title: Pig RCA saline_D

city: New Orleans

first: Sergiy

last: Sukhanov

state: Louisiana

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University School of Medicine

description: 10X Visium

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The downstream analyses were performed using R toolkit Seurat and Ingenuity pathway analysis (IPA) software (Qiagen). Cell type distribution and calculation of cell type ratio were predicted by mixed cell deconvolution analysis driven by Seurat using human atherosclerotic RCA single cell RNA seq dataset (accession number GSE131778).
Assembly: Sscrofa.11.1.105
Supplementary files format and content: Tab-separated values files, matrix files, json files, and png image files.

organism: Sus scrofa

source_name: Right coronary artery

growth_protocol: FH pigs were fed with high-fat diet for 6 months.

extract_protocol:
ST was conducted by following Visium/10x genomics pipeline. RNA extraction step was performed using Visium Spatial Gene Expression Slide & Reagents Kit, (4 rxns, cat# 1000187).
Second strain synthesis & denaturation, cDNA amplification and cleanup, cDNA quantification and QC were performed using reagents from Visium Spatial Gene Expression Slide & Reagents Kit (cat# 1000187). CDNA library was constructed with Visium library construction kit (cat#1000190). Library quantification was performed with KAPA library quantification kit (Roche, KR0405).
dual index (i5/i7) RNA-seq

treatment_protocol: IGF-1 (or saline) was injected daily at 50 ug/kg/day

value: Right coronary artery

tag: breed

value: Rapacz familial hypercholesterolemic (FH) swine

tag: Sex

value: female

tag: age

value: 20 months

tag: diet

value: high-fat

value: saline


title: Pig RCA saline_C

status: Public on Dec 03 2023

type: SRA

country: USA

description: 10X Visium

library_source: transcriptomic single cell

molecule: total RNA

tag: tissue

tag: treatment


title: Pig RCA IGF1_B

description: 10X Visium


title: cytarabine resistance HL60 cells [miRNA-seq]

city: Kaohsiung

first: Yu-Hsin

last: Tseng

address: No.100, Tzyou 1st Rd., Sanmin Dist.

department: Department of Pediatrics

country: Taiwan

institute: Kaohsiung Medical University Hospital

description: An Illumina NGS system

library_source: transcriptomic

data_processing:
Sequencing data was processed using the Illumina software program BCL2FASTQ 2.20. Subsequently, the trimmomatic program was implemented to filter poor quality reads and trim poor quality bases on the basis of the quality score. Qualified reads after filtering low-quality data were analyzed using miRDeep2 software and were aligned to the reference genome downloaded from the University of California Santa Cruz Genome Browser. miRNAs were mapped to few genomic locations; therefore, only reads that mapped perfectly to the genome less than or equal to five times were used for miRNA identification.
Assembly: not provided
Supplementary files format and content: *.txt: Tab-delimited text files include RPM values.

organism: Homo sapiens

growth_protocol: Cells are maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% antibiotic–antimycotic reagents under a humidified atmosphere of 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted from HL60 and R-HL60 cells using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA, USA) and according to the instruction manual. The RNA samples were submitted to Welgene Biotech. Co., Ltd. (Taipei, Taiwan, R.O.C) for small RNA sequencing analysis. RNA quantity was determined using an ND-1000 spectrophotometer (Nanodrop Technology, Wilmington, DE, USA) and RNA quality was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
miRNA sequencing libraries were prepared using the QIAseq miRNA Library Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol, and were sequenced using an Illumina NGS system.

treatment_protocol: The R-HL60 cell line was established through the continuous treatment of parental HL60 cells with increasing concentrations of cytarabine.

tag: cell line

tag: cell type

value: AML cell line

tag: genotype

value: WT

value: Cytarabine

tag: phenotype

value: Cytarabine resistant


title: parental HL60 cells [miRNA-seq]

description: An Illumina NGS system

value: No treatment

value: Parental


title: Pig RCA IGF1_A

description: 10X Visium


title: MCF7_2

city: Darlinghurst

first: Heloisa

middle: Helena

last: Milioli

state: NSW

address: 384, Victoria St

department: Cancer

country: Australia

institute: Garvan Institute of Medical Research

description:
Human (hg19)
Library preparation and QC validation complete
Qiagen miRNeasy Micro Kit

data_processing:
The next generation sequencing data was processed on the Illumina System.
Genome-guided alignment to a human reference (GRCh38) was performed using Rsubread.
Feature counts were computed in R using the package Rsubread.
The differential gene expression analysis was conducted with edgeR and limma packages in the R environment.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: Cell line

extract_protocol:
MCF7 cells (Michigan Cancer Foundation) and ZR75-1 cells (American Type Culture Collection) lines were verified through short tandem repeat profiling and tested negative for mycoplasma contamination. Parental cell lines were cultured in RPMI 1640 media (Thermo Fisher) supplemented with 10% fetal bovine serum (GE Healthcare) and 20 mM HEPES (Thermo Fisher). HMEC cells were purchased from ATCC and transformed into HMLER cells by the sequential addition of hTERT, SV40-ER and RAS as previously described21. Cells were cultured in serum-free mammary epithelial growth medium (MEGM) and MEGM Single Quots (Lonza, cat no. CC-4136: 1 ml bovine pituitary extract (BPE), 0.5 ml GA-1000 (30 mg/ml Gentamicin and 15 µg/ml Amphotericin), 0.5 ml insulin, 0.5 ml hydrocortisone and 0.5 ml hEGF). Cells were maintained at 37oC with 5% CO2. HCC38 cells were purchased from ATCC and cultured in RPMI containing 10% FBS containing penicillin/streptomycin (PS; 5.000 units penicillin and 5 mg streptomycin/ml in H2O, Sigma Aldrich, cat no. P4333). All cell lines were routinely tested to confirm the absence of mycoplasma contamination.
Cells were grown in P150 plates for 48h-72h, depending on growth kinetics, till plates reached 80% confluence. At harvest time, cells were washed twice with cold PBS1x (Invitrogen), scraped and collected in eppendorfs. Cells were spun down, washed once more with cold PBS1x, removing the supernatant, followed by snap freezing in liquid nitrogen. Frozen cell pellets (1 x 10^6 cells) were used for RNA extraction of RNA using the commercial RNeasy Kit (Qiagen). Quality of RNA was assessed using a bioanalyzer Eukaryote Total RNA Nano chip. Samples that scored above RIN:9 were used to generate the mRNA library, using a  TruSeq Stranded mRNA LT - Set A kit (Illumina:   RS-122-2101). CD44-low versus CD44-high cell lines: MCF-7, ZR75-1, HMLER and HCC38. Samples were submitted for depth pair-end sequencing (Illumina HiSeq 2500 v4.0) at the Garvan Molecular Genetics.
Samples were submitted for depth pair-end sequencing (Illumina HiSeq 2500 v4.0) at the Garvan Molecular Genetics. The next-generation sequencing data were processed on the Illumina System.

value: breast cancer

tag: condition

tag: volume (ul)

tag: concentration (ng/ul)


title: ChIP-seq_NIH-3T3_FH_V5_rep1

city: Beijing

first: ji

last: yiliang

address: No. 10 right outside the Western headlines

department: Department of Immunology

country: China

institute: Capital Medical University

library_source: genomic

data_processing:
ChIP-seq: the ChIP-seq data were mapped to Mus musculus (mm10) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters.
Assembly: mm10
Supplementary files format and content: WIG

molecule: genomic DNA

organism: Mus musculus

source_name: Embryo

growth_protocol: NIH-3T3 cells were transiently transfected  with plasmid.

extract_protocol:
cells were crosslinked in adherent conditions with 1% formaldehyde for 15 minutes at room temperature and quenched with glycine to a final concentration of 125 nM. Fixed cells were lysed in nuclei lysis buffer to extract nuclei and sheared by sonication to 300-500-bp-sized fragments. Sheared chromatin was incubated with antibodies and protein A/G-Dynabeads for 12 hours at 4 ℃. The beads were washed with RIPA150, RIPA500, RIPA-LiCl and TE buffer , respectively. The beads were resuspended with NLB buffer. After de-crosslinked at 65 ℃ for 6 hours, DNA fragments were digested with RNase A and proteinase K. Purified DNA fragments were generated libraries followed by high throughput sequencing using Illumina Novaseq6000
Purified DNA fragments were generated libraries followed by high throughput sequencing using Illumina Novaseq6000.

value: Embryo

value: Fibroblast

value: overexpress FH

tag: antibody


title: HCC38-Abi-N1

description: Human (hg38)

source_name: Cell line HCC38

growth_protocol: HCC38 cells were purchased from ATCC and cultured in RPMI containing 10% FBS containing penicillin/streptomycin (PS; 5.000 units penicillin and 5 mg streptomycin/ml in H2O, Sigma Aldrich, cat no. P4333). All cell lines were routinely tested to confirm the absence of mycoplasma contamination. HCC38 CD44Hi cells treated with control siRNA or two different siRNAs targeting AR (AR ex1, AR ex7). HCC38 CD44Hi cells also followed treatment with AR antagonists vehicle (DMSO), Seviteronel, Abiraterone or Enzalutamide.

extract_protocol:
Cells were grown in P150 plates and treated with AR antagonists. At harvest time, cells were washed twice with cold PBS1x (Invitrogen), scraped and collected in eppendorfs. Cells were spun down, washed once more with cold PBS1x, removing the supernatant, followed by snap freezing in liquid nitrogen. Frozen cell pellets (1 x 10^6 cells) were used for RNA extraction using the commercial RNeasy Kit (Qiagen). The quality of RNA was assessed using a bioanalyzer  Eukaryote Total RNA Nano chip. Samples that scored above RIN:9 were used to generate the mRNA library.
Samples were submitted for pair-end sequencing at Macrogen Oceania PL. The next-generation sequencing data were processed on the Illumina System.

value: Abiraterone


title: ChIP-seq_NIH-3T3_vector_V5_rep1

value: vector


title: control, large group, stage 35, sample 2

status: Public on Dec 02 2023

city: Boston

first: Megan

middle: M

last: Sperry

state: MA

address: 3 Blackfan Circle

institute: Wyss Institute at Harvard University

data_processing:
Trim adapter and polyX tails: The RNA-seq raw reads are single-end reads. The reads were trimmed for adapter “CTGTCTCTTATACACATCTCCGAGCCCACGAGAC” and polyX tails, then filtered by sequencing Phred quality (>= Q15) usingfastp(Chen et al. 2018).
Read alignment to rRNA: We downloaded theXenopus laevisrRNA sequences NCBI nucleotide database. Bowtie2 index was build by using thebowtie2-buildmodule(Langmead and Salzberg 2012). We aligned the adapter-trimmed reads to Xenopus laevis rRNA using Bowtie2 (Langmead and Salzberg 2012). We extracted the reads that were not mapped toXenopus laevisrRNA usingsamtools(H. Li et al. 2009).
Aligning reads to the genome: We downloaded theXenopus laevisgenome sequences and gene annotation from theNCBI genome database, version 10.1. We then used thegenomeGeneratemodule of theSTARaligner(Dobin et al. 2013)to generate the genome indexes. We setSTARaligner option sjdbOverhang = 75 for 76-bp reads, as was ideal. We aligned the adapter-trimmed reads to the genome using STAR aligner with the two-pass option. Reads were mapped across the genome to identify novel splice junctions in the first-pass. These new annotations were then incorporated into the reference indexes and reads were re-aligned with this new reference in the second pass. While more time-intensive, this step could aid in aligning across these junctions, especially in organisms where the transcriptome was not as well annotated. To estimate the gene expression from the gene alignments, we used RSEM, a tool for accurate quantification of gene and isoform expression from RNA-Seq data (B. Li and Dewey 2011). The resulted gene count table is at rsem_gene_counts.tsv.
Filtering, normalization, and transformation: To filter out low expressing genes, we kept genes that had counts per million (CPM) more than 1.8 in at least 3 samples. There were 21720 genes after filtering. We then normalized counts by weighted trimmed mean of M-values (TMM)(Robinson and Oshlack 2010). If no normalization is needed, all the normalization factors would be 1. Here the normalization factors were between 0.94 and 1.05. To use linear models in the following analysis, we performed Voom transformation(Law et al. 2014)to transform counts into logCPM.
Differential expression analysis: To discover the differential genes, we uselimma, an R package that powers differential expression analyses(Ritchie et al. 2015). We performed moderated t-tests to detect genes that were differentially expressed
Assembly: Xenopus laevis (NCBI genome database, version 10.1)
Supplementary files format and content: tab-delimited file includes a gene count table
Supplementary files format and content: tab-delimited file includes logCPM normalized values

organism: Xenopus laevis

source_name: whole embryo

growth_protocol: Xenopus laevis embryos were fertilized in vitro according to standard protocols in 0.1X Marc’s Modified Ringer’s solution and kept at 14°C.

