title: WT+N51AK58A-replicate3

city: Montpellier FRANCE

first: Julie

last: Carnesecchi

address: 1919, route de Mende team JCL team JCL

department: IGMM

institute: CNRS

description: Library name: JC18WNK

data_processing:
The quality of the raw reads and the presence of adapter sequences was checked using FastQC (version 0.12.1). Filtering of low-quality reads and adapter trimming was performed using Trimmomatic (version 0.39) with the following command: trimmomatic PE -phred33 -summary statsSummaryFile InputFile_1.fq.gz InputFile 2.fq.gz OutputFile_1_PairedTrimmed.fastq.gz OutputFile_1_UnpairedTrimmed.fastq.gz OutputFile_2_PairedTrimmed.fastq.gz OutputFile_2_UnpairedTrimmed.fastq.gz ILLUMINACLIP:Adapters-P5-P7.fa:2:30:10:2:True LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Prior to read alignment using RNA STAR (version 2.7.10b), the index of the genome was generated: STAR --runMode genomeGenerate --genomeDir STARIndex genomeFastaFiles Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa --sjdbGTFfile Drosophila_melanogaster.BDGP6.46.112.gtf --sjdbOverhang 149 --genomeSAindexNbases 12. Reads were aligned on the Drosophila genome with the following command: STAR --runMode alignReads genomeDir STARIndex --readFilesIn OutputFile_1_PairedTrimmed.fastq OutputFile_2_PairedTrimmed.fastq --outSAMtype BAM SortedByCoordinate.
Aligned reads were counted using HTSeq (version 0.11.3): htseq-count -f bam -r pos -m union -s no -a 255 -t exon InputFile.bam Drosophila_melanogaster.BDGP6.46.112.gtf > HTSeqCounts.txt. Further differential expression analysis was carried out on R Studio using DESeq2 (version 1.42.1) under standard conditions.
Assembly: Drosophila_melanogaster.BDGP6.46.112.gtf
Supplementary files format and content: tab-deliimited text file of Htcounts, one file per samples

organism: Drosophila melanogaster

source_name: embryonic cells

extract_protocol:
Total RNAs were extracted from three independent replicates from Drosophila S2R+ cells expressing GFPnls, myc-UbxWT, myc-UbxN51A or myc-UbxN51A+K58A or in co-expression (Gal4-UAS, actin promoter) using Qiagen RNAeasy extraction kit and Dnase digestion on column
Material handling and mRNA-Seq directional libraries with poly(A) selection (Illumina) were performed by Novogene service

treatment_protocol: transient transfection

value: embryonic cells

value: S2R+ Drosophila cells

value: overexpressing GFP-Ubx-WT+N51AK58A


title: WT+N51AK58A-replicate1

status: Public on Jun 08 2025

type: SRA

country: France

description: Library name: JC16WNK

library_source: transcriptomic

molecule: polyA RNA

tag: tissue

tag: cell type

tag: treatment


title: Late passage Senescence HFF cells, rep 2

city: Galveston

first: Steven

middle: G

last: Widen

state: Texas

address: 301 University Blvd

department: BMB

country: USA

institute: University of Texas Medical Branch

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
RNA-Seq reads were aligned to the human GRCh38  reference using the STAR software version 2.7.10a with the parameters recommended for the ENCODE consortium.
Human gene read counts were obtained from the STAR quantMode GeneCounts feature using the Gencode v41 annotation file.
Assembly: GRCh38
Supplementary files format and content: Tab delimited table of raw gene read counts per sample.

molecule: total RNA

organism: Homo sapiens

source_name: Foreskin fibroblast

extract_protocol:
Qiagen RNeasy Mini Kit. (Germantown, MD).
Poly-A plus RNA was enriched from ~0.1ug of total RNA and used to generate libraries using New England Biolabs NEBNext Ultra II Kit.

value: Foreskin fibroblast

tag: passage

value: Late passage

tag: Sex

value: Male

tag: age

value: Neonatal

value: No treatment


title: WT+N51AK58A-replicate2

description: Library name: JC17WNK


title: Arabidopsis, nrpb2-3 ssrp1-2 SSRP1-3×HA,HA, 12DAG, Rep1

city: Xianyang

first: Weiye

last: Qian

state: Shanxi

address: Yangling District

country: China

institute: State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University

description: Library name: 12DAG_nrpb2-3 ssrp1-2 SSRP1-3×HA_HA_G1_Rep1,ChIP

library_source: genomic

data_processing:
(1)Filter:ChIP-seq reads were trimmed using the fastp tool (version 0.23.4)  with a quality score threshold of >20 for the final base.Reads shorter than 35 bp after trimming were discarded.(2)Alignment:The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using Bowtie2 and sorted and indexed using the samtools suite (version 1.17).(3)Remove: PCR duplicates were removed using Picard (version 3.0.0). (4)Callpeak:Peaks were identified using the “callpeak” function of MACS2 (version 2.2.6,). (5)Coverage tracks were calculated: normalizing using RPGC (effective genome size 119482912) –bin size 10, normalization method using RPGC reads per genome coverage), creating bigwig files.(6)Plot:The metagene results were drawn using deepTools(version 3.5.2).
Assembly: TAIR 10
Supplementary files format and content: BigWig files were generated using the Deeptools  (version 3.5.2).The BigWig files for making plot were  assessed by merging results from 'bigwigcompare' of two independent biological replicates, employing the 'mean' operation.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 12DAG seedling

growth_protocol: All the lines used in this article are in Columbia-0 background.Plants were grown under standard long day conditions and ~21°C unless stated differently.

extract_protocol:
1)Crosslink protein-DNA interactions with formaldehyde; 2) Fragment chromatin via sonication or enzymatic digestion; 3) Immunoprecipitate target protein-DNA complexes using specific antibodies; 4) Reverse crosslinking and purify DNA, followed by library construction for sequencing .
ChIP-Seq libraries were prepared using Ovation® Ultralow System V2 Library Preparation Kit (PART NO. 0344, 0344NB).

value: 12DAG seedling

tag: chip-antibody

value: 88836(Thermo USA)

tag: genotype


title: LFU mediated rejuvenated late passage HFF cells, rep 1

value: LFU


title: Arabidopsis, nrpb2-3, 12DAG, , Rep2

description:
Library name: nrpb2-3_R2
Treatment

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

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

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


title: WT+N51A-replicate1

description: Library name: JC13WN

value: overexpressing GFP-Ubx-WT+N51A


title: WT+N51A-replicate2

description: Library name: JC14WN


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

description:
Library name: Columbia-0_R3
Control


title: Arabidopsis, ssrp1-2 SSRP1-3×HA, HA,12DAG, Rep1

description: Library name: 12DAG_ssrp1-2 SSRP1-3×HA_HA_G1_Rep1,ChIP


title: Arabidopsis, ssrp1-2,NRPB1, 12DAG, Rep1

description: Library name: 12DAG_ssrp1-2_NRPB1_Rep1,ChIP

value: E4646 (AbClonal China)


title: WT+N51A-replicate3

description: Library name: JC15WN


title: Arabidopsis, nrpb2-3, 12DAG, , Rep1

description:
Library name: nrpb2-3_R1
Treatment


title: Arabidopsis, ssrp1-2 SSRP1-3×HA, HA,12DAG, Rep2

description: Library name: 12DAG_ssrp1-2 SSRP1-3×HA_HA_G1_Rep2,ChIP


title: LFU treated early passage HFF, rep 3

value: early passage


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

description:
Library name: Columbia-0_R2
Control


title: N51A-replicate3

description: Library name: JC9N

value: overexpressing GFP-Ubx-N51A


title: Late passage Senescence  HFF cells, rep 1


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

description:
Library name: Columbia-0_R1
Control


title: N51A-replicate1

description: Library name: JC7N


title: N51A-replicate2

description: Library name: JC8N


title: WT-replicate3

description: Library name: JC6W

value: overexpressing GFP-Ubx-WT


title: WT-replicate1

description: Library name: JC4W


title: LFU treated early passage HFF, rep 1


title: WT-replicate2

description: Library name: JC5W


title: LFU treated early passage HFF, rep 2


title: GFP-replicate3

description: Library name: JC3G

value: overexpressing nlsGFP


title: GFP-replicate1

description: Library name: JC1G

value: embryonic cells


title: Untreated early passage HFF, rep 3


title: Arabidopsis, nrpb2-3,H3K4me3, 12DAG, Rep1

description: Library name: 12DAG_nrpb2-3_H3K4me3_Rep1,ChIP

value: 04-745( Millipore USA)


title: Arabidopsis, ssrp1-2,H3K4me3, 12DAG, Rep1

description: Library name: 12DAG_ssrp1-2_H3K4me3_Rep1,ChIP


title: DM-MuSC from patient sDM6, Differentiation day 3

city: Leuven

first: Wilhelm

last: Bouchereau

email: wilhelm.bouchereau@kuleuven.be, patrick.lomonte@univ-lyon1.fr, benedicte.chazaud@inserm.fr, armelle.corpet@univ-lyon1.fr

state: Vlaams brabant

address: ON4 - Herestraat 49 PB 804

department: Stamcelinstituut Leuven

country: Belgium

institute: KU-Leuven

description:
Library name: RD3_D6P4
Column name in raw_counts_All_Samples_Salmon.csv : RD3_D6P4_quant

data_processing:
Sequencing was performed on an Element AVITI™ system.
RNA-seq paired-reads were aligned and quantified using salmon (version 1.9.0) on gencode v41 for index generation.
Counts were processed and analysed on R (version 4.4.1) using Deseq2 package (version 1.44.0).
Assembly: Human genome GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: skeletal muscle

growth_protocol: MuSCs derived from healthy controls were directly extracted by mechanical and enzymatic digestion from fresh muscle biopsies. After an expansion period, they were frozen and stored in liquid nitrogen until further use. After thawing, MuSCs were purified at the first passage of primary culture using anti-CD56 coated magnetic beads (Miltenyi Biotech 130-050-401) to obtain pure myogenic cell cultures as described previously (Gitiaux et al., 2018). Cell purity was checked by flow cytometry (BD FACSCanto II) using anti-CD56 antibodies (APC-conjugated anti-CD56 antibodies, BD Pharmingen #555518) and isotypic control (BD Pharmingen #555751). MuSCs were cultured in complete medium (Skeletal Muscle Cell Growth Medium #23060 Promocell, supplemented with Mix C-39365, Promocell), 10% of heat-inactivated Fetal Bovine Serum (FBS, Sigma-Aldrich) and 1% of Penicillin/streptomycin (Gibco, 14190169). Cells were passaged upon reaching 80% confluency using 0.05% trypsin-EDTA (Gibco, 25300-054) digestion then seeded back onto new supports.

extract_protocol:
QIAGEN Rneasy mini kit was used to extract and purify RNA according to manufacturer instructions (Qiagen, 74104).
NEBNext® Ultra™ II Directional RNA Library kit (New England Biolabs) was used to prepare an RNA-seq library.

treatment_protocol: Analysis of proliferation of MuSCs was performed as follows: MuSCs were seeded at 3000 cells/cm². The next day, medium was changed with fresh medium. 24 hours later, 50% of the medium was replaced with fresh medium. Analysis of differentiation capacities of MuSCs was performed as follows: cells were seeded in labtek at 1500 cells/cm2 in growth medium. The next day, medium was changed with differentiation medium consisting of skeletal muscle cell basal medium (Promocell, C-23260) supplemented with 10 μg/mL insulin (Sigma-Aldrich, I2643), FBS 0.5% and 1% of Penicillin/streptomycin. 50% of the medium was replaced with fresh medium with cytokines every day for 3 days.

