title: Testes, cKO-2, Day 10

city: China

first: hongwei

last: Wei

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: South China University of Technology

description: Library name: SAMPLE4

data_processing:
Adapter sequences were removed from raw sequencing data using cutadapt1 software. Meanwhile, reads with length between 25 and 35 bp were kept for downstream analysis. Then reads were aligned to rRNA sequences so as to remove rRNA reads using bowtie2 software, remaining reads were used to align to GRCm38 using STAR. The trinucleotide periodicity of ribosomes and codon usage frequency were estimated using revised riboWaltz3 package. Read counts were calculated using featureCounts software. Raw counts were further normalized in DESeq24 package. Translational efficiencies were determined as the ratio of (normalized abundance determined by ribosome profiling)/(normalized abundance determined by RNA-seq) as previously repored5. Different translational efficiencies were estimated using DESeq24 package, genes with fold changes > 1.5 and padj < 0.05 were regarded as significant. GO and KEGG analysis were performed using clusterProfiler6 package in R software. References
Assembly: Ensembl_release106
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Library strategy: Ribo-seq

molecule: other

source_name: Testes

extract_protocol:
QEZ-seq® 1.0 kit is used to obtain ribosome footprinting form mouse testes.
QEZ-seq® 1.0 kit （NeoRibo Cat#1012S) is based on an advanced protocol for ribosome footprinting, as described in previous studies (Nature Structural & Molecular Biology, 30, 1816–1825, 2023), Delivering high-resolution mapping of ribosome-protected mRNA fragments.

value: Testes

value: tissue


title: MDM2 sKO-4

status: Public on Jun 01 2025

type: SRA

city: Wuhan

first: ZHIYI

last: CHEN

address: WuHan

country: China

institute: WuHan University

description:
Library name: sample6
T4

library_source: transcriptomic

data_processing:
Sequence reads were flitered by fastp
Trimmed sequence reads were mapped to mm39 using STAR
Read count extraction were performed using RSEM
Assembly: mm39
Supplementary files format and content: count maritx for six samples

molecule: polyA RNA

organism: Mus musculus

source_name: testis

extract_protocol:
Total RNA was used as input material for the RNA sample preparations.
Enriching mRNA using mRNA Capture Beads (oligo dT magnetic beads).

tag: tissue

value: testis

tag: age

value: postnatal day 5 (P5)

tag: genotype

value: sKO


title: Testes, cKO-3, Day 10

description: Library name: SAMPLE6

data_processing:
StringTie v1.3.1
For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software
Assembly: Ensembl_release106
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 FPKM values for each Sample

molecule: total RNA

extract_protocol:
The RNeasy micro-RNA isolation kit (Qiagen, Valencia, CA, USA) was used to isolate and purify total RNA from the testes. 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit following manufacturer's protocols.


title: Testes, cKO-1, Day 10

description: Library name: SAMPLE3

library_source: other


title: MDM2 sKO-1

description:
Library name: sample3
T1


title: Testes, cKO-2, Day 10

description: Library name: SAMPLE5


title: Testes, Control-2, Day 10

description: Library name: SAMPLE2


title: MDM2 WT-1

description:
Library name: sample1
C1

value: wild type


title: Testes, cKO-1, Day 10

description: Library name: SAMPLE4


title: MDM2 WT-2

description:
Library name: sample2
C2


title: Testes, Control-3, Day 10

description: Library name: SAMPLE3


title: DC2,NI,replicate4

city: Paris

first: Okan

last: Ayas

address: 1 avenue Claude Vellefaux

country: France

institute: INSERM

description:
Library name: Sample 33
Column name in raw_counts.tsv : 17_DC2_NI

data_processing:
Sequence reads were aligned to GRCh38 reference genome using Kallisto from Pachter lab
Read counts were imported using tximport in R4.3.2
Counts were normalized and the differentially expression analysis was conducted using DESeq2
The gene functional annotation was performed using ClusterProfiler
Assembly: GRCh38
Supplementary files format and content: raw_counts.tsv contains the raw counts for all samples

organism: Homo sapiens

source_name: PBMC

growth_protocol: pDC and DC2  were cultured in medium RPMI 1640 with GlutaMAX, 10% of FBS, 1% of MEM nonessential amino acid, 1% of sodium pyruvate and 1% of penicillin-streptomycin

extract_protocol:
ARN extraction was performed using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol
RNA libraries for RNAseq were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit following manufacturer’s protocol

treatment_protocol: 1 x 105 cells (pDC or DC2) were plated in V-bottom 96-well plates in presence of medium alone (RPMI 1640 medium with GlutaMAX, 10% FBS, 1% of MEM nonessential amino acid, 1% of sodium pyruvate, and 1% of penicillin-streptomycin), the TLR7/TLR8 agonist R848 (Resiquimod), SARS-CoV-2 strain 220/95, Delta or Omicron BA.1, at 100 and 400 genome copies per cell

value: PBMC

tag: cell type

tag: treatment

value: Unstimulated


title: Testes, Control-2, Day 10

description: Library name: SAMPLE2


title: Testes, Control-1, Day 10

description: Library name: SAMPLE1


title: DC2,Delta,replicate4

description:
Library name: Sample 35
Column name in raw_counts.tsv : 19_DC2_delta

value: SARS-CoV-2 Delta


title: DC2,Delta,replicate3

description:
Library name: Sample 31
Column name in raw_counts.tsv : 15_DC2_delta


title: sorted astrocyte, BB, Cre+, mouse3

city: Piscataway

first: Brian

last: Daniels

state: NJ

address: 604 Allison Road

department: Cell Biology and Neuroscience

country: USA

institute: Rutgers, The State University of New Jersey

data_processing:
Raw data quality was evaluated by FastQC.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
the gene hit counts table was used for downstream differential expression analysis via DESeq2. The Wald test was used to generate p-values and log2 fold changes.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes unique gene hit counts for each sample

source_name: Whole brain

extract_protocol:
Total RNA from sorted astrocytes was harvested using Qiagen RNeasyMicro kit following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols

treatment_protocol: Ripk3-2XFVfl/fl Aldh1l1 Cre+ mice and Cre− littermate controls were treated intraperitoneally with B/B Homodimerize for 24 hours prior to perfusion with PBS and harvesting of whole brain and magnetic sorting of astrocytes

value: Whole brain

value: Astrocyte

value: Ripk3-2XFVfl/fl Aldh1l1 Cre+

value: BB Homodimerizer


title: Testes, Control-1, Day 10

description: Library name: SAMPLE1


title: Cas9 LSK Tet2 KO HSPCs transduced with non-targeting sgRNAs, 2

city: Boston

first: Peter

middle: G

last: Kim

state: MA

address: 360 Longwood Ave, LC8202

department: Medical Oncology

institute: Dana Farber Cancer Institute

description:
Library name: ntc_tet_lsk2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger 7.1.0 (10x Genomics), and further analyzed using Seurat v3 and Monocle 3.
Assembly: Mouse mm10
Supplementary files format and content: tab separated value, barcode, and matrix files

source_name: blood

extract_protocol:
Lin-Sca+Kit+ cells were sorted using the Sony MA900 sorter based on the expression of BFP or RFP expression, which measures sgRNA transduction. 10000 cells were isolated per sample.
Library was prepared using the single cell 5' reagent kit (10x Genomics) according to manufacturer's instructions. Library was sequenced on an Illumina Nvaseq SP.

treatment_protocol: Cas9 WT or Tet2 HSCs were transduced with control or Ncoa4 sgRNAs and Lin-Sca+Kit+ HSPCs were sorted 12-weeks post-transplantation from a pool of 5 mouse per arm.

value: blood

value: hematopoietic stem progenitor cells

value: Tet2 KO

value: Control sgRNA


title: DC2,R848,replicate3

description:
Library name: Sample 30
Column name in raw_counts.tsv : 14_DC2_R848


title: sorted astrocyte, BB, Cre-, mouse4

value: Ripk3-2XFVfl/fl Aldh1l1 Cre-


title: sorted astrocyte, BB, Cre+, mouse1


title: sorted astrocyte, BB, Cre-, mouse3


title: sorted astrocyte, BB, Cre+, mouse4


title: DC2,R848,replicate4

description:
Library name: Sample 34
Column name in raw_counts.tsv : 18_DC2_R848


title: Cas9 LSK Tet2 KO HSPCs transduced with non-targeting sgRNAs, 1

description:
Library name: ntc_tet_lsk1
10x Genomics


title: sorted astrocyte, BB, Cre-, mouse1


title: Cas9 LSK WT HSPCs transduced with Ncoa4 sgRNAs

description:
Library name: ncoa4_wt_lsk
10x Genomics

value: WT

value: Ncoa4 sgRNA


title: DC2,NI,replicate3

description:
Library name: Sample 29
Column name in raw_counts.tsv : 13_DC2_NI


title: Cas9 LSK WT HSPCs transduced with non-targeting sgRNAs

description:
Library name: ntc_wt_lsk
10x Genomics


title: pDC,BA.1,replicate5

description:
Library name: Sample 28
Column name in raw_counts.tsv : 12_pDC_BA1

value: pDC

value: SARS-CoV-2 Omicron BA.11


title: PDA30364_MEKi+CD40_Tx1 scTCR seq

city: Heidelberg

first: Rienk

last: Offringa

state: Baden-Wuerttemberg

address: Im Neuenheimer Feld 280

department: Division of Molecular Oncology of Gastrointestinal Tumors

country: Germany

institute: DKFZ Heidelberg

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1
Assembly: mm10-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: TILs from murine PDAC tumors

extract_protocol:
Tumors were harvested, minced into smaller pieces with a scalpel and digested using the human tumor dissociation kit with gentleMACS Octo tissue dissociator (Miltenyi) according to the manufacturer’s instructions (program ‘37C_h_TDK_3’). Following 1 h digestion, tumor cell suspensions were poured through a 100 μm strainer pre-coated with 2.5% BSA/PBS. Next, cells were washed twice over a 70 µm cell strainer and frozen in liquid nitrogen in freezing media (fetal bovine serum + 10% DMSO) until processing for single-cell RNA sequencing.
Library was performed according to the manufacter’s instructions (10x Genomics, v1 chemistry according to the manufacturer’s protocol (#CG000086 Rev K)). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. For gene expression library construction, 50 ng mass of sample were fragmented, end-repaired and A-tailed. For V(D)J library construction, cDNA was first enriched using T-cell mixes 1 by PCR amplification, followed by SPRIselect reagent size selection. Then, T-cell mix 2 was used for further enrichment by PCR amplification, followed by SPRIselect reagent size selection. Post target enrichment, quality control was checked on Agilent Bioanalyzer High Sensitivity Chip and quantified using Qubit Fluorometer and Qubit dsDNA HS Assay kit. For V(D)J library construction, 50 ng mass of sample were fragmented, end-repaired and A-tailed. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: T-cells

value: TILs from murine PDAC tumors

tag: strain

value: 8-14 weeks old


title: PDA30364_MEKi+CD40_Tx2 scTCR seq


title: PDA30364_C3 scTCR seq


title: Pex5_WT_AM_3

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

description: Library name: Pex5_WT_AM_3

data_processing:
Sequenced libraries were mapped with STAR aligner to ensemble mouse reference genome GRCm38.p5 (release 91). FeatureCounts was used to quantify mapped reads per gene. Raw gene counts were processed in R v4.3.2 with DESeq2 v1.40.1  to generate normalized read counts to visualize as heat maps and determine differentially expressed genes (DEG) with greater than 0.5 absolute log2 fold change and lower than 0.05 adjusted P value.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including gene name and raw counts per sample

source_name: lung

extract_protocol:
Total RNA was isolated from 50,000 sorted BAL AMs using RNeasy plus micro kit (Qiagen) according to the manufacturer’s protocol.
Libraries were prepared using SMART-Seq RNA Stranded sample kit (Takara Bio) and sequenced by Illumina NovaSeq 6000 Sequencing System at the Functional Genomics Center Zurich. Sequencing was done using single-end 100 bp reads with final sequencing depth of 20 M reads per sample on average.