extract_protocol:
A sample consisted of 15 pooled tadpoles from each treatment and each was repeated 3 times. Tissue was extracted using TRIzol (Thermo Fisher Scientific) as per the manufacturer’s protocol, and total RNA quality and quantity was assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific).
RNA library preparation was done with the Illumina Stranded Total RNA with Ribo-Zero Plus. Libraries were then multiplexed, and an rRNA depletion run using single-end, 75-nucleotide sequencing was performed on Illumina HiSeq 2500.

treatment_protocol: Stage 25 embryos (reared at 14°C prior to exposure) were treated with 90 µM thioridazine in 0.1x MMR from NF stage 12.5 to 35. During the treatment, experimental and control embryos were kept at 18°C.

value: whole embryo

tag: developmental stage

value: Stage 35


title: control, large group, stage 35, sample 3


title: control, large group, stage 35, sample 1


title: ChIP-seq_NIH-3T3_vector_V5_rep2


title: thioridazine-treated, large group, stage 35, sample 2

value: thioridazine


title: thioridazine-treated, large group, stage 35, sample 3


title: thioridazine-treated, large group, stage 35, sample 1


title: control, small group, stage 35, sample 3


title: control, small group, stage 35, sample 1


title: thioridazine-treated, small group, stage 35, sample 3


title: thioridazine-treated, small group, stage 35, sample 2


title: control, small group, stage 35, sample 2


title: ChIP-seq_NIH-3T3_FOXA1_V5_rep2

value: overexpress FOXA1


title: control, large group, sample 1

data_processing:
Trim adapter and polyX tails: The RNA-seq raw reads are single-end reads. The reads were trimmed for adapter “CTGTCTCTTATACACATCTCCGAGCCCACGAGAC” and polyX tails, then filtered by sequencing Phred quality (>= Q15) usingfastp(Chen et al. 2018).
Read alignment to rRNA: We downloaded theXenopus laevisrRNA sequences NCBI nucleotide database. Bowtie2 index was build by using thebowtie2-buildmodule(Langmead and Salzberg 2012). We aligned the adapter-trimmed reads to Xenopus laevis rRNA using Bowtie2 (Langmead and Salzberg 2012). We extracted the reads that were not mapped toXenopus laevisrRNA usingsamtools(H. Li et al. 2009).
Aligning reads to the genome: We downloaded theXenopus laevisgenome sequences and gene annotation from theNCBI genome database, version 10.1. We then used thegenomeGeneratemodule of theSTARaligner(Dobin et al. 2013)to generate the genome indexes. We setSTARaligner option sjdbOverhang = 75 for 76-bp reads, as was ideal. We aligned the adapter-trimmed reads to the genome using STAR aligner with the two-pass option. Reads were mapped across the genome to identify novel splice junctions in the first-pass. These new annotations were then incorporated into the reference indexes and reads were re-aligned with this new reference in the second pass. While more time-intensive, this step could aid in aligning across these junctions, especially in organisms where the transcriptome was not as well annotated. To estimate the gene expression from the gene alignments, we used RSEM, a tool for accurate quantification of gene and isoform expression from RNA-Seq data (B. Li and Dewey 2011). The resulted gene count table is at rsem_gene_counts.tsv.
Filtering, normalization, and transformation: To filter out low expressing genes, we kept genes that had counts per million (CPM) more than 1.8 in at least 3 samples. There were 21720 genes after filtering. We then normalized counts by weighted trimmed mean of M-values (TMM)(Robinson and Oshlack 2010). If no normalization is needed, all the normalization factors would be 1. Here the normalization factors were between 0.94 and 1.05. To use linear models in the following analysis, we performed Voom transformation(Law et al. 2014)to transform counts into logCPM. We identified and constructed 2 surrogate variable (SV) by surrogate variables analysis (Leek and Storey 2007). We then adjusted the effects of replicates and the SV.
Differential expression analysis: To discover the differential genes, we uselimma, an R package that powers differential expression analyses(Ritchie et al. 2015). We performed moderated t-tests to detect genes that were differentially expressed
Assembly: Xenopus laevis (NCBI genome database, version 10.1)
Supplementary files format and content: tab-delimited file includes a gene count table
Supplementary files format and content: tab-delimited file includes logCPM normalized values

treatment_protocol: Stage 25 embryos (reared at 14°C prior to exposure) were treated with 90 µM thioridazine in 0.1x MMR from NF stage 12.5 to 25. During the treatment, experimental and control embryos were kept at 18°C.

value: Stage 25


title: thioridazine-treated, small group, stage 35, sample 1


title: control, large group, sample 3


title: control, small group, sample 2


title: control, small group, sample 1


title: control, small group, sample 3


title: thioridazine-treated, large group, sample 3


title: thioridazine-treated, small group, sample 3


title: thioridazine-treated, large group, sample 2


title: thioridazine-treated, large group, sample 1


title: thioridazine-treated, small group, sample 2


title: thioridazine-treated, small group, sample 1


title: control, large group, sample 2


title: MIA PaCa-2 cells, shARF6, Day 14, Rep1, ATAC-seq

city: Barcelona

first: Ritobrata

last: Ghose

address: Carrer del Doctor Aiguader, 88, CRG 5th Floor Reception

country: Spain

institute: Center for Genomic Regulation

description: 50bp paired-end reads; 50M reads per sample

data_processing:
Paired-end 50 bp reads were adaptor-trimmed using TrimGalore (version 0.6.5). Trimmed reads were aligned to the hg19 genome (UCSC) using BowTie 2 Aligner (version 2.4.2) with the following parameters: very-sensitive–2000. Aligned reads were filtered using SAM tools (version 1.11) to retain proper pairs with a MapQ value ≥ 30. Read pairs aligned with ChrM were discarded. Duplicate read pairs were removed using the Picard (version 2.23.8). The read alignment was offset as previously described. Peaks were called using MACS2 (version 2.2.7.1) with false discovery rate (FDR) < 0.01. Differentially accessible regions were determined using the DiffBind package (version 3.0.7) in R (version 4.0.2) with false discovery rate (FDR)  < 0.005. Genomic annotation of differential regions was performed using HOMER (version 4.11). Normalised read coverage values were obtained using deepTools (version 3.5.0). Coverage density heatmaps were generated using deepTools with the option reference point and considering flanking regions 1 kb upstream and downstream from the centre of the peaks.
Assembly: GRCh37
Supplementary files format and content: differential peaks compared to NT in a .csv format showing fold change

source_name: MIA PaCa-2

growth_protocol: Cells were maintained in DMEM (with 10% FBS).

extract_protocol:
On days 3, 7, 14 and 21 cells were trypsinised, centrifuged and cell pellets flash frozen using liquid nitrogen. Storage of cell pellets was at -70 oC. Once samples from all time points were collected, 50,000 MIA PaCa-2 cells for each treated condition/replicate infected was collected and treated with transposase Tn5 (Nextera Tn5 Transposase; Illumina Cat #FC-121-1030). DNA was purified using AMPure XP beads to remove large fragments (0.5 × beads; >1kb) and small fragments (1.5 × beads; < 100bp). Samples were then amplified using NEBNext high-Fidelity 2x PCR Master Mix (New England Labs #M0541) with primers containing a barcode to generate the libraries
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentiviruses containing shNT, shARF6 or shASAP1 were added to cells overnight, media replaced and then cells selected with Puromycin for 2 days.

value: MIA PaCa-2

value: Pancreatic ductal adenocarcinoma

value: ARF6 knockdown

value: lentiviruses containing shRNA

tag: time

value: Day 14


title: MIA PaCa-2 cells, shASAP1, Day 7, Rep3, ATAC-seq

value: ASAP1 knockdown

value: Day 7


title: MIA PaCa-2 cells, shARF6, Day 21, Rep2, ATAC-seq

value: Day 21


title: MIA PaCa-2 cells, shARF6, Day 21, Rep1, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 3, Rep3, ATAC-seq

value: Day 3


title: MIA PaCa-2 cells, shARF6, Day 21, Rep3, ATAC-seq


title: MIA PaCa-2 cells, shASAP1, Day 7, Rep1, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 7, Rep3, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 7, Rep1, ATAC-seq


title: MIA PaCa-2 cells,shASAP1, Day 3, Rep3, ATAC-seq


title: MIA PaCa-2 cells, shASAP1, Day 3, Rep2, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 3, Rep2, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 14, Rep3, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 7, Rep2, ATAC-seq


title: MIA PaCa-2 cells, shASAP1, Day 21, Rep3, ATAC-seq


title: MIA PaCa-2 cells, shASAP1, Day 3, Rep1, ATAC-seq


title: MIA PaCa-2 cells, shASAP1, Day 21, Rep2, ATAC-seq


title: MIA PaCa-2 cells, shASAP1, Day 21, Rep1, ATAC-seq


title: MIA PaCa-2 cells, shASAP1, Day 14, Rep1, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 3, Rep1, ATAC-seq


title: MIA PaCa-2 cells, shASAP1, Day 14, Rep3, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 14, Rep2, ATAC-seq


title: MIA PaCa-2 cells, shNT (Control), Day 7, Rep3, ATAC-seq

value: WT (non-targeting)


title: MIA PaCa-2 cells, shNT (Control), Day 7, Rep2, ATAC-seq


title: MIA PaCa-2 cells, shASAP1, Day 7, Rep2, ATAC-seq


title: MIA PaCa-2 cells, shNT (Control), Day 3, Rep2, ATAC-seq


title: MIA PaCa-2 cells, shNT (Control), Day 3, Rep3, ATAC-seq


title: MIA PaCa-2 cells, shNT (Control), Day 3, Rep1, ATAC-seq


title: MIA PaCa-2 cells, shNT (Control), Day 21, Rep3, ATAC-seq


title: MIA PaCa-2 cells, shNT (Control), Day 21, Rep1, ATAC-seq


title: MIA PaCa-2 cells, shNT (Control), Day 21, Rep2, ATAC-seq


title: MIA PaCa-2 cells, shNT (Control), Day 14, Rep3, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 7, Rep3, RNA-seq

description: 50M reads per sample

data_processing:
Single-end, 50-bp-long reads were aligned to the GRCh37.p13 Homo Sapiens reference genome using the STAR Aligner (version 2.7.6a). Gene level counts were obtained by STAR using the --quantMode GeneCounts option, using gene annotations downloaded from Gencode (Release 19 GRCh37.p13). Differential expression analysis was performed in R (version 4.0.2) using the DESeq2 package (version 1.30.0). Genes with adjusted p-value < 0.05 were considered differentially expressed. The lfcShrink() function from DESeq2 was used for visualization purposes. Gene Set Enrichment Analysis (GSEA) was performed using the clusterProfiler package (version 3.18.0) in R (version 4.0.2). PROGENy analysis was performed in R (version 4.0.3) using DESeq2 normalised counts data as input for the progeny package (version 1.12.0). Network propagation using PropaNet was performed in Python (version 2.7) using DESeq2 normalised counts data, and a network of TFs and differentially expressed target genes using ChEA3 enrichment analysis. PropaNet ranks TFs using influence maximisation, followed identification of most important TFs through network propagation.
Assembly: GRCh37
Supplementary files format and content: normalised counts in a .csv format

molecule: polyA RNA

extract_protocol:
On days 3, 7, 14 and 21 cells were trypsinised, centrifuged and cell pellets flash frozen using liquid nitrogen. Storage of cell pellets was at -70 oC. Once samples from all time points were collected, RNA extraction was performed using the Invitrogen PureLink RNA Mini Kit (Thermo Fisher Scientific #12183018A), as per the manufacturer’s protocol.
Sequencing libraries were prepared using the poly(A) selection method at the CRG Genomics Core Facility.


