title: miniSOG-DDX6_HEK293T, arsenite-stress, omit probe, post-enrichment, rep2

first: Ziqi

last: Ren

address: Chengfu Road No.292

department: College of Chemistry and Molecular Engineering

institute: Peking University

description: Column Name: mS-DDX6_AS_noprobe_enrich2

data_processing:
The adaptors sequence in reads were removed by Cutadapt (v.1.18) and quality controlled by FastQC (v0.11.8) to ensure the adaptors were completely removed. Then reads were mapped by hisat2 (v2.1.0) to the human genome assembly GRCh38 (hg38) with Homo_sapiens.GRCh38.87.gtf annotations using the command: hisat2 -x $refGenome -1 $clean_file1 -2 $clean_file2 -p 8 2>$AligDir/$output.log|samtools view -hb >$AligDir/$output.bam
The mapped reads were then sorted by command: samtools sort -n $output.bam -O BAM -o $outputSort -T $outputSort.temp -@ 4 -m 2G 2>$outputSort.log
The sorted reads were counted by htseq-count (v0.7.2) using the command: htseq-count -s no -f bam $outputSort $refGTF >$output 2>$output.log. Same library was re-detected with deeper sequencing depth on Illumina platform to get enough reads for analysis. The final counts used for further analysis were counted by the sum of counts from the two sequencing testment.
Assembly: GRCh38 (hg38)
Supplementary files format and content: HEK293T_allcounts.xlsx, contains counts of all genes (sum of two rounds of sequencing) from HEK293T stable cells stably expressing TIA1-miniSOG, G3BP2-miniSOG or miniSOG-DDX6 under all condition

growth_protocol: HEK293T cells were cultured in complete medium consisting of Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum at 37°C with 5% CO2.

extract_protocol:
RNAs were extract following the TRIzol Reagent manufacturer’s instructions, digested with 1-2 μL DNaseI at 37°C for 30 min, and then incubated with click reagents consisting of 0.1 mM biotin-azide, 2 mM THPTA, 0.5 mM CuSO4 and 5 mM sodium ascorbate. After 10 min of CuAAC reaction at room temperature, RNAs were purified with RNA Clean&Concentrator kit  and eluted with pre-warmed nuclease-free water. The RNA integrity was detected by Fragment Analyzer. Approximately 1 μg RNA was kept as pre-enrichment samples, while the remaining was purified with streptavidin beads and the post-enrichment samples were purified by TRIzol Reagent.
Total RNAs were used for library construction and libraries were constructed by NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) following the manuyfacturer's instructions.

treatment_protocol: HEK293T cells stably expressing TIA1-miniSOG, G2BP2-miniSOG or miniSOG-DDX6 were cultured to 90% confluency. To induce stress, cells were incubated in complete media supplemented with  0.5 mM sodium arsenite for 40 min in 37°C. Cells were then washed once with 1× HBSS and the medium was replaced by HBSS containing 10 mM propargylamine (PA)  and 0.5 mM sodium arsenitel. For unstressed samples, cells were rinsed with HBSS once and then incubated in HBSS containing 10 mM PA. After 5 min of incubation under 37°C, cells were illuminated with blue LED (emission peak 465-475 nm, 24 mW/cm2) for 15 min at room temperature, samples without PA probe were set as control.

tag: cell line

value: miniSOG-DDX6 stably expression

value: 0.5 mM arsenite, 1 hr


title: MB3807-rna

status: Public on Sep 29 2024

type: SRA

city: Houston

first: Marco

last: Gallo

state: TX

address: 1102 Bates Avenue

department: Pediatrics

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
Fastqs were processed to hic files using Juicer v1.6.
Contact domains were annotated from hic files using Arrowhead from Juicer Tools v1.19.02 with parameters ‘--ignore-sparsity -k SCALE’ for the following data resolutions (kb): 10, 25, 50, 100.
Loops were annotated from hic files using HiCCUPS from Juicer Tools v1.19.02 with parameters ‘--cpu -m 4096 --ignore-sparsity -k SCALE’ for resolutions (kb): 10, 25.
Compartments were annotated from hic files using the leading eigenvectors of the Juicer Tools Pearsons with parameters ‘SCALE BP 50000 -p’
Boundary scores were annotated from 50-kb contact matrices using Robustad v1.0
RNA-seq alignment: reads aligned to hg38 (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set) using HISAT2 (v2.1.0) with parameters ‘--rna-strandness RF --downstream-transcriptome-assembly’
RNA-Seq quantification: SAM output was sorted, converted to BAM, and indexed using samtools (v1.9). A counts table was prepared using the count function of HTSeq (v0.13).
RNA-Seq differential expression testing: Limma with Voom transformation (v3.44)
RNA-Seq coverage: BigWig tracks were generated using DeepTools bamCoverage with parameters --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --binSize 1. Separate files for positive and negative strand were generated with parameters --filterRNAstrand "forward" or  --filterRNAstrand "reverse"
Assembly: hg38, GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set
Supplementary files format and content: TSV; BoundaryScores.max.50kb.tsv: Summary table of RobusTAD scores for all samples
Supplementary files format and content: BDG; BoundaryScores.max.50kb.bedgraph: BEDGRAPH format values from RobusTAD boundary quantification
Supplementary files format and content: WIG; BoundaryScores.max.50kb.wig: WIGGLE format values from RobusTAD boundary quantification
Supplementary files format and content: TSV; TADBoundaryCalls.50kb.tsv: Summary table of RobusTAD boundaries for all samples
Supplementary files format and content: WIG; eigenvalue_allChr_50kb.wig: Eigenvalues of leading PC indicating genome compartmentalization
Supplementary files format and content: TSV; compartment_eigenvalues.tsv: Summary table of eigenvalues for all samples
Supplementary files format and content: HIC; inter_30.hic: Hi-C contact maps generated by Juicer
Supplementary files format and content: BigWig; pos.bw: RNA-seq coverage corresponding to the positive strand
Supplementary files format and content: BigWig; neg.bw: RNA-seq coverage corresponding to the negative strand
Supplementary files format and content: TSV; limma.*.wrt.*.tsv: Differential expression calls between tumor subgroups generated using limma
Supplementary files format and content: TSV; union_arrowhead_scores.tsv: Summary table of Arrowhead contact domain scores for all samples
Supplementary files format and content: BEDPE; merged_loops.bedpe: Loop calls generated using HiCCUPS
Supplementary files format and content: TSV; union_hiccups_scores.tsv: Summary table of HiCCUPS loop scores for each sample

molecule: total RNA

organism: Homo sapiens

source_name: brain

growth_protocol: The majority of samples were uncultured, primary patient tissue. The brain tissue culture was grown as described previously (Michealraj et al. Cell. 2020; PMID: 32445698).

extract_protocol:
Approximately 2.5M cells were used for In-situ Hi-C library approach (Rao et al. Cell. 2014; PMID: 25497547) with library preparation performed as described previously (Johnston et al. Genome Research. PMID: 31249064). Hi-C libraries were sequenced at 150 bp PE with a Hi-Seq X instrument (Illumina) at McGill Genome Centre (Montreal, QC).
In-situ Hi-C
Kapa RNA HyperPrep kit prepared and sequenced at Ontario Institute for Cancer Research (OICR)
Paired-end, stranded RNA-Seq

tag: tissue

value: brain

tag: Sex

value: F

tag: disease

value: medulloblastoma

tag: disease subgroup


title: mouse cardiomyocyte_siRNA-ppp2r5d_1

status: Public on Sep 30 2024

type: RNA

city: Shanghai

first: Fang

last: Lin

address: 150 Ji Mo Lu, Pu Dong

department: Shanghai East Hospital

country: China

institute: Tongji University School of Medicine, Shanghai

description: gene expression 64 hours after transfection

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was   fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x   Agilent fragmentation buffer and 2x Agilent blocking agent following the   manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of   2x Agilent hybridization buffer was added to the fragmentation mixture and   hybridized to Agilent  Mouse Gene Expression (8x60K) Microarray Kit for 17 hours at 65°C in a   rotating Agilent hybridization oven. After hybridization, microarrays were washed 1   minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C   GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray   Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area   61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set   to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1   (Agilent) using default parameters to obtain background subtracted and spatially   detrended Processed Signal intensities as the raw data. Raw data were normalized   in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2   samples flagged as Detected were maintained.

label: Cyanine 3

organism: Mus musculus

source_name: Cardiomyocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color   Low RNA Input Linear Amplification PLUS kit (Agilent) according to the   manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,   Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop   ND-1000 Spectrophotometer.

growth_protocol: Cells were cultured in DMEM (Hyclone) supplemented with 2% fetal bovine serum (FBS) at 37 °C in a humidified 5% CO2 – 95 % air atmosphere.

extract_protocol: Total RNA was prepared using the mirVanaTM RNA Isolation Kit (Thermo Scientific, AM1556) following the manufacturer's recommendations. The RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific), and the RNA integrity was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The interfering RNA against Ppp2r5d (Case) or the negative control siRNA (Control) were transfected into MCMs with Lipofectamine™ RNAiMAX transfection reagent. Forty-eight hours after transfection, the medium was changed to glucose-free media. The samples were then collected for a microarray gene expression study after overnight incubation.

tag: treatment


title: mouse cardiomyocyte_siRNA-nc_1

value: siRNA-nc


title: MB4079-rna

value: M


title: miniSOG-DDX6_HEK293T, arsenite-stress, omit probe, post-enrichment, rep1

city: Beijing

description: Column Name: mS-DDX6_AS_noprobe_enrich1

tag: genotype


title: gw null-2 -/- rep.2

city: Bunkyo-ku

first: Eriko

last: Matsuura

state: Tokyo

address: Yayoi

department: IQB

country: Japan

institute: The University of Tokyo

data_processing:
Basecalling with Zebracall　（version：1.0.11.83）
Raw data with adapter sequences or low-quality sequences was filtered. We first went through a series of data processing to remove contamination and obtain valid data. This step was completed by SOAPnuke software developed by BGI. SOAPnuke software filter parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --minReadLen 100", steps of filtering: 1. Filter adapter: if the sequencing read matches 25.0% or more of the adapter sequence (maximum 2 base mismatches are allowed), cut the adapter; 2. Filter read length: if the length of the sequencing read is less than 100 bp, discard the entire read; 3. Remove N: if the N content in the sequencing read accounts for 0.1% or more of the entire read, discard the entire read; 4. Filter low-quality data: if the bases with a quality value of less than 20 in the sequencing read account for 40.0% or more of the entire read, discard the entire read; 5. Obtain Clean reads: the output read quality value system is set to Phred+33.
Reads were mapped to Drosophila melanogaster BDGP6.28 genome using STAR (Version 2.7.0a)
Mapped reads were counted using featureCounts or RSEM
Assembly: Drosophila melanogaster BDGP6.28
Supplementary files format and content: Feature count text files contain two columns: 1. gene name, 2.read counts
Supplementary files format and content: RSEM count text files contain two columns: 1. transcript name, 2.read counts

organism: Drosophila melanogaster

source_name: Whole body of first instar larvae

extract_protocol:
First instar larvae were collected and extract total RNA by RNA basic kit (FastGene)
Total RNA libraries were prepared using the Strand-Specific mRNA Library Preparation method by BGI. mRNA was first purified using oligo dT-beads, fragmented, and then used to synthesize cDNA. The resulting double-stranded cDNA fragments underwent end-repair, followed by the addition of a single 'A' nucleotide to the 3' ends of the blunt fragments. Next, adaptors were ligated to the cDNAs, which were subsequently amplified by PCR.

treatment_protocol: Fly culture and crosses were carried out at room temperature.