value: lung

value: alveolar macrophages


title: pDC,Delta,replicate5

description:
Library name: Sample 27
Column name in raw_counts.tsv : 11_pDC_delta

value: PBMC

value: SARS-CoV-2 Delta


title: Cas9 LSK Tet2 KO HSPCs transduced with Ncoa4 sgRNAs

description:
Library name: ncoa4_tet_lsk
10x Genomics


title: DC2,BA.1,replicate3

description:
Library name: Sample 32
Column name in raw_counts.tsv : 16_DC2_BA1


title: pDC,R848,replicate5

description:
Library name: Sample 26
Column name in raw_counts.tsv : 10_pDC_R848


title: DC2,R848,replicate5

description:
Library name: Sample 38
Column name in raw_counts.tsv : 22_DC2_R848


title: PDA30364_C2 scTCR seq


title: PDA30364_C1 scTCR seq


title: Pex5_WT_AM_2

description: Library name: Pex5_WT_AM_2


title: pDC,NI,replicate5

description:
Library name: Sample 25
Column name in raw_counts.tsv : 9_pDC_NI

value: Unstimulated


title: PDA-OVA_MEKi+CD40_Tx5 scTCR seq


title: PDA-OVA_MEKi+CD40_Tx4 scTCR seq


title: sorted astrocyte, BB, Cre-, mouse2

value: Whole brain

value: Astrocyte

value: BB Homodimerizer


title: PDA-OVA_MEKi+CD40_Tx3 scTCR seq


title: pDC,BA.1,replicate4

description:
Library name: Sample 24
Column name in raw_counts.tsv : 8_pDC_BA1


title: PDA-OVA_MEKi+CD40_Tx2 scTCR seq


title: Pex5_VavCre_AM_3

description: Library name: Pex5_VavCre_AM_3

value: Vav1cre/+ Pex5fl/fl


title: PDA30364_MEKi+CD40_Tx3 scTCR seq


title: PDA-OVA_C3 scTCR seq


title: pDC,R848,replicate4

description:
Library name: Sample 22
Column name in raw_counts.tsv : 6_pDC_R848


title: Pex5_VavCre_AM_2

description: Library name: Pex5_VavCre_AM_2


title: PDA-OVA_MEKi+CD40_Tx1 scTCR seq


title: PDA-OVA_C2 scTCR seq


title: Pex5_VavCre_AM_1

description: Library name: Pex5_VavCre_AM_1


title: pDC,NI,replicate4

description:
Library name: Sample 21
Column name in raw_counts.tsv : 5_pDC_NI


title: pDC,BA.1,replicate3

description:
Library name: Sample 20
Column name in raw_counts.tsv : 4_pDC_BA1


title: Day +28 post-transplant peripheral blood scRNAseq capture rxn #2

city: Seattle

first: Julie

last: Boiko

state: Washington

address: 1101 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description: Library name: Sample 6

data_processing:
Cell Ranger
Assembly: GRCm38
Supplementary files format and content: Seurat object in RDS format; combines all samples/timepoints

source_name: Peripheral blood

extract_protocol:
10X Genomics 3' dual-index protocol
10X Genomics 3' dual-index protocol

value: Peripheral blood


title: PDA-OVA_C1 scTCR seq


title: PDA30364_MEKi+CD40_Tx2 scRNA seq


title: PDA30364_MEKi+CD40_Tx3 scRNA seq


title: PDA30364_MEKi+CD40_Tx1 scRNA seq


title: Day +28 post-transplant peripheral blood scRNAseq capture rxn #1

description: Library name: Sample 5


title: Pex5_WT_AM_1

description: Library name: Pex5_WT_AM_1


title: sorted astrocyte, BB, Cre+, mouse2

value: Ripk3-2XFVfl/fl Aldh1l1 Cre+


title: pDC,Delta,replicate3

description:
Library name: Sample 19
Column name in raw_counts.tsv : 3_pDC_delta


title: pDC,Delta,replicate4

description:
Library name: Sample 23
Column name in raw_counts.tsv : 7_pDC_delta


title: PDA30364_C2 scRNA seq


title: PDA30364_C1 scRNA seq


title: PDA30364_C3 scRNA seq


title: Day +21 post-transplant peripheral blood scRNAseq capture rxn #2

description: Library name: Sample 4


title: pDC,R848,replicate3

description:
Library name: Sample 18
Column name in raw_counts.tsv : 2_pDC_R848


title: Day +21 post-transplant peripheral blood scRNAseq capture rxn #1

description: Library name: Sample 3


title: PDA-OVA_MEKi+CD40_Tx4 scRNA seq


title: PDA-OVA_MEKi+CD40_Tx3 scRNA seq


title: pDC,NI,replicate3

description:
Library name: Sample 17
Column name in raw_counts.tsv : 1_pDC_NI


title: PDA-OVA_MEKi+CD40_Tx5 scRNA seq


title: Day +14 post-transplant peripheral blood scRNAseq capture rxn #2

description: Library name: Sample 2


title: PDA-OVA_MEKi+CD40_Tx2 scRNA seq


title: Day +14 post-transplant peripheral blood scRNAseq capture rxn #1

description: Library name: Sample 1


title: PDA-OVA_MEKi+CD40_Tx1 scRNA seq


title: pDC,BA.1,replicate2

description:
Library name: Sample 16
Column name in raw_counts.tsv : 16_pDC_BA1_first


title: occm-30 cell, Day 14 [occm-om14d]

city: Beijing

first: yiping

last: huang

address: 22 zhongguancun south street

department: School of stomatology

institute: Peking University

data_processing:
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent of bases with qualities of <20. The clean reads were then aligned to mouse genome (version: mm10 NCBI) using the hisat2. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016.] HTseq [Anders S, Pyl P T, Huber W. HTSeq–A Python framework to work with high-throughput sequencing data[J]. Bioinformatics, 2014: btu638.] was used to count gene and lncRNA counts and RPKM method was used to determine the gene expression.
We applied DESeq algorithm [Anders S, et al. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106. doi: 10.1186/gb-2010-11-10-r106]to filter the differentially expressed genes, after the significant analysis, Pvalue and FDR analysis under the following criteria [Benjamini Y, et al. Controlling the false discovery rate in behavior genetics research. Behav Brain Res. 2001 Nov 1;125(1-2):279-84. ]
Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the target gene of the differentially expressed miRNA in the experiment [Ashburner M, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25-9.]. We downloaded the GO annotations from NCBI (http://www.ncbi.nlm.nih.gov/), UniProt (http://www.uniprot.org/) and the Gene Ontology (http://www.geneontology.org/). Fisher’s exact test was applied to identify the significant GO categories and FDR was used to correct the p-values.
Pathway analysis was used to find out the significant pathway of the differential genes according to KEGG database. We turn to the Fisher’s exact test to select the significant pathway, and the threshold of significance was defined by P-value and FDR. [Draghici S, et al. A systems biology approach for pathway level analysis. Genome Res. 2007 Oct;17(10):1537-45. Epub 2007 Sep 4.]
Assembly: mm10
Supplementary files format and content: FPKM/TPM values for each Sample

extract_protocol:
TRIzol reagent was used to isolate total RNA in accordance with manufacturer's protocols.
the RNA sequencing library are completed according to instructions with the library preparation kit

tag: cell line

value: cementoblast

value: wt

value: cementogenic differentiation for 14 days


title: PDA-OVA_C3 scRNA seq

value: T-cells


title: pDC,R848,replicate2

description:
Library name: Sample 14
Column name in raw_counts.tsv : 14_pDC_R848_first

value: pDC


description: Library name: Sample 5


title: BRI-2251

first: Soumya

last: Raychaudhuri

address: 75 Francis St

institute: Brigham and Women's Hospital

description: Library name: BRI-2251

data_processing:
The AIM-Seq data was processed using Cell Ranger version 6.1.1 with default parameters and alignment to hg38 reference genome. The donor of origin for each cell was determined using Demuxlet version 1.0 with doublet-prior of 0.168. Cells with null or ambiguous demuxlet result, fewer than 10 counts of the hashtag oligos, or fewer than 50 total RNA counts were filtered. To account for staining differences between the hashtag oligos and different sequencing depths of the two 10X runs, the counts for each hashtag oligo in each 10X run were scaled to have the same median value. Next we added a pseudocount to the hashtag oligo counts and log10 transformed this data. Then we ran Gaussian Mixture models separately for each hashtag oligo with K=2 clusters. Each cell was assigned to a single condition if it was in the high cluster for one oligo and the low clusters for all others, a doublet if it was in the high cluster for more than one oligo, or an empty droplet if it was in the low cluster for all oligos. Empty droplets or doublets based on the hashtag oligo clustering were filtered, as were doublets based on demuxlet. Genes detected in fewer than 10 cells were filtered prior to running TCAT.
Assembly: hg38
Supplementary files format and content: Single-cell RNA, ADT, hashing counts matrices and per-cell metadata, including TCR clonotypes.
Library strategy: CITE-seq

source_name: Blood

extract_protocol:
PBMCs from 5 healthy donors were quickly thawed and placed in pre-warmed xVIVO15 cell culture medium (Lonza) supplemented with 5% heat-inactivated FBS. To reduce cell clumping, PBMCs were incubated in xVIVO15 containing 50 U/mL of benzonase nuclease (Sigma-Aldrich) for 15 minutes at 37 degrees and filtered using a 70 µm cell strainer. Washed and nuclease treated cells were seeded in a 96 well cell culture plate at a concentration of 2.5 x 106/mL. Peptide stimulations were performed using the CEFX Ultra SuperStim Pool (JPT Peptide Technologies, Product Code: PM-CEFX-1) at a final concentration of 1.25 µg/mL per peptide for 22 hours at 37 degrees and 5% CO2. Recombinant anti-CD28 and anti-CD49d antibodies (BioLegend) were added at a final concentration of 5 µg/mL and 0.625 µg/mL, respectively, to provide co-stimulation for peptide reactive T-cells. Separately mock-stimulated cells were treated with anti-CD28 and anti-CD49d antibodies at the same concentration. Peptide responsive T-cells were detected by the expression of the surface activation markers PD-L1, OX40, and CD137 via flow cytometry. Following the stimulation, peptide treated and mock-stimulated cells were washed in cell staining buffer (PBS + 2mM EDTA + 2% FBS) to end the stimulation. Fc receptor blocking was performed using a 1:50 dilution of Human TruStain FcX (Biolegend) in cell staining buffer for 10 minutes at 4 degrees. Cell viability staining was performed using a 1:500 dilution of Zombie Yellow Fixable Viability Dye (BioLegend) prepared in PBS for 30 minutes at 4 degrees. Surface staining was performed using 1:100 dilutions of BV421 conjugated anti-CD3, FITC conjugated anti-CD4, BV786 conjugated anti-PD-L1, PE conjugated anti-OX40, and APC conjugated anti-CD137 (BioLegend) for 25 minutes at 4 degrees in cell staining buffer. Following cell staining, antigen reactive and non-reactive T-cells were identified using a BD FACSAria II cell sorter and collected in cRPMI medium (100 U/mL penicillin-streptomycin + 2 mM L-glutamine + 10 mM HEPES + 0.1 mM non-essential amino acids + 1 mM sodium pyruvate + .05 mM 2-Mercaptoethanol) supplemented with 20% FBS. Sorted T cell populations were then labeled with 75 uL of TotalSeq oligo conjugated hashing antibody mix, incubated for 30 minutes at 4 degrees with gentle mixing after 15 minutes, and pooled in equal quantities. Staining with the TotalSeq-C Human Universal Cocktail (BioLegend) was then performed according to the manufacturer's instructions. The cells were then resuspended in PBS supplemented with .04% FBS at a final concentration of 500 cells/µL and submitted for single-cell profiling on the Chromium Next GEM instrument.
Library preparation was completed for the hashtag oligos, single-cell rna-seq, cite-seq, and TCR-repertoire sequencing following the manufacturer’s instructions.

value: Blood

value: T

tag: library type

value: mRNA


title: occm-30 cell, Day 0 [occm-nc]

value: without cementogenic differentiation


title: occm-30 cell, Day 7 [occm-om7d]

value: cementogenic differentiation for 7 days


title: sRNA_tas2-3_Rep2

first: Han

last: Wang

address: No.5 Yiheyuan Road

description: Library name: sRNA_tas2-3_Rep2

data_processing:
Analysis of degradome sequencing data was conducted using pRNASeqTools v0.8.
Assembly: Araport 11
Supplementary files format and content: The processed data files are in bedgraph format, containing the phasing score of 21 nt phasiRNA sites in WT and mutants.

organism: Arabidopsis thaliana

source_name: 12-day seedlings

growth_protocol: Seeds were germinated on 1/2 MS medium, maintained at 22 °C under long-day conditions (16 hours of light and 8 hours of darkness).

