CONV-RT hypoxia, 24 hr


title: Tumor, CONV-RT hypoxia, late, biol rep 4

value: CONV-RT hypoxia, late


title: Tumor, No-RT physioxia, late, biol rep 2

value: No-RT physioxia, late


title: BL14

city: Indianapolis

first: Aladdin

last: Hassanein

state: IN

address: 545 Barnhill Dr, Suite 232

department: Surgery

institute: Indiana University

data_processing:
NextSeq reads were trimmed using fastp (version 0.20.1) with parameters “-l 17 --detect_adapter_for_pe -g -p”
The resulting reads were mapped against GRCm39 using HISAT2 (version 2.2.1) with parameters “--rna-strandness F“
Read counts for each gene were created using featureCounts from the Subread package (version 2.0.2) with the parameters “-O -M --primary -p --largestOverlap -s 2 -B” and Gencode M29 as the annotation
Differential expression analysis was performed using the DESeq2 package (version 1.34.0) in R/Bioconductor (R version 4.1.2)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file of raw gene count values for each Sample

source_name: Murine tail (post-TNT day 28)

extract_protocol:
RNA was extracted using NucleoSpin RNA kit from Macherey-Nagel
Ribosomal RNA was depleted using Illumina Ribo-Zero Plus rRNA Depletion kit protocol (catalog no. 20037135).  Libraries were prepared by Illumina TruSeq Stranded Total RNA Library Preparation Kit protocol (catalog no. 20020597).  The libraries were analyzed by Agilent 4200 TapeStation, and pooled.  The pooled libraries were loaded on a NextSeq 500/550 High Output v2.5 run with a 75-cycle sequencing module (catalog no. 20024906) to generate paired-end reads.  The demultiplexing of the reads was performed using bcl2fastq version 2.20.0.

value: Murine tail (post-TNT day 28)

tag: age

value: 12 wk


title: BL18


title: BL17


title: m6Apool2_IP_humanBJ_rep1

extract_protocol:
Yeast total RNA samples were prepared by adjusting previously published protocols. After fast freezing the yeast cells in liquid nitrogen, yeast cells were resuspended in equal amounts of phenol:Chloroform:Isoamyl alcohol (Sigma Aldrich), buffer AE (50mM sodium acetate, 10mM EDTA 1% SDS), and glass beads in Eppendorf tube. The tube was vortexed for 15 minutes in a bullet blender, heated to 65 °C for 30 minutes, followed by another round of 5 minutes vortex and 30 minutes heating to 65 °C. Samples were placed on ice for 5 minutes and centrifuged for 10 minutes (12000g, 4 °C). The supernatant was isolated, re-extracted with phenol:Chloroform:Isoamyl alcohol, and precipitated with sodium acetate and isopropanol. For all types of mammalian cell lines, total RNA was extracted with BIO TRI RNA reagent (Bio-lab). Enrichment for mRNA was done by two rounds of poly-A selection using Oligo(dT) beads (Dynabeads mRNA DIRECT) in both total RNAs from yeast and mammals.
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)
m6A-seq2


title: m6Apool1_IP_humanBJ_rep2


title: 18mpizhigu_3

source_name: Bone

treatment_protocol: Femoral and tibia cortical bone were harvested with nonosseous tissue, including bone marrow. Then, the cortical bones were dissected into fragments, which were subsequently washed and centrifuged 3 times with culture medium.

value: Bone

value: Wild type (WT)

value: No treatment


title: BL12


title: m6Apool1_IP_humanBJ_rep1


title: Tumor, No-RT hyperoxia, 24 hr, biol rep 3

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: No-RT hyperoxia, 24 hr


title: Tumor, No-RT hypoxia, 24 hr, biol rep 1

value: No-RT hypoxia, 24 hr


title: 1mwtAtransfer_3

treatment_protocol: Long bones (femur and tibia) and parietal bones from 1-month-old and 18-month-old mice were prepared as previously described and cut into fragments. The samples were washed with α-MEM with 2% P/S. The bone fragments from young and old mice were maintained in α-MEM supplemented with 1% P/S in 6-well plates. After 24 hours of ex vivo culture in a 37 °C and 5% CO2 humidified incubator, the culture medium in each well was collected and added to different recipients, one of which was 1-month bone fragments with the original culture medium removed before medium transfer. After another 48 hours of culture, the recipient bone fragments receiving culture medium from young and old mouse bone fragments were collected for subsequent RNA-seq analysis.