value: skeletal muscle

value: Primary skeletal muscle stem cell derived from dermatomyositis patient

value: Differentiation day 3

tag: patient

tag: patient sex

value: M

tag: patient age_(in_years)


title: Arabidopsis, Columbia,H3K4me3, 12DAG, Rep1

description: Library name: 12DAG_Columbia_H3K4me3_Rep1,ChIP


title: Untreated early passage HFF, rep 1

value: Foreskin fibroblast

value: Male

value: Neonatal


title: Untreated early passage HFF, rep 2

value: No treatment


title: DM-MuSC from patient sDM1, Differentiation day 3

description:
Library name: RD3_D1P3
Column name in raw_counts_All_Samples_Salmon.csv : RD3_D1P3_quant

value: F


title: Pseudomonas aeruginosa UCBPP-PA14 trmA mutant strain; bio rep 3

city: Lak Si

first: Jurairat

last: Chittrakanwong

address: Kamphaeng Phet 6

department: Applied Biological Sciences

country: Thailand

institute: Chulabhorn Graduate Institute

library_source: other

data_processing:
The raw sequence reads were processed using the data analytical pipeline for AQRNA-seq to generate the raw tRNA abundance matrix.
The raw tRNA abundance matrix was normalized using the median of ratios method implemented in the DESeq2 v 1.36.0 package in R Statistical Programming Environment v 4.2.1.
Assembly: GCF_000014625.1
Supplementary files format and content: Excel files include tRNA genes and raw counts for each sample.
Supplementary files format and content: Excel files include tRNA genes and normalized counts for each sample.

molecule: other

organism: Pseudomonas aeruginosa

source_name: Bacterial cells

growth_protocol: Bacteria were grown to exponential phase in LB broth at 37 °C with shaking at 180 rpm.

extract_protocol:
Total RNA was extracted from exponential phase cells using Trizol reagent (Thermo Fisher scientific). Large RNAs were depleted from the total RNA solution by precipitation using 35% ethanol. Small RNA species including tRNAs in aqueous solution was then transferred into a new tube and precipitated by adding absolute ethanol at -70 °C for 2 h. tRNAs were then purified using HPLC.
cDNA libraries were constructed following a revised version of the Absolute Quantification RNA Sequencing (AQRNA-seq) protocol.
Other; AQRNA-seq

value: Bacterial cells

value: trmA mutant


title: HC-MuSC from patient SK230, Differentiation day 3

description:
Library name: RD3_S0P2
Column name in raw_counts_All_Samples_Salmon.csv : RD3_S0P2_quant

value: Primary skeletal muscle stem cell derived from healthy control patient


title: bone marrow transplantation mouse, Tet2+/-, Oridonin 1 month

city: Guangzhou

first: Lu

last: Lu

address: No.12,Airport Road,Baiyun District

institute: Guangzhou University of Chinese Medicine

description:
Library name: sample 4
Column name in all_Samples.csv:Tet2_ori_1

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according tothe manufacturer’s instructions. After cluster generation, the library preparations weresequenced on an Illumina Novaseq platform and 150 bp paired-end reads weregenerated.
Assembly: mm10
Supplementary files format and content: csv files include FPkMvalues for each Sample.

organism: Mus musculus

source_name: heart

extract_protocol:
RNA quantification and qualification ①RNA degradation and contamination was monitored on 1% agarose gels. ② RNA purity was checked using the NanoPhotometer®spectrophotometer (IMPLEN, CA, USA) . ③RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1µg RNA per sample was used as input material for the RNAsample preparations. Sequencing libraries were generated using NEBNext® UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’srecommendations and index codes were added to attribute sequences to each sample.Briefly, mRNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. Fragmentation was carried out using divalent cations under elevatedtemperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strandcDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H ). Second strand cDNA synthesis was subsequentlyperformed using DNA Polymerase I and RNase H. Remaining overhangs wereconverted into blunt ends via exonuclease/polymerase activities. After adenylation of3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure wereligated to prepare for hybridization. In order to select cDNA fragments ofpreferentially 250~300 bp in length, the library fragments were purified with AMPureXP system (Beckman Coulter, Beverly, USA). Then 3µlUSER Enzyme (NEB, USA)was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5min at 95°Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNApolymerase, Universal PCR primers and Index (X) Primer. At last, PCR productswere purified (AMPure XP system) and library quality was assessed on the AgilentBioanalyzer 2100 system.

value: heart

value: male

value: Oridonin

tag: time

value: 2 months


title: DM-MuSC from patient sDM3, Differentiation day 3

description:
Library name: RD3_D3P5
Column name in raw_counts_All_Samples_Salmon.csv : RD3_D3P5_quant


title: DM-MuSC from patient sDM5, Differentiation day 3

description:
Library name: RD3_D5P3
Column name in raw_counts_All_Samples_Salmon.csv : RD3_D5P3_quant


title: bone marrow transplantation mouse, Tet2+/-, Oridonin 2 month

description:
Library name: sample 5
Column name in all_Samples.csv:Tet2_ori_2


title: HC-MuSC from patient CT7, Differentiation day 3

description:
Library name: RD3_H7P3
Column name in raw_counts_All_Samples_Salmon.csv : RD3_H7P4_quant


title: Pseudomonas aeruginosa UCBPP-PA14 trmA mutant strain; bio rep 2


title: bone marrow transplantation mouse, Tet2+/-, vector 2 month

description:
Library name: sample 3
Column name in all_Samples.csv:Tet2_2

value: vector


title: HC-MuSC from patient CT6, Differentiation day 3

description:
Library name: RD3_H6P4
Column name in raw_counts_All_Samples_Salmon.csv : RD3_H6P4_quant

value: skeletal muscle


title: Arabidopsis, spt16-2,H3K4me3, 12DAG, Rep1

description: Library name: 12DAG_spt16-2_H3K4me3_Rep1,ChIP

value: 12DAG seedling

value: 04-745( Millipore USA)


title: Pseudomonas aeruginosa UCBPP-PA14 trmA mutant strain; bio rep 1


title: DM-MuSC from patient sDM6, Differentiation day 1

description:
Library name: RD1_D6P4
Column name in raw_counts_All_Samples_Salmon.csv : RD1_D6P4_quant

value: Primary skeletal muscle stem cell derived from dermatomyositis patient

value: Differentiation day 1

value: M


title: DM-MuSC from patient sDM5, Differentiation day 1

description:
Library name: RD1_D5P3
Column name in raw_counts_All_Samples_Salmon.csv : RD1_D5P3_quant


title: GFP-replicate2

description: Library name: JC2G

value: embryonic cells

value: S2R+ Drosophila cells

value: overexpressing nlsGFP


title: DM-MuSC from patient sDM3, Differentiation day 1

description:
Library name: RD1_D3P5
Column name in raw_counts_All_Samples_Salmon.csv : RD1_D3P5_quant

value: F


title: bone marrow transplantation mouse,wide-type control, vector 1 month

description:
Library name: sample 1
Column name in  all_Samples.csv: WT_1

value: WT


title: Pseudomonas aeruginosa UCBPP-PA14 wild-type strain; bio rep 2

value: Bacterial cells

value: Wild type


title: HC-MuSC from patient SK236, Differentiation day 3

description:
Library name: RD3_S6P2
Column name in raw_counts_All_Samples_Salmon.csv : RD3_S6P2_quant

value: Primary skeletal muscle stem cell derived from healthy control patient

value: Differentiation day 3


title: DM-MuSC from patient sDM1, Differentiation day 1

description:
Library name: RD1_D1P3
Column name in raw_counts_All_Samples_Salmon.csv : RD1_D1P3_quant


title: D2mdx-6wk-4

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

description:
Library name: TS20
DMD diseased Mouse at 6 weeks

data_processing:
Base calling was performed using bcl2Fastq
The quality of the raw fastq reads from sequencer were evaluated using FastQC version 0.11.5 followed by adapter and quality trimming using Trimgalore. Overall quality analysis summary reports were analyzed using MultiQC v1.6.
STAR 2.5.3a was used to map the reads to the reference mouse genome
The mapped reads were counted using RSEM (version 1.3.2), with a reference genomic feature file (Gene transfer format, GTF).
Deseq2 version 1.26 (R 3.6), was used for normalization and differential expression evaluation. Principal Component Analysis (PCA) was evaluated using the plotPCA function of DESeq2. Visualization of the first 2 Principal components was performed using the ggplot2 (version 3.3.5) package.  We set a threshold for log2 fold change (Log2FC) change of greater than an absolute value of 0.6 to select for the genes with significant differential expression. Gene lists were sorted by Log2FC (highest to lowest) to obtain the ranked list of differentially expressed genes and a padj value cutoff of 0.05 was used to assess statistical significance. Heatmaps were  created using pheatmap (version 1.0.12), and volcano plots using EnhancedVolcano
Assembly: GRCm38-mm10
Supplementary files format and content: AllSamples.TPM.csv

source_name: Heart

growth_protocol: Mice were euthanized via CO2 inhalation and cervical dislocation at designated ages corresponding to specific stages of disease progression. Muscles were surgically removed, mounted on cork with tragacanth gum, flash-frozen in liquid nitrogen-chilled isopentane and stored at –80°C. For all assays, samples were collected from matched regions of the same muscles by collecting cryosections (Leica CM1950 cryostat) for RNA analyses.

extract_protocol:
Total RNA was extracted using TRIzol RNA isolation (Life Technologies) from frozen muscle samples. RNA was purified using RNeasy mini elute columns (Qiagen) and DNAse treated using Turbo DNA-free kit (Invitrogen). Purified, DNAse-treated RNA was quantified by NanoDrop and quality was assessed using Qbit RNA Assays (Thermofisher) and BioAnalyzer nano chips (Agilent) (RIN>7.8, Average 8.30.32).
RNAseq library preparation and sequencing was performed using the TruSeq mRNA stranded kit (Illumina) and the Illumina HiSeq4000 Flow Cell with an average coverage of 63.05 million read pairs per sample at 2x75 base pair read length.

value: Heart

value: DMD

value: 6 weeks


title: HC-MuSC from patient SK230, Differentiation day 1

description:
Library name: RD1_S0P2
Column name in raw_counts_All_Samples_Salmon.csv : RD1_S0P2_quant

value: skeletal muscle


title: HC-MuSC from patient SK236, Differentiation day 1

description:
Library name: RD1_S6P2
Column name in raw_counts_All_Samples_Salmon.csv : RD1_S6P2_quant


title: D2mdx-6wk-3

description:
Library name: TS8
DMD diseased Mouse at 6 weeks


title: Pseudomonas aeruginosa UCBPP-PA14 wild-type strain; bio rep 1


title: PA14 trmA mutant rep3

data_processing:
Sequence reads were mapped to Pseudomonas aeruginosa PA14 strain whole genome using STAR. HTSeq count script was performed to obtain read counts. Differential expression was calculated using DeSeq2 package.
Assembly: GCF_000014625.1
Supplementary files format and content: tab-delimited text files include locus tag and raw counts for each sample.
Supplementary files format and content: tab-delimited tab file include locus tag and RPKM value for each sample.

growth_protocol: PA14 wild-type and trmA mutant strains were grown in LB broth at 37 °C and 180rpm. Exponential phase cells were pelleted using centrifugation to extract total RNA.

extract_protocol:
The cell pellets were lysed in Trizol reagent. Total RNA was isolated using Purelink RNA mini kit (Ambion). The extracted total RNA was treated with DNaseI followed by analysis using Agilent 2100 Bioanalyzer (Agilent Technologies).
Depletion of rRNA was performed using NEBNext rRNA depletion kit. The library was prepared using NEBNext Ultra II Directional RNA library preb kit.

