title: peritoneal dialysis effluent, three-year dialysis

city: Guangzhou

first: Siqi

last: Zheng

state: Guangdong province

address: Zhongshan 2nd Road

department: nephrology

institute: Guangdong Provicial People's Hospital

description: Library name: sample1

data_processing:
Utilize 10X Genomics Cell Ranger 3.1.0 for sequencing data quality control and quantification. Start by conducting quality control, eliminating low-quality reads, and mapping reads to the reference genome for gene annotation. Post UMI correction and statistical analysis, derive an unfiltered feature barcode matrix to pinpoint viable cells and assess gene expression.
Based on the output of Cell Ranger, we further analyzed it using Seurat 4.0 in the R software package. According to the standards: 1. The number of genes identified in the cell is 500-5000, 2. The total number of UMI is less than 25000, 3. The expression level of mitochondrial genes is less than 10%, and low-quality cells are excluded. Perform principal component analysis on the comprehensive data and select the top 50 principal components for subsequent analysis. Then, the soft k-means clustering algorithm in Harmony is used to cluster the reduced dimensional data, and finally, singleR is used to identify cell types by comparing them with cell types in the reference database.
In order to understand the molecular expression characteristics of different cell subpopulations, rank sum test was used to analyze gene differential expression in different cell subpopulations. According to the following criteria: 1. In the target or control subpopulation, genes are expressed in more than 25% of cells; 2. P-value ≤ 0.01; 3. The gene expression fold log2FC is ≥ 0.36, which means the fold of gene upregulation is ≥ 1.28, screen for upregulated differentially expressed genes.
In order to investigate the roles of immune cells and peritoneal mesothelial cells in PD-related fibrosis, we conducted enrichment analysis, trajectory analysis, and cell communication analysis. Enrichment analysis includes Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. We map differentially expressed genes to each term in the GO database and calculate the number of differentially expressed genes for each term to obtain a list of differentially expressed genes with a certain GO function. Then apply hypergeometric testing to identify GO entries that are significantly enriched in differentially expressed genes compared to the background. And KEGG enrichment analysis is similar to GO. Then, we used the monocle tool to analyze the gene expression matrix generated by 10X Genomics to simulate the dynamic changes of cells, and visualized the cell trajectories of different cell subpopulations, differentiation states, and samples. Finally, we used cellphoneDB software to analyze ligand receptor expression information and quantity in cells, in order to further construct a cell interaction network diagram and predict communication relationships between cells.
Assembly: Ensembl_release02
Supplementary files format and content: output of Cell Ranger (barcodes, genes, matrix files)

source_name: peritoneal dialysis effluent

extract_protocol:
The dialysate was centrifuged at 3000rpm at 4℃ for 15 minutes, and the cell pellet was washed twice with PBS buffer. Finally, it was resuspended in culture medium containing 10% BSA.Using Countess ®  II Automated Cell Counter counts cells in cell suspension and adjusts the concentration of live cells to the desired concentration
Load the single cell suspension onto the 10X Genomics GemCode single cell instrument, which can produce single cell gel beads (GEMs). Generate a library from cDNA and sequence Chromium Next GEM Single Cell 30 Kit v3.1. After the gel beads were dissolved in GEM, the primers were released and mixed with the cell lysate and the main mixture. Reverse transcribe the full-length cDNA of the barcode from polyadenylation mRNA and then amplify it. The library is sequencing on Illumina.

treatment_protocol: three years of peritoneal dialysis

value: peritoneal dialysis effluent

value: lymphoid cell, mononuclear phagocyte,epithelila cell

value: macrophage,T lymphocyte, B lymphocyte, peritoneal mesothelial cell, myofibroblast(activated fibroblast),NK cell


title: 004-Tumor-1808_ROI_RPL22 negative_immune low

status: Public on Dec 10 2025

type: SRA

city: Chapel Hill

first: Andrew

middle: B

last: Gladden

state: NC

address: 160 N. Medical Drive

department: Pathology & Laboratory Medicine

country: USA

institute: The University of North Carolina at Chapel Hill

description:
Library name: 004-Tumor-1808
raw_counts.txt

library_source: transcriptomic

data_processing:
Nanostring quality control process
Assembly: FASTQ files processed into DCC files by geomxngspipeline build 2.3.3.10
Supplementary files format and content: Nanostring genome assembly
Supplementary files format and content: DCC and rawcount
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: FFPE endometrial tumor

growth_protocol: No growth protocol

extract_protocol:
Nanostring antigen retrieval protocol
Nanostring library construction protocol

treatment_protocol: No treatment protocol

tag: tissue

value: Endometrium

tag: genotype

value: MLH1 deficient

tag: rpl22 status

value: negative

tag: immune status

value: immune low


title: Donor 55 – SIRPG WT CD4+ T cells, Day 2

city: Boston

first: Flavien

last: Marguerie

address: 60 Fenwood Road

department: Rheumatology and Immunology

institute: Brigham and Women's Hospital

description:
Library name: 55CD4SIRPGWTD2
Wild-type CD4+ T cells, sorted

data_processing:
Data processing tool: Sequence reads were processed using fastp for quality control and adapter trimming, and Salmon (v1.3.2) for transcript quantification in quasi-mapping mode.
Mapping: Trimmed sequence reads were mapped to the GRCh38.p14 transcriptome.
Differential expression analysis: DESeq2 (v1.46.0) was used for differential gene expression analysis.
Gene Ontology (GO): GO enrichment was performed using the clusterProfiler (v4.10.0) R package
Analysis tool for protein-protein interactions: Protein-protein interaction analysis was done using the STRING database (v12.0).
Assembly: GRCh38.p14 (Human genome assembly)
Supplementary files format and content: The processed data is in CSV format, including FPKM values for each sample

source_name: PBMCs

extract_protocol:
RNA was isolated from PBMCs using Qiagen's RNeasy Mini Plus Kit, and lysates were stored at -80°C until further processing.
RNA-seq libraries were prepared using the SMARTer mRNA-Seq Library Prep Kit, following the manufacturer's protocols. This method was used for preparing RNA libraries for SmartSeq2 protocol.

value: PBMCs

tag: cell type

value: CD4+ T cells

value: SIRPG WT

tag: treatment

value: Anti-CD3, IL-2

tag: time

value: Day 2


title: 006-Tumor-2201_ROI_RPL22 positive_immune high

description:
Library name: 006-Tumor-2201
raw_counts.txt

value: positive

value: immune high


title: Donor 50 – SIRPG KO CD8+ T cells, Day 4

description:
Library name: 50CD8SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD8+

value: CD8+ T cells

value: SIRPG KO

value: Day 4


title: 003-Immune-2201_ROI_RPL22 negative_immune low

description:
Library name: 003-Immune-2201
raw_counts.txt


title: Donor 50 – SIRPG WT CD8+ T cells, Day 4

description:
Library name: 50CD8SIRPGWTD4
Wild-type CD8+ T cells, sorted


title: Donor 55 – SIRPG KO CD8+ T cells, Day 4

description:
Library name: 55CD8SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD8+


title: Donor 50 – SIRPG KO CD8+ T cells, Day 2

description:
Library name: 50CD8SIRPGKOD2
CRISPR-mediated SIRPG knockout, sorted CD8+


title: DMSO_3

city: Aurora

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

description: Library name: DMSO_3

data_processing:
Fastq files were processed using the nf-core/rnaseq pipeline (version 3.12.0, https://nf-co.re/rnaseq/3.12).
Sequencing adapters were removed using Cutadapt (version 3.4) as part of the trimgalore package (version 0.6.7).
Reads were aligned using STAR (version 2.7.9a) to the mouse transcriptome (GRCh38, gene annotation from Ensembl release 104).
Gene quantification was performed using Salmon (version 1.10.1).
Tables with transcript and gene counts were generated by the tximport R package (version 1.26.0) under R version 4.2.2.
Assembly: GRCh38
Supplementary files format and content: Txt file containg gene counts

source_name: MCF7 ER Y537S

growth_protocol: Cells were grown in phenol-red free MEM supplemented with 5% charcoal stripped FBS, 2 mM glutamine, non-essential amino acids, pen/strep, 1 nM insulin, and 1 nM DHT

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kits. Samples were quantitated and quality assessed using Nanodrop 2000 before submission to RNA sequencing core.
Universal Plus mRNA-Seq library preparation kit with NuQuant was used with 200 ng RNA input to generate libraries.

treatment_protocol: Cells were treated with DMSO or 30 uM Enzalutamide for 96 hours before harvest

tag: cell line

value: MCF7 ER Y537S

value: ER+ breast cancer

value: ER Y537S Knock-in

value: DMSO

tag: batch


title: Donor 50 – SIRPG WT CD8+ T cells, Day 2

description:
Library name: 50CD8SIRPGWTD2
Wild-type CD8+ T cells, sorted


title: MR2R-34

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Library name: Sample 7

data_processing:
De-multiplexing and generation of FASTQ files were performed using Illumina CASAVA v1.8.2.
FastQC v0.11.7 (RRID: SCR_014583) was used to examine the quality of raw reads and cutadapt v1.18 was used for trimming the sequencing adaptors (5’- AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’, -trim-n). Reads unlikely to be properly sequenced mature miRNA transcripts were discarded (reads shorter than 16 nt or longer than 25 nt with –m 16 –M 25 in cutadapt).
Alignment and quantification of mature miRNAs based on miRBase v22 (RRID: SCR_003152) were performed with miRDeep2 v0.1.0 with mapper.pl parameters –e –h –m –i –j and quantifier.pl parameter –k –j –d -P. For mature miRNAs associated with multiple precursor miRNAs, the max counts were used.
We performed miRNA-seq sample quality assessments and miRNA filtering separately for each sample type (endobronchial biopsies and bronchial brushes). We limited the analysis to the miRNA samples with previously analyzed (GSE109743, dbGaP:phs003185.v1.p1) matched mRNA expression profiles (n=160 biopsies, n=89 brushes). The raw counts were converted into log2 counts per million of miRNA reads mapped (logCPM) and quantile normalized with voom. miRNAs with logCPM less than 1 in more than half of the samples were removed. We excluded samples (n=4 biopsies, n=2 brushes) if sequencing quality metrics were outside 2 standard deviations from the mean. The quality metrics we used included the first and the second principal components from the PCA using filtered miRNA expression, the mean Pearson expression correlation with all other samples across the filtered miRNAs, and the transcript integrity number (TIN) of the matched mRNA sequencing sample (calculated using RSeQC v3.0.0, RRID: SCR_005275). Finally, 156 biopsies and 87 brush samples from 30 patients were retained.
The gene filter and normalization described above were performed on the final high-quality samples with matching mRNA data (n=525 miRNAs in biopsies and n=489 miRNAs in brushes). The residual miRNA expressions adjusting for sequencing batch were computed with limma (RRID: SCR_010943) for downstream analysis.
Assembly: hg38
Supplementary files format and content: PCGA_miRNA_raw_count_table_BX.csv: Comma-separated value (CSV) table of raw counts, 2656 miRNAs x 156 samples
Supplementary files format and content: PCGA_miRNA_residual_table_BX.csv: Comma-separated value (CSV) table of residuals, 525 rows x 156 columns

source_name: bronchial biopsy

extract_protocol:
miRNA was extracted from biopsies or brushing samples using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.
miRNA sequencing libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEBioLabs). Sequencing adapters that target the 3’ hydroxyl group of small RNAs were ligated and the transcripts were reverse transcribed and PCR-amplified into single-stranded cDNA libraries. The libraries were pooled, and size selected for small RNA fragments on PAGE gel in groups of 6-10.

