title: HGT1_2

city: Boston

first: Yingtian

last: Xie

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

description: Library name: HGT1_2

library_source: genomic single cell

data_processing:
fastq files were run through cellranger-atac pipepline
QC and downstream analysis were done by R packages Seurat and Signac
Assembly: hg38
Supplementary files format and content: tab-separated values representing genomic locations of DNA fragments from single-cell ATAC sequencing experiments

source_name: bladder

extract_protocol:
For each of the two HGT1 cases, a 40 μm section was obtained and nuclei isolation was performed as previously described (Font-Tello et al. 2020; Cejas and Long 2022). In brief, the section was suspended in 300 μl of cold buffer comprising 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. The homogenate tissue was transferred to a pre-chilled 1.5 ml microfuge tube and incubated on ice for 10 min. Lysates were filtered through a 40 μm cell strainer, and nuclei were centrifuged for 10 min at 1500 RCF at 4°C. Nuclei were resuspended in 300 μl of buffer containing 0.1% Tween-20 and enumerated using a hemocytometer with Trypan blue stain. Approximately 7000 nuclei per sample were targeted.
Nuclei were processed following the 10× Genomics Chromium Single Cell ATAC protocol (Chromium Single Cell ATAC Library & Gel Bead Kit, 10× Genomics) according to the manufacturer’s instructions. Libraries were sequenced as 150 bp paired-end reads on an Illumina NovaSeq XP platform.

value: bladder


title: B4G12 cells, siControl1

status: Public on Jun 10 2026

type: SRA

city: Beijing

first: Junyi

last: Wang

address: 69th Yongding Road

department: Ophthalmology

country: China

institute: The Third Medical Center, Chinese PLA General Hospital

description:
Library name: Sample1
siControl1_FPKM

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomicbenchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38 using CLC genomic benchwork with default parameters
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: table-delimited text file include raw counts for each Sample
Supplementary files format and content: xls files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: human corneal endothelial cells

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat# 74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyze (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
The purified Total RNA was subjected to a series of steps including mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3'-end adenylation, adapter ligation, and PCR enrichment to complete the construction of the sequencing sample library. The concentration of the constructed library was detected using a Qubit® 2.0 Fluorometer, and the library fragment size was verified by an Agilent 4200 TapeStation. Sequencing was performed on an Illumina NovaSeq 6000 platform with a PE150 (Paired-End 150 bp) sequencing mode.  Approximately 8 Gb of clean data per sample. The proportion of bases with a quality score higher than 20 (Q20) in each read direction shall be no less than 90%.

tag: tissue

value: human corneal endothelial cells

tag: cell line

tag: cell type

value: corneal endothelial cells

tag: genotype

value: WT

tag: treatment

value: siRNA treatment


title: B4G12 cells, siControl3

description:
Library name: Sample3
siControl3_FPKM


title: HGT1_1

state: MA

country: USA

description: Library name: HGT1_1

molecule: genomic DNA


title: B4G12 cells, siNAMPT1

description:
Library name: Sample4
siNAMPT1_FPKM

value: NAMPT knockdown


title: PECHiC_differentiation_NE_rep2

city: London

first: Mikhail

last: Spivakov

address: Du Cane Road

country: United Kingdom

institute: MRC Laboratory of Medical Sciences (LMS)

description:
Library name: PECHiC_differentiation_NE_rep2
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: NE

library_source: genomic

data_processing:
Read processing, alignment, and filtering were performed using the Hi-C User Pipeline (HiCUP, (Wingett et al. 2015), modified to consider both across- and within-read ligation junctions (https://github.com/StevenWingett/HiCUP/tree/combinations, v0.7.4,  (Freire-Pritchett et al. 2021)). CHiCAGO input files were generated using chicagoTools v1.30.0 (Cairns et al. 2016) for bins of DpnII fragments spanning ~5 kb, leaving the captured (‘baited’) PE-harbouring fragments unbinned to increase resolution. CHiCAGO (v1.30.0) was run as previously described (Cairns et al. 2016; Freire-Pritchett et al. 2021) on combined replicates from each time point/condition. The ‘other ends’ of detected contacts were annotated with transcription start sites downloaded from GENCODE (v.36 Frankish et al.). CHiCAGO results were summarised across samples using makePeakMatrix.R from ChicagoTools with default parameters.
Assembly: GRCh38
Supplementary files format and content: A table of CHiCAGO interaction scores for pooled duplicates in each time point/condition (naive, day1, day3, day5, day7, day10, day14, primed, DE, NE).  Only interactions that exceed the CHiCAGO score threshold of 5 in at least one condition are reported in the table.
Library strategy: Capture-C

source_name: HNES1 cells

growth_protocol: All cells were grown at 37 °C, 5 % CO2. HNES1 hPSCs were maintained in the naive state as described in (Rostovskaya 2022). In brief, cells were cultured on irradiated mouse embryonic fibroblast (MEF) feeder cells in N2B27 supplemented with 1 µM PD0325901, 10 ng/ml human LIF (made in-house), 2 µM Gö6983 (Tocris Bio-Techne), and 2 µM XAV939 (Tocris Bio-Techne). N2B27 basal medium was prepared as follows: Neurobasal and DMEM-F12 in the ratio 1:1; 0.5% N2 supplement; 1 % B27 supplement (with vitamin A); 2 mM L-glutamine; 100 mM 2-mercaptoethanol (all from ThermoFisher Scientific). Cells were passaged through single-cell dissociation using TrypLE Express (ThermoFisher Scientific). 0.5 µL/mL Geltrex (ThermoFisher Scientific) was added to the medium during passaging. 10 µM ROCK inhibitor (Y-27632, Millipore) was added for 24 hours after replating. Naive-to-primed transition was performed as described in (Rostovskaya et al. 2019; Rostovskaya 2022). For this, naive hPSCs were passaged once in feeder-free conditions, adding 1 µL/mL Geltrex to the medium during passaging, otherwise as described above. Upon reaching confluency, cells were plated at a density of 1.6 x 104/cm2 in the medium for naive hPSC maintenance supplemented with 10 µM ROCK inhibitor, on plates pre-coated with 1% Geltrex. After 48 h, the medium was exchanged to N2B27 supplemented with 2 µM XAV939. The medium was refreshed daily. At confluency, cells were passaged using TrypLE Express at a 1:2 ratio in the transition medium supplemented with 10 µM ROCK inhibitor for 24 h, on Geltrex pre-coated plates. The H9 cells were grown in mTeSR-E8 basal media (StemCell Technologies), in feeder-free conditions using Geltrex (1:100 dilution in DMEM-F12, ThermoFisher Scientific) as a coating matrix.

extract_protocol:
Cells were dissociated into single-cell suspensions using TrypLE. 1 million cells per condition were fixed in 1X D-PBS (Sigma-Aldrich) containing 2 % paraformaldehyde (Electron Microscopy Sciences) for 10 min at room temperature.
Crosslinking was quenched with incubation in 0.125 M glycine for 5 min at room temperature followed by 5 min on ice. Cells were pelleted by centrifugation, washed with PBS, and lysed for 30 min on ice in Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, protease inhibitors). All centrifuging steps during the lysis, prior to DpnII digestion, were carried out in a swinging-bucket centrifuge at 4°C, 300 x g for 5 min.The released nuclei were permeabilised and digested overnight with DpnII (NEB). Restriction overhangs were filled in with biotin-dATP (Jena Bioscience), and proximity ligation was performed for 4 h at 16 °C using T4 DNA ligase (Invitrogen). Crosslinks were reversed overnight at 65 °C with proteinase K, and DNA was purified with AMPure XP beads (Beckman Coulter). DNA was fragmented by tagmentation to generate fragments ≤1,000 bp fragments, and biotinylated junctions were enriched using MyOne C1 streptavidin beads (Life Technologies). Libraries were amplified directly on beads with 5 PCR cycles, purified with AMPure XP beads, and subjected to poised enhancer capture using a custom-designed Agilent SureSelect system, following the manufacturer’s protocol. Libraries were sequenced as 150 bp paired-end reads.

treatment_protocol: The primed state was reached by day 14 of the transition. Cells were harvested for PECHi-C experiments in duplicate on day 0 (in the naive conditions), 1, 3, 5, 7, 10, and 14 of the transition. Differentiation was performed with HNES1 hPSC after 14 days of the naive-to-primed transition. Neuroectoderm was induced according to (Chambers et al. 2009). N2B27 basal medium was prepared as follows: Neurobasal and DMEM-F12 in the ratio 1:1; 0.5 % N2 supplement; 1 % B27 supplement (with vitamin A); 2 mM L-glutamine; 100 mM 2-mercaptoethanol (all from ThermoFisher Scientific). hPSCs were dissociated to single cells and plated at 2.5x105/cm2 to Geltrex-coated plates (ThermoFisher Scientific) in N2B27 supplemented with 1 mM A8301 (Tocris Bio-Techne) and 500 nM LDN193189 (Axon Medchem). 10 mM ROCK inhibitor (Y-27632, Millipore) was added for 24 h after plating. Cells were cultured in the differentiation conditions for 10 days. To obtain a pure neuroectoderm cell population, the cells were stained for the expression of CD56 (BD, Cat. 345812) and absence of EpCAM (Biolegend, Cat. 324212), and sorted using flow cytometry. Definitive endoderm was induced according to (Loh et al. 2014). CDM2 basal medium was prepared as follows: IMDM and F12 in the ratio 1:1, 2 mM L-Glutamine, 1 % chemically defined lipid concentrate (all from ThermoFisher Scientific), 0.1 % BSA or polyvinyl alcohol, 15 mg/mL transferrin, 450 mM monothioglycerol, 0.7 mg/mL insulin (all from Sigma). hPSCs were plated at 4x104/cm2 to Geltrex-coated plates in their culture medium with 10 mM ROCK inhibitor. After 24 h, the medium was exchanged to CDM2 basal medium supplemented with 100 ng/mL Activin A, 3 µM CHIR99021, 10 ng/mL FGF2 (all produced in house), 100 nM PI-103 (Tocris, Bio-Techne), 3 ng/mL BMP4 (Peprotech), 10 µg/mL heparin (Sigma-Aldrich) for one day; then for the next two days the following supplements were applied: 100 ng/mL Activin A, 100 nM PI-103, 20 ng/mL FGF2, 250 nM LDN193189, 10 µg/mL heparin. To obtain a pure definitive endoderm cell population, the cells were stained with antibodies against CXCR4 (BD) and CD117 (RnD Bio-Techne) and sorted using flow cytometry.