value: Whole body of first instar larvae

value: gw null-2 -/-


title: Serum_82w_rep4

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

institute: Hirosaki University

description: gene expression in serum of 82-week-old mouse

hyb_protocol: SurePrint G3 mouse miRNA microarray slides (8 × 60 K, Ver.21.0) were hybridized with the Cy3-labeled miRNA in a hybridization solution prepared with a Gene Expression Hybridization Kit (Agilent Technologies) for 20 hours at 55°C in a rotating hybridization oven (Agilent Technologies), according to the manufacturer’s instructions. After hybridization, microarray slides were washed for 5 min at room temperature with GE Wash Buffer 1 (Agilent Technologies) and for 5 min at 37°C with GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G4900DA) (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2 μm high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0 (Agilent Technologies) using default parameters (Protocol name: miRNA_1105_Oct12 and Grid name: 070155_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Serum

label_protocol: Cyanine 3(Cy3)-labeled miRNAs were synthesized from each 1.8 ng of serum RNA in 8-week-old, 82-week-old, or 102-week-old mice using a miRNA Complete Labeling Reagent and Hyb kit (Agilent Technologies), according to the manufacturer’s instructions.

extract_protocol: The serum obtained above was filtered through a 0.20 μm filter, and RNAs derived from EVs were extracted from 200 μl of serum using exoRNeasy midi kit (cat. no. 77144, Qiagen). The concentration of extracted EVs-derived RNAs was determined using Qubit™ microRNA Assay Kits (cat. no. Q32880, ThermoFisher Scientific) and Qubit 4 Fluorometer (cat. no. Q33238, ThermoFisher Q33238, ThermoFisher Scientific) according to the manufacturer's protocol. To confirm the size of RNAs in serum EVs, the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.) and the Agilent RNA 6000 Pico kit (cat. no. 5067-1513, Agilent Technologies, Inc.) were used to perform RNAs electrophoresis according to the manufacturer's protocol.

treatment_protocol: Blood obtained from the heart was collected in BD Microtainer tubes with serum separator additive BD Microgard closure (Becton Dickinson Biosciences). Blood was then centrifuged at 6000 × G at room temperature for 3 min, and serum was collected.

tag: gender

value: male

tag: age

value: 82 weeks


title: Serum_102w_rep3

description: gene expression in serum of 102-week-old mouse

value: 102 weeks


title: gw null-2 -/- rep.1


title: MB4010-rna


title: Serum_102w_rep1


title: gw null-2 -/+ rep.2

value: gw null-2 -/+


title: Serum_102w_rep2


title: MB3724-rna

value: SHH


title: Serum_82w_rep2


title: MB3716-rna


title: miniSOG-DDX6_HEK293T, arsenite-stress, label, pre-enrichment, rep2

description: Column Name: mS-DDX6_AS_label_input2


title: gw null-2 +/+ rep.2

value: gw null-2 +/+


title: Serum_82w_rep3


title: miniSOG-DDX6_HEK293T, arsenite-stress, label, pre-enrichment, rep1

description: Column Name: mS-DDX6_AS_label_input1


title: Serum_82w_rep5


title: MB3761-rna


title: Serum_8w_rep5

description: gene expression in serum of 8-week-old mouse

value: 8 weeks


title: Serum_8w_rep2


title: Serum_8w_rep4


title: MB3760-rna


title: MB3697-rna


title: gw null-2 +/+ rep.1


title: Serum_82w_rep1


title: Serum_8w_rep1


title: ruvcRNA3

city: Wuhan

first: Xinya

last: Du

state: Hubei

address: Huazhong Agricultural University, No. 1, Shishishan Street, Hongshan District

institute: Huazhong Agricultural University

data_processing:
RNA extraction, library construction, sequencing , and analysis were performed by Beijing Novogene
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp 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.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package 3.24.3). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as he threshold for significantly differential expression.
Assembly: ASM912v1 Ralstonia solanacearum
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Ralstonia solanacearum

source_name: Cell precipitation

growth_protocol: Strains were grown on Casamino Acids-Peptone-Glucose (CPG) medium at 28℃ 190 revolutions per minute (rpm) to OD600=1

extract_protocol:
Total RNA was extracted from the frozen the cell precipitation with TRNzol reagent.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Centrifugation at 12000 revolutions per minute (rpm) to collect bacterial cell precipitation and quick-frozen preservation

value: Cell precipitation

value: RuvC mutant


title: Serum_8w_rep3


title: miniSOG-DDX6_HEK293T, arsenite-stress, label, post-enrichment, rep2

description: Column Name: mS-DDX6_AS_label_enrich2

value: miniSOG-DDX6 stably expression

value: 0.5 mM arsenite, 1 hr


title: ruvcRNA2


title: ruvcRNA1


title: GMI1000RNA2

value: wild type


title: gw null-2 -/+ rep.1


title: miniSOG-DDX6_HEK293T, unstressed, omit probe, post-enrichment, rep2

description: Column Name: mS-DDX6_basal_noprobe_enrich2

value: unstressed


title: miniSOG-DDX6_HEK293T, arsenite-stress, label, post-enrichment, rep1

description: Column Name: mS-DDX6_AS_label_enrich1


title: miniSOG-DDX6_HEK293T, unstressed, omit probe, post-enrichment, rep1

description: Column Name: mS-DDX6_basal_noprobe_enrich1


title: GMI1000RNA3


title: MB3692-rna

value: brain

value: medulloblastoma


title: Ac, HiC_seq-7

city: Shenzhen

first: Hao

last: Chen

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology (SUSTech)

library_source: genomic

data_processing:
The genome size of dinoflagellate A. carterae was first estimated by using genome survey sequencing and the genome was firstly assembled using Pacbio HiFi sequencing reads and further refined with Hi-C technology to determine the contig position on scaffolds. A contig-level assembly of the resulting PacBio CCS reads with default parameters was obtained using Hifiasm software. Assembled contigs were further joined into scaffolds at the pseudo-chromosome level using Hi-C sequencing data with Juicer (default parameters) and 3D-DNA (-m haploid -q 0 -r 0).
Repeat sequences were annotated using a combination of homology-based and de novo methods. RepeatMasker (v4.0.7) and RepeatProteinMask (v4.0.7) were used to identify known repeat sequences through searching against RepBase v21.12 library. On the other hand, in the de novo step, de novo repeat sequence libraries were established using RepeatModeler and LTR_FINDER v1.06, followed by de novo prediction with the Repeatmasker program. Protein-coding genes were identified using a combination of homology-based, de novo and transcriptome-based strategies.
Raw DIP-seq and 5hmU-chemical-seq data were first processed using TrimGalore (version 0.6.7) to remove adapters and low-quality bases (-q 25). The cleaned sequence reads were then mapped to the de novo reference genome (Acart.genome.v1) using Bowtie2 local alignments. Resultant SAM formatted files were converted to the BAM format using Samtools. Enriched regions were identified with MACS2 (-g 1.2e9 -q 0.05). Motif discovery was performed using MEME (-mod zoops -minw 4 -maxw 10 -nmotifs 10 -dna) and the genomic distribution of peaks was analyzed using Bedtools.
For RNAseq data of 2-4P treatment, TrimGalore (version 0.6.7) was used to remove adapters and low-quality base (-q 25) at first. Pre-processed reads of RNA-seq were subjected to alignment against Acart.genome.v1 using software STAR (version 2.7.10a), allowing for no more than 2 mismatches. The sorted mapping files of RNA-seq were used for quantification with StringTie (v2.1.7). Next, the obtained read counts were converted to TPM (transcripts per million). The R package DESeq2 was used to perform differential gene expression of RNA-seq datasets.
For WGBS analysis, bisulfite-treated reads were filtered to remove adaptors and low-quality bases. The resulting clean reads were aligned to the A. carterae genome (Acart.genome.v1) using BS-Seeker2 (v2.1.8, --aligner=bowtie2 --local). The CGmap output file generated by BS-Seeker2 for methylation calling from the mapping result was utilized in downstream analysis.
Assembly: Ac.genome.v1.fa.gz

molecule: genomic DNA

organism: Amphidinium carterae

source_name: Ac, HiC_seq

growth_protocol: Dinoflagellate Amphidinium carterae and  Symbiodinium sp. were cultured in f/2 medium at a constant temperature of 23°C. The lighting conditions were maintained under a 12:12 hour light-dark cycle with a photon flux density of 50µmol·m-2·s-1.

extract_protocol:
Total RNA was extracted from A. carterae and Symbiodinium sp. using RNAzol®RT (MRC) according to the manufacturer’s protocol.  Genomic DNA of A. carterae and Symbiodinium sp. were extracted via a CTAB method. Briefly, cell pellets were resuspended in 600 µl of preheated CTAB extraction buffer (100 mM Tris pH 8.0, 20 mM EDTA pH 8.0, 2 M NaCl, 2% (w/v) CTAB, 2% (w/v) Polyvinylpyrrolidone. Next, 10 µl of 20 mg/ml RNase A (NEB) was added, and the mixture was incubated at 37°C for 2 hours, followed by the addition of 20 µl of Proteinase K (NEB) and another incubation at 65°C overnight. Equal volumes of phenol: chloroform: isoamyl alcohol (25: 24: 1) (Solarbio Life Sciences, Beijing, China) were added. After centrifugation, the upper phase was transferred to a new Eppendorf tube, mixed with 2/3 volume of isopropanol, and then centrifuged at 13000 rpm for 10 minutes. The pellet was washed with 700 µl of 75% ethanol and 80% ethanol sequentially. Finally, the DNA was eluted in 20 µl of ddH2O.
1. A. carterae Genome Construction: gDNA extracted from A. carterae was sent to Beijing Genomics Institute (BGI, Shenzhen, China) for Pacbio HiFi and Hi-C library construction. 2. Transcriptome Sequencing: For short-read RNA-seq and long-read sequencing of A. carterae, isolated total RNA from A. carterae cells was sent to BGI for strand-specific mRNA library and PacBio library construction. 3. 2,4-Pyridinedicarboxylic Acid Treatment: Total RNA of A. carterae was treated with Ribo-off® rRNA depletion kit (N409, Vazyme Biotech, Nanjing, China) and sent to BGI or Novogene Company (Beijing, China) for stranded RNA-seq library construction. 4. 5hmU-DIP and 5fU-DIP Library Construction: A. carterae gDNA was sonicated, end-repaired, adapter-ligated using the VAHTS® Universal DNA Library Prep Kit for Illumina V3 (ND607, Vazyme Biotech, Nanjing, China), and subjected to 5hmU-DIP using anti-5hmU antibody and Protein A/G beads, followed by protease K digestion and DNA purification. For the parallel 5fU-DIP, ACT+BF4- oxidation was performed first to fully convert gDNA 5hmU into 5fU, with the subsequent steps identical to the 5hmU-DIP procedures. 5. 5hmU-Chemical-Seq: For the 5hmU-chemical-seq approach, we employed both commercial and modified adapters. The modified adapters were designed with a 5'-end amino group and a 3'-phosphorylated oligodeoxynucleotide, annealed to create final adapters 5N3A3 and 5N3A4. A. carterae gDNA was fragmented, end-repaired, and ligated to these pre-annealed adapters. After ligation, DNA purification was performed, followed by ACT+BF4- oxidation treatment. The oxidized DNA samples were then biotinylated, purified, and captured using streptavidin magnetic beads. After washing, the DNA was eluted and amplified for subsequent sequencing. For controls, non-oxidized DNA was prepared using commercial adapters and amplified using the VAHTS® Universal DNA Library Prep Kit for Illumina V3.  6. WGBS Library Construction: A. carterae gDNA was sent to Novogene Biotech Co., Ltd (China) for WGBS libraries construction according to a standard protocol. Briefly, gDNA was spiked with unmethylated lambda DNA and sheared to average 200 bp size, followed by bisulphite treatment using the Accel-NGS® Methyl-Seq DNA Library Kit (Swift Biosciences). Following this treatment, the DNA was subjected to end-repair, adapter ligation, and PCR amplification.

