title: Resistant-treated replicate 2 (RNA-seq)

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

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.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each Sample

source_name: Miapaca2 cell line

growth_protocol: All parental and resistant cell lines were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MiaPaca2 parental and resistant cell lines were used for preparing total RNA to perform RNA seq

tag: phenotype

value: LDHA inhibitor resistant

value: LDHA inhibitor


title: HCAEC, KnD-CON_rep1

status: Public on Aug 02 2022

type: SRA

city: Suzhou

first: Hongbiao

last: Huang

address: Zhongnan street 92

country: China

institute: Children’s Hospital of Soochow University

library_source: transcriptomic

data_processing:
The reference genome was built using Hisat2 (v2.0.5).
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on hg38.
Read count extraction and normalization were performed using Hisat2.
Assembly: hg38
Supplementary files format and content: *.txt: Tab-delimited text files include FPKM values.

molecule: total RNA

organism: Homo sapiens

source_name: HCAEC

growth_protocol: HCAECs were maintained in RPMI‑1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using AMPure XP system following manufacturer's protocols.

tag: cell line

value: HCAEC

tag: cell type

value: Coronary artery endothelial cells

tag: genotype

value: Knockdown control

tag: treatment

value: Day 7 after lentiviruses transfection


title: HCAEC, KnD-CON_rep2


title: HCAEC, shNFAT2_rep2

value: NFAT2 knockdown


title: Resistant-treated replicate 1 (RNA-seq)

city: Birmingham

country: USA


title: HCAEC, OE-NFAT2_rep2

value: NFAT2 overexpression


title: HCAEC, OE-CON_rep2

value: Overexpression control


title: HCAEC, shNFAT2_rep1


title: Resistant-untreated replicate 3 (RNA-seq)

value: untreated


title: HCAEC, OE-CON_rep1


title: HCAEC, TNFa 8h_rep2

value: WT

value: TNFa stimulated 8 hours


title: Resistant-untreated replicate 2 (RNA-seq)


title: HCAEC, TNFa 8h_rep1


title: HCAEC, TNFa 2h_rep1

value: TNFa stimulated 2 hours


title: Parental-treated-replicate 2 (RNA-seq)

value: Parental


title: Resistant-treated replicate 3 (RNA-seq)


title: HCAEC, TNFa 2h_rep2


title: HCAEC, TNFa 0h_rep1

value: TNFa stimulated 0 hour


title: Resistant-untreated replicate 1 (RNA-seq)


title: HCAEC, TNFa 0h_rep2


title: Parental-treated-replicate 1 (RNA-seq)


title: HCAEC, TNFa 4h_rep2

value: TNFa stimulated 4 hours


title: Parental-treated-replicate 3 (RNA-seq)


title: HCI-EC-23_8hrE2_rep3

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
Sequencing reads were aligned to the hg38 build of the human genome using HISAT2.
SAMtools was used to convert SAM files to BAM files.
Genes were defined by the University of California Santa Cruz (UCSC) Known Genes and reads mapped to known genes were assigned with featureCounts.
Within each cell line, read counts were normalized and analyzed for differential expression via the DESeq2 package in R while controlling for the sequencing platform by using the design formula (= ~Sequencer + Treatment), where sequencer reflects the sequencing platform and treatment is 10 nM E2 or DMSO.
Assembly: hg38
Supplementary files format and content: Gene counts (raw, unnormalized) in a tab-delimited text file.

molecule: polyA RNA

growth_protocol: HCI-EC-23 and Ishikawa was cultured in RPMI 1640 (Gibco, 11875119) supplemented with 10% fetal bovine serum (Gibco, 26140079) and 1% penicillin-streptomycin (Gibco, 15140163). Hormone deprived media consisted of phenol red-free RPMI1640 (Gibco, 11835055) supplemented with 10% charcoal-stripped fetal bovine serum (Sigma Aldrich, F6765) and 1% penicillin-streptomycin (Gibco, 15140163). HCI-EC-23 or Ishikawa cell lines were cultured in hormone-deprived media for at least five days prior to experiments using hormones. Cells were incubated at 37°C with 5% CO2.

extract_protocol:
RNA was harvested by washing cells with PBS and lysing cells with buffer RLT plus (Qiagen, 1053393) supplemented with 1% beta-mercaptoethanol (Sigma-Aldrich, M3148). RNA was then purified using the Zymo Quick-RNA Miniprep kit (Zymo Research, R1055).
RNA-seq libraries were generated using the KAPA Stranded mRNA HyperPrep kit (Roche, KK8580/08098115702) using 500 ng of RNA.

treatment_protocol: Media was changed and cells were treated with either 0.1% DMSO (vehicle) or 10 nM E2 in hormone-deprived media for 8 hours.

value: endometrioid adenocarcinoma

value: 10 nM E2


title: HCAEC, OE-NFAT2_rep1


title: Parental-Untreated replicate 3 (RNA-seq)


title: MRC-5-Exo-2

city: Beijing

first: liu

last: peipei

address: No. 2, Cherry Blossom Garden East Street, Chaoyang District

department: Department of Pulmonary and Critical Care Medicine

institute: China-Japan FriendshipHospital

data_processing:
Use Cutadapt (version 2.7) to process sequencing adapters, short reads with low quality, more N, and less than 16bp
Reads with UMIs less than 12 bp and reads without UMIs were processed using perl5 (version 26), and UMIs were identified.
Use  bowtie (version 1.2.2) to compare to the miRBase database respectively
Differential expression analysis was performed using the edgeR R package (1.10.1)
Assembly: miRBase 22.0
Supplementary files format and content: Supplementary_files_format_and_content: UMIs-count.xlsx

source_name: lung

extract_protocol:
total RNA was extracted from exosomes using the miRNeasy Micro Kit (Qiagen, 217084).
we generated sequencing libraries using the QIAseq miRNA Library Kit (Qiagen) for Illumina and performed on the Illumina Novaseq platform to sequencing (Illumina).

tag: tissue

value: lung

value: the cell culture supernatant was collected to isolate exosomes.


title: MRC-5-Exo-3


title: AN10001730_1

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

country: France

institute: Centre Léon Bérard

description: targeted RNA-seq

data_processing:
Illumina bcl2fastq is used for generation of FASTQ files
HTG EdgeSeq Parser software (version 5.1) is used for alignment to a priori defined target sequences.  Requirements include %Q30 >= 85%, %PF >= 75%, and 180 < CD < 290
Post-sequencing quality control using three quality control metrics: 1) Percent of reads allocated to the Positive control probe must not exceed 15%, 2) Total aligned reads must exceed 1,500,000, and 3) Relative Standard Deviaion (CV) of counts within a sample must exceed 0.1 (CV is calculated after removal of counts from ANT and POS control probes and log2 transformation after addition of 2 to avoid taking the log of 0). A log2 CPM normalization is then processed.

source_name: targeted RNA of patient number 25

extract_protocol:
sample preparation: 10mm2 of 5 micrometer FFPE tumour macrodissection tissue were lysed using HTG Lysis Buffer, followed by proteinase K digestion, and then transferred to an HTG EdgeSeq platform according to manufacturer protocols (HTG Molecular Diagnostics, Inc., Tucson, AZ).
The Oncology Biomarker Panel was used to  capture RNA expression levels of gene targets  on the HTG EdgeSeq platform according to manufacturer protocols (HTG Molecular Diagnostics, Inc., Tucson, AZ). The resulting DNA probes were quantitatively amplified with polymerase chain reaction adding extended primers ,including sequencing primer and sample barcode sequences.
Library samples were cleaned up to remove excess primers, quantitated, pooled and sequenced using Illumina NextSeq500 sequencer using 50-cycles single end ((Illumina, Inc.).

value: oral cavity squamous cell carcinoma

tag: site

value: FLOOR OF MOUTH

tag: age

tag: Sex

value: Male

tag: smoking/drinking status

value: SD

tag: pni

value: NO

tag: lvi

value: YES

tag: pt

tag: pn

tag: cd8_% stain 1 positive cells

tag: pdl1_28.8_% stain 1 positive cells

tag: ido1_% stain 1 positive cells

value: LOW

tag: os (month)

tag: os (event)

tag: dfs (month)

tag: dfs (event)

tag: hot score

value: COLD


title: Parental-Untreated replicate 1 (RNA-seq)

tag: cell line

tag: phenotype

tag: treatment

value: untreated


title: Parental-Untreated replicate 2 (RNA-seq)


title: Lung, Frozen

city: Los Angeles

first: Gianni

last: Carraro

state: CA

address: 8700 Beverly Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

description:
Normal
Cells isolated from dissected and FACS sorted human lung distal material

library_source: transcriptomic single cell

data_processing:
Raw reads were aligned to the transcriptome by Cell Ranger, using STAR, using a hg38 transcriptome reference from Ensemble 93 annotation. Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts. The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns.
Assembly: hg38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Lung

extract_protocol:
Cells were captured and RNA obtained using a 10X Chromium device and following the Standard 10X protocol for a v3 Reagent Kit, as recommended by the manufacturer.
Reverse transcription was performed in a Veriti 96-well thermal cycler. Barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit, and sequencing performed on a NovaSeq 6000 (Illumina).

tag: tissue

value: Lung

tag: cell type

value: Epithelial

value: Frozen


title: MSCs-Exo-1

source_name: umbilical cord

value: umbilical cord

value: mesenchymal stem cells

tag: genotype

value: WT


title: MSCs-Exo-3


title: Lung, Fresh

value: Fresh


title: MSCs-Exo-2

value: the cell culture supernatant was collected to isolate exosomes.