value: HNES1 cells

tag: time point

value: day 14 cells differentiated in neuroectoderm (NE)

value: Differentiation in NE


title: PECHiC_differentiation_NE_rep1

description:
Library name: PECHiC_differentiation_NE_rep1
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: NE


title: PECHiC_differentiation_DE_rep2

description:
Library name: PECHiC_differentiation_DE_rep2
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: DE

value: day 14 cells differentiated in definitive endoderm (DE)

value: Differentiation in DE


title: PECHiC_Primed_cells_rep2

description:
Library name: PECHiC_Primed_cells_rep2
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: primed

source_name: H9 cells

value: H9 cells

value: primed cells


title: PECHiC_Primed_cells_rep1

description:
Library name: PECHiC_Primed_cells_rep1
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: primed


description:
Library name: PECHiC_naive-to-primed_transition_Day14_rep2
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day14

value: day 14 of the transition

value: naive-to-primed transition


description:
Library name: PECHiC_naive-to-primed_transition_Day14_rep1
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day14


title: PECHiC_differentiation_DE_rep1

description:
Library name: PECHiC_differentiation_DE_rep1
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: DE


description:
Library name: PECHiC_naive-to-primed_transition_Day10_rep1
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day10

value: day 10 of the transition


description:
Library name: PECHiC_naive-to-primed_transition_Day7_rep2
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day7

value: day 7 of the transition


description:
Library name: PECHiC_naive-to-primed_transition_Day7_rep1
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day7


description:
Library name: PECHiC_naive-to-primed_transition_Day5_rep2
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day5

value: day 5 of the transition


description:
Library name: PECHiC_naive-to-primed_transition_Day3_rep2
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day3

value: day 3 of the transition


description:
Library name: PECHiC_naive-to-primed_transition_Day3_rep1
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day3


description:
Library name: PECHiC_naive-to-primed_transition_Day1_rep1
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day1

value: day 1 of the transition


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep5_TechRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled

data_processing:
Read processing, alignment, and filtering were performed using the Hi-C User Pipeline (HiCUP, (Wingett et al. 2015), modified to consider both across- and within-read ligation junctions (https://github.com/StevenWingett/HiCUP/tree/combinations, v0.7.4,  (Freire-Pritchett et al. 2021)). CHiCAGO input files were generated using chicagoTools v1.30.0 (Cairns et al. 2016) for bins of DpnII fragments spanning ~5 kb, leaving the captured (‘baited’) PE-harbouring fragments unbinned to increase resolution. CHiCAGO (v1.30.0) was run as previously described (Cairns et al. 2016; Freire-Pritchett et al. 2021) on samples pooled across technical and biological replicates. The ‘other ends’ of detected contacts were annotated with transcription start sites downloaded from GENCODE (v.36 Frankish et al.). CHiCAGO results were summarised across samples using makePeakMatrix.R from ChicagoTools with default parameters.
Assembly: GRCh38
Supplementary files format and content: A table of CHiCAGO interaction scores for pooled triplicates for each condition (DMSO, PROTAC, and catalytic inhibitor). Only interactions that exceed the CHiCAGO score threshold of 5 in at least one condition are reported in the table.
Library strategy: Capture-C

source_name: HNES1 cells after 5 days of naive-to-primed transition

growth_protocol: HNES1 hPSCs were maintained in the naive state as described in (Rostovskaya 2022). In brief, cells were cultured on irradiated mouse embryonic fibroblast (MEF) feeder cells in N2B27 supplemented with 1 µM PD0325901, 10 ng/ml human LIF (made in-house), 2 µM Gö6983 (Tocris Bio-Techne), and 2 µM XAV939 (Tocris Bio-Techne). N2B27 basal medium was prepared as follows: Neurobasal and DMEM-F12 in the ratio 1:1; 0.5% N2 supplement; 1 % B27 supplement (with vitamin A); 2 mM L-glutamine; 100 mM 2-mercaptoethanol (all from ThermoFisher Scientific). Cells were passaged through single-cell dissociation using TrypLE Express (ThermoFisher Scientific). 0.5 µL/mL Geltrex (ThermoFisher Scientific) was added to the medium during passaging. 10 µM ROCK inhibitor (Y-27632, Millipore) was added for 24 hours after replating. Naive-to-primed transition was performed as described in (Rostovskaya et al. 2019; Rostovskaya 2022). For this, naive hPSCs were passaged once in feeder-free conditions, adding 1 µL/mL Geltrex to the medium during passaging, otherwise as described above. Upon reaching confluency, cells were plated at a density of 1.6 x 104/cm2 in the medium for naive hPSC maintenance supplemented with 10 µM ROCK inhibitor, on plates pre-coated with 1% Geltrex. After 48 h, the medium was exchanged to N2B27 supplemented with 2 µM XAV939. The medium was refreshed daily. At confluency, cells were passaged using TrypLE Express at a 1:2 ratio in the transition medium supplemented with 10 µM ROCK inhibitor for 24 h, on Geltrex pre-coated plates.

treatment_protocol: Naive HNES1 cells were seeded at a density of 1.6 x 104/cm2 on plates coated with 1 % Geltrex and cultured in PXGL conditions. After 24 h in PXGL, either 1 µM UNC1999 (a catalytic inhibitor of the EZH1/2 subunits of PRC2), 2.5 µM UNC6852 (a PROTAC degrader of the EED subunit of PRC2), or an equivalent volume of DMSO (control) was added. After 24 h, cells were withdrawn from PXGL and cultured in N2B27 medium supplemented with XAV939 supplemented with either 1 µM UNC1999, 2.5 µM UNC6852, or DMSO. This time point was designated “day 0” of the transition experiment. Medium and inhibitors were replaced every day until day 5. Cells were harvested on day 5 in triplicate for PECHi-C experiments.

value: catalytic inhibitor UNC1999


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch2_ BioRep5
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled

value: HNES1 cells after 5 days of naive-to-primed transition


description:
Library name: PECHiC_naive-to-primed_transition_Naive_rep2
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: naive

value: day 0 of the transition (naive cells)


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep5_TechRep3
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep5_TechRep2
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch2_ BioRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep5_TechRep1
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


title: Huh7 cells  WT1

city: guanghzou

first: wancui

last: zhu

state: State...

address: zhongshan

institute: Sun Yat-sen University

description:
Library name: sample5
Huh7 sensitive control rep1

data_processing:
Raw reads in FASTQ format were first processed through fastp (version 0.20.0) to remove adapter-containing reads, reads containing N bases, and low-quality reads (Qphred ≤ 20 bases accounting for >50% of the read length).
Assembly: GRCh38 (Ensembl release 111)
Supplementary files format and content: FPKM_values.csv: CSV file containing FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for each gene of each sample.

source_name: not

extract_protocol:
Total RNA was extracted with the Cell RNA Rapid Extraction Kit from GOONIE (400-100-100T) according to the manufacturer’s instructions.
RNA libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following the manufacturer's protocols. Briefly, mRNA was enriched using oligo(dT) beads, fragmented, and used for first-strand and second-strand cDNA synthesis. After end repair, A-tailing, and adapter ligation, the products were purified and PCR amplified to create the final library.

value: not

value: Hepatocellular carcinoma cells

value: WT

value: control

tag: batch


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep4_TechRep3
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep4_TechRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep4_TechRep2
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep4_TechRep1
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep3_TechRep2
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep3_TechRep3
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep3_TechRep1
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch2_ BioRep5
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled

value: PROTAC UNC6852


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep5_TechRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep5_TechRep3
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


title: PAG117_Inf_E2

status: Public on Jun 11 2026

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
raw reads were processed using Trimmomatic v0.36 to remove adapter sequences and low-quality bases (Phred quality score < 20).
 Filtered reads were then mapped to the human reference genome (Ensembl GRCh38 release-84) using STAR v2.5.0c.
Transcripts abundances were estimated as transcripts per million
Only genes with a minimum of 1 TPM in 10 samples per experimental condition were retained for downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: TPM

source_name: PAG117 Inf E2 Malaria Symptomatic stage mRNA Year2 Sample

extract_protocol:
globin-mRNA depletion using the GlobinClear kit (Thermo Fisher)
KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems) and 100 bp paired-end sequencing using the TruSeq SBS Kit v3 - HS (Illumina)

value: Blood

tag: visit

value: Malaria Symptomatic stage


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep5_TechRep2
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep4_TechRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep4_TechRep3
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep4_TechRep1
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch2_ BioRep3
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep3_TechRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


title: T29_INXBX

city: Redwood City

first: Dmitry

last: Velmeshev

state: CA

address: 3200 Bridge Parkway

department: Oncology

institute: Galvanize Therapeutics

description:
Library name: T29_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)

library_source: transcriptomic single cell

data_processing:
BDRhapsody pipeline+Seurat
Assembly: GRCh38
Supplementary files format and content: combined raw counts matrix (RNA)
Supplementary files format and content: gene names
Supplementary files format and content: cell names
Supplementary files format and content: combined raw counts matrix (AbSeq)
Supplementary files format and content: protein names
Supplementary files format and content: cell metadata

molecule: polyA RNA

source_name: Lung

extract_protocol:
Single cell dissociation
BDRhapsody

value: Lung

tag: donor

tag: age

tag: provider

value: Galvanize Therapeutics

tag: collection date

tag: collection location

value: Spain

tag: Sex

value: Male

tag: study group

value: PEF Treatment

value: Ablation after diagnostic biopsy

tag: histologic subtype

value: Squamous cell carcinoma

tag: ethnicity

value: Hispanic or Latino

tag: race

value: White

tag: nsclc clinical_stage


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep3_TechRep3
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled

tag: cell line

value: HNES1 cells after 5 days of naive-to-primed transition


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep3_TechRep2
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch2_ BioRep3
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled

value: catalytic inhibitor UNC1999


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep3_TechRep1
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch2_ BioRep5
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled

value: DMSO


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep5_TechRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep5_TechRep3
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep5_TechRep2
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch2_ BioRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch2_ BioRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep5_TechRep1
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep4_TechRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


title: T07_RESRU

description:
Library name: T07_RESRU
BDRhapsody scRNA+AbSeq (Immune discovery panel)

tag: tissue

value: IB


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep5_TechRep1
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled

tag: treatment


title: T07_INXBX

description:
Library name: T07_INXBX
BDRhapsody scRNA+AbSeq (Immune discovery panel)


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep4_TechRep3
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_PROTAC_Batch1_ BioRep4_TechRep2
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_PROTAC_total_pooled


title: T02_RESRT

description:
Library name: T02_RESRT
BDRhapsody scRNA+AbSeq (Immune discovery panel)

value: Adenocarcinoma


description:
Library name: Day5_PECHiC_PRC2perturb_CatalyticInhib_Batch1_ BioRep3_TechRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_UNC1999_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep4_TechRep1
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep4_TechRep2
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch2_ BioRep3
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep3_TechRep4
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


title: E4/4_M_D4F_4

city: Minneapolis

first: Ling

last: Li

email: lil@umn.edu, linglilab@umn.edu

state: MN

address: 2001 6th Street SE Rm 4-208

department: Department of Experimental and Clinical Pharmacology

institute: University of Minnesota

description: Library name: 18793

data_processing:
Raw sequencing reads were evaluated and trimmed using Trimmomatic.
Trimmed reads were mapped to the mouse reference genome GRCm38 using HISAT2.
RNA-seq raw counts for each gene were extracted using FeatureCounts.
Assembly: GRCm38
Supplementary files format and content: xlsx file includes raw counts for each sample.

