title: Leucocyte-MV4-11(sorted from co-cultre),bio rep2

city: Kunming

first: ZHENFEI

last: ZHONG

state: Yunnan

address: East Outer Ring Road,Chenggong District

institute: Institute of Biomedical Research, Yunnan University

description: Library name: Leucocyte(co-cultred) replicate2

data_processing:
Raw sequences were first quality-checked by FastQC v0.12.1 and MultiQC v1.16.
Sequences passed quality check were then aligned to the genome reference (hg38) by STAR v2.7.9a (parameter- outSAMtype: BAM SortedByCoordinate; quantmode TranscriptomeSAM GeneCounts)
The gene expression levels were estimated by rsem-calculate-exprssion of RSEM v1.3.1
The expression results were further analyzed by DESeq2 package(v1.30.1) in R.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene raw counts generated by RSEM for each sample.
Supplementary files format and content: Other tab-delimited text files contain combined raw counts for different samples.

source_name: cell line

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen) following manufacturer’s protocols. 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (Vazyme) following manufacturer’s protocols.

value: cell line

value: AML cell line


title: SMG10_T

status: Public on Mar 04 2026

type: SRA

city: Beijing

first: Zhigang

last: Cai

address: No.22 Zhongguancun South Avenue, Haidian Disrict

country: China

institute: Peking University

description: Library name: Sample 10

library_source: transcriptomic

data_processing:
featureCounts v 2.0.6
Assembly: GRCh38
Supplementary files format and content: tab-delimited format includes fpkm counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Human Submandibular gland Tissue

extract_protocol:
RNA was extacted from TRNzol Universal Reagent (DP424).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

tag: tissue

value: Human Submandibular gland Tissue


title: Female Baseline CSF Sample

city: NEW ORLEANS

first: Vahideh

last: Tarhriz

state: LA

address: Perdido,

department: Cardiovascular Research Center of Excellence

country: USA

institute: Louisiana State University Health Science Center

description:
Library name: FB-CSF
CSF-derived exosomal RNA from female baseline mouse

data_processing:
Reads with short or missing UMIs filtered using Perl5 v26. Reads were aligned to miRBase, piRNABank, and Rfam using Bowtie v1.3.0. UMI counts were summarized and normalized using edgeR and converted to CPM (Counts per million). Expression matrices were created for differential expression, PCA, and GO/KEGG pathway analysis using R clusterProfiler. Mouse genome: mm10 (GRCm38) was used for alignment and annotation. The processed data includes expression matrices in .xlsx/.txt format, including CPM and log2-transformed counts for miRNAs, piRNAs, and other ncRNAs.
Assembly: Differential expression results and pathway enrichment results provided in Excel format (.xlsx), grouped by condition (e.g., FD vs FB, MD vs MB).
Supplementary files format and content: Raw-data.xlsx

organism: Mus musculus

source_name: CSF

growth_protocol: Not applicable – exosomes were isolated from adult mouse plasma and CSF (not cultured).

extract_protocol:
Total RNA was extracted using the Qiagen miRNeasy Micro Kit according to the manufacturer’s instructions.
Libraries were prepared using the QIAseq miRNA Library Kit with UMIs for unique molecular tagging, avoiding PCR duplication. Adapters and low-quality reads removed using Cutadapt v2.7.

treatment_protocol: DOCA-salt treatment was applied to hypertensive groups; baseline mice received no treatment.

value: CSF

tag: Sex

value: Female

tag: genotype

value: Wild-type

tag: treatment

value: Baseline

tag: batch


title: Leucocyte-MV4-11(sorted from co-cultre),bio rep3

description: Library name: Leucocyte(co-cultred) replicate3

tag: cell line

tag: cell type


title: Female DOCA+Salt CSF Sample

description:
Library name: FD-CSF
CSF-derived exosomal RNA from female DOCA+Salt mouse

value: DOCA+Salt


title: Leucocyte-MV4-11(sorted from co-cultre),bio rep1

description: Library name: Leucocyte(co-cultred) replicate1


title: 2WTCT4,rep1

city: Suzhou

first: Tao

last: Zhang

state: Jiangsu

address: No.28 Kehua Road

institute: Suzhou Vocational Health College

description: Library name: Sample4

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1)
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and RPKM values for each Sample

source_name: HEK 293T

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with high glucose, supplemented with 10% fetal bovine serum (FBS), 50 U/mL penicillin, and 50 mg/mL streptomycin, and maintained at 37 °C in 5% CO₂.

extract_protocol:
RNA was harvested using Magzol Reagent (Magen，R4801-02). 1.4ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS mRNA Capture Beads（N401）+ VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605-02 following manufacturer's protocols.

treatment_protocol: For synchronization, cells were plated in 6-well plates and treated with 200 nM dexamethasone (DEX, Sigma-Aldrich, MO, USA) in PBS for 0.5 hours.

value: HEK 293T

value: human embryonic kidney (HEK) derived cell line

value: Wildtype

value: dexamethasone shock for 30 minutes


title: HUVEC, Senescence, 2

city: Shanghai

first: xuelian

last: wang

address: Ruijin er road No.197

institute: Ruijin hospital

description: Library name: S -2

data_processing:
Reads were aligned to the human genome, and gene expression levels were quantified. Differential expression analysis was performed using the DESeq2 R package with an FDR threshold of < 0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values

source_name: umbilical vein

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (Invitrogen) according to standard protocols.
Poly(A) RNA was selected from 1 μg total RNA and libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following the manufacturer’s instructions.

value: umbilical vein

value: HUVEC

value: endothelial cell

value: wild-type

value: S


title: Leucocyte-MV4-11, control, bio rep3

description: Library name: Leucocyte(control) replicate3

value: cell line


title: SMG10_O

description: Library name: Sample 9

source_name: Human Submandibular gland Organoids

value: Human Submandibular gland Organoids


title: Male DOCA+Salt Plasma Sample

description:
Library name: MD-Plasma
Plasma-derived exosomal RNA from male DOCA+Salt mouse

source_name: Plasma

value: Plasma

value: Male


title: Male Baseline Plasma Sample

description:
Library name: MB-Plasma
Plasma-derived exosomal RNA from male baseline mouse


title: 2WTCT0,rep1

description: Library name: Sample1


title: Leucocyte-MV4-11, control, bio rep1

description: Library name: Leucocyte(control) replicate1

value: AML cell line


title: SMG4_T

description: Library name: Sample 8

value: Human Submandibular gland Tissue


title: Non-infected_rep_2

city: Paris

first: Olivier

last: Espeli

address: 11 place Marcelin Berthelot

department: CIRB

country: France

institute: College de France

description:
Library name: CP203-001T0012
THP-1–derived macrophages non-infected for 24 h (biological replicate 2). Column names in processed data files: R2THP1 = Non-infected_rep_2

data_processing:
Raw reads in FASTQ format were processed by BMKGene. Adapter sequences and low-quality bases were removed using Trimmomatic. Clean reads were aligned to the human reference genome (GRCh38) using HISAT2. Transcript abundance was quantified with featureCounts, and expression levels were normalized as FPKM values. Differential expression analysis between conditions was performed using DESeq2.
Assembly: Homo_sapiens.GRCh38_release95.genome.fa.
Supplementary files format and content: Table S3.xlsx – Mapping statistics - gene-level counts matrix (tab-delimited) with the first column as gene ID and subsequent columns corresponding to each sample; All_gene_fpkm – normalized expression values (FPKM) matrix with the first column as gene ID and subsequent columns for each sample. - DEG number statistics -  All DEG –  DEG for each strain compared to Non Infected macrophages (NI) with annotations

growth_protocol: THP-1 (ATCC TIB-202) monocytes at 4.75×10^5 cells/mL were differentiated into macrophages using phorbol 12-myristate 13-acetate (PMA, 20 ng/mL; Sigma-Aldrich, P1585) and cultured at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted from infected THP-1–derived macrophages using TRIzol reagent (Invitrogen, 15596018) followed by chloroform phase separation. The RNA was treated with DNase I (Sigma, AMPD1-1KT) to remove genomic DNA contamination. RNA integrity and purity were assessed prior to library preparation.
Library preparation and sequencing were performed by BMKGene. Total RNA was enriched for mRNA using oligo(dT)-attached magnetic beads and fragmented. First- and second-strand cDNA synthesis was performed using random hexamer priming, followed by purification with AMPure XP beads. Double-stranded cDNA was end-repaired, adenylated, and ligated to sequencing adapters. Size-selected fragments (300–400 bp) were PCR-amplified to generate the final libraries. Library quality was assessed using Qubit 2.0 and Agilent 2100 Bioanalyzer. Sequencing was performed on an Illumina NovaSeq 6000 platform in paired-end 150 bp (PE150) mode by BMKGene.

treatment_protocol: Macrophages were infected with AIEC strains at MOI 100 using 120 µL of bacterial culture at OD600 = 0.5. Cells were centrifuged for 10 min at 900 rpm to promote phagocytosis and incubated for 10 min at 37°C, 5% CO2.

value: THP1 derived macrophage

value: wildtype THP1

value: uninfected control

value: Batch 1


title: Female DOCA+Salt Plasma Sample

description:
Library name: FD-Plasma
Plasma-derived exosomal RNA from female DOCA+Salt mouse

value: Female

value: Wild-type

value: DOCA+Salt


title: SMG4_O

description: Library name: Sample 7


title: 2WTCT0,rep2

description: Library name: Sample2

value: HEK 293T

value: human embryonic kidney (HEK) derived cell line

value: Wildtype

value: dexamethasone shock for 30 minutes


title: Leucocyte-MV4-11, control, bio rep2

description: Library name: Leucocyte(control) replicate2

value: cell line


title: ACC22_T

description: Library name: Sample 6

source_name: Human ACC Tissue

value: Human ACC Tissue


title: Female Baseline Plasma Sample

description:
Library name: FB-Plasma
Plasma-derived exosomal RNA from female baseline mouse

value: Plasma

value: Baseline


title: ACC22_O

description: Library name: Sample 5

source_name: Human ACC Organoids

value: Human ACC Organoids


title: CEA106S_rep_2

description:
Library name: CP203-001T0010
THP-1–derived macrophages infected with AIEC strain CEA106S for 24 h (biological replicate 2). Column names in processed data files: R2C106S = CEA106S_rep_2

value: AIEC strain CEA106S infection


title: csHSP90B1 CAR NK92(sorted from co-cultre),bio rep1

description: Library name: CAR(co-cultred) replicate1

value: csHSP90B1 CAR NK92


title: Non-infected_rep_1

description:
Library name: CP203-001T0011
THP-1–derived macrophages non-infected for 24 h (biological replicate 1). Column names in processed data files: R1THP1 = Non-infected_rep_1

value: THP1 derived macrophage

value: wildtype THP1


title: csHSP90B1 CAR NK92(sorted from co-cultre),bio rep2

description: Library name: CAR(co-cultred) replicate2


title: csHSP90B1 CAR NK92, control, bio rep3

description: Library name: CAR(control) replicate3


title: ACC4_T

description: Library name: Sample 2


title: CEA212U_rep_2

description:
Library name: CP203-001T0008
THP-1–derived macrophages infected with AIEC strain CEA212U for 24 h (biological replicate 2). Column names in processed data files: R2C212U = CEA212U_rep_2

value: AIEC strain CEA212U infection

value: Batch 1


title: csHSP90B1 CAR NK92(sorted from co-cultre),bio rep3

description: Library name: CAR(co-cultred) replicate3


title: 01_ZS761_HNF4a (ChIP)