value: bronchial biopsy

tag: pcga id

tag: patient id

tag: flowcell

tag: dysplasia grade

value: moderate dysplasia

tag: molecular subtype

value: Proliferative

tag: progression status

value: regressive

tag: median tin


title: Donor 50 – SIRPG KO CD4+ T cells, Day 4

description:
Library name: 50CD4SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD4+

value: PBMCs

value: CD4+ T cells


title: Donor 50 – SIRPG WT CD4+ T cells, Day 4

description:
Library name: 50CD4SIRPGWTD4
Wild-type CD4+ T cells, sorted

value: SIRPG WT

value: Anti-CD3, IL-2


title: 003-Immune-1808_ROI_RPL22 negative_immune low

description:
Library name: 003-Immune-1808
raw_counts.txt

value: Endometrium

value: MLH1 deficient

value: negative

value: immune low


title: 902-MR284

description: Library name: Sample 6

value: normal

value: Secretory

value: progressive/persistent


title: Donor 50 – SIRPG WT CD4+ T cells, Day 2

description:
Library name: 50CD4SIRPGWTD2
Wild-type CD4+ T cells, sorted

value: Day 2


title: Donor 50 – SIRPG KO CD4+ T cells, Day 2

description:
Library name: 50CD4SIRPGKOD2
CRISPR-mediated SIRPG knockout, sorted CD4+

value: SIRPG KO


title: Donor 49 – SIRPG KO CD8+ T cells, Day 4

description:
Library name: 49CD8SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD8+

value: CD8+ T cells

value: Day 4


title: MR2R-70

description: Library name: Sample 10

value: bronchial biopsy

value: Normal

value: unknown


title: 001-Immune-2201_ROI_RPL22 positive_immune high

description:
Library name: 001-Immune-2201
raw_counts.txt

value: positive

value: immune high


title: Donor 49 – SIRPG WT CD8+ T cells, Day 4

description:
Library name: 49CD8SIRPGWTD4
Wild-type CD8+ T cells, sorted

value: PBMCs

value: SIRPG WT

value: Anti-CD3, IL-2


title: Donor 55 – SIRPG KO CD4+ T cells, Day 2

description:
Library name: 55CD4SIRPGKOD2
CRISPR-mediated SIRPG knockout, sorted CD4+

value: CD4+ T cells


title: MR2R-37

description: Library name: Sample 4

value: hyperplasia

value: Proliferative

value: normal/stable


title: Donor 49 – SIRPG KO CD8+ T cells, Day 2

description:
Library name: 49CD8SIRPGKOD2
CRISPR-mediated SIRPG knockout, sorted CD8+


title: 001-Immune-1808_ROI_RPL22 positive_immune low

description:
Library name: 001-Immune-1808
raw_counts.txt

value: Endometrium

value: MLH1 deficient

value: immune low


title: MR2R-71

description: Library name: Sample 9

value: Secretory


title: MR2R-33

description: Library name: Sample 8

value: mild dysplasia

value: regressive


title: Donor 49 – SIRPG KO CD4+ T cells, Day 4

description:
Library name: 49CD4SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD4+

value: SIRPG KO

value: Day 4


title: Donor 49 – SIRPG WT CD8+ T cells, Day 2

description:
Library name: 49CD8SIRPGWTD2
Wild-type CD8+ T cells, sorted

value: CD8+ T cells

value: Day 2


title: Donor 49 – SIRPG WT CD4+ T cells, Day 4

description:
Library name: 49CD4SIRPGWTD4
Wild-type CD4+ T cells, sorted

value: PBMCs


title: 009-Tumor-2244_ROI_RPL22 negative_immune low

description:
Library name: 009-Tumor-2244
raw_counts.txt

value: negative


title: MR_280

description: Library name: Sample 3

value: bronchial biopsy

value: normal


title: MR176

description: Library name: Sample 2


title: Donor 49 – SIRPG KO CD4+ T cells, Day 2

description:
Library name: 49CD4SIRPGKOD2
CRISPR-mediated SIRPG knockout, sorted CD4+

value: CD4+ T cells

value: Anti-CD3, IL-2


title: 002-Immune-2201_ROI_RPL22 positive_immune low

description:
Library name: 002-Immune-2201
raw_counts.txt

value: positive


title: Donor 49 – SIRPG WT CD4+ T cells, Day 2

description:
Library name: 49CD4SIRPGWTD2
Wild-type CD4+ T cells, sorted

value: SIRPG WT


title: MR146

description: Library name: Sample 1

value: moderate dysplasia

value: Proliferative


title: 007-Tumor-2244_ROI_RPL22 positive_immune high

description:
Library name: 007-Tumor-2244
raw_counts.txt

value: Endometrium

value: MLH1 deficient

value: immune high


title: Donor 36 – SIRPG KO CD8+ T cells, Day 4

description:
Library name: 36CD8SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD8+

value: SIRPG KO


title: 002-Immune-1808_ROI_RPL22 positive_immune high

description:
Library name: 002-Immune-1808
raw_counts.txt


title: Donor 36 – SIRPG WT CD8+ T cells, Day 4

description:
Library name: 36CD8SIRPGWTD4
Wild-type CD8+ T cells, sorted

value: Day 4


title: MR_174

description: Library name: Sample 5

value: Normal

value: progressive/persistent


title: MR70

description: Library name: Sample 87

data_processing:
De-multiplexing and generation of FASTQ files were performed using Illumina CASAVA v1.8.2.
FastQC v0.11.7 (RRID: SCR_014583) was used to examine the quality of raw reads and cutadapt v1.18 was used for trimming the sequencing adaptors (5’- AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’, -trim-n). Reads unlikely to be properly sequenced mature miRNA transcripts were discarded (reads shorter than 16 nt or longer than 25 nt with –m 16 –M 25 in cutadapt).
Alignment and quantification of mature miRNAs based on miRBase v22 (RRID: SCR_003152) were performed with miRDeep2 v0.1.0 with mapper.pl parameters –e –h –m –i –j and quantifier.pl parameter –k –j –d -P. For mature miRNAs associated with multiple precursor miRNAs, the max counts were used.
We performed miRNA-seq sample quality assessments and miRNA filtering separately for each sample type (endobronchial biopsies and bronchial brushes). We limited the analysis to the miRNA samples with previously analyzed (GSE109743, dbGaP:phs003185.v1.p1) matched mRNA expression profiles (n=160 biopsies, n=89 brushes). The raw counts were converted into log2 counts per million of miRNA reads mapped (logCPM) and quantile normalized with voom. miRNAs with logCPM less than 1 in more than half of the samples were removed. We excluded samples (n=4 biopsies, n=2 brushes) if sequencing quality metrics were outside 2 standard deviations from the mean. The quality metrics we used included the first and the second principal components from the PCA using filtered miRNA expression, the mean Pearson expression correlation with all other samples across the filtered miRNAs, and the transcript integrity number (TIN) of the matched mRNA sequencing sample (calculated using RSeQC v3.0.0, RRID: SCR_005275). Finally, 156 biopsies and 87 brush samples from 30 patients were retained.
The gene filter and normalization described above were performed on the final high-quality samples with matching mRNA data (n=525 miRNAs in biopsies and n=489 miRNAs in brushes). The residual miRNA expressions adjusting for sequencing batch were computed with limma (RRID: SCR_010943) for downstream analysis.
Assembly: hg38
Supplementary files format and content: PCGA_miRNA_raw_count_table_BR.csv: Comma-separated value (CSV) table of raw counts, 2656 miRNAs x 87 samples
Supplementary files format and content: PCGA_miRNA_residual_table_BR.csv: Comma-separated value (CSV) table of residuals, 489 rows x 87 columns

source_name: bronchial brushing

value: bronchial brushing


title: Donor 36 – SIRPG WT CD8+ T cells, Day 2

description:
Library name: 36CD8SIRPGWTD2
Wild-type CD8+ T cells, sorted

value: PBMCs

value: CD8+ T cells

value: Day 2


title: Donor 36 – SIRPG KO CD8+ T cells, Day 2

description:
Library name: 36CD8SIRPGKOD2
CRISPR-mediated SIRPG knockout, sorted CD8+


title: 006-Immune-2244_ROI_RPL22 positive_immune low

description:
Library name: 006-Immune-2244
raw_counts.txt

value: immune low


title: MR61

description: Library name: Sample 86

value: severe dysplasia


title: Donor 36 – SIRPG KO CD4+ T cells, Day 4

description:
Library name: 36CD4SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD4+

value: CD4+ T cells

value: Anti-CD3, IL-2


title: MR2R-16

description: Library name: Sample 85

value: mild dysplasia


title: Donor 36 – SIRPG WT CD4+ T cells, Day 4

description:
Library name: 36CD4SIRPGWTD4
Wild-type CD4+ T cells, sorted

value: SIRPG WT


title: Donor 32 – SIRPG KO CD8+ T cells, Day 4

description:
Library name: 32CD8SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD8+
The sample pair (32CD8SIRPGWTD4 and 32CD8SIRPGKOD4) was excluded because sequencing did not work for one of the two samples.


title: 004-Immune-2244_ROI_RPL22 positive_immune high

description:
Library name: 004-Immune-2244
raw_counts.txt

value: Endometrium

value: positive


title: 853-MR94

description: Library name: Sample 84


title: Donor 32 – SIRPG WT CD8+ T cells, Day 4

description:
Library name: 32CD8SIRPGWTD4
Wild-type CD8+ T cells, sorted
The sample pair (32CD8SIRPGWTD4 and 32CD8SIRPGKOD4) was excluded because sequencing did not work for one of the two samples.


title: Donor 32 – SIRPG WT CD8+ T cells, Day 2

description:
Library name: 32CD8SIRPGWTD2
Wild-type CD8+ T cells, sorted


title: Donor 32 – SIRPG KO CD8+ T cells, Day 2

description:
Library name: 32CD8SIRPGKOD2
CRISPR-mediated SIRPG knockout, sorted CD8+


title: 003-Tumor-0949_ROI_RPL22 positive_immune low

description:
Library name: 003-Tumor-0949
raw_counts.txt

value: MLH1 deficient


title: MR_75

description: Library name: Sample 83

value: moderate dysplasia


title: 008-Tumor-2244_ROI_RPL22 positive_immune low

description:
Library name: 008-Tumor-2244
raw_counts.txt


title: 003-Immune-2244_ROI_RPL22 negative_immune low

description:
Library name: 003-Immune-2244
raw_counts.txt

value: negative


title: MR59

description: Library name: Sample 82


title: Donor 32 – SIRPG WT CD4+ T cells, Day 2

description:
Library name: 32CD4SIRPGWTD2
Wild-type CD4+ T cells, sorted


title: 002-Tumor-0949_ROI_RPL22 negative_immune low

description:
Library name: 002-Tumor-0949
raw_counts.txt


title: Donor 30 – SIRPG KO CD8+ T cells, Day 4

description:
Library name: 30CD8SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD8+

value: SIRPG KO

value: Day 4


title: Donor 32 – SIRPG KO CD4+ T cells, Day 2

description:
Library name: 32CD4SIRPGKOD2
CRISPR-mediated SIRPG knockout, sorted CD4+


title: MR_89

description: Library name: Sample 80

value: bronchial brushing


title: Donor 30 – SIRPG WT CD8+ T cells, Day 4

description:
Library name: 30CD8SIRPGWTD4
Wild-type CD8+ T cells, sorted

value: PBMCs


title: 002-Immune-2244_ROI_RPL22 positive_immune low

description:
Library name: 002-Immune-2244
raw_counts.txt


title: Donor 30 – SIRPG KO CD8+ T cells, Day 2

description:
Library name: 30CD8SIRPGKOD2
CRISPR-mediated SIRPG knockout, sorted CD8+

value: CD8+ T cells


title: 001-Tumor-0949_ROI_RPL22 positive_immune high

description:
Library name: 001-Tumor-0949
raw_counts.txt

value: immune high


title: Donor 30 – SIRPG WT CD8+ T cells, Day 2

description:
Library name: 30CD8SIRPGWTD2
Wild-type CD8+ T cells, sorted

value: Day 2


title: MR69

description: Library name: Sample 79


title: Donor 30 – SIRPG KO CD4+ T cells, Day 4

description:
Library name: 30CD4SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD4+


title: 005-Immune-2244_ROI_RPL22 positive_immune high

description:
Library name: 005-Immune-2244
raw_counts.txt


title: Donor 30 – SIRPG KO CD4+ T cells, Day 2

description:
Library name: 30CD4SIRPGKOD2
CRISPR-mediated SIRPG knockout, sorted CD4+


title: 001-Immune-2244_ROI_RPL22 positive_immune high

description:
Library name: 001-Immune-2244
raw_counts.txt


title: Donor 30 – SIRPG WT CD4+ T cells, Day 4

description:
Library name: 30CD4SIRPGWTD4
Wild-type CD4+ T cells, sorted


title: Donor 30 – SIRPG WT CD4+ T cells, Day 2

description:
Library name: 30CD4SIRPGWTD2
Wild-type CD4+ T cells, sorted


title: 006-Tumor-1675_ROI_RPL22 positive_immune low

description:
Library name: 006-Tumor-1675
raw_counts.txt

value: immune low


title: MR2R-58

description: Library name: Sample 77

value: hyperplasia


title: MR83

description: Library name: Sample 76


title: 005-Tumor-1675_ROI_RPL22 positive_immune low

description:
Library name: 005-Tumor-1675
raw_counts.txt


title: 006-Tumor-0871_ROI_RPL22 negative_immune low

description:
Library name: 006-Tumor-0871
raw_counts.txt


title: human PCLS (snRNAseq)

