title: HN137PCR, biol rep3

city: Singapore

first: Lih Feng

last: Cheow

address: 15 Kent Ridge Cres

department: iHealthtech

country: Singapore

institute: National University of Singapore

description:
HN137PCR_c
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt

data_processing:
Raw transcripts were quantified using Salmon v.1.5.2 using the parameters -l A --gcBias --seqBias --numGibbsSamples 20 -p 8, with the hg38 genome and GENCODE version 38 as reference
Quantified transcripts were imported to R with tximeta and differential analysis was performed with DESeq2, filtering out genes with less than 10 supporting reads.
Z-scores were calculated with the scale() function after variance normalization with variance stabilizing transformation (VST) to account for count variations caused by highly expressed or lowly expressed genes. The resulting output is a matrix where rows represent genes, columns represent samples, and values represent Z-score. The mean Z-score of the three replicates was calculated as the representative Z-score for each individual PDC.
Assembly: hg38
Supplementary files format and content: Raw transcript count by gene, gene Z-score matrix, and sample metadata

growth_protocol: Cells were cultured with RPMI medium supplied by 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin. Medium was replaced every 2-3 days. Cells were cultured in 37°C and 5% CO2 and passaged when cultures reached ~90% confluency. Cells were tested for mycoplasma and positive cell lines were quarantined and treated with PlasmocureTM (InvivoGen) according to the manufacturer’s protocols. Cells were confirmed to be mycoplasma negative two weeks after treatment. Treatment was then stopped, and cells were still confirmed to be mycoplasma negative two weeks after treatment cessation. Cells are only used for experiments after being confirmed to be mycoplasma negative two weeks after treatment cessation.

extract_protocol:
Total RNA was extracted with the Qiagen RNAeasy Plus Mini Kit (Cat. No. 74136) and quantified with NanoDrop. Triplicates for each cell line (using different passage number) were used
RNA-seq library preparation and directional mRNA-sequencing was carried out by NovogeneAIT

value: Primary patient derived oral cancer cell line

value: Primary Cisplatin Resistant tumor


title: CD8+ NRT cells, scRNA-seq analysis, transcriptomic

status: Public on Nov 18 2024

type: SRA

city: Nanjing

first: Yuncheng

last: Bei

state: Jiangsu

address: Zhongshan Road No.321

department: Oncology

country: China

institute: Nanjing Drum Tower Hospital

library_source: transcriptomic single cell

data_processing:
Illumina NovaSeq 6000 reads were trimmed and clipped for quality control in Trimmomatic v0.27
read quality was checked for each sample using FastQC.
High-quality reads were then imported into TopHat v2.0.8 for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline of Partek Genomics Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq release 2013-5-10). Exclusions included a minimum RPKM value of 1.0 in at least two of the 16 samples (potentially duplicates of one sample group). RPKM values were log2-transformed with an offset value of 1.0.
Assembly: Genome_build: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37).
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: All cells were cultured in AIM-V medium with 10% human AB serum (Valley biomedical, Cat no. HP1022), 50 ng/ml OKT-3 (eBioscience, Cat no. 14-0037-82), 20 IU/ml rhIL-2 (Genscript, Cat no. Z00368-50), 12.5 ng/ml rhIL-7, and 12.5 ng/ml rhIL-15 (Genscript, Cat no. Z00377-50). All cells were incubated at 37oC in 5% CO2.

extract_protocol:
A pool of ~750,000 barcodes are sampled separately to index each cell’s transcriptome. It is done by partitioning cell harvested after neoantigen-specific stimulation into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated cDNAs share a common 10x Barcode. GEMs are generated by combining barcoded Single Cell 5’ Gel Beads, a Master Mix with cells, and Partitioning Oil on Chromium Next GEM Chip G. To achieve single cell resolution, cells are delivered at a limiting dilution, such that the majority (~90 – 99%) of generated GEMs contains no cell, while the remainder largely contain a single cell. Immediately following GEM generation, the Gel Bead is dissolved and any co-partitioned cell is lysed. Oligonucleotides containing an Illumina R1 sequence (read 1 sequencing primer), a 16 nt 10x Barcode, a 10 nt unique molecular identifier (UMI), and  13 nt template switch oligo (TSO) are released and mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents and poly(dT) RT primers. Incubation of the GEMs produces 10x Barcoded, full-length cDNA from polyadenylated mRNA.
Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size prior to 5’ Gene Expression library construction. primers, a sample index, and Illumina R2 sequence (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and Sample Index PCR. The final libraries contain the primers priming sites used in Illumina sequencers
10X5'+VDJ and single-cell RNA-Seq

treatment_protocol: PBMC were isolated from healthy donors, and unfractionated PBMC were firstly exposed to GM-CSF plus IFN- 2A for DC differentiation, and LPS and TLR7/8 ligand R848 (Resiquimod) for DC maturation. Subsequently candidate neopeptides were added. Antigen-pulsed DC facilitated T-cells activation. Finally, exogenous IL-7 was used for sustained expansion of CD4+ and CD8+ antigen-responsive T-cells.

tag: tissue

value: PBMC

tag: cell type

value: CD8+ T cell

tag: treatment

value: neoantigen-specific activation


title: NRAS/AKT TIL, Isotype, scRNA-seq

city: Hong Kong

first: Nickolas

last: Teo

address: 1/F, Laboratory Block, 21 Sassoon Road

department: SBMS

country: Hong Kong

institute: HKU

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were perfomed using Cell Ranger v6.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Mus musculus

source_name: HCC tumor

extract_protocol:
2g of tumor tissue were extracted from cancerous livers, cut into small pieces, and dissociated into cell suspensions using gentleMACS Dissociator (Miltenyi Biotec) in dissociation buffer containing 0.5mg/ml of Collagenase IV (Gibco) and 100μg/ml of DNase I (Goldbio) at 37℃. Single cell suspensions were collected after filtering through a 70μm cell strainer. Immune cells were enriched via a density-gradient centrifugation approach using Percoll (Cytiva), and red blood cells were removed using a Red Blood Cell Lysing Buffer (Sigma). The tumor infiltrating leukocytes were then stained with a fluorescent conjugated antibody specific to CD45 (clone 30-F11, Biolegend) for 20 min at 4°C. Live, single, immune (CD45+) cells were then sort-purified with BD Influx into FBS-containing tubes, and were kept on ice until the cells were further processed for scRNAseq.
Single cell encapsulation and cDNA libraries were prepared with  Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index) and Chromium Next GEM Chip K Single Cell Kit, following manufacturer's instructions

treatment_protocol: NRAS/AKT-driven HCC was induced in B6 mice via HTVI. Mice were culled at 4 weeks after tumor induction for profiling of tumor infiltrating leukocytes

value: HCC tumor

value: Tumor infiltrating leukocytes

tag: sorted cells

value: immune (CD45+) cells

value: Isotype

tag: disease state

value: NRAS/AKT HCC-bearing mice


title: NRAS/AKT spleen, scRNA-seq

description: 10x Genomics

source_name: Spleen

extract_protocol:
Single cell suspensions in complete RPMI (RPMI 1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin) were collected by flushing the bone marrow, or smashing the spleen, and filtering through a 70μm cell strainer. Red blood cells were removed using a Red Blood Cell Lysing Buffer (Sigma). The immune cells were then stained with a fluorescent conjugated antibody specific to CD45 (clone 30-F11, Biolegend) for 20 min at 4°C. Live, single, immune (CD45+) cells were then sort-purified with BD Influx into FBS-containing tubes, and were kept on ice until the cells were further processed for scRNAseq.
Single cell encapsulation and cDNA libraries were prepared with  Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index) and Chromium Next GEM Chip K Single Cell Kit, following manufacturer's instructions

value: Spleen

value: Spleen cells


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient  355

city: Beijing

first: ruoyan

last: Li

address: Yiheyuan street

institute: Peking University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hybrid reference  genome containing human (UCSC hg19) and EBV (NCBI NC_00705.1) reference sequence using Bowtie 2 with default parameters.
Reads mapped to human reference were used to quantify gene expression levels of host genes. We initially used RSEM to calculate the TPM value of each gene and then transformed TPM into log2(TPM+1).
We defined genes with TPM>1 as expressed genes and filtered cells with expressed gene < 2000. Meanwhile, we calculated a house keeping gene score (HKGS) for each cell based on previously defined gene list and filtered cells with HKGS <3.5.For the remining cells, we calculated the aggregate expression Ea of each gene where Ea=log2(average(TMP1...k)+1) and excluded genes with Ea <4. Finally, we calculaed the relative expression value Er of each gene in the form of Eri,j=Ei,j-average[Ei,1...n].
Reads mapped to human reference were used to quantify gene expression levels of host genes. We initially used RSEM to calculate the TPM value of each gene and then transformed TPM into log2(TPM+1).
Reads mapped to EBV genome were retrieved to quantify gene expression levels of virus using Cufflinks. And we used gene coding sequence (CDS) regions to define transcripts of EBV genes in this study.
For 10X genomics, scRNA data generated from 10X Genomics platform was processed using CelllRanger (Version 2.1.0). Firstly,  "CellRanger mkfastq" was used to de-multiplexes raw base call (BCL) files into FASTQ files. Second, "CellRanger count" was used to perform alignment and quantify  gene expression level of single cells through barcode recognizing and UMI counting. For merging cells from different tumors, we used "CellRanger aggr" pipeline and normalized by equalizing the read depth of different libraries. The output was converted to a Seurat object using R Seurat package (version 2.1.0) for further analyses.
For bulk RNA-seq samples, 18 NPC tissues were obtained. Total RNA were isolated by the commercial RNA/DNA extracted kit (Omega,USA) , the cDNA library preparation and sequencing  as reported previously (Lijuan Hu, 2016, Front. Med.). Combining with reported data (Lijuan Hu, 2016, Front. Med.; Li zhang, Mol. Cancer Res.,2018), in total, 141 cases RNA-seq data were for downstream processing. Firstly, paired-end reads from the 141 bulk RNA-seq data were mapped to he human-EBV hybrid genome using TopHat (version 2.1.1) with default parameters. Cufflinks (version 2.2.1) tool suite was then used to quantify gene expression levels [].Briefly, we applied Cuffquant to the BAM file of each sample to calculate gene and transcript expression. Then, the results of all the samples were combined and normalized using Cuffnorm, generating the final expression matrix. This expression matrix was used for further analyses.
We adopted a previous reported sliding-average stragy (Itay etc. 2016, Science) to normalize specific gene expression patterns and infer CNVs.
To infer CNV based on low-pass whole genome sequencing,  paired end reads from low-pass whole sequencing was mapped to hg19 (UCSC) using BWA with default parameters. We removed PCR duplicates using "Samtools rmdup" followed by calculating the coverage depth at each covered base using "Samtools depth". We segmentaed the genome into small windows with 0.5Mb in size and calculated total depth in each window. The total depth of each window was further normalized by the sequencing data volume. Using the Loess normalization, we corrected bias from genomic GC content and calculated depth ratios across he whole genome of tumor samples using total depth of white blood cell samples as controls. Circular binary segmentation (CBS) algorithm documented in R DNA Copy package was used to merge windows with similar depth ratios into genomic segments. The adjacent segments were further joined using MergeLevels.
Genome_build: hg19,NC_007605.1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for host genes of NPC16,NPC17 and NPC36 with full-length method Smart-seq2:NPC16-17-36.list.matrix
Supplementary_files_format_and_content: tab-delimited text files include TPM values for viru genes NPC16,NPC17 and NPC36 with full-length method Smart-seq2:NPC16-17-36.EBV.list.matrix
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC33 with 10x Genomics Chemistry:NPC33-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC36 with 10x Genomics Chemistry:NPC36-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC46 with 10x Genomics Chemistry:NPC46-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC47 with 10x Genomics Chemistry:NPC47-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC49 with 10x Genomics Chemistry:NPC49-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  all the NPC cases of bulk RNA-seq including 18 new patients:Bulk_RNA-seq_genes.fpkm_table.txt