organism: Mus musculus

source_name: brain

extract_protocol:
Total RNA was extracted from tissue homogenate using the Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio Rad 7326830) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: brain

tag: genotype

value: male


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep3_TechRep3
Column name in the processed data file  Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep3_TechRep2
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


description:
Library name: Day5_PECHiC_PRC2perturb_DMSO_Batch1_ BioRep3_TechRep1
Column name in the processed data file Peakmatrix_chicago_score_PRC2perturbation_allSamples.txt: Day5_PRC2_DMSO_total_pooled


title: ATAC-SEM-Rep3-3117687_JWH003

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description: Library name: sample 9

data_processing:
For KAS-ATAC-seq/ATAC-seq, reads were trimmed for trim_galore(version v0.4.4, "--paired --clip_R1 15 --clip_R2 15") and aligned to human genome hg38(Gencode GRCh38.p12) by BWA (version 0.7.12-r1039, default parameter).
The duplicated reads were then marked with biobambam2 (v2.0.87) and only non-duplicated proper paired reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2). After removing mitochondrial DNA reads, the rest of reads were classified into four groups including nucleosome free, mono-, di-, and tri-nucleosome by fragment size. The bigwig files were generated using the center 80-bp of fragments and scaled to 20 million nucleosome free reads.
We observed reasonable nucleosome free peaks and pattern of nucleosome peaks surrounding nucleosome free peaks on IGV.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Blood

growth_protocol: SEM and K562 cells were grown in RPMI 1640 (Cellgro) with L-Glutamine, 10% Fetal Bovine Serum (FBS) (Hyclone), and 1% penicillin/streptomycin at 37 °C in 5% CO2.

extract_protocol:
150,000 SEM or K562 cells were lysed by ATAC-RSB+++ on ice for 3 mins. 1mL of ATAC-RSB+ was added to dilute the solution. Nuclei were pellet by centrifugation for 5 minutes, 500g, at 4 degrees. The buffer was discarded while the pellet was resuspended with 10mM N3-Kethoxial in PBS and incubated at 37 degrees, with shaking at 500rpm for 10 minutes. Nuclei were washed by 1mL DPBS and centrifuged for 5 minutes, 500g at 4 degrees to remove the buffer. Following N3-Kethoxial labeling, the transposition reaction was carried out at 37 degrees for 30 minutes. The reaction was terminated by adding 250ul of DNA Binding Buffer from DNA Clean and Concetrator-5 Kit (Zymo). The DNA was eluted by 43ul of 25mM K3BO3. Next, 2.5ul 20mM DBCO-PEG4-biotin (Sigma) was added and incubate the mixture for 1.5hrs, 37 degrees at 500rpm. After the completion fo the Clikc reaction, 2.5ul RNasA for 5 minutes at 37 degrees. The DNA was purified by the DNA by Clean and Concentrator Kit (Zymo). DNA was eluted by 50ul 25mM K3BO3.  The modified DNA was enriched with MyOne Streptavidin C1 beads and incubated for 15 minutes, washed, then purified the DNA with 20ul dH2O.
DNA was indexed with 25ul NEBNext HiFi 2x Master Mix (MO543S), 1ul 62.5uM Nextera primer Forward, and 1ul 62.5uM barcoded Nextera primer Reverse. The PCR was caried out for 12 cycles and purified by AMPure XP beads (Beckman Coulter).

value: Blood

value: SEM


title: ATAC-SEM-Rep2-3117686_JWH002

description: Library name: sample 8


title: ATAC-SEM-Rep1-3117685_JWH001

description: Library name: sample 7


title: Huh7 cells  SR1

description:
Library name: sample7
Huh7 sorafenib-resistant rep1

value: not

tag: cell type

value: Hepatocellular carcinoma cells

value: SR

value: sorafenib

tag: batch


title: RA-FLS, DMSO-treated, replicate 1

city: Seoul

first: Yong Joon

last: Lee

address: 50 Yonsei-ro, Seodaemun-gu

department: Department of Biotechnology

country: South Korea

institute: Yonsei University

description:
Library name: DMSO_1
RNA sequencing of primary RA-FLS treated with DMSO

data_processing:
For quality control of raw sequencing data, FastQC v0.11.7 was used.
Sequence reads were trimmed to remove low-quality bases, adapters and contaminants using Trimmomatic 0.38.
Trimmed sequence reads were mapped to the human reference genome (GRCh38) using HISAT2 version 2.1.0.
Transcript assembly and quantification of gene expression from mapped reads were performed using StringTie version 2.1.3b.
Assembly: GRCh38
Supplementary files format and content: Gene-level read count matrix generated from RNA-seq analysis. Rows represent genes (Gene_Symbol) and columns correspond to samples including Control-1, Control-2, Control-3, IL-17-1, IL-17-2, IL-17-3, PA20-1, PA20-2, and PA20-3.
Supplementary files format and content: Comma-separated values (CSV) file containing gene expression read counts for each sample.

source_name: Synovium

growth_protocol: RA-FLS cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humid atmosphere with 5% CO2 at 37°C.

extract_protocol:
Extraction of cellular RNA was conducted with RNeasy Mini Kit (Qiagen, Hilden, Germany)
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina). Polyadenylated mRNA was enriched using oligo-dT beads, fragmented, and reverse-transcribed into cDNA. Sequencing adapters were ligated to cDNA fragments followed by PCR amplification. Libraries were subjected to paired-end sequencing on an Illumina platform.

treatment_protocol: RA-FLS were divided into three groups: control (DMSO), IL-17 group (IL-17 + DMSO), and PA group (IL-17 + PA). Cells were pretreated with DMSO or Polygonum aviculare L. extract (PA, 20 µg/mL) for 1 h and subsequently stimulated with IL-17 for 18 h.

value: Synovium

value: Fibroblast-like synoviocytes

tag: disease state

value: Rheumatoid arthritis


title: KASATAC-SEM-Rep3-3349965_SMF303

description: Library name: sample 6


title: KASATAC-SEM-Rep2-3349964_SMF302

description: Library name: sample 5


title: KASATAC-K562-Rep3-3349968_SMF306

description: Library name: sample 3


title: KASATAC-SEM-Rep1-3349963_SMF301

description: Library name: sample 4


title: F05650303-1

city: Birmingham

first: Lin

last: Jin

address: 1720 2nd Ave South

institute: University of Alabama at Birmingham

description: Library name: Jin_F7

data_processing:
FASTQ files were generated through BaseSpace using Illumina's bcl2fastq software.
Raw paired-end FASTQ files were quality- and adapter-trimmed using Trimmomatic v0.36 in paired-end mode with parameters: PE -threads 8 -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Paired trimmed reads were retained for downstream analysis.
Trimmed paired-end reads were aligned to the human hg38 reference genome using STAR v2.7.3a with parameters: --readFilesCommand zcat --runThreadN 8 --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outSAMattributes All --outFilterIntronMotifs RemoveNoncanonical --quantMode GeneCounts --limitBAMsortRAM 64000000000.
Gene-level read counts were generated from STAR coordinate-sorted BAM files using htseq-count with the hg38 refGene GTF annotation file and parameters: -f bam -r pos -s reverse -t exon -i gene_id -m union -a 10.
Count tables were used for downstream differential gene expression analysis.
Assembly: UCSC hg38
Supplementary files format and content: tab-delimited text file consisting of raw counts (transcript abundances) for each sample for each Ensembl Gene ID

source_name: primary skin fibroblast

growth_protocol: Immortalized human skin fibroblasts or primary human skin fibroblasts (passages 2–5) were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified 5% CO₂ incubator. Cells were maintained by replacing the medium every 2–3 days and subcultured before reaching full confluence to preserve normal morphology and proliferative capacity.

extract_protocol:
Total RNA was extracted from cultured fibroblasts using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and purity were assessed by spectrophotometry, and samples were stored at –80°C until further use
Using the NEBNext Ultra II RNA Library Prep Kit for Illumina with poly(A) selection, we begin with high-quality total RNA and enrich mRNA using oligo-dT magnetic beads to capture polyadenylated transcripts, followed by washing and elution; we then fragment the purified mRNA under heat and prime it for reverse transcription to generate first-strand cDNA, after which we perform second-strand synthesis to produce double-stranded cDNA (optionally incorporating strand specificity), and subsequently carry out end repair and dA-tailing to create adapter-compatible ends; we ligate sequencing adapters, purify the library using magnetic beads (with optional size selection), and amplify it by PCR with indexed primers to enrich adapter-ligated fragments, and finally we assess library size distribution and concentration before pooling and sequencing on an Illumina platform.

treatment_protocol: Cells were treated either with or without TGF‑β or with compoound F05650303 for 48 hours.

value: primary skin fibroblast

value: fibroblast

value: wt


title: KASATAC-K562-Rep1-3349966_SMF304

description: Library name: sample 1


title: KASATAC-K562-Rep2-3349967_SMF305

description: Library name: sample 2


title: Diff UC protK-Rnase_Urine_Cancer_1

city: Ghent

first: sandor

last: Dedeyne

address: C. Heymanslaan 10

country: Belgium

institute: University Ghent

description: Library name: RNA022718

data_processing:
BCL files were processed using the Illumina Bcl2fastq (v. 2.20) software to generate and demultiplex fastq files. Raw reads were assessed for quality using FastQC (v. 0.11.9). The unique molecular identifier (UMI) sequences in the Pico v3 SMART UMI adapters were first extracted and added to the read name with UMI-tools (v. 1.0.0). Next, the sequencing data were processed with an in-house developed and validated pipeline using cutadapt (v. 1.16), SAMtools (v. 1.9), and STAR (v. 2.7.3a) to obtain deduplicated, high-quality and aligned RNA counts against the human genome (hg38). Ribosomal contamination was assessed using the BBMap tool (v. 38.87). Additional QC statistics were generated by using multiQC (v. 1.9) software package. Gene counts were determined with HTSeq (v. 0.11.0) in reverse stranded mode, only considering uniquely mapping reads. Ensembl release 91 was used to annotate reads within human genes.
Assembly: hg38
Supplementary files format and content: Tab seperated format, rows are genese, columns are samples, first 3 columns are ensembl ID, hgnc symbol and external gene name extacted from biomart