value: trmA mutant


title: HC-MuSC from patient CT7, Differentiation day 1

description:
Library name: RD1_H7P3
Column name in raw_counts_All_Samples_Salmon.csv : RD1_H7P4_quant


title: DM-MuSC from patient sDM5, Proliferation

description:
Library name: RP_D5P3
Column name in raw_counts_All_Samples_Salmon.csv : RP_D5P3_quant

value: Primary skeletal muscle stem cell derived from dermatomyositis patient

value: Proliferation


title: DM-MuSC from patient sDM6, Proliferation

description:
Library name: RP_D6P4
Column name in raw_counts_All_Samples_Salmon.csv : RP_D6P4_quant

value: M


title: PA14 trmA mutant rep2


title: D2mdx-6wk-1

description:
Library name: TS1
DMD diseased Mouse at 6 weeks


title: HC-MuSC from patient CT6, Differentiation day 1

description:
Library name: RD1_H6P4
Column name in raw_counts_All_Samples_Salmon.csv : RD1_H6P4_quant

value: Differentiation day 1


title: DM-MuSC from patient sDM3, Proliferation

description:
Library name: RP_D3P5
Column name in raw_counts_All_Samples_Salmon.csv : RP_D3P5_quant


title: DM-MuSC from patient sDM1, Proliferation

description:
Library name: RP_D1P3
Column name in raw_counts_All_Samples_Salmon.csv : RP_D1P3_quant


title: D2mdx-6wk-2

description:
Library name: TS3
DMD diseased Mouse at 6 weeks


title: HC-MuSC from patient SK236, Proliferation

description:
Library name: RP_S6P2
Column name in raw_counts_All_Samples_Salmon.csv : RP_S6P2_quant


title: HC-MuSC from patient SK230, Proliferation

description:
Library name: RP_S0P2
Column name in raw_counts_All_Samples_Salmon.csv : RP_S0P2_quant


title: B10mdx-6wk-3

description:
Library name: TS12
Wild type 6 weeks


title: bone marrow transplantation mouse, Tet2+/-, vector 1 month

description:
Library name: sample 2
Column name in all_Samples.csv:Tet2_1

value: heart

value: male

value: vector

value: 2 months


title: Pseudomonas aeruginosa UCBPP-PA14 wild-type strain; bio rep 3

value: Bacterial cells


title: bone marrow-derived macrophages cells Tet2 deficient control, treatment Day 2,ChIP

description: Library name: mouse Tet2 deficient,oridonin treatment, ChIP

data_processing:
Sequencing quality was assessed using Fastp (v0.23.1), and key metrics including read number, total bases, GC content, Q20/Q30 base percentages.
Assembly: mm39
Supplementary files format and content: bigWig

source_name: bone marrow-derived macrophages

extract_protocol:
Chromatin immunoprecipitation sequencing was performed on primary mouse bone marrow–derived macrophages to assess histone modifications using antibodies against H3K4me3 (Cell Signaling Technology, #5326 and #9751). Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature and quenched with 0.125 M glycine. Chromatin was extracted and sheared by sonication to 200–500 bp fragments.
After elution and reversal of crosslinks, DNA was purified and used for library construction with the NEBNext Ultra II DNA Library Prep Kit (NEB). Libraries were quality-checked using an Agilent 2100 Bioanalyzer and sequenced on an Illumina NovaSeq 6000 platform (paired-end, 150 bp). Raw reads were saved in FASTQ format.

value: bone marrow-derived macrophages

value: Oridonin

value: Day 2


title: B10mdx-6wk-2

description:
Library name: TS11
Wild type 6 weeks

value: Heart

value: WT


title: HC-MuSC from patient CT7, Proliferation

description:
Library name: RP_H7P3
Column name in raw_counts_All_Samples_Salmon.csv : RP_H7P4_quant

value: Primary skeletal muscle stem cell derived from healthy control patient

value: F


title: PA14 wild type rep2

value: Wild type


title: PA14 wild type rep1


title: HC-MuSC from patient CT6, Proliferation

description:
Library name: RP_H6P4
Column name in raw_counts_All_Samples_Salmon.csv : RP_H6P4_quant

value: skeletal muscle


title: B10mdx-6wk-1

description:
Library name: TS10
Wild type 6 weeks

value: 6 weeks


title: Endothelial cells from mice cortex in ASD24h group, replicate 1 [ASD24h_1]

status: Public on Jun 07 2025

city: Beijing

last: Changqing

address: No.10 Xitoutiao Road, Youanmenwai Avenue, Fengtai District

institute: Capital Medical University

description:
Library name: Sample 10
ASD24h_1

data_processing:
Quality control was performed using fastp (v0.19.7).
Reads were aligned to the mm10 reference genome using HISAT2 (v 2.0.5).
Read counting was conducted using the featureCounts tool from the Subread package.
Differential analysis was performed using DESeq2 (v 1.20.0) .
TPM involves calculating Reads Per Kilobase (RPK) for each gene, followed by normalization using the total sum of RPKs across all genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include readcount values for each Sample ...

source_name: cerebral cortex

growth_protocol: All the mice were of specific pathogen-free (SPF) grade and were housed in a laminar flow animal facility with a constant temperature of 24 °C, a humidity level of 30%-70%, and a 12-hour day-night cycle.

extract_protocol:
Upon completion of sleep deprivation, mouse cerebral cortex was rapidly dissected on ice. Tissue dissociation was performed using Type Ⅱ collagenase, followed by endothelial cell isolation via CD31+ magnetic bead sorting. mRNA was enriched using oligo(dT) magnetic beads for subsequent RNA sequencing.
Total RNA serves as starting material. mRNA with polyA tails is enriched via Oligo(dT) magnetic beads. Enriched mRNA is fragmented in Fragmentation Buffer with divalent cations, then used as template for first-strand cDNA synthesis by M-MuLV reverse transcriptase with random primers. RNaseH degrades RNA strands, and DNA polymerase I synthesizes second-strand cDNA. Double-stranded cDNA is purified, end-repaired, A-tailed, and ligated with adapters. AMPure XP beads select 370–420bp fragments, which are PCR-amplified and purified to obtain high-quality libraries. For QC, Qubit 2.0 quantifies libraries (diluted to 1.5 ng/μl), Agilent 2100 checks insert sizes, and qRT-PCR ensures effective concentrations >2nM, meeting sequencing requirements.

treatment_protocol: Male C57BL/6J mice were acclimated for 3 days under a 12-hour light/dark cycle (lights on at 07:00) before undergoing acute sleep deprivation for 6, 12, or 24 hours on day 4. The control group underwent no interventions and was maintained under normal housing conditions.

value: cerebral cortex

value: Male

value: Endothelial cells

tag: strain

value: ASD

tag: time point


title: Endothelial cells from mice cortex in ASD24h group, replicate 3 [ASD24h_3]

description:
Library name: Sample 12
ASD24h_3


title: Endothelial cells from mice cortex in ASD12h group, replicate 3 [ASD12h_3]

description:
Library name: Sample 9
ASD12h_3


title: Endothelial cells from mice cortex in ASD6h group, replicate 2 [ASD6h_2]

description:
Library name: Sample 5
ASD6h_2


title: Endothelial cells from mice cortex in ASD24h group, replicate 2 [ASD24h_2]

description:
Library name: Sample 11
ASD24h_2


title: Endothelial cells from mice cortex in ASD12h group, replicate 1 [ASD12h_1]

description:
Library name: Sample 7
ASD12h_1


title: Endothelial cells from mice cortex in control group, replicate 2 [Control_2]

description:
Library name: Sample 2
Control_2

value: Control


title: Endothelial cells from mice cortex in ASD6h group, replicate 3 [ASD6h_3]

description:
Library name: Sample 6
ASD6h_3


title: Endothelial cells from mice cortex in control group, replicate 1 [Control_1]

description:
Library name: Sample 1
Control_1


title: Endothelial cells from mice cortex in ASD6h group, replicate 1 [ASD6h_1]

description:
Library name: Sample 4
ASD6h_1


title: PA14 trmA mutant rep1

value: trmA mutant


title: KaedeRed, 72h post-photoconversion, rep 3

city: Cambridge

first: Colin

middle: YC

last: Lee

address: Wellcome Genome Campus, Hinxton

country: United Kingdom

institute: Molecular Immunity Unit

description:
Library name: MR72-3
Kaede-red CD11b+ cells (macrophages) 72h post-photoconversion replicate 3

data_processing:
Fastq files from sequencing libraries were trimmed of the first 3 nucleotides of the R1 strand. Contaminating adaptor sequences and poor-quality bases were removed using Trim Galore (Babraham bioinformatics). Libraries were only trimmed for quality.
Quality of resulting files were assessed by FastQC and aligned to the mm10 genome using HISAT2, followed by gene-level quantification using the Featurecount function from the Rsubread package in R.
Assembly: mm10
Supplementary files format and content: Raw counts matrix (txt) - individual libraries
Supplementary files format and content: Raw counts matrix (txt) - combined

source_name: Tumour

extract_protocol:
RNA extraction was performed using RNeasy plus mico kit (Qiagen) according to the manufacturer’s instructions. Genomic DNA contamination was removed using Optimal DNA depletion columns (Qiagen).
Libraries were prepared using the SMARTer stranded total RNAseq mammalian pico input kit (Takara) according to the manufacturer’s instructions. 5 ng of total RNA was used for production of libraries. Library strategy: Total RNA-seq, 2 x 150bp paired-end sequencing performed on Novaseq6000 (Illumina)

value: Tumour

value: Sorted Live CD45Positive TER119Negative KaedePositive CD11bPositive NK1.1Negative cells

value: Control (NA)

tag: batch


title: KaedeRed, 72h post-photoconversion, rep 4

description:
Library name: MR72-4
Kaede-red CD11b+ cells (macrophages) 72h post-photoconversion replicate 4


title: KaedeRed, 72h post-photoconversion, rep 2

description:
Library name: MR72-2
Kaede-red CD11b+ cells (macrophages) 72h post-photoconversion replicate 2


title: KaedeRed, 72h post-photoconversion, rep 1

description:
Library name: MR72-1
Kaede-red CD11b+ cells (macrophages) 72h post-photoconversion replicate 1


title: KaedeGreen, 72h post-photoconversion, rep 3

description:
Library name: MG72-3
Kaede-green CD11b+ cells (macrophages) 72h post-photoconversion replicate 3


title: Endothelial cells from mice cortex in control group, replicate 3 [Control_3]

description:
Library name: Sample 3
Control_3


title: KaedeGreen, 72h post-photoconversion, rep 4

description:
Library name: MG72-4
Kaede-green CD11b+ cells (macrophages) 72h post-photoconversion replicate 4


title: KaedeGreen, 72h post-photoconversion, rep 2

description:
Library name: MG72-2
Kaede-green CD11b+ cells (macrophages) 72h post-photoconversion replicate 2


title: PA14 wild type rep3

value: Bacterial cells


title: KaedeGreen, 72h post-photoconversion, rep 1

description:
Library name: MG72-1
Kaede-green CD11b+ cells (macrophages) 72h post-photoconversion replicate 1


title: KaedeRed, 24h post-photoconversion, rep 3

description:
Library name: MR24-3
Kaede-red CD11b+ cells (macrophages) 24h post-photoconversion replicate 3


title: KaedeRed, 24h post-photoconversion, rep 4

description:
Library name: MR24-4
Kaede-red CD11b+ cells (macrophages) 24h post-photoconversion replicate 4


title: KaedeRed, 24h post-photoconversion, rep 2

description:
Library name: MR24-2
Kaede-red CD11b+ cells (macrophages) 24h post-photoconversion replicate 2


title: bone marrow-derived macrophages cells Tet2 deficient control, treatment Day 0,ChIP

description: Library name: mouse Tet2 deficient,ChIP

value: bone marrow-derived macrophages

value: Vector

value: Day 2


title: KaedeRed, 24h post-photoconversion, rep 1

description:
Library name: MR24-1
Kaede-red CD11b+ cells (macrophages) 24h post-photoconversion replicate 1


title: Endothelial cells from mice cortex in ASD12h group, replicate 2 [ASD12h_2]

description:
Library name: Sample 8
ASD12h_2


title: KaedeGreen, 24h post-photoconversion, rep 2

description:
Library name: MG24-2
Kaede-green CD11b+ cells (macrophages) 24h post-photoconversion replicate 2


title: KaedeGreen, 24h post-photoconversion, rep 3

description:
Library name: MG24-3
Kaede-green CD11b+ cells (macrophages) 24h post-photoconversion replicate 3


title: KaedeGreen, 24h post-photoconversion, rep 4

description:
Library name: MG24-4
Kaede-green CD11b+ cells (macrophages) 24h post-photoconversion replicate 4


title: tumor, radiotherapy

city: La Jolla

first: Joseph

last: Califano

address: 3855 Health Sciences Dr.