city: Trieste

first: Davide

last: Selvestrel

address: Padriciano 99

country: Italy

institute: International Centre for Genetic Engeneering and Biotechnology (ICGEB)

description:
Library name: Human_sn_PCLS
Singleron

library_source: transcriptomic single cell

data_processing:
Illumina-compatible NGS libraries generated were sequenced on an Illumina NovaSeq 6000 instrument using a paired-end 150bp approach. The reads were demultiplexed on Illumina’s BaseCloud, and fastq files were used to initiate data analysis.
All the sampleswere mapped and expression levels summarized using Celescope pipeline version 2.3.0.
Assembly: Human samples were mapped against the GRCh38.v1.8.0 version of the Homo sapiens genome, while mouse sample was mapped against the Mus musculus GRCm39.v1.8.0 reference genome.
Supplementary files format and content: DDC_sn_PCLS.Rda - Rda file containing mouse snRNAseq data as Seurat object
Supplementary files format and content: Human_sn_PCLS.Rda - Rda file containing human snRNAseq  data as Seurat object. Human_sc_PCLS.Rda - Rda file containing human scRNAseq  data as Seurat object

molecule: polyA RNA

source_name: PCLS in EM for 144 h

growth_protocol: Human and mouse PCLS were cultured ex vivo

extract_protocol:
The single nuclei suspension from liver tissue was obtained using GEXSCOPE® Single Nucleus RNA Library Kit V2 (Singleron Biotechnologies). Briefly, on ice the tissue was immersed in 1ml of cold nucleus separation solution and cut into small pieces. Further homogenization was achieved by performing 10 strokes with a loose pestle (pestle A) and a tight pestle (Pestle B) (KIMBLE® KONTES® Dounce Tissue Grinder, cat. nr. 885300-0002).  The sample was then incubated on ice for 15 minutes where the state of nuclei extraction was monitored every 5 minutes under a light microscope. Following extraction, the nuclei suspension was filtered using a 30-µm sterile strainer (Miltenyi, cat. nr.130-098-458). The nuclei suspension was centrifuged at 200xg for 2 minutes at 4°C, and the supernatant was centrifuged at 500xg for 5 minutes at 4°C. The resulting pellet containing nuclei was resuspended in 0.25 ml of cold nuclei suspension buffer. The quality of the nuclei was assessed by Trypan Blue staining (0.4% w/v, Gibco) under a light microscope. The nuclei were counted using acridine/propidium iodide with a Luna FX7 automated cell counter (Logos Biosystems, Villeneuve d’Ascq, France).
A total of 45 000 nuclei were loaded onto a microfluidic chip (Singleron GEXSCOPE® Single Nucleus RNA Library Kit V2) for a minimal capture of 10 000 nuclei. Briefly, barcoded beads containing a unique Cell Barcode were loaded into the chip, and nuclei were lysed. After nuclei lysis, polyadenylated RNA was captured onto the Barcode Beads by the poly (dT) sequence. Barcode Beads with captured mRNA molecules were collected and subjected to reverse transcription reaction. The cDNA was then amplified and QC. For scRNA-seq, six human PCLS cultured for 144 hours were collected and dissociated for 3 minutes with TriplE. The digestion was stopped, and the cells were washed three times with PBS. A suspension of 3.5 × 10⁵ cells/mL was prepared in PBS, and the cells underwent library preparation. The scRNA-seq libraries were constructed using the GEXSCOPE® Single Cell RNA Library Kit (Singleron Biotechnology) following the manufacturer's protocol for a minimal capture of 10.000 cells.

value: PCLS in EM for 144 h

value: Liver cells


title: HUDEP-2 cells, Controlsh, biol rep 3

city: Bethesda

first: Yang

last: Du

state: MD

address: 4301 Jones Bridge Road

department: Pediatrics

institute: Uniformed Services University of the Health Sciences

description: Library name: Sample 6

data_processing:
FastQC (version v0.11.8) was applied to check the quality of raw reads. Trimmomatic (version v0.38) was applied to cut adaptors and trim low-quality bases with default setting. STAR Aligner version 2.7.1a was used to align the reads. Picard tools (version 2.20.4) was applied to mark duplicates of mapping. The StringTie version 2.0.4 was used to assemble the RNA-Seq alignments into potential transcripts.
Assembly: hg38
Supplementary files format and content: tab file includes FPKM values for each sample

growth_protocol: HUDEP-2 cells were maintained in StemSpan SFEM supplemented with 3 units/ml EPO, 50ng/ml SCF, 10-6 M dexamethasone, and 1 µg/ml Doxycycline.

extract_protocol:
RNA was extrated using NucleoSpin RNA Plus kit (Takara Bio).
Sequencing libraries were generated using the NEBNext Ultra II Directional Library Prep Kit (NEB) after PolyA selection

treatment_protocol: Cells transduced by lentiviral shRNAs were selected with puromycin (2 μg/ml) at 24 hours after infection for a duration of 48 hours.

value: Eryhroid cells

value: WT


title: Donor 32 – SIRPG KO CD4+ T cells, Day 4

description:
Library name: 32CD4SIRPGKOD4
CRISPR-mediated SIRPG knockout, sorted CD4+

value: CD4+ T cells

value: Anti-CD3, IL-2


title: HUDEP-2 cells, Controlsh, biol rep 2

description: Library name: Sample 5


title: Donor 32 – SIRPG WT CD4+ T cells, Day 4

description:
Library name: 32CD4SIRPGWTD4
Wild-type CD4+ T cells, sorted

value: SIRPG WT


title: MR_52

description: Library name: Sample 75

value: normal


title: MR32

description: Library name: Sample 81

value: moderate dysplasia


title: 005-Tumor-0871_ROI_RPL22 positive_immune high

description:
Library name: 005-Tumor-0871
raw_counts.txt

value: Endometrium

value: MLH1 deficient

value: positive


title: MR95

description: Library name: Sample 74

value: bronchial brushing


title: HUDEP-2 cells, MEN1sh2, biol rep 3

description: Library name: Sample 3

value: MEN1 knockdown


title: 004-Tumor-1675_ROI_RPL22 positive_immune low

description:
Library name: 004-Tumor-1675
raw_counts.txt


title: MR_30

description: Library name: Sample 73


title: 004-Tumor-0871_ROI_RPL22 positive_immune low

description:
Library name: 004-Tumor-0871
raw_counts.txt


title: MR_34

description: Library name: Sample 78


title: NOB25_HCT_1

city: Denver

first: Parsa

last: Haque

state: Colorado

address: 1635 Aurora Ct, Aurora, CO 80045

description: Library name: Sample 3_biol rep 3

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulated data.
Assembly: NCBI/UCSC/Ensembl
Supplementary files format and content: Gene counts for each sample in xlsx file

source_name: colorectal carcinoma

growth_protocol: HCT-116 was maintained DMEM, 10% FBS and 10% P/S at 5% humidity and 37C

extract_protocol:
RNA was harvested usingRNeasy Mini Kit (Qiagen), on-column DNase treatment and purity was quantified. 2ug of protein was submited for RNA seq analysis.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: HCT-116, cultured in 10% exosome-free FBS DMEM, was treated with vehicle (1xPBS), N-OB or OB EVs at 10^7 EV particles/ml for two consecutive days.

value: colorectal carcinoma

value: epithelial colonocyte

value: Wild-type

value: Obese EV BMI 46


title: HUDEP-2 cells, Controlsh, biol rep 1

description: Library name: Sample 4


title: 003-Immune-1675_ROI_RPL22 positive_immune high

description:
Library name: 003-Immune-1675
raw_counts.txt

value: immune high


title: OB46_1

description: Library name: Sample 2_biol rep 3

value: Non-obese EV BMI-25


title: NOB25_HCT_3

description: Library name: Sample 3_biol rep 1


title: HUDEP-2 cells, MEN1sh2, biol rep 1

description: Library name: Sample 1

value: Eryhroid cells


title: MR_60

description: Library name: Sample 71


title: 598-MR67

description: Library name: Sample 72


title: 003-Immune-0871_ROI_RPL22 positive_immune high

description:
Library name: 003-Immune-0871
raw_counts.txt


title: OB46_2

description: Library name: Sample 2_biol rep 2


title: human PCLS (scRNAseq)

description:
Library name: Human_sc_PCLS
Singleron

value: PCLS in EM for 144 h

value: Liver cells


title: MR35

description: Library name: Sample 70

value: severe dysplasia


title: 002-Immune-1675_ROI_RPL22 negative_immune low

description:
Library name: 002-Immune-1675
raw_counts.txt

value: negative

value: immune low


title: MR2R-26

description: Library name: Sample 69

value: metaplasia


title: Vehicle_HCT_1

description: Library name: Sample 1_biol rep3


title: 002-Immune-0871_ROI_RPL22 negative_immune low

description:
Library name: 002-Immune-0871
raw_counts.txt

value: Endometrium

value: MLH1 deficient


title: PT10_10uM_OTA+5uM_tBHQ_3

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Library name: PT10_TO3

data_processing:
Read quality was assessed using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and then reads were aligned to the Ensembl GRCh38 patch release 27 genome using the HISAT2 aligner .
Reads were imported into R, summarized as reads/gene using the Bioconductor Rsubread package , and then analyzed using the limma-voom  pipeline. An additional fold change criterion was included in the analysis to restrict to those genes with likely biologically meaningful changes in expression .
Assembly: GRCh38 patch release 27 genome
Supplementary files format and content: All counts are provided in a single file called Counts.txt, with samples in columns and genes in rows. The first column provides the Ensembl Gene ID for that row.

source_name: kidney

growth_protocol: Human primary tubule epithelial cells were cultured in DMEM (Gibco, 1130-032) with 1x ITS-A (Gibco, 51300044), 50 nM hydrocortisone (Sigma, H6909) and 1x Antimicrobic-Antimycotic (Gibco, 2520056) until confluence. Cells were passaged using 0.05% trypsin-EDTA (Gibco, 25200056) and neutralized with defined trypsin inhibitor (Gibco, R007100), centrifuged at 400g for 5 minutes, and re-plated with supplemented DMEM solution. Cells are incubated at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004) and converted to cDNA with 20 the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, 634891).
Sequencing libraries were constructed using the SMARTer ThruPlex DNA-Seq Kit (Takara, R400676) and sequenced on a NovaSeq 6000 or NovaSeq X instrument (Illumina, San Diego, CA).

treatment_protocol: PTECs, in triplicate, were plated in two 24-well plates (Costar, 3548) in supplemented DMEM medium and grown to confluence. Treatment group samples were pre-treated for 48 hours with DMEM medium and either sulforaphane (Sigma, S4441), or tBHQ (Sigma, 112941) and controls were treated with supplemented DMEM medium. Then, plates were treated for 72 hours with ochratoxin-A (Sigma, O1877) in either supplemented DMEM, supplemented DMEM + sulforaphane, or supplemented DMEM + tBHQ. Following 72-hour incubation, cells were lysed with Buffer RLT (Qiagen, 74004).