title: 1mwtAtransfer_2


title: ADP_1_100_1

value: Stimulated with 1 uM ADP


title: Tumor, FLASH-RT physioxia, 24 hr, biol rep 4

value: FLASH-RT physioxia, 24 hr


title: BL10


title: BL9


title: Tumor, FLASH-RT physioxia, late, biol rep 3

value: FLASH-RT physioxia, late


title: 1mwtAtransfer_1


title: 1mwtBcontrol_2


title: m6Apool2_Input_humanBJ_rep2

value: BJ

value: input


title: 18mpizhigu_2


title: Tumor, No-RT hyperoxia, 24 hr, biol rep 2

value: Tumor

value: U-87 MG


title: m6Apool2_Input_humanBJ_rep1


title: 1mwtBcontrol_3


title: m6Apool2_IP_ESC_CAST-HOUS_rep2

source_name: mice cell lines ESC hybrid

value: ESC hybrid

value: IP


title: m6Apool2_IP_ESC_CAST-HOUS_rep1


title: m6Apool1_Input_humanBJ_rep2


title: Tumor, FLASH-RT hyperoxia, late, biol rep 3

value: FLASH-RT hyperoxia, late


title: 18mpizhigu_1

value: Bone


title: BL7

value: Murine tail (post-TNT day 28)

value: 12 wk

value: TNTSham


title: Tumor, No-RT hyperoxia, 24 hr, biol rep 1

value: glioblastoma

value: radiotherapy - 20 Gy electrons


title: m6Apool1_Input_humanBJ_rep1


title: BL6


title: m6Apool2_IP_mice3T3_rep2

source_name: mice cell line 3T3


title: Tumor, CONV-RT hyperoxia, 24 hr, biol rep 4

value: CONV-RT hyperoxia, 24 hr


title: BL8


title: Fontan4, snATAC-seq

city: Philadelphia

first: Liming

last: Pei

state: Pennsylvania

address: 3501 Civic Center Blvd. CTRB 6018

department: Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia/University of Pennsylvania

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver biospsy

extract_protocol:
Frozen human liver samples were homogenized in 0.1X lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 1% BSA, 1mM DTT, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1U/μl RNase inhibitor) using a Dounce Homogenizer (Active Motif, 40401), followed by 5 min of incubation on ice.  Nuclei quality was examined under microscope after this step.  Next, nuclei were centrifuged at 500 rcf for 5 min at 4°C.  Supernatant was carefully disregarded, and nuclei was resuspended in 500ul pre-chilled wash buffer containing 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 1% BSA, 1mM DTT, 0.1% Tween-20, and 1U/μl RNase inhibitor.  The washing step was repeated twice.  After washing, all nuclei passed through 40um Flowmi cell strainer (Bel-Art, H13680-0040).
Library was performed according to the manufacture’s instructions (Single Cell Multiome ATAC + Gene Expression, 10x Genomics). Briefly, Nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). Incubation of GEMs produces Barcoded transposed DNA (for ATAC) which contains an illumina P5 sequence, a 16 nt 10x Barcode and a Spacer sequence. In the same partition, cDNA (for GEX) from poly-A mRNA contains illumine R1 primer sequence, 16 nt 10x Barcode, 12 nt unique molecular identifier (UMI). During the ATAC library construction, P7 and a sample index i7 were added to transposed DNA (for ATAC). The pooled barcoded cDNA (for GEX) was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the GEX library construction illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and sample indexes i5 and i7 were added.

value: Liver biospsy

value: Liver cells

tag: subject status

value: patient with Fontan circulation (FC)


title: m6Apool2_IP_mice3T3_rep1

tag: fraction


title: BL4

tag: group


title: BL2


title: BL5


title: m6Apool1_IP_ESC_CAST-HOUS_rep2


title: m6Apool1_IP_ESC_CAST-HOUS_rep1


title: m6Apool1_IP_mice3T3_rep2


title: Control1, snATAC-seq

description: 10x Genomics

value: healthy patients undergoing resection ot transplant for hepatoblastoma


title: Control3, snATAC-seq

description: 10x Genomics


title: WT.Spleen

city: Nutley

first: Ying

last: Wang

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health Center for Discovery and Innovation

description: 10x Genomics

data_processing:
Gene-level counts for all samples/cells were quantified using cellranger-3.1.0 aligning to the mm10 cellranger reference
Single cell data was then imported into R for downstream analysis with Seurat using the Read10X() function
Cells with mitochondrial content > 5% and fewer than ~200 features were removed from downstream analysis. The data were then log-normalized, scaled, and variable features were identified using the standard Seurat pipeline.
runPCA() was used to reduced the dimensionality of the data. The optimal number of dimensions to keep in the analysis was determined using the JackStraw() and ScoreJackStraw() functions. Following PCA, runUMAP() was used to produce UMAP plots.
Clusters were determined using the FindNeighbors() and FindClusters() functions. After determining clusters, per-cluster markers were identified using FindAllMarkers()
Assembly: Refdata-cellranger-mm10-3.0.0
Supplementary files format and content: CellRanger count filtered feature barcode HDF5 files

source_name: Spleen

growth_protocol: Donor CD8 and CD4 T cells were enriched from the spleen and liver of Balb/c recipients 21 days after HSCT using positive selection beads (Mitenyi Biotech).

