title: Hepatocytes, wt, cdcdhfd, repl 2

description:
52
raw_counts_HC_Hif1a_ko.txt
12602

value: wt

value: Adult

value: hfd


title: DPP-5-WT-2

status: Public on Aug 22 2023

type: SRA

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

country: USA

institute: The University of Chicago

library_source: transcriptomic

data_processing:
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures in kallisto.
Statistical tests for differential expression were performed using sleuth.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated file includes tpm levels of individual transcripts for each sample as well as statistical results for differential gene abundance between genotypes.

molecule: total RNA

organism: Mus musculus

source_name: colonic organoid

growth_protocol: Colonic epithelial crypts were isolated from colons of wildtype or Tnfr2-/- mice, embedded within Matrigel, and grown with a layer of Intesticult media. The resulting organoids were passaged 5 times before filtration through a 70-µm nylon mesh filter and subsequent seeding for the experiment. Organoids of both wildtype and knockout genotypes were isolated at 1, 2, 3, 5, and 7 days post-passage.

extract_protocol:
Organoids were placed in Trizol and homogenized. The Direct-zol kit (Zymo) was used to isolate total RNA.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit to generate single-end reads 1x75bp on a NextSeq High Output Run.

tag: days post passage

tag: genotype

value: WT


title: Lung, FASNKO, rep 1

city: New York

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The samples were sequenced using Illumina HiSeq4000 sequencer with single 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the mm9 mouse reference genome by TopHat2 (Version2.0.11) .
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes read counts at gene level for each sample

source_name: Lung

growth_protocol: To generate the AEC2-specific FASN knockdown mice, FASN loxp/loxp homozygous mice were crossed with SftpcCreERT2+/+ mice to generate FASN loxp/loxp SftpcCreERT2+/- mice (FASNKO). FASN-/- SftpcCreERT2+/- littermates served as controls(Ctrl). All animals were housed in pathogen-free environment in humidity and temperature-controlled rooms on a 12-12-h light-dark cycle. Mice were given food and water freely.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen) and was purified by the RNeasy Plus Mini Kit (Qiagen), together with DNA digestion with the RNA free DNase set (Qiagen).RNA quality was determined by 260:280 ratio and the RNA integrity number (RIN) determined by an Agilent Technologies 2100 Bioanalyzer. Only high quality RNA samples with a 260:280 ratio > 1.6 and a RIN > 7 were used for the library construction using the TruSeq Stranded mRNA Library Preparation kit (Illumina), according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tamoxifen (T5648, Sigma-Aldrich) was prepared as a 20 mg/ml stock solution in sunflower seed oil (S5007, Sigma-Aldrich). Mice were injected once a day for 3 days (100 mg/kg), followed by a 3-day rest period, and then injected again for another 3 days at 5 weeks of age. Age and sex-matched mice were used for experiments after 8 weeks of age.

tag: tissue

value: Lung

tag: cell line

tag: cell type

value: Alveolar type 2 cells

value: AEC2-specific FASN knockdown


title: RNA-seq_Tcf7-KO_rep2_LP

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Genome_build: mm10
Supplementary_files_format_and_content: First colum: entrz ID; second column: gene symbol; columns thereafter: RPKMs for each sample in log2 scale

source_name: small intestine lamina propria

extract_protocol:
Total RNA was extracted with miRNeasy Micro kit (50) (1071023; Qiagen)
RNA-Seq libraries were prepared through the Smart-seq2 method (PMID: 24385147) as previously described (PMID: 29466755).

value: small intestine lamina propria

tag: strain


title: DPP-5-KO-2


title: RNA-seq_Tcf7-KO_rep1_LP


title: Hepatocytes, wt, cdcdcd, repl 5

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

department: LIMES

country: Germany

institute: University of Bonn

description:
45
raw_counts_HC_Hif1a_ko.txt
12595

data_processing:
The Agilent high-sensitivity D5000 assay was used to measure the size distribution of cDNA libraries on a Tapestation 4200 system (Agilent).
The cDNA libraries were quantified using a high-sensitivity dsDNA assay (Qubit).
To quantify the abundances of transcripts from the bulk RNA-seq data, Kallisto pseudo alignment was applied
Kallisto read counts were used fortheDESeq2 pipeline
Assembly: GRCm38.p5 (M16)
Supplementary files format and content: txt raw count matrix with transcripts as rows and samples as columns, done with kallisto and import to DESeq2 (see manuscript for more information)

source_name: liver

growth_protocol: in vivo

extract_protocol:
Adult mice were anesthetized and perfused with ice-cold PBS. For livers, 300 mg were collected, cut into small pieces, and incubated with 1 ml of double-concentrated digestion mix (PBS containing 1 mg/ mlcollagenase D (Roche), 100 U/mlDNase I (Sigma-Aldrich), 2.4 mg/ mlof dispase (Invitrogen) and 3% fetal calf serum (FCS) (Invitrogen) for 30 min at room temeprature before the mechanical disruption 100-μm filter.  The cell suspension was diluted in 3ml of FACS buffer (0,5% BSA, 2mmol EDTA in PBS).  Cells were stained by antibody mixes and sorted using FACS ARIATM III cell sorter (BD Biosciences) directly into 500ul QIAzol lysis buffer (Qiagen).
SmartSeq2 protocol

treatment_protocol: smaples taken from mice experiencing different types of diets (Maternal Obesity Model)

value: liver

value: Hepatocytes

tag: age

tag: maternal diet

value: cdcd

tag: offspring diet

value: cd

tag: condition

value: cdcdcd

tag: biologicalreplicate

tag: merged


title: DPP-5-WT-1


title: Mouse colonic organoids, Tnfr2-/-, TNF-treated

description:
10X Genomics
rowData.txt
colData.txt
exprsData.mtx

library_source: transcriptomic single cell

data_processing:
Illumina software was used for basecalling.
UMI abundances were obtained from cellranger 5.0.0
Matrix files were loaded into monocle 3.0 for sample merging, normalization, and clustering.
Jensen-Shannon specificity scores were used to identify the top gene markers of each cluster.
Assembly: mm10
Supplementary files format and content: Sparse Matrix (mtx) file of merged UMI counts with each row representing a gene and each column a cell barcode, can be read into R with readMM function in the Matrix package
Supplementary files format and content: Tab-delimited text (txt) files providing gene names (row data) or cell clustering and sample information (column data), matched to the sparse Matrix file

molecule: polyA RNA

source_name: colonic organoids

growth_protocol: Primary colonic epithelial organoids were isolated from the distal end of 16w old wildtype and Tnfr2-/- mice. The colon (1cm from the dentate line) was cut longitudinally, minced, and incubated with prewarmed digestion solution (0.2 Wunsch units/ml Liberase TM + 200 Kuntz units/ml DNase I in DMEM/F12 + 15 mM HEPES) for 30 min at 37 degrees C with 180 rpm agitation. After vigorous pipetting and straining through 70-µm-pore cell strainer, tissue was washed with DMEM/F12 supplemented with 10% FBS. Fragments were mixed with Matrigel, and the matrix was allowed to solidify. Cultures were submerged in murine Intesticult media, which was refreshed every 3 days.

extract_protocol:
At 7 days post-passage, organoid cultures were dissociated with a 10-minute incubation with 1X TrypLE at 37 degrees C. Cells were passed through a 40-micron nylon mesh. The single-cell suspension was depleted of apoptotic cells using the Annexin V Dead Cell Removal Kit (StemCell Technologies).
Single-cell 3' libraries were generated using the 10X Chromium platform. Paired-end sequencing was performed on a HiSeq 4000.

treatment_protocol: Select cultures were treated with tumor necrosis factor (20 ng/ml) after passage 5. Treatment began 1 day after passage and was stopped 6 days after passage.

value: colonic organoids

tag: treatment

value: TNF


title: Hepatocytes, wt, cdcdcd, repl 4

description:
41
raw_counts_HC_Hif1a_ko.txt
12591


title: RNA-seq_Ctrl_rep2_LP


title: DPP-7-WT-1


title: Mouse colonic organoids, Wildtype, TNF-treated


title: DPP-3-WT-2


title: Hepatocytes, wt, cdcdcd, repl 3

description:
33
raw_counts_HC_Hif1a_ko.txt
12583


title: RNA-seq_Tcf7-KO_rep2_PP

source_name: Peyer's patches

value: Peyer's patches


title: DPP-5-KO-1


title: Hepatocytes, Hif1a ko, hfdcdcd, repl 1

description:
53
raw_counts_HC_Hif1a_ko.txt
12603

value: Hif1a ko

value: hfdcd

value: hfdcdcd

value: hfdcdcd_Hif1a ko_Hepatocytes


title: Mouse colonic organoids, Tnfr2-/-, Untreated

value: Vehicle


title: RNA-seq_Tcf7-KO_rep1_PP


title: DPP-3-KO-2


title: RNA-seq_Ctrl_rep2_PP


title: Hepatocytes, wt, cdcdcd, repl 2

description:
32
raw_counts_HC_Hif1a_ko.txt
12582

value: wt

value: Adult


title: Mouse colonic organoids, Wildtype, Untreated

value: WT


title: Senescent MAF replicate 3 BMAL1-ChIP-seq

city: Rochester

first: Sarah

middle: Katherine

last: Jachim

state: MN

address: 222 3rd Ave SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

library_source: genomic

data_processing:
Paired-end sequencing reads were mapped to the mouse genome (mm10) using Burrows-Wheeler Aligner v0.5.9
Post-mapping, additional filtering using in-house scripts was performed and only read pairs with one or both ends mapping uniquely to the genome were retained for downstream analysis
Reads arising from PCR amplifications were discarded as duplicate reads using Picard MarkDuplicates v1.67
Candidate BMAL1 binding regions were identified using peaks detected by the software package “Model-Based Analysis of ChIP-Seq”
Statistically significant peaks were selected for analysis using a false discovery rate (FDR) cutoff of <=1%.
Assembly: mm10
Supplementary files format and content: BED files (except for Input samples)

molecule: genomic DNA

source_name: Primary MAF

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 3% O2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor pico (Diagenode).
The libraries were prepared from purified ChIP and input DNAs using NEBNext High-Fidelity PCR mix (NEB) with Nextera PCR primers with molecular indices (Nextera DNA Sample Preparation Kit).

treatment_protocol: Control cells were sham irradiated, and Senescent cells were exposed to 20gy x-ray irradiation using a RS2000 X-Ray Inducer (RAD Source Technologies). Cells were treated with 100nM dexamethasone (Sigma) for two hours, and collected 12 hours later.

value: Primary MAF

value: Mouse Adult Fibroblast

tag: chip antibody

value: Rabbit anti-BMAL1 (Cell signalling Cat# 14020)


