title: scARC library, group 35, 6 hr_GEX

description:
Library name: GEX_scARC_Library_35_6
Library 35, 6 hr post stimulation, contains cell lines CD0000035, CD0000050,  CD0000056


title: Urine cells,  membranous nephropathy patient, GEX

status: Public on Feb 18 2025

type: SRA

city: Berlin

first: Jan

last: Klocke

address: Charitéplatz 1

department: Nephrology and Intesive Care

country: Germany

institute: Charité Universitätsmedizin Berlin

library_source: transcriptomic

data_processing:
fastqc to check quality of sequencing reads
cellranger (v3.1) mkfastq to demultiplex fastq files
cellranger (v3.1) count to align sequencing files to a reference transcriptome
Assembly: Assembly: GRCh38
Supplementary files format and content: provide library.csv and feature_ref.csv for cellranger (v3.1) count of ADT samples
Supplementary files format and content: Tab-separated UMI counts in matrix.mtx. List of genes in features.tsv List of cell barcodes in barcodes.tsv
Library strategy: CITE-seq

molecule: total RNA

organism: Homo sapiens

source_name: urine

extract_protocol:
Samples were collected either as first morning void urine or via urinary catheter (using the pooled urine output of 4 hours) and stored on ice. Incubation with Actinomycin D for 30 min on ice was applied to prevent subsequent alteration of transcriptomes followed by blocking Fc receptors using human FcR blocking reagent (Miltenyi, Bergisch Gladbach, Germany). Cells were then incubated with fluorescent dyes and fluorochrome-conjugated monoclonal antibodies for fluorescence-activated cell sorting (FACS). The following antibodies and dyes were used for cell labeling: Calcein AM (BD Biosciences, San Jose, CA, USA, 564061), Hoechst 33342 (BD Biosciences, San Jose, CA, USA, 561908), AnnexinV-PE (Biolegend, San Diego, CA, USA, 640908), CD45-APC/Vio770 and CD66b-PE/Vio770 (both Miltenyi, 130-110-635 and 130-119-768). Cells were washed, filtered through a 70 µm cell strainer and labeled with To-Pro3 iodide (T3605, Life technologies, Eugene, Oregon) for dead cell discrimination immediately prior to sorting. Samples were sorted using a Sony MA900 (Sony, Tokyo, Japan) with a 100µm nozzle into phosphate buffered saline (PBS) / 1 % BSA gating To-Pro3-AnnexinV- Hoechst33342+CalceinAM+ singlets for obtaining single viable urinary cells. Urinary granulocytes, which make up a large fraction of the urinary cellular signal (median 58% in FACS gating) but for which a renal tissue origin is not verifiable, and which may interfere with downstream analysis, were excluded. Relative single cell counts in sorted suspensions were counted using a MACSQuant Analyzer (Miltenyi). Cells were centrifuged, resuspended, and re-counted on a hemocytometer. Cell suspensions were subjected to single-cell sequencing following the 10x Genomics protocol for Chromium Next GEM Single Cell  v3.1 chemistry targeting between 1000 - 10000 cells depending on sample cell count.
According to manufacturer recommendation of Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1

tag: tissue

value: urine

tag: patient

value: membranous nephropathy patient

tag: library type

value: rna


title: Urine cells, pool of 4 AKI patients, GEX

value: pool of 4 AKI patients


title: scARC library, group 35, 0 hr_GEX

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

country: USA

institute: NorthShore University HealthSystem

description:
Library name: GEX_scARC_Library_35_0
Library 35, unstimulated, contains cell lines CD0000035, CD0000050,  CD0000056

library_source: transcriptomic single cell

data_processing:
10x Genomics Chromium single cell Multiome sequencing libraries were sequenced at UMGC on Novaseq S4 platform targeting pair-end (2 x 150bp) 50k reads per nuclei for ATAC library and 25K reads per nuclei for gene expression library. Briefly, after raw data collection, Illumina’s BCL2FASTQ software was used to de-multiplex and assemble the fastq files corresponding to reads (R1/R2) and indices (i5/i7) for Cell Ranger ARC. The fastq files were subsequently processed by 10x Genomics Cell Ranger ARC (v2.0.2) and aligned twice to both the human GRCh38.p14 genome and a contingent of human GRCh38.p14 and mouse GRCm38 provided by 10x Genomics for efficient identification and removal of rodent astrocytes. For snATAC-seq, the per-library Transcription Start Sites (TSS) enrichment score is usually between 7-9 and the Fraction of high-quality Reads overlapping Peaks (FRiP) is usually between 40%-80%. We excluded cells with >15% of the reads mapped to mitochondrial genes, cells with > 8,000 or < 400 number of features, and cells with > 40,000 or <500 number of UMI counts (filtered by 400 < nCount < 8,000 using Seurat).
For each library that contains cells derived from 3-4 iPSC lines, barcode-level identification was performed separately for snRNA-seq (GEX) and snATAC-seq data with genotyping information of all donors. Briefly, the BAM files generated from GEX and ATAC assays (gex_possorted_bam.bam and atac_possorted_bam.bam) were processed by demuxlet (Kang et al., 2018) with known genotype information provided as .vcf files. Barcodes (cells) identified as singlets with P1 likelihood (p1LLK) < 1x10-8 were collected, and only barcodes positively identified in both GEX and ATAC assays were retained for downstream analysis.
snRNA-seq (GEX) data were processed by extracting gene expression data from the .h5 files generated by Cell Ranger ARC. Only barcodes (cells) confidently assigned to individual iPSC lines were retained. With Seurat 5.1.0(Hao et al., 2024), for cell type assignmentsTo assign cell type identity, Leiden clustering was performed at the library level based on the first 30 PCs (or appropriate as determined by the elbowplot) and subsequently by comparing cell clusters and their marker gene expressions (GAD1, GAD2, SLC17A6, SLC17A7, NEFM) and added as metadata. The library-level gene expression matrices were subsequently collated in Seurat 5.1.0(Hao et al., 2024) as one large object with cell line-specific metadata assigned. Harmony (Korsunsky et al., 2019) was used to integrate the library-level gene matrices and removed sequencing batch-derived effects.
For snATAC-seq data, the aggregation function of Cell Ranger ARC was used to merge and generate new fragment files for MACS2-based peak calling with the CallPeaks() function in Signac(Stuart et al., 2021) with default settings. We made two merged fragment files, one containing all libraries from batch 024 (18 cell lines) and the other from batch 018, 024, 025, and 029 (76 cell lines). From each fragment file, we iterated througugh the combinations of cell types (NEFM+ glut, NEFM- glut, GABA) and stimulation stages (0 hr, 1 hr, 6 hr), which generated nine peak sets (cell type x time). We further generated a union peak set from batch 024 by setting CallPeaks(combine.peaks = TRUE) for peak analysis across different cell types. Finally, peaks that fell within the ENCODE blacklisted regions were removed. We also removed peaks that fall within chromosomes X and Y and the mitochondrial genome regions.
Assembly: hg38/GRCh38
Supplementary files format and content: CellRanger 2.0.2 output directory sans .bam files
Supplementary files format and content: h5, count matrices snATAC and snRNA-seq
Supplementary files format and content: .cloupe, 10x Genomics Loupe data file

source_name: Neuron

growth_protocol: We differentiated iPSC lines into both excitatory and inhibitory neurons and co-cultured with rate glial cells. For excitatory neuron differentiation, we used the method to derive Ngn2-glutamatergic neuron {Zhang, 2013 #6824}  with minor modifications. On DIV0, 60-80% confluent iPSCs were dissociated into single cells using accutase and replated into Matrigel-coated 6-w plate at 5 x 105 cells per well in mTeSRPlus media with 5M ROCK inhibitor, together with appropriate amount of rtTA virus and Ngn2-puro virus. On DIV1, media was refreshed with mTeSRplus containing 5M ROCK inhibitor and 2g/ml doxycycline. On DIV2 - DIV4, cells were treated with neural culture media (Neuralbasal media with 1x B27Plus and 1x Glutamax) supplemented with 2g/ml puromycin, 2g/ml doxycycline to remove non-transduced cells. On DIV5 - DIV6, puromycin was withdrawn and cells were treated with neural culture media with 2ug/ml doxycycline. On DIV7, cells would be ready for replating. For generating excitatory neurons, we used the method to derive Ascl1/Dlx2-GABAergic neurons {Yang, 2017 #7817} with minopr modifications. On DIV0, 60-80% confluent iPSCs were dissociated into single cells using accutase and replated into Matrigel-coated 6-w plate at 7 x 105 cells per well in mTeSRPlus media with 5M ROCK inhibitor together with rtTA virus, Ascl1-puro virus and Dlx2-hygro virus. On DIV1, media was refreshed with mTeSRplus containing 5M ROCK inhibitor and 2g/ml doxycycline. From DIV2 - DIV4, cells were treated with neural culture media supplemented with 2g/ml puromycin, 150g/ml hygromycin and 2g/ml doxycycline to remove non-transduced cells. On DIV5 - DIV6, cells were treated with neural culture media with 2g/ml doxycycline and 2M AraC. Cells would be ready for replating on DIV7. To co-culture the excitatory and inhibitory neurons,  on DIV7, separately cultured Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons and primary rat cortical astrocytes (Thermofisher; N7745100) were dissociated using accutase at 37C for 15-20min. Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons and astrocytes were replated at 5:5:1 ratio onto Matrigel pre-coated 12-well plate in neural culture media supplemented with 2g/ml doxycycline, 10ng/ml BDNF, 10ng/ml GDNF, 10ng/ml NT-3 and 1% FBS. For each co-culture,  we pooled cells from 3-4 donor lines with equal proportion. On DIV8, we refilled cells with more media. From DIV9 – DIV33, media was refreshed every three days with half volume change. Doxycycline was withdrawn at DIV14 and 1uMµM AraC was added in the media from DIV8-DIV17 to ensure neuron purity. DIV33 neurons were used for KCI stimulation.

extract_protocol:
After stimulation, cells were briefly washed with 1x PBS and dissociated in accutase at 37C for 40min with gentle shaking. After accutase incubation, we pipetted cells multiple times and filtered suspension twice with 40m tip filter (Sigma# BAH136800040-50EA) to obtain single cells. The washed cells were subjected to fresh nuclei isolation following 10x Genomics’ protocols (CG000365 and CG000338). For each library, around 15,000 freshly isolated nuclei were loaded for GEM capture targeting 10,000 nuclei recovery.
The pre-amplified DNAs (for snATAC-seq) and cDNAs (for snRNA-seq) were shipped to University of Minnesota Genomics Center  (UMGC) for sn-multiomics sequencing library construction following 10x Genomics’ standard protocol.

treatment_protocol: To model neuron activation, we followed previously used protocol to treat the cells with KCI {Boulting, 2021 #8234}. Briefly, 24hr before stimulation, old media was aspirated and DIV33 neuron co-culture were silenced in neural culture media supplemented with 1M TTX and 100M DL-AP5. The next day, we added fresh culture media with warmed depolarization solution (10mM HEPES, 170mM KCl, 1mM MgCl2, 2mM CaCl2) to initiate KCI stimulation. We prepared three conditions with different treatment duration (0hr, 1hr and 6hr). After stimulation, cells were dissociated for 10x Genomics’ sn-Multiomics sequencing library preparation.