extract_protocol:
CD8 and CD4 T cells were enumerated and mixed at 1:1 ratio. Same numbers of cells from different mice of the same group were pooled, generating 4 samples for scRNA-seq library preparation: WT spleen, WT liver, Id3 spleen, Id3 liver.
scRNA-seq libraries were generated using Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3 following the manufacturer’s manual (10X Genomics). 10,000 cells from each sample were loaded onto the Chromium Chip B to generate single-cell gel beads-in-emulsion (GEM) for a target recovery of 6,000 single cells. mRNA from single cells were reverse transcribed, barcoded and amplified via PCR for library construction.

value: Spleen

value: TCells

value: ID3 WT

value: WT


title: m6Apool1_IP_mice3T3_rep1

first: Ran

last: Shachar

address: 234 Herzl St.

institute: Weizmann Institute of Science

data_processing:
alignment using STAR (V. 2.5.3a)
Read coverages were obtained using the R package txtools (https://github.com/AngelCampos/txtools)
Assembly: SK1-YPS138, hg19-mm9, CAST-HOUS
Supplementary files format and content: rds

value: IP


title: m6Apool2_Input_ESC_CAST-HOUS_rep2

value: ESC hybrid

value: input


title: Fontan3, snATAC-seq

description: 10x Genomics


title: Fontan4, snRNA-seq

description: 10x Genomics


title: KO.Spleen

description: 10x Genomics

value: ID3 KO

value: KO


title: Fontan2, snATAC-seq

description: 10x Genomics


title: m6Apool2_Input_ESC_CAST-HOUS_rep1


title: BL1

value: Murine tail (post-TNT day 28)

value: 12 wk

value: TNTSham


title: KO.Liver

description: 10x Genomics

source_name: Liver

value: Liver


title: Fontan3, snRNA-seq

description: 10x Genomics

value: Liver biospsy


title: m6Apool2_Input_mice3T3_rep2


title: Fontan2, snRNA-seq

description: 10x Genomics

value: Liver cells


title: Fontan1, snATAC-seq

description: 10x Genomics

value: patient with Fontan circulation (FC)


title: WT.Liver

description: 10x Genomics


title: m6Apool2_Input_mice3T3_rep1


title: Fontan1, snRNA-seq

description: 10x Genomics


title: m6Apool1_Input_ESC_CAST-HOUS_rep2


title: Control3, snRNA-seq

description: 10x Genomics

value: healthy patients undergoing resection ot transplant for hepatoblastoma


title: 1mwtBcontrol_1

value: Bone

tag: strain

value: Wild type (WT)

value: No treatment


title: unstimulated, isotype, mouse 3

value: naive CD8 T cells

value: wild type

value: isotype + isotype


title: m6Apool1_Input_ESC_CAST-HOUS_rep1

value: ESC hybrid

value: input


title: Control1, snRNA-seq

description: 10x Genomics


title: m6Apool1_Input_mice3T3_rep2


title: m6Apool1_Input_mice3T3_rep1


title: IL13 7 dpi

city: Milwaukee

first: Santiago

last: Alvarez Argote

state: WI

address: 8701 Watertown Plank Rd, Physiology, Medical College of Wisconsin

department: Physiology

institute: The Medical College of Wisconsin, Inc.

data_processing:
Libraries were sequenced at the Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine of the Medical College of Wisconsin on a NovaSeq 6000 using one S4 lane with 2X150nt reads.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: Excel workbook (.xlsx) file of gene expression for clusters with enough cells to categorize and compare leukocytes clusters.
Supplementary files format and content: Excel workbook (.xlsx) file of gene expression for clusters with enough cells to categotize and compare macrophage subclusters.

source_name: Cardiac Ventricle

extract_protocol:
Hearts were collected at 4 or 7 days post injury and non-cardiomyocytes were dissociated from ventricles by enzymatic digestion. Viable leukocytes were collected by fluorescence-activated cell sorting.
Single cell capture, cDNA synthesis, barcoding, and library preparation was performed using the 10x Chromium system using V3.1 chemistry.

treatment_protocol: Daily intraperitoneal injection of recombinant IL13 starting at day 2 after myocardial infarction at a dose of 200ng/mouse/day

value: Cardiac Ventricle

value: Leukocytes


title: PBS 7 dpi

value: PBS


title: ID53

data_processing:
Adapters were trimmed from fastq files with trim_galore
Trimmed reads were aligned to GRCm39 using bwa-mem2
Reads aligning to mitochondrial were removed from alignment files. Filtered reads were then de-duplicated with Picard. De-duplicated alignments were then filtered for quality >= 10.
BAM files were processed with R. 300 bp windows of read counts for each sample  were calculated using functions from the csaw package. ENCODE blacklisted regions were excluded from window counts.
Local windows were filtered for enrichment over background using a cutoff of 3-fold enrichment. Read counts for all windows passing the filter were then normalized using TMM normalization from the edgeR package. Differential accesibility was then tested for the specified contrasts by using the glmQLFtest function. Following differential accessibility testing, p-values from adjecent regions were merged using the mergeResults function from csaw in order to create regions of consistently dysregulated accessibility.
Assembly: GRCm39 vM27
Supplementary files format and content: differential accessibility (tab-delimited)
Supplementary files format and content: gzipped bedGraph files with normalized log2CPM

source_name: TCells

growth_protocol: Naïve CD4 T cells were stimulated with anti-CD3/CD28 conjugated microbeads (Mitenyl Biotech) and cultured in Th1 polarization medium made with IMDM medium containing 10% FBS with the supplement of 10ng/ml IL2, 10ng/ml IL12 and 10ug/ml anti-IL4.