source_name: NPC tissue

extract_protocol:
Fresh tumors were transported in RPMI-1640 immediately on ice after resection. Rising the NPC biopsies with PBS(pH7.4), tumor tissues were minced into tiny cubes about 1-2mm3. Enzymatically dissociated the pieces of tissues into single-cell suspension. Then the cells were used for staining and FACS. The targeting single cell was sorted into a  96-well plate which containing lysis buffer including oligo dT30 primer, dNTP mix, 0.1% Triton-100 and RNase inhibitor.
The full-length cDNA is synthesized through the template-switching oligo and SS II reverse transcriptase (Invitrogen). cDNA is amplified using KAPA HiFi HotStartReadyMix (KAPA Biosysytems). Full length cDNA libraries were barcoded using the TruePreTM DNA Library Prep Kit V2 protocol (Vazyme Biotech Co.). For 10x gemomic experiments, we followed the 10X genomics chemistry.

value: NPC primary tumor

value: nasopharynx

tag: tumor stage

tag: age


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient  293


title: NRAS/AKT bone marrow, scRNA-seq

description: 10x Genomics

source_name: Bone marrow

value: Bone marrow

value: Bone marrow cells


title: HN137PCR, biol rep1

description:
HN137PCR_a
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt

tag: cell line


title: HR-1-Input

city: nanjing

first: yongfei

last: li

address: No.155 Hanzhong Road

department: Department of Mastopathy

institute: The Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of TCM)

data_processing:
library strategy: meRIP-seq
Agilent 2100 Bioanalyzer was used to detect library quality
The library concentration was diluted to 8 pM and the hiseq300/4000 PE Cluster Kit (# pe-410-1001, Illumina) was used to generate clusters in Illumina cBot
Illumina HiSeq 4000 was used for sequencing
 statistic analysis; HISAT2
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: peaks_mRNA.xlsx

source_name: breast cancer cell

growth_protocol: The breast cancer cell line BT474 and BT474.TtzmR were cultured routinely in DMEM (Gibco-Invitrogen, Carlsbad, CA, USA), with 10% Fetal Bovine Serum (FBS), with Penicillin Streptomycin (Gibco) at 37C in an atmosphere of 5% CO2 in air.

extract_protocol:
Enrichment of RNA fragments containing m6A methylation sites by immunoprecipitation with anti-n6-methyadenosine (m 6A) antibodies
The sequencing libraries of post-m6a mRNA and input mRNA were constructed respectively with KAPA Stranded mrna-seq Kit

tag: cell line background

value: resistant cells


title: SiglecFhi coculture, replicate 3

description:
SiglecF_hi_CC_3
RIL_coculture_counts.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore.
Trimed reads were mapped to UCSC mouse genome mm10 using STAR
Gene counts were quantified by featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each sample

growth_protocol: RIL-175 cells were cultured in complete RPMI (RPMI 1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin)

extract_protocol:
High-quality total RNA was extracted using RNeasy Mini Kit (Qiagen)
PolyA enrichment RNA seq

treatment_protocol: RIL-175 cells were cultured overnight with or without the presence of sort-purified TANs

value: SiglecFhi coculture


title: HR-1-IP

tag: antibody

value: anti-m6A antibody


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient  292


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient  288


title: HS-1-IP

value: sensitive cells


title: SiglecFhi coculture, replicate 2

description:
SiglecF_hi_CC_2
RIL_coculture_counts.txt


title: C4-2 cells, TIZ 16 h, repeat 3

city: Augusta

first: Chunhong

last: Yan

state: GA

address: 1410 Laney Walker Blvd

department: Georgia Cancer Center

country: USA

institute: Augusta University

data_processing:
BCL files generated by sequencing were converted to FASTQ files for the downstream analysis. Reads passed the quality control were aligned to the reference genome through Tuxedo Suite starting with TopHat aligner. The generated BAM files in a comparative setup were imported to the Cufflinks and Cuffdiff tools for outputting differentially-expressed genes with log2 fold changes.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: prostate

growth_protocol: C4-2 cells were cultured in RPMI 1640 supplemented with 10% of FBS.

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qigene). 0.8- 1ug of total RNA samples with an RNA integrity number > 5 were processed for cDNA library preparations.
Libraries were prepared using the TruSeq Standard Total RNA Ribo-zero kit from Illumina following the manufacturer's protocol.

treatment_protocol: The cells were treated with 20 uM of TIZ or DMSO for 16 h.

value: prostate

value: prostate cancer cells

tag: genotype

value: WT

value: TIZ


title: SiglecFhi coculture, replicate 1

description:
SiglecF_hi_CC_1
RIL_coculture_counts.txt


title: C4-2 cells, TIZ 16 h, repeat 2


title: HN137Met, biol rep3

description:
HN137Met_c
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt

value: Primary patient derived oral cancer cell line

value: Metastatic tumor


title: HN137Met, biol rep2

description:
HN137Met_b
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt


title: HN137Met, biol rep1

description:
HN137Met_a
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt


title: SiglecF- coculture, replicate 3

description:
SiglecF_neg_CC_3
RIL_coculture_counts.txt

value: SiglecF- coculture


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient  271


title: HN137Pri, biol rep3

description:
HN137Pri_c
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt

value: Primary tumor


title: C4-2 cells, TIZ 16 h, repeat 1


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient  282


title: HN137PCR, biol rep2

description:
HN137PCR_b
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt

value: Primary Cisplatin Resistant tumor


title: SiglecF- coculture, replicate 2

description:
SiglecF_neg_CC_2
RIL_coculture_counts.txt


title: HN137Pri, biol rep2

description:
HN137Pri_b
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt


title: SiglecF- coculture, replicate 1

description:
SiglecF_neg_CC_1
RIL_coculture_counts.txt


title: C4-2 cells, DMSO 16 h, repeat 3

value: DMSO control


title: HN137Pri, biol rep1

description:
HN137Pri_a
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt


title: No TAN coculture, replicate 2

description:
No_TAN_CC_2
RIL_coculture_counts.txt

value: No coculture


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient  211

value: NPC primary tumor

value: nasopharynx


title: HN120PCR, biol rep3

description:
HN120PCR_c
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt


title: C4-2 cells, DMSO 16 h, repeat 1


title: C4-2 cells, DMSO 16 h, repeat 2


title: No TAN coculture, replicate 1

description:
No_TAN_CC_1
RIL_coculture_counts.txt


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 138


title: ATAC_URF_3

city: Rehovot

first: Ido

last: Goldstein

address: POB 12

department: Institute of Biochemistry, Food Science and Nutrition

country: Israel

institute: The Hebrew University of Jerusalem

library_source: genomic

data_processing:
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Assembly: mm10

molecule: genomic DNA

source_name: Liver

growth_protocol: Mice were subjected to either a 4-week alternate day fasting (ADF) regimen or unrestricted feeding (URF). At the end of the experiment mice were divided to 3 groups: the first group was euthanized after a 24 h fasting period (ADF_f or URF_f). The second group fasted for 24 h followed by ad libitum refeeding for 24 h at the end of which they were euthanized (ADF_re or URF_re). The third group did not experience any type of fasting (unrestricted feeding). Each group has 3 replicates.

extract_protocol:
To isolate nuclei, liver samples (50 mg) were homogenized in hypotonic sucrose buffer (250 mM sucrose, 10 mM Tris-Hcl pH 7.8, 0.1% Igepal, 3mM MgCl2, 10mM KCl, 0.2 mM Dithiothreitol, 0.5 mM spermidine, protease inhibitor cocktail) in a dounce homogenizer. Homogenate was filtered through a 20 µM filter, spun and washed (10 mM Tris-Hcl pH 7.5, 3 mM MgCl2, 10 mM NaCl, 0.1% tween-20). 50,000 nuclei were included for next steps as described (Korenfeld et al., 2023). Each sample was sequenced at a depth of at least 50X10^6 reads (paired-end).
ATAC-seq libraries were prepared using specific DNA Barcodes and Q5 High-Fidelity DNA Polymerase from New England Biolabs. Libraries were amplified using 13 cycles on the thermocycler. PCR-amplified DNA was purified using a MinElute PCR purification kit from Qiagen following manufacturer’s instructions. Post amplification libraries were size selected at 150-400nt in length using magnetic AMPure XP beads from Beckman Coulter.

value: Liver

value: wt

value: unrestricted feeding


title: HN120PCR, biol rep2

description:
HN120PCR_b
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt


title: Sort-purified SiglecFhi TAN, replicate 2

description:
Purified_SiglecF_hi_2
Purified_TAN_counts.txt

source_name: Tumor-associated-neutrophil

value: Tumor-associated-neutrophil

value: SiglecFhi TAN


title: ATAC_URF_2


title: HN120Met, biol rep3

description:
HN120Met_c
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt


title: Sort-purified SiglecFhi TAN, replicate 1

description:
Purified_SiglecF_hi_1
Purified_TAN_counts.txt


title: ATAC_URF_1


title: HN120PCR, biol rep1

description:
HN120PCR_a
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt


title: Zebrafish endothelial cells 3 dpf 1

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: zebrafish endothelial cells

data_processing:
Cell Ranger v2.1 was used to de-multiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files, perform the alignment, barcode counting, and UMI counting.
Assembly: GRCz11
Supplementary files format and content: Tab-seprated values files

organism: Danio rerio

source_name: Whole body

extract_protocol:
Whole Tg(kdrl:EGFP) zebrafish embryos were digested into single cell suspensions, EGFP-positive cells were isolated using FACS
Single-cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v2 (10X Genomics) according to manufacturer’s protocol.

value: Whole body

value: embryo


title: Sort-purified SiglecF- TAN, replicate 2

description:
Purified_SiglecF_neg_2
Purified_TAN_counts.txt

value: SiglecF- TAN


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient  259


title: Sort-purified SiglecF- TAN, replicate 1

description:
Purified_SiglecF_neg_1
Purified_TAN_counts.txt


title: Treated GA CL young 5

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

data_processing:
Sequencing raw data (bcl) were demultiplexed and transformed in fastq files using cassava v1.8.2.
The fastq files were aligned against the reference genome by RNAstar v2.5.3a.
The raw sequencing counts per gene were generated using htseq_count v2.16.2 using Mus_musculus.GRCm38.93_proteinCoding_lincRNA.gtf
Assembly: GRCm38
Supplementary files format and content: raw_count_s38g27554_mouseGastroc.csv
Supplementary files format and content: comma-separated file containing count data per gene (row) per mouse (column)

source_name: muscle

extract_protocol:
RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical).
Libraries were quantified with the Quant-iT Picogreen (Invitrogen, 10545213) on a FilterMax F3 (Molecular Devices, F3). Size pattern was assessed with Fragment Analyzer-96 with the DNF-474-0500 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, DNF-474-0500).
Libraries (Average size: 295 bp) were pooled at an equimolar ratio and clustered at a concentration of 9 pM on a single read sequencing flow cell.