value: Neuron

tag: cell line

tag: cell type

value: cultured glutamatergic and GABAergic neurons derived from iPS cells

tag: batch


title: scARC library, group 33, 6 hr_GEX

description:
Library name: GEX_scARC_Library_33_6
Library 33, 6 hr post stimulation, contains cell lines CD0000033, CD0000034, CD0000052, CD0000055


title: scARC library, group 33, 1 hr_GEX

description:
Library name: GEX_scARC_Library_33_1
Library 33, 1 hr post stimulation, contains cell lines CD0000033, CD0000034, CD0000052, CD0000055


title: scARC library, group 33, 0 hr_GEX

description:
Library name: GEX_scARC_Library_33_0
Library 33, unstimulated, contains cell lines CD0000033, CD0000034, CD0000052, CD0000055


title: scARC library, group 05, 6 hr_GEX

description:
Library name: GEX_scARC_Library_5_6
Library 05, 6 hr post stimulation, contains cell lines CD0000002, CD000005, CD000006


title: H3K27me3_HL_E135_Shox2trac_INACTIVE_Rep1

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

description:
Library name: Sample146
sorted cells ChIP-seq H3K27me3

library_source: genomic

data_processing:
TruSeq adapter sequences and bad quality bases were removed using CutAdapt v1.18 (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q30 -m15). Reads were then mapped to mm39_dsmCherry_P2A_CRE_EYFP custome genome using Bowtie2 v2.3.5.1 with default parameters. Reads were then filtered for a MAPQ≥30 using Samtools view v1.10 and the coverage was obtained after extension of the reads by 200 bp using MACS2 v2.2.7.1 (callpeak --nomodel --call-summits --extsize 200). Coverage was normalized by the number of million tags used by MACS2. broad peak calling was performed by MACS2 using the following parameters --broad --nolambda --broad-cutoff 0.05 --nomodel --gsize mm --extsize 200 -B 2.
Assembly: custom genome: mm39_dsmCherry_P2A_CRE_EYFP
Supplementary files format and content: BigWig + MACS2 Peaks

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic Hindlimb

growth_protocol: Forelimbs and Hindlimbs from E10.5, E11.5, E12.5 and E13.5 Shox2trac embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted based on the dmCherry and EYFP fluorescent signal.

extract_protocol:
After sorting, cells were centrifuged for 5’ at 400g at 4°C and supernatant was discarded. Cells for ChIP-seq were resuspended in 10% FCS/PBS and fixed in 1% PFA at room temperature. The fixation was blocked by the addition of 1M glycine, cells were isolated by centrifugation (1000g, at 4°C for 8’), resuspended in cold lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 5 mM MgCl2, 1mM EGTA, Protease Inhibitor (Roche, 04693159001)) and incubated on ice for 10’ to isolate the cell nuclei. The nuclei were isolated by centrifugation (1000g, at 4°C for 3’), washed in cold 1X PBS, centrifuged again (1000g, at 4°C for 1’) and stored frozen at -80°C after removal of the PBS supernatant.
500000 fixed nuclei were sonicated to a 200-500bp length with the Bioruptor Pico sonicator (Diagenode).  H3K27me3 (Milipore Cat# 07-449, RRID:AB_310624) ChIP were performed as previously described (Lee et al. 2006; Rouco et al. 2021) with the addition of 5mM of Na-Butyrate to all buffers. Libraries were then prepared following the Illumina ChIP TruSeq protocol and sequenced as 50bp single-end reads on an Illumina NovaSeq 6000. Libraries were prepared starting with below <10ng quantities of ChIP-enriched DNA as starting material and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications. Libraries were validated on a Tapestation 2200 (Agilent) and a Qubit fluorimeter (Invitrogen – Thermofisher Scientific). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 or an Illumina NovaSeq 6000 sequencer.

tag: background

value: Embryonic Hindlimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: dmCherry-/EYFP-

tag: biological replicate


title: H3K27me3_HL_E135_Shox2trac_DECOM_Rep1

description:
Library name: Sample145
sorted cells ChIP-seq H3K27me3

value: dmCherry-/EYFP+


title: scARC library, group 05, 1 hr_GEX

description:
Library name: GEX_scARC_Library_5_1
Library 05, 1 hr post stimulation, contains cell lines CD0000002, CD000005, CD000006


title: scARC library, group 05, 0 hr_GEX

description:
Library name: GEX_scARC_Library_5_0
Library 05, unstimulated, contains cell lines CD0000002, CD000005, CD000006


title: ST8798_RP

first: Clemens

last: Schmitt

address: Augustenberger Platz 1

department: Hematology, Oncology and Tumor Immunology

institute: Charité Universitätsmedizin

description: Library name: AS-222828-LR-34437

data_processing:
Trim adapter sequences or low-quality ends using cutadapt
Filter rRNA sequences using sortmerna.
Align reads against reference genomes (GRCh38 or GRCm38 relase 88 for human and mouse, respectively) using STAR RNA-seq aligner 2.5.2b with --twopassMode Basic
convert sam files to bam files using Samtools
Count transcripts using summarizeOverlaps function from R/Bioconductor package GenomicAlignments with counting mode "Union"
Assembly: Convert raw counts to log2 scale using rlog method in R/Bioconductor package DESeq2
Supplementary files format and content: tab-separated txt file with raw read count

source_name: Lymph Node

growth_protocol: The primary Emu-myc lymphomas were transplanted and passaged in vivo  exclusively in strain matched C57BL6 mice.

extract_protocol:
Zymo Quick DNA/RNA Miniprep kit
Samples for RNA sequencing were prepared with the Illumina TruSeq Stranded RNA Kit

treatment_protocol: Treatment Naive

value: Lymph Node

value: primary lymphoma

value: E mu-myc B-cell lymphoma

tag: treatment response

value: RP


title: scARC library, group 63, 0 hr_ATAC

description:
Library name: scARC_Library_63_0
Library 63, unstimulated, contains cell lines CD0000004, CD0000063, CD0000064, CD0000065

library_source: genomic single cell


title: H3K27me3_HL_E135_Shox2trac_MAINTAIN_Rep1

description:
Library name: Sample144
sorted cells ChIP-seq H3K27me3

source_name: Embryonic Forelimb

value: Embryonic Forelimb

value: dmCherry+/EYFP+


title: scARC library, group 63, 6 hr_ATAC

description:
Library name: scARC_Library_63_6
Library 63, 6 hr post stimulation, contains cell lines CD0000004, CD0000063, CD0000064, CD0000065


title: AB9842_RP

description: Library name: AS-222826-LR-34437


title: scARC library, group 63, 1 hr_ATAC

description:
Library name: scARC_Library_63_1
Library 63, 1 hr post stimulation, contains cell lines CD0000004, CD0000063, CD0000064, CD0000065


title: BC3237_RP

description: Library name: AS-222827-LR-34437


title: scARC library, group 51, 6 hr_ATAC

description:
Library name: scARC_Library_51_6
Library 51, 6 hr post stimulation, contains cell lines CD0000051, CD0000060, CD0000062, CD0000066


title: AB3988_RP

description: Library name: AS-222825-LR-34436


title: scARC library, group 51, 0 hr_ATAC

description:
Library name: scARC_Library_51_0
Library 51, unstimulated, contains cell lines CD0000051, CD0000060, CD0000062, CD0000066


title: scARC library, group 35, 0 hr_ATAC

description:
Library name: scARC_Library_35_0
Library 35, unstimulated, contains cell lines CD0000035, CD0000050,  CD0000056


title: scARC library, group 51, 1 hr_ATAC

description:
Library name: scARC_Library_51_1
Library 51, 1 hr post stimulation, contains cell lines CD0000051, CD0000060, CD0000062, CD0000066


title: scARC library, group 35, 1 hr_ATAC

description:
Library name: scARC_Library_35_1
Library 35, 1 hr post stimulation, contains cell lines CD0000035, CD0000050,  CD0000056


title: scARC library, group 05, 6 hr_ATAC

description:
Library name: scARC_Library_5_6
Library 05, 6 hr post stimulation, contains cell lines CD0000002, CD000005, CD000006


title: scARC library, group 33, 1 hr_ATAC

description:
Library name: scARC_Library_33_1
Library 33, 1 hr post stimulation, contains cell lines CD0000033, CD0000034, CD0000052, CD0000055


title: ST7836_RP

description: Library name: AS-222824-LR-34436


title: scARC library, group 33, 6 hr_ATAC

description:
Library name: scARC_Library_33_6
Library 33, 6 hr post stimulation, contains cell lines CD0000033, CD0000034, CD0000052, CD0000055


title: AB7822_RP

description: Library name: AS-222822-LR-34436


title: AB7069_RP

description: Library name: AS-222821-LR-34436


title: scARC library, group 33, 0 hr_ATAC

description:
Library name: scARC_Library_33_0
Library 33, unstimulated, contains cell lines CD0000033, CD0000034, CD0000052, CD0000055


title: ST9891_RP

description: Library name: AS-222823-LR-34436


title: scARC library, group 05, 0 hr_ATAC

description:
Library name: scARC_Library_5_0
Library 05, unstimulated, contains cell lines CD0000002, CD000005, CD000006


title: TBX5 Het, atrial, d45, rep1

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description:
Library name: TBX5 Het, atrial, d45, rep1
10X Genomics
barcodes.tsv: barcode-3

data_processing:
Raw fastq files were processed with Cellranger (v6.1.1) count.
Samples from a single timepoint were aggregated using Cellranger aggr.
In the aggregated matrices, barcodes ending in -1 and -2 are wiltype, -3 and -4 are TBX5 heterozygous mutants, -5 and -6 are TBX5 homozygous mutants.
Assembly: Human hg38
Supplementary files format and content: The output of Cellranger count as gzipped tsv files with feature and barcode sequences corresponding to row and column indices respectively

source_name: WTC11 iPSC parental line

growth_protocol: iPSCs were maintained in mTeSR Plus media on growth factor-reduced (GFR) matrigel

extract_protocol:
Cells on day 20 or day 45 were singularized using 0.25%Trypsin, counted and loaded on a 10X Chromium chip according to manufacturer's instructions
Next GEM Single Cell 3' v3.1

treatment_protocol: iPSC lines were differentiated to cardiomyocytes using the Stemdiff Atrial Cardiomyocyte Differentiation Kit

tag: timepoint

value: Day 45

value: WTC11 iPSC parental line

value: Atrial cardiomyocyte

value: TBX5 Heterozygous mutant

value: batch 3


title: MKN45 cells, Treat

city: Shenyang

first: Angting

last: Ke

state: Liaoning

address: No. 4, Chongshan East Road, Huanggu District

department: Department of Surgical Oncology

country: China

institute: Fourth Affiliated Hospital of China Medical University

description: Library name: PPM_45

data_processing:
The sequencing data (Raw data)underwent quality control using fastp (v2.0) to removeadapters, trim low-quality reads (score < 20), and discard reads with an N content exceeding 10%The resulting processed data is referred to as clean data. Clean reads were aligned to the referencegenome using HISAT2 (v2.1.0), and alignment quality was assessed using RSeQC (v3.0.1).
Assembly: hg38

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Library preparation simplifies with a kit combining double-strand synthesis, end repair, and dA-tailing. mRNA is enriched with VAHTS mRNA Capture Beads（Vazyme, China） , then fragmented, and used for double-stranded cDNA synthesis. The cDNA is then purified, and adapters are ligated. Libraries are quality-checked using the Agilent Bioanalyzer and Qubit.

treatment_protocol: Cells were treated with 0.3μM periplocymarin  or 0.1%DMSO for 24h

value: Gastric cancer cell

tag: treatment

value: Periplocymarin


title: WT, atrial, d45, rep2

description:
Library name: WT, atrial, d45, rep2
10X Genomics
barcodes.tsv: barcode-2

value: Wildtype

value: batch 4


title: TBX5 Het, atrial, d45, rep2

description:
Library name: TBX5 Het, atrial, d45, rep2
10X Genomics
barcodes.tsv: barcode-4


title: MKN45 cells, Control

description: Library name: NC_45

value: DMSO


title: AB7067_RP

description: Library name: AS-222820-LR-34435


title: AB6397_RP

description: Library name: AS-222819-LR-34435


title: AB6614_RP

description: Library name: AS-222818-LR-34435


title: scARC library, group 35, 6 hr_ATAC

description:
Library name: scARC_Library_35_6
Library 35, 6 hr post stimulation, contains cell lines CD0000035, CD0000050,  CD0000056

value: Neuron

value: cultured glutamatergic and GABAergic neurons derived from iPS cells


title: HGC27 cells, Treat

description: Library name: PPM_27


title: AB6165_RP

description: Library name: AS-222817-LR-34435

value: Lymph Node

value: primary lymphoma


title: TBX5 Hom, atrial, d20, rep2

description:
Library name: TBX5 Hom, atrial, d20, rep2
10X Genomics
barcodes.tsv: barcode-6

value: Day 20

value: TBX5 Homozygous mutant

value: batch 2


title: HGC27 cells, Control

description: Library name: NC_27


title: TBX5 Hom, atrial, d20, rep1

description:
Library name: TBX5 Hom, atrial, d20, rep1
10X Genomics
barcodes.tsv: barcode-5

value: batch 1


title: B16-IFNA9 Tumours (Day 8) mouse 3 biol rep 4

city: Perth

first: Jesse

middle: David

last: Armitage

state: WA

address: 35 Stirling Hwy, Crawley

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

description: Library name: MJ43_S56

data_processing:
Raw FASTQ files were processed using CellRanger (Version 3.0.2, 10x Genomics) and aligned to the mm10 genome assembly. The CellRanger count pipeline was run with default parameters.
Assembly: mm10
Supplementary files format and content: Barcode-level count data in .h5 file format

source_name: Whole Tumour

extract_protocol:
Tumours were harvested and diced using a scalpel before being resuspended in RPMI supplemented with 3 mg/mL collagenase III (Worthington Biochemicals, USA) and 5 μg/mL DNAse I (Sigma-Aldrich, USA) for 30 mins at 37o C. Samples were neutralised in RPMI-10% FCS. Resulting single cell suspensions were passed through a 100 μM nlyon filter and centrifuged before being finally resuspended in FACS buffer (1x PBS, 1% Bovine Serum Albumin (BSA, Bovagen, USA), 5 mM EDTA).
Single cell suspensions from digested tumours were processed with V3 chemistry using the Chromium Next GEM Single Cell 3’ Gel Bead Kit v3.1 (16 rxns, PN-1000122, 10X Genomics) Chip G and Chromium Next GEM Single Cell Library Prep Kit (16 rxns, PN-1000190, 10X Genomics), according to manufacturer’s protocol.