institute: Moores Cancer Center, UC San Diego

description: TCRB TCR-seq

data_processing:
All data analysis provided by Adaptive Biotechnologies, after proprietary sequence processing steps, in their sequence viewer interface, immunoSEQ Analyzer, were exported as a summary .tsv file for each sample. TCRbeta gene segment locus calls were made using the Adaptive pipeline as part of their automated data processing pipeline.
Assembly: mm10
Supplementary files format and content: tsv file for each sample;  contains amino acid sequence, percent frequency count, cdr3 length and more
Library strategy: TCR-seq

source_name: tumor

extract_protocol:
Cells were sorted into low retention 1.5ml collection tubes, containing 500 μl of a1:1 solution of PBS:FBS supplemented with RNAse inhibitor (1:100). Following sorting, ice-cold PBS was added to make up to a volume of 1400 μl. Cells were then centrifuged for 5 minutes (600 g at 4 °C) and the supernatant was carefully removed leaving 5 to 10 μl. 25 μl of resuspension buffer (0.22 μm filtered ice-cold PBS supplemented with ultra-pure bovine serum albumin (0.04%) was added to the tube and the pellet was gently but thoroughly resuspended. Following careful mixing, 33 μl of the cell suspension was transferred to a PCR-tube for processing as per the manufacturer’s instructions
library preparation was performed as per the manufacturer’s recommendations for the 10x Genomics 5’TAG v1.0 chemistry with immune profiling technology.

value: tumor

tag: cell line

value: oral squamous cell carcinoma

value: female

value: radiotherapy


title: tumor, control

description: TCRB TCR-seq

value: control


title: tumor, sham surgery

description: TCRB TCR-seq

value: sham surgery


title: sentinel lymph node, sham surgery

description: TCRB TCR-seq

source_name: sentinel lymph node

value: sentinel lymph node


title: tumor, PD1 therapy

description: TCRB TCR-seq

value: PD1 therapy


title: KaedeGreen, 24h post-photoconversion, rep 1

description:
Library name: MG24-1
Kaede-green CD11b+ cells (macrophages) 24h post-photoconversion replicate 1


title: ATAC_CK2

city: Wuhan

first: Qiutao

last: Xu

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

description: Library name: ATAC_CK2

data_processing:
For ATAC-seq data analysis, adapter sequences were trimmed from raw reads using fastp (v0.24.0). Cleaned reads were aligned to the rice reference genome (MSU7.0) using Bowtie2. Reads mapping to mitochondrial and chloroplast genomes were filtered to exclude organellar DNA contamination. Peak calling was performed with MACS2 (v2.2.9.1) using the following parameters: --nomodel --keep-dup all --shift -75 --extsize 150.
Assembly: Rice Genome Annotation Release 7
Supplementary files format and content: bigWig, narrowPeak

organism: Oryza sativa Japonica Group

source_name: Panicle

extract_protocol:
For ATAC-seq, three grams of 14-day-old seedlings were harvested, and nuclear proteins were extracted using a nuclear protein extraction kit (NH101-01).
For ATAC-seq, libraries were prepared with the TruePrep DNA Library Prep Kit V2 for Illumina.

value: Panicle


title: ATAC_Treat2

description: Library name: ATAC_Treat2


title: tumor, lymphatic channel ablation

description: TCRB TCR-seq

value: lymphatic channel ablation


title: Cerebrum tissue, 7 months old, mKO in 5xFAD background

city: SAN ANTONIO

first: Sijia

last: He

address: 7703 Floyd Curl Dr.

institute: uthealth sa

description: Library name: mKO_5xFAD

library_source: transcriptomic single cell

data_processing:
Analysis of sequencing data was performed using PIPseeker software (v3.0.5) to generate gene expression matrices starting from processed FASTQ sequences, which include barcode identification, reference mapping, cell calling, and gene expression matrix generation.
The gene expression matrices were then imported into R for downstream analysis using the Seurat package (v4.1.4)
Assembly: GRCm39
Supplementary files format and content: barcodes
Supplementary files format and content: freatures
Supplementary files format and content: Matrix

source_name: Cerebrum

growth_protocol: Mice were housed in groups of ≤5 mice/cage in a temperature and humidity-controlled environment under a 12-h light /12-h dark cycle.

extract_protocol:
Tissues were harvested at about 7 month of age post cardiac perfusion, snap-frozen, and single nuclei from cerebrum tissues were isolated using a gradient centrifugation-based method.
Nuclei were pooled from 3 mice per genotype for each snRNAseq sample, and the PIPseq T20 3′ Single Cell RNA Kit v4.0 was used for cDNA library construction based on a particle-templated emulsification method. Libraries were pooled and sequenced using an Illumina NovaSeq 6000 instrument with 1% PhiX using an S4 flow cell (150 pair-end module).

treatment_protocol: Tamoxifen was administered to induce cGAS deletion at 2 month of age.

value: Cerebrum

value: cGAS microglial KO


title: Cerebrum tissue, 7 months old, loxp in 5xFAD background

description: Library name: Loxp_5xFAD

value: Control


title: WT_rep2

description: Library name: WT_rep2

data_processing:
For ChIP-seq, raw data were first cleaned using FastP (v0.232) to remove low-quality reads and adapters. Cleaned reads were then mapped to the rice genome using Bowtie2 (version 2.3.5.1) with default settings. Samtools (v1.9) was used to remove duplicated reads, and histone modification peaks were called using MACS software (version 2.2.7.1) with default parameters (-f BAMPE -B -q 0.05). Wig files generated by deepTools (v2.5.3) (BPM normalization) were visualized in IGV (version 2.3.88). Differential histone modification peaks were analyzed using DiffBind (v3.5) with default parameters. Peaks annotation was performed using annotatePeaks.pl of Homer (v4.11).
Assembly: Rice Genome Annotation Release 7
Supplementary files format and content: bigWig, narrowPeak

source_name: Leaf

extract_protocol:
For ChIP-seq, chromatin was isolated using Buffer S, consisting of 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 1% SDS.
ChIP-seq libraries were prepared using the Illumina TruSeq ChIP Sample Prep Set A kit.

value: Leaf


title: tumor, immunoradiotherapy

description: TCRB TCR-seq

value: immunoradiotherapy


title: sentinel lymph node, radiotherapy

description: TCRB TCR-seq


title: WT_rep1

description: Library name: WT_rep1


title: sentinel lymph node, PD1 therapy

description: TCRB TCR-seq


title: ATAC_CK1

description: Library name: ATAC_CK1


title: HBMVEC, PFF α-Syn, 6, 72h

city: Daegu

first: Mookyung

last: Cheon

address: 61, Cheomdan-ro, Dong-gu

department: Dementia Research Group

country: South Korea

institute: Korea Brain Research Institute

description:
Library name: Sample HBMVEC_Agg72_6
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg72_6

data_processing:
Raw reads were quality-checked and adapter-trimmed using Trimmomatic v0.38.
Reads were aligned to the human reference genome (GRCh38, Ensembl release 102) using HISAT2 v2.1.0.
BAM files were coordinate-sorted with samtools v1.7.
Gene counts were generated using HTSeq-count v0.12.4.
Assembly: Human genome GRCh38 (Ensembl release 102).
Supplementary files format and content: tab-delimited text includes raw counts for eash Sample.

source_name: brain microvasculature

growth_protocol: Primary human brain microvascular endothelial cells (HBMVECs) were cultured in complete classic media with 2% culture boost and 1% penicillin-streptomycin on attachment factor-coated plates at 37°C and 5% CO₂ for 2–3 days.

extract_protocol:
After treatment, cells were washed with PBS and total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and integrity were assessed using Quant-IT RiboGreen and TapeStation RNA ScreenTape. Only samples with RIN > 7.0 were used.
0.5 μg of total RNA per sample was used to construct libraries with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina). rRNA was removed using the Ribo-Zero kit, mRNA was fragmented, and cDNA was synthesized with SuperScript II and random primers. Libraries were PCR-enriched, quantified, and quality-checked before sequencing.

treatment_protocol: HBMVECs were treated with PBS (control), monomeric α-synuclein, or pre-formed fibrils (PFF) of α-synuclein for 24 or 72 hours.

value: brain microvasculature

value: primary HBMVEC

value: brain microvascular endothelial cells

value: WT

value: PFF α-Synuclein (0.5 μg)


title: ATAC_Treat1

description: Library name: ATAC_Treat1


title: ChIP_Kbhb_Treat_rep2

description: Library name: ChIP_Kbhb_Treat_rep2


title: srt2_rep2

description: Library name: srt2_rep2


title: sentinel lymph node, lymphatic channel ablation

description: TCRB TCR-seq

value: oral squamous cell carcinoma

value: female


title: ChIP_Kbhb_CK_rep2

description: Library name: ChIP_Kbhb_CK_rep2


title: ChIP_Kbhb_Treat_rep1

description: Library name: ChIP_Kbhb_Treat_rep1


title: sentinel lymph node, immunoradiotherapy

description: TCRB TCR-seq


title: HBMVEC, PFF α-Syn, 5, 72h

description:
Library name: Sample HBMVEC_Agg72_5
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg72_5


title: ChIP_Kbhb_CK_rep1

description: Library name: ChIP_Kbhb_CK_rep1


title: HBMVEC, PFF α-Syn, 3, 72h

description:
Library name: Sample HBMVEC_Agg72_3
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg72_3


title: srt2_rep1

description: Library name: srt2_rep1


title: Kbhb_treat_input

description: Library name: Kbhb_treat_input


title: Input2

description: Library name: Input2


title: WT_H3K9ac_rep1

description: Library name: WT_H3K9ac_rep1


title: HBMVEC, PFF α-Syn, 1, 72h

description:
Library name: Sample HBMVEC_Agg72_1
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg72_1


title: non sentinel lymph node, sham surgery

description: TCRB TCR-seq

source_name: non sentinel lymph node

value: non sentinel lymph node

value: sham surgery


title: hda705_H3K9ac_rep2

description: Library name: hda705_H3K9ac_rep2


title: non sentinel lymph node, PD1 therapy

description: TCRB TCR-seq

value: PD1 therapy


title: HBMVEC, PFF α-Syn, 2, 72h

description:
Library name: Sample HBMVEC_Agg72_2
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg72_2