treatment_protocol: Compounds (resuspended in 1% Sodium Carboxymethyl cellulose) were administered daily via oral gavage, starting prior to the injury and continuing for 5 days post-injury. The concentration of NAM (200mg/kg per day) and PN (4mg/kg day) were used. Vehicle-treated mice received an equivalent volume of 1% Sodium Carboxymethyl cellulose.

value: gastrocnemius

value: muscle

tag: group

value: Controlateral leg

tag: time

tag: Sex

value: male

value: Young

tag: mouseid


title: HN120Met, biol rep1

description:
HN120Met_a
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt

value: Primary patient derived oral cancer cell line

value: Metastatic tumor


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient  258

value: NPC primary tumor


title: HN120Pri, biol rep3

description:
HN120Pri_c
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt

value: Primary tumor


title: Treated GA CL young 4


title: Treated GA CL old 6

value: Old


title: C1-D7

city: Vestec

first: Lukas

last: Valihrach

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science

description: 10x Genomics

data_processing:
The raw sequencing data were processed using the recommended set of Spaceranger function (v1.2.2, 10X Genomics) for processing of fresh frozen samples. Binary base call files were demultiplexed using mkfastq function with default parameters, to generate FASTQ files.
The resulting fastq files were mapped separately to spaceranger reference (mm10/GRCm38) using count function, which takes a microscope slide image and fastq files, performs alignment, tissue detection, fiducial detection, and barcode/UMI counting.
Assembly: mm10/GRCm38
Supplementary files format and content: bardcodes.tsv: list of spatial barcodes
Supplementary files format and content: features.tsv: list of gene Ids
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: *.json: json file of tisue aligned to fiducial frame
Supplementary files format and content: *.tif: image of tissue
Library strategy: Spatial transcriptomics

source_name: brain

extract_protocol:
Mice were deeply anesthetized with pentobarbital and perfused transcardially with cold (4–8C) isolation buffer.. The forebrain hemisphere was isolated by dissection of the olfactory lobes and the midbrain structure (bregma from ~ +3 to -4 mm). Dissected forebrains were embedded in optimal cutting temperature (OCT) medium, rapidly placed on dry ice to freeze, and then transferred to -80C for a maximum of six weeks of storage. The forebrains were sectioned coronally (10 um thickness) using Leica CM1950 cryostat (Leica Microsystems). Sections collected for 10X Visium Spatial Gene Expression processing were stored at -80C.
Sequencing libraries were prepared strictly according to the manufacturer’s manual “Visium Spatial Gene Expression Reagent Kits User Guide” (CG000239).

treatment_protocol: Prior to the induction of MCAO, mice were anaesthetized with 3% isoflurane (Aerrane, Baxter) and amaintained in 2% isoflurane using a vaporizer (Tec-3, Cyprane Ltd.). A skin incision between the orbit and the external auditory meatus was made, and a 1-2 mm hole was drilled through the frontal bone 1 mm rostral to the fusion of the zygoma and the squamosal bone, about 3.5 mm ventrally to the dorsal surface of the brain. The middle cerebral artery (MCA) was exposed after the dura was opened and removed. The MCA was occluded by short coagulation with bipolar tweezers (SMT) at a proximal location, followed by transection of the vessel to ensure permanent occlusion. During the surgery, body temperature was maintained at 37 ± 1C using a heating pad. This MCAO model yields small infarct lesions in the parietal cortical region. Intact cortical tissue from 3 months old mice was used as control.

value: brain

tag: model

value: pMCAO

tag: strain

value: 3 month

tag: condition

value: 7 days


title: HN120Pri, biol rep2

description:
HN120Pri_b
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt

tag: cell type


title: Zebrafish endothelial cells 3 dpf 2

description: zebrafish endothelial cells

tag: tissue

value: Whole body


title: Control GA Injured young 5

value: Injured leg

tag: treatment

value: Control


title: FO

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: iPS-Hep org CHIR

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

value: iPSC derived hepatocyte organoids


title: D1-D3

description: 10x Genomics

value: 3 days


title: HO_Grape

source_name: iPS-Hep org Wnt(+)


title: Zebrafish endothelial cells 34 hpf

description: zebrafish endothelial cells

value: embryo


title: 623_recurrent

city: Basel

first: Sabrina

middle: Annie

last: Hogan

address: Hebelstrasse 20

institute: University of Basel

hyb_protocol: Gene expression code sets were hybridized in a thermocycler for 18 h at 65 °C prior to being processed in the nCounter Prep Station (Nanostring Technologies, USA)

scan_protocol: Gene expression was assessed using the nCounter PanCancer IO 360 panel comprising 770 genes  (including 10 house-keeping genes, NanoString Technologies, Seattle, WA), using 50 ng of total RNA per tumor sample

data_processing:
each panel was normalised separately using the limma package and  between-samples cyclic loess normalization
The matrix table displays log2 transformed cpm

label: Iso360 panel

source_name: GMB

label_protocol: slides were stained using a mixture of conjugated antibodies for identification of tissue morphology: anti-GFAP-594 (Novus Biologicals, NBP2-33184DL594; 1:1000) and anti-CD64 (purified with Abcam purification kit (ab102784) and conjugated with AlexaFluor647 (ab269235); 1:50) for the labeling of tumor cells and myeloid cells, respectively. In addition, Syto83 was used for DNA labeling (ThermoFisher Scientific, USA, 1:25)

growth_protocol: GBM tissue samples were collected directly in the operating theater during primary (first) and recurrent (second) surgeries and immediately stored in RNAlater stabilization solution (Thermo Fisher Scientific, USA) on ice and stored at -80 °C until further use.

extract_protocol: Tumors were mechanically dissociated in lysis buffer using a syringe equipped with a 23G needle, and total RNA was extracted using the AllPrep DNA/RNA/protein mini Kit (Qiagen, USA, Cat. No. / ID: 80004) according to the manufacturer’s protocol

value: recurrent

tag: relapse time (d)

tag: patientid


title: B1-D1

description: 10x Genomics

tag: age

value: male

value: 1 day


title: Treated GA CL old 5

value: gastrocnemius

value: muscle

value: Controlateral leg


title: HN120Met, biol rep2

description:
HN120Met_b
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt

tag: cell line

value: Primary patient derived oral cancer cell line

tag: disease state

value: Metastatic tumor


title: 623_primary

value: primary


title: C1-control

description: 10x Genomics

value: brain

value: control

value: 3 month


title: Control GA CL old 6

value: Old


title: 3mo_INSGAS_072321_43

city: Nashville

first: Holly

last: Algood

address: 1301 24th Ave South

department: Research

institute: Department of Veterans Affairs

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-36

hyb_protocol: Hybridization master mix (8ul) added to each RNA sample (5ul); Capture ProbeSet then aliquoted (2ul each) into each RNA sample tube. After flick to mix and brief spin, hybridized at 65C in prewarmed themocycler for 16-24 h

scan_protocol: nCounter cartridge was loaded with 30ul of hybridization product (diluted from 15ul initial product); nCounter profiler was used as an epifluorescence scanner Per: manufacturer protocol (nanoString).

data_processing: Multiple fields of view (FOVs) are imaged within each sample lane; Fields of View (FOVs) are processed internally, counting the number of each fluorescent reporter tag, and the results are exported as a comma separated values (CSV) file, called an RCC (Reporter Code Count) file.

source_name: Glandular Stomach

label_protocol: Immobilized fluorescent reporters in the cartridge (Nanostring nCounter Cartridge)

growth_protocol: Not Applicable

extract_protocol: On average, 1/4 total stomach tissue were prepared for the extraction of total RNA, Trizol method was used for extraction (including GentleMACs disocciator) followed by Qiagen RNAeasy clean up per manufacturers instructions.

treatment_protocol: Some mice were infected with H. pylori at 2 months of age for 3 months; uninfected mice were age matched (5 mo old).

value: InsGAStg/tg

tag: infection

value: Infected

tag: lymphoid follicles

value: No

tag: dysplasia

value: Signs

tag: cancer


title: 3mo_INSGAS_072321_41

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-35

tag: genotype


title: day 7 [snRNA-Seq]

description: 10x Genomics

data_processing:
Libraries were controlled for contamination using fastq_screen v0.11.1. Reads were mapped against the mouse genome GRCm38 and counted using annotation genecode.vM8 using STAR v2.7.3a with parameters “--soloType CB_UMI_Simple --soloFeatures GeneFull –soloCBmatchWLtype 1MM_multi_pseudocounts –soloUMIdedup 1MM_Directional –soloUMIfiltering MultiGeneUMI”. Empty droplets were filtered out using emptyDrops command from DropletUtils package (v 1.14.1) with lower parameter set to 1000. Background RNA was removed using SoupX package (v 1.5.2) set at the default parameters.
Assembly: mm10/GRCm38
Supplementary files format and content: bardcodes.tsv: list of cell barcodes
Supplementary files format and content: features.tsv: list of gene Ids
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format

extract_protocol:
Injured forebrain hemispheres were frozen on dry ice and stored at -80 °C until processing. For each condition, three hemispheres were collected and pooled during the single-nucleus suspension preparation. All steps for nuclei isolation were performed on ice, with instruments and plastics pre-chilled on ice, or centrifugation steps at 4°C. The frozen brain tissues were combined with 2 ml of lysis buffer (10 mM Tris, pH = 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1 % NP-40; 0.2 U/ul RNaseOUT; 0.32 M Sucrose; 1x protease inhibitor, Roche) and transferred to 2 ml Dounce tissue grinder (Sigma). Tissues were homogenized by 20 strokes with pestle A, followed by 20 strokes with pestle B and filtered using 30 um filter (Celltricks). Tissue grinder was rinsed with 1 ml HEB buffer (Hibernate A, ThermoFisher; 10 ul/ml GlutaMAX, ThermoFisher; 0.32 M Sucrose) and the wash filtered into the same tube. Homogenates were split by careful pipetting of 1.2 ml into two 2 ml tubes prefilled with 500 ul sucrose cushion (1.2 M sucrose; 10 mM Tris; 10 mM NaCl; 3 mM MgCl2; 0.2 U/ul RNase OUT) and centrifuged at 13000 g for 20 minutes at 4°C. Supernatants were removed, except 100 ul to keep the pellets covered. Pellets with the remaining supernatant were resuspended in 1 ml sucrose solution (1.0 M sucrose; 10 mM Tris; 10 mM NaCl; 3 mM MgCl2; 0.2 U/ul RNase OUT), pipetted into 2 ml tubes prefilled with 500 ul sucrose cushion and again centrifuged at 13000 g for 20 minutes at 4°C. Supernatants were removed and the pellets resuspended in 1 ml of Nuclei Wash Buffer (DPBS without calcium and magnesium; 0.5 % BSA; 0.2 U/ul RNase OUT; all ThermoFisher) and transferred into 1.5 ml tubes. Samples were centrifuged at 500 g for 5 minutes, the pellets resuspended in 1 ml of Nuclei Wash Buffer and centrifuged again. The final pellets with nuclei were resuspended in 1 ml of Nuclei Wash Buffer and filtered using 30 um filter. Nuclei stained with Propidium Iodide were counted using CellDrop Automated Cell Counter (Denovix) at default settings. Nuclei suspensions were diluted to final concentrations of 1000 nuclei/ul and single-nucleus RNA-Seq (snRNA-Seq) libraries were prepared.
Single-nucleus RNA-Seq (snRNA-Seq) libraries were prepared using Chromium Next GEM Single Cell 3' Kit v3.1 (1000268, 10X Genomics) according to the manufacturer’s protocol.