treatment_protocol: To inhibit the synthesis of 5hmU in A. carterae, cells in the exponential stage were diluted to a concentration of 1 × 10^5 cells/ml in a 6-well plate and treated with 0.5 mM 2,4-pyridinedicarboxylic acid (2-4P) in f/2 medium.

tag: experimental

value: Ac, HiC_seq


title: Ac, HiC_seq-8


title: Ac, HiC_seq-6


title: MB3690-rna

value: F


title: Ac, HiC_seq-5


title: miniSOG-DDX6_HEK293T, unstressed, label, pre-enrichment, rep2

description: Column Name: mS-DDX6_basal_label_input2


title: MB3689-rna

value: M


title: Ac, HiC_seq-4


title: Ac, HiC_seq-3


title: MB3687-rna


title: MB3670-rna


title: miniSOG-DDX6_HEK293T, unstressed, label, pre-enrichment, rep1

description: Column Name: mS-DDX6_basal_label_input1


title: Ac, HiC_seq-1


title: miniSOG-DDX6_HEK293T, unstressed, label, post-enrichment, rep2

description: Column Name: mS-DDX6_basal_label_enrich2


title: miniSOG-DDX6_HEK293T, unstressed, label, post-enrichment, rep1

description: Column Name: mS-DDX6_basal_label_enrich1


title: MB3695-rna


title: GMI1000RNA1


title: MB3693-rna


title: MB3667-rna


title: G3BP2-miniSOG_HEK293T, arsenite-stress, omit probe, post-enrichment, rep2

description: Column Name: G3BP2-mS_AS_noprobe_enrich2

value: G3BP2-miniSOG stably expression


title: MB3662-rna


title: WT_d1_DLK_UN_3

city: San Francisco

first: Trent

middle: A.

last: Watkins

state: CA

address: 675 Nelson Rising Lane, Rm 214A

institute: University of California at San Francisco

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: A single tab-delimited text file contains counts for all samples.

source_name: retina

extract_protocol:
At 3, 7, or 10 days days post-crush (dpc), the retinae were quickly dissected out in 1X PBS and snap frozen in dry ice-ethanol bath and stored in -80°C until ready to be processed for RNA extraction. RNA was extracted using the Qiagen RNeasy micro kit (#74004).
RNA libraries were prepared according to Novogene procedures by polyA capture (or rRNA removal) and reverse transcription of cDNA.

value: retina

tag: time

value: 1 d

value: wildtype

value: ddDLK; uninjured


title: WT_d1_DLK_UN_2


title: WT_d3_YFP_UN_5

value: 3 d

value: ddYFP; uninjured


title: MB3661-rna

value: SHH


title: WT_d3_YFP_CR_5

value: ddYFP; optic nerve crush


title: WT_d3_DLK_CR_5

value: ddDLK; optic nerve crush


title: WT_d3_YFP_UN_4


title: WT_d1_DLK_UN_4


title: G3BP2-miniSOG_HEK293T, arsenite-stress, omit probe, post-enrichment, rep1

description: Column Name: G3BP2-mS_AS_noprobe_enrich1

value: 0.5 mM arsenite, 1 hr


title: MB3612-rna


title: Ac, HiC_seq-2


title: WT_d3_YFP_CR_4


title: WT_d3_YFP_CR_3


title: G3BP2-miniSOG_HEK293T, arsenite-stress, label, pre-enrichment, rep2

description: Column Name: G3BP2-mS_AS_label_input2


title: WT_d3_YFP_UN_3


title: WT_d3_YFP_UN_2


title: G3BP2-miniSOG_HEK293T, arsenite-stress, label, post-enrichment, rep2

description: Column Name: G3BP2-mS_AS_label_enrich2


title: G3BP2-miniSOG_HEK293T, arsenite-stress, label, post-enrichment, rep1

description: Column Name: G3BP2-mS_AS_label_enrich1


title: SW620_4G

city: Tel Aviv

first: Ariel

last: Munitz

address: Klachkin 35

country: Israel

institute: Tel Aviv University

data_processing:
RNA libraries were generated using CEL-seq Library protocol, and sequenced on Illumina NextSeq 550, 50 single-end run.
The reads  were mapped to the homo sapiens, GRCh38 genome using Tophat2 version 2.1.0.
Only uniquely mapped reads were counted to genes, using 'HTSeq- count' package version 0.6.1 with ‘union’ mode.
Normalization was conducted using DESeq2 R package version 1.10.0.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: SW620 conditioned media donor 4

growth_protocol: Human eosinophils were isolated from the peripheral blood of healthy donors using MACS eosinophil negative selection isolation kit (Miltenyi Biotec) according to the manufacturer’s instructions. Eosinophil purity was assessed by flow cytometry using APC-conjugated anti-CD45, PE-conjugated anti–Siglec-8, APC-Cy7-conjugated CCR3 antibodies and DAPI. Eosinophil purity and viability were >95%.

extract_protocol:
Human eosinophil RNA was isolated using TRIzol (Ambion) supplemented with RNasin ribonuclease inhibitor (Promega). RNA was extracted by the addition of chloroform followed by centrifugation and addition of absolute ethanol to the top layer. Thereafter, the fluid was transferred to PureLink RNA mini kit (Invitrogen) and processed according to manufacturer’s instructions. TheRNAintegrity number (RIN) was analyzed using Bioanalyzer and only samples of RIN>6.3 were used. RNA libraries were generated using Cell-seq Library protocol, and sequenced on Illumina HiSeq2500, 50 single-end run. Sample preparation, sequencing, quality control, and normalization were conducted by the "Technion Genome Center," Life Science and Engineering Interdisciplinary Research Center, Technion, Haifa, Israel.
RNA libraries were prepared for sequencing using Cell-seq protocols

treatment_protocol: Human peripheral blood eosinophils were stimulated with IL-3 (0-100 ng/ml, Peprotech, Rehovot, IL) in the presence or absence of tumor cell conditioned media for 24 hrs. Thereafter, the cells were centrifuged (1500 rpm, 5 min, 4°C) and the cells (2 X 105 cells) were suspended in 200 ml of HBSS supplemented with 1% BSA, 0.1% sodium azide. The cells were stained with mouse anti-human CD11a/CD18-APC or isotype matched control (Biolegend, USA). Data were analyzed using Kaluza analysis software on 10,000-15,000 acquired events. Surface molecule expression was calculated by defining the delta mean fluorescent intensity between the specific antibody stain and the isotype-matched control antibody.

tag: subject

value: donor 4

value: Peripheral human blood

tag: cell type

value: Eosinophils

value: SW620 conditioned media


title: WT_d3_DLK_UN_4


title: MB3510-rna

value: brain

value: medulloblastoma


title: TIA1-miniSOG_HEK293T, arsenite-stress, omit probe, post-enrichment, rep2

description: Column Name: TIA1-mS_AS_noprobe_enrich2

value: TIA1-miniSOG stably expression


title: WT_d3_YFP_CR_1

value: retina


title: WT_d3_YFP_UN_1


title: SW620_3G

source_name: SW620 conditioned media donor 3

value: donor 3


title: WT_d3_YFP_CR_2

value: wildtype


title: WT_d3_DLK_CR_4


title: SW620_25G

source_name: SW620 conditioned media donor 25

value: donor 25


title: G3BP2-miniSOG_HEK293T, arsenite-stress, label, pre-enrichment, rep1

description: Column Name: G3BP2-mS_AS_label_input1

value: G3BP2-miniSOG stably expression


title: WT_d3_DLK_UN_2

value: 3 d

value: ddDLK; uninjured


title: WT_d3_DLK_CR_3


title: SW620_23G

source_name: SW620 conditioned media donor 23

value: donor 23


title: WT_d3_DLK_CR_2

value: ddDLK; optic nerve crush


title: TIA1-miniSOG_HEK293T, arsenite-stress, label, pre-enrichment, rep2

description: Column Name: TIA1-mS_AS_label_input2

value: 0.5 mM arsenite, 1 hr


title: WT_d3_DLK_UN_3


title: TIA1-miniSOG_HEK293T, arsenite-stress, omit probe, post-enrichment, rep1

description: Column Name: TIA1-mS_AS_noprobe_enrich1


title: WT_d1_DLK_UN_5

value: 1 d


title: SW620_18G

source_name: SW620 conditioned media donor 18

value: donor 18

value: Peripheral human blood


title: WT_d3_DLK_CR_1


title: TIA1-miniSOG_HEK293T, arsenite-stress, label, post-enrichment, rep2

description: Column Name: TIA1-mS_AS_label_enrich2


title: WT_d3_DLK_UN_1


title: TIA1-miniSOG_HEK293T, arsenite-stress, label, pre-enrichment, rep1

description: Column Name: TIA1-mS_AS_label_input1


title: P_d10_YFP_CR_5

value: Pten-fl/fl

value: ddYFP; optic nerve crush


title: P_d10_YFP_UN_5

value: ddYFP; uninjured


title: CS + Control time(dpi):4 rep:A [P15]

city: Harpenden

first: Daniel

last: Smith

state: Hertfordshire

address: West Common

department: IDE

country: United Kingdom

institute: Rothamsted Research

description: 150bp paired reads

data_processing:
HiSAT2 mapping using HPC EasyBuild v2.2.1-foss-2019b to IWGSC Chinese Spring v2.1
SAMtools format conversion, sorting & indexing using HPC Easybuild v1.10-GCC-9.3.0
Gene counts using HPC Easybuild SubRead featureCounts v2.0.0-GCC-8.3.0 and IWGSC annotation v43 for assembly v2.1, collated in file: takeAllCounts_wheat.tsv
Library normalisation and differential expression (DE) calling was carried out using the Bioconductor package DESeq2
Gene Ontology (GO) enrichment analysis was performed with web tools at GeneOntology (http://www.geneontology.org)using the Panther knowledgebase
Assembly: Chinese Spring Wheat IWGSC v2.1, annotation v43
Supplementary files format and content: takeAllCounts_wheat.tsv, featureCount gene counts

molecule: polyA RNA

organism: Triticum aestivum

source_name: Chinese Spring

growth_protocol: Wheat seeds cv. Chinese Spring were surface sterilised with sodium hypochlorite and pre-germinated in a controlled environment growth chamber cabinet (20 °C day, 16 °C night, 16 hr light cycle) for two days. Three pre-germinated seeds were transplanted onto a square petri dish plate (12 cm x 12 cm) containing 1.5 % (w/v) water agar. Plates were placed horizontally in a growth cabinet (20 °C day, 16 °C night, 16 hr light cycle).

extract_protocol:
Following confocal assessment, 1 cm root samples at the same stage of fungal colonisation (harvested from the same plate) were pooled together to create a single sample for RNA extraction. RNA was extracted from frozen root material using the E.Z.N.A.® Plant RNA Kit with the associated RNase-free DNase I Set (Omega-Biotek, USA), following the standard protocol provided. RNA quality was assessed based on the RNA Integrity Number (RIN), measured using the Bioanalyser 2100 with the corresponding RNA 6000 Nano Kit (Agilent, USA), as per manufacturer instructions.
mRNA library preparation was carried out by Novogene (China) using the Novogene RNA Library Prep Set (PT042) for polyA enrichment.