title: Resistant-treated replicate 3 (ATAC-seq)

library_source: genomic

data_processing:
The reads were first mapped to the hg38 human genome set using Bowtie2 version 2.1.0 . The mitochondria reads, duplicate reads and non-unique reads were removed bdfore peak calling.MACS2 was used for peak calling using BAMPE mode.
The mitochondria reads, duplicate reads and non-unique reads were removed bdfore peak calling.MACS2 was used for peak calling using BAMPE mode.
Genome_build: hg38
Supplementary_files_format_and_content: peak txt file

molecule: genomic DNA

extract_protocol:
Cells were trypsinized and purified by centrifugation before being place in nuclei isolation buffer (lysis buffer) containing 0.1% IGEPAL. Nuclei were then counted and 250,000 nuclei were used in ATAC-seq library preparation
Libraries were constructed as described in ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide by Buenrostro et al. 2015 Curr Proc Mol Biol

treatment_protocol: MiaPaca2 parental and resistant cell lines were used for preparing nuclei to perform ATAC seq

value: LDHA inhibitor resistant

value: LDHA inhibitor


title: HCAEC, TNFa 4h_rep1

value: HCAEC

value: Coronary artery endothelial cells

value: TNFa stimulated 4 hours


title: THP-1 cells + S. aureus BEV (ε-PL)_rep3 [SPL3]

first: Dian

last: Jiao

state: Beijing

address: Tsinghua University Beijing China

institute: Tsinghua University

data_processing:
The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3).
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters. The processed reads from each sample were aligned using HISAT2 against the reference genome.
The gene expression analyses were performed with StringTie (v1.3.3b)
DESeq(v1.28.0) was used to analyze the DEGs between samples.
Assembly: Homo sapiens hg38 reference genome
Supplementary files format and content: Tab separated text output from featureCounts with read counts per gene for each sample.

growth_protocol: THP-1 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with Trizol ( Invitrogen ) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen). RNA integrity number (RIN) > 7.0 and a 28S:18S ratio > 1.8.RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China). The triplicate samples of all assays were generated and sequenced by CapitalBio Technology (Beijing, China).
The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries.

treatment_protocol: The final protein concentration of 1 μg/ml BEVs isolated from E. coli or 10 μg/ml BEVs isolated from S. aureus were added to each well.

value: leukemia monocyti cells

value: S. aureus BEVs (epsilon-poly-L–lysine) stimulation

tag: time

value: Day 0


title: THP-1 cells + S. aureus BEV (ε-PL)_rep2 [SPL2]


title: THP-1 cells + S. aureus BEV (UC)_rep3 [SUC3]

value: S. aureus BEVs (UC) stimulation


title: Resistant-treated replicate 1 (ATAC-seq)


title: THP-1 cells + S. aureus BEV (ε-PL)_rep1 [SPL1]


title: THP-1 cells + S. aureus BEV (UC)_rep2 [SUC2]


title: THP-1 cells + E. coli BEV (ε-PL)_rep2 [EPL2]

value: E. coli BEVs (epsilon-poly-L–lysine) stimulation


title: THP-1 cells + E. coli BEV (ε-PL)_rep1 [EPL1]


title: MRC-5-Exo-1

value: lung


title: THP-1 cells + E. coli BEV (UC)_rep3 [EUC3]

value: E. coli BEVs (UC) stimulation


title: Resistant-untreated replicate 3 (ATAC-seq)

value: untreated


title: THP-1 cells + E. coli BEV (UC)_rep2 [EUC2]


title: Resistant-untreated replicate 1 (ATAC-seq)


title: THP-1 cells + E. coli BEV (UC)_rep1 [EUC1]


title: THP-1 cells Control_rep3 [NC3]

value: PBS stimulation


title: Parental-treated-replicate 3 (ATAC-seq)

value: Parental


title: Parental-treated-replicate 1 (ATAC-seq)


title: THP-1 cells Control_rep1 [NC1]

value: WT


title: A2780 cells,Treat,48h,rep3

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
FastQC was used for quality control of sequencing data, and soapnuke(V2.1) software was used for data filtering to obtain clean reads.
The sequenced data were compared with the reference genome using hisat2 software
TPM method was used to calculate genes expression, and DESeq2 was used to analyze differential genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: ovary

growth_protocol: A2780 cells were cultured in DMEM supplemented with 10% fetal bovin serum (FBS) at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
Trizol method
The RNAs containing PolyA were enriched with oligo(dT). The enriched fragments were fragmented, and then reverse transcribed to synthesize cDNA. Finally, The synthesized cDNA can be sequenced after the library is amplified with adaptor sequences.

treatment_protocol: The RNA samples included 6 replicates (3 for A2780-untreated and 3 for A2780-treated with 40 ng/ml human recombinant CRMP2 (r-CRMP2) for 48 h. The r-CRMP2 was added into the DMEM cultural medium to maintain cells growth.

value: ovary

value: Ovarian cancer cells

value: human recombinant CRMP2


title: Parental-treated-replicate 2 (ATAC-seq)

value: LDHA inhibitor


title: Resistant-treated replicate 2 (ATAC-seq)

value: LDHA inhibitor resistant


title: Parental-Untreated replicate 3 (ATAC-seq)


title: THP-1 cells + E. coli BEV (ε-PL)_rep3 [EPL3]


title: A2780 cells,Treat,48h,rep2


title: Resistant-untreated replicate 2 (ATAC-seq)


title: MTZ-62.5uM-1

type: RNA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

hyb_protocol: The hybridization protocol for the nCounter XT CodeSet gene expression TGx-DDI assay panel was completed according to the NanoString nCounter® XT Assay User Manual, section 2 (MAN-10023-11, July 2016).

scan_protocol: Direct digital detection and counting of the TGx-DDI biomarker genes, plus eight housekeeping genes (G6PD, GUSB, HPRT1, LDHA, NONO, PGK1, PPIH, and TFRC) were completed using the nCOunter Digital Analyzer accoring to instructions from the manufacturer found in the nCounter Analysis System User Manual.

data_processing: Barcodes were counted for each target, and the data were exported. The counts of each target were analyzed using nSolver Analysis version 3.0 for quality control and normalization. Quality Control (QC) metrics, background correction and data normailzation were completed following NanoString's Gene Expression Data Analysis Guidelines (MAN-C0011-04) using the nSolver software. Normalized data were subjected to TGx-DDI classification analysis.

source_name: Human TK6 Cells

label_protocol: The TGx-DDI nCounter® assay was conducted using 100 ng of high quality, purified RNA. All non-cytotoxic concentrations of each test chemical were included in this analysis, in addition to the corresponding vehicle controls for each treatment. The highest two concentrations of MTZ and NIT were excluded (i.e., 500 µM and 1,000 µM), in addition to the highest concentration of NOV (i.e., 1,000 µM) due to levels of cytotoxicity exceeding the threshold of 50% cell death. The nCounter® assay was performed in triplicate for each treatment and matched control. Caffeine (CA; 2 mM) served as a negative control, while bleomycin (BL; 10 µM) and ionizing radiation (IR; 4 Gy) were used as positive controls. nCounter® experiments were conducted as previously reported (Li et al., 2017) and full details of the nCounter® methods have been previously reported (GK Geiss et al., 2008). The nCounter® experiments were conducted following the instructions outlined in the NanoString nCounter® XT Assay User Manual (MAN-10023-11, July 2016). Briefly, optimized sequences for the TGx-DDI biomarker genes, plus eight housekeeping genes, including G6PD, GUSB, HPRT1, LDHA, NONO, PGK1, PPIH, and TFRC, were chosen based on stability and detectable expression levels and were included in a custom-designed CodeSet manufactured by NanoString. Unique barcodes were counted for each target, and the data were exported for analysis. The counts for each target were analyzed for quality control and normalization using nSolver™ Analysis version 4.0. Normalized data were exported and subjected to further analysis, which is described below in the Statistical and Bioinformatic Analyses for TGx-DDI Classification section.

growth_protocol: TK6 cells, a spontaneously transformed human lymphoblastoid cell line, were cultured in suspension in RPMI 1640 supplemented with 10% fetal bovine serum and treated with case study chemicals, as described previously (Li et al., 2015; Li et al., 2017). Concisely, exponentially growing cells were treated at a density of 4-5×105 cells per mL in parallel 96-well plates. Following the 4 hour exposure, cells were washed and collected for RNA extraction for subsequent gene expression analysis using NanoString nCounter® and BioSpyder TempO-Seq® gene expression analysis.

extract_protocol: RNA extraction was performed using the protocol accompanying the TRIzol™ reagent (Invitrogen, part of ThermoFisher Scientific, Waltham, MA USA), which was then purified via an RNA cleanup step using an RNeasy column according to the manufacturer’s instructions (Qiagen, Germantown, MD USA). Purified RNA was quantified and analyzed for quality using a NanoDrop™ spectrophotometer and an Agilent BioAnalyzer, respectively.

treatment_protocol: Human TK6 cells (ATCC, Manassas, Virginia, USA) were exposed to ten concentrations of each test chemical in triplicate, as follows: 2.0, 3.9, 7.8, 15.6, 31.3, 62.5, 125, 250, 500, and 1,000 µM, in addition to matched vehicle controls. Cells were exposed to the extended concentration range of each chemical for 4 hr in parallel 96-well plates  for evaluation of DNA damage by CometChip® and for the collection of cells for gene expression analysis using nCounter® and TempO-Seq® for TGx-DDI classification. Concisely, exponentially growing cells were treated at a density of 4-5×105 cells per mL in parallel 96-well plates. Following the 4 hr exposure, cells were washed and collected for RNA extraction for subsequent gene expression analysis using NanoString nCounter® and BioSpyder TempO-Seq® gene expression analysis.