source_name: Urine

extract_protocol:
Total and small RNA were isolated from samples using the miRNeasy Micro kit (urine and cell culture medium) and miRNeasy Serum/Plasma Advanced kit (blood plasma) according to manufacturer’s instructions (cat. no. 217084 and 217204, Qiagen, Valencia, CA, USA), and eluted in 12 µL DNase/RNase-free water. To allow for a proper method comparison during RNA sequencing, synthetic spike-in controls were added as previously described 43,44. In short, per initial amount of biofluid input volume, 2 µL Sequin spike-in control [JV1] (Garvan Institute of Medical Research) and 2 µL RNA extraction Control (RC) spike-ins (Integrated DNA Technologies) were added to the lysate. Following RNA isolation, 2 µL of External RNA Control Control Consortium (ERCC) and 2 µL Library Prep (LP) spike-ins were added. RNA samples were stored at -80 °C until further use.
treated to remove residual genomic DNA by adding 1 µL of HL-dsDNase (#70800-202, ArcticZymes, 2 U/µL) and 1 µL reaction buffer (#66001, ArcticZymes) to 12 µL RNA, followed by 10 min incubation at 37 °C, and 10 min incubation at 55 °C to inactivate the DNase. Total RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian (#634487, Takara), including a ribosomal RNA depletion step at the cDNA level, as originally published in 53, with some modifications as reported 54. 8 µL of DNase treated RNA was fragmented for 4 min at 94 °C, followed by the ‘highly degraded RNA’ workflow. Library quality control was performed with the Fragment Analyzer high sense small fragment kit (Agilent Technologies, sizing range 50-1000 bp). Libraries were quantified using the KAPA Library Quantification Kit (#KK4854, Roche), followed by equimolar pooling and Qubit quantification. The loading concentration of the pool was 0.58 nM with 2% phiX on an S2 100 cycles flow cell (paired-end 2 x 50 nucleotides) on a NovaSeq 6000 instrument (Illumina)

value: Urine

tag: preparation protocol

value: Diff UC protK-Rnase


title: Diff UC protK-Rnase_Urine_Cancer_2

description: Library name: RNA022719


title: Diff UC protK-Rnase_Urine_Cancer_3

description: Library name: RNA022720


title: Diff UC protK-Rnase_Urine_Healthy_3

description: Library name: RNA022717


title: Diff UC protK-Rnase_Urine_Healthy_1

description: Library name: RNA022715


title: Diff UC protK-Rnase_Urine_Healthy_2

description: Library name: RNA022716


title: Diff UC_Urine_Cancer_2

description: Library name: RNA022713

value: Diff UC


title: treat2

city: Shanghai

first: Ji

last: Wu

state: Shanghai

address: No. 800, Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: Sample 4

library_source: other

data_processing:
After obtaining the Clean data, the data quality was analyzed using FastQ to obtain the corresponding biological information. The filtered sequences were subjected to bioinformatics analysis using the STAR program (v020201).
Assembly: GRCm38
Supplementary files format and content: table-delimited text file includes raw counts for each sample

molecule: other

source_name: spermatogonial stem cells

extract_protocol:
Cells were crosslinked with 1% formaldehyde (10 min, RT). Chimeric reads were enriched as described
RNA was randomly cleaved using micrococcus nuclease, dephosphorylated at the 3 'end, and labeled with pCp biotin. Subsequently, the 3' phosphate group was removed by treatment with Fast alkaline phosphatase (AP), while the 5 'end was phosphorylated by T4 polynucleotide kinase (PNK), enabling the RNA fragments obtained at close range to be ligated under in situ and non-denataturated conditions. After extracting and fragmenting the total RNA (approximately 90nt fragments), the RNA fragments containing biotin were enriched and then transformed into a library of specific strands (approximately 260 bp in length) for sequencing

value: spermatogonial stem cells

value: Differentiation


title: Diff UC_Urine_Cancer_1

description: Library name: RNA022712


title: treat1

description: Library name: Sample 3


title: Diff UC_Urine_Healthy_3

description: Library name: RNA022711


title: ctrl2

description: Library name: Sample 2

value: WT


title: ctrl1

description: Library name: Sample 1


title: Diff UC_Urine_Healthy_2

description: Library name: RNA022710


title: Diff UC_Urine_Healthy_1

description: Library name: RNA022709


title: DGUC Bottom-up_Urine_Cancer_3

description: Library name: RNA022708

value: DGUC Bottom-up


title: Basolateral Amygdala single-nucleus RNA-seq, Male

first: Elizabeth

middle: Kathleen

last: Lucas

state: AL

department: Psychiatry and Behavioral Neurobiology

description:
Library name: snRNA_male
single-nucleus 3' gene expression RNA-seq; male

data_processing:
Raw sequencing data were processed with CellRanger v7.0.0 using the refdata-gex-mm10-2020-A mouse reference to produce raw and filtered feature-barcode matrices.      .
Background RNA contamination was estimated and corrected with SoupX v1.6.2.
Low-quality nuclei were removed if mitochondrial transcripts exceeded 5%, low quality clusters, and non-basolateral amygdala clusters were removed during a pre-clustering step.
Likely doublets were identified with scDblFinder v1.20.2.
Clustering was performed stepwise on non-neuronal, excitatory neurons, and inhibitory neurins using Seurat v5.1.0 using the scTransform algorithm prior to recombination in a unified UMAP space. 7830 combined variable features were used,  with clustering parameters for non-neuronal (PCs = 1–75, k = 30, resolution = 0.1); inhibitory (PCs = 1–75, k = 30, resolution = 0.2); excitatory (PCs = 1–75, k = 75, resolution = 0.3) and combined (PCs = 1–100) clustering.
Differential expression was performed within Seurat using the Wilcoxon statistic for pairwise comparisons.
Spatial transcriptomic mapping was performed using a house branch of tangram v1.0.4 that exposed PyTorch loss curves on the Allen Brain Institute ABCA-1, ABCA-2, and ABCA-3 datasets using an inclusive convex hull wrapping the basolateral amygdala complex annotated in the common coordinate framework
Reintegration was performed using a house branch of scvi-tools v1.3.3 exposing PyTorch loss curves for the scVI and scANVI models.
Reference atlas alignment was performed using MapMyCells with the Allen Institute/10x Genomics CCN20230722 Whole Mouse Brain taxonomy.
Assembly: mm10; 10x Genomics refdata-gex-mm10-2020-A
Supplementary files format and content: 10x H5 feature-barcode matrices; AnnData H5AD object containing pooled/integrated processed expression data, annotations, and embeddings; CSV analysis tables; and plain-text file-structure summaries.
Supplementary files format and content: Shared study-level processed files are listed in the STUDY supplementary file field; sample-specific raw/filtered Cell Ranger matrices, summaries, and post-QC matrices are listed in the SAMPLES processed data file columns.

source_name: basolateral amygdala

growth_protocol: Adult C57BL/6J male and female mice were maintained until vaginal lavage and cytology was performed (or sham for males) to identify proestrus and diestrus estrous cycle stages.

extract_protocol:
C57BL/6J male mice and female mice (The Jackson Laboratory Strain #000664; RRID: IMSR_JAX:000664) in proestrus or diestrus were anesthetized and euthanized by rapid decapitation. Brains were removed, sectioned at 1 mm, and 1.25 mm punches of the lateral septum were collected, snap-frozen, and stored at -80 C. Basolateral amygdala  punches were pooled by experimental group before nuclei isolation. Nuclei were isolated using detergent-based lysis, filtered through a 35 um filter, washed, and resuspended in Hibernate AB. Nuclei were stained with 7-AAD, and singlets were sorted by flow cytometry.
Suspensions were processed using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10x Genomics Cat #1000121) and sequenced on an Illumina NovaSeq 6000 using v1.5 chemistry (28 10 10 90 cycles), targeting >50,000 reads per nucleus.

treatment_protocol: All animals were naive to explicit treatment arm.

value: basolateral amygdala

tag: strain

value: naive

value: replicate 1


title: DGUC Bottom-up_Urine_Cancer_2

description: Library name: RNA022707


title: Basolateral Amygdala single-nucleus RNA-seq, Female Diestrus

description:
Library name: snRNA_female_diestrus
single-nucleus 3' gene expression RNA-seq; female; diestrus


title: Basolateral Amygdala single-nucleus RNA-seq, Female Proestrus

description:
Library name: snRNA_female_proestrus
single-nucleus 3' gene expression RNA-seq; female; proestrus


title: DGUC Bottom-up_Urine_Cancer_1

description: Library name: RNA022706


title: DGUC Bottom-up_Urine_Healthy_3

description: Library name: RNA022705


title: M509459_ABE

city: Bethesda

first: Michael

last: Erdos

state: MD

address: 50 South Dr

department: NHGRI

institute: NIH

description:
Library name: Sample36
column name in WC2_mm_20220616.tpm: M509459_ABE

data_processing:
Aligned the processed reads to the GRCm38 genome assembly using STAR v2.73a with default parameters
Quantified expression levels of gencode.vM24 genes using QoRTs (v1.3.6).
Generated a raw read count matrix of gene by library
Assembly: GRCm38
Supplementary files format and content: read counts per gene per sample

source_name: tibia

extract_protocol:
TriZol extraction, followed by DNAse digestion
RNAseq libraries were prepared using Truseq stranded mRNA library kits

value: Male

value: tibia

value: retro-orbital P14 inj ABE


title: M4WT109560_ABE

description:
Library name: Sample35
column name in WC2_mm_20220616.tpm: M4WT109560_ABE


title: DGUC Bottom-up_Urine_Healthy_2

description: Library name: RNA022704


description:
Library name: PECHiC_naive-to-primed_transition_Day10_rep2
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day10

value: HNES1 cells

tag: time point

value: day 10 of the transition

value: naive-to-primed transition


title: M409458_ABE

description:
Library name: Sample34
column name in WC2_mm_20220616.tpm: M409458_ABE


title: DGUC Bottom-up_Urine_Healthy_1

description: Library name: RNA022703


title: M409446_saline

description:
Library name: Sample33
column name in WC2_mm_20220616.tpm: M409446_saline

value: retro-orbital P14 inj saline


title: The Original ExoQuick V2_Urine_Cancer_3

description: Library name: RNA022696

value: Urine

value: The Original ExoQuick V2


title: The Original ExoQuick V2_Urine_Cancer_2

description: Library name: RNA022695


title: M309451_saline

description:
Library name: Sample31
column name in WC2_mm_20220616.tpm: M309451_saline


title: M209511_saline

description:
Library name: Sample30
column name in WC2_mm_20220616.tpm: M209511_saline


title: The Original ExoQuick V2_Urine_Healthy_3

description: Library name: RNA022693


title: M1WT509424_saline

description:
Library name: Sample29
column name in WC2_mm_20220616.tpm: M1WT509424_saline