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings using the TRIzol method (Takara, 9108).
sRNA-seq: Small RNAs (sRNAs) of varying lengths were separated by 15% Urea-PAGE, and the 15-40bp bands were excised post-electrophoresis. The gel slices were soaked overnight at 4℃ in 0.4M NaCl solution, followed by ethanol precipitation.

value: 12-day seedlings


title: DC2,BA.1,replicate2

description:
Library name: Sample 12
Column name in raw_counts.tsv : 12_DC2_BA1_first

value: PBMC

value: SARS-CoV-2 Omicron BA.11


description: Library name: Sample 3


title: sRNA_tas2-3_Rep1

description: Library name: sRNA_tas2-3_Rep1


title: DC2,Delta,replicate2

description:
Library name: Sample 11
Column name in raw_counts.tsv : 11_DC2_delta_first

value: SARS-CoV-2 Delta


title: sRNA_tas2-2_Rep2

description: Library name: sRNA_tas2-2_Rep2


title: sRNA_tas2-2_Rep1

description: Library name: sRNA_tas2-2_Rep1


title: sRNA_tas2-1_Rep1

description: Library name: sRNA_tas2-1_Rep1


description: Library name: Sample 1


title: sRNA_tas2-1_Rep2

description: Library name: sRNA_tas2-1_Rep2


title: pDC,Delta,replicate2

description:
Library name: Sample 15
Column name in raw_counts.tsv : 15_pDC_delta_first


description: Library name: Sample 2


title: sRNA_tas3a/b/c_Rep2

description: Library name: sRNA_tas3a/b/c_Rep2


title: DC2,NI,replicate2

description:
Library name: Sample 9
Column name in raw_counts.tsv : 9_DC2_NI_first

value: Unstimulated


title: DC2,R848,replicate2

description:
Library name: Sample 10
Column name in raw_counts.tsv : 10_DC2_R848_first


title: IL-27-3

city: Hangzhou

first: Yi

last: Ma

address: No.258, kaixuan RD

institute: Zhejiang University school of medicine

description: Library name: IL-27-3

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Macrophge

growth_protocol: The macrophage was plated in 10 cm Petri dishes containing DMEM medium with L-glutamine (Gibco), 10% fetal calf serum (FCS) (Gibco), 1% penicillin-streptomycin (Beyotime), and 10% L929 supernatant, and cultured for 6 days in a 37°C incubator with 5% CO2. On day 6, cells were harvested, resuspended in complete DMEM, and seeded into multi-well plates at 5×10⁵ or 1×10⁶ cells/mL.

extract_protocol:
Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

treatment_protocol: In vitro experiment, this study stimulated macrophages with 100 ng/ml IL-27 (6h) and 20 ng/ml IL-4 (12h).

value: Macrophge

value: WT


title: PDA-OVA_C2 scRNA seq

value: TILs from murine PDAC tumors

value: 8-14 weeks old


title: pDC,NI,replicate2

description:
Library name: Sample 13
Column name in raw_counts.tsv : 13_pDC_NI_first


title: sRNA_WT_tas2batch_Rep2

description: Library name: sRNA_WT_tas2batch_Rep2


title: sRNA_tas3a/b/c_Rep1

description: Library name: sRNA_tas3a/b/c_Rep1


description: Library name: Sample 4

value: Peripheral blood


title: DC2,BA.1,replicate1

description:
Library name: Sample 8
Column name in raw_counts.tsv : 8_DC2_BA1_first


title: IL-27-2

description: Library name: IL-27-2


title: sRNA_WT_tas3batch_Rep2

description: Library name: sRNA_WT_tas3batch_Rep2


title: sRNA_WT_tas3batch_Rep1

description: Library name: sRNA_WT_tas3batch_Rep1


title: DC2,Delta,replicate1

description:
Library name: Sample 7
Column name in raw_counts.tsv : 7_DC2_delta_first


title: IL-27-1

description: Library name: IL-27-1


title: DC2,R848,replicate1

description:
Library name: Sample 6
Column name in raw_counts.tsv : 6_DC2_R848_first


title: IL-4-3

description: Library name: IL-4-3


title: mRNA_tas2-3_Rep2

description: Library name: mRNA_tas2-3_Rep2

data_processing:
Analysis of degradome sequencing data was conducted using pRNASeqTools v0.8.
Assembly: Araport 11
Supplementary files format and content: The processed data files are in TXT format, containing the raw counts of all mRNA sequencing genes.

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings using the TRIzol method (Takara, 9108).
Initially, polyA-tailed RNAs were selectively enriched from the total RNA pool using oligo d(T) beads. These enriched RNAs were subsequently fragmented into random segments. Utilizing these segments as templates and dNTPs as building blocks, double-stranded cDNA was synthesized. Following purification, end repair, and adapter ligation, cDNA segments measuring 370-420bp were selected for amplification to create the RNA sequencing library.


title: mRNA_tas2-3_Rep1

description: Library name: mRNA_tas2-3_Rep1


title: DC2,NI,replicate1

description:
Library name: Sample 5
Column name in raw_counts.tsv : 5_DC2_NI_first


title: mRNA_tas2-2_Rep1

description: Library name: mRNA_tas2-2_Rep1


title: IL-4-2

description: Library name: IL-4-2


title: pDC,BA.1,replicate1

description:
Library name: Sample 4
Column name in raw_counts.tsv : 4_pDC_BA1_first


title: IL-4-1

description: Library name: IL-4-1


title: mRNA_tas3a/b/c_Rep2

description: Library name: mRNA_tas3a/b/c_Rep2


title: mRNA_tas3a/b/c_Rep1

description: Library name: mRNA_tas3a/b/c_Rep1


title: mRNA_tas2-1_Rep1

description: Library name: mRNA_tas2-1_Rep1


title: NC-3

description: Library name: NC-3

value: non


title: PDA-OVA_C1 scRNA seq

value: T-cells


description: Library name: Sample 6


title: pDC,Delta,replicate1

description:
Library name: Sample 3
Column name in raw_counts.tsv : 3_pDC_delta_first

value: pDC


title: sRNA_WT_tas2batch_Rep1

description: Library name: sRNA_WT_tas2batch_Rep1


title: pDC,R848,replicate1

description:
Library name: Sample 2
Column name in raw_counts.tsv : 2_pDC_R848_first


title: mRNA_WT_tas2batch_Rep1

description: Library name: mRNA_WT_tas2batch_Rep1


title: NC-2

description: Library name: NC-2


title: mRNA_WT_tas2batch_Rep2

description: Library name: mRNA_WT_tas2batch_Rep2


title: mRNA_WT_tas3batch_Rep1

description: Library name: mRNA_WT_tas3batch_Rep1


title: degradome_tas2-3_Rep2

description: Library name: degradome_tas2-3_Rep2

data_processing:
Analysis of degradome sequencing data was conducted using pRNASeqTools v0.8.
Assembly: Araport 11
Supplementary files format and content: BEDGRAPH

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings using the TRIzol method (Takara, 9108).
sRNA-seq: Small RNAs (sRNAs) of varying lengths were separated by 15% Urea-PAGE, and the 15-40bp bands were excised post-electrophoresis. The gel slices were soaked overnight at 4℃ in 0.4M NaCl solution, followed by ethanol precipitation. RIP-seq: WT and mutant seedlings underwent treatment with cell lysis buffer (1M Tris-HCl, 5M NaCl, 10% NP-40, 1M MgCl2, 1M DTT, proteinase inhibitor cocktail (100x), RNase inhibitor) to extract total protein. Subsequently, AGO1 antibody (Agrisera, #AS09527) and Protein A dynabeads (Thermo, 10001D) were utilized to enrich AGO1 protein. Following this enrichment process, RNA extraction and construction of the small RNA (sRNA) sequencing library were conducted as previously described. mRNA-seq: Initially, polyA-tailed RNAs were selectively enriched from the total RNA pool using oligo d(T) beads. These enriched RNAs were subsequently fragmented into random segments. Utilizing these segments as templates and dNTPs as building blocks, double-stranded cDNA was synthesized. Following purification, end repair, and adapter ligation, cDNA segments measuring 370-420bp were selected for amplification to create the RNA sequencing library. degradome-seq: The comprehensive protocol for constructing the degradome sequencing library is elaborated in Li, Yong-Fang et al.


title: NC-1

description: Library name: NC-1


title: mRNA_WT_tas3batch_Rep2

description: Library name: mRNA_WT_tas3batch_Rep2


title: mRNA_tas2-1_Rep2

description: Library name: mRNA_tas2-1_Rep2


title: mRNA_tas2-2_Rep2

description: Library name: mRNA_tas2-2_Rep2


title: KO_TAC5

first: MENGMENG

last: Zhao

address: Wuhan University

institute: Wuhan University

description:
Library name: D964B
KO_TAC5

data_processing:
CLC Genomics Workbenchv 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: heart

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA seg were prepared using SMARTER mRNA-Seq LibraryPrep Kit following manufacturer's protocols.

value: heart

value: KCP knockout

value: transverse aortic constriction surgery


title: pDC,NI,replicate1

description:
Library name: Sample 1
Column name in raw_counts.tsv : 1_pDC_NI_first


title: KO_TAC4

description:
Library name: D142_D958
KO_TAC4


title: 176_RSB057_V13

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

description: Library name: 176

data_processing:
STAR alignment to human genome version GRCh38.p13
Assembly: GRCh38.p13
Supplementary files format and content: Count table, tab-delimited text file

extract_protocol:
Qiagen RNAeasy
NovaSeq PE150

tag: description


title: degradome_WT_Rep2

description: Library name: degradome_WT_Rep2


title: 175_RSB057_V12

description: Library name: 175


title: degradome_tas3a/b/c_Rep1

description: Library name: degradome_tas3a/b/c_Rep1


title: 174_RSB057_V10

description: Library name: 174


title: KO_TAC3

description:
Library name: D139B
KO_TAC3


title: 173_RSB057_V09

description: Library name: 173


title: input_tas3a/b/c_Rep1

description: Library name: input_tas3a/b/c_Rep1

data_processing:
Analysis of degradome sequencing data was conducted using pRNASeqTools v0.8.
Assembly: Araport 11
Supplementary files format and content: BIGWIG

source_name: 15-day seedlings

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings using the TRIzol method (Takara, 9108).
WT and mutant seedlings underwent treatment with cell lysis buffer (1M Tris-HCl, 5M NaCl, 10% NP-40, 1M MgCl2, 1M DTT, proteinase inhibitor cocktail (100x), RNase inhibitor) to extract total protein. Subsequently, AGO1 antibody (Agrisera, #AS09527) and Protein A dynabeads (Thermo, 10001D) were utilized to enrich AGO1 protein. Following this enrichment process, RNA extraction and construction of the small RNA (sRNA) sequencing library were conducted as previously described.


