title: CQ2_Nthy, PM2.5


title: CQ1_Nthy, PM2.5

status: Public on Dec 08 2024

type: SRA

city: chongqin

first: xiaomeng

last: li

state: nanchong

address: 266 Fangzheng Avenue, Shuitu Street

country: China

institute: Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing 1 ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content 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 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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two 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. 2 (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre_x0002_defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA independently.
GATK (v4.1.1.0) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 ; FS > 30.0; DP < 10.
Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(4.1.0) software was used to analysis the AS event.
PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions.
WGCNA (Weighted correlation network analysis) is a systematic biological method used to describe the gene association modes among different samples. it can be used to identify gene sets that are highly synergistic changed, and identify candidate biomarkers or therapeutic targets based on the coherence of gene sets and the correlation between gene sets and phenotypes. The R package WGCNA is a set of functions used to calculate various weighted association analysis, which can be used for network construction, gene screening, gene cluster identification, topological feature calculation, data simulation and visualization. WGCNA is suitable for multisample data. Generally, more than 15 samples are required. One input file is sample information, that is, a matrix describing the traits of the sample: the traits used for association analysis must be numeric; If it is a regional or categorical variable, it needs to be converted to a 0-1 matrix. The other is gene expression data. For transcriptome sequencing, FPKM can be used as gene expression data.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: thyroid

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

tag: tissue

value: thyroid

tag: cell line

value: Nthy

tag: cell type

value: Normal thyroid cells

tag: treatment


title: HEK293 cells_hnRNPA1_siRNA_rep3

city: Los Angeles

first: Su Jeong

last: Kim

state: CA

address: 3715 McClintock Ave

country: USA

institute: USC

data_processing:
The unaligned raw reads were processed on the PartekFlow platform (Partek Inc., St. Louis, MO, USA).
Raw sequencing reads were trimmed based on their quality scores (minimum Phred score 20, minimum read length 25 nt from both end) before being mapped to the human genome hg38 using STAR version 2.7.8a. Aligned reads were then quantified to transcriptome (GENECODE genes- release 40). using Partek’s E/M method and genes with fewer than 10 reads in all samples were excluded from the subsequent analyses. Median ratio algorithms and DeSeq2 were used for normalization and differential expression analysis.
Assembly: hg38
Supplementary files format and content: Partek_HEK_hnRNPA1siRNA_gene.xlsx

source_name: Human Embryo Kidney

growth_protocol: The HEK293 cells were cultured in DMEM + 10% FBS (FBS; ThermoFisher Scientific, Waltham, MA, USA) at 37° C in 5% CO2.

extract_protocol:
cells were washed with PBS and RNA was harvested using Trizol reagent.
Total RNA from RNA immunoprecipitation was checked for degradation in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). Libraries were prepared using a TruSeq Stranded Total RNA kit from Illumina (Illumina, San Diego, CA, USA)

value: Human Embryo Kidney

tag: cellular comparment for rna-seq

value: total

tag: genotype

value: hnRNPA1 knockdown


title: HEK293 cells_hnRNPA1_siRNA_rep2


title: HEK293 cells_control_siRNA_rep4

value: control


title: Control HG-stimulated MPC5 Cell Replicate 3 [N2-1]

city: Hefei

first: Ling

last: Jiang

state: Anhui

address: Meishan Road

institute: AHMU

data_processing:
Solexa pipeline version 1.8
The quality of the raw sequencing data was assessed using FastQC software v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), before the adapter sequences and poor quality bases were trimmed from the reads using the Cutadapt software v1.17
The Hisat2 software v2.0.4 (http://ccb.jhu.edu/software/hisat2) and StringTie software v1.2.2 (http://ccb.jhu.edu/software/stringtie) (33) were used to calculate fragments per kilobase of transcript per million mapped reads (FPKM) values, which represented the final expression levels of the genes. Differential gene expression level analyses were performed using the Ballgown package in R v2.10.0 (https://www.r-project.org) (32). An average FPKM value >0.5 was chosen as the cut-off for gene expression in the samples.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with expression gene counts for every gene and every sample

organism: Mus musculus

source_name: Control HG-stimulated MPC5 Cell

growth_protocol: MPC5 were purchased from the Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences. MPC5 was cultured at 33 ℃ in RPMI 1640 containing 10% fetal bovine serum and 20 U/ml mouse recombinant interferon-g (IFN-g) medium. In order to induce differentiation, the podocytes were maintained for 7 days under non-permissive conditions without IFN-γ at 37°C for the experiment. SiRNA (Hanbio Biotechnology Co., Ltd, China) was transfected into MPC5 cells by adding Lipofectamine RNAiMAX Reagent (Invitrogen) as recommended by the manufacturer. We used the negative scrambled siRNA (Hanbio Biotechnology Co., Ltd, China) as a control. The diluted siRNA and Lipofectamine RNAiMAX were combined and incubated for 20 min. The mixture was then added to the cells in OPTI-MEM medium. After incubation for 6 h, the cells were replaced by a complete medium. In this study, different treatments were used as followed: NG (5.5 mM glucose), MG (24.5 mM mannitol+ 5.5 mM glucose), HG (30 mM glucose),

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney podocyte

tag: genotype/variation

tag: treattment

value: HG-stimulated


title: WT3

city: Hangzhou

first: Wenlong

last: Lin

state: Zhejiang

address: 66 Yuhang Tang Road

institute: Zhejiang University

description: Library name: Sample 6

data_processing:
Clustering and sequencing (Novogene Experimental Department) The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome 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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Mouse colon

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Eight- to ten-week-old IEC-conditional Nedd4l knockout mice and their littermates were treated with 2% DSS (MP Biomedicals) in drinking water (w/v) for 7 days and sacrificed for further study

value: Mouse colon

value: WT

value: 2% DSS


title: HEK293 cells_control_siRNA_rep3


title: WT2 [colonic tissues without isolation]

description: Library name: Sample 5


title: WT1

description: Library name: Sample 4


title: CK2_IOSE, control

source_name: ovary

value: ovary

value: IOSE

value: Ovarian epithelial cells


title: cKO3

description: Library name: Sample 3

value: Nedd4l knockout


title: CK2_Nthy, control


title: HEK293 cells_control_siRNA_rep2


title: HEK293 cells_Total_hnRNPA1_rep2

data_processing: CLAM (CLIP-seq Analysis of Multi-mapped reads) v1.2.0 . Specifically, we ran the CLAM realigner command (parameters: --read-tagger-method median --retag --strandness opposite --winsize 100 --max-tags -1) to format files for CLAM processing. Then, we called peaks with the CLAM peakcaller command using only uniquely mapping reads (parameters: --binsize 500 -p 6 --qval-cutoff 0.05 -u).

extract_protocol:
RNA immunoprecipitation to examine RNAs bound to RNA binding protein was performed according to the nature protocol. Briefly, HEK293 cells were harvested in polysome lysis buffer (100mM KCl, 5mM MgCl2, 10mM HEPES, pH7.0, 0.5% Nonidet P-40, 1mM DTT, 100Uml-1 RNasin RNase inhibitor, 2mM vanadyl ribonucleoside complexes solution), protease inhibitor cocktail. Cell lysates were incubated on ice for 10 min, then centrifuged at 16,000g for 15min at 4C. The supernatants were incubated with dynabeads G that were already incubated with antibodies targeting hnRNPA1 or normal IgG controls (Invitrogen) for 4h at 4C with rotation. Beads were washed with polysome lysis buffer and polysome lysis buffer including 1M urea four times, respectively. The washed beads were incubated with polysome lysis buffer with 0.1% SDS and 30mg proteinase K at 50C for 39min. The bounds RNAs were eluted and subjected to reverse transcription followed by RT-PCR or next generation sequencing to identify individual mRNAs isolated with the hnRNPA1.
Total RNA from RNA immunoprecipitation was checked for degradation in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). Libraries were prepared using a TruSeq Stranded Total RNA kit from Illumina (Illumina, San Diego, CA, USA); given the high level of degradation, no further fragmentation was necessary during library preparation, and 12 cycles of final enrichment PCR were run for all samples regardless of the starting amount of RNA used. Final library products were quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc., Waltham, MA, USA), and the fragment size distribution was determined with the Bioanalyzer 2100. All but one of the samples yielded good libraries, though final molar concentrations varied between them. The libraries were pooled equimolarly, and the final pool was quantified via qPCR using the NEBNext Library Quant Kit for Illumina (New England BioLabs, Ipswich MA), according to manufacturer’s instructions. The pool was sequenced in an Illumina NextSeq 550 platform, in Paired-End 2x150 cycles format. Sample QC, library preparation and sequencing were performed at the USC Genome Core.