title: HBMVEC, PFF α-Syn, 6, 24h

description:
Library name: Sample HBMVEC_Agg24_6
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg24_6


title: H3K9hb_ZH11_rep2

description: Library name: H3K9hb_ZH11_rep2


title: WT_H3K9ac_rep2

description: Library name: WT_H3K9ac_rep2

value: Panicle


title: H3K9hb_ZH11_rep1

description: Library name: H3K9hb_ZH11_rep1


title: hda705_rep2_K9bhb

description: Library name: hda705_rep2_K9bhb


title: HBMVEC, PFF α-Syn, 4, 72h

description:
Library name: Sample HBMVEC_Agg72_4
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg72_4


title: HBMVEC, PFF α-Syn, 5, 24h

description:
Library name: Sample HBMVEC_Agg24_5
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg24_5


title: non sentinel lymph node, lymphatic channel ablation

description: TCRB TCR-seq

value: lymphatic channel ablation


title: sentinel lymph node, control

description: TCRB TCR-seq

value: sentinel lymph node

value: control


title: non sentinel lymph node, radiotherapy

description: TCRB TCR-seq

value: radiotherapy


title: Infection_Input

description: Library name: Infection_Input


title: non sentinel lymph node, immunoradiotherapy

description: TCRB TCR-seq


title: hda705_H3K9ac_rep1

description: Library name: hda705_H3K9ac_rep1

value: Leaf


title: HBMVEC, PFF α-Syn, 4, 24h

description:
Library name: Sample HBMVEC_Agg24_4
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg24_4


title: hda705_rep1_K9bhb

description: Library name: hda705_rep1_K9bhb


title: ChIP_IF_rep2

description: Library name: ChIP_IF_rep2


title: HBMVEC, PFF α-Syn, 3, 24h

description:
Library name: Sample HBMVEC_Agg24_3
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg24_3


title: ChIP_IF_rep1

description: Library name: ChIP_IF_rep1


title: HBMVEC, PFF α-Syn, 2, 24h

description:
Library name: Sample HBMVEC_Agg24_2
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg24_2


title: ChIP_CK_rep2

description: Library name: ChIP_CK_rep2


title: ChIP_CK_rep1

description: Library name: ChIP_CK_rep1


title: H3K9ac_WT_rep2

description: Library name: H3K9ac_WT_rep2


title: HBMVEC, PFF α-Syn, 1, 24h

description:
Library name: Sample HBMVEC_Agg24_1
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Agg24_1


title: sln, irt, rep4, CSP

description:
10x Genomics
8b_TamSLN_IRT_SLN
8b_feature_ref.csv

data_processing:
Quality control, alignment, and quantification of reads were performed using Cell Ranger v.(7.0.1) software from 10X Genomics. Mouse sequences were aligned to the mouse reference genome prepared by 10X Genomics (mm10-2020-A GENCODE vM23/Ensembl 98). Downstream analysis was performed with Seurat v4 (PMID: 34062119). Quality filtering was performed on the cells, with cells being retained if they contained more than 600 features, fewer than 4000 features, and less than 10% mitochondrial reads. Reads were normalized usin SCTransform (v2) (PMID: 31870423). Samples were integrated using the FindIntegrationAnchors procedure implemented in Seurat V4. Cells were clustered using the Louvain modularity optimization algorithm. Cell types were assigned based on automated cell type annotation tools (SingleR (PMID: 30643263) and CellTypist (PMID: 38134877)), along with being informed by prior biological knowledge of expected cell types and marker genes. Cell type marker genes were computed using the FindAllMarkers function in Seurat. Subtyping of cell types was performed using Seurat’s FindSubCluster function.
Assembly: mm10
Supplementary files format and content: RDS file; S4 Seuart object with cell level data containing RNA/AC/SCT/integrated assays, metadata and pca/umap reductions
Library strategy: CITE-seq

extract_protocol:
Tissues were harvested and samples were transferred into microcentrifuge tubes containing 1 mL TRIzol. RNA was then isolated using Qiagen RNeasy Mini Columns (74004; Qiagen, Germantown, MD) according to the manufacturer’s recommendations and including an on-column DNase I digestion. Yield and integrity of RNA was confirmed by reading absorbance at 260, 280, and 230 nm using a NanoDrop ND-1000 (NanoDrop Technologies; ThermoFisher Scientific, Inc., Wilmington, DE, USA) and with the Agilent 2200 Tapestation (Agilent Technologies, Inc.).
Library preparation and paired-end 150 bp (PE150, Illumina) RNA sequencing was performed by Novogene (Novogene Corporation, Sacramento, USA).

value: 4-6 weeks old

value: immunoradiotherapy

tag: library type

value: CSP


title: H3K9ac_WT_rep1

description: Library name: H3K9ac_WT_rep1

tag: tissue


title: RNA_IF_rep2

description: Library name: RNA_IF_rep2

data_processing:
For, RNA-seq,  FastP (v0.232) was employed to remove low-quality reads and adapters. Subsequently, the cleaned reads were mapped to the rice genome (MSU 7.0) using FeatureCounts (version 2.0.3). DESeq2 (v1.36.0) was utilized to calculate genes with differential expression.
Assembly: Rice Genome Annotation Release 7
Supplementary files format and content: read_count_matrix.txt

extract_protocol:
For RNA-seq, total RNA was extracted using TRIzol reagent.
RNA libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit.


title: RNA_IF_rep3

description: Library name: RNA_IF_rep3


title: sln, irt, rep1, CSP

description:
10x Genomics
8a_TamSLN_IRT_SLN
8a_feature_ref.csv

tag: cell type


title: HBMVEC, monomeric α-Syn, 5, 72h

description:
Library name: Sample HBMVEC_Mono72_5
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono72_5

value: brain microvasculature

value: primary HBMVEC

value: brain microvascular endothelial cells

tag: treatment

value: monomeric α-Synuclein (0.5 μg)


title: RNA_CK_rep3

description: Library name: RNA_CK_rep3


title: tumor, irt, rep2, CSP

description:
10x Genomics
6b_TumorTam_IRT_SLN
6b_feature_ref.csv

value: tumor

value: oral squamous cell carcinoma

value: female


title: RNA_IF_rep1

description: Library name: RNA_IF_rep1


title: RNA_Hbkb_treat_rep3

description: Library name: RNA_Hbkb_treat_rep3


title: sln, ctrl, rep1, CSP

description:
10x Genomics
7a_TamSLN_Ctrl_SLN
7a_feature_ref.csv


title: RNA_CK_rep1

description: Library name: RNA_CK_rep1


title: RNA_Hbkb_treat_rep2

description: Library name: RNA_Hbkb_treat_rep2


title: RNA_Hbkb_treat_rep1

description: Library name: RNA_Hbkb_treat_rep1


title: HBMVEC, monomeric α-Syn, 2, 72h

description:
Library name: Sample HBMVEC_Mono72_2
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono72_2

value: WT


title: HBMVEC, monomeric α-Syn, 3, 72h

description:
Library name: Sample HBMVEC_Mono72_3
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono72_3


title: HBMVEC, monomeric α-Syn, 4, 72h

description:
Library name: Sample HBMVEC_Mono72_4
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono72_4


title: non sentinel lymph node, control

description: TCRB TCR-seq

value: non sentinel lymph node


title: tumor, irt, rep1, CSP

description:
10x Genomics
6a_TumorTam_IRT_SLN
6a_feature_ref.csv


title: RNA_Hbkb_CK_rep3

description: Library name: RNA_Hbkb_CK_rep3

value: Panicle


title: tumor, ctrl, rep2, CSP

description:
10x Genomics
5b_TumorTam_Ctrl_SLN
5b_feature_ref.csv


title: tumor, ctrl, rep1, CSP

description:
10x Genomics
5a_TumorTam_Ctrl_SLN
5a_feature_ref.csv


title: RNA_Hbkb_CK_rep1

description: Library name: RNA_Hbkb_CK_rep1


title: HBMVEC, monomeric α-Syn, 1, 72h

description:
Library name: Sample HBMVEC_Mono72_1
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono72_1


title: HBMVEC, monomeric α-Syn, 6, 72h

description:
Library name: Sample HBMVEC_Mono72_6
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono72_6


title: sln, ctrl, rep2, CSP

description:
10x Genomics
7b_TamSLN_Ctrl_SLN
7b_feature_ref.csv

value: sentinel lymph node


title: sln, irt, rep4, GEX

value: mRNA


title: HBMVEC, monomeric α-Syn, 5, 24h

description:
Library name: Sample HBMVEC_Mono24_5
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono24_5


title: RNA_CK_rep2

description: Library name: RNA_CK_rep2


title: HBMVEC, monomeric α-Syn, 6, 24h

description:
Library name: Sample HBMVEC_Mono24_6
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono24_6


title: sln, irt, rep1, GEX


title: sln, ctrl, rep2, GEX


title: HBMVEC, monomeric α-Syn, 2, 24h

description:
Library name: Sample HBMVEC_Mono24_2
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono24_2


title: tumor, irt, rep2, GEX

value: control


title: 21NL

type: RNA

city: Nanjing

first: Dongqing

last: Li

address: No.12, Jiangwangmiao Street, Xuanwu District, Nanjing, China

institute: Hospital for Skin Diseases, Institute of  Dermatology, Chinese Academy of Medical Sciences &  Peking Union Medical College

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing:
Affymetrix GeneChip Command Console (AGCC) processes raw data by first collecting intensity values from CEL files.
It then performs background correction and normalization to adjust for systematic biases.
Finally, the software summarizes probe-level data to generate gene expression values for downstream analysis.

label: biotin

source_name: perilesional skin

label_protocol: Affymetrix protocol

extract_protocol: Psoriatic lesion adipose samples, along with adjacent and healthy skin samples, were processed to extract RNA.

value: perilesional skin


title: HBMVEC, monomeric α-Syn, 3, 24h

description:
Library name: Sample HBMVEC_Mono24_3
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono24_3


title: 21L

source_name: lesion

value: lesion


title: RNA_Hbkb_CK_rep2

description: Library name: RNA_Hbkb_CK_rep2


title: 20NL


title: 19NL


title: sln, ctrl, rep1, GEX

value: 4-6 weeks old

value: immunoradiotherapy


title: 20L


title: HBMVEC, Control, 6, 72h

description:
Library name: Sample HBMVEC_Con72_6
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con72_6

value: brain microvasculature

value: PBS


title: tumor, irt, rep1, GEX


title: 19L


title: HBMVEC, monomeric α-Syn, 1, 24h

description:
Library name: Sample HBMVEC_Mono24_1
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono24_1

value: primary HBMVEC

value: brain microvascular endothelial cells


title: tumor, ctrl, rep2, GEX

value: tumor


title: HBMVEC, monomeric α-Syn, 4, 24h

description:
Library name: Sample HBMVEC_Mono24_4
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Mono24_4

value: monomeric α-Synuclein (0.5 μg)


title: HBMVEC, Control, 5, 72h

description:
Library name: Sample HBMVEC_Con72_5
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con72_5


title: tumor, ctrl, rep1, GEX

value: oral squamous cell carcinoma

value: female


title: LZ_eYFP.4 [TOB816A63]

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

institute: The Francis Crick Institute

data_processing:
Aligned to Mouse Ensembl transcriptome version GRCm38.86 using STAR version 2.5.2 and RSEM 1.3.0
Raw counts normalised using DESEQ2 version 1.18.1 using R version 3.4.3
Assembly: Ensembl GRCm38
Supplementary files format and content: VST log2 normalised expression values. Rows = genes; Columns = samples.
Supplementary files format and content: raw counts. Rows = genes; Columns = samples.

