title: BY4741 strain, WT, highty level  L-A virus, No3 isolate, rRNA depleted

description:
Library name: Fungi budding yeasts Saccharomycetes isolate9
Expression_counts: rRNADep_high level L-A virus_No3_isolate


title: Normal fibroblast from NSCLC patient 20150707

status: Public on May 01 2025

type: genomic

city: Taipei

first: Chao-Chi

last: Ho

address: 1 Jen Ai Road, Section 1

department: Department of Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital and National Taiwan University College of Medicine

description: DNA methylation data of normal fibroblast from NSCLC patient

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Normal fibroblast

label_protocol: Standard Illumina Protocol

growth_protocol: 800 cells per well were seeded to ultra-low adherent 24-wel plates (Corning) with MCDB201 medium (Invitrogen), and exposed to condition medium from cultured NFs and CAFs.

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: The medium was supplemented with epidermal growth factor (20ng/ml, Sigma) and bFGF (20ng/ml, Invitrogen).

tag: cell type

value: Normal fibroblast

tag: age

tag: smoking

value: Ever

tag: gender

value: Male

tag: histology

value: LUAD

tag: Stage

value: Late


title: Chow_hippocampus_3

type: SRA

city: Nanjing

first: jin

last: wang

address: No. 321 Zhongshan Road

department: Department of Endocrinology

country: China

institute: Drum Tower hospital affiliated to Nanjing university medical school

library_source: transcriptomic

data_processing:
miRNA sequences, tRNA sequences and piRNA sequences were obtained from miRBase v21(Kozomara and Griffiths-Jones, 2014), GtRNAdb (Chan and Lowe, 2016) and piRNA bank (Lakshmi and Agrawal, 2008), respectively. Bowtie was used to align clean reads to these reference sequences for annotation.
Assembly: miRBase v21; GtRNAdb; piRNA bank
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Adipose tissue derived EVs and hippocampus were extracted from male mice of the C57BL/6J backgrounds and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: Sex

value: male

tag: tissue

value: brain

tag: genotype

value: WT

tag: treatment

value: Chow diet


title: Chow_hippocampus_2


title: BY4741 strain, WT, highty level  L-A virus, No2 isolate, rRNA depleted

first: Tien-Hsien

last: Chang

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

institute: Academia Sinica

description:
Library name: Fungi budding yeasts Saccharomycetes isolate8
Expression_counts: rRNADep_high level L-A virus_No2_isolate

data_processing:
Sequencing data were aligned to the yeast reference genome yeast_R64 by STAR read mapper (versionL2.1.11b).  Differential-expression analysis was done using HTseq/RSEM.
Assembly: Sequencing data were aligned to the yeast reference genome yeast_R64
Supplementary files format and content: text file includes raw counts for each sample

organism: Saccharomyces cerevisiae

growth_protocol: Independent colonies from each of the  L-A-, L-A+, and L-A++ isolates were cultured in liquid YPD (2% dextrose, 2% peptone and 1% yeast extract) medium overnight.

extract_protocol:
Total RNA was isolated using MasterPureTM Yeast RNA Purification Kit (Lucigen) and treated with DNase I at 37˚C for 30 m.
For rRNA depleted method was using QIAseq FastSelect RNA Library kit (334215) and TruSeq Stranded mRNA sample prep kit (RS-122-2101) at the Genomics Core Facility, Institute of Molecular Biology, Academia Sinica, Taiwan. For the poly(A) RNA enriched approach, was using SureSelect XT HS2 mRNA Library Preparation Kit with Index Primer Pairs 97-192, 96 Reactions (G9997B) (Agilent, Santa Clara, CA, USA) and the SureSelect XT HS2 mRNA Library Preparation kit (Agilent, Santa Clara, CA, USA) was used for library construction, followed by HighPrep PCR clean-up system. (MagBio Genomics, Gaithersburg, MD, USA)(W3852001-1).done at Welgene Biotech Co., Ltd. (Taipei, Taiwan).


title: Brain arteries from SAH7d animal, rep. 4

type: RNA

city: Puerto Real

first: Maria del Carmen

last: González Montelongo

state: Cádiz

address: Calle Esparraguera 111

country: Spain

institute: University of Cádiz

description:
Gene expression data from SAH7d animals
H4

hyb_protocol: Hybridazation (GeneChip Hybridization Oven 654,Thermo Fisher Scientific, Inc.) and, washing and staining (GeneChip Fluidics Station 450, Thermo Fisher Scientific, Inc.), were performed following protocols outlined in the user manual for cartridge arrays

scan_protocol: Scanning with a GeneChip® Scanner 3000 7G system (Thermo Fisher Scientific, Inc.) was performed following protocols outlined in the user manual for cartridge arrays.

data_processing: CEL files were analyzed by Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fisher Scientific, Inc.)

label: Biotin

organism: Rattus norvegicus

source_name: Brain rat arteries under SAH induction procedure

label_protocol: Total RNA was amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific, Inc.)

growth_protocol: 13 samples or brain arteries were collected from experimental groups. Control (3), Sham7d (5) and SAH7d (5).

extract_protocol: The homogenization of the arteries was performed using the RNeasy® Micro Kit (Qiagen). The RNA isolation process was completed using the QIAcube platform (Qiagen)

treatment_protocol: Arteries were cleaned under a magnifying glass in ice-cold RNAses-free Hank’s solution, immediately frozen in liquid nitrogen and stored at -80 ºC.

value: Brain arteries cleaned from connective tissues

value: Wistar

value: six months old

value: under SAH induction procedure


title: BY4741 strain, WT, mid level  L-A virus, No3 isolate, rRNA depleted

description:
Library name: Fungi budding yeasts Saccharomycetes isolate6
Expression_counts: rRNADep_ mid level  L-A virus_No3_isolate


title: HFD_EVs_3

source_name: adipose tissue derived extracellular vesicles

value: HFD diet


title: HFD_EVs_2

value: adipose tissue derived extracellular vesicles


title: BY4741 strain, WT, mid level  L-A virus, No2 isolate, rRNA depleted

description:
Library name: Fungi budding yeasts Saccharomycetes isolate5
Expression_counts: rRNADep_ mid level  L-A virus_No2_isolate


title: Chow_hippocampus_1


title: Brain arteries from SAH7d animal, rep. 3

description:
Gene expression data from SAH7d animals
H3


title: Normal fibroblast from NSCLC patient 20150902

value: Never

value: Female

value: Early


title: Brain arteries from SAH7d animal, rep. 1

description:
Gene expression data from SAH7d animals
H1


title: Brain arteries from Sham7d animal, rep. 5

description:
Gene expression data from Sham7d animals
S5

source_name: Brain rat arteries under surgical control procedure

value: under surgical control procedure


title: Brain arteries from Sham7d animal, rep. 2

description:
Gene expression data from Sham7d animals
S2

value: Male


title: Brain arteries from Sham7d animal, rep. 4

description:
Gene expression data from Sham7d animals
S4


title: Brain arteries from Sham7d animal, rep. 3

description:
Gene expression data from Sham7d animals
S3


title: Brain arteries from SAH7d animal, rep. 2

description:
Gene expression data from SAH7d animals
H2


title: Normal fibroblast from NSCLC patient 0330

value: Normal fibroblast

value: LUAD


title: Normal fibroblast from NSCLC patient 20150505

value: Ever

value: Late


title: BY4741 strain, WT, highty level  L-A virus, No1 isolate, rRNA depleted

description:
Library name: Fungi budding yeasts Saccharomycetes isolate7
Expression_counts: rRNADep_high level L-A virus_No1_isolate

value: WT


title: HFD_EVs_1

value: male


title: Chow_EVs_3

value: Chow diet


title: Normal fibroblast from NSCLC patient 20150519


title: Normal fibroblast from NSCLC patient 20150428

value: LUSC


title: BY4741 strain, WT, without L-A virus, No2 isolate, rRNA depleted

description:
Library name: Fungi budding yeasts Saccharomycetes isolate2
Expression_counts: rRNADep_without L-A virus_No2_isolate


title: BY4741 strain, WT, mid level  L-A virus, No1 isolate, rRNA depleted

description:
Library name: Fungi budding yeasts Saccharomycetes isolate4
Expression_counts: rRNADep_ mid level  L-A virus_No1_isolate


title: Chow_EVs_2


title: BY4741 strain, WT, without L-A virus, No3 isolate, rRNA depleted

description:
Library name: Fungi budding yeasts Saccharomycetes isolate3
Expression_counts: rRNADep_without L-A virus_No3_isolate


title: Normal fibroblast from NSCLC patient 20150331_1


title: RNA_CD8_Day7_m38_Rep1

city: New York

first: Endi

middle: K

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: RNA_CD8_Day7_m38_Rep1
RNA_rawCounts.txt

data_processing:
For all sequenced data, paired-end reads were trimmed for adaptors and removal of low-quality reads using Trimmomatic (v.0.36). Trimmed reads were mapped to the Mus musculus genome (mm10 assembly) using Bowtie2 (v2.2.9). Read counts for features (peak regions for ATAC-seq and exons for RNA-seq) were generated using the summarizeOverlaps function from the GenomicAlignments package (v1.10.1). Differential analyses were executed with DESeq2 (v1.14.1) using the UCSC Known Gene models as reference annotations. Features were considered differential if they showed a P value (Padj) < 0.05, adjusted for multiple hypothesis correction.
For peak calling, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to center the reads on the transposon binding event. Shifted, concordantly aligned paired mates were used for peak calling by MACS2 at a P value of 0.01. IDR calculations using scripts provided by the ENCODE project were performed on all pairs of replicates using an oracle peak list called from merged replicates for each condition, keeping only reproducible peaks showing an IDR value of 0.05 or less. Overlapping peaks from different conditions were merged using the following conditions: if a peak overlapped with more than one other peak, the peak with the highest overlap (calculated as the percentage of overlap width out of the total width of the narrower peak) was merged; if the overlap of two peaks was > 75%, non-overlapping portions were removed; if the overlap was 75% or less, then both peaks were merged to create a single peak encompassing both peak ranges. A union of both merged overlapping peaks and unique reproducible peaks for each condition was used to generate the final atlas and was used for further analysis.
Assembly: mm10
Supplementary files format and content: RNA_rawCounts.txt
Supplementary files format and content: ATAC_rawCounts.txt
Supplementary files format and content: ATAC_peaks.txt

source_name: Spleen

extract_protocol:
For RNA-seq: We isolated 20,000–50,000 sorted splenic lymphocytes for RNA-sequencing. CD8+ T cells were sorted from wild-type mice at d0 (naive: TCRβ+CD8+CD62LhiCD44lo), d7, or d35 PI (effector and memory: TCRβ+CD8+CD62LloCD44hiTetramer+). For ATAC-seq, 7,000-50,000 cells were collected. Fresh cells were washed in cold PBS and lysed. Transposition occurred at 42 °C for 45 min.
For RNA-seq: RNA was isolated from sorted cell populations using Trizol (Invitrogen), and total RNA was amplified using the SMART-seq V4 Ultra Low Input RNA kit (Clontech). Subsequently, 10 ng of amplified cDNA was used to prepare Illumina HiSeq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using eight cycles of PCR. For ATAC-seq: DNA was purified using the MinElute PCR purification kit (Qiagen) and amplified for five cycles. Additional PCR cycles were evaluated by real-time PCR. The final product was cleaned by Ampure Beads at a 1.5 × ratio.

value: Spleen

tag: epitope

value: CD8 +T

value: MCMV

tag: day


title: BY4741 strain, WT, without L-A virus, No1 isolate, rRNA depleted

description:
Library name: Fungi budding yeasts Saccharomycetes isolate1
Expression_counts: rRNADep_without L-A virus_No1_isolate


title: Chow_EVs_1

value: adipose tissue derived extracellular vesicles


title: Normal fibroblast from NSCLC patient 20150303

description: DNA methylation data of normal fibroblast from NSCLC patient

value: Never

value: Other


title: Brain arteries from Control animal, rep. 3

description:
Gene expression data from control animals
C3

source_name: Brain rat arteries without any surgical procedure

value: Brain arteries cleaned from connective tissues

value: Wistar

value: six months old

value: without any surgical procedure


title: Normal fibroblast from NSCLC patient 20150203_2

value: Normal fibroblast

value: Female

value: LUAD


title: Normal fibroblast from NSCLC patient 20101221

value: Early


title: Brain arteries from Control animal, rep. 2

description:
Gene expression data from control animals
C2

value: Male


title: Pilot 4 CD4+CD8- cells, CITE

status: Public on Apr 30 2025

city: La Jolla

first: Bjoern

last: Peters

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description:
Library name: HIPC_Pilot_Hu_4_8D_CITE
10X Genomics

library_source: other

data_processing:
Raw reads were aligned and quantified using the Cell Ranger Multi pipeline (version 5.0.0) against the GRCh38 (2020-A) human reference genome and the VDJ was aligned with refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0. GEX and HTO data were aggregated as feature/barcode matrices and imported into the R environment using Seurat where additional QCs and downstream analysis were conducted. Before creating the Seurat object, in the GEX matrix, TCR genes belonging to each category of TCR alpha, beta, gamma and delta were averaged across the cells to prevent the formation of individual TCR gene expression clusters in downstream analysis.
Assembly: GRCh38 v2020-A
Supplementary files format and content: Cell Ranger output files: features.tsv, barcodes.tsv, matrix.mtx, filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein

source_name: PBMC

extract_protocol:
Freshly collected HLA-DR+CD3+CD4+CD8-, HLA-DR-CD3+CD4+CD8- and CD3+CD4-CD8- cells were resuspended in ice-cold PBS with 0.04% BSA in a final concentration of 1800 cells/μL. Single-cell suspensions were then immediately loaded on the 10X Genomics Chromium Controller with a loading target of 30,000-60,000 cells.
Libraries were generated using the Chromium Next Gem Single Cell 5′ Reagent Kit v2 (Dual Index) per the manufacturer’s instructions, with additional steps for the amplification of HTO barcodes and V(D)J libraries (10X Genomics). Libraries were sequenced on Illumina NovaSeq with a sequencing target of 30,000 reads per cell RNA library, 5000 reads per cell HTO barcode library, and 5000 reads per cell for V(D)J libraries.