value: kidney

value: primary proximal tubule epithelial cells


title: Vehicle_HCT_3

description: Library name: Sample 1_biol rep1

value: colorectal carcinoma


title: Vehicle_HCT_2

description: Library name: Sample 1_biol rep2

value: epithelial colonocyte


title: MR_86

description: Library name: Sample 68

value: bronchial brushing

value: normal


title: NOB25_HCT_2

description: Library name: Sample 3_biol rep 2

value: Wild-type

value: Obese EV BMI 46


title: PT10_10uM_OTA+5uM_tBHQ_1

description: Library name: PT10_TO1


title: 001-Immune-1675_ROI_RPL22 negative_immune low

description:
Library name: 001-Immune-1675
raw_counts.txt


title: PT10_10uM_OTA+5uM_tBHQ_2

description: Library name: PT10_TO2


title: 001-Immune-0871_ROI_RPL22 positive_immune low

description:
Library name: 001-Immune-0871
raw_counts.txt

value: positive


title: PT10_5uM_tBHQ_3

description: Library name: PT10_T3


title: PT10_5uM_tBHQ_2

description: Library name: PT10_T2


title: PT10_10uM_OTA+20uM_SFN2_3

description: Library name: PT10_SO3


title: 006-Tumor-1884_ROI_RPL22 positive_immune high

description:
Library name: 006-Tumor-1884
raw_counts.txt

value: immune high


title: PT10_5uM_tBHQ_1

description: Library name: PT10_T1


title: MR_90

description: Library name: Sample 65


title: 518-MR56

description: Library name: Sample 67


title: PT10_10uM_OTA+20uM_SFN2_2

description: Library name: PT10_SO2


title: HUDEP-2 cells, MEN1sh2, biol rep 2

description: Library name: Sample 2

value: Eryhroid cells

value: MEN1 knockdown


title: PT10_10uM_OTA+20uM_SFN2_1

description: Library name: PT10_SO1


title: 006-Tumor-1364_ROI_RPL22 positive_immune high

description:
Library name: 006-Tumor-1364
raw_counts.txt


title: OB46_3

description: Library name: Sample 2_biol rep 1

value: Non-obese EV BMI-25


title: MR2R-42

description: Library name: Sample 64

value: mild dysplasia


title: PT10_20uM_SFN2_3

description: Library name: PT10_S3


title: PT10_20uM_SFN2_2

description: Library name: PT10_S2


title: 005-Tumor-1884_ROI_RPL22 positive_immune low

description:
Library name: 005-Tumor-1884
raw_counts.txt

value: immune low


title: 875-MR98

description: Library name: Sample 63

value: metaplasia


title: PT10_10uM_OTA_2

description: Library name: PT10_O2


title: PT10_10uM_OTA_3

description: Library name: PT10_O3


title: MR29

description: Library name: Sample 62


title: PT10_20uM_SFN2_1

description: Library name: PT10_S1


title: MR2R-64

description: Library name: Sample 61

value: severe dysplasia


title: 005-Tumor-1364_ROI_RPL22 negative_immune low

description:
Library name: 005-Tumor-1364
raw_counts.txt

value: Endometrium

value: MLH1 deficient

value: negative


title: PT10_10uM_OTA_1

description: Library name: PT10_O1

value: kidney

value: primary proximal tubule epithelial cells


title: 004-Tumor-1364_ROI_RPL22 positive_immune high

description:
Library name: 004-Tumor-1364
raw_counts.txt


title: 004-Tumor-1884_ROI_RPL22 positive_immune low

description:
Library name: 004-Tumor-1884
raw_counts.txt


title: PT10_Control_3

description: Library name: PT10_C3

value: Control


title: MR42

description: Library name: Sample 66

value: bronchial brushing


title: 002-Immune-1884 002_ROI_RPL22 positive_immune high

description:
Library name: 002-Immune-1884 002
raw_counts.txt


title: MR7

description: Library name: Sample 57

value: moderate dysplasia


title: MR2R-21

description: Library name: Sample 60


title: THP-1 derived M2, PFUnDA, 48h,replication 2

city: 北京

first: 丽娟

last: 游

state: 北京Beijing

address: 潘家园南里7号楼

country: China

institute: 国家食品安全风险评估中心

description: Library name: PFUnDA2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: M2, PFUnDA, 48h,replication 2

growth_protocol: Human monocytic THP-1 cells (TIB-202) were purchased from the American Type Culture Collection (ATCC) and maintained in complete Roswell Park Memorial Institute (RPMI) 1640 medium with 10% (vol/vol) fetal bovine serum (FBS) and 1% (vol/vol) penicillin/streptomycin. A peroxisome proliferator-activated receptor response element (PPRE)-eGFP-THP-1 cell line was established using the PPRE-H2B-eGFP plasmid. The PPRE-eGFP-THP-1 cell line was maintained in RPMI 1640 complete medium supplemented with 10% (vol/vol) FBS and 1% (vol/vol) penicillin/streptomycin. All cells were cultured in an environment of 37°C, 5% CO2, and 95% humidity.

extract_protocol:
Total RNA was extracted from  cultured cells withTRIzol reagent.mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: In this experiment, PPRE-eGFP THP-1 cells were seeded at a density of 70,000 cells per well in black-walled 96-well plates (model: 960096, n=3) to induce their differentiation into M2 macrophages. During the differentiation induction period, the cells were exposed to perfluorinated compounds. After 48 hours of treatment,

value: M2 Macrophage

value: 100μM PFUnDA


title: PT10_Control_1

description: Library name: PT10_C1


title: THP-1 derived M2, HFPODA, 48h,replication 3

institute: 国家食品安全风险评估中心

description: Library name: HFPODA3

source_name: M2, HFPODA, 48h,replication 3

value: 100μM HFPODA


title: THP-1 derived M2, PFUnDA, 48h,replication 3

institute: 国家食品安全风险评估中心

description: Library name: PFUnDA3

source_name: M2, PFUnDA, 48h,replication 3


title: 002-Immune-1364_ROI_RPL22 positive_immune high

description:
Library name: 002-Immune-1364
raw_counts.txt

value: positive

value: immune high


title: THP-1 derived M2, HFPODA, 48h,replication 2

institute: 国家食品安全风险评估中心

description: Library name: HFPODA2

source_name: M2, HFPODA, 48h,replication 2


title: MR27

description: Library name: Sample 58


title: THP-1 derived M2, PFUnDA, 48h,replication 1

institute: 国家食品安全风险评估中心

description: Library name: PFUnDA1

source_name: M2, PFUnDA, 48h,replication 1


title: 003-Immune-1884_ROI_RPL22 positive_immune low

description:
Library name: 003-Immune-1884
raw_counts.txt


title: 719-MR78

description: Library name: Sample 56

value: hyperplasia


title: THP-1 derived M2, PFOA, 48h,replication 2

institute: 国家食品安全风险评估中心

description: Library name: PFOA2

source_name: M2, PFOA, 48h,replication 2

value: 100μM PFOA


title: MR2R-4

description: Library name: Sample 59


title: THP-1 derived M2, HFPODA, 48h,replication 1

institute: 国家食品安全风险评估中心

description: Library name: HFPODA1

source_name: M2, HFPODA, 48h,replication 1


title: MR2R-1

description: Library name: Sample 55


title: 003-Immune-1364_ROI_RPL22 positive_immune low

description:
Library name: 003-Immune-1364
raw_counts.txt

value: immune low


title: THP-1 derived M2, control, replication 3

institute: 国家食品安全风险评估中心

description: Library name: CT3

source_name: M2, control, replication 3

value: 0.1% DMSO


title: THP-1 derived M2, PFOA, 48h,replication 1

institute: 国家食品安全风险评估中心

description: Library name: PFOA1

source_name: M2, PFOA, 48h,replication 1


title: THP-1 derived M2, PFOA, 48h,replication 3

institute: 国家食品安全风险评估中心

description: Library name: PFOA3

source_name: M2, PFOA, 48h,replication 3


title: THP-1 derived M2, control, replication 1

institute: 国家食品安全风险评估中心

description: Library name: CT1

source_name: M2, control, replication 1


title: 001-Immune-1884_ROI_RPL22 negative_immune low

description:
Library name: 001-Immune-1884
raw_counts.txt

source_name: FFPE endometrial tumor

value: Endometrium


title: 001-Immune-1364_ROI_RPL22 positive_immune high

description:
Library name: 001-Immune-1364
raw_counts.txt

value: MLH1 deficient


title: MR_48

description: Library name: Sample 54


title: 008-Tumor-2045_ROI_RPL22 positive_immune low

description:
Library name: 008-Tumor-2045
raw_counts.txt


title: THP-1 derived M2, control, replication 2

institute: 国家食品安全风险评估中心

description: Library name: CT2

source_name: M2, control, replication 2


title: PT10_Control_2

description: Library name: PT10_C2


title: MR_87

description: Library name: Sample 53

source_name: bronchial brushing

value: normal


title: CE_pt4_Neu_3

city: Seoul

first: Sugyeong

last: Jo

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University College of Medicine

description:
Library name: G-F10_CE_pt4_Neu_3
FFPE Spatial transcriptome sequencing

data_processing:
Library strategy: Spatial transcriptomics (GeoMx DSP)
FASTQ read data was processed through the GeoMx NGS Pipeline and converted digital count conversion files (.dcc files). Digital counts from each segment were scaled 75th percentile (quartile 3; Q3) of expression.
Assembly: hg38
Supplementary files format and content: digital count conversion (.dcc) file
Supplementary files format and content: xlsx file include Q3 normalized data
Library strategy: Spatial Transcriptomics

source_name: Blood clot

extract_protocol:
Retrieved thrombi were fixed in 4% paraformaldehyde, embedded in paraffin, and sectioned at 4 μm. Tissue slides were hybridized with Human Whole Transcriptome Atlas probes, followed by staining with morphology markers. For each tissue sample, 3–6 regions of interest (ROIs) were selected and segmented into CD68+, CD163+, or NE+MPO+ groups based on immunofluorescence signals.
Oligonucleotides from the segmented areas were released by UV light and indexed using Illumina i5/i7 dual indexing primers. PCR products were pooled and purified using AMPure XP beads (Beckman Coulter). The pooled libraries were sequenced at 100-bp paired-end read length on an Illumina NovaSeq 6000 platform.

value: Blood clot


title: CE_pt4_Neu_2

description:
Library name: G-F09_CE_pt4_Neu_2
FFPE Spatial transcriptome sequencing


title: CE_pt3_Neu_2

description:
Library name: G-F06_CE_pt3_Neu_2
FFPE Spatial transcriptome sequencing


title: 007-Tumor-2045_ROI_RPL22 negative_immune low

description:
Library name: 007-Tumor-2045
raw_counts.txt

value: negative


title: CE_pt3_Neu_3

description:
Library name: G-F07_CE_pt3_Neu_3
FFPE Spatial transcriptome sequencing


title: 006-Tumor-2045_ROI_RPL22 positive_immune high

description:
Library name: 006-Tumor-2045
raw_counts.txt


title: MR11

description: Library name: Sample 51


title: CE_pt3_Neu_1

description:
Library name: G-F05_CE_pt3_Neu_1
FFPE Spatial transcriptome sequencing


title: 004-Immune-2045_ROI_RPL22 negative_immune low

description:
Library name: 004-Immune-2045
raw_counts.txt


title: MR97

description: Library name: Sample 50


title: MR33

description: Library name: Sample 52

value: metaplasia


title: 005-Immune-2045_ROI_RPL22 negative_immune low

description:
Library name: 005-Immune-2045
raw_counts.txt


title: CE_pt2_Neu_3

description:
Library name: G-E07_CE_pt2_Neu_3
FFPE Spatial transcriptome sequencing


title: CE_pt2_Neu_2

description:
Library name: G-E06_CE_pt2_Neu_2
FFPE Spatial transcriptome sequencing


title: CE_pt2_Neu_1

description:
Library name: G-E05_CE_pt2_Neu_1
FFPE Spatial transcriptome sequencing


title: MR2R-39

description: Library name: Sample 49

value: bronchial brushing


title: 003-Immune-2045_ROI_RPL22 positive_immune low

description:
Library name: 003-Immune-2045
raw_counts.txt


title: CE_pt1_Neu_2

description:
Library name: G-E03_CE_pt1_Neu_2
FFPE Spatial transcriptome sequencing


title: CE_pt1_Neu_3

description:
Library name: G-E04_CE_pt1_Neu_3
FFPE Spatial transcriptome sequencing


title: LAA_pt5_Neu_3

description:
Library name: G-E10_LAA_pt5_Neu_3
FFPE Spatial transcriptome sequencing


title: MR_53

description: Library name: Sample 47

value: mild dysplasia


title: 649-MR74

description: Library name: Sample 48


title: CE_pt1_Neu_1

description:
Library name: G-E02_CE_pt1_Neu_1
FFPE Spatial transcriptome sequencing


title: LAA_pt5_Neu_2

description:
Library name: G-E09_LAA_pt5_Neu_2
FFPE Spatial transcriptome sequencing


title: LAA_pt5_Neu_1

description:
Library name: G-E08_LAA_pt5_Neu_1
FFPE Spatial transcriptome sequencing


title: 002-Tumor-0398_ROI_RPL22 positive_immune high

description:
Library name: 002-Tumor-0398
raw_counts.txt


title: MR93

description: Library name: Sample 46


title: LAA_pt3_Neu_3

description:
Library name: G-F01_LAA_pt3_Neu_3
FFPE Spatial transcriptome sequencing


title: 002-Immune-2045_ROI_RPL22 positive_immune high

description:
Library name: 002-Immune-2045
raw_counts.txt


title: CE_pt4_Neu_1

description:
Library name: G-F08_CE_pt4_Neu_1
FFPE Spatial transcriptome sequencing


title: LAA_pt3_Neu_2

description:
Library name: G-E12_LAA_pt3_Neu_2
FFPE Spatial transcriptome sequencing


title: 001-Tumor-0398_ROI_RPL22 positive_immune low

description:
Library name: 001-Tumor-0398
raw_counts.txt


title: LAA_pt3_Neu_1

description:
Library name: G-E11_LAA_pt3_Neu_1
FFPE Spatial transcriptome sequencing