source_name: Spleen

extract_protocol:
Cells were sorted in RTL Buffer Plus (Qiagen) containing 1% ß-mercaptoethanol (Sigma) and RNA purified using AllPrep DNA/RNA Mini and Micro Kits (Qiagen) following manufacturer’s instructions.
RNA-sequencing was performed at the The Francis Crick Institute advanced sequencing facility.

value: Spleen

value: B cells

value: Control

value: SRBCs immunisation


title: 17L


title: HBMVEC, Control, 4, 72h

description:
Library name: Sample HBMVEC_Con72_4
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con72_4

value: WT


title: 18NL

value: perilesional skin


title: 16L

value: lesion


title: 18L


title: 17NL


title: 14NL


title: LZ_eYFP.3 [TOB816A62]


title: RNA-seq, MOC1-esc1 in vivo, sgUchl5, anti-PD-1, Replicate 2

first: Robert

middle: T

last: Manguso

state: MA

address: 75 Ames Street, Rm 7053

institute: Broad Institute of MIT & Harvard

data_processing:
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
Transcript counts were quantified by pseudoalignment of trimmed reads to mm10 using Kallisto (v0.46.0)
Gene counts were aggregated from transcript counts using the tximport (v1.24.0) R package
Assembly: mm10
Supplementary files format and content: comma-separated text file includes raw gene counts in each sample

source_name: HNSCC

growth_protocol: Mouse MOC1-esc1 cell line (sgCtrl and sgUchl5) were cultured in IMDM/Hams-F12 (2:1) supplemented with 5% heat-inactivated FBS, 100 U/mL penicillin–streptomycin, 5 ng/mL EGF, 40 ng/mL hydrocortisone, and 5 mg/mL insulin.

extract_protocol:
Tumors were collected on day 15, weighed, mechanically diced, digested with a tumor dissociation kit and a gentleMACS dissociator. After filtering through a 70-μm strainer, tumor cells were isolated using the Mouse Tumor Cell isolation kit and subsequently subjected to RNA-seq
The library was constructed by Takara SMARTer Stranded Total RNA-Seq Kit v2

treatment_protocol: Control and Uchl5-deficient MOC1-esc1 cells we inoculated into wild-type C57BL/6 mice treated with or without anti-PD-1. The anti-PD-1 treatment consisted of 200 µg per mouse administered on days 6, 9, and 12.

value: HNSCC

value: tumor cells

value: Known:TP53V170E; HRASQ61L; FAT1E2054D


title: 14L


title: 13L


title: 16NL


title: HBMVEC, Control, 3, 72h

description:
Library name: Sample HBMVEC_Con72_3
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con72_3

value: brain microvasculature

value: PBS


title: RNA-seq, MOC1-esc1 in vivo, sgUchl5, anti-PD-1, Replicate 1


title: LZ_eYFP.1 [TOB816A60]


title: LZ_MizFF.3 [TOB816A58]


title: HBMVEC, Control, 2, 72h

description:
Library name: Sample HBMVEC_Con72_2
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con72_2

value: primary HBMVEC

value: brain microvascular endothelial cells


title: LZ_MizFF.2 [TOB816A57]


title: 13NL


title: HBMVEC, Control, 1, 72h

description:
Library name: Sample HBMVEC_Con72_1
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con72_1


title: HGWD+cisplatin rep3

city: Baotou

first: Jie

last: Cheng

address: Baotou Medical College

institute: Baotou Medical College

data_processing:
fastp (version 0.23.4) was used for quality control
sequence reads were aligned to the rat genome version mRatBN7.2 with HISAT2 software (v2.0.5)
StringTie (v1.3.3b) was used for novel transcripts predictio
FeatureCounts v1.5.0-p3 was used for count the reads numbers mapped to each gene
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Rattus norvegicus

extract_protocol:
RNA was extracted using  TRIzol reagent (Invitrogen, USA)
Libraries were prepared using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

value: Rat pheochromocytoma cells

value: HGWD+cisplatin


title: HBMVEC, Control, 6, 24h

description:
Library name: Sample HBMVEC_Con24_6
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con24_6


title: HGWD+cisplatin rep1


title: HGWD+cisplatin rep2


title: RNA-seq, MOC1-esc1 in vivo, sgUchl5, Untreated, Replicate 2

value: No treatment


title: RNA-seq, MOC1-esc1 in vivo, sgUchl5, Untreated, Replicate 1


title: HBMVEC, Control, 5, 24h

description:
Library name: Sample HBMVEC_Con24_5
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con24_5


title: RNA-seq, MOC1-esc1 in vivo, sgCtrl, anti-PD-1, Replicate 3


title: HBMVEC, Control, 4, 24h

description:
Library name: Sample HBMVEC_Con24_4
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con24_4


title: cisplatin rep1

value: cisplatin


title: control rep3

value: control


title: RNA-seq, MOC1-esc1 in vivo, sgCtrl, anti-PD-1, Replicate 2


title: cisplatin rep2


title: control rep1


title: RNA-seq, MOC1-esc1 in vivo, sgUchl5, Untreated, Replicate 3


title: DLD1_LIN28B_Alp_3

city: New York

first: Alice

middle: E.

last: Shin

state: NY

address: 1130 St. Nicholas Ave. 202-2

department: Herbert Irving Comprehensive Cancer Center

institute: Columbia University Irving Medical Center

data_processing:
STAR 2.7.10 was used to align trimmed fastq files to the reference genome (hg38)
the Picard CollectRnaSeqMetrics module (Picard) was used to evaluate alignments and perform initial quality control (QC)
Gene expression was quantified with HTSeq, and these data were imported into RStudio (R 3.5) for DESeq2 (RRID: SCR_015687) analysis to determine differentially expressed genes across different conditions.
Assembly: hg38
Supplementary files format and content: CSV format final expression values in transcripts per million (TPM) for each sample

source_name: Colon

growth_protocol: LoVo and DLD-1 cells were expanded in DMEM (Corning 10-013-CV) supplemented with 10% fetal bovine serum (FBS; Cytiva SH30071) and 1% penicillin-streptomycin (Sigma-Aldrich P4333).

extract_protocol:
Total RNA was extracted from frozen cell samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Cells were treated with 5 μM alpelisib (Selleck Chemicals S2814).

value: Colon

value: Colorectal cancer

value: LIN28B overexpressed

value: Alpelisib


title: HBMVEC, Control, 2, 24h

description:
Library name: Sample HBMVEC_Con24_2
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con24_2

value: WT


title: DLD1_LIN28B_Alp_2


title: HBMVEC, Control, 3, 24h

description:
Library name: Sample HBMVEC_Con24_3
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con24_3


title: DLD1_LIN28B_3


title: control rep2


title: LZ_MizFF.1 [TOB816A56]

value: Spleen

value: B cells

value: SRBCs immunisation


title: HBMVEC, Control, 1, 24h

description:
Library name: Sample HBMVEC_Con24_1
Column name in HBMVEC_All_Samples_rawcount.txt: HBMVEC_Con24_1

value: brain microvasculature


title: RNA-seq, MOC1-esc1 in vivo, sgCtrl, Untreated, Replicate 2

value: HNSCC

value: tumor cells

value: Known:TP53V170E; HRASQ61L; FAT1E2054D


title: DLD1_LIN28B_2


title: DLD1_LIN28B_1


title: DLD1_EV_3

value: EV


title: DLD1_EV_2


title: normoxic condition for 24 hours, biol rep 2

city: guangzhou

first: Song

last: Yang

address: zhongshan second load

institute: Guangdong provincial people's hospital

description:
Library name: MSC-N24-2
column name in count.txt: MSC-N24-2

data_processing:
We obtained 150-bp paired-end RNA-seq reads from the Illumina sequencing platform. Adaptors and low-quality bases were firstly trimmed by Trim Galore. Then, gene expressions were quantified by kallisto and the GENCODE database (v32).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: The hUC-MSCs were seeded in six-well plates and cultured in the following specific medium: 10 % fetal bovine serum (HyClone, SH30396.03), 1% antibiotic-antifungal solution (Invitrogen, 10378016), 1% non-essential amino acid NEAA (Invitrogen, 11140050), and DMEM / F12 medium (Gibco, C11330500BT). Cells were passaged every 3 to 4 days.

extract_protocol:
The total RNA of hUC-MSCs in each group after hypoxia treatment was extracted by RNA small extraction kit (Sangon Biotech, B618583-0050) box, and the residual genomic DNA was removed by RNase-Free DNA removal kit (Sangon Biotech, B618253-0050).
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR (1.5 nM).

treatment_protocol: To simulate hypoxic conditions, we used a three-gas incubator (ESCO, CLL-170T-8) and set specific gas components: 95 % nitrogen, 1 % oxygen, and 4 % carbon dioxide. We designed several experimental groups, and cultured cells under different hypoxia treatment times (2 hours, 6 hours, 24 hours, 72 hours). At the same time, we set up a control group, which was cultured under normoxic conditions for 24 hours. Three biological replicates were set up at each time point to ensure the accuracy and repeatability of the results.

value: Mesenchymal Stem Cells

value: normoxia


title: RNA-seq, MOC1-esc1 in vitro, sgUchl5, IFNg, Replicate 3

data_processing:
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
Transcript counts were quantified by pseudoalignment of trimmed reads to mm10 using Kallisto (v0.46.0)
Gene counts were aggregated from transcript counts using the tximport (v1.24.0) R package
Assembly: mm10
Supplementary files format and content: comma-separated text file includes raw counts for protein coding genes in each sample

extract_protocol:
Single-cell suspensions from cells cultured in a monolayer were homogenized in 600 μl RNA lysis buffer. RNA was extracted from homogenized samples using the RNA Miniprep Plus Kit in accordance with the manufacturer’s suggested protocol.
The library was constructed by Takara SMARTer Stranded Total RNA-Seq Kit v2

treatment_protocol: The MOC1-esc1 cell line were treated for 24h with either DMSO or 10ng/ml IFNγ. Cells were collected for RNA-seq after 24h treatment.