value: Metronidazole (MTZ)

tag: concentration


title: THP-1 cells + S. aureus BEV (UC)_rep1 [SUC1]

value: leukemia monocyti cells


title: A2780 cells,Treat,48h,rep1


title: A2780 cells,Control,48h,rep3

value: control


title: Parental-Untreated replicate 1 (ATAC-seq)


title: MTZ-31.3uM-3


title: breast_p9_peritumor_pEC

city: Vienna

first: Laura

middle: de

last: Rooij

address: Lazarettgasse 14

country: Austria

institute: CeMM

data_processing:
Libraries were sequenced on an Illumina HiSeq4000, and mapped to the human genome using CellRanger software (10X Genomics, version 2.1.1).
Data was further processed using R. The following quality control steps were applied: Genes expressed by fewer than 50 cells or with a row mean of <0.003 were not considered. Cells that had either fewer than 300 genes (low quality), or a number of genes exceeding 2 standard deviations above the mean (potential doublets) were removed, as well as cells with over 10% of unique molecular identifiers (UMIs) derived from the mitochondrial genome (indicative of mitochondrial damage in apoptotic cells). All further analysis of the data derived from the remaining cells was performed using BIOMEX . Briefly, data were natural-log transformed using log1p and normalized using the Seurat pack-age, as implemented in BIOMEX. After auto-scaling, the resulting data were first summarized by principal component analysis (PCA) using the flashPCA package, followed by visualization using Uniform Manifold Approximation and Projection (UMAP) and graph-based clustering using Seurat. In case of enriched EC data, clusters containing contaminating immune cells (PTPRC positive), epithelial cells (KRT15 positive), fibroblasts (DCN positive, LUM positive), smooth muscle cells (ACTA2 positive) and pericytes (RGS5 positive) were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: bcTax_EC_enriched_raw_matrix.csv; raw UMI count matrix of all endothelial cells (from the EC-enriched dataset) that passed quality control
Supplementary_files_format_and_content: bcTax_stroma_raw_matrix.csv; raw UMI count matrix of all stromal cells (from the non-EC-enriched dataset) that passed quality control

extract_protocol:
Following surgical resection, samples from the invasive tumor front and adjacent healthy breast tissue (as far away from the tumor border as possible) were immersed in 1 ml digestion medium and minced into pieces (smaller than 1 mm3), and transferred to additional 6.5 ml digestion medium consisting of KnockOut DMEM, supplemented with penicillin/streptomycin (1x), Antibiotic-Antimycotic (2x), sodium pyruvate (1 mM), MEM NEAAs (1x), heparin (10 U/ml)/ECGF, and containing 0.3% collagenase we, 0.1% collagenase II, DNase (7.5 µM) and dispase (0.25 U/ml). Samples were incubated at 37°C for 60 minutes or until digestion of both pieces was complete. To improve digestion, samples where pipetted up and down every 10 minutes. Next, 7.5 ml of cold PBS containing 0.5% bovine serum albumin (BSA) and 2 µM EDTA were added and the samples were filtered using a 100 μm strainer (Corning). Following centrifugation (300 g) at room temperature (RT) for 4 minutes, the supernatant was decanted and discarded. Single-cell suspensions were stained with viability dye (EF 506, dilution 1:1000) and fluorescent antibodies (CD45 (Pe Cy7, dilution 1:700), EPCAM (PE, dilution 1:500), CD31 (AF488, dilution 1:100) and CD102 (APC, dilution 1:50) for 30 minutes after which cell suspensions were FACS sorted into low-bind Eppendorf tubes containing 200 µl pure FBS. Stromal cells were gated for single and alive cells (negative population for viability dye), the endothelial cell population was established based on gating single viable cells, negative for CD45 and EPCAM markers and double positive for endothelial cell markers CD31 and CD102. For each sample we sorted 100K stromal cells and at least 50K enriched endothelial cells. For further pro-cessing for scRNA-seq, the samples were re-suspended in PBS containing 0.4% UltraPure BSA (50 mg/ml).
The single cell suspensions of freshly isolated tumoral (TECs) and peritumoral normal (pNECs) endothelial cells, tumoral stroma and healthy breast stroma were converted to barcoded scRNA-seq libraries using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10X Genomics)
single cell RNA-seq

tag: sample type

value: breast cancer resection specimen

tag: condition

value: peritumor

tag: type

value: pEC


title: A2780 cells,Control,48h,rep1


title: THP-1 cells Control_rep2 [NC2]

value: Day 0


title: MTZ-250uM-3


title: MTZ-31.3uM-1


title: MTZ-31.3uM-2


title: P8

city: La Jolla

first: Vasantika

last: Suryawanshi

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

data_processing:
FASTQ files were processed using Seven Bridges Genomics pipeline
Doublet removal using doublet finder package in R

source_name: PBMCs

extract_protocol:
Blood from enrollees was centrifuged at 400 x g for 10 minutes at RT to remove platelet rich plasma. PBMCs were isolated by Ficoll-Paque PLUS gradient centrifugation using SepMate-50 tubes following the manufacturer’s protocol. PBMCs were cryopreserved in freezing solution (90% FBS/10% DMSO). Once all the samples were collected, PBMCs were thawed and washed with RPMI.
Library was prepared per BD's protocol. In brief, the reagents for PCR1 including the BD 5uman Immune Response Panel and a custom panel of 488 genes were added to the beads. Samples were aliquoted into  PCR tubes and incubated for 10 cycles according to BD’s protocol for PCR1. A double size selection was performed to remove high genomic DNA fragments. AMPure XP SPRI beads to the PCR products. After incubation, the supernatant is recovered followed by purifying the supernatant withan additional AMPure XP beads (sample tags and antibodies). The RNA tube was washed twice with 80 % ethanol. 550 μl of supernatant were removed from the antibody tube followed by two washes with 500 μL of 80 % ethanol. The cDNA was eluted off the beads using 30 μL of BD elution buffer and then transferred to a 1.5 mL tube.
AbSeq

value: PBMC


title: MTZ-62.5uM-3


title: MTZ-62.5uM-2


title: MTZ-250uM-1


title: Parental-Untreated replicate 2 (ATAC-seq)

value: untreated


title: MTZ-250uM-2


title: breast_p9_tumor_TEC

value: tumor

value: TEC


title: breast_p8_peritumor_stroma

value: stroma


title: breast_p9_peritumor_stroma


title: MTZ-125uM-3


title: breast_p8_peritumor_pEC


title: P2-P3


title: P7


title: P1-P5


title: MTZ-125uM-2


title: MTZ-125uM-1


title: NOV-500uM-3

value: Novobiocin (NOV)


title: breast_p8_tumor_TEC


title: D11-DM Bulk RNA-3

city: Durham

first: Jarrett

last: Bliton

address: 6 Davis Drive

institute: Altis Biosystems

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D11-3

data_processing:
[Read Alignment]  single-cell fastq files were aligned to reference transcriptome GRCh38 with the 10X Cell Ranger pipeline (V4.0.0),
[Single cell Downstream Processing]  downstream analysis was performed with scanpy (v1.7.2).
Annotations for cell cycle phase were added following previously published methods in Moor et al 2018. Seurat v2 was used to identify 2585 highly variable genes
[Single cell Quality Filtering parameters]  , In vivo scRNASeq, In vitro scRNASeq
Minimum genes, >500, >1000
Percent mitochondrial reads, <75%, <50%
Minimum counts, >3,000, >5,000
Maximum counts, <50,000, <80,000
[Single cell Dimensional reduction, batch correction,  Leiden clustering, and UMAP visualization ]  Following filtering, read counts were log-transformed and normalized to the median read depth of the dataset. For both single cell sequencing experiments no batch correction was performed as each dataset was analyzed separately. Variability due to read count, percentage of mitochondrial reads and cell cycle phase were regressed out by simple linear regression. Highly variably genes were identified using Seurat v2. 2,585 and 4,186 highly variable genes were used for principal component analysis for the in vivo and in vitro scRNAseq datasets, respectively. Counts for each gene were scaled to have a mean of zero and unit variance. A kNN-graph was contruscted with 10 neighbors was used to calculate leiden clusters for both in vivo and in vitro scRNAseq datasets (In vivo clustering parameters: Leiden resolution = 0.5, num_neighbors = 10, num_pcs = 40; in vitro clustering parameters: Leiden resolution = 0.1, num_neighbors = 10, num_pcs = 15) and EPCAM-negative cells were removed from the in vivo dataset. PAGA was used to initialize UMAP embeddings of leiden clusters.
Regional hashtag deconvolution followed published methods for both scRNAseq datasets. Briefly, raw hashtag read counts were normalized using centered log ratio transformation followed by k-medoid clustering (k=6 medoids)19. Hashtag noise distributions were determined by removing the cluster with highest expression of a specific hashtag, then a negative binomial distribution was fit to the data of the remaining cells. Cells were considered positive for a hashtag if counts for the specific hashtag were above the distribution’s 99th percentile (p<0.01) threshold. Cells positive for multiple hashtags were excluded as likely doublets. Cells called for colon and duodenum were removed from the dataset. For in vitro data, only hashtags 1 and 3 were kept for analysis.  Hashtag 1 and hashtag 3 come from the same dataset and need to be deconvoluted from the same set of 108 fastqs.
[Bulk RNA ]  Integrated fluidic circuits (IFCs) for samples with RIN above 8 were prepared for gene expression and genotyping analysis by using the Advanta™ RNA-Seq NGS Library Prep Kit for the Fluidigm Juno™ and sequenced with the Fluidigm Biomark™ HD system. Gene level expression was obtained through pseudo alignment of reads to human genome GRCh38 using Kallisto (Bray et al., 2016). Expression values for plotting were obtained by TMM normalization across all samples using EdgeR package (Robinson et al., 2010). Sequencing data from each time point were combined and then were normalized to the dataset median and log-transformed. Principal component analysis was done with scikitlearn (v0.24.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 - raw feature counts for each dataset
Supplementary_files_format_and_content: h5ad - final processed and integrated dataset for figure generation and analysis