extract_protocol:
Cells were lysed for 3 minutes in 50ul ATAC-Resuspension Buffer containing 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin. Wash with 1ml ATAC-RSB containing 0.1% Tween-20 and pellet nuclei.
Nuclei were resuspended in 25ul transposition mix (Illumina) for transposition reaction at 37°C for 25 minutes. Transposed DNA fragments were cleaned up with the MinElute Reaction Cleanup kit (Qiagen). Libraries were prepared with NEBNext UltraII DNA Library Prep kit for Illumina.

value: TCells

value: Tcmp

value: KO

tag: time

value: 72 hr


title: ID61

value: Teff


title: WT53

value: WT


title: ID62


title: WT63


title: ID52


title: WT62


title: IL13 4 dpi


title: ID51


title: Tumor, CONV-RT hypoxia, 24 hr, biol rep 2

source_name: Tumor

value: Tumor

value: U-87 MG

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: CONV-RT hypoxia, 24 hr


title: Tumor, FLASH-RT hypoxia, late, biol rep 1

value: FLASH-RT hypoxia, late


title: Tumor, CONV-RT hypoxia, late, biol rep 2

value: CONV-RT hypoxia, late


title: Tumor, FLASH-RT hyperoxia, late, biol rep 2

value: FLASH-RT hyperoxia, late


title: Tumor, No-RT hypoxia, late, biol rep 1

value: No-RT hypoxia, late


title: Tumor, CONV-RT physioxia, 24 hr, biol rep 1

value: CONV-RT physioxia, 24 hr


title: Tumor, CONV-RT hyperoxia, 24 hr, biol rep 3

value: CONV-RT hyperoxia, 24 hr


title: Tumor, FLASH-RT physioxia, late, biol rep 2

value: FLASH-RT physioxia, late


title: Tumor, No-RT physioxia, 24 hr, biol rep 1

value: No-RT physioxia, 24 hr


title: Tumor, CONV-RT hypoxia, late, biol rep 3


title: WT52

value: TCells

value: Tcmp


title: Tumor, FLASH-RT physioxia, 24 hr, biol rep 3

value: FLASH-RT physioxia, 24 hr


title: Tumor, CONV-RT hyperoxia, late, biol rep 3

value: CONV-RT hyperoxia, late


title: PBS 4 dpi

value: Cardiac Ventricle

value: Leukocytes

value: PBS


title: WT61

value: Teff

value: WT

value: 72 hr


title: ID3

value: KO

value: 24 hr


title: WT51


title: ID1


title: ID2


title: WT2


title: WT1


title: ID63


title: Tumor, FLASH-RT physioxia, 24 hr, biol rep 2

value: Tumor

value: U-87 MG

value: glioblastoma

value: radiotherapy - 20 Gy electrons


title: Tumor, FLASH-RT physioxia, 24 hr, biol rep 1


title: Tumor, CONV-RT hypoxia, late, biol rep 1

value: CONV-RT hypoxia, late


title: Tumor, CONV-RT physioxia, late, biol rep 1

value: CONV-RT physioxia, late


title: Tumor, FLASH-RT hyperoxia, 24 hr, biol rep 2

value: FLASH-RT hyperoxia, 24 hr


title: Tumor, CONV-RT hypoxia, 24 hr, biol rep 1

value: CONV-RT hypoxia, 24 hr


title: Tumor, CONV-RT hyperoxia, late, biol rep 2

value: CONV-RT hyperoxia, late


title: Tumor, FLASH-RT hyperoxia, 24 hr, biol rep 3


title: Tumor, CONV-RT hyperoxia, late, biol rep 1


title: Tumor, CONV-RT hyperoxia, 24 hr, biol rep 1

value: CONV-RT hyperoxia, 24 hr


title: Tumor, CONV-RT hyperoxia, 24 hr, biol rep 2


title: Tumor, No-RT physioxia, late, biol rep 1

value: No-RT physioxia, late


title: Tumor, FLASH-RT hypoxia, 24 hr, biol rep 1

value: FLASH-RT hypoxia, 24 hr


title: Tumor, FLASH-RT hyperoxia, late, biol rep 1

value: FLASH-RT hyperoxia, late


title: WT3

value: TCells

value: WT


title: WT53

data_processing:
Transcript-level abundances were quantified using Salmon v1.9.0 against the GRCm39 transcriptome.
Raw transcript abundances were then imported into R and gene-level abundance for each sample was calculated using tximport::tximport()
Count matrices were then filtered for protein coding genes and technical replicates were summed. Counts were then filtered for expression using edgeR::filterByExpr()
Filtered counts were then normalized with quantile-smoothed normalization using qsmooth::qsmooth()
Differential expression was performed with limma::treat() on the log2 qsmooth-normalized counts.
Assembly: GRCm39 vM27
Supplementary files format and content: differential-expression.tsv (tab-delimited) output from limma::topTreat()
Supplementary files format and content: logcounts.tsv (tab-delimited) count matrix containing qsmooth-normalized log2(counts + 2)

extract_protocol:
Total RNA was extracted with Qiagen RNeasy Mini Kit.
mRNA was enriched with poly(A) capture. Directional mRNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Inc).