title: input_WT_Rep2

description: Library name: input_WT_Rep2

source_name: 14-day seedlings


title: input_tas3a/b/c_Rep2

description: Library name: input_tas3a/b/c_Rep2

source_name: 16-day seedlings


title: input_WT_Rep1

description: Library name: input_WT_Rep1

source_name: 13-day seedlings


title: 172_RSB057_V08

description: Library name: 172


title: KO_TAC1

description:
Library name: D131B
KO_TAC1


title: KO4

description:
Library name: D965B
KO4

value: sham


title: 171_RSB057_V07

description: Library name: 171


title: RIP_tas3a/b/c_Rep2

description: Library name: RIP_tas3a/b/c_Rep2

value: 12-day seedlings


title: RIP_tas3a/b/c_Rep1

description: Library name: RIP_tas3a/b/c_Rep1


title: degradome_tas2-3_Rep1

description: Library name: degradome_tas2-3_Rep1


title: degradome_tas3a/b/c_Rep2

description: Library name: degradome_tas3a/b/c_Rep2


title: RIP_WT_Rep2

description: Library name: RIP_WT_Rep2


title: WT Mock-treated seedling RNA Rep 3

city: Atlanta

first: Roger

last: Deal

state: Georgia

address: 1510 Clifton Road NE, Room 2006

department: Biology

institute: Emory University

data_processing:
Read 1 from sequenced libraries were trimmed with Trimmomatic and then aligned to the Col-PEK genome assembly using the STAR alignment softwa . Picard MarkDuplicates function with REMOVE_DUPLICATES=T parameter was used to  .featureCounts was then used to convert alignment files into count matrix files for downstream analyses .
Assembly: Col-PEK
Supplementary files format and content: tab delimited text file including raw read counts at each Col-PEK gene via featureCounts

source_name: 7-day-old whole seedling

growth_protocol: Plants were grown horizontally on 1/2 MS plates sealed with medical tape in growth chambers at +20°C under a 16 hour-light/8-hour dark cycle for 7 days

extract_protocol:
Total RNA from frozen tissue was isolated using the RNeasy plant mini kit (Qiagen). Isolated RNA was treated with Ambion TURBO™ DNase (Invitrogen) using manufacturer’s recommendations.
500 nanograms of DNAase-treated RNA from RNA Extraction was used as input for the RNA-Seq library prep. The QuantSeq 3’ mRNA-Seq V2 Library Prep Kit with UDI (Lexogen) was used to make sequencing libraries with manufacturer’s recommendations.

treatment_protocol: Plants were either  treated with 10uM (+) ABA for 4 hours or a Mock solution (DMSO in Water) for 4 hours, then 100mg tissue was collected and frozen in liquid N2. All tissue collected around 1500 hours.

value: 7-day-old whole seedling

value: Mock


title: WT Mock-treated seedling RNA Rep 2


title: KO3

description:
Library name: D144B
KO3


title: 170_RSB057_V06

description: Library name: 170


title: KO2

description:
Library name: D144_D965
KO2


title: RIP_WT_Rep1

description: Library name: RIP_WT_Rep1


title: WT Mock-treated seedling RNA Rep 1


title: 169_RSB057_V05

description: Library name: 169


title: degradome_WT_Rep1

description: Library name: degradome_WT_Rep1


title: 168_RSB057_V04

description: Library name: 168


title: KO1

description:
Library name: D140B
KO1


title: WT ABA-treated seedling RNA Rep 2

value: 10 uM (+) ABA


title: KO_TAC2

description:
Library name: D135B
KO_TAC2


title: 167_RSB057_V01

description: Library name: 167


title: WT ABA-treated seedling RNA Rep 1


title: WT_TAC5

description:
Library name: D382B
WT_TAC5


title: mbd9-1 Mock-treated seedling RNA Rep 3


title: 166_RSB056_V13

description: Library name: 166


title: mbd9-1 Mock-treated seedling RNA Rep 2


title: 165_RSB056_V12

description: Library name: 165


title: WT_TAC4

description:
Library name: D381B
WT_TAC4


title: mbd9-1 Mock-treated seedling RNA Rep 1


title: mbd9-1 ABA-treated seedling RNA Rep 2


title: mbd9-1 ABA-treated seedling RNA Rep 1


title: WT ABA-treated seedling RNA Rep 3


title: mbd9 Mock-treated seedling ChIP Input Rep 2

library_source: genomic

data_processing:
Reads were aligned to the Col-PEK genome assembly with Bowtie2  using --local --very-sensitive --no-mixed --no-discordant --phred33 parameters.  Samtools -view bS, -index, and -sort functions were used to process resulting alignment files  Picard MarkDuplicates function with REMOVE_DUPLICATES=T parameter was used to remove sequencing duplicates. deepTools2 bamCoverage function with parameters --normalizeUsing RPKM and --extendReads were used to create Read Per Kilobase Million (RPKM) normalized bigwig files for visualization.
Assembly: Col-PEK
Supplementary files format and content: Reads Per Kilobase Million (RPKM) normalized bigWig files showing enrichment of each protein across the entire Col-PEK genome

molecule: genomic DNA

extract_protocol:
Frozen tissue was ground in a mortar and pestle, homogenized into a slurry in 250 µl of Buffer S and moved directly to sonication. Post sonication, lysate was diluted 10x with Buffer F for use in pulldowns. 50 µl of diluted lysate was saved as input. αH2A.Z (2 μg/mL), αMBD9 (2 μg/mL) or αPIE1 (3 μg/mL) antibodies were added to diluted lysates and incubated overnight at 4°C on a nutator for end-over-end mixing. 20 µl of Protein G Dynabeads (Invitrogen) per replicate were washed in excess Buffer F, resuspended to their original volume and added to each pulldown. Samples were incubated with beads at 4°C on a nutator for 2 hours. ChIP DNA was extracted via the MinElute PCR Purification Kit (Qiagen)
Sequencing libraries were made using the ThruPLEX DNA-Seq Kit (Takara).

treatment_protocol: Plants were either untreated, or treated with 10uM (+) ABA for 4 hours or a Mock solution (DMSO in Water) for 4 hours, then tissue was collected, crosslinked, and frozen in liquid N2. All tissue collected around 1500 hours.


title: 164_RSB056_V10

description: Library name: 164


title: mbd9-1 ABA-treated seedling RNA Rep 3


title: 163_RSB056_V09

description: Library name: 163


title: WT_TAC2

description:
Library name: D378B
WT_TAC2


title: mbd9 Mock-treated seedling  PIE1 ChIP Rep 2


title: 162_RSB056_V08

description: Library name: 162


title: mbd9 Mock-treated seedling  H2A.Z ChIP Rep 1


title: mbd9 Mock-treated seedling  PIE1 ChIP Rep 1


title: WT_TAC1

description:
Library name: D372B
WT_TAC1


title: 161_RSB056_V07

description: Library name: 161


title: mbd9 Mock-treated seedling  ChIP Input Rep 1


title: 160_RSB056_V06

description: Library name: 160


title: WT Mock-treated seedling PIE1 ChIP Rep 2


title: WT2

description:
Library name: D153B
WT2


title: 159_RSB056_V05

description: Library name: 159


title: WT_TAC3

description:
Library name: D380B
WT_TAC3


title: WT Mock-treated seedling PIE1 ChIP Rep 1


title: WT1

description:
Library name: D151B
WT1


title: 158_RSB056_V04

description: Library name: 158


title: WT Mock-treated seedling MBD9 ChIP Rep 1


title: WT Mock-treated seedling MBD9 ChIP Rep 2


title: WT Mock-treated seedling H2A.Z ChIP Rep 2


title: CTX-injured 10 days FAP-exos(FAPD10-exos)

city: ChongQing

first: 檬檬

last: 杨

state: ChongQing

address: No. 1 Medical College Road, Yuzhong District

department: School of Basic Medical Sciences

institute: 重庆医科大学

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Trimmed reads were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCh38
Supplementary files format and content: Excel file includes known miRNA readscounts for each Sample
Supplementary files format and content: Excel file includes novel miRNA readscounts for each Sample

source_name: fibro/adipogenic progenitors

growth_protocol: Freshly sorted FAPs were cultured in growth medium (GM) consisting of DMEM supplemented with 20% FBS, 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted from FAPD3-exos and FAPD10-exos using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The exosomes secreted into the supernatant within one week were collected

value: fibro/adipogenic progenitors

value: muscle-interstitial progenitors

value: exosomes collection


title: WT4

description:
Library name: D149B
WT4

value: WT


title: WT Mock-treated seedling H2A.Z ChIP Rep 1


title: CTX-injured 3 days FAP-exos(FAPD3-exos)


title: WT3

description:
Library name: D156B
WT3


title: WT Mock-treated seedling Input


title: 156_RSB055_V13

description: Library name: 156


title: 157_RSB056_V01

description: Library name: 157


title: FAPD10-exos Treated RAW264.7

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Trimmed reads were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCh38
Supplementary files format and content: Excel file includes raw counts for each Sample

growth_protocol: The RAW264.7 were cultured in growth medium (GM) consisting of DMEM supplemented with 20% FBS, 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted from FAPD10-exos- or vehicle-treated RAW264.7 using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 20ng mouse recombinant il4 was added to the medium treating for 24 hours. One of the sample was added 1*10^7paticles of FAPD10-exos at the same time.

value: Monocyte macrophage leukemia cells

value: M2 Polarization


title: mbd9-1 ABA-treated seedling PIE1 ChIP Rep 2


title: Vehicle RAW264.7

description: NC


title: mbd9-1 ABA-treated seedling ChIP Input Rep 1


title: 155_RSB055_V12

description: Library name: 155

value: Peripheral blood


title: mbd9-1 ABA-treated seedling PIE1 ChIP Rep 1


title: mbd9-1 ABA-treated seedling H2A.Z ChIP Rep 2


title: 154_RSB055_V10

description: Library name: 154


title: mbd9-1 ABA-treated seedling H2A.Z ChIP Rep 1


title: CUT&Tag of Mus musculus: ESC_IgG_CUTTag

city: Shen Zhen

first: Xinyu

last: Wu

address: BGI Space-Time Research Center

institute: BGI

data_processing:
For bulk RNA-seq analysis, reads from the RNA-seq data were aligned to the Ensembl v76 (mm10) transcript annotations using STAR (v.2.7.3a) with default parameter. Gene counts and TPM (Transcript per million) were calculated using RSEM (v1.3.1).For CUT&Tag, reads were trimmed of adapters and low-quality reads were removed by fastp ref (v0.12.4) with default parameter. Trimmed data was proceeded as previously described ref. Brieﬂy reads were first aligned to the mm10 assembly using Bowtie2 (v2.4.4) with the settings --local --very-sensitive-local --no-unal --nomixed --no-discordant --phred33 -I 10 -X 700. Low quality mapped reads were removed using Samtools(v1.9)61 with the settings -q 30. Duplicated reads were collapsed using sambamba (v0.8.0). CUT&Tag sample were called peaks using MACS2 (v2.2.7.1) with the settings -f BAMPE -g mm --SPMR --nomodel --keep-dup 1 --extsize 200 -q 1e-05 .
Assembly: mm10
Supplementary files format and content: For bulk RNA-seq all sample were normolized by TPM.For CUT&Tag the BigWig files were generated using deeptools (v3.4.3) bamCoverage tools with the settings --normalizeUsing RPKM
Library strategy: CUT&TAG

source_name: cell line

extract_protocol:
For RNA-seq cells were lysed by RNAzol®RT (MRC) and total RNA was extracted following the manufacturer’s instructions.
For RNA-seq extracted RNA was sent to BGI Genomics, where library construction and sequencing were performed.For CUT&Tag library construction, NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit for Illumina (Novoprotein) was used. In brief, 105 cells were incubated 10min at room temperature with Concanavalin A-coated magnetic beads. Bead bound cells were collected by placing a tube on a magnetic stand and removing the clear liquid. The bead-bound cells were resuspended in primary antibody buffer and incubated 2h at room temperature. Tubes were placed on a magnetic rack to remove the supernatants. Secondary antibodies were added and samples were incubated at room temperature for 1h. After placing the tubes on the magnetic rack and removing the supernatants, a mixture of pA-Tn5 were added to the bead-bound cells, vortexed gently, and incubated at RT for 1 h. After removed unbound pA-Tn5 protein, the cells were resuspended in tagmentation buffer and incubated at 37 °C for 1 h. One microliter of 10% SDS was added to stop tagmentation and incubated at 55 °C for 1 h. DNA was then extracted using magnetic beads. Purified DNA fragments were amplified by PCR for 15–20 cycles and the PCR products were purified following the kit’s instructions. CUT&Tag library construction were performed in duplicate. Libraries were sequenced by Berry Genomics Co. Ltd. (Beijing, China). Primary antibodies used were anti-KLF5 (R&D Systems).