value: PBMC

tag: sample group

value: Pilot 4 CD4+CD8- cells

tag: library type

value: CITE

tag: adt

value: adt_CD4, adt_HLADR, adt_TCRGD


title: Pilot 4 CD4+CD8- cells, HTO

description:
Library name: HIPC_Pilot_Hu_4_8D_HTO
10X Genomics

value: HTO

tag: hto


title: Brain arteries from Control animal, rep. 1

description:
Gene expression data from control animals
C1


title: Pilot 4 CD4+CD8- cells, TCR

description:
Library name: HIPC_Pilot_Hu_4_8D_TCR
10X Genomics

data_processing:
Raw reads were aligned and quantified using the Cell Ranger Multi pipeline (version 5.0.0) against the GRCh38 (2020-A) human reference genome and the VDJ was aligned with refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0. GEX and HTO data were aggregated as feature/barcode matrices and imported into the R environment using Seurat where additional QCs and downstream analysis were conducted. Before creating the Seurat object, in the GEX matrix, TCR genes belonging to each category of TCR alpha, beta, gamma and delta were averaged across the cells to prevent the formation of individual TCR gene expression clusters in downstream analysis.
Assembly: GRCh38 v2020-A
Supplementary files format and content: Cell Ranger output files: features.tsv, barcodes.tsv, matrix.mtx, filtered_contig_annotations.csv

molecule: other

tag: cell type

value: TCR


title: Pilot 3 CD4+CD8- cells, CITE

description:
Library name: HIPC_Pilot_Hu_3_8D_CITE
10X Genomics

value: Pilot 3 CD4+CD8- cells


title: Normal fibroblast from NSCLC patient 20150818

tag: age

value: Ever

value: Late


title: Pilot 4 CD4+CD8- cells, GEX

description:
Library name: HIPC_Pilot_Hu_4_8D_Gex
10X Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

value: mRNA


title: Pilot 3 CD4+CD8- cells, GEX

description:
Library name: HIPC_Pilot_Hu_3_8D_Gex
10X Genomics


title: MTB20J CD4+CD8- cells, TCR

description:
Library name: MTB20J_Hu_CD3_TCR
10X Genomics

value: MTB20J CD4+CD8- cells


title: MTB20J CD4+CD8- cells, HTO

description:
Library name: MTB20J_Hu_CD3_HTO
10X Genomics


title: Pilot 3 CD4+CD8- cells, HTO

description:
Library name: HIPC_Pilot_Hu_3_8D_HTO
10X Genomics


title: Normal fibroblast from NSCLC patient 20100315

tag: smoking

value: Never


title: Pilot 3 CD4+CD8- cells, TCR

description:
Library name: HIPC_Pilot_Hu_3_8D_TCR
10X Genomics


title: MTB20L CD4+CD8- cells, HTO

description:
Library name: MTB20L_Hu_CD3_HTO
10X Genomics

value: MTB20L CD4+CD8- cells


title: Normal fibroblast from NSCLC patient 20140411

value: Normal fibroblast

tag: gender

value: Other


title: MTB20L CD4+CD8- cells, GEX

description:
Library name: MTB20L_Hu_CD3_Gex
10X Genomics


title: MTB20H CD4+CD8- cells, TCR

description:
Library name: MTB20H_Hu_CD3_TCR
10X Genomics

value: MTB20H CD4+CD8- cells


title: MTB20L CD4+CD8- cells, TCR

description:
Library name: MTB20L_Hu_CD3_TCR
10X Genomics


title: MTB20I CD4+CD8- cells, GEX

description:
Library name: MTB20I_Hu_CD3_Gex
10X Genomics

value: MTB20I CD4+CD8- cells


title: MTB20H CD4+CD8- cells, CITE

description:
Library name: MTB20H_Hu_CD3_CITE
10X Genomics

value: PBMC

value: adt_CD4, adt_HLADR


title: MTB20L CD4+CD8- cells, CITE

description:
Library name: MTB20L_Hu_CD3_CITE
10X Genomics

value: CITE


title: Normal fibroblast from NSCLC patient 20100426_1

description: DNA methylation data of normal fibroblast from NSCLC patient

value: Male

tag: histology

value: LUAD

value: Early


title: MTB20J CD4+CD8- cells, CITE

description:
Library name: MTB20J_Hu_CD3_CITE
10X Genomics


title: MTB20J D4+CD8- cells, GEX

description:
Library name: MTB20J_Hu_CD3_Gex
10X Genomics

value: MTB20J D4+CD8- cells


title: MTB20I CD4+CD8- cells, CITE

description:
Library name: MTB20I_Hu_CD3_CITE
10X Genomics


title: MTB20H CD4+CD8- cells, GEX

description:
Library name: MTB20H_Hu_CD3_Gex
10X Genomics


title: Normal fibroblast from NSCLC patient 20101228

value: Ever

value: LUSC

tag: Stage


title: Normal fibroblast from NSCLC patient 20150203_1


title: Normal fibroblast from NSCLC patient 20150318

value: Female


title: MTB20I CD4+CD8- cells, HTO

description:
Library name: MTB20I_Hu_CD3_HTO
10X Genomics

value: HTO


title: MTB20I CD4+CD8- cells, TCR

description:
Library name: MTB20I_Hu_CD3_TCR
10X Genomics

value: TCR


title: MTB20G CD4+CD8- cells, TCR

description:
Library name: MTB20G_Hu_CD3_TCR
10X Genomics

value: MTB20G CD4+CD8- cells


title: Normal fibroblast from NSCLC patient 20101231

value: Normal fibroblast

value: Never


title: MTB20G CD4+CD8- cells, CITE

description:
Library name: MTB20G_Hu_CD3_CITE
10X Genomics


title: MTB20G CD4+CD8- cells, GEX

description:
Library name: MTB20G_Hu_CD3_Gex
10X Genomics

value: mRNA


title: MTB20E CD4+CD8- cells, CITE

description:
Library name: Mtb20E_Hu_CD3_CITE
10X Genomics

value: MTB20E CD4+CD8- cells


title: MTB20G CD4+CD8- cells, HTO

description:
Library name: MTB20G_Hu_CD3_HTO
10X Genomics

value: PBMC


title: MTB20E CD4+CD8- cells, HTO

description:
Library name: Mtb20E_Hu_CD3_HTO
10X Genomics


title: MTB20H CD4+CD8- cells, HTO

description:
Library name: MTB20H_Hu_CD3_HTO
10X Genomics

value: MTB20H CD4+CD8- cells


title: MTB20E CD4+CD8- cells, TCR

description:
Library name: Mtb20E_Hu_CD3_TCR
10X Genomics


title: MTB20D CD4+CD8- cells, CITE

description:
Library name: MTB20D_Hu_CD3_CITE
10X Genomics

value: MTB20D CD4+CD8- cells

value: CITE

value: adt_CD4, adt_HLADR


title: MTB20D CD4+CD8- cells, TCR

description:
Library name: MTB20D_Hu_CD3_TCR
10X Genomics


title: MTB20D CD4+CD8- cells, HTO

description:
Library name: MTB20D_Hu_CD3_HTO
10X Genomics


title: MTB20E CD4+CD8- cells, GEX

description:
Library name: Mtb20E_Hu_CD3_Gex
10X Genomics


title: MTB20D CD4+CD8- cells, GEX

description:
Library name: MTB20D_Hu_CD3_Gex
10X Genomics


title: MTB20C CD4+CD8- cells, TCR

description:
Library name: MTB20C_Hu_CD3_TCR
10X Genomics

value: MTB20C CD4+CD8- cells


title: MTB20B CD4+CD8- cells, CITE

description:
Library name: MTB20B_Hu_CD3_CITE
10X Genomics

value: MTB20B CD4+CD8- cells


title: MTB20A CD4+CD8- cells, CITE

description:
Library name: MTB20A_Hu_CD3_CITE
10X Genomics

value: MTB20A CD4+CD8- cells


title: MTB20B CD4+CD8- cells, GEX

description:
Library name: MTB20B_Hu_CD3_Gex
10X Genomics


title: MTB20A CD4+CD8- cells, HTO

description:
Library name: MTB20A_Hu_CD3_HTO
10X Genomics


title: MTB20B CD4+CD8- cells, HTO

description:
Library name: MTB20B_Hu_CD3_HTO
10X Genomics


title: MTB20B CD4+CD8- cells, TCR

description:
Library name: MTB20B_Hu_CD3_TCR
10X Genomics


title: MTB20C CD4+CD8- cells, GEX

description:
Library name: MTB20C_Hu_CD3_Gex
10X Genomics


title: ATAC-seq, AMLE400ug/ml, rep1

city: Daejeon

first: Suyoung

last: Choi

address: 266, Munhwa-ro, Jung-gu

department: Department of Medical Science

country: South Korea

institute: Chungnam National University

description:
Library name: Sample 10
BA3
APP_qdefault_consensus.bed
BA_APP_pooled_default.bw

library_source: genomic

data_processing:
RNA-seq, Quality control (QC) and read count matrix generation were performed using Python (v3.8.10) and R in a Linux environment. Trim Galore (v0.6.7) was used for low-quality read filtering. Reads were aligned to the mm10 reference genome using STAR aligner (v2.7.11b). SAMtools (v1.7) was used to convert SAM files into BAM files. Gene count matrices were generated for downstream analysis. ATAC-seq data quality was assessed with FastQC, and reads were trimmed for adapters and low-quality bases using Trim Galore (v0.6.7). Clean reads were aligned to the mm10 genome with Bowtie2 (v2.4.4); only properly mapped reads (MAPQ >30) were retained. PCR duplicates were removed using Picard MarkDuplicates (v2.26.3). Peaks were called using MACS3 (v3.0.0a7) and visualized with Deeptools (v3.5.1). Differential peak analysis was conducted with csaw (v1.28.0), and peak annotation and visualization were performed using ChIPseeker (v1.30.0). Motif enrichment was analyzed with HOMER (findMotifsGenome.pl), and motifs with p < 0.01 were considered significant.
Assembly: mm10
Supplementary files format and content: RNA-seq csv files include raw read count metrix for each sample
Supplementary files format and content: ATAC-seq BigWig, bed, and narrowPeak for DMSO and AMLE treated sample

source_name: BMDCs

extract_protocol:
Total RNA was extracted using the Trizol method (Invitrogen, AM9738) from BMDCs.
For RNA-seq libraries, the manufacturer's protocol for the TruSeq Stranded mRNA Library Prep Kit was followed (Guide #1000000040498). RNA sequencing was performed on the Illumina HiSeq 2500, generating raw fastq.gz files of 1.7-2.2 G per sample, with 67-81 million reads after merging. ATAC-seq libraries were prepared using the ATAC-seq kit (AT53150, Active Motif) and the Omni-ATAC protocol (Corces et al., 2017, Nature Methods 14, 959-962. 10.1038/nmeth.4396). Briefly, nuclear suspensions obtained from 100,000 BMDC samples treated with AMLE or control vehicle were incubated with assembled Tn5 transposase for 30 min at 37°C. The tagged DNA was purified using a MinElute PCR Purification Kit, amplified using Nextera PCR primers, purified using SPRI beads and sequenced using a NovaSeq 6000 sequencer (Illumina).