tag: Sex

value: 7 days


title: 608_recurrent

value: recurrent


title: 3mo_INSGAS_072321_40

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-34


title: D1-D7

description: 10x Genomics

tag: model

value: pMCAO

value: male


title: Control GA Injured old 3

value: gastrocnemius

value: muscle

tag: group

value: Injured leg

tag: time

value: Control

tag: mouseid


title: day 3 [snRNA-Seq]

description: 10x Genomics

tag: tissue

tag: strain

tag: condition

value: 3 days


title: 3mo_INSGAS_072321_36

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-33


title: iHO_others

source_name: iPS-Hep org Wnt(-)

tag: cell type

value: iPSC derived hepatocyte organoids


title: 3mo_INSGASxIL17KO_072221_46

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-32

value: InsGAStg/tg x Il17raKO

value: Yes


title: Treated GA Injured young 3

tag: treatment

tag: age

value: Young


title: Treated GA CL young 3

value: Controlateral leg


title: HN120Pri, biol rep1

description:
HN120Pri_a
snCUTRUN_RNAseq_metadata.csv
snCUTRUN_RNAseq_raw_count.txt
snCUTRUN_RNAseq_Zscores.txt

tag: cell line

value: Primary patient derived oral cancer cell line

tag: disease state

value: Primary tumor


title: 599_recurrent

tag: relapse time (d)

tag: patientid


title: 3mo_INSGASxIL17KO_072221_45

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-31

tag: infection

value: Infected

tag: lymphoid follicles

tag: dysplasia

tag: cancer


title: Control GA CL old 5

tag: group

tag: Sex

value: Old


title: sham [snRNA-Seq]

description: 10x Genomics

value: brain

value: 3 month

value: sham control


title: 551_recurrent

value: recurrent


title: Treated GA CL old 4

value: gastrocnemius

value: muscle

tag: time

value: male

tag: mouseid


title: day 7 [scRNA-Seq]

description: 10x Genomics

data_processing:
Libraries were controlled for contamination using fastq_screen v0.11.1. Reads were mapped against the mouse genome GRCm38 and counted using annotation genecode.vM8 using STAR v2.7.3a with parameters “--soloType CB_UMI_Simple --soloFeatures Gene –soloCBmatchWLtype 1MM_multi_pseudocounts –soloUMIdedup 1MM_Directional –soloUMIfiltering MultiGeneUMI”. Empty droplets were filtered out using emptyDrops command from DropletUtils package (v 1.14.1) with lower parameter set to 1000.
Assembly: mm10/GRCm38
Supplementary files format and content: bardcodes.tsv: list of cell barcodes
Supplementary files format and content: features.tsv: list of gene Ids
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format

extract_protocol:
The Plp1/tdTomato mice were deeply anesthetized with pentobarbital (PTB) (100 mg/kg, i.p.), and perfused transcardially with a cold (4–8°C) isolation buffer containing (in mM): NaCl 136.0, KCl 5.4, HEPES 10.0, glucose 5.5, osmolality 290±3 mOsmol/kg. To isolate the control and ischemic areas, the brain was sliced into 600 µm coronal sections using a vibrating microtome Leica VT1200S (Leica Microsystems). The collected tissue was incubated with continuous shaking at 37°C for 45 min in 1 ml of papain solution (20 U/ml) and 0.2 ml DNase (both from Worthington) prepared in isolation buffer. After papain treatment, the tissue was mechanically dissociated by gentle trituration using a 1 ml pipette. The dissociated cells were layered on top of 5 ml of ovomucoid inhibitor solution (Worthington) and harvested by centrifugation (70 x g for 6 min). This method routinely yielded ~2 x 10^6 cells per mouse brain. Cell aggregates were removed by filtering with 70 µm cell strainers (Becton Dickinson). Three animals per condition were pooled in the preparation of cell suspension. After obtaining an aliquot for FACS, the cell suspension was spin down, concentrated, and used for library preparation. Single cell suspension from Plp1/tdTomato mice were sorted using fluorescent activated cell sorting (FACS; BD Influx). The flow cytometer was manually calibrated to deposit a single cell in the center of collection tube. Hoechst 33258 (Life Technologies) was added to the suspension of cells to check viability. 3000 Plp1+ cells from each group (control, D1, D3, D7) were collected into 96-well plates (Life Technologies) coated with BSA (ThermoFisher Scientific) and containing 5 μl of DMEM (ThermoFisher Scientific) and 15% FBS (HyClone).
Single-cell RNA-Seq (scRNA-Seq) libraries were prepared using Chromium Next GEM Single Cell 3' Kit v3.1 (1000268, 10X Genomics) according to the manufacturer’s protocol.

tag: tissue

tag: strain

value: 7 days


title: day 1 [snRNA-Seq]

description: 10x Genomics

tag: condition

value: 1 day


title: 3mo_INSGASxIL17KO_072221_44

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-30

tag: genotype

value: InsGAStg/tg x Il17raKO

value: No


title: day 1 [scRNA-Seq]

description: 10x Genomics

tag: age


title: 551_primary

value: primary


title: day 3 [scRNA-Seq]

description: 10x Genomics

value: 3 days


title: 3mo_INSGAS_072221_28

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-29

value: InsGAStg/tg

value: Signs


title: 545_recurrent


title: Control GA Injured young 4

value: Injured leg

tag: treatment

value: Control

value: Young


title: 545_primary


title: 3mo_INSGAS_072221_27

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-28

value: Infected


title: 608_primary


title: 3mo_INSGAS_072221_26

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-27


title: sham [scRNA-Seq]

description: 10x Genomics

value: brain

value: 3 month

value: sham control


title: liver endothelial cell, Cd146, P16sh 6

city: Nice

first: Kay-Dietrich

last: Wagner

address: 28 Avenue Valombrose

department: Institute of Biology Valrose

country: France

institute: INSERM

data_processing:
Data processing step: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: mm9
Supplementary files format and content: Excel file containing reads and Fpkm values for all samples and genes

source_name: liver

extract_protocol:
Trizol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.
For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: liver

tag: cell type

value: ENDOTHELIAL CELL


title: 532_recurrent

value: recurrent

tag: relapse time (d)


title: 3mo_INSGASxIL17KO_070621_33

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-26

value: Yes


title: Control GA CL young 6

value: gastrocnemius

value: muscle

value: Controlateral leg

value: male


title: liver endothelial cell, Cd146, P16sh 5


title: 599_primary

value: primary

tag: patientid


title: Control GA Injured young 3


title: Control GA CL old 4

value: Old


title: 496_recurrent


title: liver endothelial cell, Cd146, p16 overexpression 5


title: Treated GA Injured old 4

value: Injured leg


title: 3mo_INSGASxIL17KO_070621_31

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-24

value: InsGAStg/tg x Il17raKO

tag: infection


title: liver endothelial cell, Cd146, no-coding control 5


title: Control GA CL old 3

value: Control


title: Control GA CL young 5

value: Young


title: 496_primary


title: 417_primary


title: 417_recurrent


title: Treated GA Injured young 2


title: liver endothelial cell, Cd146, empty control 4


title: 3mo_INSGASxIL17KO_070621_29

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-22

value: Infected

tag: lymphoid follicles

value: Signs

value: No


title: Control GA CL old 2


title: 3mo_INSGASxIL17KO_070621_30

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-23

tag: dysplasia


title: liver endothelial cell, Cd146, empty control 5

value: liver


title: 3mo_INSGASxIL17KO_070621_32

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-25

tag: cancer


title: liver endothelial cell, Cd146, P16sh 3

value: ENDOTHELIAL CELL


title: liver endothelial cell, Cd146, p16 overexpression 3


title: 380_recurrent

value: recurrent


title: Treated GA CL young 2

tag: group


title: 380_primary


title: Control GA CL young 4

tag: Sex


title: 532_primary


title: 3mo_INSGASxIL17KO_070621_27

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-20

value: Yes


title: 3mo_INSGASxIL17KO_070621_28

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-21


title: 3mo_INSGAS_070621_20

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-18

value: InsGAStg/tg


title: 3mo_INSGAS_070621_18

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-17


title: Treated GA CL young 1

value: gastrocnemius

value: muscle

tag: time


title: liver endothelial cell, Cd146, no-coding control 3


title: 356_recurrent


title: Control GA Injured young 2

value: male

tag: mouseid


title: 3mo_INSGASxIL17KO_050521_09

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-16


title: 356_primary

value: primary


title: liver endothelial cell, Cd146, p16 overexpression 1

tag: tissue


title: 291_recurrent


title: 291_primary


title: 3mo_INSGASxIL17KO_050521_08

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-15


title: Treated GA Injured old 3

value: Old


title: 3mo_INSGAS_070621_21

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-19


title: liver endothelial cell, Cd31, p16 overexpression 5


title: liver endothelial cell, Cd146, no-coding control 1


title: Control GA CL young 3

value: Controlateral leg


title: Control GA CL old 1


title: 3mo_INSGASxIL17KO_050521_07

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-14

value: InsGAStg/tg x Il17raKO


title: Control GA Injured old 2

value: Injured leg

value: Control


title: 282_recurrent


title: 3mo_INSGASxIL17KO_050521_06

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-13

value: Infected


title: liver endothelial cell, Cd31, P16sh 3


title: 195_recurrent


title: Treated GA CL old 3


title: 282_primary


title: liver endothelial cell, Cd31, empty control 5


title: 3mo_INSGAS_050521_03

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-11

value: Signs


title: 3mo_INSGAS_050521_04

description:
Total RNA sample from glandular stomach of Helicobacter pylori infected mouse; used to quantify expression of 750 unique genes
6982-HA-12

value: No


title: liver endothelial cell, Cd31, p16 overexpression 3

value: liver


title: 195_primary


title: Uninfected INSGASxIL17RAKO_021221_10

description:
Total RNA sample from glandular stomach of mouse (uninfected control); used to quantify expression of 750 unique genes
6982-HA-10

value: Uninfected


title: Uninfected INSGASxIL17RAKO_021221_09

description:
Total RNA sample from glandular stomach of mouse (uninfected control); used to quantify expression of 750 unique genes
6982-HA-9