title: MR80

description: Library name: Sample 45

value: moderate dysplasia


title: LAA_pt2_Neu_3

description:
Library name: G-G01_LAA_pt2_Neu_3
FFPE Spatial transcriptome sequencing


title: 003-Tumor-0398_ROI_RPL22 negative_immune low

description:
Library name: 003-Tumor-0398
raw_counts.txt


title: LAA_pt2_Neu_2

description:
Library name: G-F12_LAA_pt2_Neu_2
FFPE Spatial transcriptome sequencing


title: 001-Immune-2045_ROI_RPL22 negative_immune low

description:
Library name: 001-Immune-2045
raw_counts.txt


title: LAA_pt1_Neu_2

description:
Library name: G-F03_LAA_pt1_Neu_2
FFPE Spatial transcriptome sequencing


title: MR_50

description: Library name: Sample 44


title: LAA_pt2_Neu_1

description:
Library name: G-F11_LAA_pt2_Neu_1
FFPE Spatial transcriptome sequencing


title: 006-Tumor-0636_ROI_RPL22 positive_immune low

description:
Library name: 006-Tumor-0636
raw_counts.txt


title: MR73

description: Library name: Sample 43


title: LAA_pt1_Neu_3

description:
Library name: G-F04_LAA_pt1_Neu_3
FFPE Spatial transcriptome sequencing


title: 507-MR55

description: Library name: Sample 42


title: MR2R-76

description: Library name: Sample 41

value: severe dysplasia


title: LAA_pt1_Neu_1

description:
Library name: G-F02_LAA_pt1_Neu_1
FFPE Spatial transcriptome sequencing


title: 006-Tumor-0458_ROI_RPL22 positive_immune high

description:
Library name: 006-Tumor-0458
raw_counts.txt


title: 863-MR96

description: Library name: Sample 40


title: CE_pt4_Mac2_2

description:
Library name: D-B07_CE_pt4_Mac2_2
FFPE Spatial transcriptome sequencing


title: CE_pt4_Mac2_1

description:
Library name: D-B06_CE_pt4_Mac2_1
FFPE Spatial transcriptome sequencing


title: CE_pt4_Mac1_1

description:
Library name: D-B08_CE_pt4_Mac1_1
FFPE Spatial transcriptome sequencing


title: 005-Tumor-0458_ROI_RPL22 positive_immune high

description:
Library name: 005-Tumor-0458
raw_counts.txt


title: MR64

description: Library name: Sample 39


title: 005-Tumor-0636_ROI_RPL22 positive_immune low

description:
Library name: 005-Tumor-0636
raw_counts.txt


title: CE_pt4_Mac1_2

description:
Library name: D-B09_CE_pt4_Mac1_2
FFPE Spatial transcriptome sequencing


title: 004-Tumor-0636_ROI_RPL22 positive_immune high

description:
Library name: 004-Tumor-0636
raw_counts.txt


title: CE_pt3_Mac2_1

description:
Library name: D-B02_CE_pt3_Mac2_1
FFPE Spatial transcriptome sequencing


title: CE_pt3_Mac2_2

description:
Library name: D-B03_CE_pt3_Mac2_2
FFPE Spatial transcriptome sequencing


title: CE_pt3_Mac1_2

description:
Library name: D-B05_CE_pt3_Mac1_2
FFPE Spatial transcriptome sequencing


title: CE_pt3_Mac1_1

description:
Library name: D-B04_CE_pt3_Mac1_1
FFPE Spatial transcriptome sequencing


title: CE_pt2_Mac2_2

description:
Library name: D-A03_CE_pt2_Mac2_2
FFPE Spatial transcriptome sequencing


title: MR_82

description: Library name: Sample 37


title: MR_37

description: Library name: Sample 38


title: 004-Tumor-0458_ROI_RPL22 negative_immune low

description:
Library name: 004-Tumor-0458
raw_counts.txt


title: CE_pt2_Mac2_1

description:
Library name: D-A02_CE_pt2_Mac2_1
FFPE Spatial transcriptome sequencing


title: CE_pt2_Mac1_2

description:
Library name: D-A05_CE_pt2_Mac1_2
FFPE Spatial transcriptome sequencing


title: MR12

description: Library name: Sample 35


title: CE_pt2_Mac1_1

description:
Library name: D-A04_CE_pt2_Mac1_1
FFPE Spatial transcriptome sequencing


title: CE_pt1_Mac2_3

description:
Library name: H-A10_CE_pt1_Mac2_3
FFPE Spatial transcriptome sequencing


title: 003-Immune-0636_ROI_RPL22 positive_immune high

description:
Library name: 003-Immune-0636
raw_counts.txt


title: 003-Immune-0458_ROI_RPL22 negative_immune low

description:
Library name: 003-Immune-0458
raw_counts.txt


title: 002-Immune-0636_ROI_RPL22 negative_immune low

description:
Library name: 002-Immune-0636
raw_counts.txt


title: MR36

description: Library name: Sample 36


title: CE_pt1_Mac2_2

description:
Library name: H-A09_CE_pt1_Mac2_2
FFPE Spatial transcriptome sequencing


title: CE_pt1_Mac1_3

description:
Library name: H-B01_CE_pt1_Mac1_3
FFPE Spatial transcriptome sequencing


title: CE_pt1_Mac1_2

description:
Library name: H-A12_CE_pt1_Mac1_2
FFPE Spatial transcriptome sequencing


title: 002-Immune-0458_ROI_RPL22 negative_immune low

description:
Library name: 002-Immune-0458
raw_counts.txt


title: CE_pt1_Mac1_1

description:
Library name: H-A11_CE_pt1_Mac1_1
FFPE Spatial transcriptome sequencing


title: MR13

description: Library name: Sample 34


title: LAA_pt4_Mac2_2

description:
Library name: D-A07_LAA_pt4_Mac2_2
FFPE Spatial transcriptome sequencing


title: 001-Immune-0636_ROI_RPL22 positive_immune low

description:
Library name: 001-Immune-0636
raw_counts.txt


title: LAA_pt4_Mac2_1

description:
Library name: D-A06_LAA_pt4_Mac2_1
FFPE Spatial transcriptome sequencing


title: 001-Immune-0458_ROI_RPL22 positive_immune high

description:
Library name: 001-Immune-0458
raw_counts.txt


title: LAA_pt4_Mac1_2

description:
Library name: D-A09_LAA_pt4_Mac1_2
FFPE Spatial transcriptome sequencing


title: MR2R-55

description: Library name: Sample 32


title: MR41

description: Library name: Sample 31


title: LAA_pt4_Mac1_1

description:
Library name: D-A08_LAA_pt4_Mac1_1
FFPE Spatial transcriptome sequencing


title: MR43

description: Library name: Sample 30


title: LAA_pt3_Mac2_2

description:
Library name: D-A11_LAA_pt3_Mac2_2
FFPE Spatial transcriptome sequencing


title: MR5

description: Library name: Sample 33


title: LAA_pt3_Mac1_2

description:
Library name: D-B01_LAA_pt3_Mac1_2
FFPE Spatial transcriptome sequencing


title: LAA_pt3_Mac2_1

description:
Library name: D-A10_LAA_pt3_Mac2_1
FFPE Spatial transcriptome sequencing


title: MR_31

description: Library name: Sample 29


title: CE_pt1_Mac2_1

description:
Library name: H-A08_CE_pt1_Mac2_1
FFPE Spatial transcriptome sequencing


title: LAA_pt3_Mac1_1

description:
Library name: D-A12_LAA_pt3_Mac1_1
FFPE Spatial transcriptome sequencing


title: 699-MR77

description: Library name: Sample 28


title: LAA_pt2_Mac2_2

description:
Library name: D-B11_LAA_pt2_Mac2_2
FFPE Spatial transcriptome sequencing


title: LAA_pt2_Mac2_1

description:
Library name: D-B10_LAA_pt2_Mac2_1
FFPE Spatial transcriptome sequencing


title: 005-Tumor-0989_ROI_RPL22 positive_immune low

description:
Library name: 005-Tumor-0989
raw_counts.txt


title: LAA_pt2_Mac1_2

description:
Library name: D-C01_LAA_pt2_Mac1_2
FFPE Spatial transcriptome sequencing


title: MR_54

description: Library name: Sample 27


title: 004-Tumor-1272_ROI_RPL22 positive_immune high

description:
Library name: 004-Tumor-1272
raw_counts.txt


title: LAA_pt2_Mac1_1

description:
Library name: D-B12_LAA_pt2_Mac1_1
FFPE Spatial transcriptome sequencing


title: MR2R-51

description: Library name: Sample 26


title: LAA_pt1_Mac1_2

description:
Library name: H-A06_LAA_pt1_Mac1_2
FFPE Spatial transcriptome sequencing


title: 003-Immune-1272_ROI_RPL22 positive_immune low

description:
Library name: 003-Immune-1272
raw_counts.txt


title: LAA_pt1_Mac1_3

description:
Library name: H-A07_LAA_pt1_Mac1_3
FFPE Spatial transcriptome sequencing


title: 006-Tumor-1272_ROI_RPL22 positive_immune high

description:
Library name: 006-Tumor-1272
raw_counts.txt


title: LAA_pt1_Mac2_1

description:
Library name: H-A02_LAA_pt1_Mac2_1
FFPE Spatial transcriptome sequencing


title: LAA_pt1_Mac1_1

description:
Library name: H-A05_LAA_pt1_Mac1_1
FFPE Spatial transcriptome sequencing


title: MR63

description: Library name: Sample 23


title: 003-Immune-0989_ROI_RPL22 positive_immune high

description:
Library name: 003-Immune-0989
raw_counts.txt


title: LAA_pt1_Mac2_2

description:
Library name: H-A03_LAA_pt1_Mac2_2
FFPE Spatial transcriptome sequencing


title: 004-Tumor-0989_ROI_RPL22 positive_immune low

description:
Library name: 004-Tumor-0989
raw_counts.txt


title: 002-Immune-1272_ROI_RPL22 positive_immune high

description:
Library name: 002-Immune-1272
raw_counts.txt


title: HumanLiver_S414

city: Singapore

first: Qing

last: Zhao

address: 28 Medical Dr

country: Singapore

institute: NUS

data_processing:
FastQC (v0.11.9) was used for quality control. STAR (v2.7.9a) was used for alignment to reference genome. RSEM (v1.3.1) was used for gene expression level estimation.
Assembly: GRCh38, Ensembl release 77
Supplementary files format and content: Tab-delimited text file includes TPM for each sample.

source_name: Liver

extract_protocol:
RNA was extracted from liver biopsies using Trizol reagent.
The cDNA libraries were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit from Illumina (Yeasen) as per manufacturer’s instructions.