value: BMDCs

value: 8-10 weeks old

tag: time

value: 24h, After treatment

value: AMLE (400ug/ml)

tag: strain

value: C57BL/6, WT


title: MTB20C CD4+CD8- cells, CITE

description:
Library name: MTB20C_Hu_CD3_CITE
10X Genomics


title: LR138, AML, 3M, scRNAseq, BM

description:
Library name: CNUH_LR_138
10x Genomics

data_processing:
Reads were aligned to the GRCh38 reference genome using 10x Genomics Cell Ranger (v7.2.0), and cell-specific barcodes were filtered to retain approximately 96% of the cells. Data processing, was carried out by Microgen (Daejeon, Korea), and the processed data are available (GEO accession number: TBA). Single-cell expression data were normalized and analyzed using Seurat (v5.0.1), followed by strict quality control measures. Cells with >25% mitochondrial gene content, and fewer than 200 or more than 7500 expressed genes were excluded. Clustering was performed using Louvain and UMAP, and immune and hematopoietic cell types were manually annotated. To analysis T-cells subcluster we filtered cells by CD3(-delta, -epsilon, -zeta) expression. Additional analysis identified IKZF2, CD160, and ZBTB16 as key markers of double-negative T (DNT) cells, and differential gene expression was conducted to assess T-cell status and activation. In the T cell subset, to analyzed T cell exhaustion and metabolic reprogramming we performed the Gene set enrichment analysis pathway enrichment using ssGSEA (v1.2.4) and protein-protein association networks and functional enrichment analyses with STRING (v12.0) website as default option.
Assembly: Human GRCh38
Supplementary files format and content: Barcode, metrix, and feature files

source_name: Bone marrow

extract_protocol:
Bone marrow cells were isolated form patient and gradent isoaltied into 6h. Collacted buffitr cote were storered at LN2 tank with 90% FBS with 10% DMSO solution.
Single-cell RNA sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3.1 (PN-1000121) according to the manufacturer’s protocol (CG000204 Rev D). Single-cell suspensions were loaded onto a Chromium Controller (10x Genomics, PN-120223) to generate single-cell gel beads in emulsion (GEMs). Reverse transcription was performed within the GEMs to barcode RNA transcripts, followed by cDNA amplification using the Chromium Single Cell 3' Reagent Kit v3.1 (PN-1000157). Amplified cDNA was quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Cat# Q32851), and library quality was assessed on a Bioanalyzer 2100 (Agilent Technologies, Cat# G2939BA) using the High Sensitivity DNA Kit (Agilent, Cat# 5067-4626). Libraries were sequenced on an Illumina NovaSeq 6000 platform (Illumina, Cat# 20012850), following the recommended read length for the 10x Genomics protocol

tag: tissue

value: Bone marrow

value: 3M after HSCT

tag: gvhd prevention_treatment

value: ATG

tag: hsct method

value: Sibling, matched

tag: disease classification

value: AML, M4


title: CR112, MDS, 3M, scRNAseq, BM

description:
Library name: CNUH_CR_112
10x Genomics

value: MDS (IPSS 1, INT-1 & IPSS-R 5, high risk group)


title: CR144, ALL, 3M, scRNAseq, BM

description:
Library name: CNUH_CR_144
10x Genomics

value: Haploidentical

value: ALL with BCR-ABL rearrangement


title: ER399, AML, 3M, scRNAseq, BM

description:
Library name: CNUH_ER_399
10x Genomics

value: AML, M2


title: ER135, AML, 3M, scRNAseq, BM

description:
Library name: CNUH_ER_135
10x Genomics

value: Unrelated, matched


title: 3and12moBrain_WTandSTING-KO

city: Boston

first: Katherine

last: Sulka

state: MA

address: 136 Harrison Avenue

institute: Tufts Medical School- Graduate School of Biomedical Sciences

description:
Library name: SS001
10x Genomics v3

data_processing:
Sequenced samples were processed using Cell Ranger (v3.0.2) mkfastq pipeline. FASTQ files were assigned to the mm10 transcriptome, filters, and quantified.
Assembly: mouse mm10
Supplementary files format and content: tab separated values files and matrix files

source_name: Brain

extract_protocol:
Tissues were extracted and placed is appropriate enzymatic digestion buffer for the specific tissue and incubated at 37C. Samples were passed through a 70μm strainer, brought up to 10mL in 2% DMEM, and centrifuged for 5 minutes at 500g at 4°C. Debris was removed from samples using Debris Removal (Miltenyi, 130-109-398) and after cells were pelleted, samples were lysed by resuspension in 1mL ACK lysis buffer (Fisher Scientific, NC0829166) for 1 minute at room temperature, followed by the addition of 9mL of 2% DMEM. Samples were pelleted, resuspended in PBS, and kept cold. Cells were counted (Countessa, Thermo, with Trypan Blue viability stain) and aliquoted for experimental use.
Single cell preparations were resuspended into enriched PBS (0.5% BSA). Approximately 9,000 cells were loaded into each well of the Chromium Chip A/B (10x Genomics v2 and v3, respectively), depending on the run, and then run on the Chromium controller. GEM formation quality was visualized manually before GEMs were transferred to a thermal cycler. GEM-RT cleanup and cDNA amplification steps were completed, and quantification was run inhouse. 3’ gene expression library as constructed and post-library construction quality control was completed in-house as described in 10x Manual.

value: Brain

value: 3-mo and 12-mo

tag: genotype

value: WT and STING-KO

tag: treatment

value: FACS-sorted

tag: Sex

value: male


title: ATAC-seq, DMSO0.04%, rep1

description:
Library name: Sample 7
BA1
DMSO_qdefault_consensus.bed
BA_DMSO_pooled_default.bw

value: BMDCs

value: 8-10 weeks old

value: 24h, After treatment


title: KGW10_E_EPCAM

city: Stanford

first: Andrew

last: Gentles

address: 1201 Welch Road

institute: Stanford University

data_processing:
Raw fastqs were processed using cellranger v3.1.0 (10X Genomics) vs refdata-cellranger-GRCh38-3.0.0
Assembly: Human hg38
Supplementary files format and content: Compressed cellranger outputs comprised of gene expression matrices (_matrix.mtx.gz), barcodes (_barcodes.tsv.gx) and features (_features.tsv.gz)

source_name: EPCAM positive selection

extract_protocol:
Tissue Digestion: Human fetal thymus and lung samples (pcw 16 -18) were mechanically dissected into <2 mm3 pieces using surgical scissors. Human fetal bronchus and esophagus samples (pcw 16 -18) were opened longitudinally and mechanically scraped with scalpel to harvest the inner epithelial layer of bronchus and esophagus, respectively. All tissue samples were enzymatically digested with DNAse (10 mg/ml) and Liberase (2.5 mg/ml, Sigma Aldrich) per 10 g tissue per tube using a tissue dissociator (gentleMACS, C tube, program m_spleen_02 (Miltenyi), 1-3 runs depending on tissue). Tissue fragments were transferred to a 50ml tube and incubate at 37°C for 20 min. Cells were pelleted at 110g, RT for 2 min and resuspended in 10 ml PBS. For persisting fragments, the procedure was repeated 1-2 times to yield single cells.  Cells were resuspended in MACS buffer (PBS, 1 %BSA, 2mM EDTA), filtered through a 100um cell strainer and counted. Epithelial Cell Enrichment: For fetal thymic tissue (16-18 pcw) only, cell suspension was depleted of thymocytes and other immune cells using Human CD45 MicroBeads (Miltenyi) and LD depletion columns (Miltenyi),10e8 cells/column, according to the manufacturer’s instructions. Single cell suspensions of all tissues, (CD45-depleted thymus, bronchus, lung, and esophagus) were enriched for epithelial cells using Human CD326 (EpCAM) Microbeads and LS positive selection columns (Miltenyi) according to the manufacturer’s instructions. Quality control for thymocyte depletion and epithelial cell enrichment for thymic single cell suspensions was performed by flowcytomery on Beckman FACSAria II with CD45-APC, CD3-FITC, CD205-PE, EpCAM-APC, and L/D-NearIR-APC-Cy7 prior to MACS purification. Due to epitope blockage from magnetic bead antibodies, additional markers, i.e. CD7-AF647 (thymocytes) and CD105-PerCP/Cy5.5 (thymic mesenchymal cells) were used to assess post enrichment purity.
Gel-Bead in Emulsions (GEMs) were generated from single cell suspensions using the 3′ V3 chemistry and Chromium microfluidics system (10X Genomics). After reverse transcription, barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was subjected to 0.6x SPRI beads cleanup (Beckman, B23318). 25% of the amplified cDNA was subjected to enzymatic fragmentation, end-repair, A tailing, adaptor ligation and 10X specific sample indexing as per manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) analysis. Libraries were pooled and sequenced on an NovaSeq 6000 instrument (Illumina) using the recommended sequencing read lengths of 28 bp (Read 1), 8 bp (i7 Index Read), and 91 bp (Read 2).

value: Esophagus

value: Female


title: ATAC-seq, AMLE400ug/ml, rep2

description:
Library name: Sample 11
BA4
APP_qdefault_consensus.bed
BA_APP_pooled_default.bw

value: AMLE (400ug/ml)

value: C57BL/6, WT


title: KGW1_TH_EPCAM_45

value: Thymus


title: KGW7_L_EPCAM

value: Lung

value: Male


title: KGW4_B_EPCAM

value: Bronchus


title: MTB20A CD4+CD8- cells, TCR

description:
Library name: MTB20A_Hu_CD3_TCR
10X Genomics

value: PBMC

tag: sample group

value: MTB20A CD4+CD8- cells

tag: library type

value: TCR


title: KGW11_E_EPCAM


title: KGW8_L_EPCAM


title: MTB20C CD4+CD8- cells, HTO

description:
Library name: MTB20C_Hu_CD3_HTO
10X Genomics

tag: cell type

value: MTB20C CD4+CD8- cells

value: HTO

tag: hto


title: MTB20A CD4+CD8- cells, GEX

description:
Library name: MTB20A_Hu_CD3_Gex
10X Genomics

value: mRNA


title: KGW2_TH_EPCAM_45


title: KGW5_B_EPCAM


title: ATAC-seq, DMSO0.04%, rep2

description:
Library name: Sample 8
BA2
DMSO_qdefault_consensus.bed
BA_DMSO_pooled_default.bw

value: BMDCs

tag: age


title: sissb_total_Plus_PNK_1

status: Public on Apr 28 2025

city: Urbana

first: Sihang

last: Zhou

state: IL

address: 601 S Goodwin Ave

institute: University of Illinois Urbana-Champaign

description: Library name: sample16

data_processing:
Small RNA reads were aligned to the hg38 genome using Bowtie2 and bedtools was used to generate read counts.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Kidney

growth_protocol: HEK293T cells were maintained in DMEM supplied with 10% fetal bovine serum (FBS) and 1% Pen-Strep in the cell incubator with 5% CO₂ at 37°C. A549 cells were maintained in F-12K supplied with 10% fetal bovine serum (FBS) and 1% Pen-Strep in the cell incubator with 5% CO₂ at 37°C.

extract_protocol:
Small RNA extraction was performed using mirVana™ PARIS™ RNA and Native Protein Purification Kit according to the manufacturer's instructions.
Small RNA were constructed with the NEBNext Small RNA Sample Prep kit (NEB).

treatment_protocol: For small RNA-seq, HEK293T cells were transfected with si-scramble or si-SSB using RNAimax for 48 hours.

value: Kidney

tag: cell line

value: epithelial

value: siSSB


title: KGW9_L_EPCAM

source_name: EPCAM positive selection, CD45 depletion


title: sissb_nuc_Plus_PNK_3

description: Library name: sample15


title: KGW3_TH_EPCAM_45


title: sissb_total_Plus_PNK_2

description: Library name: sample17


title: sissb_total_Plus_PNK_3

description: Library name: sample18


title: KGW6_B_EPCAM

value: Female


title: sissb_nuc_Plus_PNK_1

description: Library name: sample13


title: sissb_nuc_Plus_PNK_2

description: Library name: sample14


title: sissb_con_nuc_Plus_PNK_3

description: Library name: sample6


title: sissb_cyto_Plus_PNK_1

description: Library name: sample10


title: sissb_con_total_Plus_PNK_1

description: Library name: sample7


title: sissb_con_total_Plus_PNK_2

description: Library name: sample8


title: sissb_con_total_Plus_PNK_3

description: Library name: sample9


title: sissb_con_cyto_Plus_PNK_1

description: Library name: sample1


title: sissb_cyto_Plus_PNK_2

description: Library name: sample11


title: sissb_cyto_Plus_PNK_3

description: Library name: sample12


title: sissb_con_cyto_Plus_PNK_2

description: Library name: sample2


title: sissb_con_nuc_Plus_PNK_1

description: Library name: sample4


title: Brain arteries from Sham7d animal, rep. 1

description:
Gene expression data from Sham7d animals
S1

value: Brain arteries cleaned from connective tissues

value: Wistar

value: six months old

value: under surgical control procedure


title: sissb_con_nuc_Plus_PNK_2

description: Library name: sample5


title: sissb_con_cyto_Plus_PNK_3

description: Library name: sample3


title: IPILUNG074.T1.rna.tcell

city: San Francisco

first: Arja

last: Ray

state: California

address: 513 Parnassus Avenue

department: Pathology

institute: UCSF

description: Library name: Sample 97

data_processing:
RNAseq reads were first aligned to reference of rRNA and mitochondrial rRNA using BWA-mem
The remaining reads were aligned to the Ensembl GRCh38.85 transcriptome build using STAR
Assembly: GRCh38
Supplementary files format and content: TSV of gene TPM per sample

source_name: Lung Tumor

extract_protocol:
The mRNA was isolated via DinaBead Direct, then converted into amplified
The dsDNA went through tagmentation, amplification and clean up with  AMPure XP beads steps, using the Illumina Nextera XT DNA Library Prep Kit. Quality control analysis was performed on the resulting pooled libraries with the Agilent Bioanalyzer HS DNA chip to assess fragment size distribution and concentration