value: IFNg


title: DLD1_EV_1


title: LoVo_LIN28B_Alp_3

value: LoVo


title: normoxic condition for 24 hours, biol rep 1

description:
Library name: MSC-N24-1
column name in count.txt: MSC-N24-1


title: RNA-seq, MOC1-esc1 in vitro, sgUchl5, IFNg, Replicate 2


title: LoVo_LIN28B_Alp_2

value: Colon


title: RNA-seq, MOC1-esc1 in vivo, sgCtrl, anti-PD-1, Replicate 1


title: RNA-seq, MOC1-esc1 in vivo, sgCtrl, Untreated, Replicate 3

value: No treatment


title: LoVo_LIN28B_Alp_1

value: Colorectal cancer

value: LIN28B overexpressed


title: RNA-seq, MOC1-esc1 in vitro, sgUchl5, IFNg, Replicate 1


title: DLD1_LIN28B_Alp_1

value: Alpelisib


title: LoVo_LIN28B_3


title: hypoxic treatment for 72h, biol rep 2

description:
Library name: MSC-H72-2
column name in count.txt: MSC-H72-2

value: hypoxia


title: hypoxic treatment for 72h, biol rep 1

description:
Library name: MSC-H72-1
column name in count.txt: MSC-H72-1


title: LoVo_LIN28B_2


title: RNA-seq, MOC1-esc1 in vitro, sgUchl5, DMSO, Replicate 3

value: DMSO


title: LoVo_EV_3


title: normoxic condition for 24 hours, biol rep 3

description:
Library name: MSC-N24-3
column name in count.txt: MSC-N24-3


title: RNA-seq, MOC1-esc1 in vivo, sgCtrl, Untreated, Replicate 1


title: hypoxic treatment for 6h, biol rep 3

description:
Library name: MSC-H6-3
column name in count.txt: MSC-H6-3


title: LoVo_EV_2


title: RNA-seq, MOC1-esc1 in vitro, sgUchl5, DMSO, Replicate 1


title: LoVo_EV_1


title: hypoxic treatment for 72h, biol rep 3

description:
Library name: MSC-H72-3
column name in count.txt: MSC-H72-3


title: Raji IP rep3

data_processing:
Fastq reads aligned to human hg19 using BWA version 0.7.17. Duplicates marked, Sam to BAM file conversion and sorting bam file done with Picard version 2.1.1.
Normalised wig files generated from BAM files using in house perl script, normalised to 10million. Conversion from wig to Bigwig done with UCSC 'wigToBigWig' program
Peak called in IP relative to input called with MACS 2.1.1 using default parameters. Peaks were annotated using Homer 4.8.3
Assembly: hg19
Supplementary files format and content: normalised bigWig files

source_name: Raji

growth_protocol: Raji cells were cultured in complete B cell culture medium (BCM); P493-6 cells were cultured in BCM togather with doxycycline and beta-oestradiol.

extract_protocol:
details in the extract_protocol.txt
In each sample, DNA fragments were amplified by 14 PCR cycles. The library preparation was performed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. Subsequently, the library was sequenced in Pair End configuration (PE100) using the NovaSeq600 sequencer. Each sample received an average of 30 million reads.

value: Raji

value: human B lymphoblastoid cell line

value: Translocated c-Myc


title: Raji IP rep2


title: hypoxic treatment for 6h, biol rep 2

description:
Library name: MSC-H6-2
column name in count.txt: MSC-H6-2


title: hypoxic treatment for 6h, biol rep 1

description:
Library name: MSC-H6-1
column name in count.txt: MSC-H6-1


title: Raji inpur


title: P493-6 IP rep3

value: EREB2-5 EBV-positive lymphoblastoid cell line stably transfected with a c-myc-tet plasmid construct


title: Raji IP rep1


title: LoVo_LIN28B_1


title: P493-6 IP rep1


title: hypoxic treatment for 24h, biol rep 3

description:
Library name: MSC-H24-3
column name in count.txt: MSC-H24-3


title: P493-6 input


title: RNA-seq, MOC1-esc1 in vitro, sgCtrl, DMSO, Replicate 3

value: HNSCC

value: tumor cells

value: Known:TP53V170E; HRASQ61L; FAT1E2054D


title: LZ_eYFP.2 [TOB816A61]

value: Spleen

value: B cells

value: Control

value: SRBCs immunisation


title: RNA-seq, MOC1-esc1 in vitro, sgCtrl, IFNg, Replicate 1

value: IFNg


title: P493-6 IP rep2


title: Xenium_iri_42days_rep2

city: Saint Louis

first: Qiao

last: Xuanyuan

state: MO

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

description: 10X Xenium in situ sequencing

hyb_protocol: Probe hybridization was performed at 50 °C for 16 hrs according to the manufacturer’s protocol. Unhybridized probes were washed away and probes were ligated at 37 °C for 2 hrs. The resulting circularized probes were then amplified by 1 hr at 4 °C and 2 hrs at 37 °C with the amplification reagents provided by 10x Genomics. After washing, the auto-fluorescent signals were quenched and nuclei were stained by the nuclei staining reagents.

scan_protocol: Kidney sections on the Xenium slide were loaded onto the Xenium Analyzer instruments and imaged at Genome Technology Access Center @ McDonnell Genome Institute (GTAC@MGI) of Washington University in St. Louis. Post-Xenium slide processing followed the protocol from 10x Genomics (Demonstrated Protocol CG000160).

data_processing: Cell segmentation was performed using Baysor algorithm (https://github.com/kharchenkolab/Baysor).

label: Xenium Mouse Probe Set

source_name: Kidney tissue

label_protocol: The capture probe panel consisted of 300 custom-designed genes.

extract_protocol: For each kidney sample, 6 μm sections were mounted onto Xenium slides.

value: Kidney

value: male

tag: surgery

value: IRI 6 weeks


title: RNA-seq, MOC1-esc1 in vitro, sgCtrl, DMSO, Replicate 2


title: LX-2_PERK siRNA + palmitic acid_3

city: Toon

first: Makoto

last: Morita

address: 454 Shitsukawa

country: Japan

institute: Ehime University Graduate School of Medicine

description: Library name: Sample 6

data_processing:
Single reads (75 bp) were sequenced using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles) on the NextSeq 500 (Illumina).
Sequence data were analyzed using CLC Genomics Workbench v24 (QIAGEN) with default settings.
FASTQ files were trimmed and subsequently mapped on the human genome data of hg38.
Assembly: hg38
Supplementary files format and content: CSV files include TPM values for each sample

source_name: cell line

growth_protocol: LX-2 cells were cultured in Dulbecco’s modified Eagle’s medium free of glutamine containing 2% fetal bovine serum, 2 mM L-Glutamine, and 1% penicillin and streptomycin. Cells were incubated in a 37 ℃ humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from LX-2 cells using RNeasy Plus Mini Kit (Qiagen).
RNA-Seq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs).

treatment_protocol: RNA was collected from LX-2 cells 24 hours after palmitic acid treatment, following transfection with control or PERK siRNA.

value: cell line

value: mesenchymal


title: hypoxic treatment for 2h, biol rep 3

description:
Library name: MSC-H2-3
column name in count.txt: MSC-H2-3

value: Mesenchymal Stem Cells

value: hypoxia


title: LX-2_PERK siRNA + palmitic acid_2

description: Library name: Sample 5


title: hypoxic treatment for 24h, biol rep 1

description:
Library name: MSC-H24-1
column name in count.txt: MSC-H24-1


title: RNA-seq, MOC1-esc1 in vitro, sgCtrl, IFNg, Replicate 2


title: LX-2_PERK siRNA + palmitic acid_1

description: Library name: Sample 4


title: RNA-seq, MOC1-esc1 in vitro, sgCtrl, IFNg, Replicate 3


title: hypoxic treatment for 2h, biol rep 2

description:
Library name: MSC-H2-2
column name in count.txt: MSC-H2-2


title: RNA-seq, MOC1-esc1 in vitro, sgUchl5, DMSO, Replicate 2

value: DMSO


title: Xenium_iri_14days_rep2

description: 10X Xenium in situ sequencing

tag: Sex

value: IRI 14 days


title: RNA-seq, MOC1-esc1 in vitro, sgCtrl, DMSO, Replicate 1

value: HNSCC


title: hypoxic treatment for 2h, biol rep 1

description:
Library name: MSC-H2-1
column name in count.txt: MSC-H2-1


title: Spherocytosis

city: Zurich

first: Florence

last: Vallelian

address: Rämistrasse 100

country: Switzerland

institute: University Hospital Zürich

data_processing:
CellRangerMulti
Preprocessing in Python with scanpy
Downstream analysis in Python with scanpy
Assembly: GRCm39
Supplementary files format and content: *.h5: output of cellranger multi
Supplementary files format and content: *.bam: output of cellranger multi
Supplementary files format and content: preprocessed_*.h5ad: preprocessed samples

source_name: spleen

extract_protocol:
Spleen were mechanically minced and dissolved in PBS containing 4 mM EDTA. Minced tissue was filtered through a 70 µm cell strainer. After centrifugation 300 g, 5 min. RBC lysis was performed using the RBC lysis buffer (Biolegend, Cat. 420302) for 4 min on ice. Cells were washed once with PBS containing 4 mM EDTA.
Spleen single-cell suspensions were multiplexed and then used for GEM generation following the 10X Genomics protocol (CG000388 Demonstrated Protocol Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing Rev B) targeting a cell recovery rate of 10,000 cells. GEM generation and library preparation were performed according to the 10X Genomics protocol (CG000388).

value: spleen

value: Spta1 -/-


title: LX-2_control siRNA + palmitic acid_3

description: Library name: Sample 3


title: hypoxic treatment for 24h, biol rep 2

description:
Library name: MSC-H24-2
column name in count.txt: MSC-H24-2


title: LX-2_control siRNA + palmitic acid_2

description: Library name: Sample 2


title: Thalassemia

value: Thal +/-


title: HCAECs PPBP treated 4-4

data_processing:
Quality Control: To obtain high-quality clean reads for subsequent analysis, raw reads from the sequencing machine were filtered using fastp (version 0.18.0). The filtering parameters included removing reads containing adapter sequences, discarding reads with more than 10% unknown nucleotides (N), and eliminating low-quality reads that had more than 50% low-quality bases (Q-value ≤ 20). This quality control process ensures that only high-quality reads are retained for downstream analysis.
Alignment:For ribosomal RNA (rRNA) removal, Bowtie2 (version 2.2.8) was utilized to align short reads to an rRNA database. The reads that successfully mapped to rRNA were discarded to ensure only non-rRNA sequences remained. These clean reads were subsequently used for downstream analyses, including assembly and gene abundance calculation.Following rRNA removal, the remaining paired-end clean reads were aligned to the reference genome using HISAT2 (version 2.4) with the "–rna-strandness RF" parameter, while other settings were left as default. This alignment facilitated accurate mapping of the transcriptomic data to the reference genome for further expression analysis.
Quantification: The mapped reads for each sample were assembled using StringTie v1.3.1 in a reference-based approach. The expression abundance and variations of each transcription region were quantified by calculating the FPKM (fragments per kilobase of transcript per million mapped reads) values using RSEM software.
Assembly: mm10
Supplementary files format and content: The processed data files are provided in TXT format, containing gene expression counts for each sample. Rows represent gene identifiers (e.g., Ensembl IDs or gene symbols), and columns represent individual samples. The values in the matrix are read counts, which can be used for downstream analysis, such as differential expression.

source_name: Human Coronary Artery Endothelial Cells

growth_protocol: HCAECs were maintained in Endothelial Cell Growth Medium

extract_protocol:
Total RNA was isolated from HCAECs using RNAiso Plus
Total RNA was extracted, followed by mRNA enrichment or rRNA depletion, and then reverse transcribed into cDNA. The cDNA fragments were end-repaired, adapter-ligated, PCR amplified, and quality-checked before sequencing on the [sequencing platform].