title: DPP-3-WT-1


title: Senescent MAF replicate 3 input


title: Hepatocytes, wt, cdcdcd, repl 1

description:
31
raw_counts_HC_Hif1a_ko.txt
12581

value: liver

value: Hepatocytes

value: cdcd


title: Hepatocytes, Hif1a ko, cdcdcd, repl 2

description:
40
raw_counts_HC_Hif1a_ko.txt
12590

value: cd

value: cdcdcd

value: cdcdcd_Hif1a ko_Hepatocytes


title: RNA-seq_Ctrl_rep1_PP

value: Peyer's patches


title: Hepatocytes, Hif1a ko, cdcdhfd, repl 2

description:
17
raw_counts_HC_Hif1a_ko.txt
12567

value: Hif1a ko

value: hfd

value: cdcdhfd

value: cdcdhfd_Hif1a ko_Hepatocytes


title: Hepatocytes, Hif1a ko, cdcdcd, repl 1

description:
22
raw_counts_HC_Hif1a_ko.txt
12572


title: RNA-seq_Ctrl_rep1_LP

value: small intestine lamina propria


title: Senescent MAF replicate 2 input


title: DPP-2-WT-2


title: DPP-2-KO-2


title: N2 L3 animals, treated with grd-1 control RNAi from hatch, Replicate 3

city: Boston

first: Fasih

middle: Mubtasim

last: Ahsan

state: MA

address: 185 Cambridge Street CPZN 6500 Simches Research Building

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
Read filtering and quasi-alignment were performed using custom UNIX/bash shell scripts on the Mass General Brigham ERISOne Scientific Computing Linux Cluster. Reads were analyzed for quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (http://dx.doi.org/10.1093/bioinformatics/btw354), and filtered for adapter contamination, truncated short reads, or low-quality bases using BBDuk (https://doi.org/10.1093/nar/gkr947). Trimmed, cleaned reads were then quantified against the C. elegans reference transcriptome annotation (WBcel235, Ensembl Release 105) using Salmon, correcting for sequencing and GC content bias using the command parameters “--seqBias” and “—gcBias”, respectively (https://doi.org/10.1093/nar/gkab1049 )(https://doi.org/10.1038/nmeth.4197).
All statistical analysis and visualizations were performed using the R (https://www.r-project.org) Bioconductor (http://www.nature.com/nmeth/journal/v12/n2/abs/nmeth.3252.html) environment. Quasi-aligned transcript quantification files for each sample were collapsed into gene-level count matrices using R package tximport (https://doi.org/10.12688/f1000research.7563.1), and paired differential expression was calculated using R package DESeq2 (https://doi.org/10.1186/s13059-014-0550-8) with a design formula of “~Replicate + Treatment”, where ‘Replicate’ accounts for inter-replicate batch effect variation in the paired experimental samples. Genes were considered differentially expressed with a Benjamini-Hochberg False Discovery Rate (FDR) corrected P value < 0.05 and an absolute log2 transformed fold change of 1.5 (https://www.jstor.org/stable/2346101).
The top 100 genes contributing to variation in principal component 1 (PC1 – explanatory for the divergence seen between EV and grd-1 RNAi) were extracted and assessed for Gene Ontology (GO) term pathway overrepresentation using R package clusterProfiler (https://doi.org/10.1016/j.xinn.2021.100141). To perform transcription factor target enrichment analyses, promoter sequences 1500 bases upstream and 500 bases downstream of the transcription start site of significantly upregulated and downregulated genes were extracted using R package TxDb.Celegans.UCSC.ens11.ensGene (https://doi.org/doi:10.18129/B9.bioc.TxDb.Celegans.UCSC.ce11.ensGene). Transcription factor binding sites were retrieved from the modENCODE modMine v33 database (https://doi.org/10.1093/nar/gkr921) and filtered for presence in the promoter sequences of the differentially expressed gene sets. Total binding site ratios in both upregulated and downregulated genes were tallied (defined as the number of binding sites identified for a given transcription factor divided by all transcription factor binding site identified) and visualized using Prism 9 (Graphpad). Significance of the enrichment in observed binding site ratio versus expected ratio was calculated using a two-tailed exact binomial test with a 95% confidence level using R function binom_test(), and FDR adjusted P values were obtained using R function p.adjust().
To generate bigWig files for track visualization on the Integrated Genome Viewer (IGV), samples were aligned to the WBcel235 (Ensembl Release 105) genome using STAR
Assembly: ce11/WBcel235 (Ensembl Release 105)
Supplementary files format and content: Raw gene-level collapsed read counts for all 6 samples in matrix format (rows are samples, columns are WormBase Gene ID). Values represent raw read counts collapsed for each transcript from the WBcel235 (Ensembl Release 105) assembly to gene-level estimates using Salmon. 6 samples total (3 EV, 3 grd-1 knockdown).
Supplementary files format and content: Salmon output generated quant.sf files are included for each sample. These files include (1) the transcript Wormbase Sequence ID, (2) the transcript length, (3) the effective length averaged for each gene-level, (4) the normalized transcript per million (TPM) abundance, and (5) the raw number of reads binned per transcript.

organism: Caenorhabditis elegans

source_name: Whole organism lysate

growth_protocol: C. elegans wildtype nematodes (N2 - Bristol) were grown and maintained at 20°C on Nematode Growth Media (NGM) seeded with Escherichia coli OP50-1 as previously described (Soukas et al., 2009). Animals were synchronized by hypochlorite bleach treatment of a population of gravid adults. Animals were collected in M9 medium, centrifuged at 4400 rpm for 1 minute and resuspended in 6 mL 1.3% bleach, 250 mM NaOH for 1 minute of vigorous shaking. Bleach solution exposure and shaking step was repeated after one wash in M9. After second bleach step, pellet was resuspended in minimal M9 by gentle pipetting, and washed in M9 four times. Eggs were resuspended in 12 mL M9, and solution was left to rotate overnight for 23 hours at 20°C.

extract_protocol:
Worms were collected in TRIzol Reagent (Invitrogen), flash frozen in liquid nitrogen, and stored at -80°C prior to RNA isolation. Samples were lysed using metal beads and the Tissuelyser I system (Qiagen). RNA was isolated from lysate using Direct-zol RNA Miniprep kit (Zymo). Approximately 1 ug of RNA  was submitted to Genewiz (Azenta) for sequencing.
All total RNA quality control, mRNA-sequencing library preparation, and Illumina sequencing was performed by Genewiz (Azenta). Samples were first verified for RNA integrity scores greater than 8 using an Agilent Tapestation 4200. Illumina library preparation was performed using polyA selection for mRNA species. Approximately 20 million paired-end, 150 base pair reads were obtained per sample.

treatment_protocol: RNAi plates were prepared with standard NGM media mixed with 5 mM isopropyl-B-D-thiogalactopyranoside and 200 ug/mL carbenicillin. All RNAi clones were isolated from the genome wide E. coli HT115 Ahringer library (Horizon Discovery) and sequence verified before use. RNAi clones were obtained by seeding onto ampicillin/tetracycline treated Luria Broth (LB) plates. RNAi clones were grown overnight at 37°C with shaking for 18 hours in LB with 200 ug/mL carbenicillin. Cultures were spun down at 4400 rpm for 15 minutes, pellets resuspended in one tenth starting LB volume and dispensed onto RNAi plates no more than 48 hours prior to adding worms. Synchronized L1 animals prepared as described above were dropped onto RNAi plates with vector RNAi control or RNAi directed against the gene of interest at 20°C. Time to adulthood was measuring by evaluating the appearance of the vulvar slit in hermaphrodite animals. Three independent biological replicate experiments were performed, using independently synchronized animals and RNAi cultures for each experiment.

value: Whole organism lysate

value: Wildtype (N2 Bristol)

value: grd-1 RNAi from hatch to L3


title: Senescent MAF replicate 2 BMAL1-ChIP-seq

value: Primary MAF

value: Mouse Adult Fibroblast


title: Hepatocytes, Hif1a ko, cdcdhfd, repl 1

description:
16
raw_counts_HC_Hif1a_ko.txt
12566

value: liver

value: Adult


title: Senescent MAF replicate 1 BMAL1-ChIP-seq

value: Rabbit anti-BMAL1 (Cell signalling Cat# 14020)


title: DPP-2-WT-1

value: WT


title: Kupffer cells, wt, hfdcdcd, repl 5

description:
515
raw_counts_KC_Hif1a_ko.txt
12681

value: Kupffer cells

value: wt

value: hfdcd

value: cd

value: hfdcdcd

value: hfdcdcd_wt_Kupffer cells


title: N2 L3 animals, treated with grd-1 control RNAi from hatch, Replicate 2


title: Senescent MAF replicate 1 input


title: Hepatocytes, wt, cdcdhfd, repl 1

description:
15
raw_counts_HC_Hif1a_ko.txt
12565

value: Hepatocytes

value: cdcd

value: hfd

value: cdcdhfd


title: DPP-2-KO-1


title: N2 L3 animals, treated with EV control RNAi from hatch, Replicate 3

value: Whole organism lysate

value: Wildtype (N2 Bristol)

value: L4440 (EV) RNAi from hatch to L3


title: N2 L3 animals, treated with grd-1 control RNAi from hatch, Replicate 1

value: grd-1 RNAi from hatch to L3


title: DPP-3-KO-1


title: Kupffer cells, wt, hfdhfdhfd, repl 4

description:
514
raw_counts_KC_Hif1a_ko.txt
12680

value: liver

value: Adult

value: hfdhfd

value: hfdhfdhfd

value: hfdhfdhfd_wt_Kupffer cells


title: N2 L3 animals, treated with EV control RNAi from hatch, Replicate 2


title: Control MAF replicate 3 BMAL1-ChIP-seq

value: Primary MAF

value: Mouse Adult Fibroblast

value: Rabbit anti-BMAL1 (Cell signalling Cat# 14020)


title: DPP-1-WT-2

value: WT


title: N2 L3 animals, treated with EV control RNAi from hatch, Replicate 1


title: Control MAF replicate 2 BMAL1-ChIP-seq


title: Kupffer cells, Hif1a ko, hfdhfdhfd, repl 4

description:
504
raw_counts_KC_Hif1a_ko.txt
12670

value: Kupffer cells

value: Hif1a ko

value: hfdhfdhfd_Hif1a ko_Kupffer cells


title: DPP-1-WT-1


title: Kupffer cells, wt, hfdhfdhfd, repl 3

description:
512
raw_counts_KC_Hif1a_ko.txt
12678

value: wt

value: hfd


title: sgHsp110 K562 sample-3 RNA seq

city: Augusta

first: Nahid

middle: F

last: Mivechi

state: GA

department: Georgia Cancer Center

institute: Augusta University

description:
Hsp11OKO9
MVG9mRNA_rawcountsM.csv

data_processing:
For Lin-cKit+ cells, the sequencing was performed on the Illumina HiSeq4000 platform and one lane of Hi Seq 50bp SR for the sequencing.   For K562 cells, RNA-seq analyses was performed on a Novaseq 6000 S1 v1.5.  with PolyA+ (mRNA) using 100M paired reads (200M total)
For K562 cell: RNA-seq reads were aligned to reference genome UCSC/hg38 using STAR program with default settings.
For K562 cell: rMATs software with default setting was used to identify and quantify alternative splicing events
For Lin-cKit+ cells: The RNAseq analysis was performed on biostatistics computing cluster. The quality control of the raw FASTQ files were perfomed using FastQC v. 0.11.8. The raw reads were mapped to mouse genome mm10 using STAR aligner with default settings. The read counts and normalization was performed using R package DESeq2.
Assembly: hg38, mm10
Supplementary files format and content: MVG9mRNA_rawcountsM.csv (human samples),  hsf2 VS B6 IR RNA seq original.csv (mouse samples)

organism: Homo sapiens

source_name: sgHsp110 K562 cells

extract_protocol: RNA was isolated using the Qiagen RNeasy plus micro-kit (for mouse bone marrow Lin-cKit+Sca1+ cells) or Qiagen RNeasy plus mini-kit (for tumor cell lines)

treatment_protocol: The mice were not treated or treated 250 Rad IR. The K562 cells lines were not treated.

value: erythroleukemia cell line

value: not treated

tag: replicate

value: Replicate 3


title: Control MAF replicate 2 input


title: sgHsp110 K562 sample-2 RNA seq

description:
Hsp11OKO8
MVG9mRNA_rawcountsM.csv

value: Replicate 2


title: DPP-1-KO-1


title: Control MAF replicate 1 BMAL1-ChIP-seq


title: sgHsp110 K562 sample-1 RNA seq

description:
Hsp11OKO7
MVG9mRNA_rawcountsM.csv

value: Replicate 1


title: T.aestivum_root3day_Rep3

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

country: China

institute: Institute of Crop Sciences

data_processing:
Raw reads were trimmed with FastQC and Trimmomatic v0.334 with default parameters. The remaining reads were aligned to the International Wheat Genome Sequencing Consortium (IWGSC) reference genome (version 1.0) using HISAT2 v2.0.5. Gene expression values were computed using StringTie v1.3.3b.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: FPKM

organism: Triticum aestivum

source_name: T.aestivum root 3day

growth_protocol: 20℃/18℃(day/night) and 16 h/8 h (light/dark).

extract_protocol:
total RNA
For each sample, total RNA was prepared for sequencing with the Illumina NovaSeq 6000 platform following the manufacturer’s instructions.

treatment_protocol: There are 17 tissues of Ae.speltoides, the pistil own 4 treatments and stamen have 5 repeats, the other tissues have 3 treatments. Besides, 7 tissues of wheat, each has 3 treatments.