value: Lung Tumor


title: IPIKID070.T1.rna.tcell

description: Library name: Sample 96

source_name: Kidney Tumor

value: Kidney Tumor


title: IPIHNSC024.T1.rna.tcell

description: Library name: Sample 95

source_name: Head and neck squamouse cell carcinoma

value: Head and neck squamouse cell carcinoma


title: IPIBLAD011.T1.rna.tcell

description: Library name: Sample 92

source_name: Bladder Tumor

value: Bladder Tumor


title: IPICRC090.T1.rna.tcell

description: Library name: Sample 93

source_name: Colorectal Tumor

value: Colorectal Tumor


title: IPIGYN108.T1.rna.tcell

description: Library name: Sample 94

source_name: Gynecological Tumor

value: Gynecological Tumor


title: IPIMEL085.T1.rna.tcell.2

description: Library name: Sample 91

source_name: Melanoma

value: Melanoma


title: IPIMEL085.T1.rna.tcell.1

description: Library name: Sample 90


title: IPISRC042.T1.rna.tcell

description: Library name: Sample 89

source_name: Sarcoma

value: Sarcoma


title: IPISRC040.T1.rna.tcell

description: Library name: Sample 88


title: IPISRC038.T1.rna.tcell

description: Library name: Sample 86


title: IPISRC039.T1.rna.tcell

description: Library name: Sample 87


title: IPISRC028.T1.rna.tcell

description: Library name: Sample 82


title: IPISRC029.T1.rna.tcell

description: Library name: Sample 83


title: IPISRC023.T1.rna.tcell

description: Library name: Sample 79


title: IPISRC022.T1.rna.tcell

description: Library name: Sample 78


title: IPISRC026.T1.rna.tcell

description: Library name: Sample 80


title: IPISRC021.T1.rna.tcell

description: Library name: Sample 77


title: IPIMEL141.T1.rna.tcell

description: Library name: Sample 98


title: IPISRC020.T1.rna.tcell

description: Library name: Sample 76


title: IPIPNET022.T1.rna.tcell

description: Library name: Sample 72

source_name: Primitive Neuro-Ectodermal Tumor

value: Primitive Neuro-Ectodermal Tumor


title: IPISRC017.T1.rna.tcell

description: Library name: Sample 75


title: IPISRC016.T1.rna.tcell

description: Library name: Sample 74


title: IPIPNET015.T1.rna.tcell

description: Library name: Sample 70


title: IPIPNET010.T1.rna.tcell

description: Library name: Sample 69


title: IPIPNET007.T1.rna.tcell

description: Library name: Sample 68


title: IPIPNET016.T1.rna.tcell

description: Library name: Sample 71


title: IPIPNET004.T1.rna.tcell

description: Library name: Sample 67


title: IPIPDAC057.T1.rna.tcell

description: Library name: Sample 66

source_name: Pancreatic Ductal Adenocarcinoma

value: Pancreatic Ductal Adenocarcinoma


title: IPIPDAC006.T1.rna.tcell.2

description: Library name: Sample 65


title: IPIPDAC006.T1.rna.tcell.1

description: Library name: Sample 64


title: IPIMEL490.T1.rna.tcell

description: Library name: Sample 63


title: IPISRC032.T1.rna.tcell

description: Library name: Sample 85


title: IPIMEL460.T1.rna.tcell

description: Library name: Sample 62


title: IPIMEL323.T1.rna.tcell

description: Library name: Sample 61


title: IPIMEL180.T1.rna.tcell

description: Library name: Sample 59


title: IPIMEL291.T1.rna.tcell

description: Library name: Sample 60


title: IPISRC030.T1.rna.tcell

description: Library name: Sample 84


title: IPIMEL134.T1.rna.tcell

description: Library name: Sample 57


title: IPILUNG067.T1.rna.tcell

description: Library name: Sample 56


title: IPILUNG045.T1.rna.tcell

description: Library name: Sample 55


title: IPILUNG022.T1.rna.tcell

description: Library name: Sample 53


title: IPILUNG039.T1.rna.tcell

description: Library name: Sample 54


title: IPISI001.T1.rna.tcell

description: Library name: Sample 73

source_name: Small Intestinal Tumor

value: Small Intestinal Tumor


title: IPILUNG019.T1.rna.tcell

description: Library name: Sample 52


title: IPILUNG018.T1.rna.tcell

description: Library name: Sample 51


title: IPIKID043.T1.rna.tcell

description: Library name: Sample 50


title: IPIMEL175.T1.rna.tcell2

description: Library name: Sample 58


title: IPISRC027.T1.rna.tcell

description: Library name: Sample 81


title: IPIHNSC102.T1.rna.tcell

description: Library name: Sample 48


title: IPIHEP038.T1.rna.tcell

description: Library name: Sample 46

source_name: Hepatobiliary Tumor

value: Hepatobiliary Tumor


title: IPIHNSC083.T1.rna.tcell

description: Library name: Sample 47


title: IPIHEP031.T1.rna.tcell

description: Library name: Sample 44


title: IPIHEP032.T1.rna.tcell

description: Library name: Sample 45


title: IPIHEP029.T1.rna.tcell

description: Library name: Sample 42


title: IPIHEP028.T1.rna.tcell

description: Library name: Sample 41


title: IPIHEP024.T1.rna.tcell

description: Library name: Sample 39


title: IPIHEP020.T1.rna.tcell

description: Library name: Sample 37


title: IPIHEP021.T1.rna.tcell

description: Library name: Sample 38


title: IPIHEP012.T1.rna.tcell

description: Library name: Sample 35


title: IPIHEP019.T1.rna.tcell

description: Library name: Sample 36


title: IPIGYN149.T1.rna.tcell

description: Library name: Sample 34


title: IPIHEP025.T1.rna.tcell

description: Library name: Sample 40


title: IPIGYN141.T1.rna.tcell

description: Library name: Sample 33


title: IPIGYN122.T1.rna.tcell

description: Library name: Sample 32


title: IPIGYN115.T1.rna.tcell

description: Library name: Sample 30


title: IPIGYN097.T1.rna.tcell

description: Library name: Sample 29


title: IPIGYN079.T1.rna.tcell

description: Library name: Sample 28


title: IPIGYN117.T1.rna.tcell

description: Library name: Sample 31


title: IPIGYN023.T1.rna.tcell

description: Library name: Sample 27


title: IPIKID042.T1.rna.tcell

description: Library name: Sample 49


title: IPIGYN020.T1.rna.tcell

description: Library name: Sample 25


title: IPIGYN009.T1.rna.tcell

description: Library name: Sample 24


title: IPIGBM032.T1.rna.tcell

description: Library name: Sample 22

source_name: Glioblastoma

value: Glioblastoma


title: IPIGBM026.T1.rna.tcell

description: Library name: Sample 21


title: IPIHEP030.T1.rna.tcell

description: Library name: Sample 43


title: IPIGBM018.T1.rna.tcell

description: Library name: Sample 20


title: IPIGBM013.T1.rna.tcell

description: Library name: Sample 19


title: IPIGBM008.T1.rna.tcell

description: Library name: Sample 17


title: IPIGALL001.T1.rna.tcell

description: Library name: Sample 15

source_name: Gallbladder Tumor

value: Gallbladder Tumor


title: IPICRC119.T1.rna.tcell

description: Library name: Sample 14


title: IPICRC107.T1.rna.tcell

description: Library name: Sample 13


title: IPICRC095.T1.rna.tcell

description: Library name: Sample 11


title: IPICRC086.T1.rna.tcell

description: Library name: Sample 10


title: IPICRC104.T1.rna.tcell

description: Library name: Sample 12


title: IPICRC051.T1.rna.tcell

description: Library name: Sample 9


title: IPICRC037.T1.rna.tcell

description: Library name: Sample 8


title: IPIBLAD015.T1.rna.tcell

description: Library name: Sample 6


title: IPIBLAD005.T1.rna.tcell.2

description: Library name: Sample 4


title: IPIBLAD037.T1.rna.tcell

description: Library name: Sample 7


title: IPIBLAD010.T1.rna.tcell

description: Library name: Sample 5


title: IPIGYN021.T1.rna.tcell

description: Library name: Sample 26


title: IPIGBM036.T1.rna.tcell

description: Library name: Sample 23


title: IPIADR003.T1.rna.tcell

description: Library name: Sample 2

source_name: Adrenal Tumor

value: Adrenal Tumor


title: IPIBLAD005.T1.rna.tcell.1

description: Library name: Sample 3


title: IPIGALL002.T1.rna.tcell

description: Library name: Sample 16


title: eco4

city: ROTTERDAM

first: guige

last: xu

address: Adrianastraat 203

country: Netherlands

institute: Erasmus medical center

description:
Library name: Sample24
Column name in Raw_gene_counts_Matrix-AllSamples.txt: eco4

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

source_name: organoid

extract_protocol:
RNA was harvested using the total RNA purification kit (Promega). 1.0 ug of total RNA was used for the construction of sequencing libraries.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).

value: Intestine

value: enterocyte

value: WT

value: infect group


title: IPIADR001.T1.rna.tcell

description: Library name: Sample 1


title: mco1

description:
Library name: Sample19
Column name in Raw_gene_counts_Matrix-AllSamples.txt: mco1

value: ctrl


title: om3

description:
Library name: Sample17
Column name in Raw_gene_counts_Matrix-AllSamples.txt: om3


title: eco1

description:
Library name: Sample22
Column name in Raw_gene_counts_Matrix-AllSamples.txt: eco1


title: mco2

description:
Library name: Sample20
Column name in Raw_gene_counts_Matrix-AllSamples.txt: mco2


title: eco2

description:
Library name: Sample23
Column name in Raw_gene_counts_Matrix-AllSamples.txt: eco2


title: em4

description:
Library name: Sample15
Column name in Raw_gene_counts_Matrix-AllSamples.txt: em4


title: IPIGBM011.T1.rna.tcell

description: Library name: Sample 18


title: em3

description:
Library name: Sample14
Column name in Raw_gene_counts_Matrix-AllSamples.txt: em3


title: mm3

description:
Library name: Sample12
Column name in Raw_gene_counts_Matrix-AllSamples.txt: mm3


title: mco4

description:
Library name: Sample21
Column name in Raw_gene_counts_Matrix-AllSamples.txt: mco4


title: em2

description:
Library name: Sample13
Column name in Raw_gene_counts_Matrix-AllSamples.txt: em2


title: om2

description:
Library name: Sample16
Column name in Raw_gene_counts_Matrix-AllSamples.txt: om2


title: mm1

description:
Library name: Sample10
Column name in Raw_gene_counts_Matrix-AllSamples.txt: mm1


title: eo3

description:
Library name: Sample6
Column name in Raw_gene_counts_Matrix-AllSamples.txt: eo3


title: oo4

description:
Library name: Sample7
Column name in Raw_gene_counts_Matrix-AllSamples.txt: oo4


title: eo2

description:
Library name: Sample5
Column name in Raw_gene_counts_Matrix-AllSamples.txt: eo2


title: mo2

description:
Library name: Sample2
Column name in Raw_gene_counts_Matrix-AllSamples.txt: mo2


title: eo1

description:
Library name: Sample4
Column name in Raw_gene_counts_Matrix-AllSamples.txt: eo1


title: mo3

description:
Library name: Sample3
Column name in Raw_gene_counts_Matrix-AllSamples.txt: mo3


title: mo1

description:
Library name: Sample1
Column name in Raw_gene_counts_Matrix-AllSamples.txt: mo1


title: F1201

status: Public on Apr 27 2025

city: Tianjin

first: Caiying

last: Zhu

address: Heping District, Nanjing Road, 288

institute: Institute of Hematology and Blood Disease Hospital

description: Library name: Sample 50

data_processing:
Each Library included paired-end sequencing reads, read 1 contained transcripts sequences while read 2 contained cell-specific barcode sequences and unique molecular identifiers(UMIs). Raw reads of each library were first splitted into individual cells based on the unique barcode sequences, then UMIs sequences were aligned to the head of the corresponding read 1.
Contaminant oligonucleotide sequences such as TSO primer, polyA tail, adaptor, and low-quality sequence (N > 10%) presented in the raw reads were then cut out, and reads whose length were less than 30bp were removed using Trimmomatic (version 0.36). Next, Clean reads were aligned to mouse assembly GRCm38 genome (https://www.gencodegenes.org, release (M15)) using HISAT2 (version 2.1.0). Reads shared the same unique molecular identifiers (UMI) were considered amplified from the same transcripts. Hence, we modified a script from HTSeq (version 0.9.1) to removed duplicated transcripts based on UMI sequences and quantified genes abundance.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each single cells.