source_name: Human Jejunum

extract_protocol:
[in vivo scRNAseq]  Whole human intestines were transported to UNC Chapel Hill in ice-cold University of Wisconsin Solution, with tissue dissection beginning within eight hours of cross-clamping. First, fat and connective tissue were trimmed from the donated organs and intestines were subdivided into six regions following measurement. For the small intestine, the proximal 20 cm was deemed Duodenum. Jejunum and ileum were determined through an even split of the remaining small intestine. Two 3x3 cm2 resections were isolated from the center of jejunum and ileum for dissociation.   Resections were incubated in 10 mM NAC at room temperature for 30 min to remove mucus, then tissue was moved to ice-cold Isolation Buffer which consisted of 5.6 mM Na2HPO4, 8.0 mM KH2PO4, 96.2 mM NaCl, 1.6 mM KCl, 43.4 mM Sucrose, 54.9 mM d-sorbitol, and 100 uM Y27632, then washed several times by gently inverting the tubes. Tissues were then incubated in Isolation Buffer with 2 mM EDTA and 0.5 mM DTT, then shaken vigorously to remove crypts. Shakes were repeated several times, checking for crypts and/or villi each time. High-yield small intestinal shakes were pooled to approximate 1:1 villus to crypt tissue by cell mass. Crypts and villi were dissociated to single cells using 4 mg/ml Protease VIII in DPBS + Y27632 on ice for ~45min with trituration via a P1000 micropipette every 10 min. Dissociation was checked on a light microscope then clumps were removed using filtration.   Single cells were washed with DPBS + Y27632 then resuspended in Advanced DMEM/F12 + 1% Bovine Serum Albumin + Y-27632. AnnexinV-APC (1:100) was added for live/dead staining and one TotalSeq Anti-Human Hashtag Antibody (Biolegend Cat Nos. 394631, 394633, 394635, 394637, 394639, & 394641) per condition to allow for tracking all six conditions with a single library preparation. Cells were washed with Advanced DMEM/F12 + 1% BSA +Y27632 then resuspended in the same solution for sorting on a Sony Cell Sorter SH800Z. Cells were gated using forward and backward scatter and AnnexinV to enrich for live single epithelial cells. 25k cells were collected from each separate region, then all regions were combined before sequencing. Library prep was performed with the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1. Sequencing was performed on an Illumina NextSeq 500.
[in vitro scRNAseq]  Media was removed from ISCs expanded on collagen and from AEs on 12-well transwell inserts and washed with 1x DPBS. 1.5mls of 3mM EDTA in PBS was applied to ISCs expanded on collagen and on apical and basal reservoirs of 12-well transwell cultures until most cells were lifted off the collagen or  Transwell surface as determined by visual inspection every 2 minutes under an inverted microscope. EDTA was aspirated using a P1000 micropipette and redistributed over the Transwell surfaced to facilitate detachment of cells from the Transwell at 2-minute intervals until the majority of cells had detached. After the cells detached, 1.5mls of DPBS was applied to each well and rinsed by aspirating and re-applying the EDTA/DPBS. Cells were then aspirated and pelleted by centrifugation at 500g for 5 minutes. The supernatant was removed and replaced with 1ml of 4mg/mL cold protease in DPBS. Cells in cold protease were incubated on ice and pipetted every 2 minutes before visual examination of dissociation under an inverted light microscope. This was repeated until all cells were singlets. Following single cell dissociation, the cold protease was quenched with Advanced DMEM/F12 + 1% FBS. Cells were pelleted as described above and resuspended in Advanced DMEM/F12 +1% FBS.
[scRNAseq]  Single cells were washed with DPBS + Y27632 then resuspended in Advanced DMEM/F12 + 1% Bovine Serum Albumin + Y-27632. AnnexinV-APC (1:100) was added for live/dead staining and one TotalSeq Anti-Human Hashtag Antibody (Biolegend Cat Nos. 394631, 394633, 394635, 394637, 394639, & 394641) per condition to allow for tracking all six conditions with a single library preparation. Cells were washed with Advanced DMEM/F12 + 1% BSA +Y27632 then resuspended in the same solution for sorting on a Sony Cell Sorter SH800Z. Cells were gated using forward and backward scatter and AnnexinV to enrich for live single epithelial cells. 25k cells were collected from each separate region, then all regions were combined before sequencing. Library prep was performed with the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1. Sequencing was performed on an Illumina NextSeq 500.
[bulkRNAseq]  To investigate the dynamic changes in gene expression as ISCs differentiate into AEs in vitro, RNA-seq was performed on human intestinal epithelial monolayers immediately before seeding onto Transwells (D0) and at Days 2, 5, 7, 10, and 11  (D2, D5, D7, D10, D11) of differentiation on Transwells.  N=3 samples were collected from each time point and RNA was extracted using RNAqueous-Micro Total RNA Isolation Kit (AM1931; ThermoFisher) according to manufacturer’s protocols and stored at −80°C. RNA quality was assessed prior to library preparation by using the  Agilent 2100 Bioanalyzer to determine the RNA integrity number (RIN) (citation for RIN).
scRNAseq & BulkRNAseq

value: Intestine

tag: intestinal region

value: Jejunum


title: breast_p8_tumor_stroma


title: breast_p7_peritumor_stroma


title: NOV-500uM-2


title: breast_p9_tumor_stroma


title: NOV-500uM-1


title: breast_p7_peritumor_pEC


title: D11-DM Bulk RNA-1

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D11-1


title: breast_p7_tumor_stroma


title: P4-P6


title: D11-DM Bulk RNA-2

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D11-2


title: D10-DM Bulk RNA-3

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D10-3


title: MTZ-7.8uM-2


title: breast_p7_tumor_TEC


title: D10-DM Bulk RNA-2

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D10-2


title: MTZ-7.8uM-1


title: breast_pt6_peritumor_stroma


title: D10-DM Bulk RNA-1

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D10-1


title: breast_pt6_tumor_stroma


title: D7-DM Bulk RNA-3

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D7-3


title: breast_pt5_tumor_stroma


title: breast_pt5_peritumor_stroma


title: MTZ-3.9uM-3


title: breast_pt5_peritumor_pEC


title: MTZ-3.9uM-1


title: D7-DM Bulk RNA-2

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D7-2


title: MTZ-3.9uM-2


title: D7-DM Bulk RNA-1

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D7-1


title: breast_pt5_tumor_TEC


title: breast_pt4_tumor_stroma


title: D5-DM Bulk RNA-1

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D5-1


title: D5-DM Bulk RNA-2

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D5-2


title: MTZ-15.6uM-3


title: breast_pt4_peritumor_stroma


title: MTZ-15.6uM-2


title: MTZ-7.8uM-3


title: MTZ-15.6uM-1


title: NOV-62.5uM-3


title: A2780 cells,Control,48h,rep2

value: ovary

value: Ovarian cancer cells

value: WT


title: breast_pt4_peritumor_pEC


title: D2-DM Bulk RNA-3

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D2-3


title: NOV-62.5uM-2


title: breast_pt4_tumor_TEC


title: D2-DM Bulk RNA-2

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D2-2


title: NOV-62.5uM-1


title: D2-DM Bulk RNA-1

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D2-1


title: breast_pt3_peritumor_stroma


title: D5-DM Bulk RNA-3

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
DM-D5-3


title: D0-EM Bulk RNA-3

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
EM-Transwells-3


title: D0-EM Bulk RNA-1

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
EM-Transwells-1


title: D0-EM Bulk RNA-2

description:
Bulk_DM_replicates.gene.TMM.EXPR.matrix.csv
bulk_processed_adata.h5ad
Bulk_DM_replicates.gene.counts.matrix
EM-Transwells-2


title: breast_pt3_peritumor_pEC


title: breast_pt3_tumor_stroma


title: breast_pt3_tumor_TEC


title: breast_pt2_tumor_stroma


title: NOV-250uM-3


title: NOV-31.3uM-2


title: breast_pt2_tumor_TEC


title: NOV-250uM-2


title: breast_pt2_peritumor_pEC


title: Adar OE 12h rep 3

city: Warszawa

first: Cecilia

middle: Lanny

last: Winata

address: Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description: replicate 3

data_processing:
Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10.
Low-quality sequences and adapter content were trimmed with cutadapt v. 2.4.
Reads were aligned to the zebrafish genome assembly GRCz10  using STAR v2.7.7a and samtools v1.11
Expression quantification was performed using HTSeq v0.11.2
Differential expression was performed using DESeq2 (R v3.6.3)
Putative RNA editing sites based on DNA- and RNA-seq input were detected using REDiscover (https://github.com/lpryszcz/REDiscover). Options -q 15 -Q 20, were used, i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity, sites with more than one alternative allele were excluded from the analysis.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab delimited file format

organism: Danio rerio

source_name: whole zebrafish embryo

growth_protocol: Zebrafish embryos were maintained according to standard protocol (Westerfield et al., 2000) and staged according to standard morphological criteria (Kimmel et al., 1995).

extract_protocol:
Parental genomic DNA was extracted from adult fin-clippings of an individual male and female zebrafish of wild-type ABTL background. For the rest of the samples, 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS (Thermo Fisher Scientific, USA) and cleaned up on the Qiagen Rneasy Mini column (Qiagen, USA). Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies (USA). To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages (Winata et al., 2018), total RNA was rRNA-depleted using Ribo-Zero Magnetic Gold Kit (Human, Mouse, Rat; Epicenter).  For the 7 dpf samples, total RNA was subjected to mRNA enrichment using  NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, NEB).
genomic DNA library was constructed using Nextera XT (Illumina, USA) using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA-seq kit (Clontech Laboratories, USA) as recommended by the manufacturer. For the 7 dpf samples, library was constructed using TruSeq Stranded Total RNA library preparation kit (Illumina, USA).