value: root 3 day

tag: cultivar

value: Chinese Spring


title: Kupffer cells, Hif1a ko, hfdhfdhfd, repl 2

description:
502
raw_counts_KC_Hif1a_ko.txt
12668

value: liver

value: Adult

value: hfdhfd

value: hfdhfdhfd


title: DPP-1-KO-2


title: Control MAF replicate 1 input

value: Primary MAF

value: Mouse Adult Fibroblast


title: Kupffer cells, Hif1a ko, hfdhfdhfd, repl 3

description:
503
raw_counts_KC_Hif1a_ko.txt
12669

value: Kupffer cells

value: Hif1a ko


title: T.aestivum_root3day_Rep2


title: Kupffer cells, wt, hfdcdcd, repl 4

description:
492
raw_counts_KC_Hif1a_ko.txt
12658

value: wt

value: hfdcd

value: cd

value: hfdcdcd

value: hfdcdcd_wt_Kupffer cells


title: Control MAF replicate 3 input


title: Kupffer cells, wt, hfdcdcd, repl 3

description:
491
raw_counts_KC_Hif1a_ko.txt
12657


title: sgHsf2 K562 sample-2 RNA seq

description:
Hsf2KO5
MVG9mRNA_rawcountsM.csv

source_name: sgHsf2 K562 cells

value: erythroleukemia cell line

value: not treated

value: Replicate 2


title: Liver colorectal cancer RNA-Seq, patient #316

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

data_processing:
RNA was sequenced on an Illumina HiSeq 2500 sequencer with a 101 bp paired-end run, producing raw fastq files. Adaptor and low quality (<Q20) sequences were removed using fastq-mcf tools. Cleaned reads were then aligned to the human genome (GRCh37) using HISAT2 version 2.0.5. Read counts were retrieved using featureCounts based on Ensembl gene annotation. Read counts were normalised and differential expression analysis was conducted using DESeq2. The design formula integrated tumour type, controlling for “patient specific effect”. A Wald test identified 424 genes significantly differentially expressed genes (DEGs) with Benjamini-Hochberg (BH) adjusted P-value <0.05 and fold-change of mean RPKM ≥2. Pathway analysis was performed using an over-representation approach. DEGs were tested against Gene Ontology terms using ClusterProfiler and all annotated genes as background (BH-adjusted P-value <0.05). The online platform TIMER2.0 was used to perform expression-based deconvolution, estimating the proportion of 22 different immune cell types in each tissue sample, using the CIBERSORT-ABS values from the estimation matrix for comparisons (Wilcoxon signed-rank test, P-value <0.05).
.txt format (contains chromosome, start, end, mean.x, mean.y, mean.diff, var.x, var.y, stderr, df, statistic, pvalue, Enddist, Overlap, CpGIs_range, CpGIs_dist, CpGI_relation, Strand and GeneID)
.csv format (contains rowname, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, hgnc_symbol, CRC_TPM, LM_TPM)

source_name: Liver Metastasis

extract_protocol: Tumour core samples were dissected from surgical specimens and immediately frozen in liquid nitrogen and initially stored at -80°C. RNA was extracted from <20 mg of tissue using RNEasy Plus Mini Kit (Qiagen, Hilden, Germany), including DNAse treatment, following tissue disruption using a Retsch Mixer Mill. RNA-sequencing was performed using the Illumina HiSeq 2500 V4 platform (Illumina, San Diego, CA, USA) to produce 125bp paired end reads.    Library preparation, including ribosomal RNA depletion using RiboZero Gold, was carried out using Illumina TruSeq V2 reagents, and libraries were sequenced using an Illumina HiSeq 2500 instrument.

value: Liver Metastasis

tag: Sex

value: M


title: T.aestivum_root3day_Rep1

value: root 3 day

value: Chinese Spring


title: Liver colorectal cancer RNA-Seq, patient #314


title: T.aestivum_leaf3day_Rep3

source_name: T.aestivum leaf 3day

value: leaf 3 day


title: sgHsf2 K562 sample-1 RNA seq

description:
Hsf2KO4
MVG9mRNA_rawcountsM.csv

value: Replicate 1


title: Liver colorectal cancer RNA-Seq, patient #311


title: Kupffer cells, wt, hfdhfdhfd, repl 1

description:
483
raw_counts_KC_Hif1a_ko.txt
12649

value: liver

value: Adult

value: hfdhfd

value: hfd

value: hfdhfdhfd

value: hfdhfdhfd_wt_Kupffer cells


title: Kupffer cells, wt, hfdhfdhfd, repl 2

description:
490
raw_counts_KC_Hif1a_ko.txt
12656

value: Kupffer cells

value: wt


title: T.aestivum_leaf3day_Rep2


title: Parental K562 sample-3 RNA seq

description:
ParentalWT3
MVG9mRNA_rawcountsM.csv

source_name: Parental K562 cells

value: erythroleukemia cell line

value: Parental WT

value: Replicate 3


title: Liver colorectal cancer RNA-Seq, patient #275

value: Liver Metastasis

value: F


title: T.aestivum_leaf3day_Rep1


title: Liver colorectal cancer RNA-Seq, patient #270

value: M


title: Kupffer cells, wt, cdcdhfd, repl 4

description:
85
raw_counts_KC_Hif1a_ko.txt
12635

value: cdcd

value: cdcdhfd

value: cdcdhfd_wt_Kupffer cells


title: Parental K562 sample-1 RNA seq

description:
ParentalWT1
MVG9mRNA_rawcountsM.csv

value: not treated

value: Replicate 1


title: T.aestivum_floret_meristem_Rep3

source_name: T.aestivum floret meristem

value: floret meristem

value: Chinese Spring


title: Liver colorectal cancer RNA-Seq, patient #269


title: Kupffer cells, wt, cdcdhfd, repl 3

description:
84
raw_counts_KC_Hif1a_ko.txt
12634

value: liver

value: Adult

value: hfd


title: sgHsf2 K562 sample-3 RNA seq

description:
Hsf2KO6
MVG9mRNA_rawcountsM.csv


title: T.aestivum_floret_meristem_Rep2


title: Kupffer cells, Hif1a ko, cdcdhfd, repl 5

description:
83
raw_counts_KC_Hif1a_ko.txt
12633

value: Kupffer cells

value: Hif1a ko

value: cdcdhfd_Hif1a ko_Kupffer cells


title: T.aestivum_grain4day_Rep3

source_name: T.aestivum grain 4day

value: grain 4 day


title: Sensory epithelia D60.1

city: 8091 Zurich

first: Marta

last: Roccio

address: Frauenklinikstrasse 24

department: Department Otolaryngology, Head and Neck Surgery

country: Switzerland

institute: University Hospital Zurich,

description: 10x Genomics

data_processing:
Single cell RNA-seq reads were processed with cellranger count v6.1.2. to generate the single cell gene expression matrix. Subsequently, we filtered doublet cells using the R/Bioconductor package scDblFinder (Germain et al., 2021), and we removed low quality cells using the quality metrics computed by the package scater (McCarthy DJ, 2017). The remaining cells were analyzed using the Seurat package (Hao et al., 2021). The workflow included normalization, dimension reduction and clustering, as well as identification of marker genes for clusters and differentially expressed genes. Data processing and analysis was performed using the Sushi platform (Hatakeyama et al., 2016)
Assembly: GRCh38.p13
Supplementary files format and content: Tab-separated values files and matrix files

source_name: WTC11-SOX2-GFP iPSC

growth_protocol: iPSC differentiation to inner ear organoid followed previously described protocols (Koehler et al., 2017; Nie and Hashino, 2020) with some modification. Briefly, 70-80% confluent iPSC cultures were dissociated to a single cell suspension in E8f supplemented with 20μM ROCKi. 3500 cells were aggregated in round bottom low-binding 96 well plates (174929, Thermo Fisher / Life Technologies) by centrifugation (100g, 6 min) in 100 ul E8f medium. After overnight culture in E8f with 20uM ROCKi, addition of 100 ul E8f was used to dilute the ROCKi to 10uM on the following day.  On day 2 of culture (day 0 differentiation) the organoids, ca 500um in diameter, were collected, rinsed twice in E6 medium (A1516401, Thermo Fisher / Life Technologies) and subsequently transferred to differentiation medium E6/SB/F/B4 (see below) with 1 organoid/100ul differentiation medium/well in new round bottom low-binding plates.    Differentiation medium E6/SB/F/B4 consisted of E6 supplemented with 2% growth factors-reduced Matrigel (354230, Corning), SB-431542 at 10μM (CAY13031, Cayman Chemical) 5ng/ml FGF2 (SRP3043, Merk/Sigma-Aldrich) and BMP-4 (314-BP-010 Biotechne/R&D Systems) from 0.5-10ng/ml. Optimal concentration for placode induction with the cell line used ranged from 1.5-2.5 ng/ml. On day 3-4 of differentiation, FGF2 and LDN193189 (CAY19396, Cayman Chemical) were added to the medium at the final concentration of 20ng/ml and 10uM respectively. On day 8, the medium was supplemented with 3uM CHIR99021 (361571 Avantor/WVR) to promote otic fate. CHIR99021 was further supplemented on day 10. On day 12 of in vitro culture, the organoids were transferred to Otic maturation medium (OMM) consisting of 1:1 Neurobasal (21103049, Thermo Fisher / Life Technologies) : Advanced-DMEMF12 (12634028, Thermo Fisher / Life Technologies), supplemented with 0.5X B27 (12587010, Thermo Fisher / Life Technologies); 0.5X N2 (17502048, Thermo Fisher / Life Technologies), 1XGlutamax (35050061,Thermo Fisher / Life Technologies) and beta mercapto ethanol (21985023, Gibco/Thermo Fisher / Life Technologies) and CHIR99021 3uM. The medium was then refreshed to provide fresh CHIR on day 15 of differentiation. From day 18 onwards, the organoids were transferred in OMM with 1% Matrigel in low-binding 24 well plates. Non-tissue culture treated 24-well plates (144530 Thermo Fisher / Life Technologies) were coated for 5 minutes at room temperature with 500ul anti-adherent solution (STEMCELL Technologies). The surfactant was then removed by aspiration, wells were washed twice with 1ml PBS and dried for 5 minutes prior to use. Samples were collected at selected time points and either fixed for characterization or triturated for flow cytometry/scRNA seq.

extract_protocol: The quality and concentration of the single cell preparations were evaluated using an haemocytometer in a Leica DM IL LED microscope and adjusted to 400 cells/µl. 17,200 cells per sample were loaded in to the 10X Chromium controller and library preparation was performed according to the manufacturer’s indications (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol). The resulting libraries were sequenced in an Illumina NovaSeq sequencer according to 10X Genomics recommendations to a depth of around 40,000 reads per cell.

treatment_protocol: Organoids were collected at the defined time points in a 15 ml falcon tube and let sediment by gravity. After removing the culture medium, organoids were incubated with Accutase and DNAse1 0.5mg/ml (10104159001, sigma Aldrich) for 25-30 min at 37C in a water bath. 1 ml dissociation solution per plate (at d8) or per ½ plate (>d18). Every 5 minutes, organoids were triturated mechanically by pipetting with p1000 pipet tips 10 times. After 25-30 min cells were washed with medium containing 10uM ROCKi and centrifuged 5 minutes at 300g. The pellet was then resuspended in PBS containing 2% BSA and 10M ROCKi and passed through a cell strainer 40um pore size (352235, Corning) to eliminate clumps.  Cells were then further centrifuged and resuspended in 550ul PBS containing 2% BSA and 10uM ROCKi on ice.  Single cell isolated from day 8 organoids (200 unselected organoids) were incubated for 5 minutes at room temperature with Calcein-AM (C3099, Life Technologies) and subsequently sorted on a FACS Aria (BD) to exclude debree, doublets, and isolate single positive cells (these represented 96% of the cell suspension). Single cells from day 26 organoids (100 unselected organoids) were incubated on ice for 45 min with 40ul of an EPCAM-Pe-Cy7 antibody (25-9326 eBioscience/ThermoFisher Scientific) (0.36ug antibody), after washing, cells were sorted on a FACS Aria (BD) to purify PE-CY7+ cells. Debrees and doublets were also excluded. Day 60 organoids (48 unselected organoids experiment 1) or (8 selected organoids experiment 2) were triturated as above and incubated for 30 min with 10ul EPCAM-Pe-Cy7 antibody (0.12ug antibody) /1x106 cells (after washing, cells were sorted on a FACS Aria (BD) to purify PE-CY7+ cells. Unstained control were used to define gating stratgey. Selection of organoids was performed by live imaging of GFP fluorescence and brightfield to visualize vesicles.  After sorting, cells were centrifuged for 5 minutes at 300g to remove FACS fluids and resuspended in a 0.04% BSA in PBS buffer at the concentration of 1000 cells/ul and placed on ice prior to loading on the 10X Chromium according to manufacturer’s instruction.