title: The Original ExoQuick V2_Urine_Healthy_2

description: Library name: RNA022692


title: The Original ExoQuick V2_Urine_Healthy_1

description: Library name: RNA022691


title: M109464_ABE

description:
Library name: Sample28
column name in WC2_mm_20220616.tpm: M109464_ABE


title: The Original ExoQuick V1_Urine_Cancer_1

description: Library name: RNA022688

value: The Original ExoQuick V1


title: M109440_saline

description:
Library name: Sample26
column name in WC2_mm_20220616.tpm: M109440_saline


title: M109432_saline

description:
Library name: Sample25
column name in WC2_mm_20220616.tpm: M109432_saline


title: M109455_ABE

description:
Library name: Sample27
column name in WC2_mm_20220616.tpm: M109455_ABE


title: The Original ExoQuick V1_Urine_Cancer_3

description: Library name: RNA022690


title: The Original ExoQuick V1_Urine_Healthy_3

description: Library name: RNA022687


title: The Original ExoQuick V1_Urine_Healthy_2

description: Library name: RNA022686


title: F609472_ABE

description:
Library name: Sample24
column name in WC2_mm_20220616.tpm: F609472_ABE

value: Female


title: The Original ExoQuick V1_Urine_Healthy_1

description: Library name: RNA022685


title: F409439_saline

description:
Library name: Sample22
column name in WC2_mm_20220616.tpm: F409439_saline


title: F509471_ABE

description:
Library name: Sample23
column name in WC2_mm_20220616.tpm: F509471_ABE


title: qEV2_Urine_Cancer_3

description: Library name: RNA022684


title: F309468_ABE

description:
Library name: Sample21
column name in WC2_mm_20220616.tpm: F309468_ABE


title: qEV2_Urine_Cancer_2

description: Library name: RNA022683


title: F309422_saline

description:
Library name: Sample19
column name in WC2_mm_20220616.tpm: F309422_saline


title: F309431_ABE

description:
Library name: Sample20
column name in WC2_mm_20220616.tpm: F309431_ABE


title: qEV2_Urine_Healthy_3

description: Library name: RNA022681


title: F309418_saline

description:
Library name: Sample18
column name in WC2_mm_20220616.tpm: F309418_saline


title: qEV2_Urine_Healthy_1

description: Library name: RNA022679


title: F209536_saline

description:
Library name: Sample17
column name in WC2_mm_20220616.tpm: F209536_saline


title: F1WT609535_ABE

description:
Library name: Sample16
column name in WC2_mm_20220616.tpm: F1WT609535_ABE


title: F109466_saline

description:
Library name: Sample15
column name in WC2_mm_20220616.tpm: F109466_saline


title: The ME kit_Urine_Cancer_3

description: Library name: RNA022672

value: The ME kit


title: The ME kit_Urine_Cancer_2

description: Library name: RNA022671


title: The ME kit_Urine_Cancer_1

description: Library name: RNA022670


title: The ME kit_Urine_Healthy_3

description: Library name: RNA022669


title: F109436_ABE

description:
Library name: Sample14
column name in WC2_mm_20220616.tpm: F109436_ABE


title: 619F_WT_WT

description:
Library name: Sample12
column name in WC2_mm_20220616.tpm: 619F_WT_WT

value: wild-type

value: NT


title: The ME kit_Urine_Healthy_2

description: Library name: RNA022668


title: 611F_WT_WT

description:
Library name: Sample9
column name in WC2_mm_20220616.tpm: 611F_WT_WT


title: 615M_WT_WT

description:
Library name: Sample10
column name in WC2_mm_20220616.tpm: 615M_WT_WT


title: Total Exosome Isolation_Urine_Cancer_3

description: Library name: RNA022666

value: Total Exosome Isolation


title: Total Exosome Isolation_Urine_Healthy_3

description: Library name: RNA022663


title: 608M_WT_WT

description:
Library name: Sample8
column name in WC2_mm_20220616.tpm: 608M_WT_WT


title: Total Exosome Isolation_Urine_Healthy_2

description: Library name: RNA022662


title: Total Exosome Isolation_Urine_Healthy_1

description: Library name: RNA022661


title: exoEasy_Urine_Cancer_3

description: Library name: RNA022660

value: exoEasy


title: 603F_WT_WT

description:
Library name: Sample5
column name in WC2_mm_20220616.tpm: 603F_WT_WT


title: 602F_WT_WT

description:
Library name: Sample4
column name in WC2_mm_20220616.tpm: 602F_WT_WT


title: exoEasy_Urine_Cancer_2

description: Library name: RNA022659


title: exoEasy_Urine_Cancer_1

description: Library name: RNA022658


title: 601F_WT_WT

description:
Library name: Sample3
column name in WC2_mm_20220616.tpm: 601F_WT_WT


title: exoEasy_Urine_Healthy_3

description: Library name: RNA022657


title: 600M_WT_WT

description:
Library name: Sample2
column name in WC2_mm_20220616.tpm: 600M_WT_WT


title: exoEasy_Urine_Healthy_2

description: Library name: RNA022656


title: 599M_WT_WT

description:
Library name: Sample1
column name in WC2_mm_20220616.tpm: 599M_WT_WT


title: UV and ruxolitinib-treated dorsal skin scRNA-seq

first: Yuanyuan

last: Liu

address: Medical School of Chinese People's Liberation Army, 100039 Beijing, China.

description:
Library name: UV_ruxolitinib
Full-thickness dorsal skin single-cell gene expression library after mixed UVA/UVB irradiation and topical ruxolitinib treatment. 10x Genomics Chromium Next GEM Single Cell 3' v3.1 GEX library; read 1 contains cell barcode and UMI, read 2 contains transcript sequence. Matrix dimensions: 32285 features x 11287 cells.

data_processing:
Raw single-cell RNA-seq reads were processed with Cell Ranger v6.1.2 (10x Genomics) against the mm10 reference genome to generate gene-barcode count matrices.
Downstream analysis and visualization were performed in Seurat v5.3.0 using a standard pipeline; clusters were annotated by canonical marker genes.
Differential expression between conditions was assessed using the nonparametric Wilcoxon rank-sum test.
Pseudotime was inferred with Monocle 3; transcription-factor activity was estimated with DoRothEA regulons; ligand-receptor signaling networks were inferred with CellChat v2.2.0.
Pathway and systems biology analyses were performed with fgsea v1.22.0 using MSigDB v7.5.1 and with clusterProfiler v4.4.4 for KEGG enrichment.
Assembly: mm10
Supplementary files format and content: 10x Genomics Cell Ranger filtered feature-barcode matrix files are provided for each sample: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Supplementary files format and content: matrix.mtx.gz contains gene expression counts in Matrix Market Exchange format; features.tsv.gz contains Ensembl gene IDs, gene symbols, and feature type; barcodes.tsv.gz contains cell barcodes.

source_name: full-thickness dorsal skin

growth_protocol: Female C57BL/6J mice (8 weeks; Charles River Laboratories, Beijing, China) were housed under SPF conditions with a 12-h light/dark cycle, 22 +/- 2 C, and ad libitum chow and water. Mice were randomized to control, UV, or UV + ruxolitinib groups.

extract_protocol:
Twenty-four hours after the final exposure, full-thickness dorsal skin was excised. Fresh tissue for single-cell analysis was processed immediately into single-cell suspensions for droplet-based scRNA-seq.
Droplet-based single-cell RNA sequencing was performed on the 10x Genomics Chromium platform using Chromium Next GEM Single Cell 3' Kit v3.1 (PN 1000268) to generate gene-expression libraries. Single-cell suspensions were combined with barcoded gel beads and RT master mix, loaded onto a Chromium Next GEM Chip G with Dual Index Kit TT Set A, and processed on a Chromium Controller. After reverse transcription, emulsions were broken and cDNA was amplified to construct GEX libraries. Library yield was quantified with Qubit 3.0 and fragment size distribution was evaluated on an Agilent 2100 Bioanalyzer. Pooled libraries were sequenced on an Illumina NovaSeq 6000.

treatment_protocol: Cutaneous photoaging was induced by mixed UVA (315-400 nm, 0.60 mW/cm2) and UVB (290-315 nm, 3.5 mW/cm2) irradiation every other day for 12 weeks. For the intervention group, dorsal skin was treated immediately following irradiation with vehicle containing ruxolitinib (JAK1/2 inhibitor; ruxolitinib) formulated as 1.5% ointment.

value: full-thickness dorsal skin

value: mixed skin cells

value: wild type

value: mixed UVA/UVB irradiation plus topical ruxolitinib


title: UV-exposed dorsal skin scRNA-seq

institute: Medical School of Chinese People's Liberation Army

description:
Library name: UV
Full-thickness dorsal skin single-cell gene expression library after mixed UVA/UVB irradiation. 10x Genomics Chromium Next GEM Single Cell 3' v3.1 GEX library; read 1 contains cell barcode and UMI, read 2 contains transcript sequence. Matrix dimensions: 32285 features x 12411 cells.

value: mixed UVA/UVB irradiation


title: Exosome Purification_Urine_Cancer_2

description: Library name: RNA022653

value: Exosome Purification


title: Control dorsal skin scRNA-seq

description:
Library name: control
Control full-thickness dorsal skin single-cell gene expression library. 10x Genomics Chromium Next GEM Single Cell 3' v3.1 GEX library; read 1 contains cell barcode and UMI, read 2 contains transcript sequence. Matrix dimensions: 32285 features x 13170 cells.

value: control


title: Exosome Purification_Urine_Healthy_3

description: Library name: RNA022651


title: FemaleC26PoWeR3

city: Fayetteville

first: Pieter

middle: Jan

last: Koopmans

state: AR

address: 155 N Stadium Drive

department: Cell and Molecular Biology

institute: University of Arkansas - Fayetteville

description:
Library name: P24_S48
8-week-old BALB/c female mouse, underwent 11.5 weeks of progressive weighted wheel running (PoWeR), 25 days prior to endpoint

data_processing:
For total RNA-Seq, raw FASTQ files were imported into Partek Cloud Platform aligned to mm39 with STAR 2.7.8a with default parameters. Aligned reads were quantified to annovation model and filtered to exclude genes with maximum count of less than 5. Normalized with DESeq2 median ratio. Tested for significance using DESeq2, with lowest average coverage filter of 1 prior to false discovery correction.
Assembly: mm39
Supplementary files format and content: For total RNA-seq, DESeq2 Normalized Counts.

source_name: Skeletal Muscle, Gastrocnemius

extract_protocol:
Total RNA was extracted via Trizol-Chloroform precpitiation of RNA using Zymo Direct-Zol RNA extraction kit.
Library preparation was performed by the Oklahoma Medical Research Foundation (OMRF) Clinical Genomics Core and 150bp - PE sequenced using an Illumina NovaSeq 6000

treatment_protocol: Male and Female 7-week-old BALB/c mice were acclimated to the running wheel for one week, or remained sedentary in group housing. Mice that were acclimated to the running wheel underwent 8 weeks of PoWeR training, then a subset were innoculated with C26 colorectal cancer cells, then continued with PoWeR for remaining 3.5 weeks until endpoint. The other subset of mice remained sedentary through the entire duration.