treatment_protocol: HCAEC were seeded into well plates and treated with different concentrations of PPBP protein （0ng/mL and 4ng/mL）for 8 h

value: primary endothelial cells

value: Human Coronary Artery Endothelial Cells

value: PPBP treated


title: Xenium_iri_2days_rep2

description: 10X Xenium in situ sequencing

value: IRI 2 days


title: HCAECs PPBP treated 4-3


title: Sickle cell disease (87)

value: HbB -/-


title: Xenium_iri_2days_rep1

description: 10X Xenium in situ sequencing

value: Kidney

value: male


title: Xenium_iri_42days_rep1

description: 10X Xenium in situ sequencing

value: IRI 6 weeks


title: HCAECs PPBP treated 4-2


title: HK2-OEHNRNPF-3_1

city: Wu Han

first: LAN

last: WANG

address: 湖北省武汉市武昌区湖北中医药大学昙华林校区昙华林188号

institute: Hubei University of Chinese Medicin

description: Library name: HK2_HN_3

data_processing:
First discarded were raw reads containing more than 2-N bases. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were dropped as well. Afterwards, clean reads were aligned to the GRCh38 genome by HISAT2  allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped) .
The R Bioconductor package DESeq2 (16)was applied to screen out the differentially expressed genes (DEGs). The P value for correction <0.05 and fold change ≥ 2 or ≤ 0.5 were set as the cut-off criteria for identifying DEGs.
The alternative splicing events and regulated alternative splicing events (RAS) between tumor and normal samples were defined and quantified by using the SUVA pipeline as described previously. Differential splicing of each pair of tumor and adjacent tissues were analyzed. Frequency and Reads proportion of SUVA AS event (pSAR) of each AS events were calculated.
In order to sort out functional categories of DEGs, Gene Ontology (GO) terms and KEGG pathways were identified using KOBAS 2.0 server. Hyper geometric test and Benjamini-Hochberg FDR controlling procedure were used to define the enrichment of each term.
GSEA is an analytical method for genome-wide expression profile microarray data. Through comparing genes with predefined gene sets, it can identify functional enrichment. A gene set means a group of genes sharing localization, pathways, functions, or other features. GSEA was conducted using clusterProfiler package (version4.6.2). The fold change of gene expression between Mets group and Primary group was calculated, and the gene list was generated in accordance with the change of |log2FC|. Afterwards, we utilized GSEA-based enriched HALLMARK gene sets of the Molecular Signature Database.
Assembly: GRCh38
Supplementary files format and content: All_sample_FPKM.xlsx

source_name: HK-2 cells

growth_protocol: cell culture

extract_protocol:
We employed four parallel wells for each group of HK-2 cells: HK-2 cells transfected with the control lentivirus were cultured in a high-glucose medium containing 30 mM glucose (HG-NC) for 72 hours, while a separate group of control lentivirus-transfected HK-2 cells were cultured in a medium containing 30 mM mannitol to serve as an osmotic control (OS-NC). Similarly, HK-2 cells transfected to overexpress hnRNPF-lentivirus were maintained in a 30mM glucose medium (HG-OE) and in a mannitol medium (OS-OE) for 72 hours, respectively.
All RNA was treated to be processed with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) utilizing smartspec plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis. For each sample, 1 μg of total RNA was used for RNA-seq library preparation. mRNAs were captured by VAHTS mRNA capture Beads (Vazyme, N401).The purified RNA was treated with RQ1 DNase (Promega) to remove DNA before used for directional VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (NR605) Polyadenylated mRNAs were purified and fragmented. Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Adaptor (N323). After purification of ligation product and size fractioning to 300-500bps, the ligated products were amplified and purified, then quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

value: HK-2 cells

value: proximal tubular cell

value: HNRNPF overexpression inHK-2 cells


title: HCAECs PPBP treated 4-1


title: Xenium_iri_12hours_rep2

description: 10X Xenium in situ sequencing

value: IRI 12 hours


title: Xenium_iri_12hours_rep1

description: 10X Xenium in situ sequencing


title: Sickle cell disease (86)


title: week6_male

description: 10X Visium CytAssist

data_processing:
Visium sequencing FASTQ files were processed with Space Ranger software (v2.1)  using the mm10-2020-A mouse reference genome.
The feature barcode matrix was read using Scanpy package and we filtered out Visium spots with fewer than 500 UMI counts, resulting in a total of 19,431 usable spots. All samples was integrated using Harmony then followed by data normalization, dimensionality reduction, and clustering.
Assembly: mm10
Supplementary files format and content: The SpaceRanger output for Visium includes several folders and files (https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/output-overview). filtered_feature_bc_matrix.h5 contains sparse matrix of gene expression
Library strategy: spatial transcriptomics

source_name: Kidney

extract_protocol:
6 µm kidney sections were placed on a Superfrost™ Plus Microscope Slide from FFPE tissue blocks.
Visium CytAssist was performed according to the workflow provided by 10x Genomics:  1. Tissue sectioning for FFPE (Demonstrated Protocol CG000518) 2. Deparaffinization, Decrosslinking, Immunofluorescence Staining & Imaging (Demonstrated Protocol CG000520) 3. CytAssist enabled RNA Digestion and Tissue Removal (Demonstrated Protocol CG000520) 4. Library Construction (Demonstrated Protocol CG000495)

value: 6 weeks post Bi-IRI surgery


title: HK2-OEHNRNPF-2_1

address: 湖北省武汉市武昌区湖北中医药大学昙华林校区昙华林188号

description: Library name: HK2_HN_2


title: Xenium_iri_4hours_rep2

description: 10X Xenium in situ sequencing

value: IRI 4 hours


title: HCAECs PPBP treated 0-4

value: no treatment


title: HK2-OEHNRNPF-1_1

address: 湖北省武汉市武昌区湖北中医药大学昙华林校区昙华林188号

description: Library name: HK2_HN_1


title: day14_male

description: 10X Visium CytAssist

value: 14 days post Bi-IRI surgery


title: HCAECs PPBP treated 0-3


title: day2_male

description: 10X Visium CytAssist

value: 2 days post Bi-IRI surgery


title: Ctrl_2_1

address: 湖北省武汉市武昌区湖北中医药大学昙华林校区昙华林188号

description: Library name: HK2_NC_2

value: HK-2 cells（control plasmid）


title: Ctrl_3_1

address: 湖北省武汉市武昌区湖北中医药大学昙华林校区昙华林188号

description: Library name: HK2_NC_3


title: Xenium_iri_14days_rep1

description: 10X Xenium in situ sequencing

value: IRI 14 days


title: Xenium_control_14days_rep2

description: 10X Xenium in situ sequencing

value: Sham


title: HCAECs PPBP treated 0-2

value: primary endothelial cells

value: Human Coronary Artery Endothelial Cells


title: LX-2_control siRNA + palmitic acid_1

description: Library name: Sample 1

value: cell line

value: mesenchymal


title: hour4_male

description: 10X Visium CytAssist

value: Kidney

value: male

value: 4 hours post Bi-IRI surgery


title: hour12_male

description: 10X Visium CytAssist

value: 12 hours post Bi-IRI surgery


title: HCAECs PPBP treated 0-1


title: Ctrl_1_1

address: 湖北省武汉市武昌区湖北中医药大学昙华林校区昙华林188号

description: Library name: HK2_NC_1

value: HK-2 cells

value: proximal tubular cell


title: sham_male

description: 10X Visium CytAssist

value: sham, collected 14 days after sham operation


title: D520_001_ADT_CZINY-0216

status: Public on Jun 06 2025

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Library name: D520_001_ADT_CZINY-0216_lib
CITE-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

data_processing:
raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_background_barcodes_included:False
Assembly: GRCh38, GENCODE32
Supplementary files format and content: h5ad, count matrix

extract_protocol:
Tissue was obtained from deceased organ donors at the time of organ acquisition for clinical transplantation through an approved protocol and material transfer agreement via LiveOnNY, the organ procurement organization for the New York metropolitan area and through the Cambridge Biorepository for Translational Medicine. Each tissue was subjected to a tissue-specific protocol to maximize mononuclear cell (MNC) recovery and viability across a diversity of sites. A series of detailed protocols are available on protocols.io (https://dx.doi.org/10.17504/protocols.io.bwrjpd4n, https://dx.doi.org/10.17504/protocols.io.bwr9pd96, https://dx.doi.org/10.17504/protocols.io.bwsapeae, https://dx.doi.org/10.17504/protocols.io.bwq4pdyw, https://dx.doi.org/10.17504/protocols.io.bwq7pdzn, https://dx.doi.org/10.17504/protocols.io.bwr6pd9e, https://dx.doi.org/10.17504/protocols.io.bz4qp8vw). Each individual tissue single cell suspension (500,000 or 1,000,000 cells) was hash tagged to allow pooling of tissue samples. CITE-seq labeling used either a TotalSeq-C cocktail containing 137 protein targets (10x 5’ libraries) or TotalSeq-A cocktail containing 277 protein targets (10x 3’ libraries).
For scRNA-seq experiments, single cells were loaded onto the channels of a Chromium chip (10x Genomics). cDNA synthesis, amplification, and sequencing libraries were generated using either the Single Cell 5′ Reagent (v1 and v2) or 3′ Reagent (v3) Kits. TCRαβ and BCR paired VDJ libraries were prepared from samples made with the 5′ Reagent kit. All libraries were sequenced on either an Illumina NextSeq 500/550 or NovaSeq 6000 instrument.

tag: donor id

tag: age

value: 25 years

tag: dev stage

value: adult stage

value: female

tag: ethnicity

value: Middle Eastern/North African

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

value: never

tag: death type

value: brain stem death

tag: cause of_death

value: anoxia

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: test results.blood_sugar

value: 120 mg/dL

tag: library protocol

value: CITE 10x 5' v2

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-C Human Universal Cocktail


title: D520_001_ADT_CZINY-0218

description:
Library name: D520_001_ADT_CZINY-0218_lib
CITE-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

value: 25 years

tag: dev stage

value: adult stage

tag: Sex

value: female

tag: ethnicity

tag: tissue

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method


title: D520_001_ADT_CZINY-0224

description:
Library name: D520_001_ADT_CZINY-0224_lib
CITE-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

value: Middle Eastern/North African

value: LiveOnNY

value: FALSE

tag: smoking history

tag: death type

tag: cause of_death

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.cmv

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_genome_annotation


title: D520_001_ADT_CZINY-0223

description:
Library name: D520_001_ADT_CZINY-0223_lib
CITE-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: dev stage

tag: Sex

value: fresh

value: never

value: brain stem death

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type

tag: antibodies/tags


title: D520_001_ADT_CZINY-0219

description:
Library name: D520_001_ADT_CZINY-0219_lib
CITE-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: ethnicity

tag: tissue

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: smoking history

tag: death type

tag: cause of_death

value: anoxia

tag: body mass_index

value: positive

value: 120 mg/dL


title: D520_001_ADT_CZINY-0217

description:
Library name: D520_001_ADT_CZINY-0217_lib
CITE-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: dev stage

tag: Sex

tag: height

tag: test results.ebv

tag: test results.cmv

tag: test results.blood_sugar

tag: library protocol

value: CITE 10x 5' v2

tag: raw matrix_genome_annotation

value: UMI

value: gene symbol, antibody target


title: D520_001_ADT_CZINY-0222

description:
Library name: D520_001_ADT_CZINY-0222_lib
CITE-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: ethnicity

tag: tissue

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type

value: CITE-seq

tag: antibodies/tags


title: D520_001_ADT_CZINY-0221

description:
Library name: D520_001_ADT_CZINY-0221_lib
CITE-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

value: 25 years

tag: dev stage

value: adult stage

tag: Sex

tag: living at_sample_collection

tag: sample preservation_method

tag: smoking history

tag: death type

tag: cause of_death

tag: body mass_index

value: TotalSeq-C Human Universal Cocktail


title: D520_001_ADT_CZINY-0220

description:
Library name: D520_001_ADT_CZINY-0220_lib
CITE-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

value: female

tag: ethnicity

value: Middle Eastern/North African

tag: tissue

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: height

tag: test results.ebv

tag: test results.cmv

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_genome_annotation


title: Xenium_iri_4hours_rep1

description: 10X Xenium in situ sequencing

value: Kidney

tag: strain

tag: Sex

value: male

tag: surgery

value: IRI 4 hours


title: D520_001_ADT_CZINY-0213

description:
Library name: D520_001_ADT_CZINY-0213_lib
CITE-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: dev stage

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

value: never

value: brain stem death

value: anoxia

value: positive

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type

tag: antibodies/tags