value: cell line


title: 152_RSB055_V08

description: Library name: 152


title: 153_RSB055_V09

description: Library name: 153


title: WT ABA-treated seedling MBD9 ChIP Rep 2


title: WT ABA-treated seedling PIE1 ChIP Rep 2


title: Atrial tissue Het4

city: Houston

first: Xander

middle: H T

last: Wehrens

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

data_processing:
RNA-seq read quality from the whole-atrium total RNA samples were verified with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, Simon Andrews, Babraham Institute, Babraham, Cambridgeshire, UK) and MultiQC. All samples had mean quality scores > 35 and > 90% of reads with quality score > 30. Quality and adapter trimming of the read ends was performed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Felix Krueger, Babraham Institute). Reads were mapped to the GRCm39 mouse reference genome using the STAR package, and transcripts were quantified as Ensembl gene IDs using the RSEM package. BAM files of the aligned reads were sorted and indexed using SAMtools, and the indexed reads were viewed in Integrative Genomics Viewer to determine the relative frequencies of WT and c.2966A>G Mrc2 transcripts.
Differential expression analyses on the whole-atrium samples were performed in R using the EDASeq, limma, and edgeR packages. whole-atrial tissue data were filtered for genes with at least 1 count per million (CPM) in at least 5 samples with the sum of CPM for all 10 samples being at least 5. Sex and age of the mice from which the atria were harvested were accounted for as explanatory variables in the linear model. The data were normalized for sample library size using the weighted trimmed mean of M-values method and corrected for changes in variance across different mean CPMs using the voom method. For each of the E990G-het vs. WT contrasts, the t-statistic and p-value for each gene was determined with H0: |log2(fold change)| < log2(1.2) and Ha: |log2(fold change)| > log2(1.2).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw count, transcripts per million, and fragments per kilobase million of each gene for each sample
Supplementary files format and content: tab-delimited text file includes raw count, transcripts per million, fragments per kilobase million, and relative counts per million of each transcript variant for each gene for each sample

source_name: Cardiac atria

extract_protocol:
The atria were lysed with 250 μL TRI reagent (T9424, Sigma-Aldrich, Inc., St. Louis, MO) per atrial pair. The lysates were partially homogenized by brief mechanical homogenization at 4 °C and incubated for 5 minutes at room temperature. Total RNA was then isolated from the supernatant using the Direct-zol RNA Miniprep Kit (R2050, Zymo Research, Irvine, CA) according to the manufacturer’s protocol. 200 μL fresh TRI reagent was added to each leftover unhomogenized tissue sample, and the samples were completely homogenized by additional mechanical homogenization at 4 °C. Total RNA was extracted from these homogenates upon addition of chloroform according to the manufacturer’s protocol. The Direct-zol kit-extracted and Tri Reagent/chloroform-extracted RNA fractions from each sample were combined for RNA-seq. Total RNA sample quantity, purity, and integrity were determined by spectrophotometric absorbance at 260 nm, the 260/280 nm absorbance ratio, and gel electrophoresis, respectively.
The total-RNA samples were shipped to GENEWIZ (Azenta, South Plainfield, NJ) on dry ice for standard RNA-seq at a targeted depth of 30 million reads per sample. The yield for 9 of the 10 whole-atrium samples exceeded 30 million reads per sample; one of the atrium samples had a yield of 24.3 million reads. At Azenta, RNA sample quantity was confirmed using the Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA), and RNA integrity was confirmed using the Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA). Library preparation with stranded polyA selection was then performed.
The libraries were sequenced using a 2x150bp Paired End (PE) configuration on the Illumina® NovaSeq™ 6000 platform. Raw sequence data (.bcl files) generated from Illumina platform were converted into .fastq files, de-multiplexed using Illumina's bcl2fastq 2.17 software, and delivered by File Transfer Protocol (FTP).

value: Cardiac atria

value: MRC2 E990G-het


title: WT ABA-treated seedling ChIP Input Rep 2


title: WT ABA-treated seedling PIE1 ChIP Rep 1


title: CUT&Tag of Mus musculus: iKlf5_D2_LIF_KLF5_CUTTag


title: mbd9-1 ABA-treated seedling ChIP Input Rep 2


title: WT ABA-treated seedling MBD9 ChIP Rep 1


title: 151_RSB055_V07

description: Library name: 151


title: D1209A ABA-treated seedling ChIP Input Rep 2


title: Atrial tissue Het3


title: 149_RSB055_V05

description: Library name: 149


title: WT ABA-treated seedling H2A.Z ChIP Rep 1


title: Atrial tissue Het2


title: 150_RSB055_V06

description: Library name: 150


title: D1209A ABA-treated seedling ChIP Input Rep 1


title: D1209A ABA-treated seedling PIE1 ChIP Rep 2


title: mbd9 Mock-treated seedling  H2A.Z ChIP Rep 2


title: Atrial tissue Het1


title: WT ABA-treated seedling ChIP Input Rep 1


title: Atrial tissue WT6

value: Wild-type


title: D1209A ABA-treated seedling MBD9 ChIP Rep 2


title: D1209A ABA-treated seedling PIE1 ChIP Rep 1


title: 148_RSB055_V04

description: Library name: 148


title: D1209A ABA-treated seedling MBD9 ChIP Rep 1


title: 147_RSB055_V01

description: Library name: 147


title: D1209A ABA-treated seedling H2A.Z ChIP Rep 1


title: 146_RSB050_V13

description: Library name: 146


title: Atrial tissue WT5


title: D1209A ABA-treated seedling H2A.Z ChIP Rep 2


title: Atrial tissue WT4


title: CON2

city: Zhuhai

first: Biao

last: Liu

address: meihuadong road

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

description: Library name: Rat_CC_NC2

data_processing:
The raw sequencing reads were processed by Cell Ranger (v.3.1.0) with the default parameters.
Assembly: rn7
Supplementary files format and content: Count martrix

organism: Rattus norvegicus

source_name: corpus cavernosum

extract_protocol:
Fresh CC tissue samples of about 1×1-cm size were first immersed in 15 ml PBS with vigorous shaking to remove residual blood cells. Then, tissues were cut into pieces of 1×1-mm size and enzymatically digested with 2.5 mg/ml collagenase type I (17104-019, gibco), 4 mg/ml collagenase type IV (17018029, gibco), 0.1 mg/ml neutral protease, and 2 mg/ml DNase I (#AMPD1, Sigma-Aldrich) at 37°C for 40 min. Subsequently, the cell suspension was filtered through a 40-mm nylon mesh, and the cells were sorted by MACS with a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) to remove dead cells. The cells were resuspended in 0.05% BSA/PBS buffer before cDNA library preparation.
Standard protocol of RD  Rhapsody

value: corpus cavernosum

value: all CC cells


title: CON1

description: Library name: Rat_CC_NC1


title: 145_RSB050_V12

description: Library name: 145


title: TEMRA_P33_37_M_Exp02

city: Rochester

first: Abhinav

last: Jain

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
The reads underwent quality checked and trimmed using the in-house scripts and aligned to hg38 with Bowtie2.
Reads mapping to mitochondria, sex chromosome, and blacklisted region were excluded.
Peaks overlaps with less than 6 samples were removed.
Peaks calling were performed using MACS.
The read counts were normalized by combining voom-observation-level weight accounting for the batch effect.
Assembly: Differential were calculated using limma. The differential peaks were used for the construction of K-means clustering based on the average of the different groups.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak, and comma-separated value files.

extract_protocol:
CD8+ tetramer+ cells and CD8+ bulk populations of central memory (CD45RA– CCR7+), effector memory (CD45RA– CCR7–) and TEMRA cells (CD45RA+ CD28–) were collected via FACS.
Sorted CD8 T cells were washed with cold PBS and RSB buffer (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2) followed by washing with RSB buffer containing 0.1% NP-40 and 0.1% Tween 20. Cell pellets were resuspended in the transposase reaction mix (25μL 2 × TD buffer, 2.5μL transposase (Illumina) and 22.5μL nuclease-free water) and incubated at 37°C for 30 min. Fragmented genomic DNA was further purified with a Qiagen MiniElute kit and library amplification was performed using Nextera PCR primers.

value: Blood

value: TEMRA CD8 T cells


title: 144_RSB050_V10

description: Library name: 144


title: Atrial tissue WT3


title: 143_RSB050_V09

description: Library name: 143


title: TEMRA_P32_27_F_Exp02


title: TEMRA_P31_80_M_Exp02


title: Atrial tissue WT1


title: 142_RSB050_V08

description: Library name: 142


title: WT ABA-treated seedling H2A.Z ChIP Rep 2

value: 7-day-old whole seedling


title: TEMRA_P29_48_F_Exp02


title: Atrial fibroblast WT4

data_processing:
RNA-seq read quality from the ACF total RNA samples were verified with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, Simon Andrews, Babraham Institute, Babraham, Cambridgeshire, UK) and MultiQC. All samples had mean quality scores > 35 and > 90% of reads with quality score > 30. Quality and adapter trimming of the read ends was performed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Felix Krueger, Babraham Institute). Reads were mapped to the GRCm39 mouse reference genome using the STAR package, and transcripts were quantified as Ensembl gene IDs using the RSEM package. BAM files of the aligned reads were sorted and indexed using SAMtools, and the indexed reads were viewed in Integrative Genomics Viewer to determine the relative frequencies of WT and c.2966A>G Mrc2 transcripts.
Differential expression analyses on the ACF samples were performed in R using the EDASeq, limma, and edgeR packages. The ACF read count data were filtered for genes with at least 1 count per million (CPM) in at least 4 samples with the sum of CPM for all 9 samples being at least 4. ACF isolation batch and sex were accounted for as explanatory variables in the linear model. The data were normalized for sample library size using the weighted trimmed mean of M-values method and corrected for changes in variance across different mean CPMs using the voom method. For each of the E990G-het vs. WT contrasts, the t-statistic and p-value for each gene was determined with H0: |log2(fold change)| < log2(1.2) and Ha: |log2(fold change)| > log2(1.2).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw count, transcripts per million, and fragments per kilobase million of each gene for each sample
Supplementary files format and content: tab-delimited text file includes raw count, transcripts per million, fragments per kilobase million, and relative counts per million of each transcript variant for each gene for each sample