title: MIA PaCa-2 cells, shARF6, Day 7, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shARF6, Day 3, Rep3, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shARF6, Day 3, Rep2, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shASAP1, Day 14, Rep2, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 21, Rep3, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shARF6, Day 3, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 14, Rep2, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 21, Rep2, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shARF6, Day 7, Rep2, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 14, Rep1, ATAC-seq


title: MIA PaCa-2 cells, shARF6, Day 14, Rep2, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shARF6, Day 21, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 7, Rep1, ATAC-seq


title: MIA PaCa-2 cells, shASAP1, Day 3, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shASAP1, Day 7, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shASAP1, Day 3, Rep2, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shASAP1, Day 21, Rep3, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shARF6, Day 14, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shASAP1, Day 7, Rep3, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells,shASAP1, Day 3, Rep3, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shASAP1, Day 21, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shASAP1, Day 14, Rep2, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shASAP1, Day 14, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 7, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 3, Rep3, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 3, Rep2, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shASAP1, Day 14, Rep3, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 21, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 21, Rep2, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 21, Rep3, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 3, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 14, Rep3, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 14, Rep2, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 14, Rep1, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shASAP1, Day 7, Rep2, RNA-seq

description: 50M reads per sample


title: MIA PaCa-2 cells, shNT (Control), Day 7, Rep3, RNA-seq

description: 50M reads per sample


title: MitoticCycling elongating Input RNA rep 2

city: Cambridge

first: Jimmy

last: Ly

state: Massachusetts

address: 455 main street

department: Biology

institute: Whitehead Institute

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
Read trimming: Cutadapt (v3.7).  cutadapt -m 15 -u 8 -e 0.1 --match-read-wildcards -a TCGTATGCCGTCTTCTGCTTG -O 1
Read mapping: STAR (v2.7.1a): STAR --runMode alignReads --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
The RiboTISH pipeline was applied to aligned reads from both translation initiation site sequencing and elongating ribosome profiling to identify high confidence translation initiation sites.
Read counting: htseq-count (0.11.0): For elongating ribosome profiling and matched RNA-seq: htseq-count -f bam -t CDS.
Assembly: hg38, Gencode release 25 annotations.
Supplementary files format and content: Tab delimited files with chromosome position for the translation initiation site and counts at each site along with the associated input mRNA counts is provided for each TIS-seq dataset.  Tab delimited file with gene ID and counts within the annotated open reading frames is provided for elongating ribosome profiling and input mRNA sequencing datasets.
Library strategy: Ribosome profiling

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum and 100 U/mL penicillin/streptomycin.

extract_protocol: To collect interphase cells, media containing translation inhibitor was poured into a 50mL tube, cells were washed with PBS + 100 μg/mL cycloheximide and then trypsinized in the presence of 100 μg/mL cycloheximide for 3 minutes at 37°C. Cells were then collected using the cold media with inhibitor. For mitotic cells, after addition of cycloheximide, mitotic cells were harvested by shake off and incubated on ice. Cells were centrifuged at 500x g for 3 minutes, washed once with 20 mL PBS+cycloheximide, and the pellet was moved into a new 1.5 mL tube with 1 mL PBS+cycloheximide. Cells were lysed in 900 μL polysome lysis buffer (20 mM Tris pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% (v/v) Triton X-100, 100 μg/mL cycloheximide, 500 U/mL RNaseIn Plus, 1x cOmplete protease inhibitor cocktail) and incubated on ice for 10 minutes. To ensure efficient lysis, cells were passed through a syringe 5 times. Cell debris and nucleus was depleted by spinning the lysate at 1300x g for 10 minutes. 30 μL of the cleared lysate was added to 400 μL TRI Reagent (Invitrogen, AM9738) for input RNA sequencing library. Three 300μL aliquots were generated with the rest of the cleared lysate, flash frozen in liquid nitrogen, and stored at -80°C.

treatment_protocol: For mitotic arrest synchronization, HeLa cells were grown to 40% confluency and treated with 2mM thymidine for 24 hours. Cells were released from thymidine arrest by washing twice with warm DMEM and cultured in 8 µM STLC for 16 hours. Mitotically arrested cells were shaken off the plate and harvested. For cycling mitotic cells, HeLa cells were grown to 20% confluency and treated for 2 mM thymidine for 16 hours. Cells were then washed twice with warm DMEM, incubated at 37°C for 8 hours then 2 mM thymidine was added for another 16 hours. After washing twice with warm DMEM and incubation at 37°C for 8 hours, the cycling mitotic cells were shaken off and harvested. For interphase cells, the mitotic cells were removed by physical disruption (mitotic shake off) and the remaining cells adhered to the plate were harvested. For elongating ribosome profiling, cells were treated with 100 μg/mL cycloheximide for 2 minutes then harvested. For initiation site sequencing, cells were treated with 2 μg/mL harringtonine for 2 minutes at 37°C, followed by 12.5 μM puromycin for 2 minutes at 37°C then 100 μg/mL cycloheximide and immediately collected.

tag: cell stage

value: Mitotic Cycling

value: Cycloheximide

tag: replicate

tag: library type

value: mRNA


title: MitoticCycling elongating RPF rep 2

value: Ribosome protected mRNA fragment


title: MIA PaCa-2 cells, shNT (Control), Day 7, Rep2, RNA-seq

description: 50M reads per sample


title: MitoticCycling TIS Input RNA rep 2

value: Harringtonine-puromycin


title: MIA PaCa-2 cells, shASAP1, Day 21, Rep2, RNA-seq

description: 50M reads per sample


title: MitoticCycling elongating Input RNA rep 1


title: MitoticCycling TIS RPF rep 2


title: MitoticCycling TIS Input RNA rep 1


title: MitoticArrest TIS Input RNA rep 2

value: Mitotic Arrest


title: MitoticArrest elongating Input RNA rep 2


title: MitoticCycling elongating RPF rep 1


title: MitoticArrest elongating RPF rep 2


title: MitoticCycling TIS RPF rep 1


title: MitoticArrest TIS RPF rep 2


title: MitoticArrest elongating RPF rep 1


title: MitoticArrest TIS RPF rep 1


title: Interphase elongating RPF rep 2

value: Interphase


title: Interphase TIS RPF rep 2


title: MitoticArrest TIS Input RNA rep 1


title: Interphase TIS Input RNA rep 1


title: Interphase elongating Input RNA rep 2


title: Interphase TIS Input RNA rep 2


title: Interphase elongating Input RNA rep 1


title: MitoticArrest elongating Input RNA rep 1


title: P-M-2--2

city: Charlottesville

first: Xiaoqin

last: Wei

state: Virginia

address: 2512 Fontaine Ave

institute: University of Virginia

data_processing:
Paired-end libraries were sequenced on an Illumina HiSeq 4000 following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. Base-calling was performed using Illumina’s RTA software (version 2.5.2). Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using RNA-seq spliced read mapper Tophat2 (v2.1.1).
Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using Bowtie (v2.3.4). Pre- and post-alignment quality controls, gene level raw read count and normalized read count (i.e. FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model.
Differential expression for each gene between various groups was identified by Cuffdiff. For functional analysis, GSEA was used to identify enriched gene sets, from the hallmark and C5 databases of MSigDB, having up-regulated and down-regulated genes, using a weighted enrichment statistic and a log2 ratio metric for ranking genes.
Assembly: mm10
Supplementary files format and content: csv file include FPKM values for each Sample ...

source_name: Bronchoalveolar lavage

growth_protocol: AMs were obtained from bronchoalveolar lavage of mice and purified by adherence for 2 h in complete medium (RPMI-1640, 10% FBS, 1% Pen/Strep/glutamate) at 37 ̊C and 5% CO2. The non-adherent cells were washed off with warm PBS. The remaining adherent cells were cultured in complete medium supplemented with 10 ng/ml recombinant murine granulocyte macrophage CSF (GM-CSF).

extract_protocol:
Total RNA from in vitro cultured AMs was extracted using RNeasy Plus Mini Kit, and RNA quality was determined (RIN>7) via Agilent Bioanalyzer
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

treatment_protocol: AMs were pre-treated with DMSO (vehicle) or MSDC (10 μM) for two hours, then, cells were stimulated with or without Poly IC (5μg/mL) for 24 hours. Then, the cells were havested for RNA-seq.

tag: strain

value: Poly(I:C) MSDC

value: MSDC & Poly(I:C)

value: lung

value: Alveolar macrophages


title: P-M-2-1


title: MIA PaCa-2 cells, shARF6, Day 14, Rep3, RNA-seq

description: 50M reads per sample

value: MIA PaCa-2

value: Pancreatic ductal adenocarcinoma

value: ARF6 knockdown

value: lentiviruses containing shRNA

value: Day 14


title: Interphase elongating RPF rep 1


title: P-D-2-1

value: Poly(I:C) DMSO

value: DMSO & Poly(I:C)


title: P-D-2--2


title: M-2-2

value: MSDC


title: Interphase TIS RPF rep 1


title: D-2-1

value: DMSO


title: S335P3_SPRA6

city: Trondheim

first: Pål

last: Sætrom

address: Erling Skjalgsons gate 1

department: Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology, NTNU

data_processing:
FASTQ files were created with bcl2fastq V2.20, quality controlled with fastqc (v0.11.9) and filtered and trimmed by fastp (v0.20.0). CollectRNASeqMetrics (v2.21.5)
Trimmed sequences were  aligned to the genome reference using STAR (v2.7.3) and quality metrics were extracted with picard CollectRNASeqMetrics (v2.21.5).
Transcript counts were generated using quasi alignment (Salmon v1.3.0) to the GRCh38 transcriptome reference sequences and imported into the R statistical software and aggregated to gene expression counts using the tximport (v1.14.0)
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts (cpm) for 60218 ENSG numbers for 335 samples

source_name: whole blood

extract_protocol:
Total RNA was extracted using PAX-gene blood RNA-kits (Qiagen)
RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

tag: sampleID

tag: pregnancyid

value: whole blood

tag: samplegroup

value: SPRA

tag: timepoint

tag: grouptime

tag: lai(p)