value: Whole Tumour


title: AB5325_RP

description: Library name: AS-222816-LR-34435

value: E mu-myc B-cell lymphoma

value: RP


title: TBX5 Het, atrial, d20, rep2

description:
Library name: TBX5 Het, atrial, d20, rep2
10X Genomics
barcodes.tsv: barcode-4

value: WTC11 iPSC parental line

value: Atrial cardiomyocyte

value: TBX5 Heterozygous mutant


title: BC3802_RP

description: Library name: AS-222815-LR-34434


title: TBX5 Het, atrial, d20, rep1

description:
Library name: TBX5 Het, atrial, d20, rep1
10X Genomics
barcodes.tsv: barcode-3


title: BC1590_RP

description: Library name: AS-222814-LR-34434


title: B16-IFNA9 Tumours (Day 8) mouse 3 biol rep 2

description: Library name: MJ43_S54


title: scARC library, group 05, 1 hr_ATAC

description:
Library name: scARC_Library_5_1
Library 05, 1 hr post stimulation, contains cell lines CD0000002, CD000005, CD000006


title: WT, atrial, d20, rep1

description:
Library name: WT, atrial, d20, rep1
10X Genomics
barcodes.tsv: barcode-1

value: Wildtype


title: B16-IFNA9 Tumours (Day 8) mouse 3 biol rep 1

description: Library name: MJ43_S53


title: BC2548_RP

description: Library name: AS-222813-LR-34434


title: WT, atrial, d20, rep2

description:
Library name: WT, atrial, d20, rep2
10X Genomics
barcodes.tsv: barcode-2


title: B16-IFNA9 Tumours (Day 8) mouse 2 biol rep 4

description: Library name: MJ42_S52


title: AB7018_NR

description: Library name: AS-222811-LR-34434

value: NR


title: AB7055_NR

description: Library name: AS-222810-LR-34433


title: WT, atrial, d45, rep1

description:
Library name: WT, atrial, d45, rep1
10X Genomics
barcodes.tsv: barcode-1

value: Day 45

value: batch 3


title: B16-IFNA9 Tumours (Day 8) mouse 2 biol rep 3

description: Library name: MJ42_S51


title: B16-IFNA9 Tumours (Day 8) mouse 2 biol rep 2

description: Library name: MJ42_S50


title: B16-IFNA9 Tumours (Day 8) mouse 2 biol rep 1

description: Library name: MJ42_S49


title: B16-IFNA9 Tumours (Day 8) mouse 1 biol rep 4

description: Library name: MJ40_S44


title: AB6836_NR

description: Library name: AS-222807-LR-34433


title: AB7091_NR

description: Library name: AS-222806-LR-34433


title: B16-IFNA9 Tumours (Day 8) mouse 3 biol rep 3

description: Library name: MJ43_S55


title: 0.4 µm-pored membrane, biol rep 2

city: Sapporo

first: Takuma

last: Nohara

state: Hokkaido

department: Dermatology

country: Japan

institute: Hokkaido University

description: Library name: Sample 2

data_processing:
Reads were mapped to hg38 using STAR (v.2.7.3).
Gene expression levels were quantified using RSEM (v.1.3.1).
Read counts were analyzed through integrated differential expression and pathway analysis (iDEP9.51).
Genes with low-level expression (less than 0.5 counts per million in all samples) were removed from the analysis.
Genes that were differentially expressed between low-density and high-density conditions were identified with DESeq2 using a threshold of false discovery rate of <0.1 and a fold-change of >2.
Assembly: hg38
Supplementary files format and content: tab-separated text file includes CPM values calculated by edgeR for each Sample

source_name: HaCaT cells expressing Cas9 and LifeAct-GFP, cultured on 0.4 µm-pored membrane, biol rep 2

growth_protocol: LifeAct-KCs were cultured in Dulbecco's modified eagle medium (DMEM) supplemented with 10% FBS and 1% antibiotic with 4.5 g/L glucose and L-glutamine (Nacalai Tesque, Kyoto, Japan).

extract_protocol:
RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany).
mRNA was enriched using oligo(dT) beads. The mRNA was fragmented randomly by adding a fragmentation buffer, then the cDNA was synthesized using an mRNA template and a random hexamer primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, Rnase H, and DNA polymerase I were added to initiate second-strand synthesis. After a series of terminal repair, A-tailing, and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: HaCaT KCs were cultured on a 0.4 µm- or 3.0 µm-pored membrane for 48 hours. KCs above the membrane were then collected by a scraper.

value: HaCaT cell

value: immortal epidermal keratinocytes

value: WT

value: cultured on 0.4 um-pored PET membrane


title: 0.4 µm-pored membrane, biol rep 1

description: Library name: Sample 1

source_name: HaCaT cells expressing Cas9 and LifeAct-GFP, cultured on 0.4 µm-pored membrane, biol rep 1


title: B16-IFNA9 Tumours (Day 8) mouse 1 biol rep 3

description: Library name: MJ40_S43


title: B16-IFNA9 Tumours (Day 8) mouse 1 biol rep 2

description: Library name: MJ40_S42


title: AB5529_NR

description: Library name: AS-222804-LR-34432

value: Lymph Node

value: primary lymphoma


title: Transdifferentiated_footprinting_2

city: Tucson

first: Kevin

last: Rhine

state: AZ

address: 1703 E Mabel St

department: Pharmacology & Toxicology

institute: University of Arizona

description:
rp_NK_rep2
nk_aging_effect_fp.csv

data_processing:
Riboseq data was analyzed as described previously; see Tirosh et al. 2015 doi:10.1371/journal.ppat.1005288
Assembly: hg19
Supplementary files format and content: RNA-seq and footprinting reads for each sample in duplicate

growth_protocol: DMEM, 15% FBS, 1X MEM NEAA for fibroblast culturing; mTeSR Plus for iPSC culturing; F12/Neurobasal, dox, db-cAMP, laminin, BDNF, GDNF, NT-3 for iPSC-derived neurons, F12/Neurobasal, dox, db-cAMP, laminin, DMH1, CHIR, SB, A83-01, forskolin for transdifferentiated neurons

extract_protocol:
RiboSeq experiments were performed as described previously; see Finkel et al. 2021 doi:10.1038/s41586-020-2739-1
RiboSeq libraries were generated as described previously; see Finkel et al. 2021 doi:10.1038/s41586-020-2739-2

treatment_protocol: Footprinting cells were treated with 100 ug/mL cycloheximide for 1 min to stall translation prior to lysis

value: Transdifferentiated cortical neurons

value: 100 ug/mL cycloheximide


title: 0.4 µm-pored membrane, biol rep 3

description: Library name: Sample 3

source_name: HaCaT cells expressing Cas9 and LifeAct-GFP, cultured on 0.4 µm-pored membrane, biol rep 3


title: Transdifferentiated_RNA-Seq_2

description:
rnaseq_NK_rep2
nk_aging_effect_mrna.csv


title: B16-IFNA4 Tumours (Day 8) mouse 3 biol rep 4

description: Library name: MJ38_S36

value: Whole Tumour


title: 3.0 µm-pored membrane, biol rep 3

description: Library name: Sample 6

source_name: HaCaT cells expressing Cas9 and LifeAct-GFP, cultured on 3.0 µm-pored membrane, biol rep 3

value: cultured on 3.0 um-pored PET membrane


title: 3.0 µm-pored membrane, biol rep 2

description: Library name: Sample 5

source_name: HaCaT cells expressing Cas9 and LifeAct-GFP, cultured on 3.0 µm-pored membrane, biol rep 2


title: AB8645_NR

description: Library name: AS-222809-LR-34433

value: E mu-myc B-cell lymphoma


title: B16-IFNA4 Tumours (Day 8) mouse 3 biol rep 3

description: Library name: MJ38_S35


title: AB7133_NR

description: Library name: AS-222802-LR-34432


title: AB7290_NR

description: Library name: AS-222801-LR-34432


title: B16-IFNA9 Tumours (Day 8) mouse 1 biol rep 1

description: Library name: MJ40_S41


title: 3.0 µm-pored membrane, biol rep 1

description: Library name: Sample 4

source_name: HaCaT cells expressing Cas9 and LifeAct-GFP, cultured on 3.0 µm-pored membrane, biol rep 1


title: Transdifferentiated_footprinting_1

description:
rp_NK_rep1
nk_aging_effect_fp.csv


title: B16-IFNA4 Tumours (Day 8) mouse 3 biol rep 2

description: Library name: MJ38_S34


title: AB6619_NR

description: Library name: AS-222808-LR-34433


title: Transdifferentiated_RNA-Seq_1

description:
rnaseq_NK_rep1
nk_aging_effect_mrna.csv


title: iPSC-derived_footprinting_1

description:
rp_NGN_rep1
nk_aging_effect_fp.csv

value: iPSC-derived cortical neurons


title: BC1782_NR

description: Library name: AS-222799-LR-34431


title: iPSC-derived_RNA-Seq_2

description:
rnaseq_NGN_rep2
nk_aging_effect_mrna.csv


title: AB5766_NR

description: Library name: AS-222805-LR-34432


title: iPSC-derived_RNA-Seq_1

description:
rnaseq_NGN_rep1
nk_aging_effect_mrna.csv


title: B16-IFNA4 Tumours (Day 8) mouse 3 biol rep 1

description: Library name: MJ38_S33


title: ST9218_NR

description: Library name: AS-222797-LR-34431


title: BC1332_NR

description: Library name: AS-222798-LR-34431


title: ST8799_NR

description: Library name: AS-222803-LR-34432


title: BC1960_NR

description: Library name: AS-222796-LR-34431


title: TransdifferentiatedNeurons_deep_2

description:
featurecounts_deepRNA-Seq.csv
NK_deep_2

data_processing:
RNA-Seq data was processed using the NF-Core architecture, which compiles several RNA-seq processing steps into a single executable command
Assembly: hg38
Supplementary files format and content: Feature counts for all detected transcripts in .csv format

extract_protocol:
RNA was extracted using Trizol and then further purified using the RNA Clean&Concentrator kit
Libraries were constructed using the Illumina Stranded mRNA Prep with IDT for Illumina adaptors

treatment_protocol: Cells were either used as-is, treated for 1 h with 0.5 mM sodium arsenite, or arsenite-treated and recovered for 24 h


title: TransdifferentiatedNeurons_deep_1

description:
featurecounts_deepRNA-Seq.csv
NK_deep_1


title: B16-IFNA4 Tumours (Day 8) mouse 2 biol rep 1

description: Library name: MJ36_S25


title: iPSC-derived_footprinting_2

description:
rp_NGN_rep2
nk_aging_effect_fp.csv

value: 100 ug/mL cycloheximidede


title: B16-IFNA4 Tumours (Day 8) mouse 1 biol rep 4

description: Library name: MJ35_S24


title: Stomach,desert_type,T5

city: Fuzhou

first: Guangtan

last: Lin

state: Fujian

address: No. 29 Xinquan Road

department: Department of Gastric Surgery

institute: Fujian Medical University Union Hospital

description:
Library name: MDA_T5
Column name in Normalized_fpkm_All_Samples.txt:MDA_T5