source_name: Primary isolated atrial fibroblast

growth_protocol: Using aseptic technique in a biosafety cabinet, each excised heart was placed on a separate petri dish in Dulbecco′s phosphate-buffered saline (DPBS) with Ca2+ and Mg2+ (D8662, Sigma-Aldrich, Inc., St. Louis, MO) with 2.5X antibiotic-antimycotic solution (250 units penicillin, 250 μg streptomycin, and 0.625 μg amphotericin B per mL) (A5955, Sigma-Aldrich, Inc., St. Louis, MO), 10 μg/mL Plasmocin® Prophylactic (ant-mpp, InvivoGen, San Diego, CA), and 100 μM L-Ascorbic acid 2-phosphate (ascorbate) sesquimagnesium salt hydrate (A8960, Sigma-Aldrich, Inc., St. Louis, MO). The tissue surrounding each atrium was trimmed, and the atria were excised and placed in dissociation solution containing 1 mg (280 U) per mL collagenase, type 4 (LS004188, Worthington Biochemical Corp., Lakewood, NJ), and 0.7 mg (1 U) per mL dispase II (D4693, Sigma-Aldrich, Inc., St. Louis, MO) in DPBS with Ca2+ and Mg2+, 25% 1:1 Dulbecco′s Modified Eagle′s Medium/Ham’s F-12 (DMEM/F12) nutrient mixture (D8062, Sigma-Aldrich, Inc., St. Louis, MO), 1X antibiotic-antimycotic solution (100 units penicillin, 100 μg streptomycin, and 0.25 μg amphotericin B per mL), 5 μg/mL Plasmocin® Prophylactic, and 100 μM ascorbate. Each pair of atria from each mouse heart was placed in 1 mL dissociation solution in separate 2-mL microcentrifuge tubes. All non-sterilized reagents used for tissue dissociation, ACF isolation, and cell cultures were filter-sterilized in the biosafety cabinet before use, and all tissues and ACFs were handled in the biosafety cabinet using aseptic technique. The atria were incubated at 37°C with gentle agitation for 5 rounds of dissociation with 25 minutes for the first round and the duration incrementally decreasing by 5 minutes for each subsequent round. After each round of dissociation, the tissues were gently triturated with a 1000 μL micropipette (the pipette tip was cut to enlarge the opening for the first two rounds). The tubes then were held vertically to allow the undigested tissue to settle, and the supernatant in each tube was passed through a 40 µm cell strainer into a 50 mL centrifuge tube on ice (separate pipette tips, strainers, and centrifuge tubes for each ACF line). 1 mL of ice-cold quenching buffer [18% DMEM/F12, 2% fetal bovine serum (FBS) (35-015-CF, Corning, Tewksbury, MA), 1X antibiotic-antimycotic solution, 5 μg/mL Plasmocin Prophylactic, and 100 μM ascorbate in DPBS] was then passed through each cell strainer. 1 mL of fresh dissociation solution was added to each tube, and the procedure was repeated for each dissociation round. After the second round only, the atria were minced into several smaller pieces using scissors. After the fifth round, the 50 mL tubes were centrifuged at 1000 rpm (193 g) for 5 min at 4°C, and the supernatants were discarded. 10 mL of DPBS was then passed through each cell strainer into each 50 mL tube to rinse the strainers and wash the pelleted ACFs, and the centrifugation step was repeated. The supernatants were then discarded, and the ACFs were resuspended in growth medium (DMEM/F12 with 10% FBS, 1X antibiotic-antimycotic solution, 5 μg/mL Plasmocin Prophylactic, and 100 μM ascorbate). 80% of each ACF line was seeded in one tissue-culture treated 6-well plate well. The ACFs were incubated at 37°C for 2 hours, and the media were then aspirated from the adherent ACFs. The adherent ACFs were washed three times with DPBS and cultured at 37 °C in growth media.

extract_protocol:
Once the ACFs in the 6-well plates reached ~50% confluency, they were adapted to serum-free media by replacing half of the conditioned media with serum-free media. The following day, all conditioned media were replaced with serum-free media. The serum-free conditioned media were collected the following day, and the ACFs were lysed with TRIzol reagent (15596018, Invitrogen™, Waltham, MA), and total RNA and cellular protein was isolated using the Direct-zol RNA Miniprep Kit (R2050, Zymo Research, Irvine, CA) according to the manufacturer’s protocol. Total RNA sample quantity, purity, and integrity were determined by spectrophotometric absorbance at 260 nm, the 260/280 nm absorbance ratio, and gel electrophoresis, respectively.
The total-RNA samples were shipped to GENEWIZ (Azenta, South Plainfield, NJ) on dry ice for standard RNA-seq at a targeted depth of 30 million reads per sample. The yield for all ACF samples exceeded 30 million reads per sample. At Azenta, RNA sample quantity was confirmed using the Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA), and RNA integrity was confirmed using the Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA). Library preparation with stranded polyA selection was then performed.
The libraries were sequenced using a 2x150bp Paired End (PE) configuration on the Illumina® NovaSeq™ 6000 platform. Raw sequence data (.bcl files) generated from Illumina platform were converted into .fastq files, de-multiplexed using Illumina's bcl2fastq 2.17 software, and delivered by File Transfer Protocol (FTP).

value: Primary isolated atrial fibroblast

value: Cardiac fibroblast


title: TEMRA_P28_46_M_Exp02


title: Atrial tissue WT2


title: TEMRA_P26_57_F_Exp02


title: TEMRA_P30_24_M_Exp02


title: 140_RSB050_V06

description: Library name: 140


title: TEMRA_P25_48_F_Exp02


title: Atrial fibroblast Het5


title: TEMRA_P27_29_F_Exp02


title: CNIED

description: Library name: Rat_CC_CNI1


title: TEMRA_P23_30_M_Exp02


title: Atrial fibroblast Het4


title: TEMRA_P20_32_M_Exp01


title: TEMRA_P21_24_M_Exp01


title: Atrial fibroblast Het3


title: 138_RSB050_V04

description: Library name: 138


title: EM_P39_22_F_Exp03

value: EM CD8 T cells


title: EM_P38_23_F_Exp03


title: 141_RSB050_V07

description: Library name: 141


title: 137_RSB050_V01

description: Library name: 137


title: Atrial fibroblast Het2


title: Atrial fibroblast WT3


title: EM_P37_31_M_Exp03


title: EM_P35_26_M_Exp03


title: 134_RSB049_V10

description: Library name: 134


title: EBV-LMP2_P38_23_F_Exp03

value: EBV-LMP2 CD8 T cells


title: Atrial fibroblast WT2


title: 136_RSB049_V13

description: Library name: 136


title: 135_RSB049_V12

description: Library name: 135


title: EBV-LMP2_P39_22_F_Exp03


title: EM_P34_28_F_Exp03


title: EBV-LMP2_P35_26_M_Exp03


title: Atrial fibroblast Het1


title: 133_RSB049_V09

description: Library name: 133


title: EBV-LMP2_P36_26_F_Exp03


title: EBV-LMP2_P34_28_F_Exp03


title: 3T3 cell, AA3

city: Shenzhen, Guangdong

address: 19/F, Li Ning Center, No. 9996 Shennan Avenue, Nanshan District, Shenzhen, China

institute: Shenzhen Hujia Technology

data_processing:
The raw image data of the sequencing results were subjected to Base Calling using the software Bcl2fastq (v2.20.0.422), and preliminary quality analysis (during the sequencing process, Illumina's built-in software decides whether to retain or discard the read based on the quality of the first 25 bases of each sequencing segment, i.e., the read). Pass Filter Data, the result is stored in FASTQ file format, which contains the sequencing sequence information (line 2 of FASTQ format) and its corresponding sequencing quality information (line 4 of FASTQ format).
Filtering of low quality data using Cutadapt (version 1.9.1) to remove contamination and splice sequences.
The filtered sequencing Clean Data was compared and analyzed with the reference genome, and the selection of the appropriate reference genome is crucial to the success of the project information analysis, and the data comparison rate can reflect to a certain extent the similarity relationship between the experimentally sequenced samples and the selected reference genome.
Hisat2 (v2.2.1) software was used for the comparison of short reads with default parameters.
alternative splicing analysis of RNA-Seq data using rMATS (4.1.0)
Gene expression was calculated using Htseq software (V 0.6.1), which uses the FPKM (Fragments Per Kilo bases per Million reads) (Mortazavi, 2008) method for calculating gene expressions
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: 3T3 cell were maitained in DMEM supplemented wth 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TransZol Up Plus RNA Kit (Transgen).2 ug of total RNA was used for the construction of sequencing ibraries.
Library construction using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina kit

value: NIH 3T3 Mouse Embryonic Fibroblast Cell

value: WT

value: UVA(10 J/cm2) and α-arbutin treated


title: EBV-BRLF1_P39_22_F_Exp03

value: EBV-BMLF1 CD8 T cells


title: 3T3 cell, AA2


title: EBV-BRLF1_P37_31_M_Exp03


title: EBV-BRLF1_P38_23_F_Exp03


title: 131_RSB049_V07

description: Library name: 131

value: Peripheral blood


title: 139_RSB050_V05

description: Library name: 139


title: EM_P36_26_F_Exp03


title: 3T3 cell, AA1


title: EBV-BRLF1_P36_26_F_Exp03


title: 130_RSB049_V06

description: Library name: 130


title: EBV-LMP2_P37_31_M_Exp03


title: 3T3 cell,MOCK 3

value: UVA(10 J/cm2)


title: Atrial fibroblast WT1


title: EBV-BRLF1_P35_26_M_Exp03


title: EBV-BRLF1_P34_28_F_Exp03


title: EBV-BMLF1_P30_24_M_Exp02


title: 128_RSB049_V04

description: Library name: 128


title: 3T3 cell,MOCK 2


title: 129_RSB049_V05

description: Library name: 129


title: EBV-BMLF1_P33_37_M_Exp02


title: 132_RSB049_V08

description: Library name: 132


title: EBV-BMLF1_P24_24_M_Exp02


title: 3T3 cell,MOCK 1


title: EBV-BMLF1_P25_48_F_Exp02


title: 127_RSB049_V01

description: Library name: 127


title: CM_P39_22_F_Exp03

value: CM CD8 T cells


title: EBV-BMLF1_P23_30_M_Exp02


title: 126_RSB046_V13

description: Library name: 126


title: 3T3 cell, control 3


title: 125_RSB046_V12

description: Library name: 125


title: CM_P36_26_F_Exp03


title: CM_P37_31_M_Exp03


title: CM_P35_26_M_Exp03


title: CM_P38_23_F_Exp03


title: 3T3 cell, control 1


title: 124_RSB046_V10

description: Library name: 124


title: CM_P34_28_F_Exp03


title: LH30_5

city: Davis

first: Gaurav

last: Sarode

address: 6404A GBSF, 451 E. Health Sciences Dr.

department: Internal Medicine

institute: University of California, Davis

data_processing:
Raw reads (FASTQ) were processed through fastp (0.20.0), removing reads containing adapter and poly-N sequences and low-quality reads while simultaneously calculating Q20, Q30, and GC content
Paired-end clean reads were aligned to the reference genome(grcm38) using the Spliced Transcripts Alignment to a Reference (STAR) software (v2.6.1d)
FeatureCounts(v1.5.0-p3) was used to count the reads mapped to each gene; RPKM of each gene was calculated based on the length of the gene and reads mapped to the gene.
Assembly: grcm38 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

growth_protocol: Mice were anesthetized with isoflurane, then euthanized by cervical dislocation. The ventral incision site was wet with 70% ethanol and the abdominal cavity was opened. The small intestine was cut at the proximal end and gently pulled out of the abdominal cavity to unfurl it, removing the majority of pancreas and mesenteric fat in the process. The small intestine was released by cutting the distal end at the cecum and wet with ice-cold dissection buffer comprised of Hank’s Balanced Salt Solution without calcium/magnesium, 10 mM HEPES, and 5% FBS. Half the full length plus 2 cm of the small intestine was used for dissociation. In a glass petri dish with ice-cold dissection buffer, the intestine was cut into 4-5 smaller segments and each segment was thoroughly flushed with ice-cold dissection buffer. Each segment was then placed on a clean paper towel saturated with ice-cold dissection buffer; any remaining bits of pancreas and mesenteric fat were trimmed; any remaining lumenal content was removed by gently sliding a pair of blunt-tip surgical forceps along the segment (holding the forceps closed), and the segment was held in ice-cold dissection buffer until all segments were cleaned. Each segment was then cut open longitudinally, cut into ~0.5 cm pieces, and placed directly into a conical tube with 40 ml dissociation buffer (HBSS without calcium/magnesium, 10mM HEPES, 12.5 mM EDTA, 5% FBS, 1mM dithiothreitol), and dissociated for 30 minutes at 300 rpm and 37°C in a Corning LSE benchtop orbital shaking incubator (Corning, NY). The dissociated suspension was passed through a 70 µm cell strainer and centrifuged. The supernatant was removed and the cell pellet was washed in 25 ml ice-cold PBS (pH 7.2) with 0.5% FBS then centrifuged. The cells were washed a total of 3 times to remove as many non-IECs, e.g. lymphocytes, as possible. Live cells were counted and the cell suspension was divided across multiple aliquots. Aliquots were centrifuged, supernatant was removed, and cell pellets were flash-frozen and stored at -80°C for downstream analyses. All centrifugations were performed for 5 minutes at 300 x g and 4°C.