city: Houston

first: Jeanine

middle: L

last: Van Nostrand

state: TX

address: One Baylor Plaza M502C Van Nostrand

department: Molecular and Cellular Biology

institute: Baylor College of Medicine, Houston

description: Library name: 01_ZS761_HNF4a

library_source: genomic

data_processing:
Trim adapters from sequencing reads (TrimGalore!); Run quality control of raw sequencing reads (fastqc);
Align reads on reference genome (BWA); Sort aligned reads (Samtools); Mark duplicates (Picard);
Filtering aligned BAM files (SAMTools & BAMTools) (reads mapped to blacklisted regions, reads marked as duplicates, reads that aren’t marked as primary alignments, reads that are unmapped, reads mapped with a low mapping quality (multiple hits, secondary alignments, etc.);
Computing Normalized and Relative Strand Cross-correlation (NSC/RSC) (phantompeakqualtools); Diverse alignment QCs and bigWig file creation (CPM-normalized) (deepTools);
Peak calling for sharp, broad peaks (MACS2) and very broad peaks (epic2); Feature counting for every sample at gene and transcription start sites loci (deepTools); Peak annotation and motif QC (HOMER); Creation of Tag Directories (HOMER); Consensus Peak Analysis (Custom); Generation of antibody specific UCSC Track Hubs (Custom)
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Liver

extract_protocol:
Lysis Buffer - Active Motif
PrepX DNA Library Kit (Takara Bio) or NEB DNA Library Prep Kit

treatment_protocol: High Fat Diet containing doxycycline for 14 days

value: Liver

tag: antibody

value: AMPKCA

value: High Fat Diet 14 days


title: 01_ZS762_HNF4a (ChIP)

description: Library name: 01_ZS762_HNF4a


title: ACC10_T

description: Library name: Sample 4


title: csHSP90B1 CAR NK92, control, bio rep1

description: Library name: CAR(control) replicate1


title: 02_ZS764_HNF4a (ChIP)

description: Library name: 02_ZS764_HNF4a


title: CEA601S_rep_2

description:
Library name: CP203-001T0006
THP-1–derived macrophages infected with AIEC strain CEA601S for 24 h (biological replicate 2). Column names in processed data files: R2C601S = CEA601S_rep_2

value: AIEC strain CEA601S infection


title: CEA106S_rep_1

description:
Library name: CP203-001T0009
THP-1–derived macrophages infected with AIEC strain CEA106S for 24 h (biological replicate 1). Column names in processed data files: R1C106S = CEA106S_rep_1


title: CEA601S_rep_1

description:
Library name: CP203-001T0005
THP-1–derived macrophages infected with AIEC strain CEA601S for 24 h (biological replicate 1). Column names in processed data files: R1C601S = CEA601S_rep_1


title: CEA212U_rep_1

description:
Library name: CP203-001T0007
THP-1–derived macrophages infected with AIEC strain CEA212U for 24 h (biological replicate 1). Column names in processed data files: R1C212U = CEA212U_rep_1


title: 01_ZS767_HNF4a (ChIP)

description: Library name: 01_ZS767_HNF4a

value: Wildtype


title: ctrl Skin fibroblasts + supernatants of macrophages NETs IgA-4

city: Bethesda

first: Kan

last: Jiang

state: MD

address: 9000 Rockville Pike

institute: NIAMS/NIH

description: Library name: SUP_NETs_IgA_rep4

data_processing:
Raw sequencing data were processed using bcl2fastq/2.20.0 to generate FastQ files. Reads were aligned to the human genome (hg38) using STAR/2.7.8a, and gene expression values (FPKM) were quantified using Partek E/M annotation model in Partek Flow.
Assembly: hg38
Supplementary files format and content: Excel files include FPKM values for each samples

source_name: primary cells

growth_protocol: CD14+ were isolated from peripheral blood of control donor using Miltenyi column, cells were differentiated into M2 like macrophages for 7 days with M-CSF. Control skin fibroblasts were maintained in DMEM supplemented with 10% FBS, 1%L-Glutamine and 1% Pen Strep

extract_protocol:
RNA was siolated using Zymo RNA kit
RNA QC was performed via high sensitivity RNA screen-tape (Agilent). All samples had RNA with RIN > 7.6, with exception of sample (M2 + HS IgA-3) which had a RIN nubmer of 6.2. An input of 100ng was used from each sample. Libraries were generated using poly-A selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB#E7490) followed by using NEBNext Ultra II  RNA Library Prep Kit for Illumina (NEB#7770). 12 cycles of PCR was used during PCR enrichment. Library QC was performed using a high sensitivity D1000 screen-tape (Agilent) and libraries were quantified via picogreen. Libraries were diluted to 3nM in 0.1 TE before further diluting for sequencing.

treatment_protocol: M2 macrophages were incubated for 24 hours with equal amounts of IgA isolated from skin tissue. In parallel, control skin fibroblasts were treated at 37 °C for 24 hours with either 50 µg of NETs or purified NETs in the presence of IgA isolated from HS skin. Or, fibroblasts were incubated with 10% supernatant collected from macrophages previously exposed for 24 hours to either macrophage NETs or NETs + IgA

value: primary cells

value: Healthy Skin fibroblasts

value: WT

value: sup HS-IgA-4


title: 02_ZS763_HNF4a (ChIP)

description: Library name: 02_ZS763_HNF4a


title: csHSP90B1 CAR NK92, control, bio rep2

description: Library name: CAR(control) replicate2

value: cell line


title: HEK293-T, DMSO treated, bio rep3

description: Library name: DMSO control replicate3

value: DMSO


title: 00_Pooled_Input

description: Library name: 00_Pooled_Input


title: CEA224S_rep_2

description:
Library name: CP203-001T0004
THP-1–derived macrophages infected with AIEC strain CEA224S for 24 h (biological replicate 2). Column names in processed data files: R2C224S = CEA224S_rep_2

value: AIEC strain CEA224S infection


title: HEK293-T, DMSO treated, bio rep1

description: Library name: DMSO control replicate1


title: HEK293-T, DMSO treated, bio rep2

description: Library name: DMSO control replicate2


title: CEA224S_rep_1

description:
Library name: CP203-001T0003
THP-1–derived macrophages infected with AIEC strain CEA224S for 24 h (biological replicate 1). Column names in processed data files: R1C224S = CEA224S_rep_1


title: ctrl Skin fibroblasts + supernatants of macrophages NETs IgA-3

description: Library name: SUP_NETs_IgA_rep3

value: sup HS-IgA-3


title: 02_ZS766_HNF4a (ChIP)

description: Library name: 02_ZS766_HNF4a


title: ACC4_O

description: Library name: Sample 1

value: Human ACC Organoids


title: ctrl Skin fibroblasts + supernatants of macrophages NETs IgA-2

description: Library name: SUP_NETs_IgA_rep2

value: sup HS-IgA-2


title: TSC_m6A_IP_rep_2

city: Bangalore

first: SRIMONTA

last: GAYEN

state: Karnataka

address: GE14, new biological science building, Indian institute of Science

department: Department of Developmental biology and Genetics

country: India

institute: Indian Institute of Science, Bangalore, India

description:
Library name: Sample 5
TSC_ip.bw

data_processing:
Quality of sequenced rawdata were assessed by FastQC(v0.12.1)
Reads were trimmed for adapters using Trim_galore (v0.6.10)
Ribosomal reads were removed by ribodetector(v0.2.7)
Reads were mapped to mouse reference genome GRCm39 using STAR(v2.7.10a)
Peaks were called using MACS2(v 2.2.9.1) with paramters: --nomodel, --keep-dup-all, -g 2654621783 and statistical significance cutoff q 0.05 value.
Assembly: mm39
Supplementary files format and content: bigwig(IP samples)

source_name: TSC

growth_protocol: All cell cultures were maintained in humidified atmosphere with 5% CO2 at 37ºC. XEN cells were cultured in DMEM supplemented with 10% FBS. EpiSCS were cultured in knock out DMEM supplemented with 20% knock out serum replacement, Fgf2 and Activin A. TSCs were cultured in MEF conditioned RPMI supplemented with 20% FBS, Fgf4 and sodium pyruvate. To all the culture conditions L-glutamine, Penstrep and NEAA were also added.

extract_protocol:
Total RNA was isolated using TRIzol reagent and resuspended in ultrapure water.
MeRIP-seq libraries were constructed using NEB Next Ultra II Directional RNA library kit(NEB, E7765)

value: TSC

value: Trophoectoderm stem cell

tag: strain

value: Hybrid(Mus molossinus X Mus musculus)


title: ctrl Skin fibroblasts + supernatants of macrophages NETs IgA-1

description: Library name: SUP_NETs_IgA_rep1

value: sup HS-IgA-1


title: LF82_rep_2

description:
Library name: CP203-001T0002
THP-1–derived macrophages infected with AIEC strain LF82 for 24 h (biological replicate 2). Column names in processed data files: R2LF82 = LF82_rep_2

value: THP1 derived macrophage

value: wildtype THP1

value: AIEC strain LF82 infection

value: Batch 1


title: TSC_m6A_IP_rep_1

description:
Library name: Sample 4
TSC_ip.bw


title: HEK293-T, Thap treated, bio rep1

description: Library name: Thap treated control replicate1

value: Thap


title: EpiSC_m6A_IP_rep_2

description:
Library name: Sample 3
EpiSC_ip.bw

source_name: EpiSC

value: EpiSC

value: Epiblast stem cell

value: XmolXmus-<delta>Tsix


title: LF82_rep_1

description:
Library name: CP203-001T0001
THP-1–derived macrophages infected with AIEC strain LF82 for 24 h (biological replicate 1). Column names in processed data files: R1LF82 = LF82_rep_1


title: HEK293-T, Thap treated, bio rep2

description: Library name: Thap treated control replicate2

value: cell line


title: HEK293-T, Thap treated, bio rep3

description: Library name: Thap treated control replicate3


title: ctrl Skin fibroblasts + supernatants of macrophages NETs-4

description: Library name: SUP_NETs_rep4

value: primary cells

value: Healthy Skin fibroblasts

value: WT

value: sup ctrl-IgA-4


title: EpiSC_m6A_IP_rep_1

description:
Library name: Sample 2
EpiSC_ip.bw


title: ctrl Skin fibroblasts + supernatants of macrophages NETs-2

description: Library name: SUP_NETs_rep2

value: sup ctrl-IgA-2


title: ctrl Skin fibroblasts + supernatants of macrophages NETs-3

description: Library name: SUP_NETs_rep3

value: sup ctrl-IgA-3


title: Molm13, Quizartinib 8h, bio rep3

description: Library name: Molm13(Quizartinib 8h) replicate3

value: AML cell line

value: Quizartinib 8h


title: Liver, Background, Sample 80

city: Cincinnati

first: Erica

last: DePasquale

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology

institute: Cincinnati Children's Hospital

description:
Library name: 80B
10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing and FASTQ generation using CellRanger version 6.0.0
Generate single-cell expression matrix using CellRanger version 6.0.0
Quality control and filtering using R 4.4.0
Create Seurat objects using Seurat version 5.1.0
Sample integration, clustering, and sub-clustering using Seurat version 5.1.0
Assembly: NCBI Genome assembly GRCh38
Supplementary files format and content: Cell Ranger output files for GEX samples: tab-separated barcodes.tsv.gz, features.tsv.gz, and matrix.tsv.gz

molecule: nuclear RNA

growth_protocol: Background liver and tumor samples from patients with HB were collected under conditions appropriate for characterization and further generation of isoalted cells with institutional review board approval

extract_protocol:
Background liver and tumor tissues (25-30 mg each) were pulverized with liquid nitrogen and nuclei prepared, sorted and counted as described by Wu et. al. with addition of 0.04% BSA/PBS in the final buffer
3'v3 assay, 10x genomics, Novaseq6000 instrument

treatment_protocol: Patient samples were analyzed, diseased (HB tumor) versus normal liver were compared

value: Liver

tag: condition

value: Background


title: Liver, Tumor, Sample 80

description:
Library name: 80T
10X Genomics

value: Tumor


title: XEN_m6A_IP

description:
Library name: Sample 1
XEN_ip.bw

source_name: XEN

value: XEN

value: Extraembryonic endoderm stem cell

value: Hybrid(Mus molossinus X Mus musculus)


title: Molm13, Quizartinib 8h, bio rep2

description: Library name: Molm13(Quizartinib 8h) replicate2


title: EpiSC_STM2457_rep_2

description: Library name: Sample 14

data_processing:
Quality of sequenced rawdata were assessed by FastQC. Reads were trimmed for adapters using Trim_galore
Ribosomal reads were removed by ribodetector
Reads were mapped to mouse reference genome GRCm39 using STAR
Gene wise featureCounts was used to generate the counts file.
Assembly: mm39
Supplementary files format and content: text file and raw counts of each samples

extract_protocol:
Total RNA was isolated using TRIzol reagent and resuspended in ultrapure water.
RNA library was prepared using TruSeq stranded total RNA kit (Illumina, 15035748).