treatment_protocol: no treatment

tag: cellular comparment for rna immunoprecipitation

value: Total

tag: rip antibody


title: HEK293 cells_Total_hnRNPA1_rep3


title: HEK293 cells_Total_IgG_rep2

value: IgG


title: CK1_IOSE, control


title: CQ3_IOSE, PM2.5


title: HEK293 cells_Total_hnRNPA1_rep1


title: HEK293 cells_Total_IgG_rep1


title: cKO2

description: Library name: Sample 2


title: HEK293 cells_hnRNPA1_siRNA_rep1


title: HEK293 cells_Total_IgG_rep3


title: cKO1

description: Library name: Sample 1


title: CQ2_IOSE, PM2.5


title: CQ1_IOSE, PM2.5


title: CK3_IOSE, control


title: HEK293 cells_control_siRNA_rep1


title: HEK293 cells_mitochondria_hnRNPA1_rep3

value: mitochondria


title: HEK293 cells_mitochondria_hnRNPA1_rep4


title: WT2

description: Library name: Sample 5


title: HEK293 cells_hnRNPA1_siRNA_rep4


title: HEK293 cells_mitochondria_IgG_rep4


title: 2h-NZB-Treg-B3

city: Philadelphia

first: Jeffrey

middle: Allen

last: Haltom

state: PA

address: 3501 Civic Center Blvd

department: Center for Mitochondrial and Epigenomic Medicine

institute: Children's Hospital of Philadelphia

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 using Mus musculus GRCm38 as reference.
featureCounts (version 1.6.0)/HTSeq was used to count mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.
DESeq2 (version 1.14.1) was used to do the differential gene expression analysis.
Assembly: GRCm38
Supplementary files format and content: Raw counts in text file

molecule: polyA RNA

source_name: Treg

extract_protocol:
Isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by AccuBlue® Broad Range RNA Quantitation assay (Biotium, California, USA). Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA).
Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 40 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation D1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 430bp with an insert size of about 300bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® Novaseq platform(Illumina, California, USA) with a read length configuration of 150 PE for 40M PE reads per sample (20M in each direction).

value: Treg

value: NZB


title: 2h-NZB-Treg-B2


title: HEK293 cells_mitochondria_IgG_rep2


title: testis_CQ3, PM2.5

source_name: testis

value: testis

value: Sertoli cell


title: HEK293 cells_mitochondria_hnRNPA1_rep2


title: HEK293 cells_cytosol_hnRNPA1_rep4

value: cytosol


title: HEK293 cells_mitochondria_hnRNPA1_rep1


title: NZB-Treg-B1

value: NZB-Treg


title: testis_CQ1, PM2.5


title: NZB-Treg-A8


title: HEK293 cells_cytosol_hnRNPA1_rep3


title: HEK293 cells_cytosol_hnRNPA1_rep1


title: HEK293 cells_cytosol_hnRNPA1_rep2


title: whole animal, dve-1, L4 rep 2

city: Worcester

first: Kellianne

middle: D

last: Alexander

state: Massachusetts

address: 365 Plantation St

department: Neurobiology

institute: University of Massachusetts Chan Medical School

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence
A minimum of approximately 20 million clean reads were obtained per sample.
Raw reads were mapped using tophat2 Gapped-read mapper Galaxy Version 2.1.1.
Gene expression quantification was analyzed using cufflinks transcript assembly and FPKM estamites galaxy version 2.2.1.3.
Assembly: ce11
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: All strains were maintained under standard conditions at 25 degrees celcius on nematode growth media plates seeded with E. coli strain OP50. Animals were synchronized at L1 and collected.

extract_protocol:
around 1200 synchronized L1 larvae were collected. Total RNA was extracted with Trizol and purified by  Rneasy columns (Qiagen).
RNA libraries for RNA-seq were prepared by BGI Genomics using standard RNAseq library prep

value: whole animal

value: DVE-1 mutant

tag: time

value: L4 stage


title: testis_CK2, control

value: control


title: testis_CK3, control


title: HEK293 cells_cytosol_IgG_rep4


title: testis_CK1, control


title: testis_CQ2, PM2.5


title: whole animal, Control, L4 rep 2

value: WT


title: 2h-Treg-A5


title: HEK293 cells_cytosol_IgG_rep3


title: HEK293 cells_mitochondria_IgG_rep3


title: CQ3_926, PM2.5

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content 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 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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two 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. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways
Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a predefined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool 4 http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA independent
GATK (v4.1.1.0) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 ; FS > 30.0; DP <
Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(4.1.0) software was used to analysis the AS even
PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions
WGCNA (Weighted correlation network analysis) is a systematic biological method used to describe the gene association modes among different samples. it can be used to identify gene sets that are highly synergistic changed, and identify candidate biomarkers or therapeutic targets based on the coherence of gene sets and the correlation between gene sets and phenotypes. The R package WGCNA is a set of functions used to calculate various weighted association analysis, which can be used for network construction, gene screening, gene cluster identification, topological feature calculation, data simulation and visualization. WGCNA is suitable for multisample data. Generally, more than 15 samples are required. One input file is sample information, that is, a matrix describing the traits of the sample: the traits used for association analysis must be numeric; If it is a regional or categorical variable, it needs to be converted to a 0-1 matrix. The other is gene expression data. For transcriptome sequencing, FPKM can be used as gene expression data
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: cardiovascular

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, U
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were gen

value: cardiovascular

value: vascular endothelial cell


title: 2h-NZB-Treg-B4


title: 2h-Treg-A4


title: whole animal, Control, L4 rep 1


title: CQ2_926, PM2.5


title: HEK293 cells_cytosol_IgG_rep1


title: CQ1_926, PM2.5


title: whole animal, dve-1, L1 rep 2

value: L1 stage


title: HEK293 cells_cytosol_IgG_rep2


title: NZB-Treg-A7


title: whole animal, dve-1, L4 rep 1


title: CK2_926, control


title: 2h-Treg-A6


title: CK3_926, control


title: A-T

city: Shanghai

first: Baohui

last: Han

address: 227 South Chongqing Road

department: Department of Respiratory and Critical Care Medicine

institute: Shanghai Chest Hospital

description: Library name: sample 4

data_processing:
FastQC-11.8
Sequence reads were trimmed for adaptor sequence/low-qcccccuality sequence using TrimGalore-0.5.0 (parameter: -q 25 --phred33 --length 36 -e 0.1 --stringency 3)
Trimmed sequence reads were mapped to GRCh38 using hisat2-2.1.0
Read count extraction and normalization were performed using stringtie
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for all samples

growth_protocol: Cells were maintained in a humidified incubator at 37 °C with 5% CO2, grown in RPMI 1640 or DMEM supplemented with 10% FBS and penicillin (100 U/ml)/streptomycin(100μg/ml) (Gibco/Thermo Fisher).

extract_protocol:
Total RNA isolation were performed using TRIzol reagent (Life Technologies, Inc., USA) and RNA isolation Kit (Qiagen, Germany). mRNA isolation and residual genomic DNA degradation were performed.
100 ng mRNA from each sample was reverse-transcribed into cDNA and fragmented into 100-300-bp pieces. End-repair and adapter-ligation were performed via the NEBNext Ultra Directional RNA Library Prep Kit (NEB, USA). Amplification and sequencing were performed using PCR and Illumina Next500 (Illumina, USA).

treatment_protocol: A549 cells were treated with trametinib (10nM) or anlotinib (1μM) for 24 hours in 6-well plates, respectively.

value: non-small cell lung cancer

value: trametinib (10nM) plus anlotinib (1μM)


title: CK1_926, control


title: Treg-A2


title: AA_120_2

city: Chang Chun

first: Tongjia

last: Chu

state: Jilin

address: The First Bethune Hospital of Jilin University, No. 1 Xinmin Street, Chaoyang District, Changchun , Jilin Province

description: Library name: Sample 8

data_processing:
featureCounts v1.5.0-p3
Quality control：Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data (clean reads) were obtained by removing readscontaining adapter, reads containing ploy-N and low quality reads fromrawdata. At the same time, Q20, Q30 and GC content the clean data were calculated. All thedownstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome：Reference genome and gene model annotation files were downloaded fromgenome website directly. Index of the reference genome was built using Hisat2 v2.0.5and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a databaseof splice junctions based on the gene model annotation file and thus a better mappingresult than other non-splice mapping tools.
Quantification of gene expression level：featureCounts v1.5.0-p3 was used to count the reads numbers mapped to eachgene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: pancreas

extract_protocol:
A total amount of 1 µg RNA per sample was used as input material for the RNAsample preparations. Sequencing libraries were generated using NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’srecommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standardillumina protocols

value: pancreas

value: Tumor

value: Arachidonic acid (120microM)


title: whole animal, Control, L1 rep 2


title: A

description: Library name: sample 2

value: anlotinib (1μM)


title: AA_120_3

institute: The First Bethune Hospital of Jilin University

description: Library name: Sample 9


title: whole animal, Control, L1 rep 1


title: ctrl

description: Library name: sample 1

value: vehicle


title: Xkit_CMP_Rep#3

first: Rachel

last: Shahan

state: California

address: 610 Charles E. Young Dr. S

institute: University of California, Los Angeles

description: Library name: Xkit_CMP3

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Perform alignments with HISAT2 to the reference,Rice genome MSU annotation.
Assembly: MSU 7.0
Supplementary files format and content: xlsx file (Integrated raw counts for each gene caculated separately in different root  growth or treatment conditions)

organism: Oryza sativa

source_name: Root

growth_protocol: X.kitaake was used as wild type. Rice seeds were dehulled, sterilized with 50% bleach for 10 min, and rinsed four to five times with sterile water. All plant growth was in Yoshida’s nutrient solution solidified with gellan gum (Gelzan, Caisson Inc).Growth boxes were kept at 4°C in the dark for 2-3 days until the seeds germinate, then transferred to a percival growth chamber set to 28°C, and consistant light. Rice seedlings were grown in the percival for 1-3 days before harvesting.