source_name: Bone marrow and Spleen

extract_protocol:
Bone marrow (BM) cells were flushed from the tibiae, femora, and pelvis. Spleen (SP) cells were ground by the mortar and pestle. BM or SP cells were then stained with anti-c-Kit microbeads (catalog no. 130-091-224, Miltenyi Biotech) and c-Kit+ cells were enriched by columns. These cells were stained with CD201 (eBio1560), CD150 (TC15-12F12.2), CD48 (HM48-1), Sca-1 (D7), c-Kit (2B8), and with a lineage-marker cocktail of B220 (RA3-6B2), Gr-1 (RB6-8C5), TER-119. Cells were sorted by FACSAria III cell sorter (Becton Dickinson, US) according to surface markers or GFP expression under the single-cell sorting mode.
The scRNA-seq libraries were prepared based on a modified Smart-seq2(STRT-seq) protocol. Single cells were sorted into individual tubes of a 0.2 mL 8-strip PCR tube containing lysis buffer by FACS. In addition, the single-cell sorting mode was used for cell sorting with the appropriate side scatter pulse width (SSC-W) and side scatter pulse height (SSC-H) settings to avoid doublets. First-strand cDNAs were synthesized using 25-nucleotide oligo-dT barcoding primer and template switch oligo (TSO) primer. Following reverse transcription, the barcoded cDNAs were amplified via 20 cycles of PCR. Next, the cDNAs of each cell were pooled together and purified twice using 0.8 x Agencount AMPure XP beads. Biotin tag and indexing sequences were introduced by additional 4 cycles of PCR amplification using biotinylated primers. Purified once and sonicated (~300 bp by Covaris M220 system), then the 3' ends of the fragmented cDNA were enriched with Dynabeads Myone streptavidin C1 beads (Invitrogen). Finally, the cDNA libraries were generated using a Kapa Hyper Prep Kit (Kapa Biosystems) and sequenced on Illumina Hiseq X Ten (Novogene) using paired-end mode (2×150 bp).

treatment_protocol: Single HSCs from β-actin-GFP transgenic B6-Ly5.2 mice and 5 × 105 whole bone marrow cells (wBMCs) from B6-Ly5.2 mice were co-transplanted into lethally-irradiated B6-Ly5.2 mice (9.0 Gy)

value: Bone marrow and Spleen

value: Primary cell

value: Transplanted into lethally-irradiated B6-Ly5.2 mice


title: F1216

description: Library name: Sample 49

source_name: Bone marrow

value: Bone marrow


title: om4

description:
Library name: Sample18
Column name in Raw_gene_counts_Matrix-AllSamples.txt: om4


title: F1214

description: Library name: Sample 47


title: F1212

description: Library name: Sample 46


title: F1211

description: Library name: Sample 45


title: F1205

description: Library name: Sample 40


title: F1210

description: Library name: Sample 44


title: F1206

description: Library name: Sample 41


title: mm2

description:
Library name: Sample11
Column name in Raw_gene_counts_Matrix-AllSamples.txt: mm2


title: F1203

description: Library name: Sample 38


title: oo6

description:
Library name: Sample9
Column name in Raw_gene_counts_Matrix-AllSamples.txt: oo6


title: F1207

description: Library name: Sample 42


title: F0440

description: Library name: Sample 33


title: oo5

description:
Library name: Sample8
Column name in Raw_gene_counts_Matrix-AllSamples.txt: oo5


title: F1209

description: Library name: Sample 43


title: F0438

description: Library name: Sample 32


title: F0431

description: Library name: Sample 30


title: F0432

description: Library name: Sample 31


title: F0436

description: Library name: Sample 35


title: F1202

description: Library name: Sample 37


title: F0435

description: Library name: Sample 34


title: F0429

description: Library name: Sample 29


title: F0420

description: Library name: Sample 26


title: F0421

description: Library name: Sample 25


title: F0425

description: Library name: Sample 28


title: F1215

description: Library name: Sample 48


title: F0417

description: Library name: Sample 24


title: F0418

description: Library name: Sample 22


title: F0434

description: Library name: Sample 36


title: F0415

description: Library name: Sample 21


title: F0413

description: Library name: Sample 20


title: F1204

description: Library name: Sample 39


title: F0410

description: Library name: Sample 18


title: F0411

description: Library name: Sample 19


title: F0409

description: Library name: Sample 17


title: F0408

description: Library name: Sample 16


title: F0406

description: Library name: Sample 15


title: F0402

description: Library name: Sample 11


title: F0401

description: Library name: Sample 12


title: F0405

description: Library name: Sample 14


title: F0122

description: Library name: Sample 10


title: F0403

description: Library name: Sample 13


title: F0111

description: Library name: Sample 8


title: NZM40 KO n4

city: Christchurch

first: Carlos

middle: Christopher

last: Smith-Diaz

state: Canterbury

address: 2 Riccarton Avenue, Christchurch Central City

department: Pathology and Biomedical Science

country: New Zealand

institute: University of Otago

data_processing:
Adapters and low-quality reads were removed using Cutadapt (v1.9.1) and mapped to the human genome build hg38 using Hisat2. Raw counts and normalised data were exported from Seqmonk (Babraham Bioinformatics, Cambridge, UK).
Assembly: Homo Sapiens hg38
Supplementary files format and content: Raw Counts

growth_protocol: NZM40 WT and PXDN KO cells were seeded at 700,000 cells in 10 mL of MEM-alpha medium with reduced FBS (0.75%) in a 10 cm cell culture dish for 48 h. After 48h, cells were replenished with fresh 0.75% FBS medium for 5 hours before the medium was fully removed and replaced with 6 mL medium containing 0% FBS. After 22 h cells were washed twice with PBS, buffer was removed thoroughly and cells were harvested by scraping in residual PBS. Cells were snap frozen on dry ice and stored at -80 degrees until RNA extraction. Five biological replicates of each cell line were analysed.

extract_protocol:
RNA was extracted from cell pellets using the NucleoSpin Plus RNA isolation kit (Macherey-Nagel, Düren, Germany). The integrity and concentration of RNA samples was assessed using the TapeStation 2200 system (Agilent, Santa Clara, California)
Library preparation was carried out with the Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: pRP[CRISPR]-Neo-hCas9-U6>mPXDN[grna#22] VB201123-1155uqc vector from VectorBuilder was used to generate a CRISPR-Cas9 NZM40 PXDN KO. 200,000 cells were transfected with the Neon®Transfection system (1600V, 20 ms, 1 pulse) and seeded in antibiotic free medium after 10 min rest. 16 hours later 750 μM geneticin was added for four days to select for transfected cells. 100 units/mL of penicillin and 100 μg/mL of streptomycin were added on day three and geneticin was removed on day five. Cells were washed, tryspinized and 200 cells were seeded in a 15 cm plate. Single clone colonies were picked and expanded. DNA was extracted and 39 CRISPR-Cas9 edited clones were PCR amplified and sequenced (PXDN exon10 forward primer: 5’GTGAGGATGGGGCTGAGCCCTGGCTCTG3’; reverse primer: 5’AGAGGTGCTGGTTGGGGAGAGCGTCACGC3’). Clone 10.34 was selected and PXDN protein expression was investigated using an in-house developed ELISA and by western blotting using an anti-PXDN C-terminal polyclonal rabbit antiserum (1:500 dilution in 2 % skim milk) and a secondary goat anti-rabbit peroxidase antibody (1:10,000) and  enhanced chemiluminescence for visualization.

value: Melanoma

value: NZM40 PXDN KO


title: NZM40 KO n5


title: F0118

description: Library name: Sample 9


title: F0110

description: Library name: Sample 7


title: F0423

description: Library name: Sample 27


title: E0105

description: Library name: Sample 4


title: F0419

description: Library name: Sample 23


title: F0108

description: Library name: Sample 5


title: NZM40 KO n2


title: NZM40 KO n3


title: NZM40 KO n1


title: E0101

description: Library name: Sample 2


title: NZM40 WT n5

value: NZM40 WT


title: NZM40 WT n4


title: NZM40 WT n3


title: E0102

description: Library name: Sample 1


title: NZM40 WT n2


title: NZM40 WT n1


title: HepG2 cells, PFOS, rep 3

status: Public on Apr 25 2025

city: Raleigh

first: Michael

last: Cowley

state: NC

address: 850 Main Campus Dr

department: Biological Sciences

institute: North Carolina State University

description:
Library name: Sample 19
19_L001.txt

data_processing:
Raw reads were processed for quality control, adapter trimming, and data filtering using ‘fastp’ (Chen 2023). 12 poor-quality bases were trimmed from the 5’-end, and the remaining reads were aligned to the mouse or human reference genome (GRCmm39 version 112 and GRCh38 version 112, respectively) from the Ensembl database using ‘STAR’ aligner (Dobin et al. 2013). Genes with uniquely mapped reads were counted using the ‘htseq-count’ function from the HTSeq python package (Anders et al. 2014). The count matrix was imported to the R statistical computing software for further analysis (R Core Team 2023). Genes with fewer than 10 counts in most replicates were removed, and the remaining count data were normalized for depth and distortion. Data dispersion was estimated using the ‘DESeq2’ package and differentially expressed genes (DEGs) were identified after applying multiple testing corrections using the Benjamini-Hochberg procedure with a false discovery rate of q<0.05 (Love et al. 2014; Benjamini and Hochberg 1995). For visualization and overlap of the DEGs and the IGN, Venn diagrams and volcano plots were generated using the ‘BioVenn’ and ‘ggplot2’ R packages, respectively (Hulsen 2021a; Hulsen 2021b; Wickham 2016).
Assembly: Mouse Genome Assembly - GRCmm39 version 112; Human Genome Assembly - GRCh38 version 112. Genomes were downloaded from the Ensembl database.
Supplementary files format and content: "All_counts.csv" file contains raw gene counts for each sample obtained from HTSeq.

growth_protocol: HepG2 cells (ATCC, HB-8065) were grown in high-glucose DMEM (Gibco, 21063045) containing 10% fetal bovine serum (FBS) (Genesee Scientific, 25-514) and 100 U/mL penicillin, 100 µg/mL streptomycin (HyClone, SV30010). Cells were maintained at 37°C in a humidified atmosphere of 5% CO2. HepG2 cells did not exceed 17 passages.

extract_protocol:
Total RNA was extracted from HepG2 cells using the NucleoSpin RNA kit (Macherey-Nagel, 740955) according to the manufacturer’s. 2 μg of total RNA was submitted to the North Carolina State University Genomic Sciences Laboratory (Raleigh, NC, USA) for library construction and sequencing.
Total RNA was assessed for quality using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Chip (Agilent Technologies, USA). Purification of messenger RNA (mRNA) was performed using the oligo-dT beads provided in the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA). Complementary DNA (cDNA) libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) using the manufacturer-specified protocol. Briefly, the mRNA was chemically fragmented and primed with random oligos for first strand cDNA synthesis. Second strand cDNA synthesis was then carried out with dUTPs to preserve strand orientation information. The double-stranded cDNA was purified, end repaired and “a-tailed” for adaptor ligation. Following ligation, samples were selected with a final library size (adapters included) of 350-550 bp using sequential AMPure XP bead isolation (Beckman Coulter, USA). Library enrichment was performed and specific indexes for each sample were added during the protocol-specified PCR amplification. The amplified library fragments were purified and checked for quality and final concentration using an Agilent 2200 Tapestation with a High Sensitivity DNA chip (Agilent Technologies, USA) and a Qubit fluorometer (ThermoFisher, USA). The final quantified libraries were pooled in equimolar amounts for clustering and sequencing on an Illumina NovaSeq 6000 DNA sequencer, utilizing a 150x2 bp paired end sequencing reagent kit (Illumina, USA). The software package Real Time Analysis (RTA) was used to generate raw base call files (bcl), which were then de-multiplexed by sample into fastq files.

treatment_protocol: HepG2 cells were seeded at 20,000 cells per well in 96-well plates for cytotoxicity assays and 600,000 cells per well in 6-well plates for mRNA extraction. Four independent experiments were performed, each with technical triplicates. Cells were serum-starved for 24 hours before toxicant exposure. After 24 hours, the cells were exposed to the following: (1) Water, (2) DMSO, (3) BPA, (4) CdCl2, (5) PFOS, (6) TBTCl, or (7) TCDD. Cells were exposed for 24 hours and collected for downstream analyses. Concentrations were selected based on previously reported cytotoxicity data in the literature as follows: 50 µM, 75 µM, 150 µM, and 300 µM BPA; 0.1 µM, 0.5 µM, 1 µM, and 5 µM CdCl2; 5 µM, 10 µM, 50 µM, and 100 µM PFOS; 0.01 µM, 0.1 µM, 1 µM, and 10 µM TBTCl; and 0.5 nM, 1 nM, 5 nM, 10 nM, 50 nM, 100 nM, 500 nM, and 1000 nM TCDD (Magnifico et al. 2022; Štampar et al. 2023; Urani et al. 2014; Rosenmai et al. 2018; Eriksen et al. 2010; Hoth et al. 2005; Zeng et al. 2018; Silkworth et al. 2005; Tian et al. 2018; Phark et al. 2016). DMSO content did not exceed 0.1% of the total cell culture media volume.