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files

source_name: stomach

extract_protocol:
A total of six mouse GC samples, including three APTc tumors and three orthotopic MDA tumors, were collected for whole-transcriptome RNA sequencing to establish the mouse bulk RNA sequence cohort. Total RNA was extracted using TRIzol™ reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol.
RNA libraries for RNA-seg were prepared using TruSeq SR Cluster Kit v.3-cBot-Hs following manufacturer's protocols.

value: stomach

value: Wild type

value: Orthotopic allograft models


title: iPSC-DerivedNeurons_deep_2

description:
featurecounts_deepRNA-Seq.csv
Ngn2_deep_2


title: B16-IFNA4 Tumours (Day 8) mouse 1 biol rep 3

description: Library name: MJ35_S23


title: iPSC-DerivedNeurons_deep_1

description:
featurecounts_deepRNA-Seq.csv
Ngn2_deep_1


title: BC1954_NR

description: Library name: AS-222800-LR-34431

value: NR


title: Stomach,desert_type,T3

description:
Library name: MDA_T3
Column name in Normalized_fpkm_All_Samples.txt:MDA_T3


title: B16-IFNA4 Tumours (Day 8) mouse 1 biol rep 2

description: Library name: MJ35_S22


title: Stomach,desert_type,T2

description:
Library name: MDA_T2
Column name in Normalized_fpkm_All_Samples.txt:MDA_T2


title: G3BP1_NK_Unstress_IP_1

data_processing:
eCLIP data was analyzed using Skipper with default settings. The kDa of each ORF was matched to the closest input sample beginning at that range; for example, a 78 kDa ORF would be paired with the input sample covering the range of 75 to 150 kDa.
Assembly: hg38/mm10
Supplementary files format and content: Reproducible enriched peaks output by Skipper

extract_protocol: eCLIP experiments were performed as previously described using the antibodies indicated above in the "treatment" entry; see Blue et al. 2022 doi:10.1038/s41596-022-00680-z

treatment_protocol: Cells were either used as-is or treated for 1 h with 0.5 mM sodium arsenite; the RNA-binding protein in the file title was immuoprecipitated using the antibody listed in the "treatment" section prior to library preparation

value: MBLI #RN048PW


title: G3BP1_NGN2_Stress_IP_2


title: B16-IFNA4 Tumours (Day 8) mouse 1 biol rep 1

description: Library name: MJ35_S21


title: B16-IFNA4 Tumours (Day 8) mouse 2 biol rep 4

description: Library name: MJ36_S28


title: Stomach,desert_type,T1

description:
Library name: MDA_T1
Column name in Normalized_fpkm_All_Samples.txt:MDA_T1


title: B16-GFP Tumours (Day 8) mouse 3 biol rep 4

description: Library name: MJ34_S20


title: B16-IFNA4 Tumours (Day 8) mouse 2 biol rep 3

description: Library name: MJ36_S27


title: Stomach,inflamed_type,T5

description:
Library name: APTc_T5
Column name in Normalized_fpkm_All_Samples.txt:APTc_T5

value: Genetic mutation


title: B16-GFP Tumours (Day 8) mouse 3 biol rep 3

description: Library name: MJ34_S19


title: B16-IFNA4 Tumours (Day 8) mouse 2 biol rep 2

description: Library name: MJ36_S26


title: G3BP1_NGN2_Stress_IP_1


title: G3BP1_NGN2_Unstress_IP_2


title: Stomach,inflamed_type,T4

description:
Library name: APTc_T4
Column name in Normalized_fpkm_All_Samples.txt:APTc_T4


title: G3BP1_NGN2_Unstress_IP_1


title: Stomach,desert_type,T4

description:
Library name: MDA_T4
Column name in Normalized_fpkm_All_Samples.txt:MDA_T4


title: B16-GFP Tumours (Day 8) mouse 2 biol rep 4

description: Library name: MJ33_S16


title: Caprin1_NK_Unstress_IP_1

value: Bethyl #A303-882A


title: Caprin1_NK_Unstress_IP_2


title: B16-GFP Tumours (Day 8) mouse 3 biol rep 1

description: Library name: MJ34_S17


title: Stomach,inflamed_type,T3

description:
Library name: APTc_T3
Column name in Normalized_fpkm_All_Samples.txt:APTc_T3


title: B16-GFP Tumours (Day 8) mouse 2 biol rep 3

description: Library name: MJ33_S15


title: Caprin1_NGN2_Stress_IP_2

value: Bethyl #A303-882A; 0.5 mM sodium arsenite


title: B16-GFP Tumours (Day 8) mouse 2 biol rep 2

description: Library name: MJ33_S14


title: Stomach,inflamed_type,T1

description:
Library name: APTc_T1
Column name in Normalized_fpkm_All_Samples.txt:APTc_T1


title: B16-GFP Tumours (Day 8) mouse 2 biol rep 1

description: Library name: MJ33_S13


title: Caprin1_NGN2_Unstress_IP_2


title: Caprin1_NGN2_Stress_IP_1


title: control,Klebsiella pneumoniae,biol rep 3

city: Beijing

first: Chenxi

last: Dai

address: Dongdajie

institute: Academy of Millitary Medical Sciences

description:
Library name: KP_3
Column name in All_reads_counts_host.xlsx: KP_3,Column name in All_reads_counts_pathogen.xlsx: KP_3

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.0), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The reference genomes of the two species were merged, and then the deduplicated data were mapped to the two reference genomes of Mus musculus from ftp://ftp.ensembl.org/pub/release-87/fasta/mus_musculus/dna/ and Klebsiella Pneumoniae from https://www.ncbi.nlm.nih.gov/nuccore/CP109963 using STAR software (version 2.5.3a) with default parameters.
The reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.28.1). A p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment.
Alternative splicing events were detected by using rMATS (version 3.2.5) with a p value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: Mus musculus:GRCm38.87;Klebsiella Pneumoniae:CP109963
Supplementary files format and content: xlsx files includes counts of each gene for each sample

organism: Klebsiella pneumoniae

growth_protocol: Specific pathogen-free, female C57BL/6J mice (6 to 8 weeks old) were housed in an Animal Biosafety Level-2 (ABSL-2) laboratory.Klebsiella pneumoniae strain NY13307 was cultured using the three-generation culture method.

extract_protocol:
Total RNA was isolated from the specified biological materials using TRIzol Reagent (Thermo Scientific, cat. #15596026) following the manufacturer's recommended protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
For library preparation, the RNA of each sample was used for stranded dual RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Vazyme, China, cat. #N406 for animal, cat. #N407 for bacteria) to deplete rRNA, and then components of KCTM Digital Stranded mRNA Library Prep Kit (Seqhealth Tech. Co., Ltd. Wuhan, China) following the manufacturer’s instruction. The kit eliminates duplication bias and errors in PCR and sequencing steps, by using unique molecular identifier (UID) of 12 random bases to label the pre-amplified cDNA molecules.PCR products corresponding to fragments ranging from 200 to 500 base pairs were enriched,quantified and sequenced on a DNBSEQ-T7 platform using the PE150 mode to generate paired-end reads.

treatment_protocol: Mice were challenged via aerosolized intratracheal inoculation with Klebsiella pneumoniae strain NY13307 at two different doses: 3 × 10^8 CFU and 7 × 10^6 CFU.


title: control,Klebsiella pneumoniae,biol rep 2

description:
Library name: KP_2
Column name in All_reads_counts_host.xlsx: KP_2,Column name in All_reads_counts_pathogen.xlsx: KP_2


title: B16-GFP Tumours (Day 8) mouse 1 biol rep 4

description: Library name: MJ32_S12


title: control,Mus musculus,biol rep 3

description:
Library name: C57_3
Column name in All_reads_counts_host.xlsx: C57_3,Column name in All_reads_counts_pathogen.xlsx: C57_3

value: lung


title: B16-GFP Tumours (Day 8) mouse 1 biol rep 3

description: Library name: MJ32_S11


title: TDP-43_NK_Unstress_IP_2

value: Bethyl #A303-223A


title: Caprin1_NGN2_Unstress_IP_1


title: control,Mus musculus,biol rep 2

description:
Library name: C57_2
Column name in All_reads_counts_host.xlsx: C57_2,Column name in All_reads_counts_pathogen.xlsx: C57_2


title: B16-GFP Tumours (Day 8) mouse 3 biol rep 2

description: Library name: MJ34_S18


title: B16-GFP Tumours (Day 8) mouse 1 biol rep 2

description: Library name: MJ32_S10


title: B16-GFP Tumours (Day 8) mouse 1 biol rep 1

description: Library name: MJ32_S9


title: TDP-43_NK_Unstress_IP_1

value: Transdifferentiated cortical neurons


title: TDP-43_NGN2_Stress_IP_2

value: Bethyl #A303-223A; 0.5 mM arsenite for 1 h


title: Low dose,24h,biol rep 3

description:
Library name: L24_3
Column name in All_reads_counts_host.xlsx: L24_3,Column name in All_reads_counts_pathogen.xlsx: L24_3


title: control,Mus musculus,biol rep 1

description:
Library name: C57_1
Column name in All_reads_counts_host.xlsx: C57_1,Column name in All_reads_counts_pathogen.xlsx: C57_1


title: Stomach,inflamed_type,T2

description:
Library name: APTc_T2
Column name in Normalized_fpkm_All_Samples.txt:APTc_T2


title: CR_HOXD13_DFL_Shox2Ull_E135_Rep1

description:
Library name: Sample149
HOXD13 CUT&RUN

data_processing:
TruSeq adapter sequences and bad quality bases were removed using CutAdapt v4.9  (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q30 -m15). Reads were then mapped to mm39_dsmCherry_P2A_CRE_EYFP custome genome using Bowtie2 v2.5.4 (using the following options: --very-sensitive --no-unal --no-mixed --no-discordant --dovetail -X 1000). Reads were then filtered for a MAPQ≥30 using Samtools view v1.21 (-q30). PCR duplicates were removed with MarkDuplicates tool from Picard version 2.27.4 before the BAM conversion to BED using bamtobed bedtools  version 2.31.1. Coverage was obtained using the options --nomodel --keep-dup all --shift -100 --extsize 200 --call-summits -B 2. MACS2 output file was then normalized by million reads.
Assembly: custom genome: mm39_dsmCherry_P2A_CRE_EYFP
Supplementary files format and content: BigWig + MACS2 Peaks
Library strategy: CUT&Run

source_name: Embryonic Distal Forelimb

growth_protocol: Proximal and distal Forelimbs from E13.5 Shox2Ull and CD1 wildtype embryos were microdissected in PBS and dissociated using trypsin-EDTA 0.25% (Thermo Fischer Scientific, 25300062) supplemented with 40μl of 5% BSA for ~12min. After Trypsin inactivation with one volume of 2.5% BSA, cells were passed through a 40μm cell strainer and another volume of 2.5% BSA was added to wash the cell strainer. Cells were spun at 400g for 5min at 4 °C and resuspended in 1%BSA in PBS.

extract_protocol:
After dissociation cells were processed for CUT and RUN following the protocol described by Skene et al. 2018. After a couple of washes, 250K were isolated and used for downstream steps. Cells were incubated with Concavalin A-coted beads (Con A-coated BioMag® Plus beads #86057). Bounded cells were then incubated overnight at 4 °C with the antibody solution containing 0.02% digitonin (Apollo APOBID3301) and 0.5 µl of HOXD13 antibody (Abcam AB229234). Samples were then incubated with the buffer containing the pA-MNase (produced from Addgene pAG/MNase #123461) for 1h on ice. Digestion wash was performed on low-calcium buffer (4 µl of 100 mM CaCl2 in 196 µl of Dig-Wash Buffer) and stopped after 30 min with  2XSTOP Buffer. DNA was precipitated following standard phenol:chloroform:IAA precipitation.
Libraries were prepared by the iGE3 Genomic Platform following starting with 5 ng of CUT&RUN-enriched DNA as starting material and processed with the Illumina TruSeq ChIP Library Preparation Kit and the IDT TruSeq RNA UD Indexes v2. No size selection was performed. Library molarity and quality were assessed with the Qubit (Thermofisher Scientific) and Tapestation (Agilent Technologies - DNA High sensitivity chip). Libraries were sequenced on a NovaSeq 6000 Illumina sequencer for PE 50 reads.