value: WTC11-SOX2-GFP iPSC

value: induced pluripotent cell differentiation in inner ear organoids

value: WT

value: otic differentiation

tag: time point

value: Day 60

tag: Stage

value: sensory epithelia development


title: Liver colorectal cancer RNA-Seq, patient #87

tag: tissue

value: Liver Metastasis

value: M


title: T.aestivum_floret_meristem_Rep1

value: floret meristem


title: Liver colorectal cancer RNA-Seq, patient #208


title: Liver colorectal cancer RNA-Seq, patient #241

value: F


title: otic_D26

description: 10x Genomics

tag: cell line

tag: genotype

value: Day 26

value: otic vesicle stage


title: Kupffer cells, Hif1a ko, cdcdhfd, repl 4

description:
82
raw_counts_KC_Hif1a_ko.txt
12632

value: liver

tag: cell type

value: Adult

value: cdcd

value: hfd

value: cdcdhfd


title: Kupffer cells, Hif1a ko, cdcdcd, repl 5

description:
72
raw_counts_KC_Hif1a_ko.txt
12622

value: Kupffer cells

value: Hif1a ko

tag: age

value: cd

value: cdcdcd

value: cdcdcd_Hif1a ko_Kupffer cells


title: placode_D8

description: 10x Genomics

value: WTC11-SOX2-GFP iPSC

value: induced pluripotent cell differentiation in inner ear organoids

value: WT

value: otic differentiation

value: Day 8

value: otic placode stage


title: Parental K562 sample-2 RNA seq

description:
ParentalWT2
MVG9mRNA_rawcountsM.csv

value: erythroleukemia cell line

value: Parental WT

value: not treated

value: Replicate 2


title: organoid data from sample  40984611441

city: Philadelphia

first: Yusen

last: Zhou

state: PA

address: 3615 Civic Center Blvd

department: Department of Biomedical and Health Informatics

institute: Children's hospital of Philadelphia

data_processing:
Sequenced reads were mapped to GRCh38 human reference genome and quantified using the kallisto pseudoalignment algorithm
Read counts were calculated using TPM
Assembly: GRCh38
Supplementary files format and content: both tab-delimited text (.tsv) and HDF5 files are provided including raw count values calculated for each sample using TPM

source_name: rectum

extract_protocol:
Trizol
Total RNA with RIN values above 6 was normalized to 400ng, converted to cDNA, then used to prepare each library using the Illumina TruSeq Stranded Messenger RNA Library Kit and the IDT for Illumina Unique Dual Index Kit in an automated Sciclone Liquid Handler Instrument. Final libraries were analyzed on a Perkin Elmer Labchip GX for quantification and QC.

value: rectum

value: organoid

tag: disease state

value: NPD

tag: diagnosis

value: CTR


title: Liver colorectal cancer RNA-Seq, patient #8

value: Liver Metastasis

value: M


title: Primary colorectal cancer RNA-Seq, patient #316

source_name: Primary Tumor

value: Primary Tumor


title: Kupffer cells, Hif1a ko, hfdhfdhfd, repl 1

description:
482
raw_counts_KC_Hif1a_ko.txt
12648

value: liver

value: Kupffer cells

value: Hif1a ko

value: Adult

tag: maternal diet

value: hfdhfd

tag: offspring diet

value: hfd

tag: condition

value: hfdhfdhfd

value: hfdhfdhfd_Hif1a ko_Kupffer cells


title: T.aestivum_grain4day_Rep1

value: grain 4 day

value: Chinese Spring


title: Kupffer cells, Hif1a ko, cdcdcd, repl 4

description:
71
raw_counts_KC_Hif1a_ko.txt
12621

value: cdcd

value: cd

value: cdcdcd

tag: biologicalreplicate

tag: merged

value: cdcdcd_Hif1a ko_Kupffer cells


title: Kupffer cells, Hif1a ko, cdcdcd, repl 3

description:
70
raw_counts_KC_Hif1a_ko.txt
12620


title: organoid data from sample  40977267085

value: rectum

value: organoid

value: IBD

value: CD


title: T.aestivum_grain20day_Rep3

source_name: T.aestivum grain 20day

value: grain 20 day


title: Kupffer cells, wt, cdcdhfd, repl 2

description:
55
raw_counts_KC_Hif1a_ko.txt
12605

source_name: liver

value: liver

value: Kupffer cells

value: wt

value: cdcdhfd

value: cdcdhfd_wt_Kupffer cells


title: Primary colorectal cancer RNA-Seq, patient #314

value: Primary Tumor

value: M


title: Kupffer cells, Hif1a ko, hfdcdcd, repl 3

description:
57
raw_counts_KC_Hif1a_ko.txt
12607

value: Hif1a ko

value: Adult

value: hfdcd

value: hfdcdcd

value: hfdcdcd_Hif1a ko_Kupffer cells


title: Primary colorectal cancer RNA-Seq, patient #311


title: T.aestivum_grain20day_Rep1

value: Chinese Spring


title: T.aestivum_grain4day_Rep2

value: grain 4 day


title: organoid data from sample  40948108343

source_name: ileum

value: ileum

value: organoid

value: IBD

value: IBDU


title: Primary colorectal cancer RNA-Seq, patient #275

value: F


title: organoid data from sample  40913770182

value: NPD

value: CTR


title: T.aestivum_grain15day_Rep3

source_name: T.aestivum grain 15day

value: grain 15 day


title: Kupffer cells, Hif1a ko, hfdcdcd, repl 2

description:
47
raw_counts_KC_Hif1a_ko.txt
12597

value: liver

value: Kupffer cells

value: cd


title: Kupffer cells, Hif1a ko, cdcdhfd, repl 3

description:
54
raw_counts_KC_Hif1a_ko.txt
12604

value: Hif1a ko

value: Adult

value: cdcd

value: hfd

value: cdcdhfd

value: cdcdhfd_Hif1a ko_Kupffer cells


title: Primary colorectal cancer RNA-Seq, patient #270

value: Primary Tumor

value: M


title: Sensory epithelia D60.2

description: 10x Genomics

value: WTC11-SOX2-GFP iPSC

value: induced pluripotent cell differentiation in inner ear organoids

value: WT

tag: treatment

value: otic differentiation

value: Day 60

value: sensory epithelia development


title: organoid data from sample  40896995487

value: ileum

value: organoid

value: IBD

value: UC


title: Kupffer cells, wt, cdcdcd, repl 5

description:
42
raw_counts_KC_Hif1a_ko.txt
12592

value: liver

value: Kupffer cells

value: wt

value: Adult

value: cd

value: cdcdcd

value: cdcdcd_wt_Kupffer cells


title: organoid data from sample  40901164997

value: rectum

value: NPD

value: CTR


title: Primary colorectal cancer RNA-Seq, patient #269

value: Primary Tumor

value: F


title: T.aestivum_grain15day_Rep1

value: grain 15 day

tag: cultivar

value: Chinese Spring


title: T.aestivum_grain15day_Rep2


title: T.aestivum_grain20day_Rep2

value: grain 20 day


title: organoid data from sample  40866836736

value: ileum

value: organoid

value: IBD

value: CD


title: Primary colorectal cancer RNA-Seq, patient #241

description: CRC241_ RNA-Seq

tag: Sex


title: T.aestivum_grain10day_Rep3

source_name: T.aestivum grain 10day

value: grain 10 day


title: Primary colorectal cancer RNA-Seq, patient #208

value: M


title: Primary colorectal cancer RNA-Seq, patient #87


title: T.aestivum_grain10day_Rep2


title: Kupffer cells, wt, cdcdcd, repl 4

description:
35
raw_counts_KC_Hif1a_ko.txt
12585

value: liver

value: Kupffer cells

value: wt

value: Adult

value: cdcd

value: cd


title: organoid data from sample  40859382280

value: NPD

value: CTR


title: Primary colorectal cancer RNA-Seq, patient #8

value: Primary Tumor


title: T.aestivum_grain10day_Rep1

value: Chinese Spring


title: Kupffer cells, wt, cdcdcd, repl 3

description:
24
raw_counts_KC_Hif1a_ko.txt
12574

value: cdcdcd

value: cdcdcd_wt_Kupffer cells


title: organoid data from sample  40847777094

value: rectum

value: organoid

value: UC


title: Kupffer cells, Hif1a ko, cdcdcd, repl 2

description:
34
raw_counts_KC_Hif1a_ko.txt
12584

value: Hif1a ko

value: cdcdcd_Hif1a ko_Kupffer cells


title: UCEC-P20190911

first: Fei

last: Tang

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: BIOPIC

institute: Peking University

data_processing:
Cell Ranger 3.0.0 was used to quantify gene expression level.
The quality of cells was then assessed based on two metrics: (1) The number of detected genes per cell; (2) The proportion of mitochondrial gene counts per cell. Specifically, cells with detected gene fewer than 200 and mitochondrial unique molecular identifier (UMI) count percentage larger than 10% were filtered out. The genes detected in more than 3 cells were retained.
Assembly: GRCh38
Supplementary files format and content: UMI count for each cell in mtx format and cell barcodes/genes/metadata in csv format

source_name: UCEC

extract_protocol:
Dissociated cells were passed through a 100μm SmartStrainer and centrifuged at 400g for 5 min. To lyse red blood cells, the pelleted cells were treated with red blood cell lysis buffer (Miltenyi Biotec) on ice for 1-2 min after removing the supernatant. After washing twice with 1 x PBS (GIBCO), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS) and stained with antibodies against CD45 and 7AAD for FACS with a BD FACSAria III sorter (BD Biosciences) instrument. 10,000~20,000 cells were loaded for library construction using the 10x Chromium Single cell 5` Library (10x Genomics, V3), according to the manufacturer’s instructions. Purified libraries were subject to an Hiseq X Ten sequencer (Illumina) for sequencing with 150-bp paired-end reads.
10x Chromium Single cell 5’

value: Normal, Tumor

value: NK cells

tag: patient id

tag: cancer type

value: Uterine Corpus Endometrial Carcinoma


title: Liver colorectal cancer RRBS, patient #316

data_processing:
The quality check and processing of the sequenced RRBS reads was performed using in-house developed bioinformatics tools.     Processed sequence reads were then aligned to the reference human genome (GRCh37) using Bismark with stringent mapping criteria by allowing only one mismatch (default = 2) in the seed. The median non-CpG DNA methylation of all samples was 1.05%, indicating effective bisulfite conversion and low levels of true non-CpG methylation.     CpG sites overlapping with SNPs (dbSNP build 151) were filtered out. For CpGs with at least 5 coverage, there were 5,113,641 autosomal CpG sites that covered at least eight paired samples. A two-sample t-test with Welch correction identified 244 differentially methylated CpGs (DMCs) with at least 20% difference in methylation and P-value < 5.010-04. Gene information for all CpGs, including location of gene promoters, introns and exons, was derived using the identgeneloc program of the DMAP tool.     R packages were used for unsupervised hierarchical clustering of CpG site methylation, using ward linkage (hclust method = "ward.D2") and Euclidean distance (dist method = "euclidean"), and Principal Component Analysis (PCA) using default parameters (prcomp). The methyLImp package was used to impute missing methylation data values (maximum 2 per group for each CpG).     Genome build/assembly: GRCh37  (hg19)
.txt format (contains chromosome, start, end, mean.x, mean.y, mean.diff, var.x, var.y, stderr, df, statistic, pvalue, Enddist, Overlap, CpGIs_range, CpGIs_dist, CpGI_relation, Strand and GeneID)
.csv format (contains rowname, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, hgnc_symbol, CRC_TPM, LM_TPM)

extract_protocol: Genomic DNA was digested with MspI enzyme followed by end-repair and ligation of Illumina TruSeq sequencing adaptors. Fragments were then size-selected and bisulfite-converted using the EZ DNA methylation kit prior to 16-18 rounds of PCR amplification. The quality and size distribution of the libraries was determined using a bioanalyser and libraries were sequenced on an Illumina HiSeq2500 machine (100 bp reads, single-ended). Base-calling of the reads was performed with Illumina Real Time Analyzer (RTA) software.