extract_protocol:
For RNA isolation, root tips were ground to a fine powder in liquid nitrogen using a mortar and pestle, followed by the addition of 1 ml of RLT buffer to the powdered tissue. RNA was then isolated and purified using the RNeasy Mini Kit (QiagenTM) according to the manufacturer’s protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification, with Novogene NGS RNA Library Prep Set. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Root

value: All cell types of root


title: Treg-A3

value: Treg


title: CQ3_2B

city: Nanchong

first: Ronghua

last: Zhang

address: Sichuan Province Nanchong City Gaoping District North SiChuan Medical College

institute: North SiChuan Medical College

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing 0ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content 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 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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two 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.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome  sequencing and other high-through put experimental technologies(http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre_x0002_defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA independently
GATK (v4.1.1.0) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 ; FS > 30.0; DP < 10.
Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(4.1.0) software was used to analysis the AS event.
PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions.
WGCNA (Weighted correlation network analysis) is a systematic biological method used to describe the gene association modes among different samples. it can be used to identify gene sets that are highly synergistic changed, and identify candidate biomarkers or therapeutic targets based on the coherence of gene sets and the correlation between gene sets and phenotypes. The R package WGCNA is a set of functions used to calculate various weighted association analysis, which can be used for network construction, gene screening, gene cluster identification, topological feature calculation, data simulation and visualization. WGCNA is suitable for multisample data. Generally, more than 15 samples are required. One input file is sample information, that is, a matrix describing the traits of the sample: the traits used for association analysis must be numeric; If it is a regional or categorical variable, it needs to be converted to a 0-1 matrix. The other is gene expression data. For transcriptome sequencing, FPKM can be used as gene expression data.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: lung

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated

value: lung

value: lung epithelial cell


title: P3 neonatal ventricular cardiomyocytes_4

city: Taipei

first: Kai-Chien

last: Yang

address: No.1, Sec. 1, Ren-Ai Rd

department: Department and Graduate Institute of Pharmacology

country: Taiwan

institute: National Taiwan University, College of Medicine

data_processing:
Adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the mouse genome (mm10) with Hisat2, allowing up to two mismatches. Sequence reads aligned to the mouse genome were imported into Partek Genomics Suite version 6.6 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as FPKM (fragments per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each samples

source_name: heart

extract_protocol:
Total RNA was extracted from cardiac tissue and cells using TRIzol agent.
RNA libraries were prepared using TrueSeq RNA Sample Prep Kits (Illumina) by the manufacturer's recommendations.

value: heart

tag: strain

tag: developmental stage

value: Postnatal  day 3


title: AA_120_1

description: Library name: Sample 7


title: whole animal, dve-1, L1 rep 1

value: whole animal

value: DVE-1 mutant


title: Xkit_CMP_Rep#2

description: Library name: Xkit_CMP2

value: WT


title: P3 neonatal ventricular cardiomyocytes_3


title: CQ2_2B


title: AA_40_3

description: Library name: Sample 6

value: Arachidonic acid (40microM)


title: P3 neonatal ventricular cardiomyocytes_2


title: Xkit_CMP_Rep#1

description: Library name: Xkit_CMP1


title: T

description: Library name: sample 3

value: non-small cell lung cancer

value: trametinib (10nM)


title: Treg-A1


title: Xkit_NC_Rep#3

description: Library name: Xkit_NC3


title: CK3_2B


title: P3 neonatal ventricular cardiomyocytes_1


title: AA_40_1

description: Library name: Sample 4

value: pancreas

value: Tumor


title: Xkit_NC_Rep#2

description: Library name: Xkit_NC2


title: P1 neonatal ventricular cardiomyocytes_4

value: Postnatal  day 1


title: CK2_2B


title: CTRL_3

description: Library name: Sample 3

value: Control


title: Xkit_NC_Rep#1

description: Library name: Xkit_NC1

value: Root


title: CTRL_2

description: Library name: Sample 2


title: CK1_2B


title: P1 neonatal ventricular cardiomyocytes_3


title: Xkit_Gel_Rep#4

description: Library name: Xkit_gel4

value: All cell types of root


title: CQ3_A549

value: lung cancer cell


title: CTRL_1

description: Library name: Sample 1


title: Xkit_Gel_Rep#3

description: Library name: Xkit_gel3


title: P1 neonatal ventricular cardiomyocytes_1


title: CQ1_2B

value: lung


title: CQ2_A549


title: mEK_transplant_day12N

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
10x library equencing was performed on Illumina HiSeq X. Sequencing data were analyzed using Illumina bcl2fastq software (version 2.20.0) and converted to FASTQ format files. Subsequently, alignment was performed using the cellranger count function of Cell Ranger Single Cell software (version 7.1.0, 10x Genomics) with using STAR aligner 2.7.2a. The GRCm38 mouse reference genome, mm10 r102  was used.
Assembly: GRCm38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: kidney

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
library construction was performed by using Chromium Single Cell 3ʹ Reagent Kits v2.

value: kidney

tag: time point


title: AA_40_2

description: Library name: Sample 5


title: Xkit_Gel_Rep#2

description: Library name: Xkit_gel2


title: Adult ventricular cardiomyocytes_7

value: heart

value: Adult


title: CQ1_A549


title: Xkit_Gel_Rep#1

description: Library name: Xkit_gel1


title: GH3_A549


title: mEK_transplant_day12

description: 10x Genomics


title: Adult ventricular cardiomyocytes_6


title: GH2_A549


title: mEK_transplant_day8

description: 10x Genomics


title: Protoplast_3H_Rep#3

description: Library name: Protoplast5


title: Adult ventricular cardiomyocytes_5


title: Protoplast_3H_Rep#2

description: Library name: Protoplast4


title: MK P7

description: 10x Genomics

source_name: Kidney

value: Kidney


title: GH1_A549


title: Protoplast_3H_Rep#1

description: Library name: Protoplast3


title: P1 neonatal ventricular cardiomyocytes_2


title: MK P0

description: 10x Genomics


title: Adult ventricular cardiomyocytes_3


title: Protoplast_2-5H_Rep#2

description: Library name: Protoplast2


title: MEK E17.5

description: 10x Genomics

source_name: Embryonic kidney

value: Embryonic kidney


title: CK2_A549


title: Adult ventricular cardiomyocytes_2

value: WT


title: Protoplast_2-5H_Rep#1

description: Library name: Protoplast1


title: CK1_A549


title: MEK E15.5

description: 10x Genomics


title: Adult ventricular cardiomyocytes_1


title: CD40 and IL4 replicate 4

status: Public on Dec 07 2024

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

data_processing:
Bulk sequencing reads were aligned to the GRCm39 reference genome and transcriptome (version 105) using the STAR aligner (version 2.7.8a) and counted using featureCounts (version 2.0.0)
Reads for each sample were summed across the three technical replicates using R
Assembly: GRCm39 v 105
Supplementary files format and content: tab seperated gene counts

source_name: spleen

extract_protocol:
To determine gene expression in cDC1s, mRNA was extracted using a Direct-zol RNA MicroPrep kit (Zymo Research) as per manufacturer’s protocol.
Libraries were prepared using Illumina stranded mRNA library kits and the outputs sequenced to a depth of 20M reads per sample on a150PE on Illumina NovaSeq X Plus 10B flow cell. Library preparation and sequencing was conducted at the Australian Genome Research Facility.

treatment_protocol: CD11c+, MHC-IIint/+, CD11b−, CD24hi, B220−, CD172a−cells were then sorted using a BD FACSAriaTMIII Cell Sorter into filtered RPMI supplemented with 50% heat-inactivated FCS and pelleted. In a 24-well plate, 5 x 105cells were plated in complete Kenneth D Shortman RPMI (KDS-RPMI 1640, 10% FCS, 2mM L-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin and 50 mM 2-mercaptoethanol). To assess cDC1 gene expression in response to IL-4, cells were incubated in the presence ofa-CD40 (10mg/ml), IL-4 (60ng/mL), IFN-g(20ng/mL), or LPS (1mg/ml). Plates were then incubated at 37°C and 5% CO2for 4 hours. For RNA isolation, cells were washed and resuspended using TRIzol (Life Technologies), snap frozen and stored at -80°C.

value: spleen

value: pre-cDC

value: WT (B6)

value: anti-CD40 and IL-4


title: CD40 and IL4 replicate 3


title: CD40 and IL4 replicate 2


title: CD40 and IL4 replicate 1


title: CD40 replicate 3


title: CD40 replicate 1


title: IL4 replicate 5


title: IL4 replicate 4


title: CD40 replicate 2


title: IL4 replicate 2


title: IL4 replicate 1


title: Media replicate 4

value: media only


title: CK3_A549


title: IL4 replicate 3


title: Media replicate 1


title: UTX_wk13, replicate 3, scRNA-seq

first: Ho Chung

last: Chen

address: 609 Charles E Young Dr E

department: MIMG

description:
Library name: UTX_3_13wk
10x Genomoics

data_processing:
Single cell feature counts were generated by aligning sequencing data with the mm10 mouse reference genome (version 2020-A) using 10x Cell Ranger software (5.0.1). Filtered output matrices and barcodes were analyzed with SEURAT 4.0 on R studio (version 1.2.5033) using the Read10X function to return a unique molecular identified (UMI) count matrix for creation of a Seurat object Cells with fewer than 200 RNA count, more than 3000 unique genes and more than 12.5% mitochondria gene counts were excluded from the analysis.
Assembly: mm10
Supplementary files format and content: Matrix market-formatted raw gene-level count file
Supplementary files format and content: The list of gene names in the raw gene-level count file
Supplementary files format and content: The list of cell barcodes in the raw gene-level count file

source_name: pancreatic lymph node

extract_protocol:
pLNs were hand-picked from NOD mice and cells were labeled by anti-CD45 antibody. DAPI was used to exclude dead cells while sorting. Live CD45+ immune cells were sorted from the pLNs on the Aira sorter and resuspended at 1000 cells/ul in PBS with 2% FBS and 2mM EDTA (FACS buffer)
Sequencing library was constructed per manufacturer's protocol (10x Genomics, 3' scRNAseq)