treatment_protocol: To assess the effect of Adar KD and OE, uninjected wild-type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.

tag: strain

value: WT (ABTL)

value: whole embryo

tag: developmental stage


title: breast_pt1_tumor_stroma

value: breast cancer resection specimen


title: NOV-125uM-1


title: NOV-125uM-3


title: breast_pt1_peritumor_stroma

value: peritumor


title: NOV-31.3uM-3


title: Adar OE 12h rep 2

description: replicate 2


title: breast_pt1_tumor_TEC


title: ETOH-treated CAF3-derived exosomes

city: Shanghai

first: Yu

last: Zhang

address: Xinsongjiang Road 650, Shanghai, China

institute: Shanghai Jiaotong University, School of Medicine

data_processing:
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
Trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The raw counts were normalized by edgeR, and differentially expressed miRNAs were filtered.
miRNA targets were predicted CloudSeq’s home-made software based on the miRanda and Targetscan algorithms based on the top 5 differentially expressed miRNAs. miRNA-targets networks were plotted by cytoscape software (v2.8.0), and the GO and KEGG pathway analysis were performed based on the predicted target genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: .xlsx file includes raw reads, and normalized data, etc.

source_name: Cancer-associated fibroblasts (CAFs)

growth_protocol: CAFs were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin.

extract_protocol:
Exosomes were collected from supernatants of primary CAFs and isolated by ultracentrifugation.RNA was harvested using Trizol reagent.
The amount and purity of RNA were analysed by a NanoDrop ND-100 (Thermo Fisher Scientific). Only small RNAs of length 20-22nt were selected to prepare libraries and PCR amplification. Then the products were sequenced via Illumina HiSeq sequencer (Illumina, USA).

treatment_protocol: CAFs were pretreated with 10% CSFBS DMEM medium for 24 h in advance, then CAFs were incubated with freshly medium with 10 nM DHT (simulating the high androgen level of prostate cancer microenvironment） or ethanol (simulating the castration level of prostate cancer microenvironment after ADT) for 48 h. After exposure, CAFs were washed using PBS and cultured in complete medium containing exosome-free CSFBS with 10 nM DHT or ethanol (ETOH) for another 48 h.

value: CAFs derived from prostate cancer

value: treated with ETOH for 4 days


title: ETOH-treated CAF2-derived exosomes


title: Adar OE 12h rep 1

description: replicate 1


title: NOV-31.3uM-1


title: NIT-7.8uM-3

value: Nitrofurantoin (NIT)


title: NIT-7.8uM-1


title: NIT-7.8uM-2


title: Adar MO 12h rep 2

description: replicate 2


title: NIT-31.3uM-3


title: Adar MO 12h rep 1

description: replicate 1


title: ETOH-treated CAF1-derived exosomes


title: DHT-treated CAF3-derived exosomes

value: treated with DHT for 4 days


title: NOV-250uM-1


title: DHT-treated CAF2-derived exosomes


title: Control 12hpf rep 3

description: replicate 3


title: NOV-125uM-2


title: DHT-treated CAF1-derived exosomes


title: NIT-31.3uM-1


title: NIT-31.3uM-2


title: NIT-3.9uM-3


title: NIT-15.6uM-3


title: Adar OE 128-cell rep 2

description: replicate 2


title: Adar MO 5.3hpf rep 1

description: replicate 1


title: Adar MO 5.3hpf rep 2

description: replicate 2


title: Adar OE 5.3hpf rep1

description: replicate 1


title: Adar MO 12h rep 3

description: replicate 3


title: NOV-7.8uM-3


title: Adar OE 5.3hpf rep2

description: replicate 2


title: NIT-15.6uM-1


title: NIT-3.9uM-1


title: Adar OE 128-cell rep 1

description: replicate 1


title: Adar MO 128-cell rep 1

description: replicate 1


title: NOV-7.8uM-1


title: Adar MO 128-cell rep 2

description: replicate 2


title: Control 12hpf rep 2

description: replicate 2


title: Control 5.3hpf rep 2

description: replicate 2


title: NIT-3.9uM-2


title: NIT-15.6uM-2


title: NOV-7.8uM-2


title: Control 12hpf rep 1

description: replicate 1


title: Control 128-cell rep 2

description: replicate 2


title: Control 5.3hpf rep 1

description: replicate 1


title: Control 128-cell rep 1

description: replicate 1


title: NOV-3.9uM-3


title: NOV-2uM-3

value: 2 µM


title: NOV-3.9uM-1


title: Offspring 5.3hpf

description: offspring


title: Offspring 3.5hpf

description: offspring


title: NOV-2uM-2


title: NOV-2uM-1


title: Offspring 16-cell

description: offspring


title: Parent Female genomic

description: female parent

source_name: tail fin-clip from adult zebrafish

value: tail fin-clip from adult zebrafish

value: adult


title: NOV-3.9uM-2

value: Novobiocin (NOV)


title: NOV-15.6uM-1


title: NIT-62.5uM-3


title: NOV-15.6uM-3


title: NOV-15.6uM-2


title: Parent male genomic

description: male parent


title: NIT-62.5uM-1


title: Scrambled siRNA transfected cells - 5

city: Leuven

first: Ahmed

last: Reda

address: Herestraat 49

country: Belgium

institute: KU Leuven

description: Scrambled siRNA

data_processing:
Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using using FastX 0.0.14 and ShortRead 1.40.0 (Morgan et al, 2009). With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina (Langmead & Salzberg, 2012).
The preprocessed reads were aligned with STAR aligner v2.5.2b to the reference genome of Homo sapiens (GRCh38) (AD et al, 2013).  Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments (Li et al, 2009).
The number of reads in the alignments that overlap with gene features were counted with featureCounts 1.5.3 (Liao et al, 2014). Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id. We removed genes for which all samples had less than 1 count-per-million. Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor (Risso et al, 2011).
With the EdgeR 3.24.3 package of Bioconductor, a negative binomial generalized linear model (GLM) was fitted against the normalized counts (Robinson et al, 2007). We did not use the normalized counts directly, but worked with offsets. Differential expression was tested for with a GLM likelihood ratio test, also implemented in the EdgeR package. The resulting p-values were corrected for multiple testing with Benjamini-Hochberg to control the false discovery rate (Benjamini  & Hochberg, 1995).
Genome_build: Homo sapiens Ensembl GRCh38.88
Supplementary_files_format_and_content: RNAseq counts in XLXS file, Statistical Results in XLXS file

source_name: fertile human caput epididymis (FHCE) cell line

extract_protocol:
Cells (grown in 6-well plates and transfected) were pelleted, and then RNA was isolated by QIAGEN Rneasy mico kit (Cat No./ID: 74004) according to the provider's protocol
Per sample, an amount of 50 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 1000000040498 v00 October 2017) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library.

treatment_protocol: FHCE cells were transfected with either scrambled siRNA or CTNS siRNA for 48 hours in vitro

value: epididymal epithelial cells

tag: passage

tag: cells

value: SV40 conditionally immortalized

value: Scrambled siRNA


title: Scrambled siRNA transfected cells - 6

description: Scrambled siRNA


title: NIT-62.5uM-2


title: Scrambled siRNA transfected cells - 4

description: Scrambled siRNA


title: NIT-250uM-1


title: Scrambled siRNA transfected cells - 2

description: Scrambled siRNA


title: Scrambled siRNA transfected cells - 1

description: Scrambled siRNA


title: NIT-250uM-2


title: NIT-250uM-3


title: M3

city: Chuo-ku

first: Jun

last: Nakayama

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center

data_processing:
Raw sequencing data were processed with the CellRanger pipeline (version 3.0.2, 10X Genomics) and mapped to the human genome (GRCh38) to generate matrices of gene counts by cell barcodes.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression matrix with features and cell barcodes by Cellaranger

source_name: Human Breast Cancer Lymphnode Metastasis

extract_protocol:
Single cells were isolated from patient-derived breast using Tumor Dissociation Kit protocol (Miltenyi Biotec, 130-095-929).  Single cells  were processed using the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit according to the manufacturer’s instructions in the Chromium Next GEM Single Cell 3′ Reagents Kits V3.1 User Guide(10X Genomics). Briefly, 8,000 cells were loaded into each chip channel and partitioned into Gel Beads-in-emulsion (GEMs) on the Chromium Controller, followed by cell lysis and barcoded RNA reverse transcription.
Library preparation was performed after breaking of single-cell emulsions, and included cDNA amplification, fragmentation, hearing and 5′ adaptor and sample index attachment. Sequencing was performed on a HiSeq X (Illumina, Inc., San Diego, CA)

value: IDC


title: NIT-125uM-3


title: CTNS siRNA transfeccted cells - 6

description: CTNS siRNA

value: CTNS siRNA


title: Scrambled siRNA transfected cells - 3

description: Scrambled siRNA


title: GFPpositive 3

city: Dresden

first: Anne

last: Grapin-Botton

state: Saxony

address: Pfotenhauerstrasse 108

country: Germany

institute: Max Planck Institute of Molecular Cell Biology and Genetics, Dresde

description: P1 pups islets (from 4pups) Wnt4+

hyb_protocol: 1.5 µg of Cy5-labelled cDNA was used for the hybridization step using the Gene Expression Hybridization kit (AgilentTechnologies, #5188-5242) following the manufacturers instructions. Cy5-labelled cDNA was hybridized to Agilent Whole Mouse Genome Oligo Microarrays 4x44k (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried and scanned.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for GE 8x60k microarrays array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: GFPpositive 3

label_protocol: 500 pg of purified RNA was transcribed into cDNA by using the Ovation PicoSL WTA System V2 kit (Nugen, #3312-48) and labelled with the SureTag DNA Labeling kit (Agilent technologies, #5190-3400) following the manufacturers' instructions.