tag: medicationra

tag: medicationsle

tag: prednisolon use

tag: diseasestate

tag: disease state_and_medication_status

tag: library size


title: M-2-1

tag: treatment

tag: tissue

tag: cell type


title: S334P84_SPRA0


title: S332P83_SPRA1


title: S331P82_HEALTHY1

value: HEALTHY


title: S330P82_HEALTHY2


title: S328P81_HEALTHY1


title: D-2-2


title: S329P82_HEALTHY3


title: S326P2_HEALTHY2


title: S324P81_HEALTHY4


title: S321P80_HEALTHY2


title: S325P81_HEALTHY3


title: S322P80_HEALTHY1


title: S320P80_HEALTHY4


title: S323P81_HEALTHY5


title: S319P80_HEALTHY5


title: S317P79_HEALTHY2


title: S314P79_HEALTHY5


title: S318P79_HEALTHY1


title: S315P2_HEALTHY3


title: S313P78_HEALTHY1


title: S316P79_HEALTHY4


title: S312P78_HEALTHY2


title: S310P78_HEALTHY5


title: S308P77_HEALTHY2


title: S309P77_HEALTHY1


title: S333P83_SPRA0


title: S307P77_HEALTHY3


title: S306P77_HEALTHY4


title: S305P77_HEALTHY5


title: S327P81_HEALTHY2


title: S304P2_HEALTHY4


title: S302P76_HEALTHY2


title: S300P76_HEALTHY4


title: S301P76_HEALTHY3


title: S303P76_HEALTHY1


title: S298P75_HEALTHY2


title: S299P75_HEALTHY1


title: S297P75_HEALTHY3


title: S294P74_HEALTHY1


title: S296P75_HEALTHY4


title: S295P75_HEALTHY5


title: S293P2_HEALTHY5


title: S291P74_HEALTHY3


title: S311P78_HEALTHY3


title: S290P74_HEALTHY4


title: S289P74_HEALTHY5


title: S288P73_HEALTHY1


title: S287P73_HEALTHY2


title: S282P1_HEALTHY1


title: S284P73_HEALTHY5


title: S283P72_HEALTHY1


title: S280P72_HEALTHY4


title: S281P72_HEALTHY3


title: S286P73_HEALTHY3


title: S285P73_HEALTHY4


title: S277P71_HEALTHY2


title: S275P71_HEALTHY4


title: S271P1_HEALTHY2


title: S274P70_HEALTHY1


title: S276P71_HEALTHY3


title: S273P70_HEALTHY2


title: S270P70_HEALTHY4


title: S269P70_HEALTHY5


title: S272P70_HEALTHY3


title: S292P74_HEALTHY2


title: S268P67_HEALTHY2


title: S267P67_HEALTHY3


title: S265P69_SNRA2

value: SNRA


title: S266P67_HEALTHY4


title: S263P68_SNRA3


title: S262P66_SNRA5


title: S261P66_SNRA4


title: S258P67_HEALTHY5


title: S259P66_SNRA2


title: S260P66_SNRA3


title: S257P66_SNRA1


title: S279P72_HEALTHY5


title: S278P71_HEALTHY1


title: S252P64_SNRA5


title: S256P65_SNRA5


title: S254P65_SNRA3


title: S253P65_SNRA2


title: S255P65_SNRA4


title: S250P64_SNRA3


title: S247P35_SLE4

value: SLE


title: S251P64_SNRA4


title: S245P63_SNRA4


title: S246P35_SLE3


title: S244P63_SNRA2


title: S242P62_SLE5


title: S241P62_SLE4


title: S243P63_SNRA1


title: S264P69_SNRA1


title: S239P62_SLE2


title: S237P59_HEALTHY2


title: S240P62_SLE3


title: S236P21_SPRA5


title: S235P21_SPRA4


title: S234P54_SLE5


title: S232P54_SLE2


title: S233P54_SLE3


title: S231P17_SPRA5


title: S229P61_SPRA4


title: S230P61_SPRA5


title: S225P61_SPRA1


title: S227P61_SPRA2


title: S226P59_HEALTHY3


title: S224P60_SLE4


title: S222P60_SLE2


title: S249P64_SNRA2


title: S223P60_SLE3


title: S228P61_SPRA3


title: S248P35_SLE5


title: S221P60_SLE1


title: S219P12_SPRA4


title: S220P12_SPRA5


title: S218P12_SPRA3


title: S217P12_SPRA2


title: S216P12_SPRA1


title: S215P59_HEALTHY5


title: S238P62_SLE1


title: S214P1_HEALTHY3


title: S212P58_SPRA3


title: S213P58_SPRA4


title: S210P58_SPRA1


title: S206P57_SLE0


title: S208P4_SPRA4


title: S205P56_SLE2


title: S203P45_HEALTHY1


title: S202P55_SLE5


title: S199P55_SLE2


title: S201P55_SLE4


title: S200P55_SLE3


title: S197P54_SLE0


title: S195P52_SLE4


title: S194P52_SLE3


title: S198P55_SLE1


title: S193P52_SLE2


title: S196P53_SLE5


title: S191P52_SLE1


title: S192P45_HEALTHY2


title: S189P51_SLE2


title: S190P51_SLE4


title: S185P49_SLE3


title: S186P49_SLE4


title: S211P58_SPRA2


title: S209P4_SPRA5


title: S187P49_SLE5


title: S184P49_SLE2


title: S182P45_HEALTHY3


title: S181P49_SLE0


title: S207P4_SPRA3


title: S204P56_SLE1


title: S180P48_SLE6


title: S179P48_SLE5


title: S177P48_SLE3


title: S178P48_SLE4


title: S176P48_SLE2


title: S174P47_SLE6


title: S173P47_SLE5


title: S172P45_HEALTHY4


title: S170P47_SLE3


title: S169P47_SLE2


title: S168P47_SLE1


title: S167P46_SLE6


title: S188P50_SLE0


title: S164P46_SLE3


title: S165P46_SLE4


title: S162P46_SLE1


title: S163P46_SLE2


title: S160P44_SLE6


title: S158P44_SLE4


title: S159P44_SLE5


title: S183P49_SLE1


title: S157P44_SLE3


title: S155P44_SLE1


title: S161P45_HEALTHY5


title: S156P44_SLE2


title: S154P44_SLE0


title: S151P43_SLE4


title: S152P43_SLE5


title: S171P47_SLE4


title: S153P43_SLE6


title: S175P48_SLE1


title: S148P43_SLE1


title: S149P43_SLE2


title: S147P42_SLE6


title: S150P34_HEALTHY1


title: S166P46_SLE5


title: S144P40_SLE6


title: S142P40_SLE4


title: S141P40_SLE3


title: S140P40_SLE2


title: S145P41_SLE6


title: S139P34_HEALTHY3


title: S138P39_SLE6


title: S137P39_SLE5


title: S134P39_SLE2


title: S135P39_SLE3


title: S133P39_SLE1


title: S131P37_SLE6


title: S132P38_SLE6


title: S129P37_SLE4


title: S128P34_HEALTHY4


title: S127P37_SLE3


title: S126P37_SLE2


title: S146P42_SLE5


title: S124P36_SLE5


title: S125P37_SLE1


title: S122P36_SLE3


title: S121P36_SLE2


title: S118P33_SLE6


title: S143P40_SLE5


title: S123P36_SLE4


title: S120P36_SLE1


title: S119P35_SLE1


title: S117P34_HEALTHY5


title: S116P33_SLE5


title: S114P33_SLE3


title: S112P33_SLE1


title: S111P32_SNRA1


title: S115P33_SLE4


title: S136P39_SLE4


title: S113P33_SLE2


title: S130P37_SLE5


title: S109P32_SNRA4


title: S106P1_HEALTHY4


title: S107P19_HEALTHY1


title: RORA_OE_capture_hic_2

city: Bengbu

first: Mingsen

last: Li

state: Anhui

address: No. 2600, Donghai Avenue, Bengbu City, Anhui Province

department: Interdisciplinary Eye Research Institute (EYE-X Institute)

institute: Bengbu Medical University

data_processing:
HiCUP pipeline was used for capture Hi-C data processing, including read mapping, read filtering and removal of duplicate reads.
CHiCAGO was used to identify significant chromatin interactions (CHiCAGO score ≥ 5).
Significant differential interactions between the two groups were determined using edgeR with |log fold change| > 1 and p-value < 0.05.
Assembly: hg19
Supplementary files format and content: A Excel file containing the differential interactions between control and RORA-overexpression groups

source_name: limbal stem cells

growth_protocol: LSCs  were grown in DMEM/F-12 (1:1) medium containing  1% penicillin/streptomycin, 10% fetal bovine serum, 10 ng/ml EGF, 5 μg/ml insulin, 0.4 μg/ml hydrocortisone, 0.1 nM cholera toxin and 2 nM 3,3',5-triiodo-L-thyronine.

extract_protocol:
The chromatin DNA was digested with 100 U HindIII (NEB, #R3104S) and labeled with biotin-14-dCTP (Invitrogen, #19518018). The biotin-labeled DNA fragments were then ligated by 50 U T4 DNA ligase (NEB, # M0202S), de-crosslinked and extracted using QIAamp DNA Mini Kit (Qiagen). We then sheared the purified DNA fragments to 300-600 bp, repaired the ends and added A-tails and SureSelect adaptors. After biotin-streptavidin-mediated pull-down, DNA fragments were amplified by PCR.
We conducted capture Hi-C of promoters by the SureSelect XT Library Prep Kit ILM (Agilent Technologies, #G9981A), as per the manufacturer’s instructions, with custom-designed biotinylated RNA bait library and custom paired-end blockers. After another PCR amplification, promoter capture Hi-C libraries were purified with AMPure XP beads (Beckman Coulter, #a63880)
Promoter capture Hi-C-seq

treatment_protocol: Cells were infected with lentiviruses expressing target genes.

value: primary limbal stem cells

tag: genotype

value: RORA overexpression


title: control_capture_hic_2

value: control


title: S105P30_SNRA1


title: S104P30_SNRA2


title: S103P30_SNRA3


title: control_capture_hic_1


title: S102P30_SNRA4


title: S101P30_SNRA5


title: S99P29_SNRA2


title: S100P30_SNRA6


title: RORA-OE-input

description: RORA.peak.bed

data_processing:
Reads were trimmed by trimmomatic tool and then aligned to human hg19 reference genome using BWA software.
Duplicated reads were removed by Picard Markduplicates and only uniquely mapping reads were retained for further analysis.
MACS2 was used to call peak.
Assembly: hg19
Supplementary files format and content: Excel files containing differential H3K27ac, H3K4me3 and H3K27me3 peaks between control and RORA-overexpression groups. A BED file containing RORA binding sites in RORA-overexpressed LSCs.

extract_protocol:
chromatin was fixed with 1% formaldehyde for 10 min and sheared in a sonification buffer. Fragmented DNA was incubated with primary antibodies overnight at 4℃ and then with Protein A/G Dynabeads  for 1 h. The beads were collected and washed sequentially with the following solutions: high-salt buffer, low-salt wash buffer, and TE buffer.  Elution of the immunoprecipitated protein/DNA complexes was performed using elution buffer at 65℃ for 4 h. Next, the protein/DNA complexes were incubated with proteinase K (Invitrogen) and RNase A (Invitrogen) for 1 h. De-crosslinked DNA was purified using the PCR Purification Kit (Qiagen).
ChIP-seq DNA libraries were generated using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) according to the manufacturer’s instructions.

tag: chip antibody


title: RORA_flag_2

description: RORA.peak.bed

value: flag


title: S98P29_SNRA4

tag: sampleID


title: RORA_flag_1

description: RORA.peak.bed


title: RORA_H3K4me3_1


title: RORA_H3K4me3_2


title: S96P19_HEALTHY2

tag: pregnancyid


title: RORA_H3K27ac_2


title: S108P31_SNRA0

tag: samplegroup


title: S110P32_SNRA3

tag: timepoint


title: S95P29_SNRA6

tag: grouptime


title: S94P28_SNRA1

tag: lai(p)


title: RORA_H3K27me3_1

description: RORA_OE_H3K27me3_differential_peaks.xlsx


title: S93P28_SNRA2

tag: medicationra


title: RORA_H3K27ac_1


title: control_H3K4me3_2


title: S92P28_SNRA3

tag: medicationsle


title: RORA_H3K27me3_2


title: control_H3K4me3_1


title: RORA_OE_capture_hic_1


title: control_H3K27me3_2


title: control-input

description: RORA.peak.bed


title: S91P28_SNRA4

tag: prednisolon use


title: S90P28_SNRA5

tag: diseasestate


title: control_H3K27me3_1


title: S89P27_SNRA4

tag: disease state_and_medication_status


title: S97P29_SNRA5

tag: library size


title: control_H3K27AC_2

tag: treatment


title: S88P27_SNRA5

tag: tissue


title: control_H3K27AC_1

tag: cell type


title: PITX1-OE-3

data_processing:
trimmed reads were aligned to human hg19 reference genome with STAR software (version 2.6.1a) to acquire read counts within per gene.
TPM (Transcripts per million reads) values that represent gene expression were generated using RSEM tools (version v1.3.0).
Significantly differentially expressed genes with fold change ≥ 2 and FDR < 0.05 were determined by DESeq2 (version 1.20.0).
Assembly: hg19
Supplementary files format and content: Excel files containing the TPM value of each gene in control and RORA- and PITX1-overexpressed LSCs.