treatment_protocol: Cell were seeded a day before the METTL3 inhibitor treatment; inhibition was performed for 12 hours with STM2457(50 µM)

value: EpiSC

value: epiblast stem cell

value: Inhibitor


title: Molm13, Quizartinib 8h, bio rep1

description: Library name: Molm13(Quizartinib 8h) replicate1

value: cell line


title: Liver, Background, Sample 85

description:
Library name: HB85B
10X Genomics


title: ctrl Skin firboblasts + NETs + HS IgA-4

description: Library name: NETs_HS_IgA_rep4

value: primary cells

value: Healthy Skin fibroblasts

value: NETs + HS IgA-4


title: ctrl Skin fibroblasts + supernatants of macrophages NETs-1

description: Library name: SUP_NETs_rep1

value: WT

value: sup ctrl-IgA-1


title: Liver, Tumor, Sample 85

description:
Library name: HB85T
10X Genomics


title: EpiSC_STM2457_rep_1

description: Library name: Sample 13

value: XmolXmus-<delta>Tsix


title: EpiSC_DMSO_rep_2

description: Library name: Sample 12

value: control


title: ctrl Skin firboblasts + NETs + HS IgA-2

description: Library name: NETs_HS_IgA_rep2

value: NETs + HS IgA-2


title: ctrl Skin firboblasts + NETs + HS IgA-3

description: Library name: NETs_HS_IgA_rep3

value: NETs + HS IgA-3


title: Liver, Background, Sample 83

description:
Library name: HB83B
10X Genomics

value: Liver

value: Background


title: Molm13, control, bio rep3

description: Library name: Molm13(Control) replicate3

value: AML cell line


title: Liver, Tumor, Sample 83

description:
Library name: HB83T
10X Genomics

value: Tumor


title: Molm13, control, bio rep1

description: Library name: Molm13(Control) replicate1


title: ctrl Skin firboblasts + NETs + HS IgA-1

description: Library name: NETs_HS_IgA_rep1

value: NETs + HS IgA-1


title: EpiSC_DMSO_rep_1

description: Library name: Sample 11

value: EpiSC

value: epiblast stem cell

value: Hybrid(Mus molossinus X Mus musculus)


title: MV4-11, Quizartinib 8h, bio rep3

description: Library name: MV4-11(Quizartinib 8h) replicate3

value: cell line

value: Quizartinib 8h


title: Liver, Tumor, Sample 82

description:
Library name: HB82T
10X Genomics


title: Liver, Tumor, Sample 70

description:
Library name: HB70T
10X Genomics


title: TSC_STM2457_rep_2

description: Library name: Sample 10

value: TSC

value: trophoectoderm stem cell

value: Inhibitor


title: ctrl Skin firboblasts + NETs-4

description: Library name: NETs_rep4

value: primary cells

value: Healthy Skin fibroblasts

value: WT


title: ctrl Skin firboblasts + NETs-3

description: Library name: NETs_rep3


title: TSC_DMSO_rep_2

description: Library name: Sample 8

value: control


title: Liver, Tumor, Sample 60

description:
Library name: HB60T
10X Genomics

value: Liver


title: ctrl Skin firboblasts + NETs-2

description: Library name: NETs_rep2


title: TSC_DMSO_rep_1

description: Library name: Sample 7


title: Liver, Tumor, Sample 53

description:
Library name: HB53T
10X Genomics


title: Liver, Background, Sample 53

description:
Library name: HB53B
10X Genomics

value: Background


title: XEN_STM2457_rep_3

description: Library name: Sample 6

value: XEN

value: extraembryonic endoderm stem cell


title: ACC10_O

description: Library name: Sample 3

value: Human ACC Organoids


title: ctrl Skin firboblasts + NETs-1

description: Library name: NETs_rep1


title: MV4-11, control, bio rep2

description: Library name: MV4-11(Control) replicate2

value: AML cell line


title: Molm13, control, bio rep2

description: Library name: Molm13(Control) replicate2


title: Liver, Tumor, Sample 31

description:
Library name: HB31T
10X Genomics

value: Tumor


title: M2 + HS IgA-4

description: Library name: HS_IgA_rep4

value: M2 macrophages

value: HS IgA


title: XEN_DMSO_rep_3

description: Library name: Sample 5

value: Hybrid(Mus molossinus X Mus musculus)


title: XEN_STM2457_rep_2

description: Library name: Sample 4


title: M2 + HS IgA-3

description: Library name: HS_IgA_rep3


title: MV4-11, Quizartinib 8h, bio rep2

description: Library name: MV4-11(Quizartinib 8h) replicate2

value: cell line

value: Quizartinib 8h


title: Liver, Background, Sample 31

description:
Library name: HB31B
10X Genomics


title: MV4-11, control, bio rep1

description: Library name: MV4-11(Control) replicate1


title: FLT3-ITD+ AML patient A PBMC, bio rep3

description: Library name: PBMC ITD replicate3

source_name: blood

value: blood

value: PBMC


title: MV4-11, control, bio rep3

description: Library name: MV4-11(Control) replicate3


title: TSC_STM2457_rep_1

description: Library name: Sample 9

value: TSC

value: trophoectoderm stem cell

value: Inhibitor


title: Liver, Tumor, Sample 30

description:
Library name: HB30T
10X Genomics

value: Liver


title: M2 + HS IgA-1

description: Library name: HS_IgA_rep1

value: primary cells

value: WT


title: Liver, Tumor, Sample 17

description:
Library name: HB17T
10X Genomics


title: M2 + HS IgA-2

description: Library name: HS_IgA_rep2


title: MV4-11, Quizartinib 8h, bio rep1

description: Library name: MV4-11(Quizartinib 8h) replicate1


title: XEN_DMSO_rep_2

description: Library name: Sample 3

value: XEN

value: extraembryonic endoderm stem cell

value: control


title: FLT3-ITD+ AML patient A PBMC, bio rep2

description: Library name: PBMC ITD replicate2


title: XEN_STM2457_rep_1

description: Library name: Sample 2


title: M2 + ctrl IgA-4

description: Library name: CTRL_IgA_rep4

value: ctrl IgA


title: Liver, Background, Sample 17

description:
Library name: HB17B
10X Genomics

value: Background


title: XEN_DMSO_rep_1

description: Library name: Sample 1


title: Healthy person D PBMC, bio rep3

description: Library name: Healthy person D replicate3


title: FLT3-ITD+ AML patient A PBMC, bio rep1

description: Library name: PBMC ITD replicate1


title: Liver, Tumor, Sample 81

description:
Library name: 81T
10X Genomics

value: Tumor


title: M2 + ctrl IgA-3

description: Library name: CTRL_IgA_rep3

value: M2 macrophages


title: AAV2-neoAg and optimized AAV6-neoAg+RT #2

city: Taichung

first: ChihYang

last: H

address: No.2 Rude Rd

country: Taiwan

institute: China Medical University Hospital

description: Library name: Sample12

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1).
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each sample

source_name: ASB-XIV tumor tissue

extract_protocol:
Total RNAs were extracted from the tumor xenografts using the TRIzolTM Reagent (ThermoFisher Scientific).
RNA libraries were prepared for sequencing using Truseq stranded mRNA Library Prep kit

treatment_protocol: FeMale Balb/c mice (BIOLASCO, Taiwan) mice bearing with ASB-XIV tumors at about 100 mm3 were treated with AAV2-, AAV6- or oAAV6-neoAg cancer vaccine (intramuscular injection dose of 1*10^8 vg/mouse).Tumors were harvested on Day 30

value: ASB-XIV tumor tissue

value: ASB-XIV

value: tumor tissue

value: AAV2-neoAg and optimized AAV6-neoAg vaccination+RT


title: Healthy person D PBMC, bio rep2

description: Library name: Healthy person D replicate2

value: blood

value: PBMC


title: M2 + ctrl IgA-2

description: Library name: CTRL_IgA_rep2


title: Healthy person D PBMC, bio rep1

description: Library name: Healthy person D replicate1


title: CRC_Plasma_Donor3_2

city: Rome

first: Mattia

last: Laffranchi

address: Viale Regina Elena 291

department: Molecular Medicine

country: Italy

institute: La Sapienza University of Rome

description:
Library name: Sample_17
primary cells

data_processing:
Low-quality reads and adaptors were removed with Trim Galore (version 0.6.4_dev), while indexing and alignment were performed with STAR (version 2.7.10b) using the human reference genome (hg38) featureCounts (version 2.1.1) was used to count the number of reads per gene.
Assembly: hg38
Supplementary files format and content: comma-delimited text file containing DESeq2 normalized counts for each sample

molecule: polyA RNA

source_name: Peripheral Blood

extract_protocol:
NK cells were harvested, and total RNA was extracted using Total RNA Mini Kit (1/2) (Geneaid, cat#RBD300).
Sequencing libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit v2 (Takara Bio) and sequenced on an Illumina NovaSeq 6000 platform as paired-end 50 bp reads (performed by DNA Link Inc.).

treatment_protocol: Sorted NK cells were then co-cultured for 48 hours with 3% plasma obtained from either three different stage IV colorectal cancer (CRC) patients or matched HD controls.

value: Peripheral Blood

value: NK

value: CRC Plasma #36


title: M2 + ctrl IgA-1

description: Library name: CTRL_IgA_rep1

value: primary cells

value: WT


title: Healthy person C PBMC, bio rep3

description: Library name: Healthy person C replicate3


title: AAV2-neoAg and AAV6-neoAg+ RT #1

description: Library name: Sample 9

value: AAV2-neoAg and AAV6-neoAg vaccination+ RT


title: Healthy person C PBMC, bio rep2

description: Library name: Healthy person C replicate2


title: K562 chromatin SPLASH, biological replicate 2

city: Singapore

first: Yue

last: Wan

address: 60 Biopolis Street, Genome

country: Singapore

institute: Genome Institute of Singapore

description: Library name: K562_chr_SPLASH_rep2

data_processing:
Adaptor sequences were removed using Cutadapt, and trimmed reads shorter than 30 nucleotides from either read pair were discarded. UMIs were extracted using UMI-tools. UMI-extracted reads were then merged using SeqPrep and aligned to the human genome (hg38, Ensembl release 110) with STAR, using parameters optimized for chimera detection. Chimeric reads were subsequently extracted using CRSSANT. Chimeras overlapping any annotated splice junctions (based on Ensembl release 110) within ±2 nucleotides were removed. Only chimeric reads containing two non-overlapping chimera arms and a single chimeric gap were retained for downstream analyses. Chimeric reads identified from two technical replicates were merged prior to UMI deduplication using UMI-tools. Only uniquely mapped reads were used for intersection with annotated Alu repeat regions.
Assembly: hg38
Supplementary files format and content: Tab-delimited, UMI-deduplicated chimera reads from each biological replicate.

growth_protocol: K562 cells were cultured with RPMI supplemented with 10% fetal bovine serum. The cells were passaged every 2 to 3 days.