treatment_protocol: After four days, one root from each plant was inoculated with a fungal plug (4 cm x 0.5 cm) cut from the leading edge of a fungal colony growing on 1.5 % water agar . Five replicates were prepared for each treatment. Roots were sampled daily from 2-6 dpi. Briefly, two 1 cm root samples were harvested from the inoculated area and snap frozen in liquid nitrogen for RNA extraction

value: root

tag: cultivar

value: var. Chinese Spring


title: SW620_11G

source_name: SW620 conditioned media donor 11

value: donor 11

value: Eosinophils

value: SW620 conditioned media


title: P_d10_YFP_UN_3

value: retina


title: SW480_3F

source_name: SW480 conditioned media donor 3

value: donor 3

value: SW480 conditioned media


title: TIA1-miniSOG_HEK293T, arsenite-stress, label, post-enrichment, rep1

description: Column Name: TIA1-mS_AS_label_enrich1

value: TIA1-miniSOG stably expression


title: SNC_2_5-hic

source_name: brain tissue culture

value: brain tissue culture

value: M

value: medulloblastoma


title: P_d10_YFP_CR_3


title: SW480_25F

source_name: SW480 conditioned media donor 25

value: donor 25


title: SW620_24G

source_name: SW620 conditioned media donor 24

value: donor 24

value: Peripheral human blood


title: P_d10_YFP_CR_2

value: Pten-fl/fl

value: ddYFP; optic nerve crush


title: P_d10_YFP_UN_4

value: ddYFP; uninjured


title: P_d10_YFP_UN_2


title: SW480_21F

source_name: SW480 conditioned media donor 21

value: donor 21


title: MBSF7-hic

source_name: brain

value: brain


title: P_d10_YFP_CR_4


title: MB4174-hic


title: P_d10_DLK_UN_5

value: ddDLK; uninjured


title: P_d10_YFP_UN_1


title: P_d10_DLK_CR_5

value: ddDLK; optic nerve crush


title: SW480_11F

source_name: SW480 conditioned media donor 11

value: donor 11

value: Eosinophils


title: MB4143-hic

value: SHH


title: SW480_18F

source_name: SW480 conditioned media donor 18

value: donor 18

value: SW480 conditioned media


title: P_d10_DLK_UN_1

value: retina


title: MB4141-hic

value: M

value: medulloblastoma


title: SW403_3E

source_name: SW403 conditioned media donor 3

value: donor 3

value: SW403 conditioned media


title: P_d10_DLK_UN_4

source_name: retina

value: Pten-fl/fl


title: P_d10_DLK_UN_3


title: P_d10_DLK_CR_1


title: P_d10_DLK_CR_3


title: MB4132-hic


title: SW403_24E

source_name: SW403 conditioned media donor 24

value: donor 24

value: Peripheral human blood


title: P_d10_DLK_CR_4


title: MB4037-hic


title: SW403_23E

source_name: SW403 conditioned media donor 23

value: donor 23


title: P_d10_DLK_CR_2


title: SW403_21E

source_name: SW403 conditioned media donor 21

value: donor 21


title: MB4079-hic

value: brain


title: P_d7_DLK_CR_1

value: 7 d

value: ddDLK; optic nerve crush


title: MB4036-hic

value: F

value: WNT


title: SW403_18E

source_name: SW403 conditioned media donor 18

value: donor 18

value: Eosinophils


title: P_d7_DLK_UN_1

value: retina

value: ddDLK; uninjured


title: P_d7_DLK_UN_5


title: P_d7_DLK_CR_5


title: MB4010-hic

value: M

value: medulloblastoma


title: SW403_11E

source_name: SW403 conditioned media donor 11

value: donor 11

value: SW403 conditioned media


title: P_d7_DLK_UN_4

value: Pten-fl/fl


title: MB3807-hic


title: P_d7_DLK_UN_3


title: SW1417_4H

source_name: SW1417 conditioned media donor 4

value: donor 4

value: Peripheral human blood

value: SW1417 conditioned media


title: SW1417_3H

source_name: SW1417 conditioned media donor 3

value: donor 3


title: P_d7_DLK_CR_3

value: 7 d


title: P_d7_DLK_UN_2


title: MB3761-hic

value: brain


title: MB3760-hic


title: P_d10_DLK_UN_2


title: SW1417_25H

source_name: SW1417 conditioned media donor 25

value: donor 25


title: P_d7_YFP_UN_3

value: ddYFP; uninjured


title: P_d7_DLK_CR_2

value: ddDLK; optic nerve crush


title: MB3724-hic

value: F

value: SHH


title: P_d7_YFP_CR_3

value: retina

value: ddYFP; optic nerve crush


title: P_d7_YFP_UN_2


title: SW1417_24H

source_name: SW1417 conditioned media donor 24

value: donor 24

value: Eosinophils


title: MB3716-hic

value: medulloblastoma


title: P_d7_YFP_CR_2

value: Pten-fl/fl


title: SW1417_23H

source_name: SW1417 conditioned media donor 23

value: donor 23


title: SW1417_21H

source_name: SW1417 conditioned media donor 21

value: donor 21

value: Peripheral human blood


title: MB3697-hic


title: P_d7_YFP_CR_5


title: P_d7_YFP_UN_1


title: P_d7_YFP_CR_1


title: P_d7_YFP_UN_5


title: P_d7_DLK_CR_4


title: MB3693-hic

value: M


title: P_d7_YFP_CR_4

value: 7 d


title: SW1417_11H

source_name: SW1417 conditioned media donor 11

value: donor 11

value: SW1417 conditioned media


title: scRNA_seq_WT_lung_ILC2s

first: Yuan

last: Jin

address: 38 Xueyuan Road

institute: Peking University Health Science Center

library_source: transcriptomic single cell

data_processing:
The reads were processed using Cell Ranger (version 6.1.1) for demultiplexing, alignment to mm10, barcode processing, and cell quality control, ultimately generating a feature-barcode matrix.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: lung

extract_protocol:
Wild-type or Pac1-/- mice were sacrificed and live lung ILC2s (Lineage- CD90.2+ ST2+ Sca-1+) sorted. Next, all wild-type or Pac1-/- ILC2s were pooled, counted and viability-assessed (>98%). Subsequently, 13,000 wild-type or Pac1-/- ILC2s were partitioned into the GemCode instrument, where individual cells were lysed and mixed with beads carrying unique barcodes in individual oil droplets.
Libraries were prepared using a Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10× Genomics) according to the manufacturer’s protocol.

value: lung

value: primary cells

value: WT


title: scRNA_seq_Pac1_KO_lung_ILC2s


title: SFM_4A

source_name: serum-free media (SFM) donor 4

value: donor 4

value: serum-free media (SFM)


title: SFM_3A

source_name: serum-free media (SFM) donor 3

value: donor 3


title: MB3689-hic

source_name: brain

value: brain


title: SFM_24A

source_name: serum-free media (SFM) donor 24

value: donor 24

value: Eosinophils


title: NC3,replicate2

city: nanjing

first: Zhu

last: Hongjing

address: hanzhong road

institute: nanjing medical university

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
RNAseq reads were aligned to the mm10 genome using STAR.
Read counts for individual gene of each sample were produced with HTSeq-count
Assembly: mm10
Supplementary files format and content: txt(gene expression of all sample)

extract_protocol:
RNA was extracted using Trizol following the manufacturer's protocol.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: primary microglia


title: NC1,replicate1


title: SFM_23A

source_name: serum-free media (SFM) donor 23

value: donor 23


title: KO2, replicate2

value: Cx3cr1CreERT2 Ythdf2fl/fl


title: MB3687-hic

value: F

value: medulloblastoma


title: MB3695-hic

value: M

value: SHH


title: SFM_21A

source_name: serum-free media (SFM) donor 21

value: donor 21

value: Peripheral human blood


title: SW1417_18H

source_name: SW1417 conditioned media donor 18

value: donor 18

value: SW1417 conditioned media


title: MB3670-hic


title: MB3667-hic


title: KO1, replicate1


title: Liver, DDC diet with cMet induction through HTVi, 0 day and 5 months, n=2 each and pooled sequencing

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

description: 10X Genomics

data_processing:
For 10X dataset, sequencing reads were aligned to the mouse reference genome (mm10) and estimated cell-containing partitions and associated UMI using the Cell Ranger (v6.0.1) single-cell software suite. For Smart-seq2 dataset, nine pair-end libraries, each containing sequencing reads from dozens of single cells, were constructed. For each library, the template switch oligo (TSO) sequences were trimmed by cutadapt (v1.14) (Martin, 2011), and the low-quality bases at 3’ end of reads were trimmed by trimmomatic (v0.36) (Bolger et al., 2014). After that, demultiplex was done by fastx toolkit (v0.0.13) (http://hannonlab.cshl.edu/fastx_toolkit).
Since we introduced UMI in our Smart-seq2 protocol, we then tagged the UMI sequence to the read name of each sequence by umi_tools (Smith et al., 2017). Thus, we got tagged FASTQ files for every assessed cell. As the read2 was mainly composed of polyA sequences, we aligned only read1 of individual FASTQ files to mm10 using STAR aligner (v2.5.2b) (Dobin et al., 2013).
Htseq-count (v0.6.0) (Anders et al., 2015) were used to get UMI count table for Smart-seq2 data.
The Seurat (v4.0.1) (Satija et al., 2015; Stuart et al., 2019) R package was employed to perform scRNA-Seq data analysis.
Assembly: mm10

source_name: Liver

extract_protocol:
We collected primary hepatocytes via perfusion as reported from normal (WT mice for denoting normal liver-derived cells, n=2) and DDC-injured (Sox9-EGFP mice to trace hepatocyte-derived Sox9-positive LPLC, n=2) liver, HCC cells are collected from 5 months of DDC+cMet treatment Sox9-CreERT2:Rosa26-mTmG, and performed pooled 10X Chromium scRNA-seq (10X genomics Methods).
For 10X pipeline, isolated hepatocytes or enriched macrophages were processed using the Chromium Single Cell 30 (v3 Chemistry) platform (10X Genomics, Pleasanton, CA). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. For Smart-seq2, single hepatocyte was placed into the lysis buffer by the mouth pipette. The reverse transcription reaction was performed with 25 nt oligo (dT) primer anchored with an 8 nt cell-specific barcode and 8 nt unique molecular identifiers (UMI). After the first-strand synthesis, the second-strand cDNA was synthesized, and the cDNA was amplified by 14 cycles of PCR. The amplified cDNA of single cells was then pooled together for the following steps. Biotinylated pre-indexed primers were used to further amplify the PCR product by an additional 4 cycles of PCR to introduce biotin tags to the 3’ ends of the amplified cDNAs. Approximately 300 ng cDNA was sheared to approximately 300 bp by Covaris S2, and the 3’ terminal of the cDNA was captured by Dynabeads® MyOne Streptavidin C1 beads (Thermo Fisher). The RNA-seq library was constructed using a Kapa Hyper Prep Kit (Kapa Biosystems) and subjected to 150 bp paired-end sequencing on an Illumina HiSeq 4000 platform (sequenced by Annoroad).

value: Liver

value: primary cells

tag: strain

value: Hepatocytes

value: Sox9-CreERT2:Rosa26-mTmG (DDC&cMet treatment) and WT (normal diet)

value: DDC&cMet treatment for 0 day and 5 months


title: SFM_11A

source_name: serum-free media (SFM) donor 11

value: donor 11

value: Eosinophils

value: serum-free media (SFM)


title: MB3662-hic

value: brain


title: Liver, DDC diet, 0 day and 2 weeks, n=2 each and pooled sequencing

description: 10X Genomics

value: Sox9-EGFP (DDC diet); WT (normal diet)

value: DDC diet for 0 day and 2 weeks


title: HCT16_4D

source_name: HCT16 conditioned media donor 4

value: donor 4

value: HCT16 conditioned media


title: OA20022, Mammary Glands Cells, rep3, 18months, snATACseq

city: Farmington

first: Olga

last: Anczukow

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

description: snATAC

library_source: genomic single cell

data_processing:
scRNA fastq files were processed using cellranger pipeline v3.1.0. snATAC fastq were processed using cellranger-ATAC pipeline v1.2.0.
scRNA count matrices generated using cellranger were processed using Seurat v4. snATAC count matrices were processed using Signac v1.1.
Low Quality Cells were filtered using Seurat v4 and Doublets were filtered using Scrublet and DoubleDecon v1.1.6 for each scRNA sample. Signac v1.1 and Amulet were used to filter out low quality cells and doublets for snATAC samples.
scRNA Samples were merged together using Seurat v4 and snATAC samples were merged using Signac v1.1. Further cells were removed post reduction and clustering for both merged objects separately.
The scRNA object was annotated using Marker genes. The snATAC object was annotated using the RNA annotations.
Assembly: mm10
Supplementary files format and content: Gene/Cell Raw count matrix for merged samples post QC for scRNA. Peak/Cell Raw count matrix for merged samples post QC for snATAC. Metadata tables for both scRNA and snATAC objects.