title: 185_recurrent

value: recurrent


title: liver endothelial cell, Cd31, no-coding control 3

value: ENDOTHELIAL CELL


title: 185_primary


title: liver endothelial cell, Cd31, P16sh 2


title: Control GA Injured old 1


title: liver endothelial cell, Cd31, p16 overexpression 2


title: 182_recurrent


title: Uninfected INSGASxIL17RAKO_021221_08

description:
Total RNA sample from glandular stomach of mouse (uninfected control); used to quantify expression of 750 unique genes
6982-HA-8


title: liver endothelial cell, Cd31, no-coding control 2


title: Treated GA Injured old 2


title: 94_recurrent


title: 182_primary


title: Control GA Injured young 1

value: Young


title: Uninfected INSGASxIL17RAKO_021221_07

description:
Total RNA sample from glandular stomach of mouse (uninfected control); used to quantify expression of 750 unique genes
6982-HA-7


title: liver endothelial cell, Cd146, empty control 2


title: liver endothelial cell, Cd31, P16sh 1


title: Control GA CL young 2

value: gastrocnemius


title: Treated GA Injured old 1

value: muscle


title: 94_primary


title: Treated GA CL old 2

value: male


title: liver endothelial cell, Cd31, no-coding control 1


title: Treated GA CL old 1


title: Uninfected INSGAS_021221_05

description:
Total RNA sample from glandular stomach of mouse (uninfected control); used to quantify expression of 750 unique genes
6982-HA-5

value: InsGAStg/tg


title: Uninfected INSGAS_021221_04

description:
Total RNA sample from glandular stomach of mouse (uninfected control); used to quantify expression of 750 unique genes
6982-HA-4


title: Treated GA Injured young 1


title: liver endothelial cell, Cd31, empty control 1


title: 38_recurrent


title: 38_primary

value: primary


title: Uninfected INSGAS_021221_02

description:
Total RNA sample from glandular stomach of mouse (uninfected control); used to quantify expression of 750 unique genes
6982-HA-2


title: liver endothelial cell, Cd31, empty control 2


title: Uninfected INSGASxIL17RAKO_021221_06

description:
Total RNA sample from glandular stomach of mouse (uninfected control); used to quantify expression of 750 unique genes
6982-HA-6


title: Female pubertal n-6 polyunsaturated fatty acid mammary epitheial cells, WT2

status: Public on Nov 17 2024

city: Guelph

first: Connor

last: Buchanan

state: Ontario

address: 50 Stone Road East

department: Human Health and Nutritional Sciences

country: Canada

institute: University of Guelph

data_processing:
The pilot dataset was analyzed following the protocol from Pertea et al  (the ``new Tuxedo” package)
The reads from the samples were mapped to the reference genome GRCM38 using HISAT2
All six samples had an overall alignment rate greater than 97%.
The alignments were then passed to String Tie for transcript assembly and quantification.
The transcript abundance matrix from String Tie was then used for differential expression analysis using two different approaches: edgeR and DESeq2.
Assembly: GRCM38 using HISAT2
Supplementary files format and content: text file countains raw gene counts for each sample

source_name: inguinal mammary gland

extract_protocol:
RNA was extracted using the Purelink RNA Mini Kit (Thermo Fisher Scientific, cat # 12183018A) following the kit instructions. The purity of the RNA was assessed using the Agilent bioanalyzer 2100 where all samples had a RNA integrity number (RIN) greater than 9 (out of a 10 point scale). RNA samples were stored at -80 ℃ for later analysis.
mRNA library

treatment_protocol: Mammary epithelial cells were isolated using the Prater method. In brief, finely minced mammary glands were digested in collagenase/hyaluronidase (StemCell, cat # 07912) for 18 h at 37◦C to allow for tissue dissociation. Cells were washed in Hank’s balanced salt solution (Sigma, cat # H6648) and treated with ammonium chloride (Sigma, cat # A9434), Trypsin/EDTA (Sigma, cat # T4049), dispase (StemCell, cat # 07913) and DNAase 1 (Sigma, cat # D5025) to release the epithelial cells. Five million cells were used for total RNA extraction

value: Female

value: Puberty (6-8 weeks)

value: inguinal mammary gland

value: pooled mammary epitheial cell

value: Wildtype (FVB/NJ)

tag: diet

value: Modified AIN93G diet (Research Diets Inc.), 22% kcal from fat, 10% fat (w/w) from safflower oil

tag: time of_dietary_exposure

value: Maintained on Parental Diet (lifelong)


title: Uninfected INSGAS_021221_01

description:
Total RNA sample from glandular stomach of mouse (uninfected control); used to quantify expression of 750 unique genes
6982-HA-1

tag: genotype

value: No


title: Female pubertal n-6 polyunsaturated fatty acid mammary epitheial cells, WT3

tag: age


title: Female pubertal n-3 polyunsaturated fatty acid mammary epitheial cells, TG2

description:
The fat-1 transgene from the roundworm Caenorhabditis elegans encodes for n-3 desaturase, enabling endogenous whole-body production of n-3 PUFA from n-6 PUFA (safflower oil), including the mammary gland
TG2

value: Transgenic fat-1 (FVB/NJ)


title: Female pubertal n-6 polyunsaturated fatty acid mammary epitheial cells, WT1


title: Female pubertal n-3 polyunsaturated fatty acid mammary epitheial cells, TG1

description:
The fat-1 transgene from the roundworm Caenorhabditis elegans encodes for n-3 desaturase, enabling endogenous whole-body production of n-3 PUFA from n-6 PUFA (safflower oil), including the mammary gland
TG1


title: WT_TNP-OVA_4h_3

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

institute: Institute of Science Tokyo

data_processing:
Fastq files were subjected to adaptor trimming using cutadapt 3.5 and mapping to reference RNA (GRCm39) using STAR-2.7.10a, followed by the calculation of gene-expression count data using RSEM-1.3.1. Count data for each sample was calculated by following arguments: rsem-calculate-expression --star --star-gzipped-read-file. Count data were merged by using rsem-generate-data-matrix  function. Ensembl gene IDs were converted to gene symbol by using a GRCm39 reference gtf file and merge function under R 4.4.1. Tab-delineated raw count data file was submitted as a processed file.
Data normalization and differential expression analyses were performed using TCC (ver 1.44.0), and GO enrichment analysis was performed using clusterProfiler (ver 4.12.0) on R 4.4.0. Genes with FDR < 0.1 were considered differentially expressed genes.
Assembly: GRCm39
Supplementary files format and content: Tab-dilineated text file includes raw counts.

source_name: basophil

growth_protocol: Bone marrow-derived basophils were generated from WT and TTP-KO mice by culturing bone marrow cells in complete RPMI media [RPMI 1640 supplemented with 10% FBS (Gibco), 1 mM sodium pyruvate (Nacalai Tesque), 0.055 mM 2-mercaptoethanol (Gibco), 100 U/mL penicillin/streptomycin (Nacalai Tesque), and 0.1 mM MEM non-essential amino acids solution (Nacalai Tesque)] with 0.3 ng/mL recombinant IL-3 (BioLegend) for 7 days. On day 6 after the start of culture, hapten TNP-specific IgE [1μg/mL, clone: IgE-Lb4, purified from hybridoma (ATCC: TIB 141)] was added to the culture media to sensitize basophils.

extract_protocol:
After treatment with TNP-OVA or control OVA, cells were lysed with lithium dodecyl sulfate-based lysis buffer supplemented with DTT. Transcriptome libraries were prepared on cell lysate or total RNA sample resolved in lysis buffer. PolyA RNAs were isolated using Dynabeads M-270 Streptavidin (Thermo Fisher Scientific) conjugated with biotin-3’ WTA-EcoP-dT25 according to the previous report with some modifications (GSE110711). To 1st strand synthesis, beads were then suspended in 10 μL of 1st Strand synthesis mix [5x SSIV buffer (Thermo Fisher Scientific), 1 mM dNTP, 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 6 mM MgCl2, 1 U/μL RNaseIn Plus Rnase Inhibitor (Promega) and 10 U/μL Superscript IV (Thermo Fisher Scientific)], and incubated for 5 min at 35ºC, 30 min at 42ºC and immediately cooled on ice. Beads were washed once with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], and once with 10mM Tris-HCl (pH 8.0).
To Exonuclease I treated, beads were then suspended in 10 μL of Exonuclease I mix [10x Exonuclease I buffer (New England Biolabs), and Exonuclease I (New England Biolabs)], and incubated for 30 min at 37ºC  and immediately cooled on ice. Beads were washed twice with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], and once with 10mM Tris-HCl (pH 8.0). cDNA dC tailing was performed on-beads by TAS-Seq workflow (Shichino et al. Commun Biol 2022.).  To 2nd strand synthesis, beads were then suspended in 10 μL of 2nd Strand Mix [0.4 μM of primers (trp1-12G), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems)], and incubated for 3 min at 97ºC, 20 sec at 98ºC, 2min at 60ºC, 5 min at 72ºC and immediately cooled on ice.  To amplify the total cDNA, beads containing cDNA was resuspended with 25 uL of first PCR mix [0.4 μM of primers (illumina-i7- [BC]-trP1, NH2-3’ WTA), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems)], and the thermal cycling was performed as following condition: for 3 min at 95°C, 12 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The first PCR products were purified by an Agencort AM Pure XP kit (Beckman-Coulter) at a 0.6:1 ratio of reagents to sample, and eluted with 25 μL of nuclease-free water. 10.5 uL of purified first PCR product was mixed with the 14.5 µl of second PCR mix [0.4 μM of primers (illumina-i7, NH2-3’ WTA), and 1x KAPA Hifi Hotstart ReadyMix, and the thermal cycling was performed as following condition: for 3 min at 95°C, 5 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The second PCR products were purified by an Agencort AM Pure XP kit at a 0.6:1 ratio of reagent to sample, and eluted with 15 μL of 10 mM Tris-HCl (pH 8.0). 100 ng of the whole-transcriptome library was subjected to fragmentation/ end-repair/polyA-tailing/ligation using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) and 1.875 pmol of illumine adapter-bulk according to manufacturer instructions. Reaction products were purified using double-size selection of Agencort AM Pure XP kit (reagent: sample ratio = 0.4:1 → 0.7:1) and then eluted with 10 μL of nuclease-free water. Barcoding mix [12.5 μL; 2× NEBNext Ultra II Q5 (New England Biolabs), 1 µM ILMN-[UDI]-i5 primer, and 1 µM ILMN-[UDI]-i7 primer] was added into 7.5 μL of eluate, and PCR was performed using the following program: for 30 sec at 98ºC, 9 cycles of 10 sec at 98ºC and 75 sec at 65ºC, followed by 5 min at 65ºC and hold at 4ºC. Reaction products were purified twice using double-size selection of Agencort AM Pure XP kit (0.5:1 → 0.8:1) and eluted with 12 μL of nuclease-free water. Final transcriptome libraries, whose lengths were around 300 base pairs, were pooled and sequenced on an Illumina Novaseq 6000 S4 flowcell (Illumina).

treatment_protocol: On day 7, IL-3-cultured bone marrow cells were subjected to enrichment of CD49b+ cells by magnetic sorting using biotinylated anti-CD49b antibody (clone: DX5, BioLegend) and MojoSort Streptavidin Nanobeads (BioLegend). Basophils (5×10⁴ cells/sample) were then treated with control OVA (10 ng/mL) for 2 hours or with TNP-OVA (10 ng/mL) for 2 hours or 4 hours.