extract_protocol:
Chromatin-enriched RNA was extracted with TRIzol and further purified on Qiagen RNeasy Mini columns.
20 ug of chromatin-enriched RNA were treated with Turbo DNase (Invitrogen, 1x DNase buffer, 0.1U/μL Turbo DNase, 0.4U/ul SUPERase·In) at 37°C for 30 minutes to remove genomic DNA, followed by ribosomal-RNA (rRNA) depletion using RNase H–based methods. Briefly, 20 μg of home-made ribosomal RNA-specific single stranded DNA probes were incubated with ~20ug of gDNA-removed chromatin RNA in probing buffer (100mM Tris-HCl PH7.0, 200mM NaCl) at 95°C for 5 minutes, followed by gradual temperature decrease at 0.1°C /s ramp rate to 22°C. The annealed DNA-RNA hybrid was digested with 0.5U/μL RNaseH (NEB) in 1x RNaseH reaction buffer at 37°C for 1 hour, followed by DNA oligo removal with 0.1U/ μL Turbo DNaseI at 37°C for 1 hour. The rRNA depleted RNA was then biotinylated via a copper-free click reaction (2 mM Click-iT Biotin PEG4 alkyne, 25 °C, 1 hour) and cleaned up with RNA Clean & Concentrator-5 (Zymo). 1μg of biotin-labelled RNA was diluted to 50 ng/ μL using 20 μL of nuclease free water, mixed with 20 μL of 2× fragmentation buffer( 9 mM MgCl2, 225 mM KCl, 150 mM Tris-HCl pH 8.3), incubated at 95 °C for 5 minutes, and immediately cooled on ice for 2 minutes. 2 μL of 0.5 M EDTA was added to chelate Mg²⁺, and the fragmented RNA was used directly without purification for streptavidin pull-down and proximity ligation as described previously (Aw et al 2016) . Notably, after proximity ligation, 3ʹ adaptors were ligated to the RNA on-beads with T4 RNA ligase 2 truncated KQ (NEB) in 30 μL of ligation mix (1× RNA ligase buffer, 20 U/μL T4 RNA ligase 2 TnKQ, 33 ng/μL 3ʹ adaptor, 0.67 U/μL SUPERase·In, 15 % PEG-5000) at 25°C for 2.5 hours, followed by RNA elution and clean-up as previously described (Aw et al 2016). Eluted RNA was reverse-cross-linked by 254-nm UV irradiation for 5 minutes on ice. Reverse transcription was performed with SuperScript IV at 50 °C for 1 hour using 1 μM 3ʹ adaptor–specific primer (5’ -TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG-3’) and 1 μM template-switch oligo (TSO) containing a 10-nt unique molecular identifier (UMI) (5’ - CTT TCC CTA CAC GAC GCT CTT CCG ATCT NNNNNNNNNN TAC rGrGrG /3phos/ -3’). cDNA fragments of 150–300nt were size-selected on a 6 % urea-PAGE gel, then amplified with NEBNext Multiplex Oligos using Q5 DNA polymerase (NEB) for 12 cycles. PCR products were purified with 0.9× Agencourt AMPure XP beads, quantified with Qubit High-Sensitivity DNA kit, and submitted for high-throughput sequencing using Novaseq-X-plus machine (Illumina).

treatment_protocol: ~80 million K562 cells were washed twice with room-temperature PBS, resuspended in 8 mL of 2.5 mM psoralen-triethylene glycol azide in PBS, and incubated at 37 °C for 10 minutes with rotation. The cells were then irradiated on ice with 365-nm UV light for 1 minute, collected, washed twice with ice-cold PBS, and subjected to chromatin fractionation immediately.


title: CRC_Plasma_Donor3_1

description:
Library name: Sample_16
primary cells

value: CRC Plasma #32


title: AAV2-Vec and AAV6-Vec+ RT #2

description: Library name: Sample 8

value: AAV2-Vec and AAV6-Vec vaccination+ RT


title: HD_Plasma_Donor3_3

description:
Library name: Sample_15
primary cells

value: HD Plasma #11


title: AAV2-neoAg and AAV6-neoAg+ RT #2

description: Library name: Sample 10


title: Healthy person C PBMC, bio rep1

description: Library name: Healthy person C replicate1


title: AAV2-Vec and AAV6-Vec+ RT #1

description: Library name: Sample 7


title: K562 chromatin SPLASH, biological replicate 1

description: Library name: K562_chr_SPLASH_rep1


title: AAV2-neoAg and optimized AAV6-neoAg+RT #1

description: Library name: Sample 11


title: CRC_Plasma_Donor2_3

description:
Library name: Sample_12
primary cells

value: CRC Plasma #42


title: CPMV treatment 24h S5W9-8

city: La Jolla

first: Nicole

last: Steinmetz

state: CA

address: 9500 Gilman Drive

institute: UCSD

description: Library name: Donor_S5W9_CPMV-8

data_processing:
Single-cell data pre-processing and gene and transcript counting were performed using 10x Genomics Cellranger v7.1.0 software.
Assembly: Homo sapiens/cowpea mosaic virus (NC_003550.1)
Supplementary files format and content: csv file

source_name: Human Peripheral Blood Mononuclear Cell

growth_protocol: PBMC isolation and incubation with CPMV was performed at the NCL according to the protocol outlined in NCL method ITA-10 (https://www.cancer.gov/nano/research/ncl/protocols-capabilities)

extract_protocol:
The isolation of single cells, purification, library preparation, and sequencing were performed at NCI Sequencing Facility.
The single cell RNA-seq libraries were prepared using a Chromium Next GEM Single Cell 5’ reagent kit v2 dual index protocol according to the manufacturer’s instructions. The libraries were pooled and sequenced on a NovaSeq X Plus flowcell (Illumina) using 10 cycles for dual indices, 26 cycles for Read1, and 90 cycles for Read2 non-symmetric run according to the manufacturer’s instructions.

value: Human Peripheral Blood Mononuclear Cell

value: CPMV treatment

tag: treatment time


title: CPMV treatment 24h S5W9-7

description: Library name: Donor_S5W9_CPMV-7

treatment_protocol: PBMC isolation and incubation with CPMV was performed at the NCL according to the protocol outlined in NCL method ITA-10 (https://www.cancer.gov/nano/research/ncl/protocols-capabilities)


title: HD_Plasma_Donor3_1

description:
Library name: Sample_13
primary cells

value: HD Plasma #6


title: AAV2-neoAg and optimized AAV6-neoAg #1

description: Library name: Sample 5

value: ASB-XIV tumor tissue

value: ASB-XIV

value: tumor tissue

value: AAV2-neoAg and optimized AAV6-neoAg vaccination


title: CPMV treatment 24h S5W9-6

description: Library name: Donor_S5W9_CPMV-6


title: CRC_Plasma_Donor3_3

description:
Library name: Sample_18
primary cells

value: Peripheral Blood


title: Healthy person B PBMC, bio rep1

description: Library name: Healthy person B replicate1

value: blood

value: PBMC


title: CRC_Plasma_Donor2_2

description:
Library name: Sample_11
primary cells

value: NK

value: CRC Plasma #36


title: Healthy person A PBMC, bio rep3

description: Library name: Healthy person A replicate3


title: HD_Plasma_Donor3_2

description:
Library name: Sample_14
primary cells

value: WT

value: HD Plasma #10


title: CPMV treatment 24h S5W9-5

description: Library name: Donor_S5W9_CPMV-5


title: AAV2-neoAg and AAV6-neoAg #1

description: Library name: Sample 3

value: AAV2-neoAg and AAV6-neoAg vaccination


title: Healthy person B PBMC, bio rep3

description: Library name: Healthy person B replicate3


title: CRC_Plasma_Donor2_1

description:
Library name: Sample_10
primary cells

value: CRC Plasma #32


title: AAV2-neoAg and AAV6-neoAg #2

description: Library name: Sample 4


title: Myf6-induced iMPC clone, MyoD-KO

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: Library name: Myf6_iMPC_MyoDKO

data_processing:
CellRanger used for demultiplexing + read mapping + barcode assignment + UMI counting
R package Seurat used for quality control + normalization + dimensionality reduction + clustering
R package Seurat used for sample integration + differential gene expression analysis
R package CellChat used for cell-cell communication analysis
R package velociraptor used for RNA velocity analysis
Assembly: GRCm39
Supplementary files format and content: Filtered count matrices from CellRanger

source_name: induced myogenic progenitor cells

growth_protocol: iMPC medium (KnockOut DMEM supplemented with 10% FBS, 10% KnockOut Serum Replacement, 1% MEM Non-Essential Amino Acids Solution (100X), 1% GlutaMAX Supplement (100X), 1% Penicillin-Streptomycin (10,000 U/mL), 0.1% 2-Mercaptoethanol and 10ng/mL bFGF) with F/R/C (F: 5µM Forskolin; R: 5µM RepSox; C: 3µM CHIR99021). All cells were cultured at 37°C and 5% CO2.

extract_protocol:
One MyoD-KO and one MyoD-WT iMPC clone at passage 4 were trypsinized and resuspended in PBS containing 2% FBS after inactivation with iMPC medium and centrifugation. The number of cells in each clone was manually counted with a hemocytometer. 12,000 cells were diluted with nuclease-free water and used for scRNA-Seq libraries preparation
Libraries were prepared using the Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) Kit (10x Genomics) according to manufacturer’s instructions. Briefly, cells were loaded with barcoded Single Cell 3’ v3.1 Gel Beads onto a Chromium Next GEM Chip G targeting the recovery of approximately 10,000 cells. After the Gel Beads-in-emulsion (GEMs) were generated, the gel beads were dissolved to release the uniquely-identifiable primers used for reverse transcription to produce barcoded cDNA from the polyA mRNA. GEMs were then broken to release the first-strand cDNA: this was then purified and further PCR-amplified. Amplified cDNA was then enzymatically fragmented, end-repaired, A-tailed, size selected, ligated to adaptors, indexed via PCR (Dual Index TT Set A, PN-1000215, 10x Genomics) and again size-selected. Diluted libraries were analyzed using the 4200 TapeStation System (Agilent Technologies, G2991BA) and D1000 ScreenTapes and reagents (D1000 ScreenTape, Agilent Technologies, 5067-5582; D1000 Reagents, Agilent Technologies, 5067-5583) according to manufacturer’s instructions.

value: induced myogenic progenitor cells

value: MyoD-KO

value: cultured in F/R/C medium, generated from MEFs with Myf6 overexpression and F/R/C treatment

tag: passage


title: Myf6-induced iMPC clone, MyoD-WT

description: Library name: Myf6_iMPC_MyoDWT

value: MyoD-WT


title: S5W9 control rep7

description: Library name: Donor_S5W9_NC-7

value: Human Peripheral Blood Mononuclear Cell

value: no treatment


title: AAV2-neoAg and optimized AAV6-neoAg #2

description: Library name: Sample 6

value: ASB-XIV tumor tissue

value: ASB-XIV

value: tumor tissue


title: CPMV treatment 24h S5W9-1

description: Library name: Donor_S5W9_CPMV-1

value: CPMV treatment


title: S5W9 control rep8

description: Library name: Donor_S5W9_NC-8


title: Healthy person A PBMC, bio rep1

description: Library name: Healthy person A replicate1

value: blood

value: PBMC


title: iMPC clone, F/R/C, Myf6-induced, lenti, rep 3

description: Library name: clone_Myf6_iMPC_H8

data_processing:
Kallisto used for reference alignment + gene expression quantification
R package edgeR used for differential gene expression analysis
R package Mfuzz used for fuzzy clustering
Assembly: GRCm38.p6
Supplementary files format and content: Raw gene counts in txt format

source_name: iMPCs

growth_protocol: Before reprogramming, MEFs were cultured in 1:1 iMPC:MEF medium. iMPC medium: KnockOut DMEM, 10% FBS, 10% KnockOut Serum Replacement, 1% MEM Non-Essential Amino Acids Solution (100X), 1% GlutaMAX Supplement (100X), 1% Penicillin-Streptomycin (10,000 U/mL), 0.1% 2-Mercaptoethanol, 10ng/mL bFGF. MEF medium: DMEM (High Glucose, L-glutamine, Phenol Red, Sodium Pyruvate), 10% FBS, 1% MEM Non-Essential Amino Acids Solution (100X), 1% Penicillin-Streptomycin (10,000 U/mL), 0.1% 2-Mercaptoethanol. iMPCs clones were picked from reprogrammed cultures and cultured in iMPC medium with F/R/C (F: 5µM Forskolin; R: 5µM RepSox; C: 3µM CHIR99021).