value: Embryonic Distal Forelimb

value: Not sorted


title: TDP-43_NGN2_Stress_IP_1


title: Low dose,24h,biol rep 2

description:
Library name: L24_2
Column name in All_reads_counts_host.xlsx: L24_2,Column name in All_reads_counts_pathogen.xlsx: L24_2


title: Low dose,24h,biol rep 1

description:
Library name: L24_1
Column name in All_reads_counts_host.xlsx: L24_1,Column name in All_reads_counts_pathogen.xlsx: L24_1


title: TDP-43_NGN2_Unstress_IP_2


title: TDP-43_NGN2_Unstress_IP_1


title: CR_HOXD13_PFL_CD1WT_E135_Rep1

description:
Library name: Sample147
HOXD13 CUT&RUN

source_name: Embryonic Proximal Forelimb

value: Embryonic Proximal Forelimb

value: Wildtype


title: Low dose,18h,biol rep 3

description:
Library name: L18_3
Column name in All_reads_counts_host.xlsx: L18_3,Column name in All_reads_counts_pathogen.xlsx: L18_3


title: control,Klebsiella pneumoniae,biol rep 1

description:
Library name: KP_1
Column name in All_reads_counts_host.xlsx: KP_1,Column name in All_reads_counts_pathogen.xlsx: KP_1


title: Psoriasis, 8

city: Uppsala

first: Enikö

last: Sonkoly

address: Entrance 40, 5th floor

department: University Hospital

country: Sweden

institute: Uppsala University

description: 16-UH-3032-R-CD45-neg-P201-PPAligned.sortedByCoord.out.bam

data_processing:
Alignment was done using STAR_2.6.1d
Assembly: hg38/GRCh38
Supplementary files format and content: tab-separated raw read counts

source_name: Epidermis

extract_protocol:
Qiagen miRNeasy kit
Illumina Ribo-Zero Plus ribosomal depletion

treatment_protocol: 4 mm punch biopsies were obtained, the epidermis and dermis separated following dispase treatment and the epidermis was dissociated using trypsin and negatively sorted for CD45 using magnetic beads to enrich epidermal keratinocytes

value: Epidermis

value: CD45-negative epidermal cells


title: Low dose,18h,biol rep 2

description:
Library name: L18_2
Column name in All_reads_counts_host.xlsx: L18_2,Column name in All_reads_counts_pathogen.xlsx: L18_2


title: FL_Shox2Δlate_E145_DECOM_REP3

description:
Library name: Sample143
sorted cells RNA-seq

data_processing:
NextSeq adapter sequences and bad quality bases were removed using CutAdapt v1.18 (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q30 -m15). Unstranded reads were then mapped to the custom genom mm39_dsmCherry_P2A_CRE_EYFP. We used STAR v2.7.2b with a filtered GTF allowing to get a gene quantification simultaneously (--outSAMstrandField intronMotif --sjdbOverhang '99' --sjdbGTFfile $gtfFile --quantMode GeneCounts --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1). FPKM values were determined by Cufflinks v2.2.1 (--max-bundle-length 10000000  --max-bundle-frags 100000000 -- multi-read-correct --library-type “fr-firststrand” --no-effective-length-correction -M MTmouse.gtf). Normalized FPKM were then computed by determining coefficients extrapolated from a set of 1000 house-keeping stably expressed genes, in between the series of compared RNA-seq datasets. Coverage was computed with Bedtools v2.28.0 using uniquely mapped reads (NH:i:1 tag). When indicated, coverage profiles represent an average of the replicates, this was done by dividing each replicate by the number of millions of uniquely mapped reads (for normalization) and calculating the average coverage.
Assembly: custom genome: mm39_dsmCherry_P2A_CRE_EYFP
Supplementary files format and content: BigWig

molecule: polyA RNA

growth_protocol: Forelimbs and Hindlimbs from E10.5, E11.5, E12.5 and E13.5 Shox2trac embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted based on the dmCherry and EYFP fluorescent signal. Also entire forelimbs from E10.5, E11.5 and E14.5 Shox2trac embryos, entire forelimbs at E10.5 and E14.5 from Shox2Δearly embryos and entire forelimbs from E11.5 and E14.5 Shox2Δlate embryos were microdissected in PBS and dissociated in a cell suspension.

extract_protocol:
Forelimbs and Hindlimbs sorted cells and entire forelimbs cell suspession were centrifuged for 5’ at 400g at 4°C, supernatant was discarded and cells frozen at -80°C. Total RNA was isolated using the RNeasy Micro Kit (QIAGEN, ID:74004) following manufacturer’s instructions and then stored frozen at -80°C. Total RNA was quantified with a Qubit (fluorimeter from Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies).
The SMART-Seq v4 kit from Clontech, (#634893) was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 5 ng of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina, FC-131-1096. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell for an average of 35 mio reads / library. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 or Illumina NovaSeq 6000 sequencer.

value: Embryonic Forelimb

value: dmCherry-/EYFP+


title: Low dose,12h,biol rep 3

description:
Library name: L12_3
Column name in All_reads_counts_host.xlsx: L12_3,Column name in All_reads_counts_pathogen.xlsx: L12_3


title: Low dose,18h,biol rep 1

description:
Library name: L18_1
Column name in All_reads_counts_host.xlsx: L18_1,Column name in All_reads_counts_pathogen.xlsx: L18_1


title: FL_Shox2Δlate_E145_DECOM_REP1

description:
Library name: Sample141
sorted cells RNA-seq


title: FL_Shox2Δlate_E145_DECOM_REP2

description:
Library name: Sample142
sorted cells RNA-seq


title: Psoriasis, 6

description: 14-UH-3032-R-CD45-neg-P199-PPAligned.sortedByCoord.out.bam


title: FL_Shox2Δlate_E145_MAINTAIN_REP3

description:
Library name: Sample140
sorted cells RNA-seq

value: dmCherry+/EYFP+


title: Psoriasis, 7

description: 15-UH-3032-R-CD45-neg-P200-PPAligned.sortedByCoord.out.bam


title: Psoriasis, 4

description: 12-UH-3032-R-CD45-neg-P196-PPAligned.sortedByCoord.out.bam


title: Low dose,12h,biol rep 1

description:
Library name: L12_1
Column name in All_reads_counts_host.xlsx: L12_1,Column name in All_reads_counts_pathogen.xlsx: L12_1


title: FL_Shox2Δlate_E145_MAINTAIN_REP1

description:
Library name: Sample138
sorted cells RNA-seq


title: Low dose,12h,biol rep 2

description:
Library name: L12_2
Column name in All_reads_counts_host.xlsx: L12_2,Column name in All_reads_counts_pathogen.xlsx: L12_2


title: Psoriasis, 5

description: 13-UH-3032-R-CD45-neg-P198-PPAligned.sortedByCoord.out.bam


title: FL_Shox2Δlate_E145_MAINTAIN_REP2

description:
Library name: Sample139
sorted cells RNA-seq


title: Psoriasis, 3

description: 11-UH-3032-R-CD45-neg-P195-PPAligned.sortedByCoord.out.bam


title: Low dose,6h,biol rep 3

description:
Library name: L6_3
Column name in All_reads_counts_host.xlsx: L6_3,Column name in All_reads_counts_pathogen.xlsx: L6_3


title: Psoriasis, 2

description: 10-UH-3032-R-CD45-neg-P194-PPAligned.sortedByCoord.out.bam


title: CR_HOXD13_PFL_Shox2Ull_E135_Rep1

description:
Library name: Sample148
HOXD13 CUT&RUN


title: FL_Shox2trac_E145_DECOM_REP3

description:
Library name: Sample137
sorted cells RNA-seq


title: Low dose,6h,biol rep 2

description:
Library name: L6_2
Column name in All_reads_counts_host.xlsx: L6_2,Column name in All_reads_counts_pathogen.xlsx: L6_2


title: FL_Shox2trac_E145_DECOM_REP2

description:
Library name: Sample136
sorted cells RNA-seq


title: Psoriasis, 1

description: 9-UH-3032-R-CD45-neg-P193-PPAligned.sortedByCoord.out.bam


title: Healthy, 8

description: 8-UH-3032-R-CD45-neg-H090Aligned.sortedByCoord.out.bam


title: serum_small RNA seq_NSCLC patient replicate 3

city: Qingdao

first: chenyu

last: li

address: No. 308 Ningxia Road, Qingdao City

institute: Qingdao University

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequencing quality are examined by FastQC (pass Illumina quality filter),  and reads were trimmed 5 ,3-adaptor bases by cutadapt.
The expression profiling of tRF & tiRNA  were calculated based on counts of reads mapped.
Reads were aligned allowing for 1 mismatch only to the mature tRNA sequences,  then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
Differential expression analysis of tRF&tiRNAs between groups was performed using edgeR. For differentially expressed tRF&tiRNAs were screened with the significant threshold to 1.5-fold difference, p-value ≤ 0.05 and the mean CPM within the group ≥ 1
Assembly: HG38
Supplementary files format and content: the CPM value of detected tRF&tiRNA for each sample

source_name: seurm

extract_protocol:
Agarose electrophoresis was used to check the integrality of total RNA samples, and then the samples were  quantified on the NanoDrop ND-1000 instrument.
Total RNA samples were first pretreated as following to remove some RNA  modifications that interfere with small RNA-seq library construction: 3-aminoacyl (charged) deacylation to  3-OHfor 3-adaptor ligation, 3-cP (2 ,3-cyclic phosphate) removal to 3-OH for 3-adaptor ligation,  5-OH(hydroxyl group) phosphorylation to 5-P for 5-adaptor ligation, m1A and m3C demethylation for  efficient reverse transcription. Then pretreated total RNA was used to prepare the sequencing library in the  following steps: 1) 3-adapter ligation; 2) 5-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5)  size selection of 134∼160bp PCR amplified fragments (corresponding to 14∼40nt small RNA size range). The  libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ  as sequencing clusters and sequenced for 50 cycles on Illumina NextSeq 500 system per the manufacturer s  instructions

value: serum

tag: disease state

value: NSCLC


title: Low dose,6h,biol rep 1

description:
Library name: L6_1
Column name in All_reads_counts_host.xlsx: L6_1,Column name in All_reads_counts_pathogen.xlsx: L6_1


title: FL_Shox2trac_E145_MAINTAIN_REP3

description:
Library name: Sample134
sorted cells RNA-seq


title: Low dose,0h,biol rep 3

description:
Library name: L0_3
Column name in All_reads_counts_host.xlsx: L0_3,Column name in All_reads_counts_pathogen.xlsx: L0_3


title: serum_small RNA seq_NSCLC patient replicate 2


title: Healthy, 7

description: 7-UH-3032-R-CD45-neg-H089Aligned.sortedByCoord.out.bam


title: Low dose,0h,biol rep 2

description:
Library name: L0_2
Column name in All_reads_counts_host.xlsx: L0_2,Column name in All_reads_counts_pathogen.xlsx: L0_2


title: FL_Shox2trac_E145_MAINTAIN_REP2

description:
Library name: Sample133
sorted cells RNA-seq


title: Low dose,0h,biol rep 1

description:
Library name: L0_1
Column name in All_reads_counts_host.xlsx: L0_1,Column name in All_reads_counts_pathogen.xlsx: L0_1


title: serum_small RNA seq_healthy individual replicate 3

value: healthy


title: serum_small RNA seq_NSCLC patient replicate 1


title: Healthy, 5

description: 5-UH-3032-R-CD45-neg-H087Aligned.sortedByCoord.out.bam


title: Healthy, 6

description: 6-UH-3032-R-CD45-neg-H088Aligned.sortedByCoord.out.bam


title: serum_small RNA seq_healthy individual replicate 2


title: Healthy, 4

description: 4-UH-3032-R-CD45-neg-H086Aligned.sortedByCoord.out.bam


title: High dose,24h,biol rep 2

description:
Library name: H24_2
Column name in All_reads_counts_host.xlsx: H24_2,Column name in All_reads_counts_pathogen.xlsx: H24_2