value: Liver

tag: gender

value: Female

tag: age at_biopsy

tag: body mass_index

tag: diabetes

tag: steatosis grade

tag: fibrosis grade

tag: inflammation grade

tag: ballooning grade

tag: nafld activity_score

tag: diagnosis

value: No Pathology


title: 843-MR92

description: Library name: Sample 24

tag: tissue

tag: pcga id


title: MR18

description: Library name: Sample 22

tag: patient id

tag: flowcell


title: HumanLiver_S398

value: MASL


title: 002-Immune-0989_ROI_RPL22 negative_immune low

description:
Library name: 002-Immune-0989
raw_counts.txt

tag: genotype

tag: rpl22 status

tag: immune status


title: HumanLiver_S416

tag: gender


title: LAA_pt1_Mac2_3

description:
Library name: H-A04_LAA_pt1_Mac2_3
FFPE Spatial transcriptome sequencing


title: MR2R-13

description: Library name: Sample 25

tag: dysplasia grade

tag: median tin


title: MR2R-46

description: Library name: Sample 21


title: HumanLiver_S412

tag: age at_biopsy

tag: body mass_index

tag: diabetes


title: 005-Tumor-1272_ROI_RPL22 negative_immune low

description:
Library name: 005-Tumor-1272
raw_counts.txt


title: MR91

description: Library name: Sample 20


title: 001-immune-1272_ROI_RPL22 positive_immune high

description:
Library name: 001-immune-1272
raw_counts.txt

value: positive

value: immune high


title: HumanLiver_S409

tag: steatosis grade

tag: fibrosis grade

tag: inflammation grade


title: HumanLiver_S406

tag: ballooning grade

tag: nafld activity_score

tag: diagnosis

value: MASH


title: HumanLiver_S415

tag: tissue

value: Male


title: 006-tumor-1292_ROI_RPL22 negative_immune low

description:
Library name: 006-tumor-1292
raw_counts.txt

value: Endometrium

value: MLH1 deficient

value: immune low


title: 001-Immune-0989_ROI_RPL22 negative_immune low

description:
Library name: 001-Immune-0989
raw_counts.txt

value: negative


title: MR_40

description: Library name: Sample 19

tag: pcga id

tag: patient id

tag: flowcell


title: HumanLiver_S405


title: MR47

description: Library name: Sample 17


title: MR58

description: Library name: Sample 18

value: hyperplasia


title: HumanLiver_S401


title: HumanLiver_S402


title: MR26

description: Library name: Sample 16

value: bronchial brushing


title: HumanLiver_S397


title: HumanLiver_S413


title: HumanLiver_S399


title: HumanLiver_S404


title: HumanLiver_S411


title: HumanLiver_S396


title: MR2R-61

description: Library name: Sample 15

value: normal


title: HumanLiver_S394


title: 004-tumor-1292_ROI_RPL22 positive_immune high

description:
Library name: 004-tumor-1292
raw_counts.txt

tag: genotype

tag: rpl22 status

tag: immune status


title: MR85

description: Library name: Sample 14

tag: dysplasia grade

value: metaplasia

tag: median tin


title: HumanLiver_S403

tag: gender

tag: age at_biopsy

tag: body mass_index


title: HumanLiver_S392

tag: diabetes

tag: steatosis grade

tag: fibrosis grade


title: MR46

description: Library name: Sample 13


title: 003-tumor-0561_ROI_RPL22 negative_immune low

description:
Library name: 003-tumor-0561
raw_counts.txt


title: 006-immune-0561_ROI_RPL22 negative_immune low

description:
Library name: 006-immune-0561
raw_counts.txt


title: 726-MR79

description: Library name: Sample 12


title: HumanLiver_S390

tag: inflammation grade

tag: ballooning grade

tag: nafld activity_score


title: HumanLiver_S389

tag: tissue

tag: diagnosis


title: 003-immune-1292_ROI_RPL22 positive_immune low

description:
Library name: 003-immune-1292
raw_counts.txt


title: 005-tumor-1292_ROI_RPL22 positive_immune low

description:
Library name: 005-tumor-1292
raw_counts.txt


title: HumanLiver_S387


title: 005-tumor-0561_ROI_RPL22 positive_immune high

description:
Library name: 005-tumor-0561
raw_counts.txt


title: 324-MR28

description: Library name: Sample 11

tag: pcga id

tag: patient id

tag: flowcell


title: HumanLiver_S386


title: HumanLiver_S385


title: HumanLiver_S393


title: MR68

description: Library name: Sample 10

value: mild dysplasia


title: HumanLiver_S384

value: Liver


title: HumanLiver_S382

value: Female


title: MR2R-10

description: Library name: Sample 9


title: HumanLiver_S391


title: HumanLiver_S380


title: HumanLiver_S379

value: No Pathology


title: 001-immune-1292_ROI_RPL22 positive_immune low

description:
Library name: 001-immune-1292
raw_counts.txt

tag: genotype

tag: rpl22 status

tag: immune status


title: HumanLiver_S388

tag: gender

value: MASL


title: 001-immune-0561_ROI_RPl22 positive_immune high

description:
Library name: 001-immune-0561
raw_counts.txt

value: positive


title: HumanLiver_S378

tag: age at_biopsy


title: 692-MR76

description: Library name: Sample 8

tag: dysplasia grade

value: severe dysplasia

tag: median tin


title: HumanLiver_S376

tag: body mass_index

tag: diabetes

tag: steatosis grade


title: MR_45

description: Library name: Sample 7

value: moderate dysplasia


city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: 32-HCT-tet-PADI4-Nutlin-Doxy-IP-H3K27me3_S32

library_source: genomic

data_processing:
Sequencing reads were quality checked with FASTQC (v0.11.9)  and aligned to the GRCh37 (hg19) genome using STAR (v2.7.9a). Homer and macs2 were used for peak call. Deeptool used for bigwigfiles.
Assembly: Hg19
Supplementary files format and content: CPM-normalized bigWig files were generated using Deeptools (v3.5.1). Score represents the normalized coverage of DNA fragment at a given coordinate.
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: H1299: DMEM, 10% FBS, 1% Penn/Strep; HCT116: McCoy's 5A media, 10% tet-free FBS, 1%Penn/Strep

extract_protocol:
CUT&Tag was performed using the Epicypher CUTANA™ CUT&Tag Kit according to the manufacturer’s instructions
Barcoded libraries were made using Epicypher CUTANA CUT&Tag Library Prep Kit following manufacturer's instructions and quantified by Agilent 4200 Tapestation System.

treatment_protocol: H1299: transfect p53 or p53+PADI4. HCT116: treated with vehicle (DMSO), Nutlin, or Nutlin + Doxycycline

tag: cell line

tag: cell type

value: colorectal cancer cell line

tag: treatment

value: Nutlin + Doxycycline


title: HumanLiver_S377

tag: tissue

tag: fibrosis grade

tag: inflammation grade

tag: ballooning grade

tag: nafld activity_score

tag: diagnosis


title: HumanLiver_S375


title: 002-immune-0561_ROI_RPL22 positive_immune low

description:
Library name: 002-immune-0561
raw_counts.txt

value: Endometrium

tag: genotype

value: MLH1 deficient

tag: rpl22 status

tag: immune status


title: MR24

description: Library name: Sample 6

tag: pcga id

tag: patient id

tag: flowcell

tag: dysplasia grade


title: 31-HCT-tet-PADI4-Nutlin-Doxy-IP-IgG

description: Library name: 31-HCT-tet-PADI4-Nutlin-Doxy-IP-IgG_S31


title: HumanLiver_S374

tag: gender

tag: age at_biopsy

tag: body mass_index

tag: diabetes

tag: steatosis grade


title: HumanLiver_S373

tag: tissue

value: Male

tag: fibrosis grade


title: MR2R-69

description: Library name: Sample 5

value: hyperplasia

tag: median tin


title: HumanLiver_S371

tag: inflammation grade

tag: ballooning grade

tag: nafld activity_score


title: MR2R-31

description: Library name: Sample 4

value: bronchial brushing


title: HumanLiver_S370

tag: diagnosis


title: HumanLiver_S369


title: HumanLiver_S367


title: MR65

description: Library name: Sample 2


title: HumanLiver_S368


title: 896-MR99

description: Library name: Sample 3


title: HumanLiver_S366


title: MR_51

description: Library name: Sample 1


title: HumanLiver_S365


title: HumanLiver_S364


title: 28-HCT-tet-PADI4-Nutlin-Doxy-IP-p53

description: Library name: 28-HCT-tet-PADI4-Nutlin-Doxy-IP-p53_S28

tag: cell line

tag: cell type

tag: treatment


title: HumanLiver_S363


title: 26-HCT-tet-PADI4-Nutlin-IP-cit306

description: Library name: 26-HCT-tet-PADI4-Nutlin-IP-cit306_S26

value: Nutlin


title: HumanLiver_S362


title: HMVEC-C, DMSO, rep3

city: Shinjuku-ku

first: Toshiomi

last: Katsuki

state: Tokyo

address: Shinanomachi 35

department: Cardiology

country: Japan

institute: Keio University Hospital

description: Library name: DMSO_3

data_processing:
A NovaSeq6000 (Illumina, CA, US) was used to sequence 100 base
Sequenced reads were aligned to the reference genome (hg19)
Assembly: hg19
Supplementary files format and content: Filtered raw counts and FPKM by StringTie-Ballgown pipeline

source_name: HMVEC-C

growth_protocol: Cell culture was performed according to the manufacture's protocol.

extract_protocol:
Total RNA was dissolved in TRIZOL (Thermo Fisher Scientific, MA, USA). RNA was purified using the ReliaPrep RNA Cell Miniprep System (Promega, WI, USA). The sequencing and mapping were performed by Macrogen (Tokyo, Japan).
Libraries were constructed using a TruSeq stranded mRNA Library (Illumina) according to the manufacturer’s instructions.

treatment_protocol: HMVEC were seeded in a 6-well plate at a density of 1 × 105 cells/2.5 mL concentrations. The medium was the same as that used for the co-culture. After 48 h, 1 µM final concentration BLT-1 (Sigma-Aldrich, Darmstadt, Germany) was added to treatment wells and DMSO was added so that the final DMSO concentration was the same as the treatment group. There were six cultured treatments and controls.

value: HMVEC-C

value: heart microvascular endothelial cells

value: DMSO


title: 25-HCT-tet-PADI4-Nutlin-IP-cit306

description: Library name: 25-HCT-tet-PADI4-Nutlin-IP-cit306_S25


title: HumanLiver_S359

value: Liver

value: Female


title: HMVEC-C, DMSO, rep2

description: Library name: DMSO_2


title: HumanLiver_S372

value: MASL


title: 24-HCT-tet-PADI4-Nutlin-IP-p53

description: Library name: 24-HCT-tet-PADI4-Nutlin-IP-p53_S24


title: 30-HCT-tet-PADI4-Nutlin-Doxy-IP-cit306

description: Library name: 30-HCT-tet-PADI4-Nutlin-Doxy-IP-cit306_S30


title: 29-HCT-tet-PADI4-Nutlin-Doxy-IP-cit306

description: Library name: 29-HCT-tet-PADI4-Nutlin-Doxy-IP-cit306_S29


title: HumanLiver_S356

value: No Pathology


title: HumanLiver_S358


title: 23-HCT-tet-PADI4-Nutlin-IP-p53

description: Library name: 23-HCT-tet-PADI4-Nutlin-IP-p53_S23


title: 27-HCT-tet-PADI4-Nutlin-Doxy-IP-p53

description: Library name: 27-HCT-tet-PADI4-Nutlin-Doxy-IP-p53_S27


title: HMVEC-C, DMSO, rep1

description: Library name: DMSO_1


title: HumanLiver_S355


title: HumanLiver_S361


title: 22-HCT-tet-PADI4-vehicle-IP-cit306

description: Library name: 22-HCT-tet-PADI4-vehicle-IP-cit306_S22

value: Vehicle


title: HumanLiver_S354


title: HMVEC-C, BLT-1, rep2

description: Library name: BLT-1_2


title: Sample 25

type: genomic

city: Hospitalet de Llobregat

first: Barbara

last: Rivera

address: Granvia de l'Hospitalet de Llobregat, 199

country: Spain

institute: IDIBELL

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC (850K) Beadchip (Illumina) arrays using standard Illumina protocol

scan_protocol: Standard Illumina scanner and settings

data_processing: All methylation analyses were conducted in R (version 4.4.1). EPICv1 and EPICv2 array data were merged and preprocessed using the minfi package (version 1.52.0). Single-sample Noob normalization was performed. Probes with poor performance were excluded based on detection p-values prior to downstream analyses. Additionally, probes targeting the X and Y chromosomes, those containing single nucleotide polymorphisms (SNPs), and cross-reactive probes were filtered out. The data were further corrected for material type (FFPE/FFT) using the limma package (version 3.62.0).