value: pancreatic lymph node

value: immune cells

tag: Sex

value: female

tag: disease state

value: pre-diabetic


title: UTX_wk13, replicate 1, scRNA-seq

description:
Library name: UTX_1_13wk
10x Genomoics


title: Adult ventricular cardiomyocytes_4


title: UTX_wk13, replicate 2, scRNA-seq

description:
Library name: UTX_2_13wk
10x Genomoics


title: Media replicate 3


title: WT_wk13, replicate 2, scRNA-seq

description:
Library name: WT_2_13wk
10x Genomoics


title: WT_wk13, replicate 1, scRNA-seq

description:
Library name: WT_1_13wk
10x Genomoics


title: WT_wk13, replicate 3, scRNA-seq

description:
Library name: WT_3_13wk
10x Genomoics


title: UTX_wk8, replicate 2, scRNA-seq

description:
Library name: UTX_2_8wk
10x Genomoics


title: UTX_wk8, replicate 1, scRNA-seq

description:
Library name: UTX_1_8wk
10x Genomoics


title: UTX_wk8, replicate 3, scRNA-seq

description:
Library name: UTX_3_8wk
10x Genomoics


title: WT_wk8, replicate 3, scRNA-seq

description:
Library name: WT_3_8wk
10x Genomoics


title: WT_wk8, replicate 1, scRNA-seq

description:
Library name: WT_1_8wk
10x Genomoics


title: KO-smc1_rep2

city: Beijing

first: Ruifeng

last: Li

address: haidian

institute: Tsinghua University

library_source: genomic

data_processing:
1) The  CUT&Tag reads were mapped to reference genome by using bowtie2 with the “-p 5 -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant” options, followed by removing low mapped quality reads, mitochondrial reads, duplications. PCR duplicates were removed using picard MarkDuplicates. Macs2 was used for peak calling with the setting of “-f BAM -B --nomodel --keep-dup all”. 2)  CUT&Tag Differential Peak Analysis. The differential peak was analyzed by R package DiffBind73  with the FDR ≤ 0.01 and FC ≥ 1.5. ChIP seeker was used for peak annotation.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: spleens and lymph nodes

extract_protocol: The CUT&Tag experiments were performed as previously described(Vazyme TD903 kit) to generate DNA libraries derived from cells. Every sample has two replicates.

value: spleens and lymph nodes

value: cd8+ T cell

value: TRIM28 knockout


title: KO-smc1_rep1


title: WT_wk8, replicate 2, scRNA-seq

description:
Library name: WT_2_8wk
10x Genomoics


title: KO_Igg


title: Media replicate 2


title: WT-smc1_rep1


title: WT_Igg


title: EpiSCs transfected with shIgf2bp2

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

data_processing:
Aligned to genome/transcriptome using STAR (2.7.10a)
Genes and TEs counted using te_counts (https://github.com/oaxiom/te_counter)
Normalised using EDASeq (v2.30.0)
Differential expression using DESeq2 (v1.36.0) q-value <0.01 fold-change >2
All other analysis was performed using glbase3 (Hutchins et al., 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalised tag counts for each sample

growth_protocol: EpiSCs were cultured feeder-free on dishes coated with fetal bovine serum (FBS; NATOCOR) in FA medium (N2B27 medium, 15 ng per ml bFGF (PeproTech) and 20 ng per ml activin A (PeproTech). N2B27-based medium: DMEM/F12 (HyClone) and Neurobasal (Gibco) mixed 1:1, supplemented with N2 (Gibco), B27 (Gibco), non-essential amino acids (Gibco), GlutaMAX (Gibco), sodium pyruvate (Cellgro), penicillin/streptomycin (HyClone), 0.1mM β-mercaptoethanol (Gibco). Mouse EpiSCs were passaged using Accutase (Sigma) and seeded as single cells at approximately 50,000 cells in a well of a 6-well plate every 3 days. The medium was changed daily. Mouse ESCs were maintained feeder-free on 0.1% gelatin in N2B27 medium supplemented with 2i/LIF at the following final concentrations: 1 µM PD0325901 (Sigma), 3 µM CHIR99021 (Sigma) and 1,000U per ml leukemia inhibitory factor (LIF; Millipore). Mouse ESCs were passaged by 0.05% trypsin-EDTA (Gibco) dissociation every 3 days. To reprogram EpiSCs into rESCs, EpiSCs were dissociated into single cells using Accutase and plated at a density of 5,000 cells per well of 6-well plate coated with feeder in N2B27+FA medium supplemented with 5μM Y27632 (Selleck). The next day, N2B27+FA medium was changed into N2B27-2iL medium for 5 days. The medium was changed every day.

extract_protocol:
RNA was purified using RNAzol RT (RN190, MRC) according to the manufacturer’s instructions. The samples were prepared for sequencing with RNA-seq NEB Next Ultra RNA Library Prep Kit (7530, NEB). Samples were sequenced on an Illumina Novaseq 6000.
RNA-seq NEB Next Ultra RNA Library Prep Kit   cat.7530

treatment_protocol: Lentiviruses were generated from HEK293T cells using the jetPEI (Polyplus transfection). Mouse EpiSCs were infected with the individual lentiviral supernatant with the addition of Polybrene (Sigma) for 8 hours followed by selection with puromycin (Selleck) for 2 days before reprogramming.

value: EpiSCs


title: EpiSC to ESC RNA-seq day 6shBRD8


title: EpiSC to ESC RNA-seq day 4 shBRD8


title: EpiSC to ESC RNA-seq day 6 shLUC

value: shLUC


title: EpiSC to ESC RNA-seq day 0 shBRD8


title: EpiSC to ESC RNA-seq day 4 shLUC


title: EpiSC to ESC RNA-seq day 2 shLUC


title: WT-smc1_rep2


title: ESC H3K36me3 WT

data_processing:
cutadapt -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --quality-cutoff 10 -m 50 -o ${bn}.trim.p1.fq.gz -p ${bn}.trim.p2.fq.gz ${p1} ${p2}
bowtie2 $opts -x /export/genomic/hg38/bowtie2-indeces/hg38 -1 ${p1} -2 ${p2} | grep -E -v 'chrM|chrUn|random|RANDOM|alt' | samtools view -b -q 20 -F 1804 -f 2 | samtools sort -n >${out}.bam
macs2 callpeak -q 0.05 -t ${f} -n ${bn} -g hs -f BEDPE # &>${bn}.err
bamCoverage -p 4 --normalizeUsing CPM --minMappingQuality 30 --ignoreDuplicates -b ${in} -o ${out}
Assembly: mm10
Supplementary files format and content: bigWig files of the sequence tag density
Supplementary files format and content: BED file forma peak summits
Library strategy: CUT&Tag

extract_protocol:
Briefly, 1 × 105 cells were washed twice with wash buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5 mM spermidine and 1× protease inhibitors). Then cells were bound to concanavalin A beads (BP531, Bangs Laboratories) in binding buffer (20 mM Tris-HCl pH 7.4, 10 mM KCl, 1 mM CaCl2 and 1mM MnCl2). The bead-bound cells were washed once with buffer containing 0.01% digitonin, and primary antibodies were added to bead-bound cells in antibody buffer (4 mM EDTA and 0.2% BSA in wash buffer containing 0.01% digitonin) and rotated overnight at 4 °C. The primary antibodies below were used: anti-BRD8 (ab17969, Abcam), anti-IGF2BP2 (11601-1-AP, Proteintech), anti-H3K27me3 (07-449, Millipore), anti-H3K4me1 (ab176877, Abcam), anti-H3K4me3 (ab8580, Abcam), anti-H3K27ac (ab4279, Abcam) and anti-H3K9me3 (ab8898, Abcam). Secondary antibody (ABIN101961, Antibodies-Online) was added to bead-cells-antibody in wash buffer and further incubated at RT for 1 h. pG-Tn5 (S603-02, Vazyme) was add to cells in ‘300-wash’ buffer (20 mM Tris-HCl pH 7.4, 300 mM NaCl, 0.5 mM spermidine and 1× protease inhibitors, 0.01% digitonin) at RT for 1h. Tn5 was activated with 300-wash buffer supplemented with 10 mM MgCl2 and washed five times with 500 μl 300-wash buffer. To stop the Tn5 reaction, 10 μl of 0.5 M EDTA, 3 μl of 10% SDS and 1.5 μl of proteinase K (20 mg/ml) were added 55 °C for 1 h. DNA fragments were extracted and PCR amplified using NEBNext HiFi 2× PCR Master mix (M0541L, NEB) using the settings: 72°C, 5 min, 98°C 30 s and 12-14 cycles of: 98°C 10 s, 63°C 10 s and 72°C 30 s. 300-500 bp DNA fragments were purified with the VAHTS DNA Clean Beads (N411-02, Vazyme). Libraries were sequenced by an Illumina sequencer.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

value: ESC


title: ESC H3K27me3 WT


title: EpiSC to ESC RNA-seq day 2 shBRD8


title: ESC H3K36me3 sgBrd8


title: ESC H3K27me3 sgBrd8


title: EpiSC to ESC RNA-seq day 0 shLUC


title: ESC BRD8 Rep1


title: ESC BRD8 Rep2


title: siKLF4_REP3

type: RNA

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Unmodified microarray data obtained from GenomeStudio (Illumina) was background-subtracted and quantile-normalized using the lumi package within R

label: biotin

source_name: hADSC

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: hADSC cells were purchased from Invitrogen and maintained in in Complete MesenPRO RS™ Medium (Invitrogen).