growth_protocol: Mice were crossed to C57BL/6J and raised under SPF condition.

extract_protocol: RNA was prepared using RNeasy Plus Micro Kit (Qiagen, # 74034) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop 2000 spectrophotometer and with the Agilent 2100 Bioanalyzer.


title: NIT-125uM-2


title: GFPnegative 4

description: P1 pups islets (from 3pups) Wnt4-

source_name: GFPnegative 4


title: GFPnegative 3

description: P1 pups islets (from 4pups) Wnt4-

source_name: GFPnegative 3


title: GFPnegative 1

description: P1 pups islets (from 4pups) Wnt4-

source_name: GFPnegative 1


title: GFPpositive 4

description: P1 pups islets (from 3pups) Wnt4+

source_name: GFPpositive 4


title: GFPpositive 2

description: P1 pups islets (from 4pups) Wnt4+

source_name: GFPpositive 2


title: CTNS siRNA transfeccted cells - 4

description: CTNS siRNA


title: P3

source_name: Human Breast Cancer


title: M4


title: CTNS siRNA transfeccted cells - 3

description: CTNS siRNA


title: H20-NOV-3

value: 0 µM


title: P4


title: CTNS siRNA transfeccted cells - 5

description: CTNS siRNA


title: M5


title: M6


title: CTNS siRNA transfeccted cells - 1

description: CTNS siRNA


title: LTC_Input

city: New Haven

first: Udeme

middle: D

last: Ekong

state: CT

address: 333 Cedar Street

department: Pediatrics

institute: Yale University

data_processing:
The reads were trimmed for quality.  The trimmed reads were aligned to the reference human genome (hg38 UCSC) using bwa mem program.
The macs2 program with "callpeak" was used to call peaks.  All the input alignments were designated as "control", and the alignments for the IP'ed sample were designated as "Treatment".  The peaks were called individually for each condition.
Summits were also called.
Genome_build: hg38
Supplementary_files_format_and_content: macs2 narrowPeak file.

source_name: FACS-sorted memory Tregs

extract_protocol: Indexed libraries that met appropriate cut-offs were quantified by qRT-PCR (KAPA Biosystems) and insert size distribution determined with the LabChip GX.

treatment_protocol: ~5 – 10 ng of DNA was cleaned up using Ampure XP SPRI beads (Beckman Coulter Genomics). The DNA was then end-repaired, A-tailed, adapter ligated and PCR enriched (8 – 10 cycles).

tag: tag

value: FACS-sorted memory Tregs from blood

tag: chip antibody

tag: affectedstatus

value: Liver transplanted control


title: P6


title: LTC

value: anti-ATF6 (sc-166659, lot # K 1617, Santa Cruz Biotechnology)


title: CTNS siRNA transfeccted cells - 2

description: CTNS siRNA

tag: treatment


title: IR-2

tag: cell line

value: Ionizing Radiation (IR; positive control)

value: 4 Gy


title: IR-1


title: H20-NOV-2


title: IR-3


title: H20-NOV-1


title: NIT-125uM-1

value: Nitrofurantoin (NIT)


title: H2O-3


title: AIH_Input

value: Auto-immune hepatitis


title: M1

tag: cell type


title: M2


title: P5


title: AIH


title: P1


title: H2O-2


title: HC

value: anti-ATF6 (sc-166659, lot # K1617, Santa Cruz Biotechnology)

value: Healthy Control


title: P2


title: AR_Input

value: Acute rejection


title: NCCBC14

value: DCIS


title: H2O-1

value: Novobiocin (NOV)


title: CA-2mM-3

value: Caffeine (CA; Negative Control)


title: AR


title: NCCBC13

source_name: Human Breast

value: normal breast


title: CA-2mM-2

source_name: Human TK6 Cells


title: dnAIH_Input

value: denovo Autoimmune hepatitis


title: CA-2mM-1


title: NCCBC11


title: NCCBC7


title: dnAIH


title: BL-10uM-3

value: Bleomycin (BL, Positive Control)

value: 10 µM


title: NCCBC6


title: NCCBC5


title: BL-10uM-1


title: NIT-2uM-3

value: 2 µM


title: NCCBC3


title: HC_Input

value: FACS-sorted memory Tregs from blood


title: BL-10uM-2


title: NCCBC2


title: CON2

city: Guangzhou

first: Baisong

last: Zhao

state: Guangdong

address: No. 9 Jinsui Road, Tianhe District

department: Department of Anesthesiology

institute: Guangzhou Women and Children’s Medical Center

data_processing:
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
Genome_build: hg19
Supplementary_files_format_and_content: Number of raw junction read

source_name: whole blood

growth_protocol: All patients were followed up for 5 years, and median cubital venous blood was collected for whole transcriptome sequencing.

extract_protocol:
RNA extraction protocol
library construction protocol

treatment_protocol: Patients with caesarean delivery under combined spinal and epidural anesthesia, who had neurological complications with a final diagnosis of post-anesthesia permanent nerve damage, were selected. Patients undergoing the same operation and anesthesia process, but without neural damage were chosen as parallel control.

tag: patient

value: The patients undergoing identical operation and anesthesia process in the same period and hospital, but without neural damage manifestations were chosen as parallel control group.

tag: tissue

value: fresh venous blood


title: CON3


title: CON1


title: EXP3

value: Patients diagnosed with permanent neurological complications were present with numbness in the perineal buttocks and lateral thigh with the area not less than 15 × 10 cm during the 5 years of follow-up.


title: NIT-2uM-1

value: Nitrofurantoin (NIT)

tag: concentration


title: NIT-2uM-2


title: EXP2


title: Sample96.Roe deer.204529320114_R06C02

type: genomic

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Blood species=Roe deer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

organism: Capreolus capreolus

source_name: Blood

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: age

tag: confidenceinageestimate

tag: Sex

value: Male


title: MTZ-2uM-3

value: Metronidazole (MTZ)


title: EXP1


title: Sample95.Roe deer.204529320114_R05C02


title: In vitro activated Naive CD4 T cells, Foxo1Ctrl 2

city: BAGNEUX

first: Bruno

last: Lucas

address: 5 rue Léon BERNARD

department: Immunology

institute: Institut Cochin, CNRS UMR8104, INSERM U1016

data_processing:
STAR (v2.7.6a): STAR --genomeDir /path/to/STAR/reference/directory --sjdbGTFfile /path/to/gtf --runThreadN 20 --readFilesIn /path/to/fastq/R1 /path/to/fastq/R2 --outFileNamePrefix [sample-prefix] --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
RSEM (v1.3.1): rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output /path/to/AlignedToTranscriptome/file /path/to/rsem-prepare-reference/files [sample-rsem-suffix]
DESeq2 Pipeline: https://github.com/GENOM-IC-Cochin/RNA-Seq_analysis/releases/tag/v1.202204
Assembly: Ensembl release 101, Mus musculus GRCm38
Supplementary files format and content: *.resultsRSEM.genes.results: Tabulated files from RSEM.
Supplementary files format and content: NormalizedMatrix.tsv: Tabulated file from DESeq2.

source_name: Lymph nodes

extract_protocol: RNA was harvested using RNeasy mini plus kit (Qiagen).

treatment_protocol: 50 000 naive CD4 T cells were cultured 4 days in the presence of an anti-CD3 antibody (145-2C11, 0.1 µg per ml) and 250 000 antigen presenting cells (splenocytes from C57BL/6 CD3eKO mice).

value: Lymph nodes

value: Activated naive CD4 T cells

tag: genotype

value: In vitro activation


title: In vitro activated Naive CD4 T cells, Foxo1Ctrl 1

tag: strain


title: In vitro activated Naive CD4 T cells, Foxo1Ctrl 3


title: MTZ-2uM-2


title: In vitro activated Naive CD4 T cells, Foxo1TKO 3


title: MTZ-2uM-1


title: Sample94.Roe deer.204529320114_R04C02

value: Female


title: In vitro activated Naive CD4 T cells, Foxo1TKO 2


title: In vitro activated Naive CD4 T cells, Foxo1TKO 1


title: Sample93.Roe deer.204529320114_R03C02


title: Sample91.Roe deer.204529320114_R01C02


title: HOAC-3

value: 0 µM


title: Sample90.Roe deer.204529320114_R06C01


title: Sample87.Roe deer.204529320114_R03C01


title: Sample86.Roe deer.204529320114_R02C01


title: DMSO-1


title: Sample85.Roe deer.204529320114_R01C01


title: HOAC-2


title: HOAC-1


title: DMSO-2


title: Sample83.Roe deer.204529320088_R05C02


title: DMSO-3


title: Sample84.Roe deer.204529320088_R06C02


title: Sample82.Roe deer.204529320088_R04C02


title: Sample81.Roe deer.204529320088_R03C02


title: Sample92.Roe deer.204529320114_R02C02


title: Sample88.Roe deer.204529320114_R04C01


title: Sample73.Roe deer.204529320088_R01C01


title: NCo376_7 dpi_rep3

city: Fuzhou

first: Ning

last: Huang

state: Fujian

address: Cangshan Distrc,Shangxia Dian Road 15

institute: Fujian Agriculture and Forestry University

description: Gene expression in NCo376 at 7 day post-S. scitamineum inoculation

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

organism: Saccharum sp. complex hybrid

source_name: NCo376, 7 dpi, replicate 3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: The robust and uniform growth sugarcane plants were collected from the field and cut into single-bud stalk. These single-bud stalks were pre-treated for removing the pathogens, grew in an incubator with 28 + 0.5 °C 3000 lx, and 16 h light/8 h dark conditions until the bud sprouting and seedling grew up.