title: WT2


title: WT61


title: WT3


title: ID63

value: KO


title: WT51


title: Tumor, FLASH-RT physioxia, late, biol rep 1

value: FLASH-RT physioxia, late


title: WT52


title: Left-over carotid artery Poldip2-SMC-/-  Repeat 4

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

data_processing:
Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Differential expression analysis
(For DESeq2 with biological replicates) Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
(For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.16.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 1 were set as the threshold for significantly differential expression.
Genome_build: Mouse Reference genome (mm9) and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample as well as the fpkm values for every gene and every sample

source_name: Left-over carotid artery

growth_protocol: Mouse were fed with standard chow

extract_protocol:
Post sacrifice, the right and left carotid arteries were removed. The lumen of the carotid arteries were rapidly flushed using 29G insulin syringe containing 150uL Qiazol. The Qiazol flushings and the left-over artery samples were flash frozen in liquid Nitrogen. The RNAs were extracted using Qiagen's miREasy RNA extraction kit following standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Left-over carotid artery

value: Poldip2 SMC Knockout


title: Left-over carotid artery Poldip2-SMC-/-  Repeat 3


title: WT63


title: ID61


title: ID52


title: ID53


title: WT (RNA-seq) rep2

city: Taian

first: Aihong

last: Zhang

state: Shandong

address: 61#,Daizong Street

institute: Shandong Agricultural University

data_processing:
the sequence quality of the generated fastq data was evaluated with FastQC v0.11.5. Sequenced reads were trimmed with SOAPnuke version 1.5 using a threshold quality score >30 and read length >60.
Trimmed sequence reads were mappled to TAIR10 Arabidopsis reference genome  using TopHat2 with parameters “-p 4 --no-novel-juncs”
Following alignment, the transcript levels of chloroplast genes were calculated using ChloroSeq bioinformatic pipeline according to Castandet et al. (2016).
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana plants were grown in Murashige and Skoog (MS) medium supplemented with 2% (w/v) sucrose and 0.4% (w/v) Gellan gum (Wako) under long-day conditions (14 h light, 10 h dark) at 22 ºC and with a light intensity of 80 µmol m-2 s-1.

extract_protocol:
Total leaf RNA was isolated using Trizol reagent (Ambion, 15596018), and the RNA quality was evaluated by electrophoresis on Agilent 2100 Bioanalyzer. The rRNAs were removed from the qualified RNA samples using the Ribo-Zero Kit (Epicentre). The resulting rRNA-depleted RNA was used for preparing the RNA sequencing library with NEBNEXT Single Cell/Low input library Prep Kit (New England Biolabs)
RNA libraries for RNA-seq were prepared using NEBNext Single Cell/Low input library Prep Kit following manufacturer's protocol

value: seedlings


title: Hashtagged antibody barcode from Patient 3 & 4 [HTO]

city: Darlinghurst

first: Peter

last: Croucher

state: New South Wales

address: 384 Victoria St

department: Bone

country: Australia

institute: Garvan Insititute of Medical Research

data_processing:
Single-cell sequencing data was demultiplexed, aligned and quantified using Cell Ranger (10x Genomics) against the human reference genome (10x Genomics, July 7, 2020 release) with default parameters.
Raw hashtag data was processed using CITE-Seq count algorithm (Stoeckius et al., 2017). Cell conditions were demultiplexed using ‘HTODemux’ function implemented in Seurat (Stoeckius et al., 2018).
Filtering and quality control was performed using Seurat (Stuart et al., 2019) on data containing 15,276 cells where 14,053 cells were retained satisfying thresholds of both <10% mitochondria content and number of genes between 300 and 5000. ‘SCTransform’ was used for normalization (Hafemeister and Satija, 2019). Genes encoding BCR and TCR were removed to improve cell clustering. Principal Component Analysis (PCA) dimensional reduction was performed on variable genes identified by ‘VariableFeatures’ function and cell clusters were visualised using Uniform Manifold Approximation and Projection (UMAP) clustering implemented in Seurat (Stuart et al., 2019).
Assembly: Human GRCh38 (July 7 2020 release)
Supplementary files format and content: Demultiplexed hashtagged CITE_Seq_count output; Seurat object saved as Rdata format

organism: synthetic construct

source_name: HTO

extract_protocol:
Single cell transcriptomic libraries were generated using the 5’v2 Gene expression and immune profiling kit (10x Genomics). Viable PBMCs were sorted into 2% FBS/PBS and cell counts were performed using a haemocytometer. Up to 40,000 cells were loaded into each lane of Chromium Next GEM Chip K Single Cell Kit (10x Genomics) to achieve a recovery cell number of approximately 20,000 cells.
cDNA and TCR libraries were generated according to manufacturer’s instructions (10x Genomics).
Generated libraries were sequenced on the NovaSeq S4 flow cell (Illumina) at Read 1 = 28, i7 index = 10, i5 index = 10 and Read 2: 90 cycles according to manufacturer’s instructions.