tag: tissue

value: Liver Metastasis

value: M


title: organoid data from sample  40820223638

value: IBD

value: CD


title: Kupffer cells, wt, cdcdcd, repl 2

description:
23
raw_counts_KC_Hif1a_ko.txt
12573

value: liver

value: Kupffer cells

value: wt

value: Adult

value: cdcd

value: cd


title: Kupffer cells, wt, cdcdhfd, repl 1

description:
46
raw_counts_KC_Hif1a_ko.txt
12596

value: hfd

value: cdcdhfd

value: cdcdhfd_wt_Kupffer cells


title: UCEC-P20190722

value: Tumor


title: organoid data from sample  40812448833

value: ileum

value: organoid

value: IBDU


title: Liver colorectal cancer RRBS, patient #314

value: Liver Metastasis


title: Kupffer cells, Hif1a ko, cdcdcd, repl 1

description:
19
raw_counts_KC_Hif1a_ko.txt
12569

value: Hif1a ko

value: cdcdcd

value: cdcdcd_Hif1a ko_Kupffer cells


title: UCEC-P20190625

value: Normal

value: NK cells

value: Uterine Corpus Endometrial Carcinoma


title: Kupffer cells, wt, cdcdcd, repl 1

description:
18
raw_counts_KC_Hif1a_ko.txt
12568

value: liver

value: Kupffer cells

value: wt

value: Adult

value: cdcdcd_wt_Kupffer cells


title: Liver colorectal cancer RRBS, patient #311

value: M


title: organoid data from sample  40883389192

value: rectum

value: NPD

value: CTR


title: Liver colorectal cancer RRBS, patient #275

value: F


title: organoid data from sample  40778010682

value: ileum

value: organoid


title: Kupffer cells, wt, hfdcdcd, repl 1

description:
7
raw_counts_KC_Hif1a_ko.txt
12557

value: hfdcd

value: cd

value: hfdcdcd

value: hfdcdcd_wt_Kupffer cells


title: organoid data from sample  40765404397


title: Kupffer cells, Hif1a ko, hfdcdcd, repl 1

description:
5
raw_counts_KC_Hif1a_ko.txt
12555

value: Hif1a ko

value: hfdcdcd_Hif1a ko_Kupffer cells


title: UCEC-P20181211

value: Tumor

value: NK cells

value: Uterine Corpus Endometrial Carcinoma


title: organoid data from sample  40758951931


title: UCEC-P20190305

value: Normal, Tumor


title: Liver colorectal cancer RRBS, patient #241

value: Liver Metastasis


title: UCEC-P20190717

value: Normal


title: Kupffer cells, wt, hfdcdcd, repl 2

description:
8
raw_counts_KC_Hif1a_ko.txt
12558

value: liver

value: Kupffer cells

value: wt

value: Adult


title: organoid data from sample  40794563038

value: ileum

value: organoid

value: NPD

value: CTR


title: Liver colorectal cancer RRBS, patient #269

value: F


title: Liver colorectal cancer RRBS, patient #270

value: M


title: UCEC-P20181122


title: Liver colorectal cancer RRBS, patient #208


title: organoid data from sample  40732507585

value: rectum


title: AGR cKO ESD_3

city: Daejeon

first: Gyuri

last: Kim

address: Yuseong-gu Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Raw reads were preprocessed to remove low-quality and adapter sequences by using Trimmomatic program before analysis, and using HISAT v2.1.0, the processed reads were aligned to Mus musculus (mm10) genome.
Indexes generated by HISAT are constructed using the same BWT (Burrows–Wheeler transform)/graph FM index (GFM) as Bowtie2.
StringTie v1.3.4b were used for transcript assambly of known transcripts.
In the data preprocessing, genes with one more than zeroed read count values in the samples were excluded. From the read count data, bias, size factors and gene-wised variation were estimated. The read count data were normalized using the DESeq2 R library. The statistical significance of the differential expression data was determined using the DESeq2 nbinomWaldTest72 with a normalized count.
Assembly: mm10
Supplementary files format and content: Tab-deliminated text file includes read count, FPKM, and TPM by gene
Supplementary files format and content: Tab-deliminated text file includes read count, FPKM, and TPM by transcript

source_name: Cereberal cortex

extract_protocol:
To isolate total RNA, the astrocyte pellets were suspended in TRIzol (Invitrogen) and stored at -80°C until use. Using Quant-IT RiboGreen Kit (Invitrogen), the total RNA concentration was calculated. Using TapeStation RNA ScreenTape (Agilent), we assessed the integrity of the total RNA from the samples. Only high-quality RNA with an RIN greater than 7.0 was used for RNA library construction.
1 µg of total RNA from each sample were used independently for library preparation with an Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc.).

value: Cereberal cortex

value: Astrocyte

value: Nr3c1 flox/flox;Aldh1l1-CreERT4

value: ESD (+ 4-OHT)


title: organoid data from sample  40676788233

value: IBD

value: CD


title: THCA-P20190816

source_name: THCA

value: Normal

value: NK cells

value: Thyroid Carcinoma


title: organoid data from sample  40729892299

value: UC


title: Kupffer cells, Hif1a ko, cdcdhfd, repl 1

description:
1
raw_counts_KC_Hif1a_ko.txt
12551

value: liver

value: Kupffer cells

value: Hif1a ko

value: Adult

value: cdcd

value: hfd

value: cdcdhfd

value: cdcdhfd_Hif1a ko_Kupffer cells


title: UCEC-P20190312

value: Uterine Corpus Endometrial Carcinoma


title: Liver colorectal cancer RRBS, patient #87

value: Liver Metastasis

value: M


title: organoid data from sample  40657629592

value: rectum

value: organoid

value: IBD


title: Liver colorectal cancer RRBS, patient #8


title: THCA-P20190621

value: Tumor

value: NK cells


title: AGR cKO ESD_2

value: Cereberal cortex

value: Astrocyte

value: Nr3c1 flox/flox;Aldh1l1-CreERT3

value: ESD (+ 4-OHT)


title: UCEC-P20190213

value: Normal, Tumor


title: THCA-P20190730

value: Normal

value: Thyroid Carcinoma


title: organoid data from sample  40630176136

value: UC


title: THCA-P20190612


title: Primary colorectal cancer RRBS, patient #314

value: Primary Tumor


title: AGR cKO ESD_1

value: Nr3c1 flox/flox;Aldh1l1-CreERT2


title: Primary colorectal cancer RRBS, patient #316


title: Kupffer cells, Hif1a ko, cdcdhfd, repl 2

description:
3
raw_counts_KC_Hif1a_ko.txt
12553

value: liver

value: Kupffer cells

value: Hif1a ko

value: Adult

value: cdcd

value: hfd

value: cdcdhfd

value: cdcdhfd_Hif1a ko_Kupffer cells


title: organoid data from sample  40614622780

value: rectum

value: organoid

value: IBD

value: IBDU


title: THCA-P20190125

value: Normal, Tumor

value: NK cells


title: Cre- ESD_2

value: Cereberal cortex

value: Astrocyte

value: Nr3c2 flox/flox

value: ESD (+ 4-OHT)


title: Cre- ESD_3

value: Nr3c3 flox/flox


title: Primary colorectal cancer RRBS, patient #311

value: Primary Tumor

value: M


title: organoid data from sample  40593132699

value: ileum

value: UC


title: organoid data from sample  40611017494

value: CD


title: Primary colorectal cancer RRBS, patient #275

value: F


title: THCA-P20190118

value: Thyroid Carcinoma


title: Primary colorectal cancer RRBS, patient #270


title: AGR cKO control_3

value: Nr3c1 flox/flox;Aldh1l1-CreERT4

value: Control (+ 4-OHT)


title: THCA-P20190122

value: Normal


title: Cre- ESD_1

value: Nr3c1 flox/flox


title: organoid data from sample  40558803438

value: organoid

value: NPD

value: CTR


title: AGR cKO control_2

value: Cereberal cortex

value: Astrocyte

value: Nr3c1 flox/flox;Aldh1l1-CreERT3


title: organoid data from sample  40575357894

value: IBD

value: IBDU


title: THCA-P20190108

value: Normal, Tumor

value: NK cells


title: Primary colorectal cancer RRBS, patient #269

value: Primary Tumor


title: AGR cKO control_1

value: Nr3c1 flox/flox;Aldh1l1-CreERT2


title: organoid data from sample  40512291331

value: ileum

value: icCD


title: organoid data from sample  40539744797

value: UC


title: RC-P20191211

source_name: RC

value: Renal Carcinoma


title: Primary colorectal cancer RRBS, patient #208

value: M


title: Cre- Control_3

value: Nr3c3 flox/flox

value: Control (+ 4-OHT)


title: Primary colorectal cancer RRBS, patient #87


title: Cre- Control_2

value: Nr3c2 flox/flox


title: Primary colorectal cancer RRBS, patient #8


title: organoid data from sample  40457462089

value: rectum

value: organoid


title: RC-P20191202


title: Cre- Control_1

value: Cereberal cortex

value: Astrocyte

value: Nr3c1 flox/flox


title: organoid data from sample  40440928633

value: NPD

value: CTR


title: RC-P20191023

value: Normal, Tumor

value: NK cells


title: organoid data from sample  40438303348


title: wt 30m Rep3

city: Sevilla

last: Barrientos-Moreno

state: Sevilla

address: Avda. Americo Vespucio 24. Edif. CABIMER.Unidad de Genómica. Parque Científico y Tecnológico Cartuja

department: Department of Genome Biology

country: Spain

institute: Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC-University of Seville-University Pablo Olavide.

data_processing:
Basecalls were performed using BaseSpace Onsite v 3.22.91.158 for NextSeq output.
fastq reads mapping by Bowtie2 at usegalaxy.eu
abundance (occupancy value in wig file) calculated by DANPOS 2.2.0 (Dpos funtion)
Assembly: sacCer3
Supplementary files format and content: .wig files report nucleosome occupancy data (the content is reads density)

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 30°C in supplemented minimal medium (SMM).

extract_protocol: Briefly, cells were fixed for 15 min with 1% formaldehyde. Glycine was added to quench the reaction at a final concentration of 125 mM. Cells were sedimented, washed twice with cold PBS and stored at –80ºC until use. Extracts for MNase digestion were resuspended in 1M sorbitol/50mM Tris HCl pH 7,5 and digested 1 h with 4.5 mg of zymoliase 20T (AmsBio 120491-1). Samples were washed first with solution I (1 M sorbitol, 20mM Tris HCl pH8, 1mM EDTA, 150mM NaCl) and then with solution I 0.1mM PMSF, suspended gently in solution II (20mM Tris HCl pH 8, 1mM EDTA, 0.15M NaCl, 0.1mM PMSF, 0.2 % Triton), and treated 20 min with different concentrations of MNase (SIGMA N3755). The reaction was then stopped by adding 3mM EDTA and 4mM Tis HCl. The spheroplasts were broken with 10% SDS. To revert crosslinking, samples were incubated for 90 min at 37ºC with proteinase K and then overnight at 65ºC. DNA was extracted from samples using a standard phenol-chloroform extraction and treated with RNase A. MNase digested samples enriched in mononucleosomes were loaded in a 1% agarose gel, and the DNA corresponding to mononucleosomes was purified with a DNA purification kit.

treatment_protocol: Cells were grown to mid-log-phase and α factor was added at 1 µg/ml. Cells were then washed three times and released into fresh SMM medium with 50 µg/ml pronase.

tag: strain


title: cr 30m Rep3

description: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11,15 RAD5 cac1∆::kanMX4 rtt106∆::hygMX4 hml∆::LEU2 bar1∆::natMX4

tag: genotype

value: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11,15 RAD5 cac1{delta}::kanMX4 rtt106{delta}::hygMX4 hml{delta}::LEU2 bar1{delta}::natMX4


title: male3, untreated, low IFNg

city: Durham

first: Shane

middle: Mitchell

last: O'Neil

state: NC

address: 701 W Main St

department: Neuroscience

institute: Duke University

data_processing:
STAR v2.7.3a
GenomicAlignments::summarizeOverlaps in R
Assembly: mm39
Supplementary files format and content: comma-delimited text file including count values for each sample

source_name: brain

growth_protocol: Neurons cultured from P0 mouse brains were maintained in Neurobasal medium supplemented with B27, GlutaMAX, and penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Media were aspirated and cells washed with PBS prior to collection. Cells were lysed and RNA isolated using Qiashredder (Qiagen, cat #79654) and RNeasy kit (Qiagen, cat #74106) according to manufacturer protocol.
RNA library prep was performed using KAPA RNA HyperPrep (Roche) as per the manufacturer's protocol.

treatment_protocol: Cultured neurons were treated with vehicle, 0.02 U/mL IFN-γ, or 100 U/mL IFN-γ for 24 h at DIV 5 and/or 30 min at DIV 12.