value: basophil

value: WT

tag: treatment

value: TNP-OVA for 4 hours


title: WT_TNP-OVA_4h_1

tag: cell type


title: WT_TNP-OVA_4h_2


title: TTP-KO_TNP-OVA_4h_1

value: TTP-KO


title: TTP-KO_TNP-OVA_2h_3

value: TNP-OVA for 2 hours


title: TTP-KO_TNP-OVA_4h_2


title: Uninfected INSGAS_021221_03

description:
Total RNA sample from glandular stomach of mouse (uninfected control); used to quantify expression of 750 unique genes
6982-HA-3

value: Uninfected


title: TTP-KO_TNP-OVA_2h_2


title: WT_TNP-OVA_2h_3


title: TTP-KO_TNP-OVA_2h_1


title: WT_TNP-OVA_2h_1


title: WT_TNP-OVA_2h_2


title: Control GA CL young 1

value: gastrocnemius

value: muscle

value: Controlateral leg

value: Control

value: male

value: Young


title: TTP-KO_OVA_2h_3

value: control OVA for 2 hours


title: TTP-KO_OVA_2h_1


title: TTP-KO_OVA_2h_2


title: WT_OVA_2h_2


title: WT_OVA_2h_3


title: Female pubertal n-3 polyunsaturated fatty acid mammary epitheial cells, TG3

description:
The fat-1 transgene from the roundworm Caenorhabditis elegans encodes for n-3 desaturase, enabling endogenous whole-body production of n-3 PUFA from n-6 PUFA (safflower oil), including the mammary gland
TG3

value: Female

value: Puberty (6-8 weeks)

value: inguinal mammary gland

value: pooled mammary epitheial cell

value: Modified AIN93G diet (Research Diets Inc.), 22% kcal from fat, 10% fat (w/w) from safflower oil


title: TTP-KO_4-hour_3

data_processing:
Demultiplexed fastq files were first adaptor-trimmed by cutadapt 3.5 by following arguments: cutadapt -m 20 -O 20 -a "polyA=A{20}" -a "QUALITY=G{20}" -n 2; cutadapt -m 20 -O 3 --nextseq-trim=10 -a "r1adapter=A{18}AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=3;max_error_rate=0.100000"; cutadapt -m 20 -O 20 -g "r1adapter=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC;min_overlap=20" --discard-trimmed.  Trimmed reads were aligned to GRCm39 reference genome by STAR-2.7.10a by following arguments: STAR  --quantMode TranscriptomeSAM --outSAMtype SAM --outSAMattributes MD NH --outFilterMismatchNmax 14 --readFilesCommand gunzip -c --alignEndsType EndToEnd  --clip5pNbases 1 . Generated bam files were indexed by using SAMtools.
TO calculate the half-lives of each mRNA, bamlist.cit files were generated from bamlist file using  Gedi version 1.0.6a. Then, mRNA hlaf-lives were calculated using GRNAD-SLAM 2.0.7b by following argumants: gedi -e Slam -genomic GRCm39  -progress -plot -D -minEstimateReads 1000. Generated tsv files were submitted as processed file.
Assembly: GRCm39
Supplementary files format and content: tsv file generated by GRAND-SLAM

growth_protocol: Bone marrow-derived basophils were generated from WT and TTP-KO mice by culturing bone marrow cells in complete RPMI media [RPMI 1640 supplemented with 10% FBS (Gibco), 1 mM sodium pyruvate (Nacalai Tesque), 0.055 mM 2-mercaptoethanol (Gibco), 100 U/mL penicillin/streptomycin (Nacalai Tesque), and 0.1 mM MEM non-essential amino acids solution (Nacalai Tesque)] with 0.3 ng/mL recombinant IL-3 (BioLegend) for 7 days. On day 6 after the start of culture, hapten TNP-specific IgE [1μg/mL, clone: IgE-Lb4, purified from hybridoma (ATCC: TIB 141)] and s4U (150μM, MilliporeSigma) was added to the culture media.

extract_protocol:
Total RNA was extracted by using NucleoSpin RNA Plus XS kit (Macherey-Nagel), followed by the alkylation reaction for 15 min at 50℃ under the following condition: 30% DMSO, 10mM iodoacetamide, 50mM NaPO4 pH8. The reaction was stopped with DTT and RNA was cleaned up with Oligo Clean & Concentrator (Zymo Research). 65 ng of RNA was subjected to the construction of sequencing libraries.
NGS libraries were prepared by QuantSeq 3' mRNA-seq V2 library Prep Kit FWD with UDIs (Lexogens) and sequenced on NovaSeq 6000 sequencer.

treatment_protocol: On day 7, IL-3-cultured bone marrow cells were subjected to enrichment of CD49b+ cells by magnetic sorting using biotinylated anti-CD49b antibody (clone: DX5, BioLegend) and MojoSort Streptavidin Nanobeads (BioLegend).  Basophils were treateded for 1.5h with TNP-OVA (10 ng/mL) in the presence of s4U (150 μM) and washed twice. Subsequently, basophils were incubated for 0, 1, 2, and 4 hours in the absence of s4U and TNP-OVA.

value: basophil

value: incubation with TNP-OVA and s4U, alkylation reaction

tag: timepoint

value: 4 hours after the removal of TNP-OVA


title: WT_OVA_2h_1

value: WT


title: TTP-KO_4-hour_2

value: TTP-KO


title: TTP-KO_TNP-OVA_4h_3

value: TNP-OVA for 4 hours


title: TTP-KO_4-hour_1


title: WT_4-hour_3


title: WT_4-hour_1


title: WT_4-hour_2


title: TTP-KO_2-hour_3

value: 2 hours after the removal of TNP-OVA


title: TTP-KO_2-hour_1


title: TTP-KO_2-hour_2


title: WT_2-hour_3


title: TTP-KO_1-hour_2

value: 1 hour after the removal of TNP-OVA


title: WT_2-hour_1


title: TTP-KO_1-hour_1


title: TTP-KO_1-hour_3


title: WT_1-hour_2


title: WT_2-hour_2


title: WT_1-hour_1


title: WT_1-hour_3


title: TTP-KO_0-hour_1

value: 0 hour after the removal of TNP-OVA


title: WT_0-hour_1


title: WT_0-hour_3


title: TTP-KO_0-hour_2


title: WT_0-hour_2


title: TTP-KO_0-hour_3


title: HFpEF-FoxO1-sh, 4 pooled samples

city: Los Angeles

first: Thassio

last: Mesquita

state: California

address: 8700 Beverly Boulevard

department: Smidt Heart Institute

institute: Cedars-Sinai Medical Center

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting and aggregation were made using the Cell Ranger software 6.1.2.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Left ventricle

extract_protocol:
Cells isolated from left ventricular tissue using the gentleMACS Octo-Dissociator with heaters, gentleMACS C-tubes and Multi Tissue Dissociation Kit 2 (Miltenyi Biotec, #130-110-203). After digestion, the enzymatic reaction was quenched with DMEM (Dulbecco’s medium, 20% FBS, 1% penicillin/streptomycin) and the cell suspension was passed through a 70 µm cell strainer to remove cardiomyocytes and small fragments. Cells were spun at 600g for 5 min at room temperature. Debris was then removed using Miltenyi Biotec Cell Debris Removal Solution (Cat #: 130-109-398). After debris removal, red blood cells were lysed in ACK lysis buffer (Invitrogen) for 5 min at room temperature and resuspended in PBS containing 1% BSA.
Chromium Next GEM Single Cell 3' HT Kit v3.1 (10x Genomics, #1000370) according to the manufacturer’s protocol. Libraries were checked for quality on an Agilent 4200 TapeStation (D1000 ScreenTape) and quantified using QuantStudio 12k Flex (Collibri library quantification kit).

treatment_protocol: C56Bl6 fed with a standard diet (control), High-Fat + L-NAME diet plus AAV-scramble-sh (HFpEF-scr), and High-Fat + L-NAME diet plus AAV-FoxO1-sh (HFpEF-FoxO1-sh)

value: Left ventricle

value: cardiac cells

value: High-Fat + L-NAME diet for 6 weeks + AAV-FoxO1-sh for 4 weeks


title: Control, 4 pooled samples

description: 10X Genomics

value: control diet for 10 weeks


title: HFpEF-scr, 4 pooled samples

description: 10X Genomics

value: High-Fat + L-NAME diet for 6 weeks + AAV-scramble-sh for 4 weeks


title: HFpEF-FoxO1-sh 4

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

extract_protocol:
Left ventricular samples were harvested in ice-cold PBS, flash frozen on LN2, and RNA extracted using RNeasy kit (QIAzol, Qiagen).
RNA-Seq library construction was performed using the Swift Biosciences RNA Library Kit (Swift Biosciences, Ann Arbor, MI), following mRNA purification using NEBNext® Poly(A) mRNA Magnetic Isolation Module. Final library concentration was measured via the Qubit 1X dsDNA HS Assay kit (ThermoFisher Scientific) and library size was evaluated on the 4200 TapeStation using the Agilent D1000 ScreenTape System (Agilent Technologies).


title: HFpEF-FoxO1-sh 2


title: HFpEF-scr 4


title: HFpEF-FoxO1-sh 1


title: HFpEF-scr 2


title: HFpEF-FoxO1-sh 5


title: Control 5


title: HFpEF-scr 3


title: Control 4


title: Control 3


title: HFpEF-scr 1


title: Control 2


title: HFpEF 5

extract_protocol:
Left ventricular samples were harvested in ice-cold PBS, flash frozen on LN2, and RNA extracted using RNeasy kit (QIAzol, Qiagen).
Total RNA-Seq library construction was performed using the Swift Biosciences RNA Library Kit (Swift Biosciences, Ann Arbor, MI), following rRNA depletion using Lexogen RiboCop Depletion Kit Human/Mouse/Rat v2 (Lexogen Inc., Greenland, NH). Final library concentration was measured via the Qubit 1X dsDNA HS Assay kit (ThermoFisher Scientific) and library size was evaluated on the 4200 TapeStation using the Agilent D1000 ScreenTape System (Agilent Technologies).

treatment_protocol: C56Bl6 fed with a standard diet (control group) or High-Fat + L-NAME (HFpEF group) for 6 weeks

value: High-Fat + L-NAME diet for 6 weeks


title: HFpEF 1


title: HFpEF 2


title: HFpEF 3


title: Control 5

value: control diet for 6 weeks


title: Control 1


title: Control 4


title: Control 2


title: BSO2

city: hefei

first: Yue

last: Zhao

institute: univerisity of science and techonology of china

description:
control123vsBSO123_count.xlsx
bulk RNA for NK cells

data_processing:
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. Index of the reference genome was built using Hisat2 v2.2.1 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.2.1.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: FPKM values and gene count for each Sample

source_name: peripheral blood

extract_protocol:
For bulk RNA-seq analysis of human peripheral blood NK cells, we sorted NK cells from peripheral blood using the Human NK Cell Isolation Kit (Miltenyi Biotec) or flow cytometric sorting with a purity of more than 95%. Total intracellular RNA was extracted using TRIzol (Invitrogen).
RNA libraries for RNA-seq were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit or Fast RNA-seq Lib Prep Kit V2 following manufacture's protocols.