extract_protocol:
Total RNA was extracted from frozen mouse liver  using the AllPrep DNA/RNA Mini Kit (Cat. No- 80204 QIAGEN).
Sequencing libraries were generated using with 1 ug of total RNA by NEBNext Ultra RNA Library Prep Kit for Illumina (Cat. no-E7530LNew England Biolabs).

value: Liver

value: Het

value: Heterozygus

tag: time

value: 30 weeks


title: EM-39_2nd tr

city: Chicago

first: Jinhee

last: Kim

state: IL

address: 676 North St. Clair Street Arkes Suite 2330

department: Infectious Disease

institute: Northwestern University

data_processing:
Data were analyzed using the Partek Flow software.
Sequencing data were demultiplexed, trimmed, and aligned to hg38 with STAR 2.7.8a. Differential gene expression analysis using the quantified gene transcripts was performed with DESeq2 R package(60) comparing the samples in the 2 groups. A cut-off of FDR<0.1 was used for significance. Differentially expressed genes (DEGs) were analyzed by gene set enrichment analysis (GSEA) to identify enriched pathways and molecular processes in the ART at conception group compared to the 2nd trimester group.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for each Sample

source_name: PBMC

extract_protocol:
RNA was extracted with the RNeasy kit (Qiagen).
Due to the low RNA yield, a low-input RNA-seq library preparation was performed.

value: PBMC

tag: group of_women

value: Initiated cART at ≥ 2nd trimester


title: LH30_4


title: EM-37_cART

value: On cART at conception


title: 123_RSB046_V09

description: Library name: 123

source_name: Peripheral blood


title: EM-38_cART


title: 122_RSB046_V08

description: Library name: 122


title: 120_RSB046_V06

description: Library name: 120


title: LH30_2


title: 3T3 cell, control 2


title: EM-33_2nd tr


title: EM-36_cART


title: EM-34_cART


title: 119_RSB046_V05

description: Library name: 119


title: LH30_1


title: EM-32_2nd tr


title: EM-31_cART


title: EM-29_cART


title: EM-40_2nd tr


title: KO9

source_name: Intestinal epithelial cells

value: Intestinal epithelial cells

value: KO

value: Global ATP7B KO

value: 16 weeks


title: EM-27_cART


title: 118_RSB046_V04

description: Library name: 118


title: EM-28_2nd tr


title: KO43

value: WT

value: Wildtype


title: EM-26_2nd tr


title: 117_RSB046_V01

description: Library name: 117


title: LH30_3


title: 121_RSB046_V07

description: Library name: 121


title: EM-35_2nd tr


title: KO40


title: EM-24_2nd tr


title: 116_RSB045_V13

description: Library name: 116


title: EM-25_2nd tr


title: EM-23_cART


title: EM-22_2nd tr


title: EM-21_2nd tr


title: 115_RSB045_V12

description: Library name: 115


title: EM-30_cART


title: KO34


title: 114_RSB045_V10

description: Library name: 114


title: 113_RSB045_V09

description: Library name: 113


title: EM-18_cART


title: EM-20_2nd tr


title: EM-17_cART


title: KO33


title: EM-19_2nd tr


title: EM-16_cART


title: 112_RSB045_V08

description: Library name: 112


title: 111_RSB045_V07

description: Library name: 111


title: KO30_7


title: KO41


title: EM-14_2nd tr


title: KO30_6


title: EM-13_2nd tr


title: 110_RSB045_V06

description: Library name: 110


title: KO30_2


title: EM-12_2nd tr


title: 109_RSB045_V05

description: Library name: 109


title: EM-10_2nd tr


title: EM-9_cART


title: KO30_12


title: EM-8_cART


title: 108_RSB045_V04

description: Library name: 108


title: EM-15_cART


title: EM-6_cART


title: 107_RSB045_V01

description: Library name: 107


title: KO30_10


title: EM-7_cART


title: EM-2_2nd tr


title: KO30_1


title: EM-5_cART


title: EM-3_2nd tr


title: KO24


title: EM-1_cART


title: KO227


title: KI381_K4me3_recovery_GM07492

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: K4me3_GM07_SS24_hg38_t381t405c397_fe_k1sort.bw

data_processing:
ChIP-seq reads were mapped to the hg38 human reference genome using Bowtie2 64 with the default “--sensitive” parameter. Reads with MAPQ score greater than 20 were used in downstream analyses. We generated per-base coverage of 200 bp-extended aligned reads normalized by sequencing depth, and this was used for visualization of ChIP-seq genomic signal distribution.
To identify ChIP enriched "peak" locations, the aligned reads from biological replicates of ChIP and the corresponding input were processed by MACS2 (v2.1.0) with "call peak -g hg --nomodel --extsize 200 --SPMR --bdg --call-summits" parameter set. This also generated input-normalized, replicate-combined per-base fold enrichment signal scores, which were used in visualization of replicate-combined genomic signals.
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: bedgraph

source_name: Dermal fibroblast

growth_protocol: Human skin fibroblast cell line GM07492 (Coriell Cell Repository) was grown in MEM Alpha medium (Life Technologies, catalog number 12561-056) with 10% FBS (Sigma) and 1% Penicillin/Streptomycin mix (Corning) and incubated at 37°C with 5% CO2. This was the proliferation growth condition. For serum starvation, the proliferation culture medium was replaced with MEM Alpha with 0.1% FBS, 1% Penicillin/Streptomycin, at 37°C with 5% CO2 for 48 hours. For recovery, the 48-hour starved cells were cultured with the proliferation medium at 37°C with 5% CO2 for 24 hours.

extract_protocol:
ChIP-seq in GM07492 fibroblasts were performed during proliferating, at 48 hours into starvation, and at 24 hours into the recovery phase. Cells were crosslinked in 1% formaldehyde for 15 min at room temperature. Cell extract from one million cells was incubated with antibodies in a 200-μL reaction for 12 hours or longer at 4°C. Antibodies used in ChIP are: mouse monoclonal anti-H3K27ac antibody (Wako MABI0309, Lot 14007, RRID:AB_11126964; 2 μL per IP) and mouse monoclonal anti-H3K4me3 antibody (Wako MABI0304, Lot 14004, RRID:AB_11123891; 2 μL per IP). Immunocomplex was captured by Protein G-conjugated magnetic beads and washed. Immunoprecipitated DNA was reverse-crosslinked and used to construct high-throughput sequencing libraries.
Immunoprecipitated DNA was reverse-crosslinked and used to construct high-throughput sequencing libraries using NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370).

value: Dermal fibroblast

tag: phase

value: recovery

tag: chip antibody


title: KI405_K4me3_recovery_GM07492


title: EM-11_2nd tr


title: 103_RSB039_V09

description: Library name: 103

value: Peripheral blood


title: KO225


title: KO39


title: 104_RSB039_V10

description: Library name: 104


title: KI404_K4me3_starvation_GM07492

description: K4me3_GM07_Q_hg38_t376t404c396_fe_k1sort.bw

value: starvation


title: KI376_K4me3_starvation_GM07492


title: 102_RSB039_V08

description: Library name: 102


title: KO224

value: Liver


title: KI403_K4me3_proliferation_GM07492

description: K4me3_GM07_P_hg38_t353t403c384_fe_k1sort.bw

value: proliferation


title: 106_RSB039_V13

description: Library name: 106


title: KO25


title: KI353_K4me3_proliferation_GM07492


title: 105_RSB039_V12

description: Library name: 105


title: 101_RSB039_V07

description: Library name: 101


title: KI402_K27ac_recovery_GM07492

description: K27ac_GM07_SS24_hg38_t379t402c397_fe_k1sort.bw


title: 100_RSB039_V06

description: Library name: 100


title: KI401_K27ac_starvation_GM07492

description: K27ac_GM07_Q_hg38_t374t401c396_fe_k1sort.bw


title: KO222


title: KO223


title: KI379_K27ac_recovery_GM07492


title: KI397_Input_recovery_GM07492

value: Input


title: KI374_K27ac_starvation_GM07492


title: 99_RSB039_V05

description: Library name: 99


title: KI396_Input_starvation_GM07492


title: KI665_Bru_recovery_GM07492

description: BrU-labeled RNA

data_processing:
Bru-seq reads were aligned to the human hg38 reference genome with the Gencode v38 basic gene annotation using STAR version 2.7.9 59 with the default alignment parameters except using "--clip3pAdapterSeq AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --sjdbGTFfeatureExon gene" parameters. From raw read counts per transcript, TPMs (transcripts per million) were calculated in R as follows: TPM = 10^6 x RPK/sum(RPK), where RPK = [read count] x 1/[transcript length in kb], and sum(RPK) is the sum of RPKs for all transcripts.
Assembly: hg38
Supplementary files format and content: A text file containing read count and TPM for each gene.
Library strategy: Bru-seq

extract_protocol:
After 2 hours of BrU labeling, the culture medium was removed, and cells were harvested with Trizol LS for RNA extraction (Invitrogen #10296010). Purified total RNA was treated with TurboDNase (Ambion AM18907) and fragmented by Fragmentation Buffer (Ambion AM8740). BrU-incorporated RNA fragments were immunoprecipitated with mouse monoclonal anti-BrdU antibody 3D4 (BD Biosciences 555627 Lot 7033666).
Immunoprecipitated RNAs were used to construct DNA sequencing libraries using NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs E7760).

treatment_protocol: Bru-seq was performed by following the protocol developed elsewhere with modifications. To label RNAs in GM07492 fibroblast cells in culture, we added 5-Bromouridine (BrU, Sigma #850187, dissolved in PBS at 50 mM) directly to the culture medium at the final concentration of 2 mM and incubated cells at 37°C with 5% CO2 for 2 hours. This 2-hour labeling was performed during proliferation, at 46 to 48 hours into starvation, and at 22 to 24 hours into the recovery phase.


title: 98_RSB039_V04

description: Library name: 98


title: KO220

value: 30 weeks


title: KI663_Bru_starvation_GM07492

description: BrU-labeled RNA


title: 97_RSB039_V01

description: Library name: 97


title: KO219


title: KI662_Bru_proliferation_GM07492

description: BrU-labeled RNA


title: KO221


title: EM-4_cART

value: PBMC


title: KI661_Bru_recovery_GM07492

description: BrU-labeled RNA


title: 96_RSB038_V13

description: Library name: 96


title: 94_RSB038_V10

description: Library name: 94


title: KI658_Bru_proliferation_GM07492

description: BrU-labeled RNA


title: KO215


title: KI659_Bru_starvation_GM07492

description: BrU-labeled RNA


title: 93_RSB038_V09

description: Library name: 93


title: Ovcar8 Cisplatin, total mRNA, rep1

city: Pittsburgh

first: Katherine

last: Aird

state: PA

address: 5051 Centre Ave.