value: hepatocyte

value: PFOS


title: HepG2 cells, PFOS, rep 1

description:
Library name: Sample 17
17_L001.txt


title: HepG2 cells, PFOS, rep 4

description:
Library name: Sample 20
20_L001.txt


title: HepG2 cells, TCDD, rep 4

description:
Library name: Sample 16
16_L001.txt

value: TCDD


title: HepG2 cells, TCDD, rep 3

description:
Library name: Sample 15
15_L001.txt


title: 16363.fastq.gz,GUS2020_256_NN,95843,Liver,Semaglutide_24_w,10090

city: Maaloev

first: Jenny

last: Norlin

state: Denmark

address: Novo Nordisk Park 1

department: Translational Leads Department

country: Denmark

institute: Novo Nordisk

description: Library name: 16363.fastq.gz

data_processing:
Read counts were quantified by salmon v1.2.0, read quality of the data was evaluated using FastQC 0.11.9 and Picard, and the inter- and intra-group variability was evaluated using principal component analysis and hierarchical clustering. Differential gene expression was assessed by the R-package DESeq2.
Assembly: GRCm38 from Ensable data base, using STAR v2.7.3a
Supplementary files format and content: tsv-format, read counts

source_name: liver

extract_protocol:
20 ± 10 mg were taken from the left lateral lobe. RNA was purified using NucleoSpin kit (MACHEREY-NAGEL). Purified RNA (10 ng – 1 µg) from each sample was used to generate a cDNA library using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. The cDNA library was then sequenced on a NextSeq 500 using NextSeq 500/550 High Output Kit V2 (Illumina).
The cDNA library was sequenced on a NextSeq 500 using NextSeq 500/550 High Output Kit V2 (Illumina).

value: liver

value: male


title: HepG2 cells, TCDD, rep 1

description:
Library name: Sample 13
13_L001.txt


title: F0109

description: Library name: Sample 6


title: HepG2 cells, TCDD, rep 2

description:
Library name: Sample 14
14_L001.txt


title: 16362.fastq.gz,GUS2020_256_NN,95771,Liver,Semaglutide_16_w,10090

description: Library name: 16362.fastq.gz


title: 16252.fastq.gz,GUS2020_256_NN,95956,Liver,Semaglutide_24_w,10090

description: Library name: 16252.fastq.gz


title: 16253.fastq.gz,GUS2020_256_NN,95951,Liver,Chow_reversal_24_w,10090

description: Library name: 16253.fastq.gz


title: 16251.fastq.gz,GUS2020_256_NN,95824,Liver,Vehicle_24_w,10090

description: Library name: 16251.fastq.gz


title: E0103

description: Library name: Sample 3


title: 16249.fastq.gz,GUS2020_256_NN,95853,Liver,Semaglutide_16_w,10090

description: Library name: 16249.fastq.gz


title: 16248.fastq.gz,GUS2020_256_NN,95837,Liver,Vehicle_16_w,10090

description: Library name: 16248.fastq.gz


title: 16247.fastq.gz,GUS2020_256_NN,95919,Liver,Chow_reversal_8_w,10090

description: Library name: 16247.fastq.gz


title: 16244.fastq.gz,GUS2020_256_NN,95986,Liver,Chow_Vehicle_24_w,10090

description: Library name: 16244.fastq.gz


title: 16245.fastq.gz,GUS2020_256_NN,95904,Liver,Vehicle_8_w,10090

description: Library name: 16245.fastq.gz


title: 16250.fastq.gz,GUS2020_256_NN,95887,Liver,Chow_reversal_16_w,10090

description: Library name: 16250.fastq.gz


title: 16246.fastq.gz,GUS2020_256_NN,95817,Liver,Semaglutide_8_w,10090

description: Library name: 16246.fastq.gz


title: 16243.fastq.gz,GUS2020_256_NN,95876,Liver,Chow_reversal_24_w,10090

description: Library name: 16243.fastq.gz


title: 16241.fastq.gz,GUS2020_256_NN,95835,Liver,Vehicle_24_w,10090

description: Library name: 16241.fastq.gz


title: 16238.fastq.gz,GUS2020_256_NN,95850,Liver,Vehicle_16_w,10090

description: Library name: 16238.fastq.gz


title: HepG2 cells, PFOS, rep 2

description:
Library name: Sample 18
18_L001.txt


title: 16237.fastq.gz,GUS2020_256_NN,95937,Liver,Chow_reversal_8_w,10090

description: Library name: 16237.fastq.gz


title: 16240.fastq.gz,GUS2020_256_NN,95917,Liver,Chow_reversal_16_w,10090

description: Library name: 16240.fastq.gz


title: 16236.fastq.gz,GUS2020_256_NN,95955,Liver,Semaglutide_8_w,10090

description: Library name: 16236.fastq.gz


title: 16235.fastq.gz,GUS2020_256_NN,95948,Liver,Vehicle_8_w,10090

description: Library name: 16235.fastq.gz


title: 16230.fastq.gz,GUS2020_256_NN,95889,Liver,Chow_reversal_16_w,10090

description: Library name: 16230.fastq.gz


title: 16233.fastq.gz,GUS2020_256_NN,95794,Liver,Chow_reversal_24_w,10090

description: Library name: 16233.fastq.gz


title: 16229.fastq.gz,GUS2020_256_NN,95944,Liver,Semaglutide_16_w,10090

description: Library name: 16229.fastq.gz


title: 16225.fastq.gz,GUS2020_256_NN,95814,Liver,Vehicle_8_w,10090

description: Library name: 16225.fastq.gz


title: 16228.fastq.gz,GUS2020_256_NN,95862,Liver,Vehicle_16_w,10090

description: Library name: 16228.fastq.gz


title: 16232.fastq.gz,GUS2020_256_NN,95766,Liver,Semaglutide_24_w,10090

description: Library name: 16232.fastq.gz


title: 16360.fastq.gz,GUS2020_256_NN,95795,Liver,Semaglutide_16_w,10090

description: Library name: 16360.fastq.gz


title: 16222.fastq.gz,GUS2020_256_NN,95878,Liver,Semaglutide_24_w,10090

description: Library name: 16222.fastq.gz


title: 16223.fastq.gz,GUS2020_256_NN,95894,Liver,Chow_reversal_24_w,10090

description: Library name: 16223.fastq.gz


title: 16227.fastq.gz,GUS2020_256_NN,95786,Liver,Vehicle_8_w,10090

description: Library name: 16227.fastq.gz


title: 16219.fastq.gz,GUS2020_256_NN,95851,Liver,Semaglutide_16_w,10090

description: Library name: 16219.fastq.gz


title: 16224.fastq.gz,GUS2020_256_NN,95990,Liver,Chow_Vehicle_24_w,10090

description: Library name: 16224.fastq.gz


title: 16212.fastq.gz,GUS2020_256_NN,95860,Liver,Semaglutide_24_w,10090

description: Library name: 16212.fastq.gz


title: 16220.fastq.gz,GUS2020_256_NN,95802,Liver,Chow_reversal_16_w,10090

description: Library name: 16220.fastq.gz


title: 16213.fastq.gz,GUS2020_256_NN,95839,Liver,Chow_reversal_24_w,10090

description: Library name: 16213.fastq.gz


title: 16216.fastq.gz,GUS2020_256_NN,95852,Liver,Semaglutide_8_w,10090

description: Library name: 16216.fastq.gz


title: 16214.fastq.gz,GUS2020_256_NN,95987,Liver,Chow_Vehicle_24_w,10090

description: Library name: 16214.fastq.gz


title: 16215.fastq.gz,GUS2020_256_NN,95816,Liver,Vehicle_8_w,10090

description: Library name: 16215.fastq.gz


title: 16217.fastq.gz,GUS2020_256_NN,95958,Liver,Chow_reversal_8_w,10090

description: Library name: 16217.fastq.gz


title: 16221.fastq.gz,GUS2020_256_NN,95870,Liver,Vehicle_24_w,10090

description: Library name: 16221.fastq.gz


title: 16211.fastq.gz,GUS2020_256_NN,95819,Liver,Vehicle_24_w,10090

description: Library name: 16211.fastq.gz


title: 16209.fastq.gz,GUS2020_256_NN,95780,Liver,Semaglutide_16_w,10090

description: Library name: 16209.fastq.gz


title: 16208.fastq.gz,GUS2020_256_NN,95778,Liver,Vehicle_16_w,10090

description: Library name: 16208.fastq.gz


title: 16231.fastq.gz,GUS2020_256_NN,95813,Liver,Vehicle_24_w,10090

description: Library name: 16231.fastq.gz


title: 16206.fastq.gz,GUS2020_256_NN,95831,Liver,Semaglutide_8_w,10090

description: Library name: 16206.fastq.gz


title: 16207.fastq.gz,GUS2020_256_NN,95769,Liver,Chow_reversal_8_w,10090

description: Library name: 16207.fastq.gz


title: 16210.fastq.gz,GUS2020_256_NN,95905,Liver,Chow_reversal_16_w,10090

description: Library name: 16210.fastq.gz


title: 16202.fastq.gz,GUS2020_256_NN,95858,Liver,Semaglutide_24_w,10090

description: Library name: 16202.fastq.gz


title: 16203.fastq.gz,GUS2020_256_NN,95773,Liver,Chow_reversal_24_w,10090

description: Library name: 16203.fastq.gz


title: 16201.fastq.gz,GUS2020_256_NN,95934,Liver,Vehicle_24_w,10090

description: Library name: 16201.fastq.gz


title: 16200.fastq.gz,GUS2020_256_NN,95807,Liver,Chow_reversal_16_w,10090

description: Library name: 16200.fastq.gz


title: 16198.fastq.gz,GUS2020_256_NN,95859,Liver,Vehicle_16_w,10090

description: Library name: 16198.fastq.gz


title: 16197.fastq.gz,GUS2020_256_NN,95891,Liver,Chow_reversal_8_w,10090

description: Library name: 16197.fastq.gz


title: 16218.fastq.gz,GUS2020_256_NN,95861,Liver,Vehicle_16_w,10090

description: Library name: 16218.fastq.gz


title: 16196.fastq.gz,GUS2020_256_NN,95890,Liver,Semaglutide_8_w,10090

description: Library name: 16196.fastq.gz


title: Running-muscle(snRNA-seq)

city: Beijing

first: Wei

last: Tao

address: No.5 Yiheyuan Road

department: School of Life Sciences

institute: Peking University

description: Library name: Running-muscle(snRNA-seq)

data_processing:
For DNBelab C of MGI, the filtered gene expression count matrix was generated using PISA (version 0.12)  aligned to mm10 reference genome. For 10x Genomics, the filtered gene expression count matrix was generated using Cell Ranger (version 6.1.2) aligned to mm10 reference genome
Seurat (version 4.1.1) was used to perform the downstream analysis
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skeletal muscle

extract_protocol:
Fresh mouse skeletal muscle was frozen in liquid nitrogen
snRNA-seq libraries were prepared for sequencing using established protocols of BGI Genomics and 10X Genomics

value: skeletal muscle

tag: group

value: Running

value: slow myonuclei, myotendinous junction, endothelial cell et al.


title: Sedentary-muscle(snRNA-seq)

description: Library name: Sedentary-muscle(snRNA-seq)

value: Sedentary

value: WT


title: Young-muscle(snRNA-seq)

description: Library name: Young-muscle(snRNA-seq)

value: young


title: 16195.fastq.gz,GUS2020_256_NN,95940,Liver,Vehicle_8_w,10090

description: Library name: 16195.fastq.gz


title: 16194.fastq.gz,GUS2020_256_NN,95982,Liver,Chow_Vehicle_24_w,10090

description: Library name: 16194.fastq.gz


title: 16193.fastq.gz,GUS2020_256_NN,95782,Liver,Chow_reversal_24_w,10090

description: Library name: 16193.fastq.gz


title: Aging-muscle(snRNA-seq)

description: Library name: Aging-muscle(snRNA-seq)

value: aging


title: 16188.fastq.gz,GUS2020_256_NN,95804,Liver,Vehicle_16_w,10090

description: Library name: 16188.fastq.gz


title: 16189.fastq.gz,GUS2020_256_NN,95783,Liver,Semaglutide_16_w,10090

description: Library name: 16189.fastq.gz


title: 16192.fastq.gz,GUS2020_256_NN,95926,Liver,Semaglutide_24_w,10090

description: Library name: 16192.fastq.gz


title: 16187.fastq.gz,GUS2020_256_NN,95915,Liver,Chow_reversal_8_w,10090

description: Library name: 16187.fastq.gz


title: 16186.fastq.gz,GUS2020_256_NN,95818,Liver,Semaglutide_8_w,10090

description: Library name: 16186.fastq.gz


title: 16204.fastq.gz,GUS2020_256_NN,95989,Liver,Chow_Vehicle_24_w,10090

description: Library name: 16204.fastq.gz


title: 16184.fastq.gz,GUS2020_256_NN,95988,Liver,Chow_Vehicle_24_w,10090

description: Library name: 16184.fastq.gz


title: 16185.fastq.gz,GUS2020_256_NN,95811,Liver,Vehicle_8_w,10090

description: Library name: 16185.fastq.gz


title: 16181.fastq.gz,GUS2020_256_NN,95929,Liver,Vehicle_24_w,10090

description: Library name: 16181.fastq.gz


title: 16180.fastq.gz,GUS2020_256_NN,95953,Liver,Chow_reversal_16_w,10090

description: Library name: 16180.fastq.gz


title: 16182.fastq.gz,GUS2020_256_NN,95809,Liver,Semaglutide_24_w,10090

description: Library name: 16182.fastq.gz


title: 16183.fastq.gz,GUS2020_256_NN,95933,Liver,Chow_reversal_24_w,10090

description: Library name: 16183.fastq.gz


title: 16179.fastq.gz,GUS2020_256_NN,95856,Liver,Semaglutide_16_w,10090

description: Library name: 16179.fastq.gz


title: 16178.fastq.gz,GUS2020_256_NN,95914,Liver,Vehicle_16_w,10090

description: Library name: 16178.fastq.gz


title: 16176.fastq.gz,GUS2020_256_NN,95924,Liver,Semaglutide_8_w,10090

description: Library name: 16176.fastq.gz


title: 16177.fastq.gz,GUS2020_256_NN,95879,Liver,Chow_reversal_8_w,10090

description: Library name: 16177.fastq.gz


title: 16175.fastq.gz,GUS2020_256_NN,95826,Liver,Vehicle_8_w,10090

description: Library name: 16175.fastq.gz


title: 16174.fastq.gz,GUS2020_256_NN,95981,Liver,Chow_Vehicle_24_w,10090

description: Library name: 16174.fastq.gz


title: Skin, healthy, facial, temporal region, donor 3

status: Public on Apr 23 2025

city: Hamburg

first: Tolga

last: Düz

address: Beiersdorfstraße 1-9

country: Germany

institute: Beiersdorf AG

description: Library name: C02945D2_D3

data_processing:
Barcode mapping, read filtering, read alignment, count matrix generation, as well as image registration and tissue cutting were performed using the SAW pipeline, as outlined in the Stereo-seq paper "Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays".
Assembly: GRCh38.p13
Supplementary files format and content: raw.gef: Feature expression matrix includes the whole information over a complete chip region.
Supplementary files format and content: .tissue.gef: Feature expression matrix under the tissue coverage region
Supplementary files format and content: regist.tif: image after the registration with raw.gef matrix
Supplementary files format and content: merge.barcodeReadsCount.txt: A mapped CID list file with read counts for each CID.
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10µm sections were cut with cryostat.
The generation of Stereo-seq chips, CID sequence calling (short barcode sequence for identifying the location of captured molecules), tissue processing, in situ reverse transcription, amplification, library construction, sequencing, probe and section preparation, hybridization, and staining were all conducted by MIRXES, following the protocols detailed in the Stereo-seq paper "Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays". Single-stranded DNA (ssDNA) staining was performed, and the tissue sections were placed on the chip for fixation and permeabilization.