treatment_protocol: NK cells purified from peripheral blood were treated in vitro with BSO for 72 h; NK cells purified from peripheral blood of patients with acute leukemia were treated in vitro with GSHEE for 12h.

value: peripheral blood

value: NK cells

tag: subject status

value: healthy donor

value: BSO


title: control3


title: HFpEF-FoxO1-sh 3


title: BSO1


title: control2


title: Control 3


title: Control 1


title: Pig ESCs cultured without feeder cells (LDN-treated)

city: Seoul

first: Chang-Kyu

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
Following cluster amplification of denatured templates, paired-end sequencing (2 × 150 bp) was performed using a NovaSeq 6000 system (Illumina, San Diego, CA, USA).
Raw RNA-seq reads were demultiplexed and trimmed using the mkfastq command in CellRanger (v5.0.0; 10× Genomics).
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

organism: Sus scrofa

source_name: Pig embryonic stem cells

growth_protocol: The pig ESCs were cultured in ESC medium [DMEM/F12 containing 15% (v/v) KnockOut™ Serum Replacement (KSR), 0.1% (v/v) chemically defined lipid concentrate (LC), 1× GlutaMAXTM supplement, 0.1 mM β-mercaptoethanol, 1× MEM nonessential amino acids, and 1× antibiotic–antimycotic (all from Gibco, Gaithersburg, MD, USA) supplemented with 20 ng/mL FGF2 (R&D Systems, Minneapolis, MN, USA), 5 ng/mL ActA (R&D Systems), 1.5 µM CH (Cayman Chemical, Ann Arbor, MI, USA), and 2.5 µM IWR-1 (Sigma–Aldrich, St. Louis, MO, USA)]. Pig ESCs were subcultured every 5–7 days. Twenty-four hours before subculturing, pig ESCs were cultured with ESC culture medium containing 10 µM Y-27632 (Santa Cruz Biotechnology, Dallas, TX, USA). Expanded colonies were dissociated into small clumps using TrypLE™ Express (Gibco). These clumps were transferred onto new feeder cells and cultured with ESC medium containing 10 µM Y-27632 (Santa Cruz Biotechnology) for 24 h. Next, attached clumps were cultured with ESC medium lacking Y-27632 for 4–6 days. The medium was changed every 24 h, and pig ESCs were cultured under humidified conditions in an atmosphere containing 5% CO2 at 37 °C.

extract_protocol:
Before RNA and DNA extraction from pig ESCs cultured with feeder cells, SSEA4-positive undifferentiated pig ESCs were sorted using a MACS Cell Separation System (Miltenyi Biotec, Germany) to remove differentiated cells and feeder cells. The dissociated pig ESCs were reacted with an anti-SSEA4 antibody (1:200; MAB4304, Millipore) and anti-mouse IgG microbeads (1:5; Miltenyi Biotec). SSEA4-positive cells were sorted on an LS column (capacity, 1 × 108 magnetically labeled cells; Miltenyi Biotec) according to the manufacturer’s instructions. Total RNA was extracted from pig fetal fibroblasts, and SSEA4-positive ESCs were sorted using TRIzol reagent (Invitrogen).
cDNA library preparation and RNA-Seq analysis were performed by the National Instrumentation Center for Environmental Management (NICEM) at Seoul National University (www.nicem.snu.ac.kr, Seoul, Korea). The viability and number of cells were calculated by LUNA-FL™ Dual Fluorescence Cell Counter (Logos Biosystems, Anyang, Korea) before 10x Genomics single-cell RNA-seq library construction. The cells were loaded into chromium microfluidic chips using the Chromium Single Cell 3ʼ Reagent Kit (v3 chemistry; 10×Genomics, Pleasanton, CA, USA) and then separated into single-cell gel bead emulsions (GEMs) by the Chromium Controller (10×Genomics) according to the manufacturer’s protocol. Reverse transcription of RNA molecules captured from single cells in GEMs was performed by a C1000 Touch Thermal Cycler (Bio–Rad, Hercules, CA, USA). Then, subsequent steps, including cDNA amplification and library construction, were performed according to the manufacturer’s instructions. The cDNA libraries were quantified by a LabChip GX Touch Nucleic Acid Analyzer using a DNA High Sensitivity Reagent Kit (PerkinElmer, Waltham, MA, USA).

treatment_protocol: For adaptation to feeder-free culture, pig ESCs cultured with feeder cells were transferred to MatrixTM-coated plates (SPL Life Sciences, Pocheon, Korea) at a 1:5 to 1:10 split ratio with feeder-free (FF-) ESC medium. The cells were cultured in FF-ESC medium [DMEM/F12 containing 15% (v/v) KSR, 0.1% (v/v) LC, 1× glutamax, 0.1 mM β-mercaptoethanol, 1× MEM nonessential amino acids, and 1× antibiotic–antimycotic (all from Gibco) supplemented with 20 ng/mL FGF2 (R&D Systems), 5 ng/mL ActA (R&D Systems), 1.5 µM CH (Cayman Chemical), 2.5 µM IWR-1 (Sigma–Aldrich), and 250 nM LDN-193189 (Cayman Chemical)]. Pig ESCs were subcultured every 5–7 days. Twenty-four hours before subculturing, pig ESCs were cultured with FF-ESC culture medium containing 10 µM Y-27632 (Santa Cruz Biotechnology, Dallas, TX, USA). Next, expanded colonies were dissociated into small clumps using TrypLE™ Express (Gibco). These clumps were transferred onto new MatrixTM-coated plates and cultured with FF-ESC medium containing 10 µM Y-27632 (Santa Cruz Biotechnology) for 24 h. Next, attached clumps were cultured with FF-ESC medium lacking Y-27632 for 4–6 days. The medium was changed every 24 h, and pig ESCs were cultured under humidified conditions in an atmosphere containing 5% CO2 at 37 °C. Pig ESCs cultured over 3 passages in the absence of feeder cells were used for further analysis, including immunostaining, teratoma assay, PCR analysis, and RNA sequencing.

value: Pig embryonic stem cells


title: HFpEF 4


title: R72_T3_fruit_BABA2_Infected_2

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Trimmomatic (Bolger et al., 2014) was used to remove adapters and discard low-quality reads.
The cleaned reads were aligned to the tomato genome (ITAG4.0) using Hisat2 (version 2.2.1) (Kim et al., 2019)
Samtools (version 1.12) (Li et al., 2009) was used to sort and index Sam files into Bam format.
Read counts were generated using Htseq (version190 0.13.5) (Anders et al., 2015), and the raw count per gene was used to determine differentially expressed genes using DESeq (Anders and Huber, 2010) and default parameters. Genes with a significance p-value below 0.05 after Benjamini and Hochberg correction were considered to be differentially expressed.
Assembly: ITAG4.0
Supplementary files format and content: For each genotype, the rawcount file is provided, generated with htseq-count (Anders et al., 2015).

organism: Solanum lycopersicum

source_name: red fruits

growth_protocol: Seeds of tomato cv Micro Tom were placed in Petri dishes containing wetted tissue paper and maintained at 28°C in the dark for 3-6 days to stimulate homogeneous germination. Germinated seeds were planted in individual pot propagators containing Scott’s M3 compost and cultivated under standard tomato growth conditions (16h/8h day/night cycle; 144 25°C/20°C).

extract_protocol:
One-week after each respective BABA treatment, two leaves from four individual plants were collected and stored in liquid nitrogen. Plants were left to grow and produce red fruit. The first three fruit on all plants were marked and collected. Total RNA was isolated from 100 mg of leaves or fruits samples using  TRIzol (Thermo Fisher; catalogue number 15596026) following manufacturer's specifications.
Libraries for RNA expression analysis were prepared by Novogene following their standard protocol. After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichmen

treatment_protocol: At two-weeks, 1/3 of plants were soil drenched with 5 mM BABA (catalogue number A4420-148 7, Sigma Aldrich) to provide a final concentration of 0.5 mM in the soil. All other plants were treated with the same volume of water. One week after BABA treatment, seedlings were removed from soil, roots were gently washed, and seedlings were replanted in new compost. At twelve weeks, 1/3 of plants were soil treated to a final concentration of 0.5 mM BABA. The remaining 1/3 of plants were left as water controls. Infections of leaves with Botrytis cinerea (R16) were performed entirely as previously described (Luna et al., 2016). Infection of fruit was performed  as described in Wilkinson et al., 2018.

value: red fruits

tag: ecotype

value: Micro Tom

tag: treatment 1

value: BABA 2 wpg

tag: treatment 2

value: infected


title: BSO3


title: R66_T3_fruit_Water_Infected_2

value: Water


title: R79_T3_fruit_BABA12_Infected_1

value: BABA 12 wpg


title: Pig ESCs cultured with feeder cells

value: cultured with feeder cells


title: DPP4 KD/Hypoxia 4

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

institute: Chiba University

data_processing:
Removal of poly A tail and adapter sequences were performed using BBDuk (BBMap version 38.96) with the following settings (k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20).
Trimmed reads were mapped to hg38 using STAR version 2.7.6a with the following settings (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
Read counts for each gene were obtained using HTSeq-count version 1.99.2 with the following settings (-m intersection-nonempty -s yes).
Assembly: hg38
Supplementary files format and content: xlsx files include raw conts for each sample
Supplementary files format and content: xlsx files include RPM values for each sample

source_name: human lung fibroblasts

growth_protocol: HLFs were obtained from Lonza (Basel, Switzerland) and cultured in Dulbecco’s Modified Eagle’s Medium with high glucose supplemented with 15% fetal bovine serum.

extract_protocol:
Total RNA was isolated from HLFs and stored in Isogen (Nippon Gene, Tokyo, Japan).
Purified total RNA (200 ng) with an RNA integrity value of > 9 was used for RNA library preparation according to the instructions of the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria). Libraries were amplified via 13 cycles of polymerase chain reaction. RNA libraries were sequenced using the Illumina (San Diego, California, USA) NextSeq 500 system (75 cycles).

treatment_protocol: For siRNA transfection, DPP4-siRNA (Cat# 4392421, siRNA ID:s4255) and negative control siRNA (Cat# 4390843, Silencer™ Select Negative Control No.1 siRNA) were purchased from Thermo Fisher Scientific. Using the Lipofectamin™ RNAiMAX Transfection Reagent (Thermo Fisher Scientific), HLFs were transfected with siRNA for 72 h according to the manufacture’s protocol. After siRNA treatment, cells were ex-posed to normoxia or hypoxia. Cells in the normoxic groups were maintained at 37℃ in 21% O₂ and 5% CO₂. Cells in the hypoxia groups were separately cultured in 1% O₂ and 5% CO₂ for 48 h, using AnaeroPack-Kenki 5% (Mitsubishi Gas Chemical, Tokyo, Japan) and an oxygen indicator. Cells were used at passages 6–8 in all experiments.