institute: University of Pittsburgh School of Medicine

data_processing:
Demultiplexed and quality-filtered mRNA-Seq reads were then aligned to human reference genome (GRCh38) using STAR (v.2.6.1)
Differential expression analysis was done using DESeq2 (v2_1.6.3)
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file includes raw counts for all samples
Supplementary files format and content: Tab delimited text file includes FPKMs for all samples

growth_protocol: Ovcar8 cells were cultured in DMEM + 5% FBS

extract_protocol:
RNA was harvested by Trizol followed by a Qiagen clean up column with a DNAse step.
The cDNA libraries were prepared using NEBNext Ultra 2 RNA Library Prep Kit for Illumina (New England Biolabs; Cat.# E7775)
Next generation sequencing was performed at Novogene using a NovaSeq 6000 Sequencing System  (Illumina)

treatment_protocol: Cells were treated with DMF or 1uM cisplatin for 4 days

value: cell line

value: Ovarian Cancer

value: Cisplatin


title: Ovcar8 Cisplatin, total mRNA, rep3


title: Ovcar8 Cisplatin, total mRNA, rep2


title: KO216


title: Ovcar8 DMF, total mRNA, rep2

value: DMF


title: HEK-1

city: La Jolla

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Drive, MC 0412

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
Cutadapt 2.5 used for adapter trimming
BWA-MEM 0.7.12-r1039 used for mapping
PRIMseqTools used for downstream processing
Assembly: hg38
Supplementary files format and content: chimeric read pairs for RPA identification
Library strategy: PRIM-seq

growth_protocol: Ligation of Total RNA to Interaction Linker: Purified total RNA was fragmented with the NEBNext® Magnesium RNA Fragmentation Module (NEB, E6150S) for 2 minutes at 94 °C. The fragmented RNA was purified with a RNeasy Mini Column (Qiagen, 74104). The ends of the 200 pmols of RNA were repaired in a 200 μLs reaction containing 100 U Quick CIP (NEB, M0525S) and 1x rCutSmart buffer (B6004S). The reaction was incubated at 37 °C for 1 hour and then purified with RNeasy Mini Columns (Qiagen, 74104). To ligate the interaction linker to the total RNA, a 200 μLs reaction was mixed containing 400 pmols of App-interaction linker, 200 pmols of fragmented total RNA, 4,000 U T4 RNA Ligase 2, truncated KQ (NEB, M0373S), 1x T4 RNA Ligase buffer (NEB, M0373S), and 15% PEG 8000 (NEB, M0373S). This reaction was incubated at 16 °C overnight and then purified with RNeasy Mini Columns (Qiagen, 74104). The bottom strand of the interaction linker was added to the purified sample in a 1:1 molar ratio in 1x Annealing buffer [10x: 100 mM Tris-HCI Buffer, pH 7.5 (Invitrogen, 15567027), 500 mM NaCl (Thermo Scientific, AM9759), 10 mM EDTA pH 8.0 (Invitrogen™, AM9260G)]. The solution was heated to 75°C for 5 minutes and cooled to 25°C at 0.1°C per second.

extract_protocol:
The DNA was released from the beads with the NEBNext® Ultra™ II FS DNA Module (NEB, E7810S) using twice the reaction volume and a fragmentation time of 10 minutes. The end-repair step was not performed. Libraries were then generated with the NEBNext Ultra™ II DNA Library Kit (NEB, E7805S) without purification. After ligated with adaptors, DNA fragments are selected with 20 μLs of Streptavidin T1 beads (Invitrogen™, 65602) by incubation at room temperature for 1h with agitation. The beads were washed 3 times each with: Low Salt wash buffer [0.1% SDS (Invitrogen™, AM9820), 0.1% Triton X-100 (Sigma-Aldrich, T8787-50ML), 2 mM EDTA pH 8.0 (Invitrogen™, AM9260G), 20 mM Tris-HCl pH 8.0 (Invitrogen™, 15568025), 150 mM NaCl (Thermo Fisher Scientific, AM9759)], 1x B&W buffer (5 mM Tris-HCl pH 7.5 (Invitrogen™, 15567027), 0.5 mM EDTA pH 8.0 (Invitrogen™, AM9260G), 1M NaCl (Thermo Fisher Scientific, AM9759)), and 1x PBS pH 7.4 (Gibco™, 70011044) with 0.1% Triton X-100 (Sigma-Aldrich, T8787-50ML). 50 μLs of the pre-mixed reagents (NEB, E7805S) including 25 μLs of 2x PCR Master Mix, 5 μLs of Universal Primer, and 5 μLs of Primer Mix-Index 1 from the NEBNext Ultra II Single Indexing Kit (NEB, E7335S) were added to the beads.
The amplification was conducted with an initial denaturation of 95°C for 2 minutes then cycled 15 times with a 98°C -denaturation step for 10 seconds and a 68°C combined annealing and extension step for 90 seconds. PCR products were purified with 0.75x AMPure XP Beads (Beckman, A63880), eluted in 20 μLs of UltraPure™ DNase/RNase-Free distilled water (Thermo Scientific, 10977023), and quantified with the Qubit dsDNA HS Assay Kit (Invitrogen™, Q32851). Each library was paired-end sequenced for 150 cycles on each end on an Illumina NovaSeq 6000.

treatment_protocol: The first step is the incubation of the SMART-display protein library with an RNA library. In this step, displayed protein libraries are pulled down onto streptavidin magnetic T1 beads, and their mRNA tags are stabilized by reverse transcription to convert to double-stranded cDNA using a template-switching oligo (TSO) containing a non-palindromic restriction enzyme (BbvCI) site. Next, free biotin is added to the protein population to block the remaining binding sites on the streptavidin beads and prevent non-specific binding. Subsequently, an RNA library ligated with a biotin ligation linker (gray bars, Figure 2) designed with complementary sticky ends to the BbvCI restriction site was prepared and added to the protein library allowing the formation of RNA-protein associations. Then, the double-stranded cDNA barcode is treated with a BbvCI to generate sticky ends. The second step is to ligate the barcodes from interacting RNA-protein pairs. In this step, the interacting RNA-protein pairs will be cross-linked. Stringent washes will be applied to remove non-specifically bound proteins or RNAs. The biotin ligation linker-containing ends of the RNA library are then ligated to the sticky end of the interacting protein library. The use of a non-palindromic restriction enzyme prevents the self-ligation of the cDNA or the self-ligation of the linker sequence. At this point, RNA-protein associations have been recorded by chimeric sequences of the form cDNA-linker-RNA. The third step is to construct the sequencing library. The RNA is converted to double-stranded cDNA, allowing the chimeric sequences to transfer into the form of cDNA1-linker-cDNA2 where the cDNA1 comes from the protein and cDNA2 comes from the RNA end. The cDNAs, including those that have been ligated (cDNA1-linker-cDNA2), are subjected to enzymatic fragmentation (NEBNext Ultra II FS) and the addition of sequencing adapters. The chimeric sequences (cDNA1-linker-cDNA2) are selected for using the biotin on the linker sequence. The resulting library is amplified and subjected to paired-end sequencing. Taken together, SMART-display and REILIS constitute the entire PRIM-seq experimental pipeline.


title: Ovcar8 DMF, total mRNA, rep3


title: Greater than 3kDa fraction of senescent conditioned media_replicate2

data_processing:
Demultiplexed and quality-filtered mRNA-Seq reads were then aligned to human reference genome (GRCh38) using STAR (v.2.6.1)
Differential expression analysis was done using DESeq2 (v2_1.6.3)
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file includes FPKMs for all samples

growth_protocol: Ovcar8 cells were cultured in RPMI 1640 + 5% FBS

extract_protocol:
RNA was harvested by Trizol followed by a Qiagen clean up column with a DNAse step.
The cDNA libraries were prepared using NEBNext Ultra 2 RNA Library Prep Kit for Illumina (New England Biolabs; Cat.# E7775)

treatment_protocol: Cells were cultured in ULA plates in conditioned media and RPMI 1640 + 5% in a 1:1 ratio

value: High grade serous ovarian cancer


title: Ovcar8 DMF, total mRNA, rep1


title: Greater than 3kDa fraction of senescent conditioned media_replicate1


title: KO15

value: 16 weeks


title: Greater than 3kDa fraction of senescent conditioned media_replicate3


title: Less than 3kDa fraction of senescent conditioned media_replicate3


title: 90_RSB038_V06

description: Library name: 90

data_processing:
STAR alignment to human genome version GRCh38.p13
Assembly: GRCh38.p13
Supplementary files format and content: Count table, tab-delimited text file

extract_protocol:
Qiagen RNAeasy
NovaSeq PE150


title: Less than 3kDa fraction of senescent conditioned media_replicate2


title: 95_RSB038_V12

description: Library name: 95


title: 92_RSB038_V08

description: Library name: 92


title: KO213

value: KO

value: Global ATP7B KO


title: 91_RSB038_V07

description: Library name: 91


title: 89_RSB038_V05

description: Library name: 89


title: KO13

value: WT

value: Wildtype


title: Less than 3kDa fraction of senescent conditioned media_replicate1


title: Boiled senescent conditioned media_replicate3


title: Boiled senescent conditioned media_replicate2


title: KO18


title: iWT30_5

value: iWT

value: Intetsine Specific Wildtype


title: Pre-treated with senescent conditioned media_replicate1


title: Pre-treated with senescent conditioned media_replicate2


title: 86_RSB036_V13

description: Library name: 86

value: Peripheral blood


title: 88_RSB038_V04

description: Library name: 88


title: Boiled senescent conditioned media_replicate1

value: Boiled senescent conditioned media


title: iWT30_4

value: Liver


title: iWT30_7

value: 30 weeks


title: Senescent conditioned media_replicate3

value: Senescent conditioned media_replicate3


title: Pre-treated with senescent conditioned media_replicate3


title: Senescent conditioned media_replicate2

value: Senescent conditioned media_replicate2


title: Senescent conditioned media_replicate1

value: Senescent conditioned media


title: Pre-treated with poliferative conditioned media_replicate3


title: 85_RSB036_V12

description: Library name: 85


title: iWT30_11


title: iWT30_10


title: 84_RSB036_V10

description: Library name: 84


title: Pre-treated with poliferative conditioned media_replicate2


title: 87_RSB038_V01

description: Library name: 87


title: iKO30_7

value: iKO

value: Intetsine Specific ATP7B KO


title: 82_RSB036_V08

description: Library name: 82


title: 83_RSB036_V09

description: Library name: 83


title: Pre-treated with poliferative conditioned media_replicate1

value: High grade serous ovarian cancer


title: Proliferative conditioned media_replicate2


title: iKO30_5


title: 81_RSB036_V07

description: Library name: 81


title: Proliferative conditioned media_replicate1

value: Proliferative conditioned media


title: iKO30_11


title: 79_RSB036_V05

description: Library name: 79


title: 80_RSB036_V06

description: Library name: 80


title: Fresh media_replicate1

value: Fresh media


title: iKO30_4


title: Fresh media_replicate2

value: Fresh media_replicate2


title: iWT30_1

value: Intestinal epithelial cells


title: Crushertime whole genome sequencing

city: dallas

first: Edward

last: Grow

state: TEXAS

address: 7053 beltau lane

institute: UTSW

data_processing:
WGS reads were trimmed and filtered for quality using BBDuk and FastQC (version 0.10.1).
Processed reads were aligned to bostau7 with Bowtie2 (v2.2.6) with the following parameters: (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant).
PCR duplicates were removed using bedtools
VarScan.v2.4.2 to identify homozygous SNVs using command “--min-coverage 20 --min-var-freq 0.1  --p-value 0.05”.
Homozygous SNVs exclusively found in Dreamboy were identified using VarScan.v2.4.2.jar  compare
Assembly: Bostau7
Supplementary files format and content: VCF= Varscan output of SNVs found with indivated variant detected
Library strategy: whole genome sequencing

organism: Bos taurus

source_name: fibroblast

growth_protocol: Cells were maintained in DMEM-high glucose (Thermo-Fisher 11965118) + 10% FBS, 1X Non-essential amino acids, 1X glutamax, 1X penicillin/streptomycin at 20% oxygen, and passaged using trypsin every 2-5 days.

extract_protocol:
genomic DNA was extracted using phenol:chlorform:isoamyl alcohol and precipitated with sodium acetated and ethanol at -80C for 20 min
gDNA was tagmented using Nextera XT DNA Library Preparation Kit (Illumina catalog #FC-131-1024) and libraries were amplified by PCR

treatment_protocol: Cumulus cells were harvested with trypsinization from expanded COC complexes, semen genomic DNA was harvested directly from cryopreserved samples.

value: fibroblast

value: male