extract_protocol: RNA was extracted and prepared using Aurum Total RNA kit (Bio-Rad) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer

treatment_protocol: Cells were plated in 6-well plates and transfected with siKLFs or scramble siRNA. After two days cells RNA was collected.

tag: sirna

value: human adipose derived stem cells


title: siKLF16_REP2

description: replicate 2


title: siKLF17_REP1

description: replicate 1


title: siKLF11_REP3

description: replicate 3


title: siKLF16_REP1

description: replicate 1


title: EpiSC H3K4me3 shBrd8

value: WT


title: siKLF4_REP2

description: replicate 2


title: siKLF4_REP1

description: replicate 1


title: siKLF16_REP3

description: replicate 3


title: siKLF11_REP1

description: replicate 1


title: siCTRL REP2

description: replicate 2

value: siscramble


title: siKLF9_REP2

description: replicate 2


title: siKLF17_REP2

description: replicate 2


title: siKLF9_REP3

description: replicate 3


title: siKLF9_REP1

description: replicate 1


title: siKLF11_REP2

description: replicate 2


title: hADSC_siCTRL_REP3

description: replicate 3

source_name: hADSC, scramble

extract_protocol: RNA was extracted and prepared using Aurum Total RNA kit (Bio-Rad) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser

treatment_protocol: Cells were plated in 6-well plates and transfected with KLF2, KLF8 or scramble siRNA. After two days cells RNA was collected.

value: human adipose derived stem cells (hADSC)


title: EpiSC H3K4me1 shBrd8


title: siKLF17_REP3

description: replicate 3


title: hADSC_siKLF2_REP2

description: replicate 2

source_name: hADSC, KLF2


title: hADSC_siKLF8_REP3

description: replicate 3

source_name: hADSC, KLF8


title: hADSC_siKLF2_REP3

description: replicate 3


title: hADSC_siKLF8_REP1

description: replicate 1


title: EpiSC H3K27ac shBrd8


title: hADSC_siKLF2_REP1

description: replicate 1


title: siCTRL REP3

description: replicate 3


title: EpiSC H3K4me1 shLuc

value: shLuc


title: hADSC_siKLF8_REP2

description: replicate 2


title: EpiSC H3K27ac shLuc


title: EpiSC H3K9me3 shLuc


title: EpiSC H3K4me3 shLuc


title: EpiSC H3K27me3 shLuc Rep2


title: hADSC_siCTRL_REP2

description: replicate 2


title: EpiSC H3K27me3 shLuc Rep1


title: EpiSC H3K9me3 shBrd8 Rep2


title: EpiSC KAT5 shBrd8


title: JURKAT, 2DG, H3K18la

first: Wu

last: Wenyan

address: 1678 Dongfang Road, Pudong New District, Shanghai

institute: Shanghai Children's Medical Center

description: Library name: JURKAT_2DG_H3K18la

data_processing:
Upon removal of low-quality reads and adapters, quality control was executed using FastQ Screen (version 0.13.0) and FastQC (version 0.11.9)
The Burrows-Wheeler Aligner (version 0.7.17-r1188) was then employed to align the data to the human hg19 genome reference, with non-uniquely mapping reads being discarded.
Duplicate reads were marked with the MarkDuplicates feature in Picard (version 2.22.9, http://broadinstitute.github.io/picard).
BigWig files standardized by spike-in were generated using the bamCoverage tool of deepTools (version 3.4.3)
Assembly: hg19
Supplementary files format and content: bigWig

source_name: JURKAT

growth_protocol: RPMI 1640 medium supplemented with 10% FBS. cells were cultured in an incubator at 37°C with 5% CO2.

extract_protocol:
Cell pellets were resuspended in 50μl nuclear isolation buffer (Sigma NUC-10) with added protease inhibitors. Chromatin digestion was performed using MNase (4-5U, NEB M0247) for 9-20 minutes
Library construction was performed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following the manufacturer's protocol.

treatment_protocol: For the sodium oxamate inhibition experiment, Jurkat cells were cultured for 48 hours in standard medium, medium containing 50mM sodium oxamate, and medium supplemented with both 50mM sodium oxamate and 10mM L-sodium lactate.  For the 2DG treatment, JURKAT cells were cultured for 24 hours in standard medium or medium containing 5 mM 2DG.

value: JURKAT


title: EpiSC KAT5 shLuc


title: JURKAT, control, H3K18la (2DG_control)

description: Library name: JURKAT_control_H3K18la_2DG_control


title: EpiSC H3K9me3 shBrd8 Rep1


title: JURKAT, oxamate, H3K4me1

description: Library name: JURKAT_oxamate_H3K4me1


title: JURKAT, control, H3K4me1

description: Library name: JURKAT_control_H3K4me1


title: EpiSC H3K27me3 shBrd8 Rep2


title: EpiSC H3K27me3 shBrd8 Rep1


title: HUVEC, passage 4, CUT&RUN for SOX18

city: Oxford

first: Susann

last: Bruche

address: Institute of Developmental and Regenerative Medicine

department: Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford

description: Library name: SOX18_AN_H4

data_processing:
Data was processed using the nf-core/cutandrun v3.1 pipeline (10.5281/zenodo.5653535) with the following adjustments to the default settings: --normalisation_mode CPM and --trim_nextseq 20. The CUT&RUN hg38 blacklist published by Nordin A et al. (https://doi.org/10.1186/s13059-023-03027-3) was used during sequence alignment.
Assembly: hg38
Supplementary files format and content: BigWig files for alignment against hg19 or hg38
Library strategy: CUT&Run

source_name: HUVEC

growth_protocol: HUVEC were cultured in EBM-2 Basal Medium (CC-3156) with EGM-2 SingleQuots Supplements (CC-4176).

extract_protocol:
CUT&RUN was performed with the Cell Signaling CUT&RUN assay kit according to manufactures instructions. For SOX7 and SOX17 assays, cells were lightly crosslinked with 0.1% methanol-free formaldehyde for 2min before washing and binding to ConcavalinA beads.
Libraries were constructed using the NEBNext Ultra II kit using the modified protocol described by Nan Liu (dx.doi.org/10.17504/protocols.io.bagaibse) and NEBNext Dual Index Multiplex Oligos for Illumina.

value: HUVEC

value: Endothelial cell

tag: antibody


title: EpiSC BRD8 Rep2

tag: cell line


title: HUVEC, passage 3, CUT&RUN for SOX18

description: Library name: SOX18_AN_H3

tag: cell type


title: EpiSC IGF2BP2

tag: treatment


title: EpiSC BRD8 Rep1


title: ESC IGF2BP2


title: HUVEC, passage 4, IgG control CUT&RUN for SOX18

description: Library name: IgG_SOX18_H4


title: EpiSCs converted to ESCs ATAC-seq shBrd8 Day 6 Rep2

data_processing:
Reads were aligned to the mm10 mouse genome with bowtie2 (v2.4.5) (Langmead and Salzberg, 2012)
Peaks were called with MACS2 (v2.2.7.1) (Zhang et al., 2008)
redefine_peaks function, was used to recover low-scoring peaks by sharing peak information across samples (Ma et al., 2021)
All other analysis was performed using glbase3 (Hutchins et al., 2014).
Assembly: mm10
Supplementary files format and content: BED files containing peak summits
Supplementary files format and content: bigWig files of density trace counts

extract_protocol:
Briefly, nuclei from 50,000 cells were extracted with lysis buffer (10 mM Tris-HCl pH 7.4 10 mM NaCl, 3 mM MgCl2, and 0.2% (v/v) IGEPAL CA-630).  Tagmentation reactions were performed by addition of 50 ul reaction mix of the TruePrep DNA Library Prep Kit (Vazyme, TD502) according to the manufacturer’s instructions. DNA fragments were cleaned up using the MinElute PCR Purification Kit (Qiagen, 28004). ATAC-seq libraries were amplified with PCR for an appropriate number of cycles 17 and the sequence index was added by TruePrep® Index Kit V2 for Illumina (Vazyme, TD202). The amplified DNA libraries were purified using the VAHTS DNA Clean Beads (Vazyme, N411-02) and sequenced on an Illumina sequencer.
ATAC-seq library was generated using the Tn5 enzyme from the TruePrep DNA Library Prep Kit V2 (Vazyme, TD501-02) as previously described (Buenrostro et al., 2013). Briefly, a total of ~50,000 cells were washed once with 50 μl of cold PBS and resuspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). The nuclei were centrifuged for 10 min at 500 × g at 4 °C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase (Vazyme) and 22.5 μl nuclease-free water). Samples were PCR amplified and purified using a MinElute kit (Qiagen).


title: siCTRL REP1

description: replicate 1


title: hADSC_siCTRL_REP1

description: replicate 1


title: EpiSCs converted to ESCs ATAC-seq shBrd8 Day 6 Rep1


title: HUVEC, passage 7, CUT&RUN for SOX17

description: Library name: SOX7_RD_H7

value: SOX7 (R&D Systems, AF2766)


title: EpiSCs converted to ESCs ATAC-seq shBrd8 Day 4 Rep2


title: HUVEC, passage 6, CUT&RUN for SOX17

description: Library name: SOX7_RD_H6


title: HUVEC, passage 3, IgG control CUT&RUN for SOX18

description: Library name: IgG_SOX18_H3


title: HUVEC, passage 6, IgG control CUT&RUN for SOX7

description: Library name: IgG_SOX7_H6


title: EpiSCs converted to ESCs ATAC-seq shBrd8 Day 4 Rep1


title: EpiSCs converted to ESCs ATAC-seq shBrd8 Day 2 Rep2


title: Primary ectopic endometrial stromal cells H5

city: tartu

first: Maire

last: Peters

department: Dept. of Obstetrics and gynecology

country: Estonia

institute: University of Tartu

data_processing:
The reads underwent trimming using the Fastp program.
Reads were aligned to the GRCh37 human genome with the STAR aligner (v2.7.10a)
Read count estimation was  performed using featureCounts tool with default parameters.
Assembly: GRCh37 human genome
Supplementary files format and content: "counts_filtered_endometriosis_hypoxia_counts.xlsx" .This file contains the raw read count matrix. This file is in excel format..