label: Cy3 and Cy5

source_name: FFT

label_protocol: Standard Illumina protocol

extract_protocol: Tumoral DNA from fresh frozen tissue (FFT) samples was isolated with the DNeasy Blood and Tissue Qiagen kit and tumoral DNA from archived formalin-fixed, paraffin-embedded (FFPE) material was isolated using the QIAamp DNA FFPE Tissue Kit

tag: project

value: This study

tag: Sex

tag: tumor type

value: Minimally invasive follicular thyroid carcinoma (MIFTC)

tag: genotype

tag: tissue type

value: FFT


title: 21-HCT-tet-PADI4-vehicle-IP-cit306

description: Library name: 21-HCT-tet-PADI4-vehicle-IP-cit306_S21

value: colorectal cancer cell line


title: HumanLiver_S353

tag: gender

tag: age at_biopsy

tag: body mass_index

tag: diabetes


title: HMVEC-C, BLT-1, rep1

description: Library name: BLT-1_1


title: Sample 17

value: Follicular variant of papillary thyroid carcinoma (FVPTC)


title: 20-HCT-tet-PADI4-vehicle-IP-p53

description: Library name: 20-HCT-tet-PADI4-vehicle-IP-p53_S20


title: HumanLiver_S352

tag: tissue

value: Male

tag: steatosis grade

tag: fibrosis grade

value: MASH


title: Sample 14

value: Encapsulated angioinvasive follicular thyroid cancer (EAIFTC)


title: HumanLiver_S351

tag: inflammation grade

tag: ballooning grade

tag: nafld activity_score


title: HMVEC-C, BLT-1, rep3

description: Library name: BLT-1_3

tag: cell line

tag: cell type


title: 19-HCT-tet-PADI4-vehicle-IP-p53

description: Library name: 19-HCT-tet-PADI4-vehicle-IP-p53_S19

tag: treatment


title: Sample 30

source_name: FFPE

tag: project

tag: Sex

value: Follicular thyroid carcinoma (FTC)

value: FFPE


title: Old female chondrocyte #2

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
Library name: Sample 5
732CF, age 73, chondrocytes, female

data_processing:
Quality control was first applied to raw RNA sequencing reads by tool FastQC.
Low-quality reads and adapter sequences were filtered out by the Trimmomatic tool.
Surviving reads were then aligned to human reference genome hg38 using STAR aligner, and gene counts were quantified.
Assembly: hg38
Supplementary files format and content: *.STAR.ReadsPerGene.out.tab

source_name: Cartilage

extract_protocol:
Individual chondrocyte cultures (P0) were lysed with the QIAzol reagent (Qiagen, German Town, MD, United States), and RNA was isolated from the lysate using an RNA Easy Plus Universal Kit (Qiagen).
Library preparation and sequencing were performed according to Medgenome (CA, United States). Total mRNA was processed for next-generation sequencing performed with the Illumina HiSeq 2500 system (San Diego, CA, United States). Clontech SMARTer UltraTM Low Input RNA Kits (Mountain View, CA, United States) and NexeteraXT (San Diego, CA, United States) kits were used for library preparation.

value: Cartilage

value: Chondrocytes

tag: genotype

value: WT

tag: age group

value: Aged

tag: age

value: female


title: 18-H1299-p53-PADI4-IP-H3K27me3

description: Library name: 18-H1299-p53-PADI4-IP-H3K27me3_S18

value: Human lung cancer cell line

value: transfect p53+PADI4


title: HumanLiver_S349

value: Liver

tag: gender

tag: age at_biopsy

tag: diagnosis

value: No Pathology


title: Old female chondrocyte #1

description:
Library name: Sample 4
731CF, age 73, chondrocytes, female

tag: tissue


title: Supraspinal_Control_2

city: Milwaukee

first: Murray

last: Blackmore

state: WI

address: 561 N 16th St

department: Biomedical Sciences

institute: Marquette University

description:
Library name: CTR-C-2
10x Genomics

data_processing:
NovaSeq X Plus used for base-calling
CellRanger pipeline (10X Genomics) used for base-cell demultiplexing, alignment, read filtering, and UMI counting.
Low quality cells removed based on total UMI count
Software: CellRanger (7.0.1)
Assembly: mm10
Supplementary files format and content: .txt file of gene-barcode matrix for each sample, with genes along rows and cell-barcodes along columns.

molecule: nuclear RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
For extraction of nuclei, frozen tissue was promptly transferred from -80 °C storage to a chilled 2mL dounce (KIMBLE, Ref. DWK885300-0000) with chilled Nuclei EZ Lysis Buffer (Sigma-Aldrich N 3408). The sample was dounced 25 times with pestle A and 20 times with pestle B. The dounced sample was then transferred to a chilled 15mL conical tube and an additional 2mL of Nuclei EZ Lysis Buffer was added and gently mixed by inversion. The sample was incubated on ice for 5 minutes and centrifuged at 500G at 4 °C. The supernatant was removed, and the pellet was resuspended in 4mL of Nuclei EZ Lysis Buffer. The sample was incubated on ice and centrifuged at 500G at 4 °C for 5 minutes. Following the centrifugation, the supernatant was removed, and the pellet resuspended in 750 µl of Nuclei Suspension Buffer (NSB) (2% Bovine Serum Albumin (BSA, Sigma-Aldrich Ref. A9418), 40U/ µl RNase Inhibitor (Invitrogen Ref. AM2684), 1X PBS). For embryonic samples, which lacked AAV-derived nuclear mGl fluorescence propidium, iodide (Sigma, P4864, 1:500 dilution) was added to NSB to facilitate sorting.
5000 and 7000 nuclei were sorted directly into the Reverse Transcription Master Mix and single-nuclei libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (PN-1000269).

treatment_protocol: Adult mixed supaspinal neurons received either Sox11 or control treatment by injection of AAV2-Retro to cervical spinal cord to adult mice and were collected two weeks later.

value: Brain


title: HumanLiver_S348

value: Female

tag: body mass_index

tag: diabetes

tag: steatosis grade

value: MASL


title: Supraspinal_Sox11_2

description:
Library name: Sox11-2wk-U-3
10x Genomics


title: Supraspinal_Sox11_1

description:
Library name: Sox11-2wk-U-2
10x Genomics


title: 16-H1299-p53-PADI4-IP-cit363

description: Library name: 16-H1299-p53-PADI4-IP-cit363_S16


title: 17-H1299-p53-PADI4-IP-IgG

description: Library name: 17-H1299-p53-PADI4-IP-IgG_S17


title: HumanLiver_S347

tag: fibrosis grade

tag: inflammation grade

tag: ballooning grade


title: Young female chondrocyte #2

description:
Library name: Sample 2
36CF, age 36, chondrocytes, female

tag: cell type

value: Young


title: HumanLiver_S345

tag: nafld activity_score


title: 15-H1299-p53-PADI4-IP-cit363

description: Library name: 15-H1299-p53-PADI4-IP-cit363_S15

tag: cell line

tag: treatment


title: Young female chondrocyte #1

description:
Library name: Sample 1
24CF, age 24, chondrocytes, female

tag: genotype

tag: Sex


title: Supraspinal_Control_1

description:
Library name: CTR-C
10x Genomics


title: Cholinergic neurons, Bmal1 knockout, ZT20, biol rep 6

city: Chicago

first: Sharon

last: Tam

state: IL

address: 303 E Chicago Ave, Rm 13-270

institute: Northwestern University

description:
Library name: Sample 24
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT20_biol.rep.6

data_processing:
150bp paired-end sequencing was performed on a NovaSeq X Plus (Illumina) to a minimum depth of 30M reads.
Sequences were aligned to the mm10 transcriptome with STAR (v2.7.5) using the –quantMode Transcriptome and GeneCounts options.
Gene counts were obtained from mm10 annotations (Ensembl 98) using rsem-calculate-expression (v1.3.0).
Differential mRNA expression analysis was performed using DESeq2 (v1.32.0) after removal of genes with < 10 assigned counts. Differentially expressed transcripts were defined as having an FDR-adjusted p-value < 0.05.
Alternative splicing analysis was performed using rMATS (v4.0.2) to quantify reads across annotated splice junctions present in the mm10 assembly. Differentially spliced transcripts were defined as having an FDR-adjusted p-value < 0.05 and a minimum exon inclusion level difference > 10%.
Assembly: mm10
Supplementary files format and content: .csv file includes raw counts for Input and Samples

source_name: spinal cord cholinergic neurons

extract_protocol:
RNA was extracted using the Direct-zol RNA MicroPrep kit.
Libraries were constructed from 300 ng of RNA using the Illumina Stranded mRNA Prep kit according to the manufacturer's instructions.

value: spinal cord cholinergic neurons

value: Bmal1 knockout


title: Old female chondrocyte #3

description:
Library name: Sample 6
74CF, age 74, chondrocytes, female

tag: age group

tag: age


title: 006-Tumor-0989_ROI_RPL22 positive_immune low

last: Gladden

address: 160 N. Medical Drive

description:
Library name: 006-Tumor-0989
raw_counts.txt

data_processing:
Nanostring quality control process
Assembly: FASTQ files processed into DCC files by geomxngspipeline build 2.3.3.10
Supplementary files format and content: Nanostring genome assembly
Supplementary files format and content: DCC and rawcount
Library strategy: Spatial Transcriptomics

extract_protocol:
Nanostring antigen retrieval protocol
Nanostring library construction protocol

value: Endometrium

value: MLH1 deficient

tag: rpl22 status

value: positive

tag: immune status

value: immune low


title: HumanLiver_S344

tag: tissue

tag: gender

tag: age at_biopsy

tag: diagnosis


title: 9_DU145sh6-2-3_1

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: DU145 shRNA FZD6 #2 (7-9 triplicate)

data_processing:
Sequenced reads in FASTQ files were mapped to hg38 whole genome using STAR, and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

extract_protocol:
Total RNA was extracted using NucleoSpin RNA Plus kit (Macherey-Nagel, Bethlehem, PA) and was then reverse transcribed with an iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA).
Human FZD6 ORF was purchased from Origene (Rockville, MD). The shRNA-resistant mutant was generated using QuikChange II Site-Directed Mutagenesis Kit (Agilent, Santa Clara, CA).

value: WT


title: Cholinergic neurons, WT, ZT20, biol rep 6

description:
Library name: Sample 23
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT20_biol.rep.6

value: wild-type


title: Young female chondrocyte #3

description:
Library name: Sample 3
38CF, age 38, chondrocytes, female

value: Cartilage

value: Chondrocytes

value: female


title: HumanLiver_S343

value: Liver

value: Male

tag: body mass_index

tag: diabetes

tag: steatosis grade

tag: fibrosis grade

value: MASH


title: 13-H1299-p53-PADI4-IP-cit342

description: Library name: 13-H1299-p53-PADI4-IP-cit342_S13

tag: cell type

value: Human lung cancer cell line

value: transfect p53+PADI4


title: 8_DU145sh6-2-2_1

description: DU145 shRNA FZD6 #2 (7-9 triplicate)

tag: cell line


title: Cholinergic neurons, Bmal1 knockout, ZT8, biol rep 6

description:
Library name: Sample 22
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT8_biol.rep.6


title: HumanLiver_S342

value: Female

tag: inflammation grade

tag: ballooning grade

tag: nafld activity_score

value: No Pathology


title: 12-H1299-p53-PADI4-IP-cit306

description: Library name: 12-H1299-p53-PADI4-IP-cit306_S12

tag: treatment


title: Cholinergic neurons, WT, ZT8, biol rep 6

description:
Library name: Sample 21
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT8_biol.rep.6

value: spinal cord cholinergic neurons

tag: genotype


title: HumanLiver_S341

value: MASL


title: 7_DU145sh6-2-1_1

description: DU145 shRNA FZD6 #2 (7-9 triplicate)


title: Cholinergic neurons, Bmal1 knockout, ZT20, biol rep 5

description:
Library name: Sample 20
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT20_biol.rep.5

value: Bmal1 knockout


title: HumanLiver_S340


title: 11-H1299-p53-PADI4-IP-cit306

description: Library name: 11-H1299-p53-PADI4-IP-cit306_S11


title: 10-H1299-p53-PADI4-IP-p53-Do1

description: Library name: 10-H1299-p53-PADI4-IP-p53-Do1_S10


title: 6_DU145sh6-1-3_1

description: DU145 shRNA FZD6 #1 (4-6 triplicate)


title: 5_DU145sh6-1-2_1

description: DU145 shRNA FZD6 #1 (4-6 triplicate)


title: Cholinergic neurons, WT, ZT20, biol rep 5

description:
Library name: Sample 19
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT20_biol.rep.5


title: 9-H1299-p53-PADI4-IP-p53-Do1

description: Library name: 9-H1299-p53-PADI4-IP-p53-Do1_S9


title: HumanLiver_S338


title: Cholinergic neurons, Bmal1 knockout, ZT8, biol rep 5

description:
Library name: Sample 18
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT8_biol.rep.5


title: 4_DU145sh6-1-1_1

description: DU145 shRNA FZD6 #1 (4-6 triplicate)


title: 4-H1299-p53-IP-cit306

description: Library name: 4-H1299-p53-IP-cit306_S4

value: transfect p53


title: 3_DU145scr-3_1

description: DU145 scramble (1-3 triplicate)


title: 14-H1299-p53-PADI4-IP-cit342

description: Library name: 14-H1299-p53-PADI4-IP-cit342_S14


title: Cholinergic neurons, WT, ZT8, biol rep 5

description:
Library name: Sample 17
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT8_biol.rep.5


title: HumanLiver_S337


title: HumanLiver_S336


title: 2_DU145scr-2_1

description: DU145 scramble (1-3 triplicate)


title: 3-H1299-p53-IP-cit306

description: Library name: 3-H1299-p53-IP-cit306_S3


title: Cholinergic neurons, Bmal1 knockout, ZT20, biol rep 4

description:
Library name: Sample 16
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT20_biol.rep.4


title: 1_DU145scr-1_1

description: DU145 scramble (1-3 triplicate)


title: Cholinergic neurons, WT, ZT20, biol rep 4

description:
Library name: Sample 15
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT20_biol.rep.4


title: 2-H1299-p53-IP-p53-Do1

description: Library name: 2-H1299-p53-IP-p53-Do1_S2


title: 1-H1299-p53-IP-p53-Do1

description: Library name: 1-H1299-p53-IP-p53-Do1_S1


title: HumanLiver_S333


title: Cholinergic neurons, Bmal1 knockout, ZT8, biol rep 4

description:
Library name: Sample 14
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT8_biol.rep.4


title: STZ Endo 6mo (2)

first: Katia

last: Corano Scheri

address: 300 E. Superior St.