growth_protocol: LSCs were grown in 1:1 DMEM/F-12 medium containing  1% penicillin/streptomycin, 10% fetal bovine serum, 10 ng/ml EGF, 5 μg/ml insulin, 0.4 μg/ml hydrocortisone, 0.1 nM cholera toxin and 2 nM 3,3',5-triiodo-L-thyronine.

extract_protocol:
Total RNA were extracted by RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using  NEBNext RNA first and second Strand Synthesis Module (NEB, USA) and KAPA Library Preparation Kit (KAPA Biosystem)

tag: genotype

value: PITX1 overexpression


title: PITX1-OE-2


title: S86P26_SNRA0


title: control-P-3


title: S84P26_SNRA1


title: PITX1-OE-1


title: S83P26_SNRA2


title: control-P-2


title: S82P26_SNRA4


title: control-P-1


title: S81P26_SNRA5


title: RORA-OE-2


title: S80P25_SNRA0


title: RORA-OE-1


title: control-R-2


title: S79P24_SNRA0


title: S78P23_SPRA1


title: control-R-1


title: S77P23_SPRA2


title: MCF7 cells with GD3S overexpression, treated by Nutlin3A, replicate #5

city: Houston

first: Zheng

last: Yin

state: TX

address: 6565 Fannin St, MC: F6-300

department: Systems Medicine and Bioengineering

institute: Houston Methodist Cancer Center

data_processing:
Used Cutadapt to remove low quality bases, followed by FastQC
Used HISAT2 to map reads to reference genome
Used StringTie for read assembly
Used gffcompare to reconstruct the transcriptome
Used StringTie and ballgown to estimate expression levels for all transcripts
Assembly: Release 107 (July 2022) of the Homo Sapiens reference genome from Ensemble
Supplementary files format and content: Excel file including PRKM and raw count for each gene in each sample

extract_protocol:
Following treatment, the cells were washed with PBS, and RNA extraction was performed with a QIAGEN RNA extraction kit according to the manufacturer’s protocol.
A poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.
Poly(A) tail-containing RNAseq

treatment_protocol: MCF7 cells with or without GD3S overexpression were cultured and treated with DMSO or Nutlin3A at 10µM for 72 h

tag: cell line

tag: disease

value: Breast Cancer

value: GD3S overexpression


title: S76P22_SPRA0

tag: sampleID

tag: pregnancyid


title: MCF7 cells with GD3S overexpression, treated by Nutlin3A, replicate #6


title: S87P27_SNRA6

tag: samplegroup

tag: timepoint


title: S75P19_HEALTHY4

tag: grouptime

tag: lai(p)


title: S74P22_SPRA1

tag: medicationra

tag: medicationsle


title: MCF7 cells with GD3S overexpression, treated by Nutlin3A, replicate #4


title: S73P22_SPRA2

tag: prednisolon use

tag: diseasestate


title: S72P22_SPRA3

tag: disease state_and_medication_status

tag: library size


title: S85P19_HEALTHY3

tag: tissue


title: MCF7 cells with GD3S overexpression, treated by DMSO, replicate #3

tag: treatment


title: MCF7 cells with GD3S overexpression, treated by DMSO, replicate #2

tag: genotype


title: wildtype MCF7 cells treated by Nutlin3A, replicate #3

tag: cell line

value: Control/Wildtype


title: S71P22_SPRA4


title: MCF7 cells with GD3S overexpression, treated by DMSO, replicate #1

tag: disease


title: S68P20_SPRA1

tag: sampleID


title: S69P21_SPRA1

tag: pregnancyid


title: wildtype MCF7 cells treated by DMSO, replicate #3


title: wildtype MCF7 cells treated by Nutlin3A, replicate #2


title: S67P20_SPRA2

tag: samplegroup


title: wildtype MCF7 cells treated by DMSO, replicate #2


title: wildtype MCF7 cells treated by Nutlin3A, replicate #1


title: S70P21_SPRA0

tag: timepoint


title: S66P20_SPRA3

tag: grouptime


title: S65P20_SPRA4

tag: lai(p)


title: wildtype MCF7 cells treated by DMSO, replicate #1


title: S64P19_HEALTHY5

tag: medicationra


title: S63P18_SPRA0

tag: medicationsle


title: S62P18_SPRA1

tag: prednisolon use


title: cell multiplexing library 2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: data generated using cell plex technology from 10XGenomics

library_source: other

data_processing:
from fastq to count matrix: cellranger v7.1.0
Cell ranger is available in docker image repbioinfo/cellranger.2023.7.1.0 at https://hub.docker.com/ (docker pull repbioinfo/cellranger.2023.7.1.0)
The sample sheet required by cellranger is available in the supplementary file: multi_gex.csv. The string to execute the conversion from fastq to counts in docker are: 1) access to the docker container :docker run -v /fastq_folder_somewhere_in_your_server:/data -v /somewhere_in_your_server/the-folder_with_the_10Xgenomics_human_genome_assembly_built/:/genomes -it repbioinfo/cellranger.2023.7.1.0 /bin/bash ; 2) execute cellranger cellranger multi --id=BE1 --csv=/data/multi_gex.csv
The barcode.tsv files were edited indicating the name of the cell lines.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: 10XGenomics sparse matrix format
Supplementary files format and content: multi_gex.csv configuration file required to run cellranger multi

molecule: other

source_name: CMOs library

extract_protocol: The libraries were constructed using CellPlex technology from 10XGenomics. We used four reactions of Chromium Next GEM Single Cell 3' Kit v3.1, combined with 3' CellPlex Kit. We generated four expression libraries (1740FL-306-01-01, 1740FL-306-01-02, 1740FL-306-01-03, 1740FL-306-01-04) and  four multiplexing libraries (1740FL-306-01-09, 1740FL-306-01-10, 1740FL-306-01-11, 1740FL-306-01-12). These are the cell lines analysed and the associated CellPlex barcode:  PC9 (CMOs 303), HTB178 (CMOs 305), CRL5868 (CMOs 304), DV90 (CMOs 306), HCC78 (CMOs 307), A549 (CMOs 301), CCL-185-IG (CMOs 302), PBMC (CMOs 308). As part of the supplementary data the file multi_gex.csv describes all the required parameters to run cellranger for multiplexed samples.

value: CMOs library


title: cell multiplexing library 1


title: cell multiplexing library 3


title: S60P18_SPRA3

tag: diseasestate


title: cell multiplexing library 4


title: S58P17_SPRA0

tag: disease state_and_medication_status


title: gene expression library 3

description:
data generated using cell plex technology from 10XGenomics
PC9_barcodes.tsv, HTB178_barcodes.tsv, CRL5868_barcodes.tsv, DV90_barcodes.tsv, HCC78_barcodes.tsv, A549_barcodes.tsv, CCL-185-IG_barcodes.tsv, PBMCs_barcodes.tsv
PC9_features.tsv, HTB178_features.tsv, CRL5868_features.tsv, DV90_features.tsv, HCC78_features.tsv), A549_features.tsv, CCL-185-IG_features.tsv, PBMCs_features.tsv
PC9_matrix.mtx.gz, HTB178_matrix.mtx.gz, CRL5868_matrix.mtx.gz, DV90_matrix.mtx.gz, HCC78_matrix.mtx.gz, A549_matrix.mtx.gz, CCL-185-IG_matrix.mtx.gz, PBMCs_matrix.mtx.gz

source_name: cell line, PBMC

value: cell line, PBMC


title: S59P18_SPRA4

tag: library size


title: gene expression library 4

tag: tissue


title: S61P18_SPRA2


title: gene expression library 1


title: S57P17_SPRA1


title: TotalRNAseq_Calu3_Mock_6h_Rep3

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
RNA-seq data was analyzed using the RNA-seq module from the snakePipes package (Bhardwaj et al, Bioinformatics, 2019). A hybrid genome of human (genome build hg38, Gencode release 31) and viral genomes ( H1N1: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=370129 and SARS_Cov-2: https://www.ncbi.nlm.nih.gov/nuccore/1798174254) was used as reference for mapping and read counting. Differential gene expression analysis was done using DESeq2 (Love et al, Genome Biology, 2014), using the total number of mapped human and viral reads to calculate size factors.
Genome_build: hg38
Supplementary_files_format_and_content: Table in tsv format with raw counts

extract_protocol: Total RNA was isolated using Trizol (R2050; Zymo Research, USA), as per manufacturer’s instructions. Followed by purification using RNA Clean & Concentrator (R1017; Zymo esearch, USA) and DNase I Set (E1010; Zymo Research, USA), as per manufacturer’s instructions.

tag: agent

value: Mock

tag: time point


title: S56P17_SPRA2


title: S54P7_HEALTHY1


title: TotalRNAseq_Calu3_Mock_6h_Rep2


title: S52P15_SPRA0


title: TotalRNAseq_Calu3_Mock_6h_Rep1


title: S55P17_SPRA3


title: TotalRNAseq_Calu3_Mock_24h_Rep3


title: S53P16_SPRA0


title: TotalRNAseq_Calu3_Influenza_6h_Rep3

value: Influenza


title: TotalRNAseq_Calu3_Influenza_6h_Rep2


title: TotalRNAseq_Calu3_Mock_24h_Rep1


title: S51P15_SPRA1

value: whole blood


title: S50P15_SPRA2

value: SPRA


title: S49P15_SPRA4


title: S48P15_SPRA5


title: gene expression library 2

tag: cell line


title: TotalRNAseq_Calu3_Influenza_24h_Rep2


title: TotalRNAseq_Calu3_Influenza_24h_Rep3


title: S46P14_SPRA3


title: S47P14_SPRA2


title: TotalRNAseq_Calu3_Inactive_Covid_6h_Rep2


title: S44P14_SPRA5


title: S45P14_SPRA4


title: S43P7_HEALTHY2

value: HEALTHY


title: TotalRNAseq_Calu3_Influenza_24h_Rep1


title: TotalRNAseq_Calu3_Inactive_Covid_6h_Rep3


title: TotalRNAseq_Calu3_Inactive_Covid_6h_Rep1


title: TotalRNAseq_Calu3_Inactive_Covid_24h_Rep3


title: TotalRNAseq_Calu3_Covid_6h_Rep3


title: TotalRNAseq_Calu3_Mock_24h_Rep2


title: S40P13_SPRA3


title: S37P13_SPRA6


title: S41P13_SPRA2


title: TotalRNAseq_Calu3_Inactive_Covid_24h_Rep2


title: TotalRNAseq_Calu3_Covid_24h_Rep3


title: S42P14_SPRA6


title: TotalRNAseq_Calu3_Inactive_Covid_24h_Rep1


title: S38P13_SPRA5


title: S39P13_SPRA4


title: TotalRNAseq_Calu3_Covid_6h_Rep2


title: TotalRNAseq_Calu3_Influenza_6h_Rep1


title: S36P12_SPRA0


title: S35P11_SPRA0


title: TotalRNAseq_Calu3_Covid_6h_Rep1


title: TotalRNAseq_Calu3_Covid_24h_Rep1


title: TotalRNAseq_Calu3_Covid_24h_Rep2


title: S34P11_SPRA1


title: S32P11_SPRA2


title: ChIPseq_WSN_6h_rep2_Input

description: ChIP-seq

data_processing:
ChIP-seq reads were aligned to the human genome build hg38 using the ChIP-seq module from the snakePipes package (Bhardwaj et al., Bioinformatics, 2019). Duplicate and discordant reads were removed. Peak calling was done with MACS2 (model- based analysis of ChIP- Seq) (Zhang et al., Genome Biol, 2008) using "--keep-dup all", "--nomodel", "--extsize". Gene annotations and transcript start site (TSS) information for human genes were from taken from Gencode annotation release 31. Reads overlapping the TSS regions (TSS +/- 100bp) were counted using bedtools2 (Quinlan & Hall, Bioinformatics, 2010). Differential analysis of TSS density was done using DESeq2 (Love et al., Genome Biol, 2014). Size factors were calculated based on the signal in genomic bins of corresponding Input samples similar to (Arrigoni et al., Communications Biology, 2018). Profile plots were generated using deeptools2 (Ramirez et al., Nucleic Acids Res, 2016) using bigwig files that were normalized using the size factors calculated based on the corresponding input samples.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files with normalized read coverage

extract_protocol: Calu3 cells were infected with Influenza or SARS CoV-2 virus for various time points before harvesting them for chromatin profiling. The ChIP-seq library preparation was done as in Arrigoni et al. Communications Biology (2018).

tag: antibody


title: ChIPseq_WSN_6h_rep2_H3K27Ac

description: ChIP-seq

value: H3K27Ac, Diagenode (C15410196)


title: S29P11_SPRA5

tag: sampleID


title: S33P7_HEALTHY3

tag: pregnancyid


title: ChIPseq_WSN_6h_rep1_581_Pol2

description: ChIP-seq

value: RNA PolII (RPB1) Cell Signaling 14958


title: S28P10_SPRA0

tag: samplegroup


title: ChIPseq_WSN_24h_rep2_Input

description: ChIP-seq


title: ChIPseq_WSN_24h_rep2_H3K27Ac

description: ChIP-seq


title: WT-3

city: Tai-an

first: Yuan Yuan

address: No. 61 Dai Zong Street

institute: College of Horticultural Science and Engineering, Shandong Agricultural University

description: To investigate the molecular mechanisms of greasification and apple quality maintenance, we sequenced the transcriptome of apples stored for 10 d after EGCG treatment during the most significant period of greasification differences.