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified byRNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: The buds were injected with S. scitamineum 5 × 10^6 spores/mL.

value: bud


title: Sample78.Roe deer.204529320088_R06C01


title: Sample75.Roe deer.204529320088_R03C01


title: Sample77.Roe deer.204529320088_R05C01


title: Sample76.Roe deer.204529320088_R04C01


title: NCo376_5 dpi_rep3

description: Gene expression in NCo376 at 5 day post-S. scitamineum inoculation

source_name: NCo376, 5 dpi, replicate 3


title: NCo376_7 dpi_rep1

source_name: NCo376, 7 dpi, replicate 1


title: Sample79.Roe deer.204529320088_R01C02


title: NCo376_3 dpi_rep3

description: Gene expression in NCo376 at 3 day post-S. scitamineum inoculation

source_name: NCo376, 3 dpi, replicate 3


title: NCo376_7 dpi_rep2

source_name: NCo376, 7 dpi, replicate 2


title: NCo376_5 dpi_rep1

source_name: NCo376, 5 dpi, replicate 1


title: Sample71.Roe deer.204529320098_R05C02


title: NCo376_3 dpi_rep2

source_name: NCo376, 3 dpi, replicate 2


title: Sample72.Roe deer.204529320098_R06C02


title: NCo376_0 dpi_rep3

description: Gene expression in NCo376 at 0 day post-S. scitamineum inoculation

source_name: NCo376, 0 dpi, replicate 3


title: YC71-374_7 dpi_rep3

description: Gene expression in YC71-374 at 7 day post-S. scitamineum inoculation

source_name: YC71-374, 7 dpi, replicate 3


title: NCo376_3 dpi_rep1

source_name: NCo376, 3 dpi, replicate 1


title: YC71-374_5 dpi_rep3

description: Gene expression in YC71-374 at 5 day post-S. scitamineum inoculation

source_name: YC71-374, 5 dpi, replicate 3


title: NCo376_0 dpi_rep1

source_name: NCo376, 0 dpi, replicate 1


title: NCo376_5 dpi_rep2

source_name: NCo376, 5 dpi, replicate 2


title: NCo376_0 dpi_rep2

source_name: NCo376, 0 dpi, replicate 2


title: Sample69.Roe deer.204529320098_R03C02


title: YC71-374_3 dpi_rep3

description: Gene expression in YC71-374 at 3 day post-S. scitamineum inoculation

source_name: YC71-374, 3 dpi, replicate 3


title: YC71-374_5 dpi_rep2

source_name: YC71-374, 5 dpi, replicate 2


title: Sample74.Roe deer.204529320088_R02C01

source_name: Blood


title: Sample68.Roe deer.204529320098_R02C02


title: Sample67.Roe deer.204529320098_R01C02


title: Sample66.Roe deer.204529320098_R06C01


title: Sample70.Roe deer.204529320098_R04C02


title: Sample65.Roe deer.204529320098_R05C01


title: DIV28_MN_TTX_RNA_rep2

city: Piscataway

first: Tulsi

last: Patel

state: New Jersey

address: 683 Hoes Lane West

department: Neuroscience and Cell Biology

institute: Rutgers University

data_processing:
RNA: Reads were trimmed for adaptors and low-quality positions using Trimgalore (Cutadapt v0.6.2)88. Reads were aligned to the mouse genome (mm10) and gene-level counts were quantified using RSEM (v1.3.0)89 rsem-calculate-expression using default parameters and STAR (v2.5.2b) for alignment.
ATAC: Reads were trimmed for adaptors and low-quality positions using Trimgalore (Cutadapt v0.6.2)88. Reads were aligned to the mouse genome (mm10) with bwa mem (v0.7.1.7)91 with default parameters. Duplicates were removed with samtools (v1.7.2)92 markdup and properly paired mapped reads were filtered. Accessible regions were called using MACS2 (v2.2.7.1)93 with the parameters -f BAMPE -g mm -p 0.01 --shift -36 --extsize 73 --nomodel --keep-dup all --call-summits. Accessible regions that overlapped genome blacklist regions were excluded from downstream analysis.
Assembly: mm10
Supplementary files format and content: RNA-seq RSEM gene level outputs with expected counts, TPM, FPKM
Supplementary files format and content: ATAC-seq bed files containing called peaks

source_name: stem cell derived motor neurons

growth_protocol: Motor neurons were differenitiated using standard protocols (Wichterle and Peljto, 2008), dissociated, and co-cultured with primary astrocytes derived from mouse cortex at P2 for 28 days in the presence of neurotrophic factors.

extract_protocol:
Nuclei were extracted using an optimized version of the INTACT protocol (Mo et al., 2016)
ATAC-seq libraries were build as described (Buenrostro et al., 2015) and RNA-seq libraries were built with Clontech SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian with ZAPr ribosomal depletion

treatment_protocol: For testing role of activity, cells were treated with TTX (1uM) for the entire 28 day co-culture

value: C57BL/6- Chat-Cre;SUN1-GFP-3xMYC

value: 1uM TTX

tag: tissue/cell type

value: stem cell derived motor neurons

tag: molecule subtype

value: nuclear RNA


title: DIV28_MN_TTX_RNA_rep3


title: YC71-374_7 dpi_rep1

source_name: YC71-374, 7 dpi, replicate 1


title: YC71-374_7 dpi_rep2

source_name: YC71-374, 7 dpi, replicate 2


title: DIV28_MN_TTX_RNA_rep1


title: YC71-374_5 dpi_rep1

source_name: YC71-374, 5 dpi, replicate 1


title: Sample64.Roe deer.204529320098_R04C01


title: YC71-374_3 dpi_rep2

source_name: YC71-374, 3 dpi, replicate 2


title: YC71-374_0 dpi_rep2

description: Gene expression in YC71-374 at 0 day post-S. scitamineum inoculation

source_name: YC71-374, 0 dpi, replicate 2


title: YC71-374_3 dpi_rep1

source_name: YC71-374, 3 dpi, replicate 1


title: Sample63.Roe deer.204529320098_R03C01


title: YC71-374_0 dpi_rep1

source_name: YC71-374, 0 dpi, replicate 1


title: DIV28_MN_RNA_rep1


title: Sample62.Roe deer.204529320098_R02C01


title: Itgb7 KO-2

first: Chen

last: Shiyang

address: Room 413, New biochemistry building, YueYang Road

institute: Shanghai Institute of Biochemistry and Cell Biology (CAS)

data_processing:
Illumina bcl2fastq v2.17.1.14 software used for basecalling.
Sequences from scRNA-seq were processed with Cell ranger (v.2.1.1) software (10X Genomics). In short, demultiplexing, UMI (unique molecular identifier) collapsing and alignment to the mm10 mouse transcriptome was performed.
Data were then normalized using a deconvolution-based method by computing size factors and to remove cell-specific biases.
Data were scaled and UMI counts regressed out with the ScaleData function.Then the Genes used for the principal component analysis. PCA was performed with RunPCA, and significant PCs determined based on the Scree plot
Differentially expressed genes for each cluster were then identified using the Wilcox test in Seurat and the top genes ( Q value <0.05 and  log fold change>0.5) were used to identify different cell types.
Genome_build: mm10
Supplementary_files_format_and_content: Genes.tsv/Barcodes.tsv/Matrix.mtx files for each sample

source_name: small intestine

extract_protocol:
Single cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip and Library Kits (V2, 10X Genomics, Pleasanton) as per the manufacturer’s protocol.
Libraries were prepared with the Chromium Single Cell 3' Reagent Version 2 Kit. Libraries were sequenced on an Illumina Hiseq Xten (2 × 150) platforms at the Omics Core of Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai, China.

value: small intestine

value: epithelial cell


title: Itgb7 KO-3


title: DIV28_MN_RNA_rep2


title: Itgb7 KO-1


title: Sample60.Roe deer.204529320091_R06C02


title: DIV7_MN_RNA_rep1


title: WT-3

value: wild-type


title: WT-2


title: Sample61.Roe deer.204529320098_R01C01


title: Sample59.Roe deer.204529320091_R05C02


title: DIV0_MN_RNA_rep2


title: DIV7_MN_RNA_rep2


title: DIV0_MN_RNA_rep3


title: DIV28_MN_TTX_ATAC_rep2

value: Tn5 Tagemented DNA


title: DIV0_MN_RNA_rep1


title: Sample58.Roe deer.204529320091_R04C02


title: Sample57.Roe deer.204529320091_R03C02


title: WT-1


title: DIV28_MN_TTX_ATAC_rep1


title: HO rep-2

city: shanghai

first: HONG

last: QIN

address: 130# Dongan road

institute: Fudan Univercity

description: HO rep-2

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads from RNA-seq were aligned to the mouse mm10 reference assembly by using HISAT2 with parameters "--rna-strandness RF". Not uniquely mapped reads were removed.
For differential gene expression analysis, we counted reads mapped to Ensembl genes using HTSeq with the following command: htseq-count -f bam -r pos -s reverse -a 10 -t exon -i gene_id -m union.
Fold-change and p values were calculated by the R package DESeq2.
To quantify the expression level of genes, we acquired the FPKM using StringTie with options '-e -B -A –rf'.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including FPKM values for each replicate.