source_name: Ectopic endometrium

growth_protocol: The cells were cultured in phenol red-free DMEM supplemented with 10% charcoal-stripped FBS with penicillin/streptomycin/amphotericin B (100 U/mL, 100 μg/mL, and 0.25 μg/mL, respectively) at 37 °C under 20% O2 and 5% CO2; passaging of primary eutopic endometrial stromal cells was performed twice per week at 1/4 ration, while primary ectopic endometrial stromal cells were grown for longer periods to gain enough confluency for further passaging.

extract_protocol:
The RNA extraction was performed using the RNeasy Mini Kit, together with DNase I treatment (Qiagen), following the manufacturer’s instructions
The DNA libraries were constructed following the Smart-seq2 protocol described previously (Picelli et al. 2013) with 100 ng of each RNA sample, then enzymatically fragmented and tagged using Nextera XT kit (Illumina Inc) and IDT® for Illumina® DNA Unique Dual Index barcodes.

treatment_protocol: 48-h culturing in phenol red-free DMEM supplemented with 10% charcoal-stripped FBS with penicillin/streptomycin/amphotericin B under different oxygenation conditions - normoxia (20% oxygen, 5% carbon dioxide, 75% nitrogen) or hypoxia (1% oxygen, 5% carbon dioxide, 95% nitrogen)

tag: study group

value: endometriosis

tag: compound

value: Hypoxia

tag: oxygenation


title: EpiSCs converted to ESCs ATAC-seq shBrd8 Day 2 Rep1

tag: genotype


title: Primary eutopic endometrial stromal cells H5

source_name: Eutopic endometrium


title: Primary ectopic endometrial stromal cells N5

value: Normoxia


title: EpiSCs converted to ESCs ATAC-seq shBrd8 Day 0 Rep2


title: EpiSCs converted to ESCs ATAC-seq shBrd8 Day 0 Rep1


title: EpiSCs converted to ESCs ATAC-seq shLUC Day 6 Rep1


title: EpiSCs converted to ESCs ATAC-seq shLUC Day 6 Rep2


title: EpiSCs converted to ESCs ATAC-seq shLUC Day 4 Rep1


title: Primary eutopic endometrial stromal cells H4


title: Primary ectopic endometrial stromal cells H4


title: EpiSCs converted to ESCs ATAC-seq shLUC Day 4 Rep2


title: Primary eutopic endometrial stromal cells N5


title: Primary ectopic endometrial stromal cells H3


title: Primary eutopic endometrial stromal cells H3


title: EpiSCs converted to ESCs ATAC-seq shLUC Day 2 Rep1


title: Primary ectopic endometrial stromal cells N4


title: Primary eutopic endometrial stromal cells N4


title: Primary ectopic endometrial stromal cells N3


title: EpiSCs converted to ESCs ATAC-seq shLUC Day 2 Rep2


title: EpiSCs converted to ESCs ATAC-seq shLUC Day 0 Rep1


title: Rice root cells - sc_306

description:
Library name: Sample 4
10X Genomics kit v3.1

data_processing:
Processed by COPILOT (https://github.com/ohlerlab/COPILOT)
Assembly: MSU 7.0
Supplementary files format and content: Seurat object

source_name: Root

growth_protocol: Kitaake was used as wild type. Rice seeds were dehulled, sterilized with 50% bleach for 10 min, and rinsed four to five times with sterile water. All plant growth was in Yoshida’s nutrient solution solidified with gellan gum (Gelzan, Caisson Inc).Growth boxes were kept at 4°C in the dark for 2-3 days until the seeds germinate, then transferred to a percival growth chamber set to 28°C, and consistant light. Rice seedlings were grown in the percival for 1-3 days before harvesting.

extract_protocol:
For each sample, ~1 cm root tips were harvested from 15 - 40 roots and placed into a 35 mm petri dish containing a 70 μm cell strainer and 4.5 mL enzyme solution (4% [w/v] cellulase [ONOZUKA R-10, GoldBio], 1.5% Macerozyme R10 [GoldBio], 0.24% Pectolyase [Sigma P3026], 0.4 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol). The digestion was incubated on an 85 rpm shaker at 28°C for 2.5 hours with additional pipette mixing every 30 minutes. The resulting cell solution was filtered twice through 40 μm cell strainers and centrifuged for 5 minutes at 500g in a swinging bucket rotor. The pellet was washed with 2mL washing solution (0.4 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol), centrifuged again at 500g for 3 minutes, and the pellet resuspended in washing solution at a concentration of ~2000 cells/uL. We loaded 16,000 cells, with the aim to capture 10,000 cells per sample with the 10X Genomics Chromium 3` Gene expression v3 or v3.1 (HT, 32,000 -> 20,000) kits.
Cell barcoding and library construction were performed following the manufacturer’s instructions. cDNA and final library quality were verified using a Bioanalyzer High Sensitivity DNA Chip (Agilent) and sequenced on an Illumina NovaSeq 6000 instrument to produce 100bp paired-end reads.

treatment_protocol: For soil growth conditions, Wedowee sand loam soil from Johnston county, Notrh Carolina (15% clay, 75% sand,15g/kg organic C, 1g/kg total N, CEC = 6.4 meg/100g,base salt = 83%, P = 199 g/m3, K = 78 g/m3, Ca = 804 g/m3, pH = 5.8) was used . Soil was air dried, crushed and then passed through a sieve with a 2 mm mesh size. To allow packing of soil to certian bulk densities, the soil was lightly sprayed with sterilized water, mixed thoroughly. Non-compacted soil condition is 1.1 g/ cm-3 (1.1 BD), Compacted soil conditions is 1.6 g/ cm-3 (1.6 BD). Soils were packed in 3D-printed mesocosms at bulk density of 1.1 BD or 1.6 BD and then saturated with water. Germinated rice seedlings (maximum 4 seedlings per mesocosm)with equivalent length radicles were inserted below the soil surface, and then grown in  a percival growth chamber set to 28°C, and consistant light for 2-3 days before harvesting.

tag: tissue

value: Root

value: All cell types of root

value: WT (Kitaake)


title: corticosterone rep2

city: Berkeley

first: Yeara

last: Jo

address: 485 Weill Hall

institute: University of California, Berkeley

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Raw sequencing data were aligned to mouse genome mm10 (Genome  Reference Consortium GRCm38) by using Spliced Transcripts Alignment to a Reference  (STAR) aligner with the following parameters: “--outFilterType BySJout  --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --  outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20  --alignIntronMax 1000000 --alignMatesGapMax 1000000”.
Transcript data from STAR were analyzed using RSEM for gene and transcript level quantification
Genome_build: Mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text files include TPM (Transcripts Per Million) values for each sample

source_name: Bone marrow

extract_protocol:
At 3.5 days post culture, pro-DCs defined as Lin-CD11b-/loCD11c- cells (Lin includes B cells (CD19, B220), T cells (Thy1.2, CD3, CD4, CD8, CD127), NK cells (NK1.1), red  blood cells (Ter119), granulocytes (Gr-1), monocytes (CD11b), and dendritic cells (MHCII)) were purified by using fluorescence-activated cell sorting (FACS) from culture and RNA was harvested using Qiagen Rneasy Micro Kit.
Illumina TruSeq RNA Library Prep Kit v2 was used with the whole available RNA for each sample to construct sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 7 weeks old female C57Bl/6J mice were intravenously infected with 2x10^6 plaque forming units of lymphocytic choriomeningitis virus strain Clone-13. Bone marrow cells were harvested in duplicates at 8 days post infection and cultured in the presence of 100ng/ml Flt3L. For Gmeb1 knockdown, BM cells were enriched by using an EasySep Mouse Streptavidin Rapidspheres isolation Kit and biotin-conjugated anti-CD11b. Franctions unbound to streptavidin beads were cultured in the presence of Flt3L, and at day 2 post culture, the culture was enriched by using an EasySep Mouse Streptavidin Isolation Kit, biotin-conjugated anti-Gr-1, anti-CD19, and anti-CD127. Fractions unbound to streptavidin beads were transduced with retroviral particles encoding Gmeb1-targeting or control shRNA at days 2 and 3 post culture. For corticosterone treatment, bone marrow cells were cultured in the presence of vehicle or 50nM corticosterone. Pro-DCs transduced with retroviruses encoding control or Gmeb1-targeting shRNA were subsequently analyzed on a HiSeq 4000 instrument using a single read 100bp protocol. Pro-DCs treated with vehicle or 50nM corticosterone was sequenced using NOVA-seq with a paired end 50bp protocol.