extract_protocol:
To extract total RNA from cells in culture, cells were trypsinized for 5 minutes at 37°C, washed 1x with PBS and the RNA isolated using the RNeasy Mini Kit, including DNAse digestion. Samples were stored at -80°C until library preparation.
Library preparation from RNA was performed either at the Functional Genomics Center Zurich (FGCZ) of University of Zurich and ETH Zürich (Myf6-induced lentiviral reprogramming) or at Novogene UK (TetO-Myf6 and MyoD-KO reprogramming). At the FGCZ, the RNA quality was determined with a Fragment Analyzer (Agilent Technologies) and only samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. The TruSeq Stranded mRNA (Illumina) was used for library preparation. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR.  The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent Technologies): the product was a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20 before sequencing. At Novogene, RNA quality was measured with the 5400 Fragment Analyser (Agilent Technologies) and only samples with RNA Integrity Number (RIN)≥ 9.1 were used for library preparation. Library preparation was carried out with a modified kit based on the TruSeq RNA Library Prep Kit (Illumina). Briefly, mRNA was purified from the total RNA samples by polyA enrichment using polyT oligo-attached magnetic beads. RNA was then fragmented and the first cDNA strand synthesized using random hexamer primers. The second strand of cDNA was then synthesized using dTTP (non-directional library), end-repaired, A-tailed, ligated with adapters, size selected, digested with USER enzyme, amplified and purified. The library concentration was checked with Qubit Fluorometer and RT-qPCR, while library fragment size was checked on a bioanalyzer.

treatment_protocol: On day 0 of the reprogramming process, medium was changed with iMPC medium only or with dox and/or F/R/C (dox: 2µg/mL doxycycline hyclate; F: 5µM Forskolin; R: 5µM RepSox; C: 3µM CHIR99021).

value: iMPCs

value: Pax7-CreERT2 x Rosa26-LSL-tdTomato x CAG-rtTA3

value: iMPC medium +F/R/C, generated from MEFs with Myf6 overexpression and F/R/C treatment

tag: time

value: established clone


title: CPMV treatment 24h S5W9-3

description: Library name: Donor_S5W9_CPMV-3


title: HD_Plasma_Donor2_4

description:
Library name: Sample_9
primary cells

value: Peripheral Blood

value: NK

value: WT

value: HD Plasma #11


title: HD_Plasma_Donor2_2

description:
Library name: Sample_7
primary cells

value: HD Plasma #6


title: CRC_Plasma_Donor1_1

description:
Library name: Sample_4
primary cells

value: CRC Plasma #32


title: CRC_Plasma_Donor1_3

description:
Library name: Sample_6
primary cells

value: CRC Plasma #42


title: AAV2-Vec and AAV6-Vec #1

description: Library name: Sample 1

value: ASB-XIV tumor tissue

value: AAV2 and AAV6 treatment


title: CPMV treatment 24h S5W9-4

description: Library name: Donor_S5W9_CPMV-4

value: Human Peripheral Blood Mononuclear Cell


title: Healthy person A PBMC, bio rep2

description: Library name: Healthy person A replicate2

data_processing:
Raw sequences were first quality-checked by FastQC v0.12.1 and MultiQC v1.16.
Sequences passed quality check were then aligned to the genome reference (hg38) by STAR v2.7.9a (parameter- outSAMtype: BAM SortedByCoordinate; quantmode TranscriptomeSAM GeneCounts)
The gene expression levels were estimated by rsem-calculate-exprssion of RSEM v1.3.1
The expression results were further analyzed by DESeq2 package(v1.30.1) in R.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene raw counts generated by RSEM for each sample.
Supplementary files format and content: Other tab-delimited text files contain combined raw counts for different samples.

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen) following manufacturer’s protocols. 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (Vazyme) following manufacturer’s protocols.


title: Molm13 cell line, bio rep2

description: Library name: Molm 13 replicate2

source_name: cell line

value: cell line

value: AML cell line


title: HD_Plasma_Donor2_3

description:
Library name: Sample_8
primary cells

value: HD Plasma #10


title: AAV2-Vec and AAV6-Vec #2

description: Library name: Sample 2

value: ASB-XIV

value: tumor tissue


title: CPMV treatment 24h S5W9-2

description: Library name: Donor_S5W9_CPMV-2

value: CPMV treatment


title: Molm13 cell line, bio rep1

description: Library name: Molm 13 replicate1


title: iMPC clone, F/R/C, Myf6-induced, lenti, rep 2

description: Library name: clone_Myf6_iMPC_H7

value: iMPCs

value: Pax7-CreERT2 x Rosa26-LSL-tdTomato x CAG-rtTA3

value: iMPC medium +F/R/C, generated from MEFs with Myf6 overexpression and F/R/C treatment

value: established clone


title: HD_Plasma_Donor1_4

description:
Library name: Sample_3
primary cells

value: Peripheral Blood

value: NK

value: WT

value: HD Plasma #11


title: RS4;11 cell line, bio rep2

description: Library name: RS4;11 replicate2

value: ALL cell line


title: Healthy person B PBMC, bio rep2

description: Library name: Healthy person B replicate2

value: blood

value: PBMC


title: S5W9 control rep6

description: Library name: Donor_S5W9_NC-6

value: Human Peripheral Blood Mononuclear Cell

value: no treatment


title: CRC_Plasma_Donor1_2

description:
Library name: Sample_5
primary cells

value: CRC Plasma #36


title: MV4-11 cell line, bio rep2

description: Library name: MV4-11 replicate2

value: cell line

value: AML cell line


title: S5W9 control rep5

description: Library name: Donor_S5W9_NC-5


title: RS4;11 cell line, bio rep1

description: Library name: RS4;11 replicate1


title: MEFs +Myf6+F/R/C, Day 12, lenti, rep3

description: Library name: D12_Myf6_FRC_H8

source_name: Thy1+ MEFs

value: Thy1+ MEFs

value: iMPC medium +Myf6+F/R/C

value: Day 12


title: HD_Plasma_Donor1_2

description:
Library name: Sample_1
primary cells

value: HD Plasma #6


title: MV4-11 cell line, bio rep1

description: Library name: MV4-11 replicate1


title: HD_Plasma_Donor1_3

description:
Library name: Sample_2
primary cells

value: HD Plasma #10


title: MEFs +Myf6+F/R/C, Day 12, lenti, rep2

description: Library name: D12_Myf6_FRC_H7

value: Pax7-CreERT2 x Rosa26-LSL-tdTomato x CAG-rtTA3


title: MEFs +Myf6+F/R/C, Day 12, lenti, rep1

description: Library name: D12_Myf6_FRC_H5


title: iMPC clone, F/R/C, Myf6-induced, lenti, rep 1

description: Library name: clone_Myf6_iMPC_H5

value: iMPCs

value: iMPC medium +F/R/C, generated from MEFs with Myf6 overexpression and F/R/C treatment

value: established clone


title: S5W9 control rep2

description: Library name: Donor_S5W9_NC-2


title: S5W9 control rep4

description: Library name: Donor_S5W9_NC-4


title: S5W9 control rep3

description: Library name: Donor_S5W9_NC-3


title: In-vivo WM4237-1 scRNAseq Day92 Dabrafenib/Trametinib treated

city: Philadelphia

first: Yeqing

last: Chen

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description: Library name: BC_WM4237-1_EP_scRNAseq

data_processing:
The reads alignment was performed using Cell Ranger v8.0.0 (10x Genomics). For in-vivo PDX samples, the raw sequencing reads were first aligned to a human-mouse combined reference genome (refdata-gex-GRCh38_and_GRCm39-2024-A) to identify mouse reads contamination. Cells with more than 20% of counts originating from mouse genome were excluded. For barcoded samples, the raw sequencing reads were aligned to a customized reference genome by incorporating our barcode vector sequence into the human genome (GRCh38-2024-A). Otherwise, the raw sequencing reads were aligned to the human genome (GRCh38-2024-A) directly.
Assembly: GRCh38-2024-A
Supplementary files format and content: rds

source_name: In-vivo PDX

growth_protocol: WM4237-1 cells are cultured in TU2% media consisting of 80% MCDB 153, 10% Leibovitz’s L-15, 2% FBS, 2.4 mM CaCl2, and passaged using 0.05% trypsin-EDTA. Melanoma cells (5 × 10⁵ in 100 μL of a 1:1 mixture of RPMI and Matrigel [Corning]) were subcutaneously injected into the right flanks of 6–8-week-old male NSG mice. Tumor growth was monitored using calipers, and volumes were calculated using the formula (W² × L)/2.

extract_protocol:
Post-treatment WM4237-1 cells were trypsinized, washed, and processed with Dead Cell Removal Kit (Miltenyi Biotec) following manufacturer’s instructions. Tumor chunks from three replicates were pooled, minced, and dissociated (0.2–1 g) using the Tumor Dissociation Kit and gentleMACS Octo Dissociator (Miltenyi Biotec) with heating. Cells were filtered (70 μm nylon mesh), centrifuged (250 × g, 7 min), RBC-lysed with 1 mL ACK buffer (Quality Biological, 118-156-101), diluted, and centrifuged again (250 × g, 5 min). Pellets were processed with the Mouse Cell Depletion Kit and Dead Cell Removal Kit (Miltenyi Biotec). Final pellets were resuspended in 80 µL PBS, kept on ice, and used for cell counting and scRNA-seq.
Single cell droplets were generated using the Chromium Next GEM single cell 3’ kit v3.1 (10x Genomics). cDNA synthesis and amplification, library preparation and indexing were done using the 10x Genomics Library Preparation kit (10x Genomics), according to manufacturer’s instructions. Overall library size was determined using the Agilent Bioanalyzer 2100 and the High Sensitivity DNA assay and libraries were quantitated using KAPA real-time PCR. Libraries were pooled and sequenced on the NovaSeq 6000 (Illumina, San Diego, CA) using a S2 300 cycle kit (Illumina), paired end run with the following run parameters: 26 base pair x 8 base pair (dual index) x 280 base pair.

treatment_protocol: WM4237-1 cells were treated for one week with media containing 0.3 µM dabrafenib and 30 nM trametinib refreshed every two days. Once tumors reached approximately 100-500 mm³, mice were treated with a rodent diet supplemented with 150 mg/kg dabrafenib and 1.5 mg/kg trametinib (Bio-Serv, S7581). Tumors were harvested at defined time points and pooled for single-cell sample preparation.

value: In-vivo PDX

value: Melanoma

value: BRAF V600E

value: Dabrafenib/Trametinib


title: In-vivo WM4237-1 scRNAseq Day21 Dabrafenib/Trametinib treated

description: Library name: BC_WM4237-1_D21_scRNAseq


title: In-vivo WM4237-1 scRNAseq Day0 Treatment naïve

description: Library name: BC_WM4237-1_D0_scRNAseq

value: Treatment naïve


title: CPMV treatment 24h Q7V4-8

description: Library name: Donor_Q7V4_CPMV-8

value: Human Peripheral Blood Mononuclear Cell

value: CPMV treatment


title: Proton irradiated 3

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

description: Library name: P-3

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of A. nidulans FGSC A4 with hisat2 (version 2.1.0).
DESeq2 (version 1.24.0) was used to determine differentially expressed genes.
RPKM values were calculated with the edgeR package (“rpkm” function).
Assembly: genome: https://fungidb.org/common/downloads/release-65/AnidulansFGSCA4/fasta/data/FungiDB-65_AnidulansFGSCA4_Genome.fasta; gff: https://fungidb.org/common/downloads/release-65/AnidulansFGSCA4/gff/data/FungiDB-65_AnidulansFGSCA4.gff)
Supplementary files format and content: excell file includes count and RPKM values for each Sample

organism: Aspergillus nidulans

source_name: mycelium

growth_protocol: Conidia were collected using 0.001 v/v % Tween 80 solution and were spread out (50 µL conidia suspension containing 107 conidia/mL) on Barratt’s minimal agar plates (10 mL in a Petri-dish with diameter 55 mm) covered with a cellophane sheet. Plates were pre-incubated at 37 °C for 20 h. These young, still growing (but not yet conidia-forming) cultures were irradiated.