value: brain

tag: cell line

value: primary culture

tag: cell type

value: neurons

value: WT

tag: treatment 1

value: untreated

tag: treatment 2

value: low IFNg


title: organoid data from sample  40411969992

tag: disease state

tag: diagnosis


title: THCA-P20181226

value: Thyroid Carcinoma


title: male3, untreated, high IFNg

value: high IFNg


title: RC-P20190925

value: Renal Carcinoma


title: Primary colorectal cancer RRBS, patient #241

value: Primary Tumor

value: F


title: cr 60m Rep2

value: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11 RAD5 cac1[delta]::kanMX4 rtt106[delta]::hygMX4 hml[delta]::LEU2 bar1[delta]::natMX4

tag: time point

value: 60 minutes after release of G1 until G2 phase


title: organoid data from sample  40404416536

value: ileum

value: organoid

value: NPD

value: CTR


title: wt 60m Rep2

value: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11 RAD5 bar1[delta]::HISG


title: RC-P20190923

value: Normal, Tumor

value: NK cells


title: male3, high IFNg, untreated

value: brain

value: primary culture

value: neurons

value: WT


title: organoid data from sample  40486531731

value: IBD

value: CD


title: organoid data from sample  40393074187


title: RC-P20191223

value: Renal Carcinoma


title: RC-P20190919


title: cr G1 Rep2


title: organoid data from sample  40374915445

value: UC


title: male3, high IFNg, low IFNg

value: high IFNg

value: low IFNg


title: male3, high IFNg, high IFNg


title: wt G1 Rep2


title: male3, untreated, untreated

value: untreated


title: male2, untreated, untreated


title: organoid data from sample  40369756936

value: rectum

value: organoid


title: RC-P20181224


title: cr 60m Rep1

value: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11 RAD5 cac1[delta]::kanMX4 rtt106[delta]::hygMX4 hml[delta]::LEU2 bar1[delta]::natMX4

value: 60 minutes after release of G1 until G2 phase


title: RC-P20191021

value: Normal, Tumor


title: RC-P20181217

value: NK cells


title: organoid data from sample  40349687284

value: NPD

value: CTR


title: male2, untreated, low IFNg

value: brain

value: primary culture

value: neurons


title: organoid data from sample  40323143838

value: IBD


title: PACA-P20191204

source_name: PACA

value: Tumor

value: Pancreatic Cancer


title: wt 60m Rep1

value: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11 RAD5 bar1[delta]::HISG


title: cr G1 Rep1


title: male2, untreated, high IFNg

value: WT

value: high IFNg


title: wt G1 Rep1


title: organoid data from sample  40310528543

value: rectum


title: PACA-P20191125


title: organoid data from sample  40292643748

value: organoid


title: PACA-P20190515


title: Tyrosol_treated_3

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of A nidulans FGSC A4 with hisat2 (version 2.1.0).
DESeq2 (version 1.24.0) (Love et al. 2014) was used to determine differentially expressed genes.
RPKM values were calculated with the edgeR package (“rpkm” function).
Assembly: genome: http://www.aspergillusgenome.org/download/sequence/A_nidulans_FGSC_A4/current//A_nidulans_FGSC_A4_version_s10-m04-r14_chromosomes.fasta.gz; gff3:   http://www.aspergillusgenome.org/download/gff/A_nidulans_FGSC_A4/A_nidulans_FGSC_A4_version_s10-m04-r14_features_with_chromosome_sequences.gff.gz
Supplementary files format and content: excell file includes count and RPKM values for each Sample

organism: Aspergillus nidulans

source_name: mycelium

growth_protocol: Barratt's minimal broth, 220 rpm, 37 °C

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

treatment_protocol: 35 mM tyrosol treated and untreated exponentially growing phase cultures

value: mycelium

value: FGSC A4 wild type

value: Tyrosol treated


title: RC-P20190918

value: Normal, Tumor

value: NK cells

value: Renal Carcinoma


title: male2, high IFNg, low IFNg

value: brain

value: low IFNg


title: Tyrosol _treated_2


title: organoid data from sample  40285199382

value: CD


title: male2, high IFNg, high IFNg

value: primary culture

value: neurons


title: organoid data from sample  40256130640

value: NPD

value: CTR


title: Tyrosol_treated_1


title: PACA-P20190306

value: Tumor

value: Pancreatic Cancer


title: PACA-P20190225


title: male1, untreated, low IFNg

value: WT

value: untreated


title: PACA-P20181128


title: organoid data from sample  40238256845

value: ileum

value: organoid


title: Untreated_2

value: mycelium

value: FGSC A4 wild type


title: Untreated_3


title: organoid data from sample  40241871131

value: rectum


title: PACA-P20181121

value: NK cells


title: Untreated_1


title: OV-P20190304

source_name: OV

value: Normal, Tumor

value: Ovarian Cancer


title: organoid data from sample  40221702489

value: IBD

value: IBDU


title: S288C rad6Δ+peroxide [SM110F]

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description: monosome footprints

data_processing:
Base calling and demultiplexing was performed at the NHLBI DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and then trimmed to the start of the linker sequence by Cutadapt. These files are the raw data files uploaded on the GEO database.
Reads were aligned to a library of non coding RNA genes and those not matching were retained.
A custom python script is used to remove PCR duplicates by comparing the 7-nucleotide unique molecular identifiers (UMIs) in the libraries.
After trimming UMIs by Cutadapt, reads were aligned to human transcriptome by bowtie1 and mapped reads were processed by using custom python scripts.
Assembly: R64-1-1
Supplementary files format and content: Wiggle files for ribosome occupancy
Library strategy: Ribo-seq

source_name: MATa SUC2 gal2 mal2 mel flo1 flo8-1 hap1 ho bio1 bio6 rad6::kanMX4

growth_protocol: SUB280 strain derivatives were grown in synthetic defined (SD) medium composed of D-Glucose (BD Difco, #215510), yeast nitrogen base (BD Difco, #291940) and drop-out amino acid medium without Leu and Trp (Sigma, #Y0750). SUB280 rad6Δ RAD6 and SUB280 rad6Δ RAD6(C88A) cells were grown in SD media supplemented with drop-out amino acid supplements without Leu, Trp and Ura (Sigma, #Y1771). S288C strain derivatives were grown in SD complete media by using drop-out amino acid supplements without Leu and Trp (Sigma, #Y0750) and supplementing it back with L-leucine (Sigma, #L800) and Tryptophan (Sigma, #T8941). Starter cultures were grown at 30°C overnight and then diluted to an OD600 of 0.001 (rad6Δ cells) or 0.0001 (WT cells) and were grown to a final OD600 between 0.5 and 0.6 for ~16 hours.

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells. Ribosome profiling lysates were clarified, treated with RNase I, and run over sucrose gradients to extract either the monosome or the disome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos in some cases. In others, Ribo-Zero was used. RNA-Seq samples were prepared with the Illumina Truseq Stranded ribo-zero kit.

treatment_protocol: Unless noted otherwise, the cultures were treated with freshly diluted H2O2 (peroxide) (Sigma, #216763), achieving a final concentration of 0.6 mM, for 30 minutes.

value: 0.6 mM hydrogen peroxide,30 min


title: organoid data from sample  40205268033

value: NPD


title: male1, high IFNg, untreated

value: brain

value: primary culture

value: neurons

value: high IFNg


title: male1, high IFNg, low IFNg

value: WT

value: low IFNg


title: ESCA-P20191129

source_name: ESCA

value: Esophageal Cancer


title: OV-P20181225

source_name: FTC

value: Tumor

value: Fallopian Tube Carcinoma


title: male2, high IFNg, untreated

value: untreated


title: organoid data from sample  40187474238

source_name: rectum

value: rectum

value: organoid

value: icCD


title: S288C rad6Δ [SM109F]

description: monosome footprints

value: MATa SUC2 gal2 mal2 mel flo1 flo8-1 hap1 ho bio1 bio6 rad6::kanMX4


title: male1, high IFNg, high IFNg


title: organoid data from sample  40184868943

value: IBD

value: IBDU


title: male1, untreated, untreated


title: S288C WT+peroxide [SM108F]

description: monosome footprints

source_name: MATa SUC2 gal2 mal2 mel flo1 flo8-1 hap1 ho bio1 bio6

value: 0.6 mM hydrogen peroxide,30 min


title: female2, untreated, untreated

value: brain


title: ESCA-P20191125

value: Normal, Tumor

value: NK cells


title: female2, untreated, low IFNg

value: primary culture

value: neurons


title: ESCA-P20190613

value: Normal


title: organoid data from sample  40167315587

value: ileum

value: CD


title: S288C WT [SM107F]

description: monosome footprints

value: MATa SUC2 gal2 mal2 mel flo1 flo8-1 hap1 ho bio1 bio6


title: SUB280 rad6Δ RAD6 (C88A)+peroxide [SM106F]

description: monosome footprints

source_name: MATa lys2-801 leu2-3,112 ura3-52 his3- Δ200 trp1-1[am] ubi1-Δ1::TRP1 ubi2-Δ2::ura3 ubi3-Δub-2 ubi4-Δ2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3] [pYES RAD6(C88A)-HA, URA3]

value: MATa lys2-801 leu2-3,112 ura3-52 his3- {delta}200 trp1-1[am] ubi1-{delta}1::TRP1 ubi2-{delta}2::ura3 ubi3-{delta}ub-2 ubi4-{delta}2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3] [pYES RAD6(C88A)-HA, URA3]


title: female2, untreated, high IFNg

value: WT

value: untreated

value: high IFNg


title: male1, untreated, high IFNg


title: ESCA-P20190410

value: Esophageal Cancer


title: SUB280 rad6Δ RAD6 (C88A) [SM105F]

description: monosome footprints


title: organoid data from sample  40120371040

value: rectum

value: organoid

value: NPD

value: CTR


title: ESCA-P20190404

value: Normal, Tumor


title: SUB280 rad6Δ RAD6+peroxide [SM104F]

description: monosome footprints

source_name: MATa lys2-801 leu2-3,112 ura3-52 his3- Δ200 trp1-1[am] ubi1-Δ1::TRP1 ubi2-Δ2::ura3 ubi3-Δub-2 ubi4-Δ2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3] [pYES RAD6-HA, URA3]

value: MATa lys2-801 leu2-3,112 ura3-52 his3- {delta}200 trp1-1[am] ubi1-{delta}1::TRP1 ubi2-{delta}2::ura3 ubi3-{delta}ub-2 ubi4-{delta}2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3] [pYES RAD6-HA, URA3]

value: 0.6 mM hydrogen peroxide,30 min


title: organoid data from sample  40103927684

source_name: ileum

value: IBD

value: UC


title: female2, high IFNg, low IFNg

value: brain

value: primary culture

value: neurons

value: low IFNg


title: female2, high IFNg, high IFNg

value: WT


title: SUB280 rad6Δ RAD6 [SM103F]

description: monosome footprints

value: untreated


title: organoid data from sample  40085042880

value: ileum


title: organoid data from sample  40066983148


title: BC-P20190403

source_name: BRCA

value: NK cells

value: Breast Cancer


title: SUB280 hel2Δ+peroxide [SM100F]

description: monosome footprints

source_name: MATa lys2-801 leu2-3,112 ura3-52 his3- Δ200 trp1-1[am] ubi1-Δ1::TRP1 ubi2-Δ2::ura3 ubi3-Δub-2 ubi4-Δ2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3] hel2:kanMX4

value: MATa lys2-801 leu2-3,112 ura3-52 his3- {delta}200 trp1-1[am] ubi1-{delta}1::TRP1 ubi2-{delta}2::ura3 ubi3-{delta}ub-2 ubi4-{delta}2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3] hel2:kanMX4


title: BC-P20190123


title: organoid data from sample  40021655987

value: rectum

value: organoid


title: female1, untreated, low IFNg


title: female1, untreated, untreated


title: organoid data from sample  40002596246

value: NPD

value: CTR


title: SUB280 hel2Δ [SM099F]

description: monosome footprints


title: vascular smooth muscle cells saphenous vein dog C

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

data_processing:
RNA-seq reads were aligned to the reference genome using STAR version 2.4.2a
Read groups were added to the BAM files with Picard's AddOrReplaceReadGroups
The BAM files are sorted with Sambamba v0.4.5 and transcript abundances were quantified with HTSeq-count version 0.6.1p1, using the union mode.
Genome_build: canfam3.1
Supplementary_files_format_and_content: raw counts

organism: Canis lupus familiaris

extract_protocol:
cells were trypsinized and stored in RLT. Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)

value: vascular smooth muscle cells


title: female1, untreated, high IFNg

value: high IFNg


title: T1-0689-3

first: zhang

last: xin

address: No.2 West Yuanmingyuan Road

department: Institute of Plant Protection

institute: Chinese Academy of Agricultural Sciences

description: HD73 cells, cdsR knockdown, T1, repeat 3

data_processing:
The raw sequence data were quality filtered using the fastp software.
Filtered fastq files were used for mapping to the reference genome using Rockhopper version 2.0 software with default parameters.
rRNA reads were eliminated by using SortMeRNA v2.1 program together with silva database.
reads were mapped to ribosomal RNA genes by Hisat2.
The DESeq2 suite of programs was used to analysis differential transcripts from in a pairwise fashion.
Assembly: Bacillus thuringiensis serovar kurstaki str. HD73 (NCBI Reference Sequence: NC_020238.1)
Supplementary files format and content: Reads were mapped to ribosomal RNA genes by Hisat2. After that, FeatureCount was employed to do expression calibration.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HD73 cells, cdsR knockdown, T1

growth_protocol: HD73 and cdsR deletion mutant were cultured in SSM medium until T-1, T0, and T1, respectively. T0 indicates the end of the exponential growth phase and Tn indicates the number of hours before (-) or after T0. The samples were crushed to extract total RNA for sequencing.