tag: strain background

value: Bone marrow

tag: age

value: 7 weeks

tag: gender

value: female

value: 8 days post infection

tag: infection

value: LCMV Cl13

value: 50nM corticosterone


title: Rice root cells - sc_305

city: Los Angeles

description:
Library name: Sample 3
10X Genomics kit v3.1


title: Rice root cells - sc_304

description:
Library name: Sample 2
10X Genomics kit v3.1


title: Primary ectopic endometrial stromal cells N2


title: Rice root cells - sc_303

description:
Library name: Sample 1
10X Genomics kit v3.1


title: corticosterone rep1

tag: time


title: EpiSCs converted to ESCs ATAC-seq shLUC Day 0 Rep2

value: EpiSCs

value: WT

value: shLuc


title: Primary eutopic endometrial stromal cells H2


title: Primary ectopic endometrial stromal cells H2


title: vehicle rep2

value: vehicle


title: HUVEC, passage 7, IgG control CUT&RUN for SOX7

description: Library name: IgG_SOX7_H7

value: HUVEC

value: Endothelial cell


title: Primary eutopic endometrial stromal cells N3

value: endometriosis


title: comC_mutant_Rep4

city: Richmond

first: Ping

last: Xu

state: VA

address: 521 North 11th street

department: Philips Institute for Oral Health Research

institute: Virginia Commonwealth Univ. School of Dentistry

description: replicate 4

data_processing:
Standard Illumina pipeline. Real Time Analysis (RTA v. 1.18.66.3) software used for image processing, intesity extraction and basecalling based on intensities. CHASTITY software used for quality filter of basecalling.
Reads obtained from RNA-sequencing were aligned against the Streptococcus sanguinis SK36 genome using EDGE-pro.
Differential genes analysis was executed by DESeq2.
Genome_build: Streptococcus sanguinis reference genome
Supplementary_files_format_and_content: tab-delimited text file includes gene name and ID, fold change of expression, p-value

organism: Streptococcus sanguinis

growth_protocol: Cells were incubated at 37°C under microaerobic conditions in TH-HS media and harvested at mid-log phase. The comC mutant was supplemented with kanamycin (500 µg/ml) for selection of the antibiotic resistance cassette.

extract_protocol:
Cells were lysed and RNA was extracted by FastPrep lysing matrix beads. Clean-up and DNase I treatment was conducted by QIAGEN RNeasy mini kit, according to the manufacterer's protocol. Illlumina RiboZero Magnetic Kit for bacteria was used to deplete ribosomal RNA from 2 µg of total RNA.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) was used for the RNA-seq library preparation according to the manufacturer’s protocol. Briefly, ribosomal-depleted RNA was fragmented followed by first-strand cDNA synthesis from random primers using ProtoScript II Reverse Transcriptase (New England BioLabs). Second strand cDNA was synthesized and purified. End repair was performed on the double-stranded cDNA and primed with the addition of 5’-phosphorylated dA-tailed ends using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase (New England BioLabs). This was immediately followed by adaptor ligation (New England BioLabs) and purified. Samples were PCR-amplified for 12 cycles with Phusion HiFi polymerase (New England Biolabs) with paired-end primers and a randomly chosen unique barcode (NEB Next Multiplex Oligs for Illumina - Index Primers 2, 11, 12, 13, 15, 16, 18, 20, 21, 22). Agencourt AMPure XP Beads (Beckman Coulter) were used for all purification steps.

tag: strain

value: parent strain:SK36

tag: growth phase

value: mid-log


title: Primary eutopic endometrial stromal cells N2

value: Normoxia


title: comC_mutant_Rep1

description: replicate 1


title: vehicle rep1


title: comC_mutant_Rep3

description: replicate 3


title: Primary ectopic endometrial stromal cells H1

value: Hypoxia


title: SAMPLE 5_HCT116 shALKBH_2_1

type: genomic

city: Guangzhou

first: Dingcheng

last: Shen

address: 26 Yuancun Erheng Road

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850 Beadchip using standard Illumina protocol

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

data_processing:
The array data (.IDAT files) was analyzed using ChAMP package in R for deriving the methylation level . The methylation status of all the probes was denoted as β value, which is the ratio of the methylated probe intensity to the overall probe intensity
Unmethylated and methylated signal intensities are provided as raw data

label: cy3, cy5

source_name: HCT116 shALKBH_2

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from HCT116 cells using Qiagen DNeasy Kit according to standard instructions

tag: genotype/variation


title: IbTLD-H2O2

first: Jeng-Shane

last: Lin

address: No. 1, Sec. 4, Roosevelt Road

department: Plant Biology

institute: National Taiwan University

data_processing:
Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0 and expected to generate  20M per sample.
Trimmomatics was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks for gene expression estimation.
For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles.
The reference genome and gene annotations were retrieved from Ensembl database.
Genome_build: Nicotiana tabacum Ntab-TN90
Supplementary_files_format_and_content: W38-TLD file includes FPKM values for each Sample

organism: Nicotiana tabacum

source_name: Seedlings

growth_protocol: Tobacco (Nicotiana tabacum L. cv. W38) was grown in a controlled environment at 22°C under 16 h light/8 h dark with cool fluorescent light at 100 μmolm-2 s-1.

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual.
Library construction of all samples were used by Agilent's SureSelect Strand Specific RNA Library Preparation Kit

treatment_protocol: The 12-day-old seedlings were treated with 10 mM H2O2 for 6 hrs.

tag: cultivar

value: trangenic tobacco overexpressing IbTLD

value: treated with 10 mM H2O2 for 6 hrs


title: Wild-type_SK36_Rep4 (control for comC)

description: replicate 4

source_name: Wild-type SK36


title: comC_mutant_Rep2

description: replicate 2


title: IbTLD-control

value: untreated


title: Wild-type_SK36_Rep3 (control for comC)

description: replicate 3


title: Primary ectopic endometrial stromal cells N1


title: W38-H2O2

value: Wild-type


title: HUVEC, passage 7, CUT&RUN for SOX7

description: Library name: SOX17_H7

tag: cell line

tag: antibody

value: SOX17 (R&D Systems, AF1924)


title: Primary eutopic endometrial stromal cells N1


title: Wild-type_SK36_Rep2 (control for comC)

description: replicate 2


title: W38-control

tag: treatment


title: HUVEC, passage 7, IgG control CUT&RUN for SOX17

description: Library name: IgG_SOX17_H7

tag: cell type


title: Primary eutopic endometrial stromal cells H1

tag: study group

tag: compound


title: SGA_10th_7

status: Public on Dec 06 2024

city: Udine

first: Raffaella

last: Picco

address: P.le Kolbe 4

department: Department of Medicine

country: Italy

institute: University of Udine

data_processing:
Reads were mapped to the Human reference genome downloaded from Ensembl (version 107) using STAR (v2.7.3a).
Transcript assembly and quantiﬁcation were done with StringTie (v2.1.5).
Differentially expressed genes (DEGs) were identiﬁed using the DESeq2 R package (v1.40.2)
Assembly: GRCh38 (Ensembl 107)
Supplementary files format and content: tab-delimited text file includes TPM values for each sample and quantified gene
Supplementary files format and content: tab-delimited text file with raw gene counts for every gene and every sample

source_name: biopsies

extract_protocol:
Total RNA was extracted with Tri Reagent (Molecular Research Center) from 30mg villous placental tissue
RNA concentration, integrity and purity were tested by Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit). 10ng RNA were DNAseI digested (NEB), rRNA depleted (using Ribo-Zero method) and reverse transcribed obtaining cDNA. Adapter were ligated to fragmented cDNA after end-repair and A-Tailing following DNBSEQ protocol (MGI-Tech). 18 rounds of PCR amplification were performed to enrich the cDNA fragments. Then the PCR products were purified with Ampure XP Beads (Agencourt). ssCirDNA was obtained after denaturation and circularization. DNA balls were generated from each library following BGI specifications (SOP-SS-025)

value: placental villous tissue

tag: fetus size

value: small for gestational age, below the 10th percentile


title: HUVEC, passage 6, IgG control CUT&RUN for SOX17

description: Library name: IgG_SOX17_H6


title: SAMPLE 3_HCT116 shALKBH_1_1

source_name: HCT116 shALKBH_1


title: HUVEC, passage 6, CUT&RUN for SOX7

description: Library name: SOX17_H6


title: NORM_9

tag: tissue

value: appropriate for gestational age


title: Wild-type_SK36_Rep1 (control for comC)

description: replicate 1


title: SAMPLE 6_HCT116 shALKBH_2_2


title: SAMPLE 4_HCT116 shALKBH_1_2


title: NORM_7


title: SGA_10th_5


title: SAMPLE 1_HCT116 shNC_1

source_name: HCT116 shNC_1

value: shNC


title: NORM_5


title: SAMPLE 2_HCT116 shNC_2

source_name: HCT116 shNC_2


title: SGA_10th_2


title: SGA_10th_3


title: NORM_4


title: SGA_10th_4


title: SGA_10th_1


title: NORM_2


title: SGA_10th_8


title: NORM_1


title: NORM_3


title: SGA_3rd_2

value: small for gestational age, below the 3rd percentile


title: SGA_3rd_4


title: SGA_3rd_3


title: SGA_3rd_5


title: SGA_10th_9


title: SGA_10th_6


title: NORM_8


title: SGA_3rd_1


title: NORM_6


title: AX4 tgrB1L846F_20hr : replicate 2

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
After demultiplexing, we used Genialis Web tool  (https://www.genialis.com/ ) to perform data processing. The data was preprocessed by running BBDuk (ver 3. 1.2) on paired-end reads to trim illumina adaptor sequence (Minimum length = 30, Kmer length = 23, Maximum Hamming distance for kmers =1, k_trim “r”, quality_trim “r”, trim_quality = 28) and mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, -m 1, --best, --strata. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 1 more time.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable)
Assembly: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary files format and content: Processed data files are tab-separated files with two columns: the first containing gene names and the second its expression. Files ending with “_preprocessed_mapped_expression_rc.tab.gz" contain raw expression values while files ending with "_ preprocessed_mapped_expression_rpkum_polya.tab.gz" contain normalized expression values.