value: Skin

value: Sebaceous gland

value: Healthy

tag: ethnicity

value: Caucasian

value: Female

tag: reference

tag: parameters

value: Multi-mapped reads parameter was switched on during the count matrix generation step.


title: Skin, healthy, facial, temporal region, donor 2

description: Library name: C02945C6_D2

tag: tissue


title: Skin, healthy, facial, temporal region, donor 1

description: Library name: C02945A1_D1


title: Rep2_WT70h

status: Public on Apr 22 2025

city: Hanover

first: Jay

middle: C

last: Dunlap

state: NH

address: 702 Remsen

department: Molecular and Systems Biology

institute: Geisel School of Medicine at Dartmouth

data_processing:
Conventional basecalls with Sanger / Illumina 1.9 (Rep1) Check if the same for the other Reps
After sequencing, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads.
Ribosomal rRNA was removed with SortMeRNA version 4.3.4
RNA-seq data were mapped to the GRCm38 assembly via STAR version 2.7. with the options --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM to produce bam files with reads aligned to both the transcriptome and the reference.
The RNA-Seq data were quantified using RSEM version 1.3.1 with options --bam --paired-end --forward-prob .5 to produce transcripts-per-million (TPM) counts for each gene from transcriptome alignments
Assembly: Mus_musculus.GRCm38.dna.primary_assembly.fa
Supplementary files format and content: Gene TPM expression files output from RSEM
Supplementary files format and content: Analysis results from rhythmicity calling algorithm ECHO
Supplementary files format and content: Analysis results from rhythmicity calling algorithm ECHO for use in R shiny app

source_name: synchronized mature adipocytes

growth_protocol: Starting at 10 hours post-synchronization, one 35mm dish with fully confluent, synchronized mature adipocytes was removed with two-hour resolution. Cells were gently scraped and lysate was flash-frozen in liquid nitrogen for one minute and stored immediately in -80C freezer. Samples were defrosted once for RNA isolation.

extract_protocol:
Total RNA extracted using Qiagen RNAeasy Tissue Mini Kit
TruSeq Stranded Total RNA library kit with ribo-Depletion

treatment_protocol: No treatments were applied to any samples.

value: inguinal-derived mature adipocytes

tag: strain

value: Homozygous for Per2:Luc


title: Rep2_WT68h


title: 16190.fastq.gz,GUS2020_256_NN,95868,Liver,Chow_reversal_16_w,10090

description: Library name: 16190.fastq.gz

value: liver


title: Rep2_WT66h


title: Rep2_WT64h


title: Rep2_WT60h


title: Rep2_WT58h


title: Rep2_WT54h


title: Rep2_WT52h


title: Rep2_WT50h


title: Rep2_WT48h


title: Rep2_WT46h


title: Rep2_WT44h


title: 16205.fastq.gz,GUS2020_256_NN,95882,Liver,Vehicle_8_w,10090

description: Library name: 16205.fastq.gz

value: male


title: Rep2_WT42h


title: Rep2_WT40h


title: Rep2_WT34h


title: Rep2_WT36h


title: Rep2_WT38h


title: Rep2_WT30h


title: Rep2_WT32h


title: Rep2_WT72h


title: Rep2_WT26h


title: Rep2_WT24h


title: Rep2_WT28h


title: Rep2_WT22h


title: Rep2_WT18h


title: Rep2_WT20h


title: Rep2_WT12h


title: Rep1_WT70h


title: Rep1_WT72h


title: Rep2_WT14h


title: Rep1_WT68h


title: Rep1_WT62h


title: Rep1_WT54h


title: Rep1_WT56h


title: Rep1_WT64h


title: Rep1_WT52h


title: Rep1_WT50h


title: Rep1_WT44h


title: Rep2_WT56h


title: Rep1_WT42h


title: Rep1_WT48h


title: Rep1_WT40h


title: Rep1_WT38h


title: Rep1_WT46h


title: Rep1_WT28h


title: Rep1_WT34h


title: Rep1_WT32h


title: Rep1_WT26h


title: Rep1_WT30h


title: Rep1_WT24h


title: Rep1_WT22h


title: Rep1_WT18h


title: Rep1_WT20h


title: Rep2_WT62h


title: Rep1_WT16h


title: Rep1_WT14h


title: Rep1_WT66h


title: Rep1_WT12h


title: sihnRNPL3

status: Public on Apr 18 2025

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description: Library name: Sample12

data_processing:
Raw reads were assessed for Phred quality scores using the FASTQC program and low bases and adaptor sequences were trimmed off using Fqtrim retaining reads of 76 bp length only.
Processed reads were aligned against the human reference genome (GRCh38.p10) with Gencode v27 annotation (gencode.v27.annotation.gtf.gz) using STAR v2.5.1b. STAR was run in a two-pass mode, allowing an alignment to the transcriptome coordinates by setting the option --quantMode to TranscriptomeSAM.
Gene levels were quantified using RSEM v1.3.0 in defautl settings.
Assembly: GRCh38
Supplementary files format and content: txt file with the gene TPM levels

growth_protocol: The MCF-7 cancer cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Sigma) supplemented with 10% Fetal Bovine Serum (Euroclone) and 1% L-Glutamine 100x 200mM (Euroclone).

extract_protocol:
RNA extraction was performed forty-eight hours after siRNA transfection following the TRIzol™ Reagent protocol (Thermo Fisher Scientific). RNA was quantified using the NanoDrop system. Retrotranscription was performed following the protocol of SuperScript™ IV VILO™ Master Mix (Invitrogen).
The total RNA was processed for RNA-sequencing analysis with the TruSeq Stranded Total RNA gold (Illumina) following the manufacturer’s instruction and sequenced on the NovaSeq6000 (Illumina).

treatment_protocol: MCF-7 cell lines were transiently transfected with siRNA 20nM using the Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific, 13778150).

value: Breast cancer cell

value: siRNA against hnRNPL


title: Rep1_WT58h


title: sihnRNPL1

description: Library name: Sample10


title: ctl_hnRNPL3

description: Library name: Sample9

value: Control


title: ctl_hnRNPL2

description: Library name: Sample8


title: ctl_hnRNPL1

description: Library name: Sample7


title: sicircCDYL3

description: Library name: Sample6

value: siRNA against circCDYL


title: sicircCDYL1

description: Library name: Sample4


title: sicircCDYL2

description: Library name: Sample5


title: Rep1_WT36h


title: ctl_circCDYL2

description: Library name: Sample2


title: copepodid, wild-source, l. salmonis, 8

city: St. Andrews

first: Marc

last: Trudel

state: NB

address: 125 Marine Science Dr

country: Canada

institute: Department of Fisheries and Oceans Canada

description: Library name: CP_W9

data_processing:
FastQC was completed on all raw sequence files for quality control.
Sequences were trimmed using the TruSeq3-PE-2 adapter sequence in Trimmomatic (version 0.39).
Splice-aware mapping was completed using STAR (Spliced Transcripts Alignment to the Reference). Two alignments were made on the sample set. Once for the L. salmonis genome and another for the S. salar genome.
FeatureCount was used to generate raw read counts.
EdgeR and DEseq2 were used to normalize and generate differential expression data.
The RNAseq short variant discovery pipeline from Genome Analysis Toolkit 4 (GATK4) was used to identify SNPs and In/Dels. Filtered using: QD< 2.0, QUAL< 30.0, SOR> 3.0, FS> 60.0, MQ< 40.0, MQRankSum< -12.5 and ReadPosRankSum< -8.0.
Pilot GWAS was completed using PLINK (version 1.9): missingness per individual (0.1), missingness per marker/SNP (0.1), minor allele frequency (0.05) and Hardy-Weinberg equilibrium (1x10-6).
Assembly: LSalAlt2s
Assembly: Ssal_v3.1: GCA_905237065.2
Supplementary files format and content: tab-delimited text file, includes raw counts for all samples. L. salmonis alignment.
Supplementary files format and content: tab-delimited text file, includes raw counts for all samples. S. salar alignment.

organism: Lepeophtheirus salmonis

source_name: whole

growth_protocol: Laboratory cultured L. salmonis: 6 generations. S. salar in flow-through tanks.

extract_protocol:
RNA was extracted using a modified phenol-chloroform method described in (Chomczynski, 1993). Extracted RNA was then treated using TURBO DNase and followed by the RNeasy MinElute Cleanup Kit™ (Qiagen) as per manufacturers instructions prior to submission for RNA sequencing.
Library construction and subsequent sequencing was completed by Genome Quebec.

treatment_protocol: Reduced tank flow and exposed S. salar to L. salmonis for 1 hr at 50 copepodid/fish.