source_name: Mammary Glands

growth_protocol: Virgin female young (3-4 months old) and older (17-18 months old) C57BL/6J mice (JAX #000664) were maintained under regular conditions, with 12hr/12hr light/dark cycle, and food (LabDiet 5K0G) and water ad libitum. Young and older animals were housed together for at least a month prior to tissue collection to synchronize estrus cycles.

extract_protocol:
Fresh mammary glands (each sample prepared from mammary glands pooled from three mice) were surgically excised, finely minced and incubated in a digestion solution (DMEM/F12, 10% heat-inactivated FBS, 1.5 mg/ml collagenase IV, 0.2% trypsin, 5 ug/ml insulin, 2.5 ug/ml gentamycin) for 15 min at 37°C. Following brief centrifugation, undigested tissues were further digested at 37C for 20 min prior to centrifugation; while the digested, aqueous fraction was collected, pelleted, resuspended in DMEM/F12 +FBS, and stored on ice. Pellets from both fractions were combined and incubated in a solution of DMEM/F12 and 1U/ml DNase I for 2-5 min at room temperature. Cells were then pulse-centrifuged three times at 520g as previously described (PMID: 23378653 and PMID: 25245692). Cells found in the pellet and supernatant fractions at each step were separated and collected. Epithelial cells (which are enriched in the pellet fraction) were further digested for 10 min at 37C in a solution containing TrypLE and 1U/ml DNase I. Cells found in the supernatant fraction were subjected to red blood cell lysis in ACK buffer. Live cells (calcein+ and PI-) from both fractions were isolated using flow cytometry and were combined at a 1:1 ratio for downstream library preparations.
For scRNA-seq, single cell capture, barcoding and library preparation were performed using the 10X Chromium v.3 chemistry, according to the manufacturer’s protocol (#CG00183). cDNA and single cell libraries for RNA-seq were checked for quality on an Agilent 4200 TapeStation, quantified by KAPA qPCR, and sequenced on a Novaseq6000 instrument (Illumina) to an average depth of 50,000 reads per cell. For snATAC-seq, nuclei suspensions were incubated in a transposase-containing mix, nuclei were counted, and 9,250 nuclei were loaded into one lane of a 10X Chromium microfluidic chip. Single nuclei capture, barcoding and library preparation were performed using the 10X Chromium v.1 chemistry, according to the manufacturer’s protocol (#CG000168).  Libraries for snATAC-seq were checked for quality on an Agilent 2100 Bioanalyzer, quantified by KAPA qPCR, and sequenced on a Novaseq6000 instrument (Illumina) to an average depth of 25,000 read pairs per nucleus.

value: Mammary Glands

value: Mammary Cells (Epithelial, Stromal and Immune)

value: 18 months

value: Female

tag: virginity status

value: Virgin

tag: replicate


title: P_d7_YFP_UN_4

source_name: retina

value: retina

value: 7 d

value: Pten-fl/fl

value: ddYFP; uninjured


title: MB3692-hic

value: M

value: medulloblastoma


title: OA20020, Mammary Glands Cells, rep3, 3months, snATACseq

description: snATAC

value: 3 months


title: NC2,replicate2

value: brain

value: primary microglia


title: MB3690-hic

value: F


title: OA20018, Mammary Glands Cells, rep2, 18months, snATACseq

description: snATAC


title: HCT16_3D

source_name: HCT16 conditioned media donor 3

value: donor 3

value: Peripheral human blood

value: Eosinophils


title: OA20016, Mammary Glands Cells, rep2, 3months, snATACseq

description: snATAC

value: Mammary Glands

value: Mammary Cells (Epithelial, Stromal and Immune)


title: MB3612-hic

value: SHH


title: OA20014, Mammary Glands Cells, rep1, 18months, snATACseq

description: snATAC

value: 18 months

value: Female

value: Virgin


title: OA20012, Mammary Glands Cells, rep1, 3months, snATACseq

description: snATAC


title: MB3510-hic


title: OA20021, Mammary Glands Cells, rep3, 18months, scRNAseq

description: scRNA


title: HCT16_23D

source_name: HCT16 conditioned media donor 23

value: donor 23

value: HCT16 conditioned media


title: HCT16_25D

source_name: HCT16 conditioned media donor 25

value: donor 25


title: OA20017, Mammary Glands Cells, rep2, 18months, scRNAseq

description: scRNA


title: HCT16_21D

source_name: HCT16 conditioned media donor 21

value: donor 21


title: OA20015, Mammary Glands Cells, rep2, 3months, scRNAseq

description: scRNA

value: 3 months


title: HCT16_18D

source_name: HCT16 conditioned media donor 18

value: donor 18


title: OA20013, Mammary Glands Cells, rep1, 18months, scRNAseq

description: scRNA


title: OA20006, Mammary Glands Cells, rep6, 18months, scRNAseq

description: scRNA


title: MB3661-hic

value: brain

value: M

value: medulloblastoma


title: OA20004, Mammary Glands Cells, rep5, 18months, scRNAseq

description: scRNA


title: HCT115_4C

source_name: HCT115 conditioned media donor 4

value: donor 4

value: Peripheral human blood

value: HCT115 conditioned media


title: OA20011, Mammary Glands Cells, rep1, 3months, scRNAseq

description: scRNA

value: Mammary Glands

value: Mammary Cells (Epithelial, Stromal and Immune)


title: Injured IVDS Round 1

city: St. Louis

first: Simon

last: Tang

state: MO

address: 425 S. Euclid Ave, Campus Box 8233, Tang Lab, Washington University School of Medicine

department: Orthopaedic Surgery

institute: Washington University in St. Louis

data_processing:
The Cell Ranger Single-Cell Software Suite (10x Genomics) was then used to perform sample demultiplexing, barcode processing, and single-cell gene counting. After demultiplexing the sequencing files with “cellranger mkfastq.gz”, “cellranger count” was used to perform alignment to mouse reference transcriptome (mm10), barcode processing and gene counting.
Assembly: mm10
Supplementary files format and content: gene list (features.tsv) and cell barcodes (barcodes.tsv) as well as gene/barcode matrices (matrix.mtx) are provided for each experimental group.

source_name: Intervertebral discs

growth_protocol: Female, 12-week old C57BL/6 (#000664) mice were purchased from the Jackson Laboratories and housed in a mouse facility under standard laboratory conditions. A chow diet and water were available at libitum.

extract_protocol:
For tail IVD extractions, mice were euthanized at 7 days post injury (dpi) in a CO2 chamber with 3% CO2 for 5 minutes and a 2 minute dwell time. Euthanized mice were submerged in 70% ethanol for 2 minutes before the IVDs were extracted. IVDs were either rendered into a single cell suspension and counted for single cell RNA sequencing
Library preparation was performed using Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3 (10X Genomics) following the manufacturer’s protocol and sequenced using Illumina NextSeq 500.

treatment_protocol: Control IVDs were isolated from mouse tails in the coccygeal “CC” region CC12/13 through CC16/17. Injured IVDs were conducted using a 30G needle to bilaterally puncture regions CC5/6 through CC9/10. Control and Injured IVDs are from the same animal. Punctures were performed by using digital palpation to identify CC5/6 through CC9/10, puncturing each level with a sterile 30G needle, and confirming the accuracy of each puncture with X-ray

value: Intervertebral discs

value: heterogeneous

value: wildtype

value: needle puncture injury

tag: group

value: injured


title: OA20003, Mammary Glands Cells, rep5, 3months, scRNAseq

description: scRNA

tag: tissue

value: Female

value: Virgin


title: Injured IVDs Round 2


title: Control IVDs Round 2

value: internal control

value: non injured


title: OA20002, Mammary Glands Cells, rep4, 18months, scRNAseq

description: scRNA

value: 18 months

tag: Sex


title: OA20005, Mammary Glands Cells, rep6, 3months, scRNAseq

description: scRNA

value: 3 months


title: Control IVDs Round 1


title: OA20001, Mammary Glands Cells, rep4, 3months, scRNAseq

description: scRNA


title: HCT115_3C

source_name: HCT115 conditioned media donor 3

value: donor 3

value: Eosinophils


title: MB0558-hic

source_name: brain

value: brain

value: F

tag: disease

value: medulloblastoma


title: OA20019, Mammary Glands Cells, rep3, 3months, scRNAseq

description: scRNA

value: Mammary Glands

value: Mammary Cells (Epithelial, Stromal and Immune)


title: HCT115_25C

source_name: HCT115 conditioned media donor 25

value: donor 25

value: Peripheral human blood

value: HCT115 conditioned media


title: Patient3 8703

type: genomic

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
The analysis was performed using SNP-FASST2 algorithm, which makes segmentation calls based on both the log2 ratio and B-allele frequency. All specimens had the Median Absolute Pairwise Difference (MAPD) value below 0.3 and the ndSNPQC value above 26, indicating good quality of data according to the Affymetrix quality control recommendations (Supplementary Table 1). Copy number gain and loss was defined as log2 ratio > 0.2 and < -0.2, respectively (Supplementary Table 2). A minimum of 20 probes in the segment was used to call copy number alterations.
log2ratio

label: biotin

source_name: Desmoid tumor Patient 3

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA and RNA were extracted in parallel from the re-embedded tumor cores using the AllPrep DNA/RNA FFPE kit including the RNaseA and DNase treatment steps respectively, according to the manufacturer’s protocol (Qiagen).

value: desmoid tumor


title: HCT115_24C

source_name: HCT115 conditioned media donor 24

value: donor 24


title: Patient3 8701


title: Patient3 8697


title: Hepatocytes, G-MDSC depletion, POD2, rep1

city: Ramat Gan

first: Niv

last: Pencovich

address: 2 Derech Sheba

department: Surgery and transplantation

institute: Sheba medical center

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the mouse genome using STAR
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count
Normalization and differential expression was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: Excel file includes the raw counts

source_name: Liver

extract_protocol:
Hepatocytes from BALB/C mice livers were extracted one or two days after hepatectomy using the two step perfusion method: mice were anaesthetized and a cannula was inserted into the inferior vena cava. The portal vein was cut, and the mouse liver was perfused with perfusion medium (Ca2+/Mg2+ ion-free HBSS buffer containing 5 mM EGTA, 25 mM HEPES) for 5 minutes and then with the addition of 0.8 mg/mL type-I collagenase, at 37 ºC for another 8 minutes. Following adequate digestion, the liver was resected and passed through a 70 μm filter, followed by centrifugation of the cells for 2 min at 50 G. RNA from the hepatocyte pellet was extracted using the QIAGEN RNAeasy mini-kit.
Inhouse poly A based RNA seq

treatment_protocol: 8 weeks old BALB/C male mice were treated with an anti-GR1 antibody or a non-targeting anti-IgG matched isotype antibody, inoculated intra-peritoneally (200µg in 100µl PBS for each injection). Two days later, another dose of the same antibodies was given, and a 70% hepatectomy was performed on all mice.