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: Cultures were subjected to a proton count of approximately 0.2-1 × 1011 p with energies exceeding 10 MeV. Irradiation of cultures was performed at the vertical beamline of the MGC-20 cyclotron. Accumulated charges of 6400 ± 20% pC was administered in each treatment.

value: mycelium

value: THS30.3 (pyrG89, AfupyrG+; pyroA+; veA+)

value: proton irradiated


title: Proton irradiated 2

description: Library name: P-2


title: Untreated 2

description: Library name: C-2

value: untreated


title: MEFs +Myf6, Day 12, lenti, rep2

description: Library name: D12_Myf6_H7

value: Thy1+ MEFs

value: iMPC medium +Myf6

value: Day 12


title: Proton irradiated 1

description: Library name: P-1


title: Untreated 3

description: Library name: C-3


title: CPMV treatment 24h Q7V4-7

description: Library name: Donor_Q7V4_CPMV-7


title: In-vitro WM4237-1 scRNAseq Dabrafenib/Trametinib treated

description: Library name: BC_WM4237-1_DT_scRNAseq

source_name: In-vitro cell line

value: In-vitro cell line


title: In-vitro WM4237-1 scRNAseq Treatment naïve

description: Library name: BC_WM4237-1_CTRL_scRNAseq


title: S5W9 control rep1

description: Library name: Donor_S5W9_NC-1

value: no treatment


title: MEFs +Myf6, Day 12, lenti, rep3

description: Library name: D12_Myf6_H8

value: Pax7-CreERT2 x Rosa26-LSL-tdTomato x CAG-rtTA3


title: MEFs +Myf6, Day 12, lenti, rep1

description: Library name: D12_Myf6_H5


title: Untreated 1

description: Library name: C-1


title: Cct7 KD 2

city: Yangzhou

first: Jiali

address: 98 Nantong West Road, Yangzhou City

institute: Northern Jiangsu People's Hospital Affiliated to Yangzhou University

description: Library name: samples 8

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to mouse genome (mm10, Ensembl) using the Star.  HTseq was used to get gene counts and FPKM method was used to determine the gene expression.
Assembly: mm10_Ensembl
Supplementary files format and content: Cct5 KD Vs Cct5 KD Ctr.csv; Cct7 KD Vs Cct7 KD Ctr.csv

source_name: E14 embryonic stem cell

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction.
The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: Poly-A containing mRNA was purified from 1ug total RNA using oligo(dT) magnetic beads and fragmented into 200-600 bp using divalent cations at 85℃ for 6 min. The cleaved RNA fragments were used for first- and second-strand complementary DNA (cDNA) synthesis . dUTP mix was used for second-strand cDNA synthesis, which allows for the removal of the second strand. The cDNA fragments were end repaired, A-tailed and ligated with indexed adapters. The ligated cDNA products were purified and treated with uracil DNA glycosylase to remove the second-strand cDNA. Purified first-strand cDNA was enriched by PCR to create the cDNA libraries. The libraries were quality controlled with Agilent 2200 and sequenced by DNBSEQ-T7 on a 150 bp paired-end run.

value: E14 embryonic stem cell

tag: sample group

value: Cct7 KD


title: CPMV treatment 24h Q7V4-6

description: Library name: Donor_Q7V4_CPMV-6


title: MEFs +Myf6+F/R/C, Day 2, lenti, rep3

description: Library name: D2_Myf6_FRC_H8

value: iMPC medium +Myf6+F/R/C

value: Day 2


title: MEFs +Myf6+F/R/C, Day 2, lenti, rep2

description: Library name: D2_Myf6_FRC_H7


title: Cct7 KD 1

description: Library name: samples 7


title: CPMV treatment 24h Q7V4-4

description: Library name: Donor_Q7V4_CPMV-4


title: CD34_WGBS_DMT207

first: Yijie

last: SHEN

address: 130 Dong'an Road

institute: Fudan University

description:
Library name: CD34_WGBS_DMT207
Whole genome bisulfite sequencing (WGBS) of genomic DNA using sodium bisulfite conversion.

data_processing:
Reads were trimed and aligned with Bismark (--bowtie2 --non_directional) to a bisulfite-converted genome. Duplicates are removed with deduplicate_bismark, and methylation extracted via bismark_methylation_extractor (--comprehensive --bedGraph).
Assembly: hg38
Supplementary files format and content: Bismark compatible coverage files containing counts of coverted and non-coverted CpGs for each sample.

source_name: Peripheral blood

growth_protocol: HUDEP-2 cells were maintained in StemSpan™ Serum Free Medium (SFEM, StemCell Technologies) supplemented with 1 µg/mL doxycycline, 1µM dexamethasone, 50 ng/mL recombinant human stem cell factor, 3 IU/mL recombinant human erythropoietin, and 1% P/S. HUDEP-2 cells were induced differentiation in Iscove's Modified Dulbecco's Medium (IMDM, Gibco) supplemented with 1 µg/mL doxycycline, 50 ng/mL rhSCF, 3 IU/mL rhEPO, 10 µg/mL insulin, 10 µg/mL heparin, 320 µg/mL holo-transferrin, 5% fetal bovine serum and 1% P/S. Human primary CD34+ cells were cultured in three-phase systems in IMDM supplemented with 3 IU/mL rhEPO, 10 µg/mL insulin, 10 µg/mL heparin, 5% human male AB serum, and 1% P/S. Phase I medium was supplemented with 1 ng/mL recombinant human IL-3, 100 ng/mL rhSCF and 200 µg/mL holo-transferrin. Phase II medium was supplemented with 100 ng/mL rhSCF and 200 µg/mL holo-transferrin. Phase III medium was supplemented with 800 µg/mL holo-transferrin.

extract_protocol:
DNA was extracted using the Dneasy Blood and Tissue (Qiagen).
DNA libraries were prepped using the NEBNext® Enzymatic Methyl-seq Kit with at least 10 ng of genomic DNA

value: Peripheral blood

value: Human hematopoietic stem cell

value: WT


title: CPMV treatment 24h Q7V4-5

description: Library name: Donor_Q7V4_CPMV-5

value: Human Peripheral Blood Mononuclear Cell

value: CPMV treatment


title: CPMV treatment 24h Q7V4-3

description: Library name: Donor_Q7V4_CPMV-3


title: CD34_RNA_seq_DMT207_Rep2

description:
Library name: CD34_RNA_seq_DMT207_Rep2
RNA-seq of oligo-dT captured mRNA
Primary_cell_FPKM.csv

data_processing:
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1. Reads were mapped to reference genome hg38 with ENCODE RNA-seq pipeline.
Assembly: hg38
Supplementary files format and content: csv files with FPKM values for each gene

extract_protocol:
Cells were homogenized using TRIzol (Life Technologies). RNA was extracted using RNeasy Mini Kit (Qiagen).
Sequencing libraries were constructed from 500 ng of DNase-treated, total RNA using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB cat# 6310) for rRNA depletion, followed by the TruSeq Stranded Total kit (Illumina cat# 20020598) for cDNA synthesis and library preparation according to manufacturer’s specifications.


title: Cct7 KD Ctr 2

description: Library name: samples 6

value: Cct7 KD Ctr


title: MEFs +Myf6, Day 2, lenti, rep2

description: Library name: D2_Myf6_H7


title: CD34_RNA_seq_DMT207_Rep1

description:
Library name: CD34_RNA_seq_DMT207_Rep1
RNA-seq of oligo-dT captured mRNA
Primary_cell_FPKM.csv


title: CD34_RNA_seq_DMSO_Rep2

description:
Library name: CD34_RNA_seq_DMSO_Rep2
RNA-seq of oligo-dT captured mRNA
Primary_cell_FPKM.csv

value: DMSO


title: CPMV treatment 24h Q7V4-1

description: Library name: Donor_Q7V4_CPMV-1


title: Cct5 KD 2

description: Library name: samples 4

value: Cct5 KD


title: MEFs +Myf6, Day 2, lenti, rep1

description: Library name: D2_Myf6_H5

value: Thy1+ MEFs

value: iMPC medium +Myf6


title: Cct7 KD Ctr 1

description: Library name: samples 5


title: CPMV treatment 24h Q7V4-2

description: Library name: Donor_Q7V4_CPMV-2


title: CD34_WGBS_DMSO

description:
Library name: CD34_WGBS_DMSO
Whole genome bisulfite sequencing (WGBS) of genomic DNA using sodium bisulfite conversion.


title: Cct5 KD 1

description: Library name: samples 3


title: MEFs +Myf6+F/R/C, Day 2, lenti, rep1

description: Library name: D2_Myf6_FRC_H5


title: HUDEP_RNA_seq_DMT207_Rep2

description:
Library name: HUDEP_RNA_seq_DMT207_Rep2
RNA-seq of oligo-dT captured mRNA
HUDEP_FPKM.csv

source_name: Umbilical cord blood

value: Umbilical cord blood

value: Human erythroid progenitor


title: MEFs before repr, lenti, rep3

description: Library name: D-1_Thy1_MEF_H8

value: Pax7-CreERT2 x Rosa26-LSL-tdTomato x CAG-rtTA3

value: 1:1 iMPC:MEF media

value: 1 day before reprogramming


title: Q7V4 control rep8

description: Library name: Donor_Q7V4_NC-8

value: no treatment


title: CD34_RNA_seq_DMSO_Rep1

description:
Library name: CD34_RNA_seq_DMSO_Rep1
RNA-seq of oligo-dT captured mRNA
Primary_cell_FPKM.csv


title: Q7V4 control rep7

description: Library name: Donor_Q7V4_NC-7


title: Cct5 KD Ctr 2

description: Library name: samples 2

value: E14 embryonic stem cell

value: Cct5 KD Ctr


title: HUDEP_RNA_seq_DMT207_Rep1

description:
Library name: HUDEP_RNA_seq_DMT207_Rep1
RNA-seq of oligo-dT captured mRNA
HUDEP_FPKM.csv


title: Q7V4 control rep6

description: Library name: Donor_Q7V4_NC-6


title: MEFs before repr, lenti, rep2

description: Library name: D-1_Thy1_MEF_H7


title: Cct5 KD Ctr 1

description: Library name: samples 1


title: HUDEP_RNA_seq_DMSO_Rep2

description:
Library name: HUDEP_RNA_seq_DMSO_Rep2
RNA-seq of oligo-dT captured mRNA
HUDEP_FPKM.csv


title: MEFs before repr, lenti, rep1

description: Library name: D-1_Thy1_MEF_H5


title: Donor3_CD34_ATAC_seq_DMT207

description:
Library name: Donor3_CD34_ATAC_seq_DMT207
ATAC-seq library generated using Tn5-mediated tagmentation from primary cells.

data_processing:
Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1. Mapping to reference genome hg38 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800.
Assembly: hg38
Supplementary files format and content: bigWig files with read coverage

extract_protocol:
50-100k cells were lysised with 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin, then incubated with Tagment DNA Enzyme (Illumina) for 30 minutes at 37C. DNA was purified with Qiagen MinElute Reaction Cleanup Kit.
Library fragments were amplified using Phusion High-Fidelity PCR Master Mix with HF Buffer (ThermoFisher cat#F531S) and indexes.

value: Peripheral blood

value: Human hematopoietic stem cell


title: Q7V4 control rep4

description: Library name: Donor_Q7V4_NC-4

value: Human Peripheral Blood Mononuclear Cell


title: Microdissected Mice Renal CCD, MUT4_Vehicle, RNA-Seq, Transcriptome 01

first: Shuo-Ming

last: Ou

address: 10 Center Dr

institute: NHLBI

description: Library name: Sample 22

data_processing:
Sequenced reads were mapped to Ensembl mouse gene set using STAR v2.7.61
Transcript abundances in TPM were caculated by  RSEM/1.3.3
Assembly: GRCm39 (Ensembl)
Supplementary files format and content: Excel file includes TPM values for each sample

source_name: Kidney

growth_protocol: Pathogen-free male C57BL/6 mice (Taconic) weighing 20-30 g had free access to ad libitum drinking water and normal rodent chow before experiment. The mice were housed one per cage, maintained on a 12:12-h light-dark cycle, and acclimated to the housing conditions for 3 days before the experimental procedures.