extract_protocol:
The total RNA was extracted using the RN43-EASYspin Plus kit (Aidlab Biotechnologies,Beijing) following the manufacturer's. The total RNA qualityand purity were analysis of Bioanalyzer 2100 system and RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA).
Ribosomal RNA was removed using Epicentre Ribo Zero™ rRNA Removal Kits (bacteria) (Epicentre, USA) .  sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

treatment_protocol: Samples of T-1 indicate samples of logarithmic phase, samples of T0 indicate samples of the end of logarithmic growth, and samples of T1 indicate samples of adaptation phase.

value: Bacterial cells

value: cdsR knockdown


title: organoid data from sample  40149430782

value: IBD

value: icCD


title: ESCA-P20190411

value: Normal, Tumor

value: Esophageal Cancer


title: biopsy data from sample 9971793399

source_name: Ileum

value: Ileum

value: biopsy

value: UC


title: T1-0689-2

description: HD73 cells, cdsR knockdown, T1, repeat 2

organism: Bacillus thuringiensis serovar kurstaki str. HD73


title: female1, high IFNg, untreated

value: brain

value: primary culture

value: neurons

value: WT

value: untreated


title: female2, high IFNg, untreated


title: vascular smooth muscle cells saphenous vein dog B


title: T1-0689-1

description: HD73 cells, cdsR knockdown, T1, repeat 1


title: vascular smooth muscle cells saphenous vein dog A


title: ESCA-P20181123

value: NK cells


title: biopsy data from sample 9940753211

value: NPD

value: CTR


title: T1-WT-3

description: HD73 cells, WT, T1, repeat 3

source_name: HD73 cells, WT, T1

value: Bacterial cells


title: biopsy data from sample 9823004282


title: T1-WT-2

description: HD73 cells, WT, T1, repeat 2


title: vascular smooth muscle cells pulmonary vein dog C

value: vascular smooth muscle cells


title: WT Senescent MAF replicate 3

data_processing:
Raw sequence data (.bcl files) generated the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequence reads were trimmed using Trimmomatic v.0.36
Trimmed sequence reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Assembly: GRCm38
Supplementary files format and content: .csv files with raw counts (one file with all KO samples and one file with all WT samples)

source_name: Primary MAF

extract_protocol: Cells were collected in TRIzol reagent (Invitrogen) and RNA was extracted according to manufacturer instructions.

value: Primary MAF

value: Mouse adult fibroblast

tag: cell subtype

value: Senescent MAF


title: vascular smooth muscle cells pulmonary vein dog B


title: biopsy data from sample 9433080982

source_name: Rectum

value: Rectum


title: biopsy data from sample 9695702256

value: IBD


title: biopsy data from sample 9325947159

value: biopsy


title: T1-WT-1

description: HD73 cells, WT, T1, repeat 1


title: WT Senescent MAF replicate 1


title: vascular smooth muscle cells femoral vein dog D


title: T0-0689-3

description: HD73 cells, cdsR knockdown, T0, repeat 3

source_name: HD73 cells, cdsR knockdown, T0

value: cdsR knockdown


title: vascular smooth muscle cells femoral vein dog B


title: vascular smooth muscle cells pulmonary vein dog A


title: WT Senescent MAF replicate 2


title: WT Control MAF replicate 2

value: Control MAF


title: vascular smooth muscle cells femoral vein dog A


title: biopsy data from sample 8766675562

value: CD


title: biopsy data from sample 9096494786

value: Ileum

value: UC


title: WT Control MAF replicate 3

value: WT


title: T0-0689-2

description: HD73 cells, cdsR knockdown, T0, repeat 2


title: T0-WT-3

description: HD73 cells, WT, T0, repeat 3

source_name: HD73 cells, WT, T0


title: T0-WT-2

description: HD73 cells, WT, T0, repeat 2


title: female1, high IFNg, low IFNg

source_name: brain

value: brain

value: primary culture

value: neurons

value: high IFNg

value: low IFNg


title: biopsy data from sample 8986797186

value: NPD

value: CTR


title: female1, high IFNg, high IFNg


title: KO Senescent MAF replicate 3

value: Primary MAF

value: Mouse adult fibroblast

value: BMAL1 -/-

value: Senescent MAF


title: WT Control MAF replicate 1


title: vascular smooth muscle cells portal vein dog C

value: vascular smooth muscle cells


title: vascular smooth muscle cells portal vein dog A


title: biopsy data from sample 8672611246

value: Rectum

value: biopsy

value: IBD


title: KO Senescent MAF replicate 1


title: T0-WT-1

description: HD73 cells, WT, T0, repeat 1

value: Bacterial cells


title: biopsy data from sample 8081214457


title: T0-0689-1

description: HD73 cells, cdsR knockdown, T0, repeat 1

value: cdsR knockdown


title: biopsy data from sample 7807216273

value: Ileum


title: vascular smooth muscle cells vena cava dog B

source_name: vascular smooth muscle cells vena cava


title: vascular smooth muscle cells vena cava dog C


title: KO Control MAF replicate 3

value: Control MAF


title: T-1-0689-2

description: HD73 cells, cdsR knockdown, T-1, repeat 2

source_name: HD73 cells, cdsR knockdown, T-1


title: biopsy data from sample 7800901725


title: KO Control MAF replicate 2


title: vascular smooth muscle cells vena cava dog A


title: KO Senescent MAF replicate 2


title: T-1-0689-3

description: HD73 cells, cdsR knockdown, T-1, repeat 3


title: T-1-0689-1

description: HD73 cells, cdsR knockdown, T-1, repeat 1


title: biopsy data from sample 7214955558

value: IBDU


title: T-1-WT-3

description: HD73 cells, WT, T-1, repeat 3

source_name: HD73 cells, WT, T-1

value: WT


title: biopsy data from sample 7143294781


title: vascular smooth muscle cells pulmonary artery dog C


title: vascular smooth muscle cells portal vein dog B


title: T-1-WT-2

description: HD73 cells, WT, T-1, repeat 2


title: biopsy data from sample 7139077478


title: vascular smooth muscle cells pulmonary artery dog B


title: biopsy data from sample 7051356862

value: CD


title: Vdrflox/flox;Krt14cre_skin_P18_1

city: Tokushima

first: Yudai

last: Joko

address: 3-18-15 Kuramoto-cho

country: Japan

institute: Tokushima University

description: RNAdia

data_processing:
The demultiplexing, barcoded processing and gene counting were performed via the snakemake pipeline dropSeqPipe version 0.4 with default parameters
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mice dorsal skin

extract_protocol:
P18 mice back skin from epidermis specific VDR knockout (VDR cKO)(Vdr flox/flox; Krt14cre) and control (Vdr flox/flox) mice were collected and placed dermis down in 0.25% trypsin for 20 min at 37°C. Cell suspensions were obtained by scraping the skin gently. The cells were then filtered with strainers (70,40 μm).
Library was performed according to the manufacter’s instructions (RNAdia 2.0 kit, Dolomite Bio, Royston, UK). Briefly, cells were loaded into a Nadia (Dolomite Bio) microfluidics cartridge at a concentration of 310 cells per microliter. Cells were lysed in droplet and emulsion formed from the microfluidics device was then isolated and droplets broken with 1H,1H,2H,2H-Perfluoro-1-octanol. Reverse transcription was then performed, and purified cDNA was used as an input for Nextera tagmentation reactions.

value: Mice dorsal skin

tag: age

value: Epidermis cell

value: Vdr flox/flox; Krt14cre


title: T-1-WT-1

description: HD73 cells, WT, T-1, repeat 1

tag: treatment


title: vascular smooth muscle cells pulmonary artery dog A


title: Vdrflox/flox_skin_P18_2

description: RNAdia

value: Vdr flox/flox


title: Vdrflox/flox_skin_P18_1

description: RNAdia


title: biopsy data from sample 6838739690

value: UC


title: whole exome sequencing of Y2031

data_processing:
Library strategy: exome-seq
Raw reads were trimmed with FastQC and Trimmomatic v0.334 with default parameters, and got the clean reads. Then the bwa software was used to map the reads to the IWGSC RefSeq V1.0.
The gatk software was used to call variation, and the variation information was saved as gVCF file.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: gVCF files were generated using gatk software, represents the variation information.

organism: Aegilops speltoides

source_name: Y2031 leaf

extract_protocol: genomic DNA

value: leaf

tag: cultivar


title: vascular smooth muscle cells aorta dog B

source_name: vascular smooth muscle cells aorta

value: vascular smooth muscle cells


title: aged_atherosclerotic_plaque_3, replicate 3, scRNAseq [TCR]

city: Birmingham

first: Daniel

middle: J

last: Tyrrell

state: AL

address: 901 19th Street South

institute: University of Alabama at Birmingham

description:
10x Genomics
barcodes.tsv
features.tsv
matrix.mtx
metadata.tsv

data_processing:
Reads were aligned to the pre-built mm10 genome references (versions: ‘mm10-2020-A’ or ‘vdj_GRCm38_alts_ensembl-5.0.0’) and the “filtered” Cell Ranger output, containing the expression profile or immune profile of cells with a correctly detected cellular barcode, was used for downstream analysis. Similar numbers of cells were recovered for both the expression profiling and immune profiling.
Analysis was performed in R (v 4.0.3). For 5’ GEX data, analysis was primarily performed using the Seurat package (v 4.0.5) (Stuart et al., 2019). Gene-barcode matrices and metadata for each sample were loaded and further filtering and clustering analyses were performed as described in the Seurat tutorials (http://satijalab.org/seurat/). The following parameter(s) were used to exclude cells with extreme values, which indicates low complexity, duplets, or apoptotic cells: less than 5% of UMIs mapping to mitochondrial genes and greater than 200 unique RNAs/cell. Counts were normalized using the default normalization approach and variable features were identified. Anchor points were then generated between all datasets and used for data integration (nfeatures = 3000). Principal component analysis (PCA) was then performed, and 16 significant PCA components were used for finding nearest neighbors followed by graph-based, semi-unsupervised clustering into distinct populations (resolution = 0.5). To identify marker genes, the clusters were compared pairwise for differential gene expression using the Wilcoxon rank-sum test for single-cell gene expression (FindAllMarkers function; default settings). Cell-type predictions were also generated with scCATCH(Shao et al., 2020), specifying mouse as species, matching to the CellMatch database to reduce memory requirements with heart and blood options included as tissues of origin. Thresholds of 0.10 were set for minimum numbers of cells for gene detection and minimum log-fold change. Cluster markers genes and scCATCH cell-type predictions were then manually reviewed. Further analysis was performed using BBrowser software (BioTuring, v3, San Diego, CA) (Le et al., 2020). Feature-barcode matrix files were imported into BBrowser. All t-distributed stochastic neighbor embedding (t-SNE) plots used default settings. Cluster marker genes and scCATCH cell-type predictions were combined with BBrowser marker feature analysis to identify and combine clusters of the same cell types into a total of 37 clusters. Marker gene expression on t-SNE plots were and significant differentially expressed genes were plotted. Differential gene expression was performed using BBrowser via the “Venice” method using -0.25 > logFC > 0.25; adjusted p-value < 0.05 (Vuong et al., 2020). Outputs were then used to create violin plots using GraphPad Prism software. The same differential gene expression output data were used to generate gene ontology biological process analysis using ShinyGO (v 0.76). Signature score analysis was performed using BBrowser and data were exported and graphs were created using Graphpad Prism software. Trajectory analysis (pseudotime analysis) was performed using BBrowser software.
Assembly: Reads were aligned to the pre-built mm10 genome references (versions: ‘mm10-2020-A’ or ‘vdj_GRCm38_alts_ensembl-5.0.0’
Supplementary files format and content: normalized features, matrix, barcodes tables contain all identified clusters and metadata contains group IDs, cluster ID, barcode ID, age, treatment, and annotated cluster ID.