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 46.5M raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads. Then about 46M clean reads  for each sample were retained for subsequent analyses.
The clean reads were mapped to the reference genome  using HISAT2 . FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs) . Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
Based on the hypergeometric distribution, GO , KEGG  pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: GDDH13_v1.1
Supplementary files format and content: fastq.gz
Supplementary files format and content: Differential screening was performed according to the expression of protein-coding genes in different samples, and there were four differential subgroups, whose numbers of detected differential genes were 1114, 1296, 780, and 558, respectively.

organism: Malus domestica

source_name: pericarp of apples

extract_protocol:
Total RNA was extracted using the TianGen kit in silico matrix column method according to the instructions. RNA purity was identified and quantified using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA) and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Transcriptome libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit according to the instructions. Transcriptome sequencing and analysis were performed by Shanghai Ouyi Biotechnology Co.

value: pericarp of apples

value: Protective organisation

tag: cell type

value: epidermal cell

tag: genotype

value: WT

tag: treatment

value: Vacuum in ddH2O2 for 5 minutes


title: ChIPseq_WSN_6h_rep1_Input

description: ChIP-seq


title: ChIPseq_WSN_6h_rep1_H3K27Ac

description: ChIP-seq


title: WT-2


title: ChIPseq_WSN_24h_rep2_581_Pol2

description: ChIP-seq


title: S27P10_SPRA1

tag: timepoint

tag: grouptime

tag: lai(p)

tag: medicationra


title: ChIPseq_WSN_24h_rep1_Input

description: ChIP-seq


title: S26P10_SPRA4

tag: medicationsle

tag: prednisolon use

tag: diseasestate

tag: disease state_and_medication_status


title: WT-1

tag: tissue


title: ChIPseq_WSN_24h_rep1_H3K27Ac

description: ChIP-seq

tag: agent

tag: time point


title: EGCG-3

tag: cell line

value: 5 μmol L-1 of EGCG in aqueous solution for 5 min.


title: S31P11_SPRA3

tag: sampleID

tag: pregnancyid

tag: library size


title: EGCG-2

tag: cell type

tag: genotype


title: S24P9_SPRA3

tag: samplegroup

tag: timepoint


title: ChIPseq_Uninf_6h_rep2_Input

description: ChIP-seq

value: Uninfected

tag: antibody


title: ChIPseq_Uninf_6h_rep2_H3K27Ac

description: ChIP-seq


title: ChIPseq_WSN_24h_rep1_581_Pol2

description: ChIP-seq


title: S30P11_SPRA4

tag: grouptime

tag: lai(p)

tag: medicationra


title: ChIPseq_WSN_6h_rep2_581_Pol2

description: ChIP-seq


title: S25P10_SPRA5

tag: medicationsle

tag: prednisolon use

tag: diseasestate


title: ChIPseq_Uninf_6h_rep1_Input

description: ChIP-seq

tag: agent


title: ChIPseq_Uninf_6h_rep1_H3K27Ac

description: ChIP-seq

tag: time point


title: EGCG-1

tag: tissue

tag: cell line

tag: treatment


title: S23P7_HEALTHY4

tag: sampleID

tag: pregnancyid

tag: disease state_and_medication_status

tag: library size


title: ChIPseq_Uninf_6h_rep1_581_Pol2

description: ChIP-seq


title: S22P9_SPRA4

tag: samplegroup

tag: timepoint


title: ChIPseq_Uninf_24h_rep2_Input

description: ChIP-seq

tag: antibody


title: ChIPseq_Uninf_24h_rep2_H3K27Ac

description: ChIP-seq


title: S21P9_SPRA5

tag: grouptime

tag: lai(p)


title: ChIPseq_Uninf_24h_rep2_581_Pol2

description: ChIP-seq


title: Influenza mice Day6_2, scRNAseq

first: Jay

last: Kolls

state: LA

institute: Tulane University

description: 10x Genomics

data_processing:
The demultiplexing , barcode processing , gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/6.1)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
mRNA was extracted from lung single cell suspension using the 10X Genomics Chromium™ Single Cell A Chip Kit Library construction was performed according to 10x Genomics Chromium™ Single Cell 3' Reagent Kit v3.1 protocol
single cell gene expression RNA-seq

value: Lung


title: ChIPseq_Uninf_6h_rep2_581_Pol2

description: ChIP-seq


title: S20P9_SPRA6

tag: medicationra

tag: medicationsle


title: Influenza mice Day6_1, scRNAseq

description: 10x Genomics


title: Influenza mice Day4, scRNAseq

description: 10x Genomics


title: S19P8_SPRA0

tag: prednisolon use

tag: diseasestate


title: ChIPseq_Uninf_24h_rep1_H3K27Ac

description: ChIP-seq

tag: agent

tag: time point


title: S18P8_SPRA1

tag: tissue


title: S17P8_SPRA2


title: K18-hACE2, PR8, Day6_4_bulk RNA

data_processing:
Trimmed sequence reads were mapped to mm10 using Banana Slug Analytics Platform (Slug Genomics, 203 UV Santa Cruz)
Cuffdiff were used for differential expression analysis (Slug Genomics, 203 UV Santa Cruz)
The Cuffdiff output was used to generate volcano plots (EnhancedVolcano) and ggplot (enrichplot)  using  R package 4.2.1
Assembly: mm10
Supplementary files format and content: Comma-delimited CSV files include differentially expressed genes for each comparisons

source_name: lung

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN, 74106) in accordance with the RNeasy Reagent manufacturer’s protocol. The concentration of RNA was determined by NanoDrop 2000. RNA quality was determined on an Agilent TapeStation 4150 using an Agilent RNA ScreenTape (Agilent, 5067-5576).
Total RNA libraries for RNA-seq were prepared using TruSeq total RNA Library Prep Kit following manufacturer's protocols.

value: lung

tag: genotype

tag: treatment

value: H1N1 infection (50PFU, A/PR/8/34(PR8))


title: CAC-C4

city: Shanghai

first: Haochen

last: Yang

state: Shanghai

address: 320 Yue-yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
The cDNA library was sequenced using the Illumina sequencing platform (Novaseq). The RNA isolation, library construction and sequencing were performed at Shanghai Biochip Co., Ltd.
Assembly: Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. We used Cutadapt software to filter the sequencing data to get high quality Clean Data for further analysis. Reads were aligned to an assembly of Mus musculus (GRCm39) using HiSat software.
Supplementary files format and content: For gene-expression analysis, the fragments of genes were counted and subsequently normalized by FPKM according to following formula.

source_name: Colon

extract_protocol:
Total RNA from was isolated with RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions and RNA integrity was determined using an Agilent Bioanalyzer4200 (Agilent technologies).
VAHTS Stranded mRNA-seq Library Prep Kit (NR612, Vazyme) was used to prepare the sequencing library according to the manufacturer's protocol.

treatment_protocol: Mouse CRC paired tumor and colon tissues were isolated from AOM/DSS CRC bearing C57BL/6 mice as described above. Tissues were immediately frozen in liquid nitrogen after isolated and then stored at -80 °C refrigerator.

value: Colon

tag: strain

tag: cell type

value: Normal colon cell

tag: disease

value: Normal

value: AOM/DSS


title: K18-hACE2, PR8, Day6_3_bulk RNA


title: ChIPseq_Uninf_24h_rep1_581_Pol2

description: ChIP-seq


title: K18-hACE2, PR8, Day6_2_bulk RNA


title: K18-hACE2, PR8, Day6_1_bulk RNA


title: ChIPseq_Covid_6h_rep2_Input

description: ChIP-seq


title: CAC-C2


title: CAC-T20

value: Tumor cell

value: colorectal cancer


title: S16P8_SPRA3

tag: sampleID

tag: pregnancyid

value: whole blood

tag: samplegroup

value: SPRA

tag: disease state_and_medication_status

tag: library size


title: CAC-T4


title: K18-hACE2, PR8, Day4_4_bulk RNA


title: ChIPseq_Covid_6h_rep2_H3K27Ac

description: ChIP-seq

tag: antibody

value: H3K27Ac, Diagenode (C15410196)


title: S15P8_SPRA4

tag: timepoint

tag: grouptime

tag: lai(p)

tag: medicationra

tag: medicationsle


title: ChIPseq_Uninf_24h_rep1_Input

description: ChIP-seq

tag: agent

tag: time point


title: ChIPseq_Covid_6h_rep2_581_Pol2

description: ChIP-seq

value: RNA PolII (RPB1) Cell Signaling 14958


title: K18-hACE2, PR8, Day4_3_bulk RNA

tag: tissue

tag: genotype

tag: treatment


title: CAC-C20

tag: strain

tag: cell type

tag: disease


title: Primary beige adipocyte,  Ets1 ChIP

city: Nanjing

first: Kai

address: #818, East Tianyuan Road

institute: Nanjing Medical University

data_processing:
Alignment by BWA
Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
Assembly: mm10
Supplementary files format and content: BigWig files
Supplementary files format and content: fastq files

source_name: SVF derived primary beige adipocyte

extract_protocol:
SVF cells were obtained from adipose tissue in the inguinal position of male C57BL/6J mice at 3-4 weeks old. Type I collagenase (2mg/ml, Sigma, SCR103) was preconfigured using DMEM basic medium (Gibco, C11995500BT) containing 2% volume of FBS (Gibco), 100 U/ml penicillin, 100 μg/ml streptomycin, and stored in the dark after removal of bacteria by filtration using a 0.22 μM filter. The volume ratio of collagenase to adipose tissue was maintained at 2:1. Then the adipose pad was cut into pieces to 1mm³ and digested in 37℃ water bath for 1h, during which the tube was reversed and mixed every five minutes. The digested adipocytes were filtered (70 μm), then centrifuged at 1000 rpm for 10 min. After re-suspension with PBS, centrifuge at the same speed and time. DMEM/F-12 (Meilunbio, MA0214) containing 10% FBS (Gibco) and 1% penicillin-streptomycin was used to culture the primary SVF, and then the cells were implanted into the pore plate of appropriate size. The medium was changed 24 h later, and then every 48 h until the cells grew to contact inhibition state. The plate-fully-covered cells then subjected to differentiation. As for beige adipogenesis, culture medium was added insulin (5μg/ml, sigma, I3536), Dexamethasone (5μM, sigma, D4902), 3,3',5-Triiodo-L-thyronine (T3, 1nM, sigma, T2977), Rosiglitazone (1μM, sigma, R2408), Isobutyl methylxanthine (0.5mM, sigma, I5879). The above differentiation medium were changed 48 h later with medium only containing insulin, T3 and rosiglitazone, and renewed every 48 h. 6 days later, the mature beige adipocyte were collected and treated according to the manufacturer’s instructions by using in situ DNA Binding Library for Illumina Cut&Tag kits (Yeasen, 12598E12).
Native nuclei were purified from adipocytes, and washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). For CUT&Tag, 1x10^5 nuclei bound to Concanavalin A-coated beads were incubated with indicated primary antibodies (Ets1, Active Motif, #39581, 1:50) and second antibodies (anti-rabbit IgG antibody, goat monoclonal: Millipore AP132). Transposase pA-Tn5 was used to induce DNA tagmentation, followed by Proteinase K digestion and PCI extraction. The ethanol precipitated DNA was immediately subjected to PCR amplification by Universal and barcoded i7 primer using NEBNext HiFi 2x PCR Master mix. The amplified library was purified without size selection. ChIP-seq libraries were prepared from 3-5ng DNA using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Post-amplification libraries were size selected at 250–450bp in length using AMPure XP beads ((Beckman Counter)) and were quantified using the Library Quantification Kit for Illiumina (Kapa Biosystems, KK4603). The CUT&Tag Library was pooled to a final concentration of 10nM and sequenced paired-end using the Illumina NovaSeq 6000.