value: Liver

value: BALB/C

value: Male

value: Hepatocytes

value: WT

value: Anti mouse Gr1 Ab, 70% hepatectomy d2


title: HCT115_23C

source_name: HCT115 conditioned media donor 23

value: donor 23

value: Eosinophils


title: Hepatocytes, G-MDSC depletion, POD2, rep2


title: Patient3 8700


title: Hepatocytes, G-MDSC depletion, POD2, rep3


title: HCT16_11D

source_name: HCT16 conditioned media donor 11

value: donor 11

value: HCT16 conditioned media


title: Hepatocytes, G-MDSC depletion, POD1, rep3

value: Anti mouse Gr1 Ab, 70% hepatectomy d1


title: Patient3 8696


title: HCT115_21C

source_name: HCT115 conditioned media donor 21

value: donor 21


title: Patient2 8690

source_name: Desmoid tumor Patient 2


title: Hepatocytes, G-MDSC depletion, POD1, rep2


title: Patient3 8704


title: HCT115_18C

source_name: HCT115 conditioned media donor 18

value: donor 18


title: Patient2 8688


title: Caco2_4B

source_name: Caco2 conditioned media donor 4

value: donor 4

value: Peripheral human blood

value: Caco2 conditioned media


title: Patient2 8689

value: desmoid tumor


title: Hepatocytes, control, POD2, rep3

value: Liver

value: Isotype-control Ab, 70% hepatectomy d2


title: Patient2 8687


title: HCT115_11C

source_name: HCT115 conditioned media donor 11

value: HCT115 conditioned media


title: Patient2 8684


title: Hepatocytes, G-MDSC depletion, POD1, rep1

value: BALB/C

value: Male

value: Hepatocytes


title: Patient2 8686


title: Hepatocytes, control, POD2, rep2

value: WT


title: Patient3 8698


title: Caco2_3B

source_name: Caco2 conditioned media donor 3

value: donor 3

value: Eosinophils


title: Patient1 9215

source_name: Desmoid tumor Patient 1


title: Hepatocytes, control, POD2, rep1


title: Patient1 9213


title: Hepatocytes, control, POD1, rep3

value: Isotype-control Ab, 70% hepatectomy d1


title: Patient1 9214


title: Patient1 9212


title: Caco2_24B

source_name: Caco2 conditioned media donor 24

value: donor 24


title: Hepatocytes, control, POD1, rep2


title: Caco2_21B

source_name: Caco2 conditioned media donor 21

value: donor 21


title: Caco2_23B

source_name: Caco2 conditioned media donor 23

value: donor 23


title: Patient1 9211


title: Patient2 8685


title: Hepatocytes, control, POD1, rep1


title: Patient1 9208


title: Caco2_11B

source_name: Caco2 conditioned media donor 11

value: donor 11


title: RNAseq_KO_IL7_IL33_NMU_replicate1

data_processing:
Sequence reads were trimmed for adaptor sequence/low quality sequence
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: lung

extract_protocol:
~500 ILC2s were sorted directly into the lysis buffer of a Single Cell Full Length mRNA-Amplification Kit (Vazyme, N712). mRNAs in the samples were then reverse transcribed to cDNAs and pre-amplified according to the manufacturer’s protocols.
The sequencing libraries were established using a TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502), according to the manufacturer’s instructions.

value: lung

tag: cell line

value: primary cells

value: IL7 plus IL33 plus NMU


title: gwnull-2_rep2

data_processing:
Basecalling with Sanger / Illumina 1.9
RNA sequence reads were analyzed on the Galaxy web platform (usegalaxy.eu). After trimming of the adaptor sequence, quality was controlled by FastQC 0.11.2.
Reads were mapped to Drosophila melanogaster BDGP6.28 genome using STAR (Version 2.7.0a)
Mapped reads were counted using featureCounts
Genome_build: Drosophila melanogaster BDGP6.28
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2.read counts

source_name: First instar laeva

extract_protocol:
First instar larvae were collected and extract total RNA by RNA basic kit (FastGene) according to the manufacturer protocol.
Total RNA libraries were prepared by using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech).

value: Whole body

value: RNA extraction


title: Patient1 8675

value: desmoid tumor


title: gwnull-2_rep1


title: Patient1 8674


title: RNAseq_WT_IL7_IL33_NMU_replicate2

tag: treatment


title: RNAseq_WT_IL7_IL33_NMU_replicate1

tag: genotype


title: gwnull-1_rep1


title: RNAseq_KO_IL7_IL33_CGRP_replicate2

value: IL7 plus IL33 plus CGRP


title: Liver-DDC+Met-2

data_processing:
Illumina Casava1.7 software used for basecalling.
Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted ). Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality). Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
The sequencing reads were mapped to the mm10 using STAR algorithm.
Htseq-count algorithm was used to count reads mapped to each gene uniquely.
DESeq2 R package was used to detect differentially expressed genes (DEGs) between groups.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver hepatocyte

extract_protocol:
Liver was perfused using three-steps methods. Cells in liver were sorted by BD FACSAriaIII. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice was feeded with DDC diet or normal diet under cMet induction through HTVi for 5 months and pooled sequencing for liver tissue. And, for discovering EP300 function in HCC initiation, mice was treated with DDC diet and HTVi of pT3-cMet plasmids in physiological saline (20ug/mL). To deplete EP300 in hepatocyte, EP300f/f mice was tail-vein injected AAV-TBG-Cre with the titer of 2.5x10^11, while control mice was injected AAV-TBG-GFP.

value: liver hepatocyte

value: DDC+Met treatment for 5 months


title: yw_rep2

value: yw


title: Patient1 9210


title: RNAseq_KO_IL7_IL33_NMU_replicate2


title: yw_rep1


title: Liver-DDC+Met-1

value: WT


title: RNAseq_WT_IL7_IL33_CGRP_replicate2


title: gwnull-1_rep2


title: RNAseq_WT_IL7_IL33_CGRP_replicate1


title: Liver-Met-3

value: Met treatment for 5 months


title: Max cKO gonadal cells

city: Hidaka-shi

first: Ayumu

last: Suzuki

state: Saitama

address: 1397-1 Yamane

department: Division of Biomedical Sciences, School of Medicine

institute: Saitama Medical University

description: 10x Genomics

data_processing:
The filterd_feature_bc_matrix (barcodes.tsv.gz, feature.tsv.gz, matrix.mtx.gz) and cloupe files were made using Cell ranger (v7.0.1).
Feature_genes_score.xlsx was made by Loupe Browser (6.5.0) and Excel.
Assembly: mn10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: E12.5 gonads

extract_protocol:
Gonads attached to mesonephros were recovered from tamoxifen-administered control male Maxfl/fl mouse embryos and those with the CreERT2 transgene. After removing the attached mesonephros, these fleshly isolated gonads were dissociated to single cell suspension using 0.05% trypsin-0.2 mM EDTA in PBS. Cells were washed and resuspended in PBS.
Library was performed according to the manufacturer’s instructions (Single Cell 3’ Reagent Kits v3, 10X Genomics).

value: E12.5 gonads

value: male

value: Max cKO (mixture of Maxfl/fl and Max fl/fl;Oct4-CreERT2)

value: treated with tamoxifen at E8.5


title: Liver-DDC+Met-3


title: Liver-Met-2


title: Con_3

city: Nantong

first: YU

last: WU

address: Nantong, 226001, PR China;

institute: Nantong Hospital of Traditional Chinese 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 mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 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_mouse/release_M20/gencode.vM20.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (v1.32.0). Pvalue <0.05 and |FoldChange|≥1.5 were set as the threshold for significantly differential expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include count and FPKM values for each Sample

source_name: liver tissue

growth_protocol: Psoraleae Fructus decoction high-dose group and saline were intragastric for 30 days.

extract_protocol:
RNA was harvested using Trizol reagent according to the manufacturer’s instructions.
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. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

treatment_protocol: After death, liver tissue was taken by laparotomy.

tag: treatmet

value: Control

value: ICR


title: RNAseq_KO_IL7_IL33_CGRP_replicate1

value: lung

value: primary cells


title: RNAseq_KO_IL7_IL33_replicate1

value: IL7 plus IL33


title: Liver-Met-1


title: Con_2


title: HCC_EP300_WT-2


title: RNAseq_WT_IL7_IL33_replicate2


title: HCC_EP300_WT-1


title: RNAseq_WT_IL7_IL33_replicate1


title: Con_1


title: RNAseq_KO_IL7_IL33_replicate2


title: Con_4


title: SPHD_4

value: high-dose  Psoraleae Fructus


title: HCC_EP300_KO-2


title: RNAseq_KO_IL7_replicate2


title: RNAseq_KO_IL7_replicate1


title: SPHD_2


title: SPHD_3


title: RNAseq_WT_IL7_replicate2


title: SPHD_1


title: HEP-K27ac-1

data_processing:
Basecalls performed using CASAVA version 1.4
aligned signals in raw (bam) files were filtered to remove reads that aligned to multiple locations,Duplicate reads were removed using DeepTools v2.1.0
Peaks were identified using MACS v1.4 with the p-value cut-off 10-5 and peaks were filtered to remove peaks that overlap with ENCODE blacklisted regions, as well as peaks mapped to chrX, chrY, chrM.
Raw signals from individual samples were converted to signal files (bigWig) using DeepTools v2.1.0
signals were quantile-normalized using Haystack, with 25-bp windows
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Liver were perfused and hepatocytes were isolated and lysed. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Purified ChIP DNA was used to prepare sequencing libraries via NEBNext Ultra DNA Library Prep Kit for the Illumina (E7370).

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: HEP-K27ac-2

value: H3K27ac (Abcam, ab12179)


title: RNAseq_WT_IL7_replicate1


title: Ac, WGBS-2

data_processing:
The genome size of dinoflagellate A. carterae was first estimated by using genome survey sequencing and the genome was firstly assembled using Pacbio HiFi sequencing reads and further refined with Hi-C technology to determine the contig position on scaffolds. A contig-level assembly of the resulting PacBio CCS reads with default parameters was obtained using Hifiasm software. Assembled contigs were further joined into scaffolds at the pseudo-chromosome level using Hi-C sequencing data with Juicer (default parameters) and 3D-DNA (-m haploid -q 0 -r 0).
Repeat sequences were annotated using a combination of homology-based and de novo methods. RepeatMasker (v4.0.7) and RepeatProteinMask (v4.0.7) were used to identify known repeat sequences through searching against RepBase v21.12 library. On the other hand, in the de novo step, de novo repeat sequence libraries were established using RepeatModeler and LTR_FINDER v1.06, followed by de novo prediction with the Repeatmasker program. Protein-coding genes were identified using a combination of homology-based, de novo and transcriptome-based strategies.
Raw DIP-seq and 5hmU-chemical-seq data were first processed using TrimGalore (version 0.6.7) to remove adapters and low-quality bases (-q 25). The cleaned sequence reads were then mapped to the de novo reference genome (Acart.genome.v1) using Bowtie2 local alignments. Resultant SAM formatted files were converted to the BAM format using Samtools. Enriched regions were identified with MACS2 (-g 1.2e9 -q 0.05). Motif discovery was performed using MEME (-mod zoops -minw 4 -maxw 10 -nmotifs 10 -dna) and the genomic distribution of peaks was analyzed using Bedtools.
For RNAseq data of 2-4P treatment, TrimGalore (version 0.6.7) was used to remove adapters and low-quality base (-q 25) at first. Pre-processed reads of RNA-seq were subjected to alignment against Acart.genome.v1 using software STAR (version 2.7.10a), allowing for no more than 2 mismatches. The sorted mapping files of RNA-seq were used for quantification with StringTie (v2.1.7). Next, the obtained read counts were converted to TPM (transcripts per million). The R package DESeq2 was used to perform differential gene expression of RNA-seq datasets.
For WGBS analysis, bisulfite-treated reads were filtered to remove adaptors and low-quality bases. The resulting clean reads were aligned to the A. carterae genome (Acart.genome.v1) using BS-Seeker2 (v2.1.8, --aligner=bowtie2 --local). The CGmap output file generated by BS-Seeker2 for methylation calling from the mapping result was utilized in downstream analysis.
Assembly: Ac.genome.v1.fa.gz