value: Skeletal Muscle, Gastrocnemius

value: BALB/c

tag: agent

value: C26 Tumor

tag: group

value: 11.5 week of PoWeR exercise training


title: FemaleC26PoWeR2

description:
Library name: P23_S47
8-week-old BALB/c female mouse, underwent 11.5 weeks of progressive weighted wheel running (PoWeR), 25 days prior to endpoint

tag: Sex

value: Female


title: Exosome Purification_Urine_Healthy_1

description: Library name: RNA022649

value: Urine


title: FemaleC26PoWeR1

description:
Library name: P22_S46
8-week-old BALB/c female mouse, underwent 11.5 weeks of progressive weighted wheel running (PoWeR), 25 days prior to endpoint


title: ExoSpin_Urine_Healthy_3

description: Library name: RNA022648

value: ExoSpin


title: WT sample L19 liver

city: Jerusalem

first: Itamar

last: Harel

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Quality control and adapter trimming of the fastq sequence files were performed with FastQC (v0.11.8), fastx-toolkits (v0.0.13), Trim Galore! (v0.6.4), and Cutadapt (3.4). Options were set to remove Illumina TruSeq adapters and end sequences to retain high-quality bases with phred score > 20 and a remaining length > 20 bp. Successful processing was verified by re-running FastQC. Reads was mapped and quantified to the killifish genome Nfu_20140520 using STAR 2.7.6a. Differential gene expression between rag2 mutant and WT fish was performed using the edgeR package (v3.32.1).
Assembly: Nfu_20140520
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Nothobranchius furzeri

source_name: Liver

growth_protocol: Fish were grown at 28°C in a central filtration recirculating system with a 12 h light/dark cycle at the Hebrew University of Jerusalem (Aquazone ltd, Israel). Fish were fed with live Artemia until the age of 2 weeks (#109448, Primo), and starting week 3, fish were fed three times a day on weekdays (and once a day on weekends), with GEMMA Micro 500 Fish Diet (Skretting Zebrafish, USA), supplemented with Artemia once a day.

extract_protocol:
Brain and liver were isolated as described in (Astre et al. 2022)
Library preparation was performed using KAPA mRNA HyperPrep Kit (ROCHE-08105936001) according to the recommended protocols. Library quantity and pooling were measured by Qubit (dsDNA HS,Q32854), Size selection at 4% agarose gel. Library quality was measured by Tape Station (HS,5067-5584). Libraries were sequenced by NextSeq 2000 P2, 100 cycle,75 bp single-end (Illumina, 20024906) with ~40 million reads per sample.

value: Liver

value: WT

tag: age

value: 3 months

value: Male


title: FemaleC26SED2

description:
Library name: P20_S44
8-week-old BALB/c female mouse remained sedentary in group housing, and received C26 colorectal cancer cell innoculation  25 days prior to endpoint

value: Sedentary


title: ExoSpin_Urine_Healthy_1

description: Library name: RNA022646


title: FemaleC26SED1

description:
Library name: P19_S43
8-week-old BALB/c female mouse remained sedentary in group housing, and received C26 colorectal cancer cell innoculation  25 days prior to endpoint


title: ExoSpin_Urine_Cancer_3

description: Library name: RNA022645


title: FemalePBSPoWeR3

description:
Library name: P18_S42
8-week-old BALB/c female mouse, underwent 11.5 weeks of progressive weighted wheel running (PoWeR), and received PBS injection  25 days prior to endpoint

value: PBS


title: ExoSpin_Urine_Cancer_2

description: Library name: RNA022644


title: WT sample L8 liver


title: FemalePBSPoWeR2

description:
Library name: P17_S41
8-week-old BALB/c female mouse, underwent 11.5 weeks of progressive weighted wheel running (PoWeR), and received PBS injection  25 days prior to endpoint


title: ExoSpin_Urine_Cancer_1

description: Library name: RNA022643


title: FemalePBSPoWeR1

description:
Library name: P16_S40
8-week-old BALB/c female mouse, underwent 11.5 weeks of progressive weighted wheel running (PoWeR), and received PBS injection  25 days prior to endpoint


title: ExoCap_Urine_Cancer_3

description: Library name: RNA022642

value: ExoCap


title: FemalePBSSED3

description:
Library name: P15_S39
8-week-old BALB/c female mouse remained sedentary in group housing, and received PBS injection  25 days prior to endpoint


title: ExoCap_Urine_Cancer_2

description: Library name: RNA022641


title: FemalePBSSED2

description:
Library name: P14_S38
8-week-old BALB/c female mouse remained sedentary in group housing, and received PBS injection  25 days prior to endpoint


title: ExoCap_Urine_Cancer_1

description: Library name: RNA022640


title: dKO sample 2 brain

source_name: Brain

value: Brain

value: ATMcGAS double mutant

value: 2 months


title: ExoCap_Urine_Healthy_3

description: Library name: RNA022639


title: MaleC26PoWeR2

description:
Library name: P12_S36
8-week-old BALB/c male mouse, underwent 11.5 weeks of progressive weighted wheel running (PoWeR), 25 days prior to endpoint

value: Skeletal Muscle, Gastrocnemius


title: ExoCap_Urine_Healthy_2

description: Library name: RNA022638


title: ExoSpin_Urine_Healthy_2

description: Library name: RNA022647


title: FemaleC26SED3

description:
Library name: P21_S45
8-week-old BALB/c female mouse remained sedentary in group housing, and received C26 colorectal cancer cell innoculation  25 days prior to endpoint

value: BALB/c


title: MaleC26PoWeR1

description:
Library name: P10_S34
8-week-old BALB/c male mouse, underwent 11.5 weeks of progressive weighted wheel running (PoWeR), 25 days prior to endpoint

value: C26 Tumor


title: MaleC26SED2

description:
Library name: P8_S32
8-week-old BALB/c male mouse remained sedentary in group housing, and received C26 colorectal cancer cell innoculation  25 days prior to endpoint


title: ExoCap_Urine_Healthy_1

description: Library name: RNA022637


title: EXO-TotalRNA_Urine_Cancer_3

description: Library name: RNA022636

value: EXO-TotalRNA


title: EXO-TotalRNA_Urine_Cancer_2

description: Library name: RNA022635


title: MaleC26SED1

description:
Library name: P7_S31
8-week-old BALB/c male mouse remained sedentary in group housing, and received C26 colorectal cancer cell innoculation  25 days prior to endpoint


title: MalePBSPoWeR3

description:
Library name: P6_S30_
8-week-old BALB/c male mouse, underwent 11.5 weeks of progressive weighted wheel running (PoWeR), and received PBS injection  25 days prior to endpoint

value: 11.5 week of PoWeR exercise training


title: EXO-TotalRNA_Urine_Cancer_1

description: Library name: RNA022634

value: Urine


title: MalePBSPoWeR2

description:
Library name: P5_S29
8-week-old BALB/c male mouse, underwent 11.5 weeks of progressive weighted wheel running (PoWeR), and received PBS injection  25 days prior to endpoint


title: M309457_ABE

description:
Library name: Sample32
column name in WC2_mm_20220616.tpm: M309457_ABE

value: tibia

value: retro-orbital P14 inj ABE


title: The Original ExoQuick V2_Urine_Cancer_1

description: Library name: RNA022694

value: The Original ExoQuick V2


title: EXO-TotalRNA_Urine_Healthy_3

description: Library name: RNA022633


title: EXO-TotalRNA_Urine_Healthy_2

description: Library name: RNA022632


title: MalePBSPoWeR1

description:
Library name: P4_S28
8-week-old BALB/c male mouse, underwent 11.5 weeks of progressive weighted wheel running (PoWeR), and received PBS injection  25 days prior to endpoint


title: MalePBSSED3

description:
Library name: P3_S27
8-week-old BALB/c male mouse remained sedentary in group housing, and received PBS injection  25 days prior to endpoint


title: MalePBSSED2

description:
Library name: P2_S26
8-week-old BALB/c male mouse remained sedentary in group housing, and received PBS injection  25 days prior to endpoint


title: Diff UC protK-Rnase_Plasma_3

description: Library name: RNA022765

value: Breast Cancer

value: Diff UC protK-Rnase


title: EXO-TotalRNA_Urine_Healthy_1

description: Library name: RNA022631


title: MalePBSSED1

description:
Library name: P1_S25
8-week-old BALB/c male mouse remained sedentary in group housing, and received PBS injection  25 days prior to endpoint

value: Male

value: Sedentary


title: Diff UC protK-Rnase_Plasma_2

description: Library name: RNA022764


title: Kelly cells treated with anti-GD2 and co-cultured with UCB NK cells, biological replicate 2

city: Guangzhou

first: Xiya

last: Tan

state: None Selected

address: 51 Dongfeng Road East, Guangzhou 510060, P. R. China.

institute: Sun Yat-sen University Cancer Center

description: Library name: GD2-UCBNK-2

data_processing:
Raw sequencing reads were generated in FASTQ format on the Illumina NovaSeq X Plus platform.
Adapter sequences and low-quality reads were removed using fastp (v0.18.0) to obtain clean reads.
Clean reads were used for downstream transcriptomic analysis.
Assembly: GRCm39 (Ensembl release 111)
Supplementary files format and content: Tab-delimited text file containing raw gene-level read counts for each sample.
Supplementary files format and content: Tab-delimited text file containing normalized gene expression values ([TPM/FPKM/CPM]) for each sample.

source_name: xenograft tumor tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent.
RNA-seq libraries for Illumina sequencing were prepared using the Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit according to the manufacturer's instructions.