value: SVF derived primary beige adipocyte

value: wild type C57

value: SVF seperated from iWAT were cultured in vitro and induced to beige differentiation. 6 days after differentiation, mature beige adipocyte were analyzed by ChIP-seq.


title: CAC-T2


title: S14P8_SPRA5

tag: sampleID

tag: pregnancyid

tag: samplegroup

tag: prednisolon use

tag: diseasestate


title: S13P8_SPRA6

tag: timepoint

tag: grouptime

tag: disease state_and_medication_status

tag: library size


title: K18-hACE2, PR8, Day4_2_bulk RNA


title: ChIPseq_Covid_6h_rep1_Input

description: ChIP-seq

tag: agent

tag: antibody


title: ChIPseq_Covid_6h_rep1_H3K27Ac

description: ChIP-seq

tag: time point


title: Lung-tdT-, bleo injuryed 2 months, scRNAseq

first: zixin

last: liu

address: 320 Yueyang road, Life Science Research Building A2112

institute: Center for Excellence in Molecular Cell Science

description:
LZ11
10x Genomics

data_processing:
Each scRNA-seq data set was processed by CellRanger (v6.1.1) pipeline to perform the alignment against the modified mouse reference genome mm10, filter the alignment and count barcodes and UMIs
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole lung

extract_protocol:
The lung epithelial cells isolation procedure included two rounds of digestion by two different enzyme cocktail (enzyme mixture 1: collagenase type I (500 U ml-1, Gibco, 17100–017), elastase (4 U ml-1, Worthington Biochemical Corporation, LS002279), and dispase (5 U ml-1, BD Biosciences, 354235) in DMEM/F12 (Gibco, 10565018); enzyme mixture 2: 0.1% Trypsin-EDTA (Gibco, 25200072) and DNase I (0.33 U ml-1; Worthington Biochemical Corporation LS002139) in DMEM/F12 (Gibco, 10565018)). In brief, the mice was euthanized by CO2 inhalation and then 10 ml of cold PBS was perfused through the right ventricle. After injecting 1.5 ml of enzyme mixture 1 through trachea, the lung lobes was collected and cut in to pieces, and additional 2.5 ml of enzyme mixture 1 was added before incubating the sample at 37 °C for 20 minutes on orbital shaker (~100 r.p.m). The digestion was ended by adding equal volume of cold DMEM/F12 with 10% of FBS (Gibco, 10099141) to the digestion medium, and the tissue was disturbed by pipetting before centrifuged at 1000g and 4 °C for 5 minutes. The supernatant was discarded and the pellet was resuspended with 2 ml of enzyme mixture 2 for incubating at 37 °C for 20 minutes. The digestion was stopped by adding equal volume of DMEM/F12 containing of 10% FBS and then filtered with 100 μm strainer and centrifuged at 1000g and 4 °C for 5 minutes. The pellet was resuspended by 2-3 ml of red blood cell lysis buffer (eBioscience, 00-4333-57) and incubated at room temperature for 3 minutes and then was stopped by adding 3 ml of cold PBS. The sample was filtered through 40 μm stainer and then centrifuged and resuspended in PBS. For MACS and FACS combined isolation, the cells was incubated with Epcam-APC (1:100, eBioscience, 17-5791-82) at 4 °C for 30 minutes and ended by adding cold PBS and centrifuged at 1000g and 4 °C for 5 minutes. For each adult lung, the pellet was resuspended in 80 μl of PBS and followed by 320 μl of anti-APC MicroBeads (Miltenyi Biotec, 130-090-855), then mixed the cells and beads well by pipetting and incubated at 4 °C for 15 minutes. After washing the sample with PBS and centrifuging at 1000g and 4 °C for 5 minutes, the pellet was resuspended in 500 ul of PBS and performed MACS positive isolation by autoMACS Pro Separator (Miltenyi Biotec). The positive selected cells were stained with DAPI and then performed FACS isolation by gating DAPI– Epcam+ tdTomato+ cells.
The cell suspense was loaded in 10x Chromium controller to generate GEMs, which were further processed into single cell 5ʹ gene expression libraries using Chromium Single Cell 5ʹ Library Kit (v2 Chemistry).

tag: tissue

value: whole lung

value: tdT- lung epithelial cells

tag: genotype

value: p63-CreER R26-tdT

value: bleo injuryed 2 months


title: S12P7_HEALTHY5

value: HEALTHY

tag: lai(p)

tag: medicationra

tag: medicationsle


title: K18-hACE2, PR8, Day4_1_bulk RNA

address: 1430 Tulane Ave

value: lung

tag: treatment

value: H1N1 infection (50PFU, A/PR/8/34(PR8))


title: K18-hACE2, SARS-CoV-2, Day6_3_bulk RNA

value: SARS-CoV-2 infection (2.0 X10^5/TCID50, WA1/2020)


title: Lung-tdT+, bleo injuryed 2 months, scRNAseq

description:
LZ10
10x Genomics

tag: cell type

value: tdT+ lung epithelial cells


title: S11P6_SPRA0

tag: sampleID

tag: pregnancyid

tag: samplegroup


title: ChIPseq_Covid_24h_rep2_Input

description: ChIP-seq


title: S10P5_SPRA1

tag: timepoint

tag: prednisolon use

tag: diseasestate


title: 7F0K, after selection, 10-3

city: Shenzhen

first: Zhe

last: Zhang

state: Guangdong

address: Gaoke Innovation Center

department: Institute of Physical and Systems Biology

institute: Shenzhen Bay Laboratory

data_processing:
Paired-end fastq files from next-generation sequencing were merged by using PEAR.
Both 5’ constant regions and 3’ constant regions of the assembled reads were trimmed by cutadapt.
We used FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and vsearch to filter sequencing reads with low quality, and count the read number of identical sequences.
The read numbers before and after selection were then summed up for each unique sequence.
The read counts were further processed by the STEAM module from DiMSum with minor adjustments. DiMSum STEAM performed statistical analyses to obtain the fitness score and error estimates for each protein variant.
Assembly: N/A
Supplementary files format and content: The txt files contain space-separated values in each line. The values from left to right are: number of mutations, mutation type, read counts before selection, read counts after selection, fitness, error estimate, amino acid sequence.
Library strategy: Sibs-Seq

organism: Escherichia coli

growth_protocol: 20 μl frozen stocks from the diluted library (～107 clones) were transferred to 20 mL EZ Rich Defined Medium containing 0.2% glucose and 50 μg/ml kanamycin. The cells were cultured at 37 °C overnight with shaking at 200 rpm.

extract_protocol:
All the cell pellets were thawed and the plasmids were extracted by using Plasmid Mini Kit I (Omega Bio-tek). The plasmids were then employed as the templates for sequencing library constructions.
The PCR products with sequencing adapters were gel-purified and sent to Novogene for next-generation sequencing.

treatment_protocol: For the first round of selection, 20 μl overnight cell culture was transferred to 20 ml EZ Rich Defined Medium containing 0.2% glucose, 50 μg/ml kanamycin, and a specific concentration of TMP for additional cell culture (12 hours at 37 °C). Meanwhile, the remaining cell culture was harvested by centrifugation and the pellets were stored at -20 °C for plasmid extraction.

tag: cell line


title: K18-hACE2, SARS-CoV-2, Day6_2_bulk RNA

city: New Orleans


title: ChIPseq_Covid_24h_rep2_H3K27Ac

description: ChIP-seq

tag: agent


title: K18-hACE2, SARS-CoV-2, Day6_1_bulk RNA


title: ChIPseq_Covid_24h_rep2_581_Pol2

description: ChIP-seq

tag: antibody


title: S9P5_SPRA2

tag: grouptime

tag: disease state_and_medication_status

tag: library size


title: 6LF2, before selection


title: S8P5_SPRA3

tag: tissue

tag: lai(p)


title: ChIPseq_Covid_24h_rep1_Input

description: ChIP-seq

tag: time point


title: 7CHQ, after selection, 25-2


title: K18-hACE2, SARS-CoV-2, Day4_2_bulk RNA

tag: genotype

tag: treatment


title: S7P5_SPRA4

tag: sampleID

tag: medicationra

tag: medicationsle


title: ChIPseq_Covid_24h_rep1_H3K27Ac

description: ChIP-seq


title: ChIPseq_Covid_6h_rep1_581_Pol2

description: ChIP-seq


title: S6P5_SPRA5

tag: pregnancyid

tag: samplegroup

tag: timepoint


title: K18-hACE2, SARS-CoV-2, Day4_1_bulk RNA


title: ChIPseq_Covid_24h_rep1_581_Pol2

description: ChIP-seq


title: 6TN7, after selection, 25-2

tag: cell line


title: K18-hACE2, naïve_4_bulk RNA


title: 7F0K, before selection


title: S4P3_SPRA4

tag: prednisolon use

tag: diseasestate


title: Slamseq_Calu3_Mock_6h_Rep2

data_processing:
Library strategy: Slam-seq
SLAM-seq analysis was done similar to (Muhar et al., Science, 2018). 3'UTR annotations were taken from Gencode annotation release 31 and merged on a gene level. The entire genomic regions of both viruses (H1N1: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=370129 and SARS_Cov-2: https://www.ncbi.nlm.nih.gov/nuccore/1798174254) were added to the human 3’UTR annotations. Adapters and polyA stretches were trimmed from raw reads using fastp (Chen et al., Bioinformatics, 2018). Trimmed reads were further processed with SlamDunk v0.3.4 16 (Neumann et al, BMC Bioinformatics,2018). "Slamdunk all" command was executed with default parameters except '-5 12 -n 100 -t 20 -m -rl 100 --skip-sam'. Differential gene expression was done with DESeq2 (Love et al, Genome Biology, 2014) using raw read counts with at least 2 T>C conversions. Size factors were calculated based on the number of mapped reads (human and viral reads) independent of T>C conversions.
Genome_build: hg38
Supplementary_files_format_and_content: Table in tsv format with raw counts

extract_protocol:
RNA was extracted using Trizol per manufactures protocol, with addition of DTT, and protection from light during the procedure to prevent S-S cross-binding.
5 ug of RNA was used for SLAMseq modifications, as described in Herzog et. al. 2017. Briefly, Iodoacetamide (Sigma I1149) was conjugated to 4SU in a 50mM pH 8.0 phosphate buffer in DMSO/Water (1:1), the reaction was quenched with DTT and RNA was reprecipitated using Ethanol and NaOAc. Libraries were prepared using Quantseq 3’ mRNA-Seq Library Prep Kit (Lexogen).