extract_protocol:
RNAs were extracted using Zymo kit and cDNAs were sythesized using SMART-Seq V4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ten-week-old WT and MUT (Thr551Ala/Ser552Ala at beta-catenin) mice were assigned to two groups without treatments

value: Kidney

value: MUT

value: Vehicle


title: HUDEP_RNA_seq_DMSO_Rep1

description:
Library name: HUDEP_RNA_seq_DMSO_Rep1
RNA-seq of oligo-dT captured mRNA
HUDEP_FPKM.csv

value: WT

value: DMSO


title: MEFs +Myf6, Day 2, lenti, rep3

description: Library name: D2_Myf6_H8

value: Thy1+ MEFs

value: iMPC medium +Myf6

value: Day 2


title: Microdissected Mice Renal CCD, MUT4_Vehicle, RNA-Seq, Transcriptome 03

description: Library name: Sample 24


title: Q7V4 control rep5

description: Library name: Donor_Q7V4_NC-5


title: Microdissected Mice Renal CCD, MUT3_Vehicle, RNA-Seq, Transcriptome 03

description: Library name: Sample 21


title: Microdissected Mice Renal CCD, MUT4_Vehicle, RNA-Seq, Transcriptome 02

description: Library name: Sample 23


title: Q7V4 control rep3

description: Library name: Donor_Q7V4_NC-3


title: Q7V4 control rep1

description: Library name: Donor_Q7V4_NC-1


title: DJ_E_C_2

city: Beijing

first: 刘

last: 硕

address: 北京市海淀区西三环北路105号

institute: capital normal university

description: Library name: DJ_E_C_2

data_processing:
Raw reads were filtered with fastp, and aligned to the reference genome using hisat250. The resulting sam file containing mapped reads were converted to the bam format by SAM tools. After that, gene counts were called from the bam files using feature Counts.
Assembly: T2T-NIP
Supplementary files format and content: counts

organism: Oryza sativa

source_name: root

growth_protocol: Seeds were soaked in tap water and germinated at 37°C in the dark for 2 days. Then cultured at 28°C in the dark

extract_protocol:
Total RNA was isolated from the root tips of rice plants using TRIzol reagent (Ambion, 15596018) according to the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection

treatment_protocol: Place the germinated seeds on a barbed wire fence and place them in an airtight container. Ethylene gas (2 ppm) was injected into the boxes using a syringe. The seedlings were cultured at 28°C in the dark for 3 days with different concentrations of CaCl2

value: root

value: Dongjin

value: calcium and ethylene


title: Donor2_CD34_ATAC_seq_DMT207

description:
Library name: Donor2_CD34_ATAC_seq_DMT207
ATAC-seq library generated using Tn5-mediated tagmentation from primary cells.


title: Donor3_CD34_ATAC_seq_DMSO

description:
Library name: Donor3_CD34_ATAC_seq_DMSO
ATAC-seq library generated using Tn5-mediated tagmentation from primary cells.


title: Donor2_CD34_ATAC_seq_DMSO

description:
Library name: Donor2_CD34_ATAC_seq_DMSO
ATAC-seq library generated using Tn5-mediated tagmentation from primary cells.


title: Microdissected Mice Renal CCD, MUT3_Vehicle, RNA-Seq, Transcriptome 02

description: Library name: Sample 20


title: Q7V4 control rep2

description: Library name: Donor_Q7V4_NC-2

value: no treatment


title: CPMV treatment 24h B3C2-8

description: Library name: Donor_B3C2_CPMV-8

value: CPMV treatment


title: A1BG vector

type: RNA

city: Yoshida-gun

first: Juan

last: Lyu

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: Second Department of Internal Medicine

country: Japan

institute: University of Fukui

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: HepG2 cell

label_protocol: Cyanine 3 (Cy3)-labeled complementary RNA (cRNA) was generated from 50 ng of total RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies, #5190-2305) according to the manufacturer’s protocol. External RNA spike-in controls were added prior to amplification. Following in vitro transcription and Cy3 labeling, cRNA was purified using the RNeasy Mini Kit (QIAGEN). cRNA yield and dye incorporation efficiency were assessed using a NanoDrop ND-2000 spectrophotometer, and cRNA quality was evaluated using an Agilent 2100 BioAnalyzer.

growth_protocol: The human liver cancer cell line HepG2 was obtained from the American Type Culture Collection (Manassas, VA, USA), and  cultured in RPMI-1640 (SigmaAldrich, St. Louis, MO, USA) containing 10% fetal bovine serum (FBS), 2 mmol/L L-glutamine, 1 μmol/L sodium pyruvate, 0.1 mmol/L nonessential amino acids, and 100 U/mL penicillin/50 μg/mL streptomycin (Gibco, Grand Island, NY, USA) at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Cat. No, 74106, QIAGEN) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were transfected with 25 nM siRNA using DharmaFECT 4 according to the manufacturer’s instructions and harvested 72 h post-transfection. For gene overexpression, CMV promoter-driven plasmids were transfected using Lipofectamine LTX, and cells were harvested 72 h after transfection.

value: A1BG vector


title: Microdissected Mice Renal CCD, MUT3_Vehicle, RNA-Seq, Transcriptome 01

description: Library name: Sample 19


title: Donor1_CD34_ATAC_seq_DMSO

description:
Library name: Donor1_CD34_ATAC_seq_DMSO
ATAC-seq library generated using Tn5-mediated tagmentation from primary cells.

value: Peripheral blood


title: CPMV treatment 24h B3C2-7

description: Library name: Donor_B3C2_CPMV-7


title: si-A1BG


title: Empty vector

value: Empty vector


title: DJ_E_4

address: 北京市海淀区西三环北路105号

description: Library name: DJ_E_4

value: ethylene


title: si-Non target

value: si-Non target


title: Donor1_CD34_ATAC_seq_DMT207

description:
Library name: Donor1_CD34_ATAC_seq_DMT207
ATAC-seq library generated using Tn5-mediated tagmentation from primary cells.

value: Human hematopoietic stem cell


title: Microdissected Mice Renal CCD, MUT2_Vehicle, RNA-Seq, Transcriptome 03

description: Library name: Sample 18

value: Kidney

value: MUT

value: Vehicle


title: CPMV treatment 24h B3C2-6

description: Library name: Donor_B3C2_CPMV-6

value: Human Peripheral Blood Mononuclear Cell


title: DJ_C_2

address: 北京市海淀区西三环北路105号

description: Library name: DJ_C_2

value: calcium


title: DJ_E_C_3

address: 北京市海淀区西三环北路105号

description: Library name: DJ_E_C_3


title: Microdissected Mice Renal CCD, MUT2_Vehicle, RNA-Seq, Transcriptome 01

description: Library name: Sample 16


title: HUDEP_ATAC_seq_DMT207_Rep2

description:
Library name: HUDEP_ATAC_seq_DMT207_Rep2
ATAC-seq library generated using Tn5-mediated tagmentation from HUDEP-2 cells.

value: Umbilical cord blood

value: Human erythroid progenitor

value: WT


title: CPMV treatment 24h B3C2-5

description: Library name: Donor_B3C2_CPMV-5


title: HUDEP_ATAC_seq_DMSO_Rep2

description:
Library name: HUDEP_ATAC_seq_DMSO_Rep2
ATAC-seq library generated using Tn5-mediated tagmentation from HUDEP-2 cells.

value: DMSO


title: Microdissected Mice Renal CCD, MUT2_Vehicle, RNA-Seq, Transcriptome 02

description: Library name: Sample 17


title: Microdissected Mice Renal CCD, MUT1_Vehicle, RNA-Seq, Transcriptome 02

description: Library name: Sample 14


title: Microdissected Mice Renal CCD, MUT1_Vehicle, RNA-Seq, Transcriptome 03

description: Library name: Sample 15


title: DJ_2

address: 北京市海淀区西三环北路105号

description: Library name: DJ_2

value: root

value: Dongjin

value: control


title: CPMV treatment 24h B3C2-4

description: Library name: Donor_B3C2_CPMV-4

value: CPMV treatment


title: HUDEP_ATAC_seq_DMSO_Rep1

description:
Library name: HUDEP_ATAC_seq_DMSO_Rep1
ATAC-seq library generated using Tn5-mediated tagmentation from HUDEP-2 cells.


title: DJ_C_1

address: 北京市海淀区西三环北路105号

description: Library name: DJ_C_1


title: Microdissected Mice Renal CCD, MUT1_Vehicle, RNA-Seq, Transcriptome 01

description: Library name: Sample 13


title: HUDEP_ATAC_seq_DMT207_Rep1

description:
Library name: HUDEP_ATAC_seq_DMT207_Rep1
ATAC-seq library generated using Tn5-mediated tagmentation from HUDEP-2 cells.


title: DJ_E_3

address: 北京市海淀区西三环北路105号

description: Library name: DJ_E_3


title: DJ_1

address: 北京市海淀区西三环北路105号

description: Library name: DJ_1


title: CPMV treatment 24h B3C2-3

description: Library name: Donor_B3C2_CPMV-3


title: CPMV treatment 24h B3C2-2

description: Library name: Donor_B3C2_CPMV-2


title: Microdissected Mice Renal CCD, WT4_Vehicle, RNA-Seq, Transcriptome 02

description: Library name: Sample 11


title: P5,mPOCs,Irradiated,t24

city: Solna

first: Tianyi

last: Li

address: Bioclinicum NKS J5:20, Solnavägen 30

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description: Library name: P30458_1049_S106

data_processing:
Fastq files were trimmed using TrimGalore (version 0.6.1) to remove the low-quality reads before mapping.
STAR aligner (version 2.7.11a) was used to map the trimmed fastq files to human genome hg38.
The bam files were aligned using featureCount function in subread package (version 2.0.3) and annotated using UCSC gtf file
Assembly: hg38
Supplementary files format and content: RawCounts.txt

source_name: Ovary

extract_protocol:
RNA extraction was performed using the RNeasy Micro Kit (Qiagen, Germany) following the manufacturer’s instructions.
Libraries were prepared using the Illumina Stranded mRNA Prep Ligation protocol (Illumina, USA) according to the manufacturer’s instruction, with 10 ng of RNA used as input.