treatment_protocol: PBMC from 4 donors were cultured for 48 hr with SARS-CoV-2 Nucleocapsid protein, spike and RBD peptide pools, respectively. Antigen specific CD4+ T cells were FACS sorted on AriaIII (BD Biosciences) at 48hrs, based on combined expression of CD25 and CD134 (OX40).  Unstimulated purified CD45RO+ ex vivo memory CD4+ T cells were used as a comparator subset. Purified cells from 4 conditions of 2 patients were then pooled (~20,000cells) and 10X single cell Transcriptomics was performed (2 lanes, 4 pooled patients).

value: convalescent donor at 3 months post SARS-CoV-2 infection

tag: data type

value: HTO

tag: molecule type

value: Synthetic barcode


title: ID62


title: ID3


title: Left-over carotid artery Poldip2-SMC-/-  Repeat 1


title: ID51


title: Left-over carotid artery Poldip2-SMC-/-  Repeat 2


title: Left-over carotid artery Poldip2-floxed  Repeat 2

value: Littermate Control


title: WT62


title: WT1


title: pbf8 (RNA-seq) rep2

value: PBF8 knockout


title: Endothelial enriched Poldip2-EC-/-  Repeat 4

source_name: Carotid artery endothelium

value: Carotid artery endothelium

value: Poldip2 EC knockout


title: Endothelial enriched Poldip2-EC-/-  Repeat 3


title: IP_Yeast_SK1mu_REP3

city: Rehovot

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae SK1

value: yeast cell

value: IP


title: ID2


title: Hashtagged antibody barcode from Patient 1 & 2 [HTO]


title: IP_Yeast_SK1mu_REP2


title: ID1


title: Endothelial enriched Poldip2-EC-/-  Repeat 1


title: Endothelial enriched Poldip2-floxed  Repeat 4


title: IP_Yeast_SK1mu_REP1


title: pbf8 (RNA-seq) rep1


title: Left-over carotid artery Poldip2-floxed  Repeat 1


title: Endothelial enriched Poldip2-EC-/-  Repeat 2


title: WT (RNA-seq) rep1


title: IP_Yeast_SK1_REP3


title: KO iBAT cold 2

city: Iowa City

first: Renata

middle: O

last: Pereira

state: Iowa

address: 169 Newton Rd

department: Internal Medicine

institute: University of Iowa

data_processing:
psuedoalignment and quantification performed using Kallisto (v0.45.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files with transcripts per million

source_name: brown adipose tissue

extract_protocol:
Total RNA was extracted from tissues with TRIzol reagent (Invitrogen) and purified with the RNeasy kit (Qiagen Inc).
Illumina TruSeq mRNA Stranded kit

value: brown adipose tissue

value: male


title: IP_Yeast_SK1_REP2


title: Endothelial enriched Poldip2-floxed  Repeat 1


title: KO iBAT cold 1


title: Endothelial enriched Poldip2-floxed  Repeat 2


title: WT iBAT cold 1

value: WT


title: KO iBAT cold 3

value: KO


title: 3226, MRTX1133 treated, bio rep 3

city: Buffalo

first: Jianxin

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

data_processing:
nf-core/rnaseq  version 3.3.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text files, contain raw read counts at isoform level.

growth_protocol: Cells were grown in Keratinocyte Serum-Free media (KSF) supplemented with 2% FBS, EGF (0.2 ng/mL) and bovine pituitary extract (30 µg/mL) (Life Technologies, Carlsbad, CA)

extract_protocol:
RNA was extracted using Quiagen Rneasy plus mini Kit.
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.

treatment_protocol: The cells were treated with 0.1% DMSO and MRTX1133 (500 nM) up to 48 hours