title: eFLWTG4_E125_REP3

description:
Library name: Sample131
entire forelimb (bulk) RNA-seq

value: entire limb (not sorted)


title: eFL_Shox2trac_E125_REP3

description:
Library name: Sample128
entire forelimb (bulk) RNA-seq


title: High dose,24h,biol rep 1

description:
Library name: H24_1
Column name in All_reads_counts_host.xlsx: H24_1,Column name in All_reads_counts_pathogen.xlsx: H24_1

value: lung


title: Healthy, 3

description: 3-UH-3032-R-CD45-neg-H085Aligned.sortedByCoord.out.bam


title: FL_Shox2trac_E145_DECOM_REP1

description:
Library name: Sample135
sorted cells RNA-seq


title: serum_small RNA seq_healthy individual replicate 1


title: Psoriasis14_preTx_LS_02

city: Sacramento

first: JAEHWAN

last: KIM

address: 10535 Hospital Way

institute: University of California, Davis

data_processing:
CellRanger version 3.1 (10X Genomics) pipelines were used for demultiplexing base calls into Fastq, filtering, barcode counting and filtering, UMI counting and alignment with reference human genome GRCh38.
The quality control, normalization, linear regression of number of UMIs and scaling were performed using Seurat (v4.0).
Seurat R package (version 4.0, https://satijalab.org/seurat/) was used for the single-cell data integration. We first merged single-cell data of samples with the common sequencer and the identical reagent kit version. To harmonize merged groups into a single dataset without batch effects, correspondences between cells in three merged datasets were identified by the FIndIntegrationAnchors function, and used for data integration with the IntegratedData function in Seurat R package.
Principal component analysis and graph-based clustering analysis were performed with Seurat R package (version 4.0, https://satijalab.org/seurat/). Sixty principal components (PCs) were selected for Uniform Manifold Approximation and Projection (UMAP) for Dimension Reduction. With a resolution of 0.8, cells were clustered by the FindClusters function. Then, differentially expressed genes of each cluster compared to all other cells were found by the FindAllMarkers function. Differentially expressed genes between psoriasis and control within each cluster were found by the FindMarkers function. The average gene expression of psoriasis vs. control cells within a cluster was calculated by the AverageExpression function.
Assembly: GRCh38
Supplementary files format and content: barcode table, gene table and gene expression matrix files generated by Cell Ranger version 3.1.

source_name: Skin

extract_protocol:
6 mm punch skin biopsy tissues from human skin were bisected, and one of the two bisected skin tissues was incubated in culture medium for harvesting emigrating cells. Harvested skin tissue was immediately placed in 0.2% Dispase II (Sigma-Aldrich) and incubated in a humidified incubator at 37 Celsius and 5% CO2 for 3 hours. Then, epidermis and dermis were separated with forceps and sliced into small pieces with #10 blade scalpels. Epidermis and dermis were separately cultured in RPMI-1640 medium with L-glutamine (Cytiva) supplemented with 10% human albumin serum (Sigma-Aldrich) and without any enzyme or antibiotic agent in a humidified incubator at 37 Celsius and 5% CO2. Nonplastic adherent cells that had emigrated out of epidermis and dermis were harvested after 48 hours. The harvested cells from epidermis and dermis were filtered through a 40-µm cell strainer (Corning) and stored on ice.
The 10x Genomics Chromium Single Cell 3′ Reagents Kit user guide (https://support.10xgenomics.com/single-cell-gene-expression/library-prep) was used to prepare the single cell suspension. The appropriate volume of each sample was diluted to recover 10,000 cells. Subsequently, the single cell suspension, Gel Beads and oils were added to the 10x Genomics single-cell chip. After droplet generation, samples were transferred into PCR tubes and we performed reverse transcription using a ProFlex PCR Thermocycler System (Applied Biosystems). After reverse transcription, cDNA was recovered using a recovery agent, provided by 10x Genomics, followed by silane DynaBead clean-up as outlined in the user guide.

value: Skin

tag: tissue type

value: LS

tag: timeline

value: Baseline


title: High dose,18h,biol rep 3

description:
Library name: H18_3
Column name in All_reads_counts_host.xlsx: H18_3,Column name in All_reads_counts_pathogen.xlsx: H18_3

tag: tissue


title: eFL_Shox2trac_E125_REP1

description:
Library name: Sample126
entire forelimb (bulk) RNA-seq


title: LuCaP96CR_VEH_scRNA

city: Boston

first: Maryam

last: Labaf

state: MA

address: 100 William T Morrissey Blvd

department: Biology

institute: University of Massachusetts Boston

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: xenograft-implant

extract_protocol:
Tissue fragments were incubated in 3 ml Accumax (Innovative Cell Technologies, AM105) for 10-20 min at room temperature on a rocking shaker. Red blood cells were lysed with ACK Lysing Buffer (Thermo Fisher Scientific, A1049201) on ice for 1 min, followed by quenching with PBS and then filtered again with a 40-μm cell strainer. Cell suspensions were washed three times and resuspended with PBS plus 0.04% BSA. The final cell viability of suspensions was determined by Countess Automated Cell Counter (Thermo Fisher Scientific).
CDNA

treatment_protocol: cells were treated with 40mg/kg testosterone ip for 7 days

value: xenograft-implant

value: human prostate cancer

value: mixed RB1 hemizygous and homozygous deletion

value: Vehicle


title: Healthy, 2

description: 2-UH-3032-R-CD45-neg-H084Aligned.sortedByCoord.out.bam

value: Epidermis


title: Healthy, 1

description: 1-UH-3032-R-CD45-neg-H081Aligned.sortedByCoord.out.bam

value: CD45-negative epidermal cells


title: eFL_Shox2trac_E125_REP2

description:
Library name: Sample127
entire forelimb (bulk) RNA-seq

value: Embryonic Forelimb


title: High dose,18h,biol rep 2

description:
Library name: H18_2
Column name in All_reads_counts_host.xlsx: H18_2,Column name in All_reads_counts_pathogen.xlsx: H18_2


title: High dose,18h,biol rep 1

description:
Library name: H18_1
Column name in All_reads_counts_host.xlsx: H18_1,Column name in All_reads_counts_pathogen.xlsx: H18_1


title: FL_Shox2trac_E145_MAINTAIN_REP1

description:
Library name: Sample132
sorted cells RNA-seq


title: PRE_91

city: Houston

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

data_processing:
The paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.8
Illumina universal adapters were trimmed from the reads using cutadapt 1.18 and read quality was checked again using FastQC 0.11.8
The trimmed reads were aligned to the Gencode GRCh38 human reference genome using TopHat2 2.1.1 (parameter: --library-type=fr-unstranded)
The BAM file with mapped reads for each sample was sorted and then used as an input for featureCounts (Subread 1.6.3) in order to generate read count data on gene/feature level (parameters: -p -t exon -g gene_id -s 0)
Genes/features were annotated using the GTF file from Gencode human GRCh38 reference
Assembly: Human GRCh38
Supplementary files format and content: Read count data generated by featureCounts (Subread 1.6.3) for each sample

source_name: Bone

extract_protocol:
Total RNA of fresh tissues was extracted with Trizol reagent (Ambion Life Technologies, catalog number 15596026) following the manufacturer’s instructions
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Corporation Inc (US) following standard Illumina protocols

value: Bone

value: metastatic breast cancer

value: PRE


title: LuCaP96CR_Hi-T_scRNA

description: 10x Genomics

value: Hi-dose testosterone


title: CHiC_eFL_Shox2trac_E125

description:
Library name: Sample124
Shox2 Agilent probes C-HiC

data_processing:
Sequencing reads were mapped to reference genome mm9, filtered and deduplicated using the HiCUP pipeline v0.6.1. The pipeline was set up with Bowtie2 v2.3.4.2 for short read mapping.  In case replicates were available, they were combined before the processing with the HiCUP pipeline. Juicer command line tools v1.9.9 was used to generate binned contact maps from valid and unique reads pairs with MAPQ≥30 and to normalize maps by Knights and Ruiz matrix balancing. For binning and normalization, only the genomic region chr3: 65,000,001-68,500,000 was considered.  Afterwards, KR normalized maps, as well as raw count maps, were exported for 5 kb resolution. Subtraction maps were produced from the KR normalized maps and scaled together across their subdiagonals. CHiC maps of count values, as well as subtraction maps, were visualized as heatmaps in which values above the 99-th  percentile were truncated for visualization purposes.
Assembly: mm9
Supplementary files format and content: Text files indicating interaction frequency of valid pairs of the binned contact map

source_name: Embryonic Forelimb

growth_protocol: Forelimbs and Hindlimbs from E11.5, E12.5 and E13.5 Shox2trac embryos were microdissected in PBS. After producing cell suspention, cells were fixed or FACS sorted based on the dmCherry and EYFP fluorescent signal.

extract_protocol:
Tissues were homogenized in typsin-EDTA solution, fixed with 2% PFA at room temperature 10 min. Then fixation was halted with 1M glycine and the cells were lysed in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 1mM EGTA, Protease Inhibitor, #04693159001). Upon PBS wash, samples were frozen and stored at -80°C. Samples were then digested with DpnII, re-ligated, de-crosslinked and purified.
The 3C-library was then sheared and adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing (50 to 100 bp paired-end) following Agilent instructions. Libraries were sequenced an Illumina HiSeq 4000 or Illumina NovaSeq 6000 sequencer.


title: PRE_84


title: b5_Sample_R813-4

data_processing:
The paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.8
Illumina universal adapters were trimmed from the reads using cutadapt 1.18 and read quality was checked again using FastQC 0.11.8
The trimmed reads were aligned to the Gencode GRCh38 human reference genome using TopHat2 2.1.1 (parameter: --library-type=fr-firststrand)
The BAM file with mapped reads for each sample was sorted and then used as an input for featureCounts (Subread 1.6.3) in order to generate read count data on gene/feature level (parameters: -p -t exon -g gene_id -s 2)
Genes/features were annotated using the GTF file from Gencode human GRCh38 reference
Assembly: Human GRCh38
Supplementary files format and content: Read count data generated by featureCounts (Subread 1.6.3) for each sample

source_name: Liver

extract_protocol:
Total RNA of fresh tissues was extracted with Trizol reagent (Ambion Life Technologies, catalog number 15596026) following the manufacturer’s instructions
RNA libraries were prepared, and transcriptome sequencing was conducted by the MD Anderson Advanced Technology Genomics Core. TruSeq RNA exome, previously known as the TruSeq RNA Access Library Prep Kit (Illumina), was used to analyze human RNA isolated from FFPE tissues.