source_name: Ac, WGBS

extract_protocol:
Total RNA was extracted from A. carterae and Symbiodinium sp. using RNAzol®RT (MRC) according to the manufacturer’s protocol.  Genomic DNA of A. carterae and Symbiodinium sp. were extracted via a CTAB method. Briefly, cell pellets were resuspended in 600 µl of preheated CTAB extraction buffer (100 mM Tris pH 8.0, 20 mM EDTA pH 8.0, 2 M NaCl, 2% (w/v) CTAB, 2% (w/v) Polyvinylpyrrolidone. Next, 10 µl of 20 mg/ml RNase A (NEB) was added, and the mixture was incubated at 37°C for 2 hours, followed by the addition of 20 µl of Proteinase K (NEB) and another incubation at 65°C overnight. Equal volumes of phenol: chloroform: isoamyl alcohol (25: 24: 1) (Solarbio Life Sciences, Beijing, China) were added. After centrifugation, the upper phase was transferred to a new Eppendorf tube, mixed with 2/3 volume of isopropanol, and then centrifuged at 13000 rpm for 10 minutes. The pellet was washed with 700 µl of 75% ethanol and 80% ethanol sequentially. Finally, the DNA was eluted in 20 µl of ddH2O.
1. A. carterae Genome Construction: gDNA extracted from A. carterae was sent to Beijing Genomics Institute (BGI, Shenzhen, China) for Pacbio HiFi and Hi-C library construction. 2. Transcriptome Sequencing: For short-read RNA-seq and long-read sequencing of A. carterae, isolated total RNA from A. carterae cells was sent to BGI for strand-specific mRNA library and PacBio library construction. 3. 2,4-Pyridinedicarboxylic Acid Treatment: Total RNA of A. carterae was treated with Ribo-off® rRNA depletion kit (N409, Vazyme Biotech, Nanjing, China) and sent to BGI or Novogene Company (Beijing, China) for stranded RNA-seq library construction. 4. 5hmU-DIP and 5fU-DIP Library Construction: A. carterae gDNA was sonicated, end-repaired, adapter-ligated using the VAHTS® Universal DNA Library Prep Kit for Illumina V3 (ND607, Vazyme Biotech, Nanjing, China), and subjected to 5hmU-DIP using anti-5hmU antibody and Protein A/G beads, followed by protease K digestion and DNA purification. For the parallel 5fU-DIP, ACT+BF4- oxidation was performed first to fully convert gDNA 5hmU into 5fU, with the subsequent steps identical to the 5hmU-DIP procedures. 5. 5hmU-Chemical-Seq: For the 5hmU-chemical-seq approach, we employed both commercial and modified adapters. The modified adapters were designed with a 5'-end amino group and a 3'-phosphorylated oligodeoxynucleotide, annealed to create final adapters 5N3A3 and 5N3A4. A. carterae gDNA was fragmented, end-repaired, and ligated to these pre-annealed adapters. After ligation, DNA purification was performed, followed by ACT+BF4- oxidation treatment. The oxidized DNA samples were then biotinylated, purified, and captured using streptavidin magnetic beads. After washing, the DNA was eluted and amplified for subsequent sequencing. For controls, non-oxidized DNA was prepared using commercial adapters and amplified using the VAHTS® Universal DNA Library Prep Kit for Illumina V3.  6. WGBS Library Construction: A. carterae gDNA was sent to Novogene Biotech Co., Ltd (China) for WGBS libraries construction according to a standard protocol. Briefly, gDNA was spiked with unmethylated lambda DNA and sheared to average 200 bp size, followed by bisulphite treatment using the Accel-NGS® Methyl-Seq DNA Library Kit (Swift Biosciences). Following this treatment, the DNA was subjected to end-repair, adapter ligation, and PCR amplification.

tag: experimental

value: Ac, WGBS


title: LPLC-K27ac-2

value: liver hepatocyte


title: FastATAC_seq_KO_NMU_CGRP_replicate2

data_processing:
The reads were aligned to the Mus musculus mm10 genome, and the peaks were called using MACS2 (version 2.1.2).
Assembly: mm10
Supplementary files format and content: bigWig files

extract_protocol:
Lung ILC2s from wild-type or Pac1-/- mice (~50,000 ILC2s) were treated under different conditions of stimulation for 6 h, and lysed using a Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711), according to the manufacturer’s instructions.
The ATAC-seq libraries were established using a Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711), according to the manufacturer’s instructions.

value: NMU plus CGRP


title: Ac, Iso-seq

source_name: Ac, Iso-seq

value: Ac, Iso-seq


title: Ac, WGBS-1


title: FastATAC_seq_KO_NMU_CGRP_replicate1


title: LPLC-K27ac-1


title: Ac, non-2-4P-ribooff-RNAseq-2

data_processing:
The genome size of dinoflagellate A. carterae was first estimated by using genome survey sequencing and the genome was firstly assembled using Pacbio HiFi sequencing reads and further refined with Hi-C technology to determine the contig position on scaffolds. A contig-level assembly of the resulting PacBio CCS reads with default parameters was obtained using Hifiasm software. Assembled contigs were further joined into scaffolds at the pseudo-chromosome level using Hi-C sequencing data with Juicer (default parameters) and 3D-DNA (-m haploid -q 0 -r 0).
Repeat sequences were annotated using a combination of homology-based and de novo methods. RepeatMasker (v4.0.7) and RepeatProteinMask (v4.0.7) were used to identify known repeat sequences through searching against RepBase v21.12 library. On the other hand, in the de novo step, de novo repeat sequence libraries were established using RepeatModeler and LTR_FINDER v1.06, followed by de novo prediction with the Repeatmasker program. Protein-coding genes were identified using a combination of homology-based, de novo and transcriptome-based strategies.
Raw DIP-seq and 5hmU-chemical-seq data were first processed using TrimGalore (version 0.6.7) to remove adapters and low-quality bases (-q 25). The cleaned sequence reads were then mapped to the de novo reference genome (Acart.genome.v1) using Bowtie2 local alignments. Resultant SAM formatted files were converted to the BAM format using Samtools. Enriched regions were identified with MACS2 (-g 1.2e9 -q 0.05). Motif discovery was performed using MEME (-mod zoops -minw 4 -maxw 10 -nmotifs 10 -dna) and the genomic distribution of peaks was analyzed using Bedtools.
For RNAseq data of 2-4P treatment, TrimGalore (version 0.6.7) was used to remove adapters and low-quality base (-q 25) at first. Pre-processed reads of RNA-seq were subjected to alignment against Acart.genome.v1 using software STAR (version 2.7.10a), allowing for no more than 2 mismatches. The sorted mapping files of RNA-seq were used for quantification with StringTie (v2.1.7). Next, the obtained read counts were converted to TPM (transcripts per million). The R package DESeq2 was used to perform differential gene expression of RNA-seq datasets.
For WGBS analysis, bisulfite-treated reads were filtered to remove adaptors and low-quality bases. The resulting clean reads were aligned to the A. carterae genome (Acart.genome.v1) using BS-Seeker2 (v2.1.8, --aligner=bowtie2 --local). The CGmap output file generated by BS-Seeker2 for methylation calling from the mapping result was utilized in downstream analysis.
Supplementary files format and content: 2-4P-TEtranscript-RNAseq.cntTable.txt

source_name: Ac-control

value: control


title: HCC-K27ac-2

value: Sox9-CreERT2; Rosa-LSL-tdTomato


title: Patient3 [STT8704_R3]

hyb_protocol: As per manufacturer (Illumina)

scan_protocol: As per manufacturer (Illumina)

data_processing: The data has been analyzed using a custom pipeline in R (version 3.6.3). For specimen quality control, we required that > 90% of probes were measured with p < 0.05 on at least 3 separate beads (using “detectionP” function in the minfi package version 1.32.0, and the “beadcount” function in the wateRmelon package version 1.30.0) (Supplementary Table 1) 32,33. We also required the samples to have log2 median intensity of the methylated and unmethylated channels > 9 (using “shinySummarize” function in the minfi package) 32. The data was normalized using Illumina preprocessing (“preprocessIllumina” function in the minfi package) 32, and we verified that the specimens had a bimodal distribution of beta values. Next, we removed individual poor quality probes (measured with p ≥ 0.01), probes associated with single nucleotide polymorphisms (“dropLociWithSnps” function in the minfi package) 32, cross-reactive probes (“xreactive_probes” function in the maxprobes package version 0.0.2)34 and probes associated with sex chromosomes. The exploratory analysis was done using 1% probes with most variable beta values. Heatmaps that visualize unsupervised clustering were plotted using ClustVis package in R (version 0.0.0.9000) 22. Beta values were used for unsupervised clustering with Euclidean distance and Ward linkage method.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

tag: age at diagnosis

tag: site of primary tumor

value: Arm

tag: driver ctnnb1 mutation


title: Ac, 5hmU-chemical-seq-2

source_name: Ac, 5hmU-chemical-seq

value: Ac, 5hmU-chemical-seq


title: FastATAC_seq_KO_NMU_replicate2

tag: cell type

value: NMU


title: Ac, 5hmU-chemical-seq-1


title: Ac, 2-4P-ribooff-RNAseq-2

value: 2,4-pyridinedicarboxylic acid (2-4P)


title: HCC_EP300_KO-1

tag: strain

value: DDC+Met treatment for 5 months


title: Patient3 [STT8697_P]


title: Ac, input-chemical-seq-2

source_name: Ac, input-chemical-seq

value: Ac, input-chemical-seq


title: Ac, non-2-4P-ribooff-RNAseq-1


title: HCC-K27ac-1


title: Ac, input-chemical-seq-1


title: Patient3 [STT8703_R2]


title: Patient3 [STT8700_R1]


title: Ac, 2-4P-ribooff-RNAseq-1


title: FastATAC_seq_KO_NMU_replicate1

value: lung

value: primary cells


title: Ac, DIP-input-2

source_name: Ac, DIP-input

value: Ac, DIP-input


title: Patient2 [STT8689_R2]

value: Buttock


title: Ac, 5fU-DIP-2

source_name: Ac, 5fU-DIP

value: Ac, 5fU-DIP


title: FastATAC_seq_WT_NMU_CGRP_replicate2

value: WT


title: FastATAC_seq_WT_NMU_replicate1


title: Ac, RNA_seq

source_name: Ac, RNA_seq

value: Ac, RNA_seq


title: Ac, 5fU-DIP-1


title: Patient3 [STT8698_P]


title: Patient2 [STT8690_R2]


title: Ac, 5hmU-DIP-2

source_name: Ac, 5hmU-DIP

value: Ac, 5hmU-DIP


title: LPLC-EP300-2

value: liver hepatocyte


title: Ac, DIP-input-1


title: Patient2 [STT8688_R1]


title: Patient1 [STT8675_R]

value: Mesentry


title: HCC-EP300-2

value: Sox9-CreERT2; Rosa-LSL-tdTomato


title: RNA-seq of RNA IP with an antibody specific for TMG

city: Manhasset

first: Sophie

last: Kwon

state: New York

address: 51 Clapham Ave

institute: Saint Mary's High School

description: Sequences from RNA IP enriched RNA to obtain sequence coverage.

data_processing:
RNA-seq reads were mapped to the reference human genome (UCSC hg19) using bowtie2 verions 2.5.3 with the following configurations -q -5 1 -3 5 to generate bedGraph files.
Assembly: hg19
Supplementary files format and content: bedGraph. Scores stand for RNA-seq read coverage

source_name: HeLa

growth_protocol: HeLa cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% FBS and 100U of penicillin/streptomycin.