source_name: atherosclerotic plaque

extract_protocol:
Samples were prepared for single-cell 5′ Gene expression and VDJ repertoire immune profiling, using the Chromium Single-Cell Controller (10X Genomics, CA). A part of the isolated cDNA was set aside for BCR target enrichment and VDJ repertoire library preparation, while another of the cDNA was processed for 5′ gene expression (GEX) library. Each library was sequenced on an Illumina NovaSeq-6000 platform to generate 151x151 paired-end reads.
Processing of raw sequencing reads for each library was carried out using the Cell Ranger pipeline (v 6.0.1, 10x Genomics, CA).

treatment_protocol: Study approval. All animal experiments were carried out in accordance with the University of Michigan Institutional Animal Care and Use Committee (protocol #00010704).    Mice and diet. C57BL/6 WT young (2-3 months) and aged (18-19 months) female mice were obtained from the National Institute on Aging rodent colony and Charles River Breeding Laboratories (stock# 027). Female Ldlr-/- mice were purchased from Jackson Laboratories (stock #002207). Female CD8-/- mice (Jackson Laboratories, stock # 002665) were a gift from Dr. Grace Chen. We chose to use female mice in these studies because we have previously demonstrated that the age-enhanced atherosclerosis phenotype is similar between males and females (Tyrrell et al., 2020a). All mice were maintained on a 12-h light-dark cycle with free access to food and water. Sizes of experimental groups were based upon our prior studies (Tyrrell et al., 2020a; Tyrrell et al., 2020b).    To generate hyperlipidemic WT C57BL/6 mice, an i.p., injection of recombinant adeno-associated virus 8-D377Y-murine Pcsk9 (mPCSK9-AAV) was used. The mPCSK9-AAV was generated at the University of Pennsylvania Vector Core. The mPCSK9-AAV was diluted in sterile saline and mPCSK9-AAV was administered i.p. at 5.0x109 vector genomes per gram body weight (i.e., 1.5x1011 vector genomes/30g mouse), similar to the intermediate dose that was previously described (Bjorklund et al., 2014). mPCSK9-AAV mice were then rested for 1 week in their home cage and then both WT C57BL/6 mPCSK9-AAV and Ldlr-/- mice were fed a Western Diet (WD; 42% calories from fat, Teklad, catalog #88137) or control low-fat diet (LFD; 13% calories from fat, LabDiet catalog #5L0D) for 10-weeks. Single cell suspensions from aortic plaques of young (4-5 months) and aged (21-22 months) C57BL/6 WT PCSK9-AAV mice were generated by isolating the aortic root and arch, mincing tissue, and digesting the aorta in 1X HBSS containing 450 U/mL collagenase I (Sigma, catalog #SCR103), 250 U/mL collagenase XI (Sigma, catalog #C7657), 120 U/mL hyaluronidase (Sigma, catalog #H3506), and 120 U/mL DNAse I (Roche, 10104159001) for 45 minutes. Suspension was filtered through 45μm cell strainer and washed with RPMI 1640 + 10% fetal bovine serum. Single cell suspensions of splenocytes were obtained by mechanical digestion of spleen by smushing through 70μm cell strainer and washing with RPMI 1640 + 10% fetal bovine serum. Single cell suspensions of aortic plaques and splenocytes were enriched for CD3+ cells using CD3ε positive selection microbead kit (Miltenyi Biotec, catalog #130-094-973) with Miltenyi MS columns (Miltenyi Biotec, catalog #130-042-201) and OctoMACSTM separator (Miltenyi Biotec, catalog #130-042-108) according to manufacturers instructions. After CD3ε enrichment, cells were washed with warm RPMI 1640 + 10% fetal bovine serum. Cells were kept in RPMI 1640 + 10% fetal bovine serum on ice for 10-30 minutes until delivery to the e Advanced Genomics Core laboratory at the University of Michigan for single cell RNA sequencing.

value: atherosclerotic plaque

value: plaque cells

value: PCSK9-AAV_10-wk WD feeding


title: whole exome sequencing of Y162

source_name: Y162 leaf


title: vascular smooth muscle cells aorta dog A


title: vascular smooth muscle cells femoral artery dog C


title: vascular smooth muscle cells aorta dog C


title: whole exome sequencing of Y2020

source_name: Y2020 leaf


title: aged_atherosclerotic_plaque_4, replicate 4, scRNAseq [TCR]


title: young_atherosclerotic_plaque_4, replicate 4, scRNAseq [TCR]


title: KO Control MAF replicate 1

last: Jachim

institute: Mayo Clinic

value: Primary MAF

value: Mouse adult fibroblast

value: BMAL1 -/-


title: biopsy data from sample 6739821734

value: Rectum

value: biopsy

value: NPD

value: CTR


title: aged_atherosclerotic_plaque_1, replicate 1, scRNAseq [TCR]


title: biopsy data from sample 6733092745

value: Ileum

value: IBD

value: icCD


title: whole exome sequencing of PI560528

source_name: PI560528 leaf


title: biopsy data from sample 6445622918


title: vascular smooth muscle cells femoral artery dog B


title: biopsy data from sample 6662556960

value: CD


title: whole exome sequencing of PI542260

source_name: PI542260 leaf


title: biopsy data from sample 6421694263

source_name: Ileum


title: young_atherosclerotic_plaque_3, replicate 3, scRNAseq [TCR]


title: vascular smooth muscle cells coronary artery dog D


title: biopsy data from sample 6195746358

value: UC


title: whole exome sequencing of PI542270

source_name: PI542270 leaf

value: leaf


title: whole exome sequencing of Ae48

source_name: Ae48 leaf


title: vascular smooth muscle cells femoral artery dog A

value: vascular smooth muscle cells


title: biopsy data from sample 6332115407


title: vascular smooth muscle cells coronary artery dog C


title: aged_atherosclerotic_plaque_2, replicate 12, scRNAseq [TCR]

value: atherosclerotic plaque


title: whole exome sequencing of PI560749

source_name: PI560749 leaf


title: biopsy data from sample 5939318740


title: biopsy data from sample 5792732371


title: vascular smooth muscle cells coronary artery dog A


title: Ae.speltoides_stamen_Rep4

data_processing:
Raw reads were trimmed with FastQC and Trimmomatic v0.334 with default parameters. The remaining reads were aligned to the International Wheat Genome Sequencing Consortium (IWGSC) reference genome (version 1.0) using HISAT2 v2.0.5. Gene expression values were computed using StringTie v1.3.3b.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: FPKM

source_name: Ae.speltoides stamen

extract_protocol:
total RNA
For each sample, total RNA was prepared for sequencing with the Illumina NovaSeq 6000 platform following the manufacturer’s instructions.

value: stamen


title: aged_spleen_3, replicate 3, scRNAseq [TCR]

source_name: spleen

value: spleen

value: splenocyte


title: Ae.speltoides_stamen_Rep5


title: young_atherosclerotic_plaque_1, replicate 1, scRNAseq [TCR]

value: plaque cells

value: PCSK9-AAV_10-wk WD feeding


title: aged_spleen_2, replicate 2, scRNAseq [TCR]


title: Ae.speltoides_stamen_Rep2


title: aged_spleen_1, replicate 1, scRNAseq [TCR]


title: endothelial cells saphenous vein dog A

source_name: endothelial cells saphenous vein

value: endothelial cells


title: endothelial cells saphenous vein dog B


title: Ae.speltoides_stamen_Rep3


title: young_atherosclerotic_plaque_2, replicate 2, scRNAseq [TCR]


title: endothelial cells pulmonary vein dog D

source_name: endothelial cells pulmonary vein


title: Ae.speltoides_stamen_Rep1


title: biopsy data from sample 4379496952

source_name: Rectum

value: Rectum

value: biopsy


title: biopsy data from sample 4538991461


title: biopsy data from sample 5395385401


title: young_spleen_3, replicate 3, scRNAseq [TCR]


title: biopsy data from sample 4304050535

value: NPD

value: CTR


title: young_spleen_2, replicate 2, scRNAseq [TCR]


title: endothelial cells pulmonary vein dog C


title: biopsy data from sample 4291720641

value: Ileum


title: Ae.speltoides_spikelet_meristem_Rep3

source_name: Ae.speltoides spikelet meristem

value: spikelet meristem


title: young_spleen_1, replicate 1, scRNAseq [TCR]


title: endothelial cells saphenous vein dog C


title: endothelial cells pulmonary vein dog B


title: biopsy data from sample 4181037523

value: IBD

value: CD


title: Ae.speltoides_spikelet_meristem_Rep1


title: endothelial cells femoral vein dog C

source_name: endothelial cells femoral vein


title: Ae.speltoides_stem20day_Rep3

source_name: Ae.speltoides stem 20day

value: stem 20 day


title: biopsy data from sample 4028176603


title: endothelial cells femoral vein dog B


title: biopsy data from sample 4001235543

value: IBDU


title: Ae.speltoides_stem20day_Rep2


title: aged_atherosclerotic_plaque_4, replicate 4, scRNAseq

source_name: atherosclerotic plaque

value: atherosclerotic plaque


title: aged_atherosclerotic_plaque_1, replicate 1, scRNAseq


title: aged_atherosclerotic_plaque_2, replicate 12, scRNAseq


title: Ae.speltoides_stem15day_Rep3

source_name: Ae.speltoides stem 15day

value: stem 15 day


title: Ae.speltoides_stem20day_Rep1


title: young_atherosclerotic_plaque_4, replicate 4, scRNAseq


title: endothelial cells vena cava dog B

source_name: endothelial cells vena cava


title: biopsy data from sample 3943331569

value: UC


title: young_atherosclerotic_plaque_3, replicate 3, scRNAseq


title: endothelial cells vena cava dog A


title: biopsy data from sample 3723636182


title: Ae.speltoides_stem15day_Rep1


title: Ae.speltoides_spikelet_meristem_Rep2


title: biopsy data from sample 3684376931


title: young_atherosclerotic_plaque_2, replicate 2, scRNAseq


title: Ae.speltoides_stem10day_Rep3

source_name: Ae.speltoides stem 10day

value: stem 10 day


title: aged_atherosclerotic_plaque_3, replicate 3, scRNAseq

value: plaque cells


title: endothelial cells coronary artery dog537

source_name: endothelial cells coronary artery


title: young_atherosclerotic_plaque_1, replicate 1, scRNAseq

value: PCSK9-AAV_10-wk WD feeding


title: biopsy data from sample 3631280583

source_name: Ileum


title: Ae.speltoides_stem10day_Rep2


title: endothelial cells femoral vein dog A

value: endothelial cells


title: biopsy data from sample 3553318929

value: Rectum


title: endothelial cells vena cava dog C


title: biopsy data from sample 3818749482

value: biopsy


title: aged_spleen_3, replicate 3, scRNAseq

value: spleen

value: splenocyte


title: Ae.speltoides_stem15day_Rep2


title: Ae.speltoides_stem10day_Rep1


title: aged_spleen_2, replicate 2, scRNAseq


title: Ae.speltoides_root3day_Rep3

source_name: Ae.speltoides root 3day

value: root 3day


title: young_spleen_3, replicate 3, scRNAseq


title: Ae.speltoides_root3day_Rep2


title: aged_spleen_1, replicate 1, scRNAseq


title: biopsy data from sample 3359263969

value: NPD

value: CTR


title: young_spleen_2, replicate 2, scRNAseq


title: endothelial cells coronary artery dog C


title: biopsy data from sample 3269365601

value: IBD

value: CD


title: biopsy data from sample 3312689543


title: biopsy data from sample 3179088571

value: Ileum


title: Ae.speltoides_pistil_Rep4

source_name: Ae.speltoides pistil

value: pistil


title: Ae.speltoides_root3day_Rep1


title: young_spleen_1, replicate 1, scRNAseq


title: Ae.speltoides_pistil_Rep3


title: biopsy data from sample 3028669805


title: endothelial cells coronary artery dog A