tag: agent

value: Mock


title: K18-hACE2, naïve_3_bulk RNA


title: Slamseq_Calu3_Mock_6h_Rep1


title: S5P4_SPRA1

value: whole blood

tag: grouptime

tag: disease state_and_medication_status


title: 6TN7, before selection


title: 6LF2, after selection, 10-2


title: K18-hACE2, naïve_2_bulk RNA

tag: tissue


title: S3P3_SPRA5

value: SPRA

tag: lai(p)

tag: library size


title: K18-hACE2, SARS-CoV-2, Day4_3_bulk RNA

tag: genotype


title: 6LYD, after selection, 400-2


title: Slamseq_Calu3_Mock_24h_Rep3

tag: time point


title: K18-hACE2, naïve_1_bulk RNA

tag: treatment


title: Slamseq_Calu3_Mock_24h_Rep2


title: 6LYD, after selection, 400-1


title: K18-hACE2, SARS-CoV-2, Day21_3_bulk RNA

value: SARS-CoV-2 infection (1.0 X10^4/TCID50, WA1/2020)


title: 7CHQ, before selection


title: S1P1_HEALTHY5

tag: sampleID

tag: medicationra


title: K18-hACE2, SARS-CoV-2, Day21_2_bulk RNA


title: 6LYD, after selection, 100-3


title: Slamseq_Calu3_Influenza_6h_Rep3

value: Influenza


title: SGC7901_miR-501_mimics

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (1.26.0).
Assembly: GRCh38
Supplementary files format and content: File include Count and  FPKM values for each sample

growth_protocol: The human gastric cancer cell line AGS and SGC7901 were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The two gastric cancer cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Gastric cancer cells were grown in 6-well plates and transfected with NC siRNAs and miR-501-mimics siRNAs. After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Two different GC cell lines were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were transfected with NC siRNAs and the miR-501-mimics (final concentration, 50 nM) by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 48 h post-transfection, cells were harvested for RNA sequencing.

tag: cell type

value: gastric cancer cell


title: K18-hACE2, SARS-CoV-2, Day21_1_bulk RNA


title: Slamseq_Calu3_Influenza_6h_Rep2


title: SGC7901_miR-501_NC

value: negative control siRNA


title: 6LYD, after selection, 100-2


title: 6LYD, after selection, 100-1


title: Slamseq_Calu3_Influenza_6h_Rep1


title: 6LYD, after selection, 400-3


title: Slamseq_Calu3_Influenza_24h_Rep3


title: ostie1-1 anther stage12 biological replicate1 [M12-1]

first: Yuxing

last: Fang

address: Peking University

institute: Peking University

description: M12 biol rep1

data_processing:
HISAT 2.2.0 was used for reads mapping (with default parameter).
featureCounts was used for count extraction and normalization.
Assembly: IRGSP-1.0/GCA_001433935.1
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

organism: Oryza sativa

source_name: anther

growth_protocol: Rice plants were grown in the field during the rice growing season in Nanjing (N 32.02°, E 118.51°).

extract_protocol:
Anthers on certain stages were picked with
RNA library was prepared with VAHTS Universal V6 RNA-seq Library Prep Kit for MGI

treatment_protocol: untreated

value: anther

tag: Stage

value: untreated


title: AGS_miR-501_mimics

source_name: AGS

value: AGS


title: ostie1-1 anther stage12 biological replicate2 [M12-2]

description: M12 biol rep2


title: Slamseq_Calu3_Influenza_24h_Rep2


title: S2P2_HEALTHY1

data_processing:
FASTQ files were created with bcl2fastq V2.20, quality controlled with fastqc (v0.11.9) and filtered and trimmed by fastp (v0.20.0). CollectRNASeqMetrics (v2.21.5)
Trimmed sequences were  aligned to the genome reference using STAR (v2.7.3) and quality metrics were extracted with picard CollectRNASeqMetrics (v2.21.5).
Transcript counts were generated using quasi alignment (Salmon v1.3.0) to the GRCh38 transcriptome reference sequences and imported into the R statistical software and aggregated to gene expression counts using the tximport (v1.14.0)
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts (cpm) for 60218 ENSG numbers for 335 samples

extract_protocol:
Total RNA was extracted using PAX-gene blood RNA-kits (Qiagen)
RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

tag: pregnancyid

tag: samplegroup

tag: timepoint

tag: medicationsle


title: AGS_miR-501_NC

tag: cell line


title: 6LYD, after selection, 25-3


title: WT anther stage12 biological replicate2 [WT12-2]

description: WT12 biol rep2

value: WT


title: 6LYD, after selection, 25-1


title: WT anther stage12 biological replicate3 [WT12-3]

description: WT12 biol rep3


title: Slamseq_Calu3_Mock_24h_Rep1

tag: agent


title: Slamseq_Calu3_Influenza_24h_Rep1


title: 6LYD, before selection


title: 1223-p5-p_S12

city: Solna

first: Emma

middle: R

last: Andersson

state: Not required for this country

address: Solnav. 9, BioMedicum

country: Sweden

institute: Karolinska Institutet

data_processing:
aligned to the mouse genome assembly version GRCm39 using package Rsubread 2.8.2
sequence reads were assigned to genes using featureCounts in the Rsubread package
raw counts were analysed using (DESeq2 1.34.0)
ComBat-seq (R package sva 3.42.0) was used to adjust for batch effects caused by different days of organoid derivation (derivation date)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file contains raw feature counts and comma separated file contains normalized counts (output of DESeq2, after batch correction)

growth_protocol: Organoids were grown following protocol Broutier et al, Nat Protoc. 2016;11:1724–1743.

extract_protocol:
Total RNA was harvested using RNeasy Plus micro kit (Qiagen, 74034) from the passage 5 of organoids.
RNA libraries for RNA-seq were prepared using TruSeq RNA SMP prep Kit-v2 SetA from Illumina (cat no. RS-122-2001) following the manufacturer’s protocol.

treatment_protocol: Organoids were not treated.

value: liver

value: cholangiocytes

value: intrahepatic cholangiocyte organoids (ICOs)

tag: mouse id

tag: liver region

value: Periphery

tag: derivation date

tag: passage


title: WT anther stage12 biological replicate1 [WT12-1]

city: Beijing

description: WT12 biol rep1

tag: tissue

tag: genotype


title: 1223-p5-h_S11

value: Hilum


title: Slamseq_Calu3_Inactive_Covid_6h_Rep3

tag: time point


title: 1225-p5-h_S10


title: 108 opools, after selection, 400-3


title: ostie1-1 anther stage10 biological replicate3 [M10-3]

description: M10 biol rep3

tag: treatment


title: 108 opools, after selection, 400-2


title: ostie1-1 anther stage10 biological replicate2 [M10-2]

description: M10 biol rep2


title: 6LYD, after selection, 25-2


title: ostie1-1 anther stage10 biological replicate1 [M10-1]

description: M10 biol rep1


title: 108 opools, after selection, 400-1


title: 1221-p5-p_S8


title: 108 opools, after selection, 100-3


title: 1219-p5-p_S6

value: Ndr (Jag1 Ndr/Ndr)


title: 108 opools, after selection, 100-2


title: WT anther stage10 biological replicate3 [WT10-3]

description: WT10 biol rep3


title: 108 opools, after selection, 100-1


title: WT anther stage10 biological replicate1 [WT10-1]

description: WT10 biol rep1


title: Slamseq_Calu3_Inactive_Covid_24h_Rep2


title: Slamseq_Calu3_Inactive_Covid_24h_Rep1


title: WT anther stage10 biological replicate2 [WT10-2]

description: WT10 biol rep2


title: Slamseq_Calu3_Covid_6h_Rep3


title: 1219-p5-h_S5


title: 108 opools, after selection, 25-3


title: Slamseq_Calu3_Covid_6h_Rep2


title: 1220-p5-h_S3


title: MVNEO2

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

country: France

institute: INSERM

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: barcodes files and matrix files

source_name: heart

extract_protocol:
Avc was microdissected from E9.5 mouse embryos; mitral valve at E16.5 and postbirth ( P0, Neonate) were microdissected. Cells were digested with TRIPLE for 5 or 10 min , blocked with 10% decomplemnted FCS and FACS sorted using tomato
libraries were prepared using the single cell 3' reagent kit from 10C genomics. Sequncing was carried out using NextSeq  500 1x57 nt

value: MV cells

value: heart

tag: strain

tag: age


title: Slamseq_Calu3_Inactive_Covid_24h_Rep3


title: 1220-p5-p_S4

tag: cell type


title: Slamseq_Calu3_Covid_6h_Rep1


title: 1224-p5-p_S1


title: MVE16,5

description: 10x Genomics


title: 108 opools, after selection, 25-2


title: Slamseq_Calu3_Covid_24h_Rep1


title: 108 opools, before selection


title: 1221-p5-h_S7


title: Slamseq_Calu3_Covid_24h_Rep3


title: 1225-p5-p_S9


title: AVCE9,5

description: 10x Genomics

value: AVC cells


title: Slamseq_Calu3_Inactive_Covid_6h_Rep1


title: MC38 tumor, RT 24h, mouse 3

status: Public on Dec 01 2023

city: Dallas

first: Sangeetha

last: Reddy

state: Texas

address: 2280 Inwood Road

institute: UT Southwestern Medical Center

data_processing:
Single end demultiplexed fastq files were generated using bcl2fastq2 v 2.17 from NextSeq550 high output v3 bcl files
Fastq files were imported, trimmed for adapter sequences followed by quality trimming using CLC Genomics Workbench v 23.0.3
High-quality reads were mapped against gene regions and transcripts annotated by ENSEMBL v99 GRCm39 using RNA-Seq Analysis tool v2.7 (CLC Genomics Workbench, reverse strand-specific option)
Assembly: ENSEMBL v99 GRCm39
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each Sample

source_name: MC38 tumor tissue

growth_protocol: RM9 and MC38 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq® Stranded mRNA-Seq Library Prep Kit (Cat. 20020594) following manufacturer's protocols.

treatment_protocol:
1 million RM9 or MC38 cells were injected subcutaneously on the right hind leg of C57BL/6 mice. Allow the tumors to develop and grow to the size of 8mm in diameter. Irradiate the tumors with a single dose of 15 Gy.
Euthanize different groups of mice at 3h, 12h, and 24h after irradiation and collect the tumor tissue for RNA extraction.

value: MC38 tumor tissue

value: adenocarcinoma

value: Irradiation, 15 Gy

tag: time

value: 24 post RT


title: MC38 tumor, RT 24h, mouse 2


title: MC38 tumor, RT 12h, mouse 4

value: 12 post RT


title: MC38 tumor, RT 24h, mouse 4


title: MVNEO1

description: 10x Genomics


title: Slamseq_Calu3_Covid_24h_Rep2


title: 108 opools, after selection, 25-1


title: MC38 tumor, RT 12h, mouse 3


title: MC38 tumor, RT 24h, mouse 1


title: MC38 tumor, RT 3h, mouse 1

value: 3h post RT


title: MC38 tumor, RT 3h, mouse 4


title: MC38 tumor, RT 12h, mouse 1


title: 1224-p5-h_S2


title: MC38 tumor, Control, mouse 4

value: no treatment


title: MC38 tumor, Control, mouse 3

value: WT


title: RM9 tumor, RT 24h, mouse 2

source_name: RM9 tumor tissue

value: RM9 tumor tissue


title: MC38 tumor, Control, mouse 2


title: RM9 tumor, RT 24h, mouse 3


title: RM9 tumor, RT 24h, mouse 1


title: MC38 tumor, Control, mouse 1


title: RM9 tumor, RT 12h, mouse 3


title: RM9 tumor, RT 12h, mouse 4


title: MC38 tumor, RT 12h, mouse 2


title: MC38 tumor, RT 3h, mouse 3


title: RM9 tumor, RT 12h, mouse 1


title: RM9 tumor, RT 12h, mouse 2


title: RM9 tumor, RT 3h, mouse 2


title: RM9 tumor, Control, mouse 4


title: RM9 tumor, RT 3h, mouse 1


title: RM9 tumor, RT 3h, mouse 3


title: RM9 tumor, Control, mouse 1


title: RM9 tumor, Control, mouse 2


title: RM9 tumor, Control, mouse 3


title: MC38 tumor, RT 3h, mouse 2