value: whole

value: wild

tag: time


title: Rep2_WT16h


title: ctl_circCDYL3

description: Library name: Sample3


title: ctl_circCDYL1

description: Library name: Sample1


title: copepodid, wild-source, l. salmonis, 5

description: Library name: CP_W6


title: copepodid, wild-source, l. salmonis, 3

description: Library name: CP_W3


title: copepodid, wild-source, l. salmonis, 6

description: Library name: CP_W7


title: copepodid, wild-source, l. salmonis, 4

description: Library name: CP_W4


title: copepodid, wild-source, l. salmonis, 2

description: Library name: CP_W2


title: copepodid, wild-source, l. salmonis, 1

description: Library name: CP_W10


title: copepodid, farm-source, l. salmonis, 8

description: Library name: CP_F5

value: farm


title: copepodid, farm-source, l. salmonis, 6

description: Library name: CP_F22


title: copepodid, farm-source, l. salmonis, 7

description: Library name: CP_F3


title: copepodid, farm-source, l. salmonis, 5

description: Library name: CP_F21


title: copepodid, farm-source, l. salmonis, 3

description: Library name: CP_F19


title: copepodid, farm-source, l. salmonis, 4

description: Library name: CP_F20


title: sihnRNPL2

description: Library name: Sample11


title: copepodid, farm-source, l. salmonis, 1

description: Library name: CP_F17


title: chalimus II, wild-source, l. salmonis, 7

description: Library name: C2_W8


title: copepodid, farm-source, l. salmonis, 2

description: Library name: CP_F18


title: chalimus II, wild-source, l. salmonis, 6

description: Library name: C2_W7


title: chalimus II, wild-source, l. salmonis, 5

description: Library name: C2_W5


title: chalimus II, wild-source, l. salmonis, 4

description: Library name: C2_W4


title: copepodid, wild-source, l. salmonis, 7

description: Library name: CP_W8


title: chalimus II, wild-source, l. salmonis, 2

description: Library name: C2_W1


title: chalimus II, wild-source, l. salmonis, 3

description: Library name: C2_W2


title: chalimus II, farm-source, l. salmonis, 7

description: Library name: C2_F7


title: chalimus II, wild-source, l. salmonis, 1

description: Library name: C2_W10


title: chalimus II, farm-source, l. salmonis, 5

description: Library name: C2_F5


title: chalimus II, farm-source, l. salmonis, 8

description: Library name: C2_F8


title: chalimus II, farm-source, l. salmonis, 6

description: Library name: C2_F6


title: chalimus II, farm-source, l. salmonis, 4

description: Library name: C2_F4


title: adult male, wild-source, l. salmonis, 8

description: Library name: AM_W9


title: adult male, wild-source, l. salmonis, 7

description: Library name: AM_W7


title: adult male, wild-source, l. salmonis, 5

description: Library name: AM_W5


title: adult male, wild-source, l. salmonis, 2

description: Library name: AM_W1


title: adult male, wild-source, l. salmonis, 1

description: Library name: AM_W10


title: adult male, farm-source, l. salmonis, 8

description: Library name: AM_F9


title: adult male, farm-source, l. salmonis, 7

description: Library name: AM_F7


title: chalimus II, farm-source, l. salmonis, 1

description: Library name: C2_F1


title: adult male, wild-source, l. salmonis, 4

description: Library name: AM_W4


title: adult male, farm-source, l. salmonis, 5

description: Library name: AM_F5


title: adult male, wild-source, l. salmonis, 3

description: Library name: AM_W3


title: adult male, farm-source, l. salmonis, 6

description: Library name: AM_F6


title: adult male, farm-source, l. salmonis, 4

description: Library name: AM_F4


title: chalimus II, wild-source, l. salmonis, 8

description: Library name: C2_W9


title: adult male, farm-source, l. salmonis, 2

description: Library name: AM_F2


title: adult female, wild-source,l. salmonis, 8

description: Library name: AF_W9

value: female


title: chalimus II, farm-source, l. salmonis, 3

description: Library name: C2_F3


title: adult female, wild-source,l. salmonis, 7

description: Library name: AF_W8


title: adult female, wild-source,l. salmonis, 6

description: Library name: AF_W7


title: adult female, wild-source,l. salmonis, 4

description: Library name: AF_W4


title: adult female, wild-source,l. salmonis, 5

description: Library name: AF_W6


title: chalimus II, farm-source, l. salmonis, 2

description: Library name: C2_F2


title: adult female, wild-source,l. salmonis, 1

description: Library name: AF_W1


title: adult female, wild-source,l. salmonis, 2

description: Library name: AF_W2


title: adult male, wild-source, l. salmonis, 6

description: Library name: AM_W6


title: adult female, farm-source, l. salmonis, 6

description: Library name: AF_F7


title: adult female, wild-source,l. salmonis, 3

description: Library name: AF_W3


title: adult female, farm-source, l. salmonis, 8

description: Library name: AF_F9


title: adult female, farm-source, l. salmonis, 5

description: Library name: AF_F6


title: adult female, farm-source, l. salmonis, 4

description: Library name: AF_F5


title: adult female, farm-source, l. salmonis, 2

description: Library name: AF_F2


title: adult female, farm-source, l. salmonis, 3

description: Library name: AF_F3


title: adult female, farm-source, l. salmonis, 1

description: Library name: AF_F1


title: adult male, farm-source, l. salmonis, 3

description: Library name: AM_F3


title: adult male, farm-source, l. salmonis, 1

description: Library name: AM_F1


title: Patient 102, 103 PBMCs, CSP

city: Chicago

first: Huiping

last: Liu

address: 303 E Superior St, Room 5-250B

institute: Northwestern University

description:
Library name: WBC_1217_CSP
WBC_1217_barcodes.tsv.gz
WBC_1217_features.tsv.gz
WBC_1217_matrix.mtx.gz

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using CellRanger v4.0.0
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

source_name: PBMCs

extract_protocol:
White blood cells from breast cancer patients or healthy controls were isolated from peripheral blood samples and sorted using FACS
Patient cells were labelled with hashtag barcode oligo and libraries were prepared per manufacturer's instructions. Briefly, cells were loaded onto a 10X Chromium controller, and library was constructed using 10X Chromium Next GEM Single Cell 5' Library and Geal Bead kits (v1.1)

value: PBMCs

tag: disease state

tag: breast cancer_subtype

tag: tumor stage

tag: ctc status

tag: alive


title: Patient 089, 090, 091, 092 PBMCs, CSP

description:
Library name: WBC_1119_CSP
WBC_1119_barcodes.tsv.gz
WBC_1119_features.tsv.gz
WBC_1119_matrix.mtx.gz

value: Healthy

tag: Sex


title: Patient 100, 101 PBMCs, GEX

description:
Library name: WBC_1214_GEX
WBC_1214_barcodes.tsv.gz
WBC_1214_features.tsv.gz
WBC_1214_matrix.mtx.gz

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using CellRanger v4.0.0
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files


title: Patient 074, 075, 076, 077 PBMCs, CSP

description:
Library name: WBC_1102_CSP
WBC_1102_barcodes.tsv.gz
WBC_1102_features.tsv.gz
WBC_1102_matrix.mtx.gz


title: Patient 089, 090, 091, 092 PBMCs, GEX

description:
Library name: WBC_1119_GEX
WBC_1119_barcodes.tsv.gz
WBC_1119_features.tsv.gz
WBC_1119_matrix.mtx.gz


title: Patient 074, 075, 076, 077 PBMCs, GEX

description:
Library name: WBC_1102_GEX
WBC_1102_barcodes.tsv.gz
WBC_1102_features.tsv.gz
WBC_1102_matrix.mtx.gz


title: Patient 102, 103 PBMCs, GEX

description:
Library name: WBC_1217_GEX
WBC_1217_barcodes.tsv.gz
WBC_1217_features.tsv.gz
WBC_1217_matrix.mtx.gz


title: Patient 427, 428, 429, 311 PBMCs biol rep 4, CSP

description:
Library name: WBC_120922X_CSP
WBC_120922X_barcodes.tsv.gz
WBC_120922X_features.tsv.gz
WBC_120922X_matrix.mtx.gz

value: Cancer

tag: race

value: NA, White, White, White

value: TNBC, LumA, LumB, LumA


title: Patient 427, 428, 429, 311 PBMCs biol rep 4, GEX

description:
Library name: WBC_120922X_GEX
WBC_120922X_barcodes.tsv.gz
WBC_120922X_features.tsv.gz
WBC_120922X_matrix.mtx.gz

value: Female


title: Patient 427, 428, 429, 311 PBMCs biol rep 2, GEX

description:
Library name: WBC_120922B_GEX
WBC_120922B_barcodes.tsv.gz
WBC_120922B_features.tsv.gz
WBC_120922B_matrix.mtx.gz


title: Patient 427, 428, 429, 311 PBMCs biol rep 3, CSP

description:
Library name: WBC_120922C_CSP
WBC_120922C_barcodes.tsv.gz
WBC_120922C_features.tsv.gz
WBC_120922C_matrix.mtx.gz


title: Patient 427, 428, 429, 311 PBMCs biol rep 2, CSP

description:
Library name: WBC_120922B_CSP
WBC_120922B_barcodes.tsv.gz
WBC_120922B_features.tsv.gz
WBC_120922B_matrix.mtx.gz


title: adult female, farm-source, l. salmonis, 7

description: Library name: AF_F8

tag: treatment


title: Patient 0621 PBMCs, GSP

description:
Library name: WBC_062123_CSP
WBC_062123_barcodes.tsv.gz
WBC_062123_features.tsv.gz
WBC_062123_matrix.mtx.gz

tag: age


title: Patient 427, 428, 429, 311 PBMCs biol rep 3, GEX

description:
Library name: WBC_120922C_GEX
WBC_120922C_barcodes.tsv.gz
WBC_120922C_features.tsv.gz
WBC_120922C_matrix.mtx.gz


title: Patient 0210, 371, CA1, CA2, CA3 PBMCs, CSP

description:
Library name: WBC_0212_CSP
WBC_0212_barcodes.tsv.gz
WBC_0212_features.tsv.gz
WBC_0212_matrix.mtx.gz

value: NA, NA, White, White, NA

value: NA, TNBC, HER2, LumA, NA


title: Patient 0621 PBMCs, GEX

description:
Library name: WBC_062123_GEX
WBC_062123_barcodes.tsv.gz
WBC_062123_features.tsv.gz
WBC_062123_matrix.mtx.gz


title: Patient 427, 428, 429, 311 PBMCs biol rep 1, GEX

description:
Library name: WBC_120922A_GEX
WBC_120922A_barcodes.tsv.gz
WBC_120922A_features.tsv.gz
WBC_120922A_matrix.mtx.gz


title: Patient 420 PBMCs, CSP

description:
Library name: WBC_050523_CSP
WBC_050523_barcodes.tsv.gz
WBC_050523_features.tsv.gz
WBC_050523_matrix.mtx.gz

value: White

value: LumB


title: Patient 0210, 371, CA1, CA2, CA3 PBMCs, GEX

description:
Library name: WBC_0212_GEX
WBC_0212_barcodes.tsv.gz
WBC_0212_features.tsv.gz
WBC_0212_matrix.mtx.gz


title: Patient 300 PBMCs

description:
Library name: WBC_0702
WBC_0702_barcodes.tsv.gz
WBC_0702_features.tsv.gz
WBC_0702_matrix.mtx.gz


title: Patient 0716b PBMCs, CSP

description:
Library name: WBC_0716B_CSP
WBC_071621B_barcodes.tsv.gz
WBC_071621B_features.tsv.gz
WBC_071621B_matrix.mtx.gz

value: TNBC


title: Patient 100, 101 PBMCs, CSP

description:
Library name: WBC_1214_CSP
WBC_1214_barcodes.tsv.gz
WBC_1214_features.tsv.gz
WBC_1214_matrix.mtx.gz


title: Patient 301, 302, 303, 304, 47 PBMCs, CSP

description:
Library name: WBC_0709_CSP
WBC_0709_barcodes.tsv.gz
WBC_0709_features.tsv.gz
WBC_0709_matrix.mtx.gz

value: White, White, White, White, Black

value: LumA, LumB, LumA, HER2, LumB


title: Patient 433 PBMCs, CSP

description:
Library name: WBC_021023_CSP
WBC_021023_barcodes.tsv.gz
WBC_021023_features.tsv.gz
WBC_021023_matrix.mtx.gz

value: Asian


title: Patient 433 PBMCs, GEX

description:
Library name: WBC_021023_GEX
WBC_021023_barcodes.tsv.gz
WBC_021023_features.tsv.gz
WBC_021023_matrix.mtx.gz


title: Patient 301, 302, 303, 304, 47 PBMCs, GEX

description:
Library name: WBC_0709_GEX
WBC_0709_barcodes.tsv.gz
WBC_0709_features.tsv.gz
WBC_0709_matrix.mtx.gz


title: Patients 407, 436, 437 PBMCs, CSP

description:
Library name: WBC_032423_CGP
WBC_032423_barcodes.tsv.gz
WBC_032423_features.tsv.gz
WBC_032423_matrix.mtx.gz

value: White, Black, Black

value: LumB, TNBC, LumB


title: Patient 427, 428, 429, 311 PBMCs biol rep 1, CSP

description:
Library name: WBC_120922A_CSP
WBC_120922A_barcodes.tsv.gz
WBC_120922A_features.tsv.gz
WBC_120922A_matrix.mtx.gz


title: skin, farm-source, time 2, s. salar, 5

description: Library name: Sk2_F5

organism: Salmo salar

source_name: skin

value: skin

value: farm


title: skin, farm-source, time 2, s. salar, 6

description: Library name: Sk2_F6


title: skin, wild-source, time 2, s. salar, 5

description: Library name: Sk2_W5

value: wild


title: gill, wild-source, time 2, s. salar, 5

description: Library name: g2_W5

source_name: gill

value: gill


title: skin, wild-source, time 2, s. salar, 1

description: Library name: Sk2_W1


title: skin, farm-source, time 2, s. salar, 3

description: Library name: Sk2_F3


title: skin, wild-source, time 2, s. salar, 6

description: Library name: Sk2_W6


title: skin, wild-source, time 2, s. salar, 2

description: Library name: Sk2_W2


title: Patients 426, 427, 429, 432 PBMCs, GEX

description:
Library name: WBC_020823_GEX
WBC_020823_barcodes.tsv.gz
WBC_020823_features.tsv.gz
WBC_020823_matrix.mtx.gz

value: PBMCs

value: Cancer

value: White, NA, White, Black

value: TNBC, TNBC, LumB, TNBC


title: Patients 426, 427, 429, 432 PBMCs, CSP

description:
Library name: WBC_020823_CSP
WBC_020823_barcodes.tsv.gz
WBC_020823_features.tsv.gz
WBC_020823_matrix.mtx.gz

value: Female


title: Patients 407, 436, 437 PBMCs, GEX

description:
Library name: WBC_032423_GEX
WBC_032423_barcodes.tsv.gz
WBC_032423_features.tsv.gz
WBC_032423_matrix.mtx.gz


title: skin, farm-source, time 2, s. salar, 2

description: Library name: Sk2_F2


title: gill, wild-source, time 2, s. salar, 2

description: Library name: g2_W2


title: gill, wild-source, time 2, s. salar, 6

description: Library name: g2_W6


title: Patient 420 PBMCs, GEX

description:
Library name: WBC_050523_GEX
WBC_050523_barcodes.tsv.gz
WBC_050523_features.tsv.gz
WBC_050523_matrix.mtx.gz

value: White


title: skin, farm-source, time 2, s. salar, 1

description: Library name: Sk2_F1


title: skin, wild-source, time 2, s. salar, 3

description: Library name: Sk2_W3


title: skin, farm-source, time 2, s. salar, 4

description: Library name: Sk2_F4


title: gill, farm-source, time 2, s. salar, 6

description: Library name: g2_F7