value: Liver

tag: group


title: High dose,24h,biol rep 3

description:
Library name: H24_3
Column name in All_reads_counts_host.xlsx: H24_3,Column name in All_reads_counts_pathogen.xlsx: H24_3


title: High dose,12h,biol rep 3

description:
Library name: H12_3
Column name in All_reads_counts_host.xlsx: H12_3,Column name in All_reads_counts_pathogen.xlsx: H12_3


title: b5_Sample_R813-2


title: PRE_80


title: High dose,12h,biol rep 2

description:
Library name: H12_2
Column name in All_reads_counts_host.xlsx: H12_2,Column name in All_reads_counts_pathogen.xlsx: H12_2


title: High dose,12h,biol rep 1

description:
Library name: H12_1
Column name in All_reads_counts_host.xlsx: H12_1,Column name in All_reads_counts_pathogen.xlsx: H12_1


title: b5_Sample_R813-1


title: PRE_76

source_name: Brain

value: Brain


title: b4_Sample_R849-78


title: High dose,6h,biol rep 3

description:
Library name: H6_3
Column name in All_reads_counts_host.xlsx: H6_3,Column name in All_reads_counts_pathogen.xlsx: H6_3

value: lung


title: PRE_71


title: CHiC_eFL_Shox2Δearly_E125

description:
Library name: Sample125
Shox2 Agilent probes C-HiC

value: entire limb (not sorted)


title: b4_Sample_R849-77


title: Stomach,desert_type,S1

description:
Library name: MDA_S1
10x Genomics

data_processing:
The 10x Genomics sequencing data were processed for alignment and quantification with the CellRanger software package (version 7.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: matrix files

extract_protocol:
Samples were washed with 1× phosphate-buffered saline (PBS), and blood residues along with peripheral non-tumor tissues were meticulously removed. The tissues were then minced into small pieces and dissociated into single cells using a tailored dissociation solution.
These single-cell suspensions were loaded onto a microfluidic chip in a 10X Genomics Chromium instrument to construct a cDNA library, as per the manufacturer’s protocols for the 10X Genomics Chromium Single-Cell 3′ kit (V3)

value: stomach

value: Wild type

value: Orthotopic allograft models


title: Stomach,desert_type,S2

description:
Library name: MDA_S2
10x Genomics


title: Stomach,desert_type,S3

description:
Library name: MDA_S3
10x Genomics


title: Stomach,inflamed_type,T3

description:
Library name: APTc_T3
10x Genomics

value: Genetic mutation


title: PRE_5

source_name: Pleural effusion

value: Pleural effusion


title: High dose,6h,biol rep 2

description:
Library name: H6_2
Column name in All_reads_counts_host.xlsx: H6_2,Column name in All_reads_counts_pathogen.xlsx: H6_2


title: Stomach,inflamed_type,T2

description:
Library name: APTc_T2
10x Genomics


title: PRE_44


title: b3_Sample_56


title: Stomach,inflamed_type,T1

description:
Library name: APTc_T1
10x Genomics


title: PRE_185


title: High dose,0h,biol rep 3

description:
Library name: H0_3
Column name in All_reads_counts_host.xlsx: H0_3,Column name in All_reads_counts_pathogen.xlsx: H0_3


title: b3_Sample_55


title: b3_Sample_54


title: High dose,0h,biol rep 2

description:
Library name: H0_2
Column name in All_reads_counts_host.xlsx: H0_2,Column name in All_reads_counts_pathogen.xlsx: H0_2


title: P2116_3_HTO

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

description: Library name: BSSE_QGF_218504

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Gene expression libraries were mapped to the mouse genome mm10 with STAR (version v2.7.10a) with default parameters, except: --outFilterType=BySJout --outFilterMultimapNmax=10 --outSAMmultNmax=1 --outFilterScoreMin=30 --soloCBmatchWLtype=1MM_multi_Nbase_pseudocounts --soloUMIlen=10 --soloUMIfiltering=MultiGeneUMI_CR --soloUMIdedup=1MM_CR --soloCellFilter=None --clipAdapterType=False --soloType=CB_UMI_Simple –soloStrand=Reverse –soloMultiMappers=EM . The mm10 genome reference was supplemented with the Homo_sapiens_JAK2_V617F construct, CreERT2, pEGFP sequences, and the sequence of the unedited CARLIN barcode. Read counting was done using Ensembl 102 gene models with the mentionned additionnal sequences. For the Homo_sapiens_JAK2_V617F construct, UMI counting was performed on the CDS exons 3 to 12, exons 13 to 25, and exons 13 to 25 on the opposite strand.
All subsequent analyses were performed using the R software (version 4.2.2) and Bioconductor 3.16 packages.
Assembly: mm10
Supplementary files format and content: CellMetadata.txt.gz is a gzipped text file containing tab-separated cell metadata, such as UMAP coordinates, clustering information, sample IDs…
Supplementary files format and content: UMIsMatrix.txt.gz is a gzipped text file with tab-separated UMI counts for each gene. Each row includes the Ensembl 102 gene annotation and raw counts per gene, while the columns represent individual cells. Counts for additional genes are listed at the end of the file.
Supplementary files format and content: HTO_full_info.txt is a text file with tab-separated HTO barcode sequences and their corresponding TotalSeq-B barcode names. The relationship between barcode names and multiplexed samples is included in this file.

source_name: Bone marrow

extract_protocol:
bone marrow cells were harvested and stained with CD4-bio, CD8-bio, Ter119-bio, CD11b-bio, Gr1-bio, B220-bio, c-kit-BV711, Sca-I-APC-Cy7, CD150-PE and CD48-AF700; and cell hashing CD45 antibodies (TotalSeq-B0301 to B0308), for sample barcoding (all from BioLegend) for 1 hour at 4°C, followed by 20-min incubation with streptavidin-PacificBlue. Cells were resuspended in staining media (PBS+ 3% FBS) containing Sytox Blue 1:5000, and HSCs (lin-, c-kit+, sca-1+, CD150+, CD48-), LSKs (lin-, c-kit+, sca-1+) and/or MyPs (lin-, c-kit+, sca-1-) were sorted using BD FacsARIA III (BD biosciences) with 85 um nozzle, into PBS + 3% FBS.
Single Cell 3′ v3 Reagent Kit (10X Genomics) with BioLegend TotalSeq-B hashtagged antibodies (HTO)

treatment_protocol: Tamoxifen inducible conditional JAK2-V617F transgenic mice (Scl;VF) were treated by intraperitoneal injection of 2 mg tamoxifen (100 mg/kg) for 5 consecutive days.

value: Bone marrow

value: tissue

value: c-kit+


title: PRE_156

source_name: Lymph node

value: Lymph node


title: High dose,0h,biol rep 1

description:
Library name: H0_1
Column name in All_reads_counts_host.xlsx: H0_1,Column name in All_reads_counts_pathogen.xlsx: H0_1


title: b3_Sample_52


title: P2116_2_HTO

description: Library name: BSSE_QGF_218503


title: b3_Sample_46

value: Bone


title: PRE_148

value: metastatic breast cancer


title: P2116_4_GEX

description: Library name: BSSE_QGF_218501


title: High dose,6h,biol rep 1

description:
Library name: H6_1
Column name in All_reads_counts_host.xlsx: H6_1,Column name in All_reads_counts_pathogen.xlsx: H6_1


title: P2116_3_GEX

description: Library name: BSSE_QGF_218500


title: b3_Sample_45

source_name: Breast

value: Breast


title: b3_Sample_44


title: PRE_127

source_name: Lung

value: Lung

value: PRE


title: P2116_2_GEX

description: Library name: BSSE_QGF_218499


title: PRE_110


title: b3_Sample_43


title: PRE_175


title: PRE_107


title: P2116_1_GEX

description: Library name: BSSE_QGF_218498


title: b3_Sample_53

source_name: Uterus

value: Uterus


title: P2116_4_HTO

description: Library name: BSSE_QGF_218505


title: PRE_106


title: RNA-Seq, Dux-N22-GSK-2

city: Kunming

first: meiqi

address: Kunming, Yunnan province

institute: LPBR

data_processing:
Raw data were filtered using fastp software (v 0.23.2), and reads were mapped to GRCm38 using HISAT2 (v 2.1.0), featureCounts (v 2.0.1) is used to count the reads mapped to each gene
Differential expression analysis between the two comparison sets was performed using DESeq2 software (1.40.2)
Analysis of transposon expression using TEtranscripts(v 2.2.3)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: mouse embryonic stem cells

growth_protocol: Mouse ES cells were cultured with the medium consist of DMEM (Gibco), 15% fetal bovine serum (FBS, Gibco (16000-004), 10ng/ml Recombinant Murine LIF, 0.1 mM non-essential amino acids (11146-050, Gibco), 0.1 mM PenStrep (15140-122, Gibco), 0.1 mM β-mercaptoethanol (21985-023, Gibco),1 mM GlutaMAX-1(35050-061, Gibco). The medium was changed daily, and cells were passaged every two days.

extract_protocol:
RNA extraction using the phenol/chloroform method,1 ug total RNA of each sample was used as the starting material to construct a transcriptome sequencing library
According to the operating instructions of VAHTS Universal V6 RNA-Seq Library Prepkit for Illumina (NR 604-01/02)

treatment_protocol: For mimicking global DNA demethylation reprogramming events, WT, Dux-KO and Dux (n=1) mESCs were treated with DMSO controls and 1 uM GSK-3484862 for 3 days. Mouse ESCs were then collected for RNA extractiona and RNA-seq.

value: mouse embryonic stem cells


title: POST_99

value: POST


title: b3_Sample_40


title: b3_Sample_41


title: b3_Sample_38


title: POST_93

value: Liver


title: b3_Sample_33


title: b3_Sample_42


title: POST_88


title: POST_90


title: RNA-Seq, WT-GSK-2


title: RNA-Seq, Dux-N22-GSK-1


title: b3_Sample_35


title: POST_62


title: POST_85


title: RNA-Seq, Dux-KO22-GSK-1


title: b3_Sample_36


title: POST_48


title: RNA-Seq, WT-GSK-1


title: b3_Sample_31


title: RNA-Seq, WT-DMSO-2


title: RNA-Seq, Dux-N22-DMSO-2


title: RNA-Seq, WT-DMSO-1


title: POST_46


title: b2_Sample_9


title: POST_43

source_name: Ascites

value: Ascites


title: b3_Sample_37


title: RNA-Seq, Dux-N22-DMSO-1


title: b2_Sample_8


title: POST_3


title: RNA-Seq, Dux-KO22-DMSO-2


title: b2_Sample_7


title: RNA-Seq, Dux-KO22-DMSO-1


title: POST_181


title: b2_Sample_76


title: POST_173


title: RNA-Seq, Duxnto1-40


title: b2_Sample_71


title: POST_172


title: b2_Sample_65


title: RNA-Seq, Duxnto1-22


title: POST_151


title: b2_Sample_62


title: RNA-Seq, Duxnto1-31


title: b2_Sample_64


title: POST_128


title: RNA-Seq, Duxnto1-17


title: RNA-Seq, Dux-KO-22


title: POST_11


title: b2_Sample_60

value: Brain


title: POST_108


title: b2_Sample_5


title: POST_116


title: P2116_1_HTO

description: Library name: BSSE_QGF_218502


title: RNA-Seq, Dux-KO-52


title: RNA-Seq, Dux-KO-15


title: PRE_155


title: b2_Sample_59


title: RNA-Seq, E14-chen-3


title: POST_1


title: RNA-Seq, Dux-KO22-GSK-2


title: b2_Sample_57


title: L98

city: Hong Kong

first: Zezhuo

last: Su

address: No. 21 Sasson Rd, Pokfulam

institute: The University of Hong Kong

description: Malignant (Significant CNV)

data_processing:
Raw reads were processed using the standard CellRanger (v3.0.0) pipline.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix from CellRanger output

source_name: Recurrent

extract_protocol:
Tumour tissues were thoroughly washed 2-3 times with HBSS (Gibco, Cat. no. 14025076) before being minced into small nodules. After an additional 2-3 washes with HBSS, the tissues were further minced into 1 mm³ nodules. The dissociation process involved an enzyme cocktail composed of 0.4% (w/v) collagenase II (Gibco, Cat. no. 17101015), 0.4% (w/v) Hyaluronidase (Sigma, Cat. no. H3884-1G), and 0.4% (w/v) dispase II (Sigma, Cat. no. D4693-1G), which was used to digest the tissues. The tumour nodules were dissociated at 37°C with shaking at 25 R.P.M for approximately 90 minutes. The resulting cell suspensions were filtered using a 40 µm nylon cell strainer (Falcon, Cat. no. 352340). Dissociated single cells were then washed 2-3 times with HBSS containing 0.1% (w/v) BSA (Gibco, Cat. no. 15260073). Red blood cells were removed using ACK Lysing Buffer (Gibco, Cat. no. Gibco). Finally, the isolated single cells were diluted to a concentration of around 100 cells/µl for scRNA-seq analysis.
The tumour nodules were dissociated at 37°C with shaking at 25 R.P.M for approximately 90 minutes. The resulting cell suspensions were filtered using a 40 µm nylon cell strainer (Falcon, Cat. no. 352340). Dissociated single cells were then washed 2-3 times with HBSS containing 0.1% (w/v) BSA (Gibco, Cat. no. 15260073). Red blood cells were removed using ACK Lysing Buffer (Gibco, Cat. no. Gibco). Finally, the isolated single cells were diluted to a concentration of around 100 cells/µl for scRNA-seq analysis.
The library was sequenced by Illumina NovaSeq 6000 using 150 nt paired-end sequencing with 100GB raw reads output per sample.