title: 3226, MRTX1133 treated, bio rep 2


title: Y814_skin_wound

city: Los Angeles

first: Denis

last: Evseenko

address: 1450 Biggy St

institute: University of Southern  California

data_processing:
Raw sequencing reads were processed using Partek Flow Analysis Software (build version 10.0.21.0210). Briefly, raw reads were checked for their quality, trimmed and reads with an average base quality score per position>30 were considered for alignment. Trimmed reads were aligned to the mouse genome (mm10) using STAR-2.7.3a with default parameters. Reads with alignment percentage >75% were deduplicated based on their unique molecular identifiers (UMIs). Reads mapping to the same chromosomal location with duplicate UMIs were removed. Transcripts were quantified using mm10 Gencode vM25 and UMI count matrix was generated with rows representing genes and columns representing each detected cell. Thereafter ‘Knee’ plot was constructed using the cumulative fraction of reads/UMIs for all barcodes. Barcodes below the cut-off defined by the location of the knee were assigned as true cell barcodes and quantified. Further noise filtration was done by removing cells having >5% mitochondrial counts. Genes not expressed in any cell were also removed as an additional clean-up step. Cleaned-up reads were normalized using counts per million (CPM) method followed by log-transformation generating count matrices for each sample. Count matrices were used to visualize and explore the samples in further details by generating tSNE plots, a non-linear dimensional reduction technique. This algorithm learns the underlying manifold of the data and places similar cells together in a low-dimensional space. K-means clustering was computed for identifying groups of cells with similar expression profiles using Euclidean distance metric based on the most appropriate cluster count with a maximum of 1000 iterations. Dot plots were generated in R (v4.0.3) using ggplot2(v3.3.3).
Genome_build: mm10 Gencode vM25
Supplementary_files_format_and_content: Sparse matrix files with genes in columns and cells in rows

source_name: skin wound

extract_protocol:
Single cell samples were prepared using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 and Chip Kits (10x Genomics) according to the manufacturer’s protocol. Briefly samples were FACS sorted using DAPI to select live cells and Ter119 exclusion followed by resuspension in 0.04% BSA-PBS. Nearly 1200cells/µl were added to each well of the chip with a target cell recovery estimate of 1000 cells. Thereafter Gel bead-in Emulsions (GEMs) were generated using GemCode Single-Cell Instrument. GEMs were reverse transcribed, droplets were broken and single stranded cDNA was isolated. cDNAs were cleaned up with DynaBeads and amplified. Finally, cDNAs were ligated with adapters, post-ligation products were amplified, cleaned-up with SPRIselect and purified libraries were sequenced on Novaseq.
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1

value: skin

value: wound

tag: genotype/variations


title: Input_Yeast_SK1mu_REP2

value: input


title: WT_skin_wound_treated

source_name: skin wound treated with R805

extract_protocol:
Single cell samples were prepared using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 and Chip Kits (10x Genomics) according to the manufacturer’s protocol. Briefly samples were FACS sorted using DAPI to select live cells followed by exclusion of Ter119+ cells and then resuspension in 0.04% BSA-PBS. Nearly 1200cells/µl were added to each well of the chip with a target cell recovery estimate of 1000 cells. Thereafter Gel bead-in Emulsions (GEMs) were generated using GemCode Single-Cell Instrument. GEMs were reverse transcribed, droplets were broken and single stranded cDNA was isolated. cDNAs were cleaned up with DynaBeads and amplified. Finally, cDNAs were ligated with adapters, post-ligation products were amplified, cleaned-up with SPRIselect and purified libraries were sequenced on Novaseq.
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1


title: Input_Yeast_SK1_REP3


title: Input_Yeast_SK1mu_REP1


title: WT iBAT cold 2


title: 3226, MRTX1133 treated, bio rep 1


title: 3226, Control, bio rep 3

value: DMSO


title: 3226, Control, bio rep 2


title: WT_skin_wound_untreated

source_name: untreated skin wound


title: 3226, Control, bio rep 1


title: 24-hr fasting rep5

first: Dongxing

last: Zhu

state: Guangdong

address: Xinzao, Panyu District

department: School of Basic Medical Sciences

institute: Guangzhou Medical University

description: Sample 2-5

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).  Sequence quality was examined using the FastQC [1] software.
The trimmed reads (trimmed 5', 3'-adaptor  bases using cutadapt [2] ) were aligned to reference genome using Hisat2 software
The transcript abundances  for each sample was estimated with StringTie [4] , and the FPKM [8] value for gene and transcript level were  calculated with R package Ballgown
The differentially expressed genes and transcripts were filtered using  R package Ballgown. The novel genes and transcripts were predicted from assembled results by comparing to  the reference annotation using StringTie and Ballgown, then use CPAT [10] to assess the coding potential of  those sequences. Then use rMATS [11] to detecting alternative splicing events and plots.
Principle Component  Analysis (PCA) and correlation analysis were based on gene expression level, Hierarchical Clustering, Gene  Ontology, Pathway analysis, Gene Ontology, Pathway analysis, scatter plots and volcano plots were performed  with the differentially expressed genes in R, Python or shell environment for statistical computing and graphics
Genome_build: GRCm38
Supplementary_files_format_and_content: The xlsx format file contains the FPKM value of gene in every sample

source_name: Aortae

extract_protocol:
Mouse aortae were carefully dissected, and fat tissue were removed. Then mouse aortae were flash frozen in liquid nitrogen and strored at -80oC, and RNA was harvested using Trizol reagent.
Total RNA from each sample was quantified using a NanoDrop ND-1000 instrument. 1- 2 ug total RNA  was used to prepare the sequencing library in the following steps: 1. Total RNA is enriched by oligo (dT)  magnetic beads (rRNA removed); 2. RNA-seq library preparation using KAPA Stranded RNA-Seq Library  Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library  strand-specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute  quantification qPCR method. To sequence the libraries on the Illumina NovaSeq 6000 instrument, the barcoded  libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified  in situ, and subsequently sequenced for 150 cycles for both ends on Illumina NovaSeq 6000 instrument.