department: Ophthalmology, Feinberg School of Medicine

description: Library name: AF-18 (6mo)

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Data was demultiplexed and counted using Cell Range
Cell Ranger output was analyzed using Seurat version 4.3
Assembly: mm10
Supplementary files format and content: Tab-delimited text file with raw counts for each sample
Supplementary files format and content: Tab-delimited matrix files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Retina

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions.
Single cell suspensions were washed in PBS/2% BSA and checked for viability > 85%
Directional mRNA libraries were prepared using NEBNext Kits per the manufacturer’s instructions
10X Genomics NEXT GEM Kit V2, 10X genomics Library Construction kit

value: Retina

value: Endothelial cells

value: STZ (Diabetic)


title: CID4411_L1_lung_tumour

city: Darlinghurst

first: Leila

last: Eshraghi

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description:
Library name: CID4411_L1_lung_tumour
10x NextGEM 3'

data_processing:
Raw bcl files were demultiplexed and mapped to the reference genome GRCh38 using the Cell Ranger Single Cell v2.0 software (10X Genomics). The EmptyDrops method from the DropletUtils package (v1.2.2) was applied for cell filtering with additional cutoffs for cells with a gene and unique molecular identifier (UMIs) count greater than 200 and 250, respectively, and a mitochondrial percentage less than 20%.
Assembly: Genome_build: GRCh38
Supplementary files format and content: cloupe.cloupe = interactive exploration of single-cell data in Loupe Browser
Supplementary files format and content: filtered_gene_bc_matrices_h5.h5 = filtered gene–barcode count matrix
Supplementary files format and content: metrics_summary.csv = summary of quality control (QC) metrics
Supplementary files format and content: web_summary.html = interactive quality-control report

source_name: lung

extract_protocol:
Tumour Dissociation kit, human (Miltenyi Biotech, cat no 130-095-929)
Single-cell sequencing was performed using the Chromium Single-Cell v2 3’ and 5’ Chemistry Library, Gel Bead, Multiplex and Chip Kits (10X Genomics) according to the manufacturer's protocol. A total of 5,000 to 7,000 cells were targeted per well. Libraries were sequenced on the NextSeq 500 platform (Illumina) with pair-ended sequencing and dual indexing. A total of 26, 8 and 98 cycles were run for Read 1, i7 index and Read 2, respectively.

value: lung

tag: disease state

value: tumour

tag: disease

value: metastatic breast cancer

tag: age

value: 40 years

tag: Sex


title: CID4411_N3_lung_normal

description:
Library name: CID4411_N3_lung_normal
10x NextGEM 3'

tag: tissue

value: normal

value: female


title: Cholinergic neurons, WT, ZT8, biol rep 4

description:
Library name: Sample 13
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT8_biol.rep.4

value: wild-type


title: HumanLiver_S332

value: Liver

tag: gender

tag: age at_biopsy

tag: diagnosis


title: HumanLiver_S331

value: Female

tag: body mass_index

tag: diabetes

tag: steatosis grade


title: STZ Retina 6mo (2)

description: Library name: AF-15 (6mo)

tag: cell type

value: Retinal cells


title: Cholinergic neurons, WT, ZT20, biol rep 3

description:
Library name: Sample 11
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT20_biol.rep.3

value: spinal cord cholinergic neurons


title: Cholinergic neurons, Bmal1 knockout, ZT20, biol rep 3

description:
Library name: Sample 12
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT20_biol.rep.3


title: STZ Retina 6mo (3)

description: Library name: AF-17 (6mo)


title: AD990_G2_BrdU

city: New York

first: Axel

last: Delamarre

state: NY

address: 411 E 67th st

institute: MSKCC

description: Library name: AD990_G2_BrdU

data_processing:
The data processing step are detailed at:  https://github.com/Axel-Delamarre/Whitehouse-Lab/blob/main/Master_CAD-C. Birefly, 1-Index DNA barcodes, 2-Identify Barcodes in Reads, 3- Extract nucleosomes positions, 4- Align to reference genome, 5-Remove hairpin artifacts, 6- Process read informations, 7- Generate contact matrices
Assembly: saccer3
Supplementary files format and content: .hic and .mcool

organism: Saccharomyces cerevisiae

source_name: WT

extract_protocol:
Cells were broken using freezer mill (Spex SamplePrep,6875D) for 5 cycles, 2 min, 15cps. After verification of breakage under the microscope, cells were resuspended in 900μL of XLB-3 (supplemented with protease inhibitors, A32955, Pierce) and cross-linked by addition of DSG at 3mM final (Disuccinimidyl glutarate, A35392, ThermoFisher) for 30min at 30C. DSG was quenched by addition of 100μL of 1M Tris HCl, pH 8 for 1min.
SQK-LSK114

value: WT

value: Nocodazole


title: STZ Endo 6mo (1)

description: Library name: AF-14+16 (6mo)


title: HumanLiver_S330

tag: fibrosis grade

tag: inflammation grade

value: No Pathology


title: HumanLiver_S329

tag: ballooning grade

tag: nafld activity_score

value: MASL


title: 002-immune-1292_ROI_RPL22 positive_immune high

city: Chapel Hill

first: Andrew

institute: The University of North Carolina at Chapel Hill

description:
Library name: 002-immune-1292
raw_counts.txt

value: Endometrium

tag: genotype

value: MLH1 deficient

tag: rpl22 status

value: positive

tag: immune status

value: immune high


title: STZ Retina 6mo (1)

description: Library name: AF-13 (6mo)

value: Retina

tag: treatment

value: STZ (Diabetic)


title: AD979_G2_BrdU

description: Library name: AD979_G2_BrdU


title: Cholinergic neurons, Bmal1 knockout, ZT8, biol rep 3

description:
Library name: Sample 10
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT8_biol.rep.3

value: Bmal1 knockout


title: AD979_G2_scc1-aid

description: Library name: AD979_G2_scc1-aid

value: IAA, Nocodazole


title: HumanLiver_S328

value: Male


title: HumanLiver_S334

value: Liver


title: Sham Retina 6mo (3)

description: Library name: AF-5 (6mo)

value: Sham (control)


title: Cholinergic neurons, WT, ZT8, biol rep 3

description:
Library name: Sample 9
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT8_biol.rep.3

value: wild-type


title: 004-tumor-0561_ROI_RPL22 positive_immune low

description:
Library name: 004-tumor-0561
raw_counts.txt

value: immune low


title: Sham Endo 6mo (2)

description: Library name: AF-4+6 (6mo)

value: Endothelial cells


title: HumanLiver_S326

value: Female

value: MASH


title: AD978_G1

description: Library name: AD978_G1

value: WT

value: Alpha-factor


title: Cholinergic neurons, Bmal1 knockout, ZT20, biol rep 2

description:
Library name: Sample 8
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT20_biol.rep.2

value: spinal cord cholinergic neurons


title: Sham Retina 6mo (2)

description: Library name: AF-3 (6mo)

value: Retinal cells


title: AD977_G2

description: Library name: AD977_G2

value: Nocodazole


title: HumanLiver_S325


title: AD765_G2

description: Library name: AD765_G2


title: HumanLiver_S324


title: Sham Endo 6mo (1)

description: Library name: AF-2 (6mo)

value: Retina


title: Cholinergic neurons, Bmal1 knockout, ZT8, biol rep 2

description:
Library name: Sample 6
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT8_biol.rep.2


title: HumanLiver_S323

value: MASL


title: Sham Retina 6 mo (1)

description: Library name: AF-1 (6mo)


title: ΔDrs2  yeast cells rep2

city: shanghai

first: Geng

last: Lv

address: huangpuqu

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description: Library name: L1EJF2003930

data_processing:
fastap
Assembly: ASM1011175v1
Supplementary files format and content: csv files include count values for each Sample

organism: Nakaseomyces glabratus

source_name: yeast cells

extract_protocol:
Total RNA was extracted from tissue samples. The concentration and purity of the extracted RNA were measured using Nanodrop 2000. RNA integrity was assessed by agarose gel electrophoresis, and the RQN value was determined using Agilent 5300.
After extracting total RNA, enrich mRNA, then fragment the mRNA, reverse-transcribe to synthesize cDNA, ligate adaptors, perform fragment selection and library enrichment, and proceed to sequencing.

value: yeast cells

value: Drs2 knockout


title: Cholinergic neurons, WT, ZT8, biol rep 2

description:
Library name: Sample 5
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT8_biol.rep.2


title: Sham Endo 3mo (3)

description: Library name: AF-12 (3mo)


title: HumanLiver_S322

value: No Pathology


title: Cholinergic neurons, Bmal1 knockout, ZT20, biol rep 1

description:
Library name: Sample 4
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT20_biol.rep.1

value: Bmal1 knockout


title: ΔDrs2  yeast cells rep1

description: Library name: L1EJF2003929


title: Sham Retina 3mo (3)

description: Library name: AF-11 (3mo)

value: Sham (control)


title: Cholinergic neurons, WT, ZT20, biol rep 1

description:
Library name: Sample 3
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT20_biol.rep.1

value: wild-type


title: HumanLiver_S321

value: Liver


title: ATCC2001 yeast cells rep3

description: Library name: L1EJF2003928


title: HumanLiver_S320


title: Sham Endo 3mo (2)

description: Library name: AF-10 (3mo)

value: Endothelial cells


title: Cholinergic neurons, Bmal1 knockout, ZT8, biol rep 1

description:
Library name: Sample 2
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Exp.ZT8_biol.rep.1


title: ATCC2001 yeast cells rep2

description: Library name: L1EJF2003927


title: Cholinergic neurons, WT, ZT20, biol rep 2

description:
Library name: Sample 7
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT20_biol.rep.2


title: HumanLiver_S319

value: Male


title: ATCC2001 yeast cells rep1

description: Library name: L1EJF2003926


title: ΔDrs2  yeast cells rep3

description: Library name: L1EJF2003931


title: HumanLiver_S316

value: MASH


title: Sham Retina 3mo (2)

description: Library name: AF-9 (3mo)


title: STZ Retina 3 mo (3)

description: Library name: AF-7 (3mo)

value: STZ (Diabetic)


title: Cholinergic neurons, Pooled input

description:
Library name: Input
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Input

value: pooled input (wild-type and Bmal1 knockout)


title: Cholinergic neurons, WT, ZT8, biol rep 1

description:
Library name: Sample 1
Column name in 'raw.counts.all.samples_Bmal1-KO.csv': Ctrl.ZT8_biol.rep.1

value: spinal cord cholinergic neurons


title: STZ Endo 3mo (3)

description: Library name: AF-8 (3mo)


title: WT cholinergic neurons, ZT20, biol rep 3

description:
Library name: Sample 18
Column name in 'raw.counts.all.samples_timecourse.csv': ZT20_biol.rep.3

data_processing:
150bp paired-end sequencing was performed on a NovaSeq X Plus (Illumina) to a minimum depth of 30M reads.
Sequences were aligned to the mm10 transcriptome with STAR (v2.7.5) using the –quantMode Transcriptome and GeneCounts options.
Gene counts were obtained from mm10 annotations (Ensembl 98) using rsem-calculate-expression (v1.3.0).
Alternative splicing analysis was performed using rMATS (v4.0.2) to quantify reads across annotated splice junctions present in the mm10 assembly. Differentially spliced transcripts were defined as having an FDR-adjusted p-value < 0.05 and a minimum exon inclusion level difference > 10%.
Rhythmic mRNA expression and rhythmic splice frequency throughout the day were assessed by JTK_Cycle analysis, allowing for period lengths of 20, 24, or 28 hours to account for 4-hr sampling frequency. Rhythmicity was determined by an FDR-adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: .csv file includes raw counts for Input and Samples

extract_protocol:
RNA was extracted using the Direct-zol RNA MicroPrep kit.
Libraries were constructed from 100 ng of RNA using the Illumina Stranded mRNA Prep kit according to the manufacturer's instructions.