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) according to manufactor's recommendations.
For RNA fragmentation, 20 ug of total RNA was incubated in 20 ul fragmentation buffer (10 mM Tris-HCl pH 7.4, 10 mM ZnCl2) at 94°C for 5 min. The fragmented RNA was then purified using the Monarch RNA cleanup kit (50 ug) (NEB) and 10 ug of RNA was immunoprecipitated with 3 ug IgG against TMG (MBL, RN019M) or non-specific IgG bound to protein A/G Dynabeads. Beads were washed three times with wash buffer (10 mM Tris-HCl, 150 mM NaCl, and 1% Empigen BB). RNA on magnetic beads was treated with FastAP (Thermo Fisher Scientific) at 37°C for 20 min and ligated to 20 pmole pre-activated 3′ adapter ( AppNNNNNCGTCGTGTAGGGAAAGAGTGTAGATddC) overnight at 37°C in RNA ligase buffer containing 15% PEG8000). RNA bound to beads was recovered by phenol/chloroform extraction and ethanol precipitation. The RNA-adapter hybrid was converted into complementary DNAs with an RT primer (5' phosphate-CAGCAGGAATGCCGAGACCGATCTACACTCTTTCCCTACACGA ), size-fractionated by electrophoresis on a 12% polyacrylamide gel containing 8 M urea and circularized by circLigase ssDNA ligase (Biosearch technologies). Circularized cDNAs were PCR-amplified with PCR primers containing demultiplexing codes (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACG, and CAAGCAGAAGACGGCATACGAGAT[5nt code)TAGCTGATGCTACGACCACAGG)  to be converted into linear DNA fragments adequate for Illumina high-throughput DNA sequencers. The samples were sequenced on Illumina NextSeq 500 Sequencer with a primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACG) to obtain 76-nt reads and with the second primer (CCTGTGGTCGTAGCATCAGCTA) to obtrain demultiplixing codes. The raw image data was transformed by base-calling into sequence data and stored in FASTQ format.

value: HeLa

value: Wild type

tag: antibody

value: precipitated by an antibody for TMG


title: FastATAC_seq_WT_NMU_replicate2

value: NMU


title: Ac, 5hmU-DIP-1


title: Patient2 [STT8687_R1]


title: LPLC-EP300-1

city: Shanghai


title: HCC-EP300-1


title: HEP-EP300-2


title: Ac, genome_survey

source_name: Ac, genome_survey

value: Ac, genome_survey


title: Patient3 [STT8696_P]

value: Arm


title: RNA-seq of RNA IP negative control with non-specific IgG

description: Sequences from an IgG control to obtain sequence coverage.

value: precipitated by non-specific IgG


title: Patient1 [STT9214_R]


title: Patient1 [STT9212_P]


title: Patient1 [STT9208_P]


title: Patient2 [STT8685_P]


title: FastATAC_seq_WT_NMU_CGRP_replicate1

city: Beijing

value: lung

value: primary cells

value: NMU plus CGRP


title: Patient2 [STT8686_R1]

value: Buttock


title: Patient1 [STT9215_R]


title: HMGB1koHepMac_EtOH_BioRep3

status: Public on Sep 28 2024

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using qubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

label: Biotin

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: HMGB1 was knocked out in hepatocytes and/or macrophages, then treated with ethanol or vehicle control.

value: female

tag: genetic intervention

value: HMGB1 knockout in hepatocytes and macrophages

tag: ethanol (etoh) treatment

value: EtOH treatment

value: liver tissue


title: Patient2 [STT8684_P]


title: HMGB1koHepMac_Control_BioRep1

scan_protocol: Refer to the Illumina beadarray Assay System Manual

value: Control (no EtOH treatment)

tag: tissue


title: HMGB1koHepMac_EtOH_BioRep2

label_protocol: Refer to the Illumina beadarray Assay System Manual

tag: Sex


title: HMGB1koMac_EtOH_BioRep3

value: HMGB1 knockout in macrophages


title: HMGB1koHepMac_Control_BioRep2


title: HMGB1koMac_EtOH_BioRep1


title: Patient1 [STT8674_P]

value: Mesentry


title: Patient1 [STT9210_P]


title: HMGB1koMac_Control_BioRep3


title: HMGB1koMac_Control_BioRep2


title: HMGB1koHep_Control_BioRep3

value: HMGB1 knockout in hepatocytes


title: HMGB1koHep_EtOH_BioRep3


title: HMGB1koHep_EtOH_BioRep1


title: HMGB1koHep_Control_BioRep1


title: HMGB1koMac_Control_BioRep1


title: HMGB1koHepMac_Control_BioRep3


title: HMGB1koHepMac_EtOH_BioRep1


title: HMGB1koHep_Control_BioRep2


title: Wildtype_EtOH_BioRep3

value: Wildtype


title: Wildtype_Control_BioRep1


title: Wildtype_EtOH_BioRep1


title: Wildtype_Control_BioRep3


title: HMGB1koHep_EtOH_BioRep2


title: Wildtype_Control_BioRep2


title: HEP-EP300-1

value: liver hepatocyte

value: WT


title: Human sample with a Bacterial  infection [408980]

city: Durham

first: Julie

last: Steinbrink

state: NC

address: 315 Trent Drive

department: Center for Applied Genomics and Precision Medicine

institute: Duke University

description: Gene expression data from peripheral blood from humans with confirmed infection

hyb_protocol: 20 ug of antisense cRNA was hybridized for 16+ hr at 45C on GeneChip Human U133A array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Midi_euk2v3_450 protocol

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 7G.

data_processing: CEL files imported in to R using affy and normalized using the multi-array method for noptical noise and non-specific binding adjustments and quantile normalization implimented in the bioconductor package gcrma

source_name: Human peripheral bloods

label_protocol: Biotinylated antisense strand cRNA was prepared according to the standard Affymetrix protocol from 2.5 ug total RNA utilizing peptide nucleic acids complimentary to globin mRNA to block amplification of those transcripts(GeneChipÂ® 1 cycle labeling kit with Globin Reduction protocol (Affymetrix) Data was Generated at Expression Analysis, Inc (Durham, NC))

extract_protocol: Total RNA extracted from PaxGene Blood tubes as per the manufacturer's protocol.

tag: infection type exposure

value: Bacterial

value: Human peripheral bloods


title: Human sample with a Bacterial  infection [408982]


title: Human sample with a Bacterial  infection [408978]


title: Human sample with a Bacterial  infection [408984]


title: Human sample with a Bacterial  infection [408983]


title: Human sample with a Bacterial  infection [408975]


title: Human sample with a Bacterial  infection [408985]


title: Human sample with a Bacterial  infection [408976]


title: Human sample with a Candidemia  infection [408973]

value: Candidemia


title: Wildtype_EtOH_BioRep2


title: Human sample with a Bacterial  infection [408974]


title: Human sample with a Bacterial  infection [408981]


title: Human sample with a Candidemia  infection [408971]


title: Human sample with a Bacterial  infection [408977]


title: Human sample with a Candidemia  infection [408970]


title: Human sample with a Candidemia  infection [408966]


title: Human sample with a Bacterial  infection [408959]


title: Human sample with a Candidemia  infection [408972]


title: Human sample with a Candidemia  infection [408969]


title: Human sample with a Candidemia  infection [408956]


title: Human sample with a Candidemia  infection [408955]


title: Human sample with a Candidemia  infection [408967]


title: Human sample with a Candidemia  infection [408957]


title: Human sample with a Candidemia  infection [408953]


title: Human sample with a Candidemia  infection [408954]


title: Human sample with a Candidemia  infection [408965]


title: Human sample with a Candidemia  infection [408951]


title: Human sample with a Candidemia  infection [408950]


title: Human sample with a Viral  infection [408946]

value: Viral


title: Human sample with a Candidemia  infection [408936]


title: Human sample with a Candidemia  infection [408945]


title: Human sample with a Candidemia  infection [408942]


title: Human sample with a Candidemia  infection [408940]


title: Human sample with a Candidemia  infection [408934]


title: Human sample with a Viral  infection [408928]


title: Human sample with a Candidemia  infection [408933]


title: Human sample with a Viral  infection [408924]


title: Human sample with a Candidemia  infection [408935]


title: Human sample with a Bacterial  infection [408941]


title: Human sample with a Viral  infection [408922]


title: Human sample with a Candidemia  infection [408944]


title: Human sample with a Viral  infection [408920]


title: Human sample with a Viral  infection [408919]


title: Human sample with a Viral  infection [408915]


title: Human sample with a Viral  infection [408930]


title: Human sample with a Viral  infection [408918]


title: Human sample with a Viral  infection [408916]


title: Human sample with a Viral  infection [408912]


title: Human sample with a Viral  infection [408914]


title: Human sample with a Viral  infection [408911]


title: HMGB1koMac_EtOH_BioRep2


title: CD8_60h_PGE2_2

city: Kyoto

first: Shuh

last: Narumiya

state: Kyoto

address: Yoshidahonmachi

department: Department of Drug Discovery Medicine

institute: Kyoto University

data_processing:
fastq files were adaptor trimmed by Trimmomatic
Trimmed reads were aligned to mm10 using HISAT2
Mapped reads with proper pairs were filtered and sort
ht-seq count was used to extract count from sorted BAM
Assembly: mm10
Supplementary files format and content: tab-delimited text files of raw count

source_name: Naïve CD8

growth_protocol: Naïve CD8 T cells were extracted from c57bl/6 mices and stimulated with anti-CD3/CD28 Dynabead (Gibco) with or without 30 nM PGE2 in the presence of 30u/ml IL2 at the indicated time.

extract_protocol:
RNA was extracted from stimulated cells using QIAGEN RNeasy plus micro kit and immediately proceed to reverse transcription
RNA-seq libraries were prepared using SMART-Seq v4 (Takara Bio) Ultra Low Input RNA for Sequencing Kit (24h samples) or Illumina TruSeq stranded mRNA (48h and 60h samples) following manufacturer's protocol.

value: splenocyte

tag: cell line

value: Primary cell

value: naive CD8

value: PGE2 30nM

tag: time


title: CD8_60h_PGE2_3

tag: genotype

tag: treatment


title: Human sample with a Viral  infection [408903]


title: Human sample with a Viral  infection [408907]


title: CD8_60h_PGE2_1


title: Human sample with a Viral  infection [408901]


title: CD8_60h_Vehicle3

value: Vehicle (DMSO)


title: CD8_60h_Vehicle2


title: CD8_48h_PGE2_3


title: CD8_60h_Vehicle1


title: Human sample with a Viral  infection [408906]


title: Human sample with a Viral  infection [408896]


title: Human sample with a Viral  infection [408905]


title: Human sample with a Viral  infection [408897]


title: Human sample with a Viral  infection [408898]


title: Human sample with a Viral  infection [408891]


title: Human sample with a Viral  infection [408889]


title: CD8_48h_PGE2_2


title: Human sample with a Viral  infection [408900]


title: CD8_48h_Vehicle3


title: CD8_48h_PGE2_1


title: CD8_48h_Vehicle2


title: Human sample with a Viral  infection [408893]


title: Biological replicate 6, pertubation: Crypt neo

description: Gene expression data from in-vitro perturbed PBMCs

source_name: Perturbed PBMCs

tag: biological replicate

tag: perturbation

value: Crypt neo

tag: perturbation class

value: Fungal

value: Perturbed PBMCs


title: CD8_48h_Vehicle1


title: CD8_24h_PGE2_2


title: CD8_24h_PGE2_3


title: CD8_24h_PGE2_1


title: Biological replicate 6, pertubation: Candida

value: Candida


title: Biological replicate 6, pertubation: E. coli

value: E. coli


title: Biological replicate 6, pertubation: Crypt gatt

value: Crypt gatt


title: Biological replicate 6, pertubation: St. Pneum

value: St. Pneum


title: CD8_24h_Vehicle3


title: CD8_24h_Vehicle2


title: CD8_24h_Vehicle1


title: Biological replicate 6, pertubation: Poly I:C

value: Poly I:C


title: Biological replicate 6, pertubation: LPS

value: LPS

value: Bacterial


title: Biological replicate 5, pertubation: Crypt gatt