value: aortae

value: 7-weeks old

value: 24 hr fast


title: 24-hr fasting rep6

description: Sample 2-6


title: Input_Yeast_SK1_REP2


title: IP_Yeast_SK1_REP1


title: Input_Yeast_SK1_REP1


title: Endothelial enriched Poldip2-floxed  Repeat 3

value: Littermate Control


title: 24-hr fasting rep4

description: Sample 2-4


title: 24-hr fasting rep3

description: Sample 2-3


title: WT_skin_wound


title: 1222, MRTX1133 treated, bio rep 3


title: 1222, MRTX1133 treated, bio rep 2


title: Pc_schizont_Mm_hepatocyte_ATAC-seq_3500

first: Haoyu

last: Wu

address: Kai Yuan Avenue 190

institute: GIBH

data_processing:
For ATAC-seq data analysis, pair-end reads were mapped to a merged genome reference of Mmul_10 and PlasmoDB44 using BWA 0.7.17-r1188 mem with default settings. Next, reads mapped to the PlasmoDB44 genome only were extracted for further analysis. Duplicates and reads with mapping quality lower than 30 were removed using samtools 1.7
Open chromatin profile tracks were generated using deeptools 3.5.0 bamCoverage function with the following setting, --normalizeUsing CPM.
Genome_build: Mmul_10 and PlasmoDB44
Supplementary_files_format_and_content: bigwig files containing genomic signals of each ATAC samples

organism:
Plasmodium cynomolgi
Mus musculus

source_name: schizonts

growth_protocol: 3 hypnozoite (GFP+/mCherry-) and 3 liver-schizonts (GFP++/mCherry++) infected hepatocyte populations were collected in two independent experiments

extract_protocol:
Sorting was performed using the AriaIIIu as described previously {Voorberg-van der Wel, Elife 2021}. Parasites were collected into PBS containing 1% BSA, centrifuged (5 min, 500g, 4 °C) and kept on ice until transposase treatment.
Transposase treatment was performed in 10ul volume containing 1xTD buffer (Nextera kit, Illumina), 0.5ul “home-made” Tn5 transposase adapter complex and 0.4mg/ml digitonin (Promega, #G9441) at 30 min at 37 °C. After column purification (MinElute PCR Purification Kit, Qiagen) transposed DNA fragments were PCR amplified (98 °C for 2 min; 13 cycles of 98 °C for 20 sec, 62 °C for 3 min; 62 °C for 5 min) using Nextera i5/i7 indexing primers (Illumina) and 2x KAPA HiFi HotStart ready-mix (KAPA Biosystems). The resulting libraries were subsequently purified with Agencourt AMPure XP bead (Beckman Coulter) first at 1:0.65 ratio to remove large DNA fragments, followed by addition of extra beads to the supernatant to 1:1.8 ratio and removal of adapter dimers.
ATAC-seq libraries were sequenced on the Illumina NextSeq 500 system (Illumina, FC-110-3001) to generate 2x38 bp paired-end reads.

tag: Stage

value: schizonts


title: Pc_schizont_Mm_hepatocyte_ATAC-seq_3300


title: 24-hr fasting rep2

description: Sample 2-2


title: Pc_schizont_Mm_hepatocyte_ATAC-seq_5000


title: 1222, Control, bio rep 3


title: Input_Yeast_SK1mu_REP3


title: Pc_hypno_Mm_hepatocyte_ATAC-seq_4500

source_name: hypnozoites

value: hypnozoites


title: 1222, Control, bio rep 2


title: control rep6

description: Sample 1-6

value: control


title: Pc_hypno_Mm_hepatocyte_ATAC-seq_1500


title: 24-hr fasting rep1

description: Sample 2-1


title: 1222, Control, bio rep 1


title: control rep4

description: Sample 1-4


title: control rep5

description: Sample 1-5


title: HPAF-II_HA-hSPDEF_IgG

first: Olaf

last: Klingbeil

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Sequencing reads were mapped to the mouse or human genome (mm10/hg19) using Bowtie2 (2.4.4)
Duplicate read removal and sorting was performed using SAMtools (1.14)
Peaks were called using MACS2 (2.2.7.1) with 5% FDR cut off and broad peak option for histone- or narrow peak option for TF- datasets
Big wig files were generated using deeptools
Assembly: mm10/hg19
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: HPAF-II human PDA cell line

extract_protocol:
CUT&RUN was performed according to manufacturer’s instructions (CUTANA ChIC/CUT&RUN Kit, EpiCypher 14-1048).
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina according to manufacturer’s instructions.

value: HPAF-II human PDA cell line

value: pancreatic ductal adenocarcinoma (PDA) cell

tag: antibody

value: IgG control, EpiCypher 13-0042


title: HPAF-II_HA-hSPDEF_GATA6_REP3

value: GATA6, R&D AF1700


title: control rep3

description: Sample 1-3

tag: tissue