value: human lung fibroblasts


title: DPP4 KD/Hypoxia 3


title: Somatic cell control

source_name: Pig fetal fibroblasts

value: Pig fetal fibroblasts

value: Somatic cell control


title: R71_T3_fruit_BABA2_Infected_1


title: DPP4 KD/Hypoxia 2


title: Input_MeDIP

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

data_processing:
Adapter trimming and Quality filtering of paired reads using fastp version 0.23.4 at default parameters
Paired end-to-end alignment using Bowtie2 at default parameters after imposing a read length constraint of minimum 100bp and maximum 1000bp. Alignment mean read length = 222bp for N-term_MeDIP, 218bp for C-term_MeDIP, 203bp for F-len_MeDIP, 228bp for Input (MeDIP). 191bp for N-term_ChIP and 151bp for Input (ChIP).
Bigwigs were created using bamCoverage by deeptools version 3.5.1 at default parameters in bin size of 50bp
Assembly: hg38 unmasked
Supplementary files format and content: Bigwig

growth_protocol: HEK293T and human fibroblasts cells were grown in DMEM supplemented with 10 % FBS and 1% antibiotic-antimycotic at 37°C and 5% CO2.

extract_protocol:
1. MeDIP-Seq: After 72 h of transfection, cells over-expressing N-term & C-term truncated forms and F-len CGGBP1 were harvested for genomic DNA isolation using phenol-chloroform-isoamyl alcohol extraction method. Genomic DNA was sonicated to obtain 700-1000 bp fragments. 1µg fragment DNA was end repaired using NEBNext Ultra II End Repair/dA-Tailing Module (NEB #E7546). PCR adapters from Oxford Nanopore Technologies (ONT #SQK-PSK004) were ligated to end repaired DNA using NEB Blunt/TA Ligase Master Mix (NEB #M0367). 1x MeDIP master mix (10 mM Sodium Phosphate Buffer, 0.14 M NaCl and 0.05% TritonX-100) was added to adapter ligated DNA which was then denatured at 95℃ for 5 mins followed by snap chilling on ice. An antibody cocktail against 5-methylcytosine (EMD Millipore #MABE146, Sigma #SAB2702243 and Novus Biologicals #NBP2–42813) was added to snap-chilled DNA and was incubated at 4℃ overnight. Protein G Plus/Protein A Agarose beads were added to the mix followed by incubation at room temperature for 2 h. Then beads were collected by centrifugation in a separate tube and were washed thrice with 1x MeDIP master mix buffer and were subjected to Proteinase K (Sigma #P2308) digestion at 56℃ for 2 h. The slurry was centrifuged and immunoprecipitated DNA in the supernatant was collected into new tubes. This DNA was subjected to 18 cycles of PCR using whole genome primers (ONT #SQK-PSK004) and LongAmp Hot Start Taq 2X Master Mix (NEB #M0533). 2. ChIP-Seq: The N-term, C-term, and FL-CGGBP1 were over-expressed in HEK293T-shB-KD, HEK293T-shA-KD, and HEK293T-CT cells, respectively. Cells were harvested for ChIP after being transfected for 72 hours. The cells were harvested using a scrapper after being crosslinked with 4% formaldehyde for 10 minutes at 37°C. They were then quenched with glycine (125 mM). Thermo Fisher Scientific #87785's 1x Halt Protease inhibitor cocktail, EDTA-free, was added to SDS lysis buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS) and the mixture was lysed for 30 minutes on ice with periodic flick-mixing. After that, DNA was sonicated for 20 cycles of 30 seconds ON and 30 seconds OFF to create DNA fragments that ranged in length from 0.15 to 0.35 kb. The fragmented DNA was diluted in ChIP-dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl) after taking out 10% DNAseparately as input. In order to pre-clear chromatin, Protein G Plus/Protein A Agarose beads (Merck Millipore #IP05) were incubated for 4hours at 4°C. After that, the DNA was incubated for an overnight period at 4°C with gentle tumbling with an antibody cocktail targeted against the N-term(Invitrogen #PA5-57317, Abcam #ab176814, Abclonal #AE005 directed towardsthe FLAG-tagged N-term). Protein G Plus/Protein A Agarose beads were then added to collect the antibodies, and the mixture was tumble-incubated for an hour at room temperature. After that, the beads were pelleted and washed with the following four buffers: LiCl IP wash buffer (0.25 M LiCl, 1% IGEPAL (NP40), 1% sodium deoxycholate, 1 mM EDTA, and 10 mM Tris–HCl); low-salt IP wash buffer (0.1% SDS, 1% Triton X–100, 2 mM EDTA, 20 mM Tris–HCl and 150 mM NaCl); and two washes of TE buffer (10 mM Tris–HCl and 1 mM EDTA). An elution buffer (1% SDS and 0.1 M NaHCO3) was used to elute the immunoprecipitated DNA in a 500ul total volume. 200 mM NaCl was added to eluted DNAand incubatedfor 8 hours at 65°C forreverse-crosslinking. Next, for one hour at 45°C, Proteinase K (Sigma #P2308) was added to the DNA along with 10 mM EDTA, 0.1 M Tris-HCl pH 6.8, and 0.1 mg/ml for protein digestion. After adding 10% v/v 3M sodium acetate at pH 5.2, ethanol precipitation was used to purify the ChIP DNA.
1. MeDIP-Seq: Library preparation was done using NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (NEB #E7645, #E7103) as per manufacturer’s instruction. DNA was quantified using Qubit and quality assessment was done using TapeStation. DNA was sequenced on Illumina HiSeq 2500 platform. 2. ChIP-Seq: Library preparation was done using NEXTFlex Rapid DNA Sequencing Bundle (NEXTflex, #5188-12) as per manufacturer’s instruction. DNA was quantified using Qubit and quality assessment was done using TapeStation. DNA was sequenced on Illumina NovaSeq 6000 platform.
MeDIP-Seq & ChIP-Seq

treatment_protocol: HEK293T cells were transduced with the following shRNA lentiviruses: non-targeting (CT), CGGBP1-targeting (KD for selected domains: shA targetting the N-terminal of CGGBP1 for C-term truncated form over-expression and shB targetting the C-terminal of CGGBP1 for N-term truncated form over-expression). For stable transduction, control- and CGGBP1-shmiR transduced cells were selected with 10 ug/ml puromycin for a week. CT cells were then transfected with Full-length overexpression plasmid using Polyplus JetOptimus (cat #101000051) transfection reagent (5ug plasmid per 10cm dish). HEK293T shB and shA cells were transfected with N-term and C-term over-expression plasmids respectively using the same protocol as for Full-length.

tag: cell line

tag: antibody

value: not applicable


title: R80_T3_fruit_BABA12_Infected_2


title: DPP4 KD/Hypoxia 1


title: F-len_MeDIP

value: EMD Millipore #MABE146, Sigma #SAB2702243 and Novus Biologicals #NBP2-42813


title: R70_T3_fruit_Water_Mock_3

value: mock


title: R67_T3_fruit_Water_Infected_3


title: R69_T3_fruit_Water_Mock_2


title: Control/Hypoxia 3


title: R86_T3_fruit_BABA12_Mock_2


title: R77_T3_fruit_BABA2_Mock_2


title: R78_T3_fruit_BABA2_Mock_3


title: Control/Hypoxia 4


title: R81_T3_fruit_BABA12_Infected_3


title: N-term_MeDIP


title: C-term_MeDIP


title: R73_T3_fruit_BABA2_Infected_3


title: control1

value: peripheral blood

value: NK cells


title: Control/Hypoxia 2


title: R65_T3_fruit_Water_Infected_1


title: N2a-Mn_total RNA

city: Nanning

first: yunfeng

last: zou

address: Shuangyong road

institute: Guangxi Medical University

data_processing:
Illumina HiSeqTM 4000 software used for basecalling.
Reads obtained from the sequencing machines included raw reads containing adapters or low  quality bases which would affect the following assembly and analysis. Thus, to get high  quality clean reads, reads were further filtered by fastp(version 0.18.0). hort reads alignment tool Bowtie2 [2] (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database.
Transcripts abundances were quantified by software StringTie in a reference-based approach. For  each transcription region, a FPKM (fragment per kilobase of transcript per million mapped  reads) value was calculated to quantify its expression abundance and variations, using  StringTie software.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include count and normalized (fpkm,rpm, tpm).

source_name: Mouse neuroblastoma cells

extract_protocol:
RNA was harvested using Trizol reagent.  Illumina HiSeqTM 4000 was used with 1 ug of total RNA (ribosomal RNA removed) for the construction of sequencing
C_S19_L005_R1_001.fastq and T_S18_L005_R1_001.fastq files were prepared with small RNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: N2a cells were cultured in  MEM medium containing 300 μM manganese for 48 hours

value: Mouse-derived neural  cells

tag: strain


title: R68_T3_fruit_Water_Mock_1


title: R83_T3_fruit_BABA12_Mock_1


title: N2a-Mn_small RNA


title: R75_T3_fruit_BABA2_Mock_1


title: B3I_T1_leaf_BABA_Infected_3

source_name: leaves

value: leaves


title: Control/Hypoxia 1


title: DPP4 KD/Normoxia 4


title: B2I_T1_leaf_BABA_Infected_2


title: B1I_T1_leaf_BABA_Infected_1


title: DPP4 KD/Normoxia 3


title: B2M_T1_leaf_BABA_Mock_2


title: DPP4 KD/Normoxia 2


title: N2a_small RNA


title: B1M_T1_leaf_BABA_Mock_1


title: 5637RE2_NSG12

city: la jolla

first: Xue

last: Wang

state: CA

address: 10010 N Torry Pines Rd

department: MCBL-H

institute: Salk Institute

data_processing:
The Fastq files of the RNA-seq data were processed to read quality control by running "FastQC" (Galaxy version 0.72) in Galaxy  (usegalaxy.org) and then to remove the adapters by running ‘Trim Galore!’ (Galaxy version 0.4.3.1). The trimmed reads were mapped to human genome 38 by ‘HISAT2’ (Galaxy version 2.1.0+galaxy 4) and the mapped reads were then counted with ‘featureCounts’ (Galaxy version 1.6.3+galaxy 2). The counts were processed to differentially expressed gene analysis with R package‘DESeq2’(Version 1.14.1).
Assembly: hg19
Supplementary files format and content: counts.txt
Supplementary files format and content: Counts of all RNA-seq files including replicates

growth_protocol: T24 cells with different PIN1 expression levels were cultured in McCoy’s 5A complete medium. 5637  with different PIN1 expression levels cells were maintained in RPMI-1640 complete medium.

extract_protocol: Total RNA was extracted according to the manufacturer’s instructions from the NucleSpin RNA purification kit (Macherey-Nagel, 740955.50) and processed to library construction with TruSeq RNA library Prep Kit (illumine).

value: human bladder cancer cell line

value: PIN1 re-expression


title: W3I_T1_leaf_Water_Infected_3

value: Micro Tom


title: 5637RE1_NSG11


title: W1I_T1_leaf_Water_Infected_1

value: infected


title: W2I_T1_leaf_Water_Infected_2

value: Water


title: DPP4 KD/Normoxia 1


title: 5637KO2_NSG10

value: PIN1 knockout


title: Control/Normoxia 4


title: W2M_T1_leaf_Water_Mock_2


title: W3M_T1_leaf_Water_Mock_3


title: Control/Normoxia 3