value: Recurrent

value: H3F3A G35W High


title: L99

description: Benign

source_name: Primary

value: Primary

value: Denosumab


title: b2_Sample_3


title: RNA-Seq, E14-chen-2


title: RNA-Seq, E14-chen-1


title: b2_Sample_2


title: L86

description: Malignant (Significant CNV)


title: GMP replicate3, scRNAseq

city: Hangzhou

first: Sheng

last: Pan

address: #866 Yuhangtang Road

institute: Zhejiang University

description: 10x Genomics

data_processing:
Barcode processing and single-cell 3’ gene counting were performed using Cell Ranger (version 3.1.0), as detailed in the 10x Genomics support documentation (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). Subsequently, scRNA-seq data were aligned to Ensembl mouse reference genome (mm10). Data filtering, dimension reduction, and clustering analysis were performed using the R package Seurat (version 3.1.1). Cells were subjected to filtering based on several criteria, including a minimum number of UMI (≥1200), a minimum of expressed genes (≥1000), library complexity (log10GenesPerUMI > 0.75), and mitochondrial gene content (<15%). Genes expressed in less than 10 cells were excluded from the analysis. Consequently, we retained 26,414 high-quality cells, each expressing an average of 3,248 genes per cell, with a total of 20,983 genes detected across all cells.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The femur, tibia, and fibula of eight to twelve-week-old Balb/C mice were dissected, carefully removing muscle and tendons. The bones were then crushed in PBS containing 0.2% BSA at pH 7.4 using a mortar and pestle. The cell suspension was passed through a 40-μm nylon mesh sieve and then lysed to remove red blood cells with red blood cell lysis buffer.  To enrich hematopoietic progenitors, the bone marrow cells were incubated with an APC-conjugated anti-c-Kit antibody (ACK2, eBioscience), washed and incubated with anti-APC microbeads (Miltenyi Biotech, Germany). After incubation, the cells were washed and re-suspended in MACS buffer and separated through a magnetic column on a magnetic separation plane (Miltenyi Biotech). Cells remained on the column were collected. For live cell analysis or sorting, the collected cells were first stained with biotin-conjugated anti-mouse lineage cocktail antibodies [Ter-119 (TER-119), Gr-1 (RB6-8C5), CD11b (M1/70), B220 (RA3-6B2), CD4 (RM4-5) and CD8 (53-6.7), Biolegend]. After washing, the cells were stained with streptavidin-conjugated fluorescein (Biolegend) and the following antibodies protected from light: c-Kit (ACK2, eBioscience), Sca-1 (El3161.7, Biolegend), CD34 (RAM34, BD), Flt3 (A2F10, BD), CD16/32 (93, BD). DAPI (Solarbio) was used to exclude dead cells. The cells were washed between each step. FACS sorting was performed using a BD LSRII sorter.  The isolated progenitor populations were defined as follows:  LMPP, Lin-c-Kit+Sca-1+CD34+Flt3+; CMP, Lin-c-Kit+Sca1-CD34+CD16/32low; GMP, Lin-c-Kit+Sca-1-CD34+CD16/32high.
The Libraries were constructed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, samples were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction.

value: Bone marrow

value: GMP

value: WT


title: b2_Sample_29

value: metastatic breast cancer


title: GMP replicate2,scRNAseq

description: 10x Genomics


title: L71

description: Benign

value: H3F3A G35W Low


title: GMP replicate1,scRNAseq

description: 10x Genomics


title: b2_Sample_28

value: Breast


title: L77

description: Benign


title: CMP, scRNAseq

description: 10x Genomics

value: CMP


title: b2_Sample_27


title: b2_Sample_22

value: Bone


title: L70

description: Benign


title: b2_Sample_23


title: L67

description: Benign

value: H3F3A G35W Negative


title: L56

description: Benign


title: adult_d1

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

data_processing:
The 10x Visium raw FASTQ data of neonatal and adult mice were processed and mapped with SpaceRanger (v1.3.0) with the manually aligned H&E images. The reference genome mm10 (i.e. refdata-mm10_gex.10x.2020.A) from SpaceRanger was used.
Next, the filtered feature barcode matrix together with the associated image at each time point were imported to Seurat (v4.1.1) and different time points were merged for neonatal and adult mice, respectively. The images were manually cropped to keep only the Visium spots covering heart tissue.
Lastly, the merged data were normalized using SCTransform method (sctransform v0.3.4) with 3000 variable genes.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz: gene expression count data
Supplementary files format and content: barcodes.tsv.gz: a list of spatial barcodes
Supplementary files format and content: features.tsv.gz: a list of gene IDs
Supplementary files format and content: .tif :  tissue H&E images
Library strategy: Spatial Transcriptomics

source_name: Heart

extract_protocol:
Fresh frozen tissue were embbeded in OCT and 10um sections were cut with cryostat
According to 10x genomics Visium protocols

treatment_protocol: Myocardial infarction (MI) was induced by a permanent ligation of the left anterior descending (LAD) coronary artery. Adult ICR mice were anesthetized using isoflurane (Abbott Laboratories, Cat# AWN-34014202) and, following tracheal intubation, were artificially ventilated. Toe pinche was performed to test the depth of anesthesia. Prior to all surgical procedures mice were administered with buprenorphine in a subcutaneous manner, as an analgesic agent (0.066 mg/kg). Lateral thoracotomy was performed at the third intercostal space by blunt dissection of the intercostal muscles. Following the exposure of the left ventricle the LAD an 8-0 silk suture was used to tie the LAD coronary artery. The suture was validated by holding in the tie for 5 seconds and the observance of an ischemic (white) area below the suture. Following this validation, the procedure ended by closing the chest cavity and skin by either suture and biological glueHistoacryl® (B. Braun Melsungen AG, Cat# LUXBBS105005/2), respectively. Following awakening, mice were warmed for several minutes in a recovery cage.

value: Heart

value: Heart cells

value: LAD ligation

tag: time


title: L109

description: Benign


title: adult_d4


title: Patient 131 liver scRNA-seq sample

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

data_processing:
Processing of raw reads was performed using the Cell Ranger software provided by 10X genomics and the hg38 human reference genome (GRCm38 v86 and corresponding GENCODE annotation file). During read alignment, PCR duplicates were removed. The UMI (unique molecular identifier) for each gene is counted to measure the gene expression levels. The cell doublet status is inferred by the software DoubletFinder. A number of quality-control metrics are evaluated to control the data quality, including the total UMI count, the total number of genes detected, the mitochondrial gene ratio, log10(gene number) per UMI, and the inferred status of cell doublet.  Low-quality cells with a total UMI count smaller than 500, a total number of genes smaller than 200, and a mitochondrial gene ratio greater than 50% are excluded for further analysis.
Assembly: GRCm38 v86
Supplementary files format and content: Filtered bc matrix from CellRanger

extract_protocol:
The sample was incubated at 37 °C for 5 min. After dissociation, 2ml of advanced DMEM+10%FBS media was added to the sample and filtered through a 70 μm cell strainer (Fisher Scientific, cat.43-10070-40) into Eppendorf tubes
The filtrate was centrifuged at 500g for 5 min, and the supernatant was removed. If the pellet was bloody, red blood cell (RBC) removal was performed using RBC Lysis Solution (1x) (Miltenyi Biotec, cat. No. 130-094-183) for 10 min at RT. Sample was then centrifuged at 500g for 5 min and pellet was resuspended in 1ml of advanced DMEM, to be combined into one Eppendorf tube.
The single-cell suspension was visualized, counted, and stored at nitrogen until 10x Genomics Single-Cell sequencing was performed.

tag: individual

value: Patient 131

value: Liver

tag: status

value: Baseline

tag: progression time

value: on treatment

tag: progression type

value: late progressor

tag: sequencing core_id


title: b2_Sample_17

tag: batch


title: Patient 153 liver scRNA-seq sample

value: Patient 153


title: b2_Sample_20


title: Patient 110 pleural effusion scRNA-seq sample

value: Patient 110

value: Pleural effusion


title: Patient 95 liver scRNA-seq sample

value: Patient 95


title: adult_d7

tag: cell type


title: b2_Sample_1

value: metastatic breast cancer


title: Patient 45 liver scRNA-seq sample

value: Patient 45


title: b1_Sample_68


title: b1_Sample_67


title: Patient 120 liver scRNA-seq sample

value: Patient 120


title: adult_d14


title: b1_Sample_58


title: b2_Sample_14

value: Bone


title: b2_Sample_13


title: less effective DSC ID6

type: RNA

city: Yokohama

first: Yumiko

last: Ishimatsu-Tsuji

address: Nishi-ku

institute: Shiseido

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized toand Agilent SurePrint G3 Human GE 8x60K ver2 microarray (G4858A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (AgilentG3_HiSen_GX_1Color protocol).

data_processing: The scanned images were analyzed with Feature Extraction Software12.1.0.3  (Agilent) using default parameters (protocol GE1-1200_June14 and Grid: 039494_D_F_20190203) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: clinical trial volunteers, Not disclosed

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Freshly isolated dermal sheath cups from clinical trial volunteers were transferred into culture plates and were incubated at 37°C and 5% CO2 in the culture medium for cell expansion.

extract_protocol: Cells were suspended in 1 ml of Isogen (Nippon Gene, Tokyo) and total RNA was extracted according to the instructions for use. RNA purification was performed using the RNeasy Mini Kit (Qiagen, Hilden). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent Tape station (Agilent Technologies, Santa Clara, CA).

value: less effective DSC

value: dermal sheath cup cells


title: less effective DSC ID5


title: less effective DSC ID2


title: b2_Sample_12

value: Breast


title: less effective DSC ID8


title: less effective DSC ID7


title: LMPP,scRNAseq

description: 10x Genomics

value: Bone marrow

value: LMPP

tag: genotype

value: WT


title: b1_Sample_49


title: b1_Sample_69

value: Liver


title: Patient 3 liver scRNA-seq sample

value: Patient 3

value: Baseline


title: b2_Sample_21


title: Patient 46 pleural effusion scRNA-seq sample

value: Patient 46

value: Progressor

value: 5 m

value: early progressor


title: primary epithelial stem cells-derived extracellular vesicles (EV), CD9+EV, rep 3

city: SKT

first: Sunyoung

last: Park

state: Seoul

country: South Korea

institute: Yonsei university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hsa (mirbase) whole genome using Bowtie2
Read count extraction using bedtools.
Quantile normalization was performed by EdgeR.
Assembly: hsa
Supplementary files format and content: tab-delimited text files include normalized values for each Sample

source_name: Salivary gland

growth_protocol: Human parotid gland derived epithelial cells were cultured in Dermacult with Y27632 (10uM), A83-01 (1 uM), and LDN193189 (0.1 uM).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small  RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

treatment_protocol: To optain exosomes, we harvested medium from nearly confluent human parotid epithleial cells culture with exosome removed dermacult omitting small molecules.

value: Salivary gland

tag: cell line

value: primary cell culture

value: epithelial stem cell

tag: type

value: CD9+ enriched


title: Patient 144 liver scRNA-seq sample

value: Patient 144

value: 3 m


title: highly effective DSC ID8

value: highly effective DSC

value: dermal sheath cup cells


title: less effective DSC ID3

value: less effective DSC


title: Patient 11 pleural effusion scRNA-seq sample

value: Patient 11

value: Pleural effusion


title: highly effective DSC ID7


title: Patient 165 pelvic bone scRNA-seq sample

source_name: Pelvic bone

value: Patient 165

value: Pelvic bone

value: late progressor


title: less effective DSC ID4


title: Patient 3 ascites scRNA-seq sample 1

value: Patient 3

value: Ascites

value: Progressor


title: less effective DSC ID1


title: primary epithelial stem cells-derived extracellular vesicles (EV), CD9+EV, rep 1

value: Salivary gland

tag: treatment


title: primary epithelial stem cells-derived extracellular vesicles (EV), total EV, rep 3

value: primary cell culture

value: WT


title: Patient 139 liver scRNA-seq sample

value: Patient 139

value: Liver

value: 8 m


title: highly effective DSC ID4

value: highly effective DSC