organism: Dictyostelium discoideum

source_name: AX4 tgrB1L846F

growth_protocol: All strains were cultured axenically in HL5.

extract_protocol:
At each time point, we harvested the cells, resuspended with 1 mL of Trizol® (life technologies, CA, USA) and extracted total RNA according to the manufacturer’s recommended protocol. We performed two rounds of poly-A selection and fragmented 100 ng of the resulting mRNA into approximately 200 bases fragments. We prepared cDNA and the second strand.
We prepared Illumina multiplexed libraries. We prepared 108 individual libraries separately (one from each sample), three categories and added a unique barcode to each library in each category at the final step of PCR amplification. We pooled equal amounts of DNA from each library in each category and sequenced one pool per lane of a flow cell on Illumina NovaSeq6000 using the manufacturer's recommended pipeline (PE, read length = 151 bases). Since the illumina sequence reads for rapgapB- and rapgapB- tgrB1- strains were low, they were sequenced twice. Therefore, we obtained 4 fastq file for each of these samples. We combined those fastq file to analyze them.

treatment_protocol: The cells were washed with phospate buffer, resuspended with PDF and plated at 1.7x10e6 cells/sq.cm on one cellulose filter on top of a paper pad soaked with PDF .

value: AX4 tgrB1L846F

tag: genotype

value: expressing tgrB1L846F in WT

tag: replicate

tag: developmental time

value: 20 hr

value: on Black filter


title: AX4 tgrB1L846F_20hr : replicate 1


title: AX4 tgrB1L846F_16hr : replicate 2

value: 16 hr


title: AX4 tgrB1L846F_16hr : replicate 3


title: AX4 tgrB1L846F_12hr : replicate 3

value: 12 hr


title: AX4 tgrB1L846F_16hr : replicate 1


title: AX4 tgrB1L846F_12hr : replicate 2


title: AX4 tgrB1L846F_20hr : replicate 3


title: AX4 tgrB1L846F_12hr : replicate 1


title: AX4 tgrB1L846F_04hr : replicate 3

value: 4 hr


title: AX4 tgrB1L846F_08hr : replicate 2

value: 8 hr


title: AX4 tgrB1L846F_08hr : replicate 3


title: AX4 tgrB1L846F_08hr : replicate 1


title: AX4 tgrB1L846F_00hr : replicate 3

value: 0 hr


title: AX4 tgrB1L846F_04hr : replicate 2


title: rapgapB- tgrB1-_20hr : replicate 1

source_name: rapgapB- tgrB1-

value: rapgapB- tgrB1-

value: rapgapB tgrB1 double crisprKO


title: rapgapB- tgrB1-_12hr : replicate 2


title: rapgapB- tgrB1-_08hr : replicate 3


title: AX4 tgrB1L846F_00hr : replicate 1


title: rapgapB- tgrB1-_16hr : replicate 3


title: rapgapB- tgrB1-_16hr : replicate 2


title: AX4 tgrB1L846F_00hr : replicate 2


title: rapgapB- tgrB1-_20hr : replicate 2


title: AX4 tgrB1L846F_04hr : replicate 1


title: rapgapB- tgrB1-_20hr : replicate 3


title: rapgapB- tgrB1-_12hr : replicate 3


title: rapgapB- tgrB1-_08hr : replicate 2


title: rapgapB- tgrB1-_16hr : replicate 1


title: rapgapB- tgrB1-_12hr : replicate 1


title: rapgapB- tgrB1-_08hr : replicate 1


title: rapgapB- tgrB1-_04hr : replicate 2


title: rapgapB- tgrB1-_04hr : replicate 1


title: rapgapB- tgrB1-_04hr : replicate 3


title: rapgapB- tgrB1-_00hr : replicate 3


title: rapgapB- tgrB1-_00hr : replicate 2


title: rapgapB- tgrB1-_00hr : replicate 1


title: rapgapB-_20hr : replicate 2

source_name: rapgapB-

value: rapgapB-

value: rapgapB crisprKO


title: rapgapB-_20hr : replicate 3


title: rapgapB-_20hr : replicate 1


title: rapgapB-_16hr : replicate 3


title: rapgapB-_16hr : replicate 1


title: rapgapB-_12hr : replicate 1


title: rapgapB-_12hr : replicate 3


title: rapgapB-_04hr : replicate 3


title: rapgapB-_08hr : replicate 1


title: rapgapB-_12hr : replicate 2


title: rapgapB-_08hr : replicate 2


title: rapgapB-_00hr : replicate 2


title: tgrC1-_20hr : replicate 1

value: tgrC1 crisprKO


title: rapgapB-_00hr : replicate 3


title: tgrC1-_16hr : replicate 2


title: tgrC1-_16hr : replicate 3


title: tgrC1-_20hr : replicate 2


title: tgrC1-_20hr : replicate 3


title: tgrC1-_16hr : replicate 1


title: tgrC1-_12hr : replicate 3


title: tgrC1-_12hr : replicate 2


title: rapgapB-_16hr : replicate 2


title: tgrC1-_08hr : replicate 3


title: tgrC1-_12hr : replicate 1


title: tgrC1-_08hr : replicate 2


title: tgrC1-_04hr : replicate 1


title: tgrC1-_08hr : replicate 1


title: rapgapB-_08hr : replicate 3


title: tgrC1-_04hr : replicate 2


title: tgrC1-_04hr : replicate 3


title: rapgapB-_04hr : replicate 1


title: rapgapB-_00hr : replicate 1


title: rapgapB-_04hr : replicate 2


title: tgrC1-_00hr : replicate 2


title: tgrC1-_00hr : replicate 1


title: Hashtag of Lung MAIT Cells, dpi 9 and 60

city: Melbourne

first: Shihan

address: 792 Elizabeth Street

institute: Peter Doherty Institute, University of Melbourne

data_processing:
FASTQ files were processed using the cellranger count pipeline from Cell Ranger version 3.1.0
Assembly: mmu 2020-A
Supplementary files format and content: features.tsv, gene Ids in TSV format
Supplementary files format and content: barcodes.tsv cell barcodes in TSV format
Supplementary files format and content: matrix.mtx raw counts as matrix
Supplementary files format and content: HTO_ref.csv referece sequences for hashtag sequencing as CSV

source_name: Lung

extract_protocol:
MAIT cells were sorted (BD FACS Aria III) from pooled lungs
cDNA libraries were generated according to the manufacturer’s instructions (10x Genomics) and then converted using the MGIEasy Universal Library Conversion Kit (BGI)

treatment_protocol: Mice intranasally infected with 80 CFU F. tularensis LVS for 6, 9, 12 or 60 days.

value: Lung

tag: age

value: 6-12 weeks

value: mix of TdT+/CD45.2- and TdT-/CD45.2+ MAIT cells

value: C57BL/6 Il17a-CRE/Rosa26-flox/flox

value: Infected


title: Gene Expression of Lung MAIT Cells, dpi 9 and 60


title: Hashtag of Lung MAIT Cells, dpi 6 and 12


title: tgrB1-_20hr : replicate 3

value: tgrB1 crisprKO

value: 20 hr


title: tgrB1-_20hr : replicate 1

value: on Black filter


title: tgrB1-_16hr : replicate 3

value: 16 hr


title: tgrB1-_16hr : replicate 2


title: tgrB1-_20hr : replicate 2


title: 4T07-TGL cells, Brd7-KO2, rep2

first: Junfeng

last: Zhang

address: 2130 W. Holcombe Blvd

department: Department of Cancer Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
STAR 2.4.2a was used to align the RNA-seq reads to the reference mouse genome (mm10) and to count the number of reads mapping to each gene in the Ensembl GRCm38.80 gene model. Differential expression analysis was performed using the DESeq2 package(v.1.10.0)in R (v.4.3.1;http://www.R-project.org/).
Assembly: mm10
Supplementary files format and content: txt files includes raw counts for each sample

source_name: 4T07-TGL cells

growth_protocol: 4T07-TGL cells were cultured in Dulbecco's Modified Eagle Medium (Gibco) with 10% fetal bovine serum (FBS, Gibco) at 37 °C in 5% CO2. All cell lines used in this study were confirmed Mycoplasma-negative using the Universal Mycoplasma Detection Kit (ATCC 30-1012K).

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini Kit (Qiagen)
RNA-seq on 4TO7-TGL cells with or without Brd7 KO was performed in the MD Anderson Advanced Technology Genomics Core (ATGC).

value: 4T07-TGL cells

value: breast cancer cells


title: 4T07-TGL cells, Brd7-KO1, rep3


title: 4T07-TGL cells, Brd7-KO1, rep1


title: tgrB1-_12hr : replicate 3

value: 12 hr


title: tgrB1-_16hr : replicate 1


title: 4T07-TGL cells, Brd7-KO1, rep2


title: tgrB1-_12hr : replicate 1


title: tgrC1-_00hr : replicate 3

value: 0 hr


title: 4T07-TGL cells, sgControl, rep3

value: Control


title: Gene Expression of Lung MAIT Cells, dpi 6 and 12


title: tgrB1-_08hr : replicate 3

value: 8 hr


title: tgrB1-_08hr : replicate 1


title: 4T07-TGL cells, sgControl, rep1


title: tgrB1-_08hr : replicate 2


title: 4T07-TGL cells, Brd7-KO2, rep1


title: 4T07-TGL cells, Brd7-KO2, rep3