value: xenograft tumor tissue

value: Kelly

value: neuroblastoma cell and NK cell co-culture


title: Diff UC protK-Rnase_Plasma_1

description: Library name: RNA022763


title: Kelly cells treated with anti-GD2 and co-cultured with UCB NK cells, biological replicate 1

description: Library name: GD2-UCBNK-1


title: Kelly cells co-cultured with UCB NK cells, biological replicate 2

description: Library name: UCBNK-2


title: Diff UC_Plasma_2

description: Library name: RNA022761

value: Diff UC


title: qEV2_Urine_Cancer_1

description: Library name: RNA022682


title: Diff UC_Plasma_1

description: Library name: RNA022760


title: qEV2_Urine_Healthy_2

description: Library name: RNA022680


title: Kelly cells co-cultured with UCB NK cells, biological replicate 1

description: Library name: UCBNK-1


title: DGUC Bottom-up_Plasma_3

description: Library name: RNA022759

value: DGUC Bottom-up


title: Kelly cells treated with anti-GD2 antibody, biological replicate 2

description: Library name: Anti-GD2-2

value: neuroblastoma cells


title: DGUC Bottom-up_Plasma_2

description: Library name: RNA022758


title: F109420_saline

description:
Library name: Sample13
column name in WC2_mm_20220616.tpm: F109420_saline

value: Female

value: retro-orbital P14 inj saline


title: Kelly cells treated with anti-GD2 antibody, biological replicate 1

description: Library name: Anti-GD2-1


title: FemalePBSSED1

description:
Library name: P13_S37
8-week-old BALB/c female mouse remained sedentary in group housing, and received PBS injection  25 days prior to endpoint

value: Skeletal Muscle, Gastrocnemius

value: BALB/c

value: PBS


title: DGUC Bottom-up_Plasma_1

description: Library name: RNA022757


title: DGUC Top-Down_Plasma_3

description: Library name: RNA022756

value: DGUC Top-Down


title: Kelly cells treated with IgG control, biological replicate 2

description: Library name: IgG_2


title: Kelly cells treated with IgG control, biological replicate 1

description: Library name: IgG_1


title: The ME kit_Urine_Healthy_1

description: Library name: RNA022667

value: Urine

value: The ME kit


title: DGUC Top-Down_Plasma_2

description: Library name: RNA022755

value: Breast Cancer


title: 617M_WT_WT

description:
Library name: Sample11
column name in WC2_mm_20220616.tpm: 617M_WT_WT

value: Male

value: tibia

value: wild-type

value: NT


title: small intestine, model, rep1 scRNA

first: Zhijie

last: Bai

state: 北京Beijing

address: Taiping Road, Haidian District

institute: beijing institute of radiation

description: Library name: 241159A_M

data_processing:
The fastq files generated by sequencing was processed by CellRanger (version 4.0) offered by 10x Genomics to obtain expression matrixes.
Assembly: GRCm39
Supplementary files format and content: barcodes.tsv.gz; features.tsv.gz; matrix.mtx.gz

source_name: small intestine

extract_protocol:
Small intestines were dissected and processed as described above. Single-cells were washed once and subjected for 10x Genomics single-cell sample preparation.
The single-cell cDNA library was constructed following the standard protocol offered by 10x Genomics. Completed cDNA library was sequenced by Illumina novaseq6000 platform.

value: small intestine


title: small intestine, control, rep1 scRNA

description: Library name: 241159A_C


title: DGUC Top-Down_Plasma_1

description: Library name: RNA022754


title: The Original ExoQuick V2_Plasma_3

description: Library name: RNA022753

value: The Original ExoQuick V2


title: 606M_WT_WT

description:
Library name: Sample7
column name in WC2_mm_20220616.tpm: 606M_WT_WT


title: small intestine, model, rep3

description: Library name: M3

data_processing:
Raw FASTQ files were first subjected to quality control using FastQC, followed by adapter trimming and low-quality read removal with Trimmomatic. High-quality reads were then aligned to the reference genome (GRCm39) using STAR aligner. Gene expression quantification was performed using featureCounts, generating a count matrix where rows represent genes and columns represent samples.
Assembly: GRCm39
Supplementary files format and content: C-M.txt

extract_protocol:
After rapid freezing with liquid nitrogen, the small intestine tissue was used to extract RNA using the Trizol method.
Total RNA served as the starting material for RNA sample preparation, where mRNA was isolated using poly-T oligo-attached magnetic beads. Fragmentation was conducted under elevated temperature in the presence of divalent cations within the First Strand Synthesis Reaction Buffer. For first strand cDNA synthesis, random hexamer primers and M-MuLV Reverse Transcriptase were employed; this step was followed by second strand synthesis using DNA Polymerase I and RNase H. Subsequently, the overhanging ends of the cDNA were converted to blunt ends. After adenylation of the 3ʹ ends, adaptors with a hairpin loop structure were ligated to the cDNA molecules. The cDNA fragments were then size-selected to a target length range of 370–420 bp using the AMPure XP system. Following size selection, PCR amplification was performed with Phusion High-Fidelity DNA Polymerase and universal primers.


title: The Original ExoQuick V2_Plasma_2

description: Library name: RNA022752


title: small intestine, model, rep2

description: Library name: M2


title: The Original ExoQuick V2_Plasma_1

description: Library name: RNA022751


title: small intestine, model, rep1

description: Library name: M1


title: The Original ExoQuick V1_Plasma_1

description: Library name: RNA022748

value: The Original ExoQuick V1


title: small intestine, control, rep3

description: Library name: C3


title: 604F_WT_WT

description:
Library name: Sample6
column name in WC2_mm_20220616.tpm: 604F_WT_WT


title: qEV2_Plasma_3

description: Library name: RNA022747

value: qEV2 (AC)


title: small intestine, control, rep2

description: Library name: C2


title: small intestine, control, rep1

description: Library name: C1


title: qEV2_Plasma_1

description: Library name: RNA022745


title: The ME kit_Plasma_3

description: Library name: RNA022741


title: CTX combo VDJ

city: New York

first: Yacine

last: Marouf

state: NY

address: 413 E 69th St

department: MCC

institute: Weill Cornell Medecine

description: Library name: CTX_combo_VDJ

data_processing:
CellRanger v6.1.1
Assembly: GRCm38-2020-A
Supplementary files format and content: h5 files for GEX and ADT
Supplementary files format and content: csv files for VDJ
Library strategy: TCR-Seq

source_name: Tumor

growth_protocol: B16-F10  tumor cells were implanted intradermally (i.d.) in the flank at doses of 2 x 105.

extract_protocol:
Mice were implanted with B16-F10 tumors. CTX and ICB treatment was administered as previously described. On day 14 post CTX treatment, all cohorts of mice were sacrificed, tumors were mechanically dissociated to obtain a single-cell suspension. Lymphocytes were separated from tumors using 40% Percoll (GE Healthcare) gradient centrifugation. Cells were treated with saturating anti-CD16/CD32 (BD) in staining buffer (2% fetal bovine serum in PBS) on ice for 15 minutes. Cells were then stained with anti-CD45 APC (BioLegend) for 20 mins on ice, TotalSeq anti-mouse hashtag antibodies (C0301, C0302, C0303, C0304, C0305; BioLegend) for 20 mins on ice followed by CITE-seq antibodies (custom made from BioLegend) for 30 mins on ice. Concentration of antibodies used according to the manufacturer’s instructions. The cells were washed 2-3 times in staining buffer (2% fetal bovine serum in PBS between each staining step. The cells were then resuspended in DAPI and FACS sorted based live CD45+ cells and next-generation TCR coupled with 10x Genomics sequencing was performed.
Following QC, the single cell suspension was loaded onto Chromium Chip A (10X Genomics PN 230027) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 1,700-6,400 cells proceeded using the Chromium Single Cell 5′ Reagent Kit (10X Genomics PN 1000006) according to the manufacturer’s protocol. cDNA amplification included 13-16 cycles and 11-50 ng of the material was used to prepare sequencing libraries with 14-16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/91 run using the NovaSeq 6000 S1 Reagent Kit (100 cycles) (Illumina). An average of 160 million paired reads was generated per sample.

treatment_protocol: Cyclophosphamide monohydrate (MilliporeSigma) mixed in sterile PBS was administered as a single dose of 250mg/kg intraperitoneally (i.p). On day 8, mice were treated with 200 microgram aPD-1 and 100 microgram  aCTLA-4 i.p. in PBS, administered twice weekly until termination of the experiment.

value: Tumor


title: CTX IgG VDJ

description: Library name: CTX_IgG_VDJ

value: CTX IgG


title: The ME kit_Plasma_1

description: Library name: RNA022739


title: The ME kit_Plasma_2

description: Library name: RNA022740


title: PBS IgG VDJ

description: Library name: PBS_IgG_VDJ

value: IgG


title: PBS combo VDJ

description: Library name: PBS_combo_VDJ


title: CTX combo ADT

description: Library name: CTX_combo_ADT

data_processing:
CellRanger v6.1.1
Assembly: GRCm38-2020-A
Supplementary files format and content: h5 files for GEX and ADT
Supplementary files format and content: csv files for VDJ
Library strategy: CITE-seq

molecule: protein


title: Total Exosome Isolation_Plasma_1

description: Library name: RNA022736

value: Total Exosome Isolation


title: CTX IgG ADT

description: Library name: CTX_IgG_ADT


title: exoEasy_Plasma_3

description: Library name: RNA022735

value: exoEasy


title: exoEasy_Plasma_1

description: Library name: RNA022733


title: CTX IgG GEX

description: Library name: CTX_IgG_mRNA


title: Exosome Purification_Plasma_2

description: Library name: RNA022731

value: Exosome Purification


title: PBS combo GEX

description: Library name: PBS_combo_mRNA


title: PBS IgG GEX

description: Library name: PBS_IgG_mRNA


title: Exosome Purification_Plasma_1

description: Library name: RNA022730


title: ExoSpin_Plasma_3

description: Library name: RNA022729

value: ExoSpin


title: cKO 3

first: Yiming

last: Zhu

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

description:
Library name: Sample7
Column name in raw_counts.txt: cKO3

data_processing:
FastQC (v0.11.9) package was used to check the quality of raw data, and the Trim-Galore (v0.6.7) for trimming the adapter sequence and filter reads with low quality.
Paired-end sequencing reads were aligned to the mouse genome (GRCm38.primary_assembly.genome) using Spliced Transcripts Alignment to a Reference (STAR) 2.7.10a.
Package featureCounts v.2.0.1 was used to count the read numbers mapped to each gene.
Assembly: mouse genome(GRCm38.primary_assembly.genome)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA from 10,000 sorted PCs was extracted using the EZ-press RNA Purification Kit PLUS (EZB, B0004-PLUS-S).
Reverse transcription, PCR preamplification, and purification of PCR products were conducted using the Discover-sc WTA Kit V2 (Vazyme Biotech). The RNA-seq library was generated by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech) using 10 ng amplified cDNAs as input following the manufacturer's protocols.

treatment_protocol: Taciflox/flox and Jchain-CreERT2;Taciflox/flox mice were injected once daily with 100 mg/kg tamoxifen in corn oil for 3 consecutive days. Ten thousand bone marrow plasma cells (PCs,CD138high B220–) were sorted from these mice using BD FACS Aria Ⅲ.