value: Ovary

value: Primary ovarian cells

value: Irradiated

tag: type

value: mPOCs


title: P5,mPOCs,Control,t24

description: Library name: P30458_1050_S107

value: Control


title: P5,mPOCs,Irradiated,t4

description: Library name: P30458_1048_S105


title: Microdissected Mice Renal CCD, WT4_Vehicle, RNA-Seq, Transcriptome 01

description: Library name: Sample 10

value: Kidney


title: P5,mPOCs,Irradiated,t1

description: Library name: P30458_1047_S104


title: Microdissected Mice Renal CCD, WT4_Vehicle, RNA-Seq, Transcriptome 03

description: Library name: Sample 12

value: Vehicle


title: BC32 control rep8

description: Library name: Donor_B3C2_NC-8

value: Human Peripheral Blood Mononuclear Cell

value: No treatment


title: CPMV treatment 24h B3C2-1

description: Library name: Donor_B3C2_CPMV-1


title: Panc 10.05 PTEN KO 2.6.2 untreated 72h

city: Amsterdam

first: Astrid

last: Bosma

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description:
Library name: 7058_23_pTEN_2_6_2-Unt-72hr_AACGAAGATC-TGTGGTCTAA
column name in genecounts.txt file: 23_pTEN_2_6_2_Unt_72hr

data_processing:
samples were aligned using HiSat2
Assembly: homo sapiens (GRCh38/hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: pancreas

extract_protocol:
RNA was extracted using RNEasy mini kit (Quiagen)
The library was prepared using the TruSeq RNA Sample Preparation kit (Illumina)

value: pancreas

value: pancreatic cancer

value: PTEN KO

value: untreated

tag: time point


title: Panc 10.05 PTEN KO 2.6.2 SHP2i+ERKi 72h

description:
Library name: 7058_31_pTEN_2_6_2-2_2_S_E-72hr_CCTCCTGTGA-CACGTCTACG
column name in genecounts.txt file: 31_pTEN_2_6_2_2_2_S_E_72hr


title: Panc 10.05 PTEN KO 2.6.2 SHP2i+ERKi 24h

description:
Library name: 7058_15_pTEN_2_6_2-2_2_S_E-24hr_AGTATCCGAT-TATTGCGCTA
column name in genecounts.txt file: 15_pTEN_2_6_2_2_2_S_E_24hr


title: Microdissected Mice Renal CCD, WT3_Vehicle, RNA-Seq, Transcriptome 03

description: Library name: Sample 9

value: WT


title: BC32 control rep6

description: Library name: Donor_B3C2_NC-6


title: BC32 control rep7

description: Library name: Donor_B3C2_NC-7


title: P5,mPOCs,Control,t1

description: Library name: P30458_1046_S103


title: Panc 10.05 PTEN KO 2.1.4 SHP2i+ERKi 72h

description:
Library name: 7058_32_pTEN_2_1_4-2_2_S_E-72hr_TATGCGTAGC-TCAGAGGCAC
column name in genecounts.txt file: 32_pTEN_2_1_4_2_2_S_E_72hr


title: Microdissected Mice Renal CCD, WT3_Vehicle, RNA-Seq, Transcriptome 02

description: Library name: Sample 8


title: BC32 control rep4

description: Library name: Donor_B3C2_NC-4


title: Panc 10.05 PTEN KO 2.1.4 SHP2i+ERKi 24h

description:
Library name: 7058_16_pTEN_2_1_4-2_2_S_E-24hr_GCAATCTGCT-ACGAACCAAG
column name in genecounts.txt file: 16_pTEN_2_1_4_2_2_S_E_24hr


title: Panc 10.05 PTEN KO 2.6.2 untreated 24h

description:
Library name: 7058_7_pTEN_2_6_2-Unt-24hr_GTATGCCACA-CCGAGTCTTC
column name in genecounts.txt file: 7_pTEN_2_6_2_Unt_24hr


title: P5,cPOCs,Irradiated,t24

description: Library name: P30458_1044_S101

value: cPOCs


title: Microdissected Mice Renal CCD, WT2_Vehicle, RNA-Seq, Transcriptome 03

description: Library name: Sample 6


title: Microdissected Mice Renal CCD, WT3_Vehicle, RNA-Seq, Transcriptome 01

description: Library name: Sample 7


title: BC32 control rep5

description: Library name: Donor_B3C2_NC-5


title: Panc 10.05 PTEN KO 2.1.4 untreated 72h

description:
Library name: 7058_24_pTEN_2_1_4-Unt-72hr_AATAGGTAGG-TGGCTTATGG
column name in genecounts.txt file: 24_pTEN_2_1_4_Unt_72hr


title: BC32 control rep3

description: Library name: Donor_B3C2_NC-3


title: Microdissected Mice Renal CCD, WT2_Vehicle, RNA-Seq, Transcriptome 02

description: Library name: Sample 5


title: Panc 10.05 PTEN KO 2.1.4 untreated 24h

description:
Library name: 7058_8_pTEN_2_1_4-Unt-24hr_GCCAACAGAC-CGTTCACGTT
column name in genecounts.txt file: 8_pTEN_2_1_4_Unt_24hr


title: P5,cPOCs,Control,t24

description: Library name: P30458_1045_S102


title: BC32 control rep2

description: Library name: Donor_B3C2_NC-2


title: Panc 10.05 WT SHP2i+ERKi 24h

description:
Library name: 7058_9_WT-2_2_S_E-24hr_ATAAGCGGAG-CTGTTCTACG
column name in genecounts.txt file: 9_WT_2_2_S_E_24hr


title: BC32 control rep1

description: Library name: Donor_B3C2_NC-1


title: P5,cPOCs,Irradiated,t1

description: Library name: P30458_1042_S99


title: Panc 10.05 WT SHP2i+ERKi 72h

description:
Library name: 7058_25_WT-2_2_S_E-72hr_ATGTTGCCAC-TAGAAGCCAT
column name in genecounts.txt file: 25_WT_2_2_S_E_72hr


title: Panc 10.05 WT untreated 72h

description:
Library name: 7058_17_WT-Unt-72hr_CGACCTTAAT-GCTCTTAGGT
column name in genecounts.txt file: 17_WT_Unt_72hr


title: P5,cPOCs,Control,t1

description: Library name: P30458_1041_S98


title: P4,mPOCs,Irradiated,t4

description: Library name: P30458_1038_S95


title: Microdissected Mice Renal CCD, WT1_Vehicle, RNA-Seq, Transcriptome 03

description: Library name: Sample 3


title: P4,mPOCs,Irradiated,t24

description: Library name: P30458_1039_S96


title: P5,cPOCs,Irradiated,t4

description: Library name: P30458_1043_S100


title: Panc 10.05 WT untreated 24h

description:
Library name: 7058_1_WT-Unt-24hr_TAACTTGGTC-GTCGTGAATC
column name in genecounts.txt file: 1_WT_Unt_24hr


title: iAT2_iMAC (multiplexed samples)

city: Parkville

first: Michael

last: See

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

country: Australia

institute: MCRI

description:
Library name: iAT2_iMAC
10x Genomics

library_source: other

data_processing:
Fastq files were processed using Cellranger 8.0.0 to demultiplex, align and quantify reads-per-cell
Assembly: GRCh38
Assembly: HRV VR283
Assembly: RSV A2
Supplementary files format and content: filtered h5 files produced by Cellranger

molecule: other

source_name: iPSC-derived in vitro cells

extract_protocol:
Uninfected or infected samples were dissociated 48 hours later using Accutase (Stem Cell Technologies, 7922). To achieve sufficient cell numbers Transwells from the same condition were pooled as appropriate. Cells were stained with Zombie R718 for 15 minutes at room temperature, then incubated with anti-CD45 antibody. Cells were then fixed with “Fixation buffer” (10X Genomics, 1000475) for 21 hours. After quenching fixation as per manufacturer’s instructions, Zombie-negative cells were sorted. In iAT2-iMac cocultures, CD45- iAT2s and CD45+ iMacs were sorted separately, then pooled after sorting 10:1. Cells were collected from the sort in Lo-bind Eppendorf tubes supplemented with RNAse inhibitor (Promega, M6101). Cells were counted then stored at -80°C, as per manufacturer’s recommendations.
After storage, monocultured iAT2s and iMacs, as well as infected iAT2s and iMacs were pooled 1:1 then all samples hybridised with Human WTA Probes BC001-BC004 as well as 26 custom spike-in probe pairs against RSV A2 genes at 40 nM per probe for all samples. Custom probes were designed according to 10X tech note CG000621_RevC and purchased as standard desalted oPools from IDT and resuspended in low EDTA TE buffer (ThermoFisher Scientific, #12090015). Samples were multiplexed prior to GEM generation using a Chromium X controller. GEMs were recovered and gene expression libraries constructed, following manufacturer’s protocols. Libraries were sequenced on an Illumina NovaSeq X plus (AGRF).

treatment_protocol: Respiratory syncytial virus A2 infection

value: iPSC-derived in vitro cells

value: BU3 NGST CRISPRi

value: iAT2s and iMacs

value: plus or minus RSV A2

tag: human wta probes

value: BC001 (iAT2_iMAC_uninf_mono), BC002 (iAT2_plus_iMAC_uninf_coculture), BC003 (iAT2_iMAC_inf_mono), BC004 (iAT2_plus_iMAC_inf_coculture)

tag: library type

value: mRNA


title: Microdissected Mice Renal CCD, WT1_Vehicle, RNA-Seq, Transcriptome 01

description: Library name: Sample 1

tag: tissue


title: siControl, Differentiated -2

city: Melbourne

first: Diji

last: Kuriakose

address: Clayton

institute: Monash University

description:
Library name: Sample8
Coulmn name in all_counts_Differentiated.txt Sample 8

data_processing:
Sequence libraries were filtered for adaptor contamination using the Cutadapt (v3.3) software tool.
Filtered reads were aligned to the mouse reference genome (mm10) using Bowtie (v.2.3.5)
Assembly: mm10
Supplementary files format and content: tab-delimited txt file

source_name: Hippocampus

growth_protocol: DMEM, 8mM HEPES, B27 supplement, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Plus sonication (Diagenode).
RNA librarries for small RNA-seq was prepared using Small RNA-seq Lib Prep Kit for Illumina V3-Abclonal according to the manufacturers instructions.

value: Hippocampus

value: Neural progenitor cells

value: primary cells

tag: genotype

value: Control

value: Differentiated


title: High flow velocity_5

city: WUxi

first: Xin

last: Gao

institute: Nanjing Agricultural University

description: Library name: G_4

data_processing:
Firstly, Cutadapt were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO)(http://www.geneontology.org), SwissProt(http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with FDR < 0.05) by R package edgeR.
hg18
Assembly: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Triplophysa orientalis

source_name: muscle tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: muscle tissue

value: skeletal muscle cells

tag: treatment

value: Overexpressing


title: High flow velocity_3

description: Library name: G_2


title: P4,mPOCs,Irradiated,t1

description: Library name: P30458_1037_S94

value: Ovary

value: Primary ovarian cells

value: Irradiated

value: mPOCs


title: S4-S5 Mutant, S4 Viewpoint, rep1

city: Mexico City

first: Angel

middle: Josue

last: Cerecedo-Castillo

state: Coyoacan

address: Circuito Exterior s/n Ciudad Universitaria

department: Molecular Genetics

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description: Library name: VP_S4_dS4S5_rep1

data_processing:
Pipe4C (v1.1.6) was utilized for preprocessing and analysis of all samples. The hg19 reference genome was used for all alignments. deepTools multiBamSummary was used to estimate scaling factors by viewpoint, which were then applied to generate bigWig files using bamCoverage.
Assembly: hg19
Supplementary files format and content: Normalized 4C counts and signal
Library strategy: 4C-Seq

source_name: Bone Marrow

growth_protocol: K562 cells were cultured in ISCOVE supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were maintained at 37 °C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Ten million cells were crosslinked with 2% formaldehyde for 10 min, followed by a 5-min quenching with glycine. Cells were washed once with PBS and then incubated for 20 min in lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% Igepal) with 1× protease inhibitors. First, three rounds of digestion were carried out with DpnII (NEB R0543S) at 37 °C in a thermomixer at 500 rpm (100 U for 4 h, 100 U overnight, and 100 U for another 4 h); the restriction enzyme was inactivated by heating to 62 °C for 20 min while shaking at 500 rpm. Next, the first ligation was performed with 2000 U of T4 DNA ligase (NEB M0202L) at 16 °C in 7 mL of Milli-Q water overnight. Samples were then phenol-chloroform extracted and ethanol precipitated. The second digestion was performed overnight with 50 U of NlaIII (NEB R0125S) or CviQI (NEB R0639S). The second ligation was carried out in a total volume of 5 mL with 3000 U of T4 DNA ligase (NEB M0202L). The ligated material was purified with SPRI beads and quantified using a Qubit dsDNA Assay Kit.
The first round of PCR amplification with viewpoint-specific primers was performed using 4 × 50 µL PCR reactions with 200 ng of 4C template and 16 PCR cycles with Phusion polymerase (NEB M0530L). A second round of PCR with universal primers containing Illumina adapters was then performed, and the material was purified with SPRI beads. Two independent libraries per condition were sequenced on an Illumina HiSeq 4000 platform as single-end 150 bp reads.

value: Bone Marrow

value: Chronic Myelogenous Leukemia

value: S4-S5 mutant