value: Bone marrow

value: Plasma cells

value: 3-day tamoxifen treatment


title: ExoCap_Plasma_3

description: Library name: RNA022726

value: Breast Cancer

value: ExoCap


title: cKO 1

description:
Library name: Sample5
Column name in raw_counts.txt: cKO1


title: cKO 2

description:
Library name: Sample6
Column name in raw_counts.txt: cKO2


title: ExoCap_Plasma_2

description: Library name: RNA022725


title: ExoSpin_Plasma_1

description: Library name: RNA022727


title: Control 4

description:
Library name: Sample4
Column name in raw_counts.txt: Control4

value: Taciflox/flox


title: EXO-TotalRNA_Plasma_3

description: Library name: RNA022723

value: EXO-TotalRNA


title: Control 3

description:
Library name: Sample3
Column name in raw_counts.txt: Control3


title: EXO-TotalRNA_Plasma_2

description: Library name: RNA022722


title: EXO-TotalRNA_Plasma_1

description: Library name: RNA022721


title: Control 2

description:
Library name: Sample2
Column name in raw_counts.txt: Control2


title: Control 1

description:
Library name: Sample1
Column name in raw_counts.txt: Control1


title: WT, dorsal skin, epidermal progenitor cells, 6-month-old telogen, RNA-seq, rep 1

city: Los Angeles

first: Ya-Chen

last: Liang

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

description:
Library name: Chuong-874
Column name in Msx2_EpdSC_DESeq2_cKO_vs_WT_counts.txt: Ch-874_S221

data_processing:
RNA-seq Data Processing and Analysis: RNA-seq analysis was conducted using the Partek® Flow® platform (Partek Inc.). Default parameters were applied unless otherwise specified.
Quality Control and Alignment: Pre-alignment quality control (QA/QC) steps were performed prior to read mapping. Reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR version 2.7.3a, followed by post-alignment QA/QC.
Quantification and Normalization: Aligned reads were quantified to the Ensembl release 103 annotation model using the Partek Expectation/Maximization (E/M) method. Gene expression values were normalized using Transcripts Per Million (TPM).
Differential Expression Analysis: Differential gene expression analysis was performed using Partek Gene-Specific Analysis (GSA). Genes with a false discovery rate (FDR) < 0.05 and an absolute fold change > 2 were considered significantly differentially expressed.
Assembly: Emsemble GRCm38/mm10 for all samples.
Supplementary files format and content: Tab-delimited text files include raw counts for each sample
Supplementary files format and content: Tab-delimited text files include GSA result for each sample

source_name: skin

growth_protocol: Mice were maintained under a 12 h light/dark cycle at 21–26 °C and 30–70 % relative humidity in the USC animal facility.

extract_protocol:
Total RNAs of indicated tissues were isolated using the standard AllPrep DNA/RNA Micro Kit protocol (Cat. 80284, Qiagen)
Library preparation using the SMARTer Stranded Total RNA-Seq Kit v3 was performed in Novogen company (CA, USA)

treatment_protocol: No treatment

value: skin

value: epidermal progenitor cell

value: wild-type


title: JJN3 cells, nontargeting control, rep 2

city: Berlin

first: Stefan

last: Habringer

address: Hindenburgdamm 30

department: Hematology, Oncology and Cancer Immunology

country: Germany

institute: Charité - Universitaetsmedizin Berlin

description:
Library name: Sample 11
JJN3_nt_2

data_processing:
Analysis with usegalaxy.org
Trim Galore
Bowtie 2
htseq-count
DESeq2
Assembly: hg38
Supplementary files format and content: rLog normalized counts

extract_protocol:
Rneasy mini prep kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification (Source: Novogene).

value: plasma cell

value: nontargeting sgRNA control

value: untreated


title: Msx2-KO, dorsal skin, hair follicle stem cells, 6-month-old telogen, RNA-seq, rep 2

description:
Library name: Chuong-877
Column name in Msx2_HFSC_DESeq2_cKO_vs_WT_counts.txt: Ch-877_S219

value: hair follicle stem cell

value: Msx2 knockout


title: Msx2-KO, dorsal skin, hair follicle stem cells, 6-month-old telogen, RNA-seq, rep 1

description:
Library name: Chuong-876
Column name in Msx2_HFSC_DESeq2_cKO_vs_WT_counts.txt: Ch-876_S218


title: JJN3 cells, KANSL2 knockdown, rep 2

description:
Library name: Sample 8
JJN3_KANSL2KD_2

value: KANSL2 knockdown


title: Msx2-KO, dorsal skin, hair follicle stem cells, 6-month-old telogen, ATAC-seq, rep 2

description: Library name: omATAC-14-2

data_processing:
ATAC-seq data were processed using the Partek® Flow® platform (Partek Inc.). Default parameters were used unless otherwise specified.
Quality Control: Pre-alignment quality control (QA/QC) algorithms were first applied. Post-alignment QA/QC was conducted after read mapping.
Read Mapping and Filtering: Reads were aligned to the mouse reference genome (Ensembl GRCm38/mm10) using BWA-MEM. Aligned reads were subsequently filtered to remove PCR duplicates, defined as reads with the same start position and sequence.
Peak Calling: Peaks were called using MACS2 with the following parameters: q-value cutoff < 0.01, no shifting model, shift size = 100, extension size = 200, and duplicate reads retained (keep dup all). Output files included both narrowPeak and bedGraph formats.
Signal Visualization: bigWig files were generated from bedGraph files using the Wig/BedGraph-to-bigWig converter. The narrowPeak files represent statistically significant peaks of chromatin accessibility as called by MACS2, based on local enrichment over background using the aligned read data.
Assembly: Emsemble GRCm38/mm10 for all samples.
Supplementary files format and content: narrowPeak file, which includes peak coordinates, signal intensity, and statistical significance for enriched regions.

extract_protocol:
Omni-ATAC-seq was performed following the published protocol (PMID: 28846090) with minor modifications. FACS-isolated HFSCs from different genetic backgrounds were resuspended in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) and incubated for 5 minutes at 4 °C. Following lysis, nuclei were diluted by adding ATAC-resuspension buffer (identical to lysis buffer but lacking NP-40 and Digitonin, and supplemented with 0.1% Tween-20). Nuclei were pelleted by centrifugation at 2,500 rpm for 5 minutes at 4 °C. The nuclear pellet was then resuspended in the transposition reaction mix containing Tn5 transposase (Illumina, 15027866) and incubated at 37 °C for 30 minutes. Transposed DNA was purified using the Zymo DNA Clean & Concentrator Kit (D4014) and eluted according to the manufacturer’s instructions.
Library amplification was performed based on the published Omni-ATAC-seq protocol (PMID: 28846090). Samples were PCR-amplified using NEBNext High-Fidelity PCR Master Mix (M0541, New England Biolabs) and 1.25 μM custom Nextera primers under the following thermal cycling conditions: 72 °C for 5 min, 98 °C for 30 s, followed by 5 cycles of 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 1 min. After the initial 5 cycles, a 5 μl aliquot was removed, combined with SYBR Green I (Invitrogen, S7563), and subjected to quantitative PCR (qPCR) to determine the optimal number of additional cycles. The final number of cycles was defined based on reaching one-fourth of the maximum fluorescence intensity. Libraries were then amplified accordingly and purified. Final DNA was eluted in 15 μl of 10 mM Tris-HCl (pH 8.0).


title: Msx2-KO, dorsal skin, hair follicle stem cells, 6-month-old telogen, ATAC-seq, rep 1

description: Library name: omATAC-14-1


title: INA 6 cells, nontargeting control, rep 3

description:
Library name: Sample 6
INA6_nt_3


title: INA 6 cells, nontargeting control, rep 2

description:
Library name: Sample 5
INA6_nt_2


title: JJN3 cells, KANSL2 knockdown, rep 1

description:
Library name: Sample 7
JJN3_KANSL2KD_1


title: Msx2-WT, dorsal skin, hair follicle stem cells, 6-month-old telogen, ATAC-seq, rep 1

description: Library name: omATAC-18


title: INA 6 cells, nontargeting control, rep 1

description:
Library name: Sample 4
INA6_nt_1


title: MPTP+SUEHP+T0070907_SC_3

city: Daejeon

first: jungim

last: Kim

address: 1672, Yuseong-daero, Yuseong-gu

department: KM Convergence Research Division

institute: Korea Institute of Oriental Medicine

description: Library name: G5_3_S_C

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Spinal cord

growth_protocol: The animals were housed under controlled environmental conditions, with a temperature of 23 ± 1 °C, a relative humidity of 50%, and a 12-hour light/dark cycle.

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: MPTP was administered intraperitoneally at a dose of 20 mg/kg  every 2 hours for a total of 4 injections. One week after the final MPTP injection, SUEHP was administered twice a week until the end of the experiment, for a total of 4 injections. CB1 antagonist (SR141714A, 3mg/kg)  or PPARγ inhibitor (T0070907, 5mg/kg) was co-treated intraperitoneally with SUEHP.

value: Spinal cord

value: Male

value: 8 Weeks


title: INA6 cells, KANSL2 knockdown, rep 3

description:
Library name: Sample 3
INA6_KANSL2KD_3


title: MPTP+SUEHP+T0070907_SC_4

description: Library name: G5_4_S_C


title: MPTP+SUEHP+T0070907_SC_2

description: Library name: G5_2_S_C


title: INA6 cells, KANSL2 knockdown, rep 2

description:
Library name: Sample 2
INA6_KANSL2KD_2


title: qEV2_Plasma_2

description: Library name: RNA022746

data_processing:
BCL files were processed using the Illumina Bcl2fastq (v. 2.20) software to generate and demultiplex fastq files. Raw reads were assessed for quality using FastQC (v. 0.11.9). The unique molecular identifier (UMI) sequences in the Pico v3 SMART UMI adapters were first extracted and added to the read name with UMI-tools (v. 1.0.0). Next, the sequencing data were processed with an in-house developed and validated pipeline using cutadapt (v. 1.16), SAMtools (v. 1.9), and STAR (v. 2.7.3a) to obtain deduplicated, high-quality and aligned RNA counts against the human genome (hg38). Ribosomal contamination was assessed using the BBMap tool (v. 38.87). Additional QC statistics were generated by using multiQC (v. 1.9) software package. Gene counts were determined with HTSeq (v. 0.11.0) in reverse stranded mode, only considering uniquely mapping reads. Ensembl release 91 was used to annotate reads within human genes.
Assembly: hg38
Supplementary files format and content: Tab seperated format, rows are genese, columns are samples, first 3 columns are ensembl ID, hgnc symbol and external gene name extacted from biomart

value: qEV2 (AC)


title: MPTP+SUEHP+T0070907_SC_1

description: Library name: G5_1_S_C


title: INA6 cells, KANSL2 knockdown, rep 1

description:
Library name: Sample 1
INA6_KANSL2KD_1


title: MPTP+SUEHP+SR141714A_SC_4

description: Library name: G4_4_S_C


title: Total Exosome Isolation_Plasma_3

description: Library name: RNA022738

value: Breast Cancer

value: Total Exosome Isolation


title: PBS combo ADT

description: Library name: PBS_combo_ADT

value: Tumor


title: exoEasy_Plasma_2

description: Library name: RNA022734

value: exoEasy


title: PBS IgG ADT

description: Library name: PBS_IgG_ADT

value: IgG