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Ultra™ II Directional RNA Library Prep Kit for Illumina® (Cat# E7760) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: 25 weeks


title: YC71-374_0 dpi_rep3

source_name: YC71-374, 0 dpi, replicate 3


title: HO rep-1

description: HO rep-1


title: Sample55.Roe deer.204529320091_R01C02

city: Los Angeles

value: Male


title: WT rep-1

description: WT rep-1


title: Sample54.Roe deer.204529320091_R06C01


title: DIV28_MN_ATAC_rep2


title: Sample53.Roe deer.204529320091_R05C01


title: DIV7_MN_ATAC_rep2


title: DIV28_MN_ATAC_rep1


title: DIV7_MN_ATAC_rep1


title: Sample52.Roe deer.204529320091_R04C01


title: HO rep-3

description: HO rep-3


title: Sample50.Roe deer.204529320091_R02C01


title: DMSO 6hr replicate2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Merged replicates: DMSO 6hr replicate1, DMSO 6hr replicate2

data_processing:
The RNA-seq reads were aligned to the hg19 human reference genome using TopHat a fast splice junction mapper for RNA-Seq reads using the ultra high-throughput short read aligner Bowtie (Langmead et al, 2009) .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Two biological replicates of total RNA were isolated from each condition.  Total RNA was isolated using the RNeasy kit (Qiagen, 74106) according to the manufacturer’s instructions.
The total RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen).  The polyA+ RNA was then used to generate strand-specific RNA-seq libraries as described previously (Zhong et al., 2011).  The RNA-seq libraries were subjected to QC analyses (final library yield, and the size distribution of the final library DNA fragments) and sequenced using an Illumina HiSeq 2000.
polyA-RNA-seq

treatment_protocol: HeLa were seeded in 6 well plates and treated with BYK or Cisplatin for 6 hours.

value: HeLa cervical cancer cell line

tag: rna-seq

value: polyA-RNA

value: DMSO (vehicle)


title: DMSO + Cisplatin 6 hr replicate1

description: Merged replicates: DMSO + Cisplatin 6 hr replicate1, DMSO + Cisplatin 6 hr replicate2

value: DMSO (vehicle) + Cisplatin


title: DIV0_MN_ATAC_rep1


title: DMSO 6hr replicate1


title: DIV0_MN_ATAC_rep2


title: DMSO + Cisplatin 6 hr replicate2


title: BYK + Cisplatin 6 hr replicate2

description: Merged replicates: BYK + Cisplatin 6 hr replicate1, BYK + Cisplatin 6 hr replicate2

value: BYK204165 + Cisplatin


title: 2yr_MN_RNA_rep2

source_name: mouse spinal cords

value: mouse spinal cords


title: 2yr_MN_RNA_rep1

value: C57BL/6- Chat-Cre;SUN1-GFP-3xMYC


title: Sample48.Roe deer.204529320104_R06C02


title: Sample56.Roe deer.204529320091_R02C02

value: Female


title: P56_MN_RNA_rep3


title: Sample47.Roe deer.204529320104_R05C02


title: BYK + Cisplatin 6 hr replicate1


title: WT rep-3

description: WT rep-3


title: WT rep-2

description: WT rep-2


title: Sample46.Roe deer.204529320104_R04C02


title: P56_MN_RNA_rep2


title: BYK 6hr replicate2

description: Merged replicates: BYK 6hr replicate1, BYK 6hr replicate2


title: Sample45.Roe deer.204529320104_R03C02


title: P56_MN_RNA_rep1


title: Sample51.Roe deer.204529320091_R03C01


title: BYK 6hr replicate1


title: P21_MN_RNA_rep3


title: Sample44.Roe deer.204529320104_R02C02


title: Sample49.Roe deer.204529320091_R01C01


title: Phaeodactylum tricornutum cells under 0.3ug/ml tunicamycin rep2

city: shantou

first: jichen

last: chen

address: university road

institute: shantou university

data_processing:
RNA-seq
illuma casava 1.7 software  used for basecalling
Sequence reads were trimmed for adaptor sequence, and masked for low complexity or low-quality sequence then mapped to mm10 whole genome using bowtie V0.12.2 with parameters
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read per kilobase of exon per magabase of library size (FPKM) were caculated using a protocol
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Phaeodactylum tricornutum

source_name: wild type under tun stress

growth_protocol: f/2 medium, 24 h light period, 22°C

extract_protocol:
0.1μg/ml tun stress, 0.3μg/ml tun stress
RNA was harvested using Trizol reagent illumina truseq RNA sample kit (Cat#FC-122-1001) was used with 1ug of total RNA for construction
RNA libraries for RNA-seq were prepared using standard illumia protocols

treatment_protocol: no tun stress

value: Phaeodactylum tricornutum CCAP 1055

value: wild type under tun stress

value: WT

value: tun stress

tag: time

value: 24 hour


title: Sample43.Roe deer.204529320104_R01C02


title: P21_MN_RNA_rep2

value: nuclear RNA


title: Phaeodactylum tricornutum cells control rep3

source_name: wild type

value: wild type

value: no treatment


title: Phaeodactylum tricornutum cells under 0.3ug/ml tunicamycin rep3


title: P21_MN_RNA_rep1


title: Sample41.Roe deer.204529320104_R05C01

value: Male


title: Sample42.Roe deer.204529320104_R06C01


title: P13_MN_RNA_rep1


title: Phaeodactylum tricornutum cells under 0.3ug/ml tunicamycin rep1


title: Sample40.Roe deer.204529320104_R04C01


title: P4_MN_RNA_rep3


title: Sample39.Roe deer.204529320104_R03C01


title: Phaeodactylum tricornutum cells control rep2


title: P4_MN_RNA_rep2


title: Phaeodactylum tricornutum cells control rep1


title: P4_MN_RNA_rep1


title: Sample38.Roe deer.204529320104_R02C01


title: VillinCre Naïve 3

city: Newark

first: Alexander

last: Lemenze

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Basecalling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and alignment (Cutadapt v2.5, STAR v2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Assembly: GRCm38
Supplementary files format and content: Tab delimited file (txt) for raw hit counts

source_name: Duodenum - Small Intestine

growth_protocol: Hpb L3  were isolated from cultures using a modified Baermann apparatus and maintained in PBS at 4C.

extract_protocol:
Intestinal epithleial cells were harvested from duodenum - small intestine, sorted by flow cytometery on DAPI-, CD45-, EpCAM+. RNA was extracted using  Qiagen RNAeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: VillinCre and VillinCre-A2BARfl/fl mice were inocualted with 200 Hpb L3 for 24hrs. PBS vehicle  was gavaged for control naïve mice

value: C57BL/6 - VillinCre

tag: genotyope

value: PBS Vehicle control

value: Intestinal Epithelial Cells, DAPI-. CD45-, EpCAM+


title: VillinCre Naïve 4


title: Sample36.Roe deer.204529320112_R06C02

source_name: Blood


title: VillinCre Naïve 2


title: VillinCre Naïve 1


title: E13.5_MN_RNA_rep1


title: E10.5_MN_RNA_rep3

value: C57BL/6- HB9-GFP

value: whole cell RNA


title: Sample34.Roe deer.204529320112_R04C02


title: Sample35.Roe deer.204529320112_R05C02


title: P13_MN_RNA_rep2

value: mouse spinal cords


title: VillinCre Hpb 4

value: Hpb 24hrs


title: E10.5_MN_RNA_rep2


title: Sample31.Roe deer.204529320112_R01C02

value: Female


title: VillinCre Hpb 3


title: Sample32.Roe deer.204529320112_R02C02


title: VillinCre Hpb 2


title: 2yr_MN_ATAC_rep2

value: C57BL/6- Chat-Cre;SUN1-GFP-3xMYC

value: Tn5 Tagemented DNA


title: E10.5_MN_RNA_rep1


title: Sample30.Roe deer.204529320112_R06C01


title: Sample37.Roe deer.204529320104_R01C01


title: Sample33.Roe deer.204529320112_R03C02


title: VillinCre Hpb 1

value: WT


title: VillinCre-A2BARfl/fl Naïve 4

value: C57BL/6 - VillinCre-A2BARfl/fl

value: A2BAR KO in intestinal epithelial cells


title: E13.5_MN_RNA_rep2

value: nuclear RNA


title: P56_MN_ATAC_rep1


title: Sample28.Roe deer.204529320112_R04C01


title: P21_MN_ATAC_rep2


title: Sample27.Roe deer.204529320112_R03C01


title: VillinCre-A2BARfl/fl Naïve 1


title: P21_MN_ATAC_rep1


title: Sample26.Roe deer.204529320112_R02C01


title: Sample25.Roe deer.204529320112_R01C01


title: VillinCre-A2BARfl/fl Hpb 4


title: P13_MN_ATAC_rep2


title: P13_MN_ATAC_rep1


title: Sample24.Roe deer.204529320095_R06C02


title: P56_MN_ATAC_rep2


title: VillinCre-A2BARfl/fl Hpb 3


title: Sample29.Roe deer.204529320112_R05C01


title: VillinCre-A2BARfl/fl Hpb 2


title: Sample23.Roe deer.204529320095_R05C02


title: SCFA - 3

city: New York

first: Julia

last: Brown

state: New York

address: 413 E 69th Street, 1252A

institute: Weill Cornell Medicine

data_processing:
Annotation, mapping and counting of the resulted reads were analyzed by SALMON with default parameters
LEfSe followed by multiple hypotheses correction using signal-to-noise rate and false discovery rate analyses was used to discover genes with differential abundance. Differences at LEfSe p < 0.05  and FDR < 0.05 were considered significant, with negative linear discriminant analysis (LDA) scores indicating genes that were upregulated in GF mice and positive LDA scores indicating genes that were upregulated in SCFA-treated mice
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx containing read counts and abundance/length

source_name: lung

extract_protocol:
Lungs were harvested and RNA was extracted using Qiagen Rneasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SCFAs

value: lung


title: VillinCre-A2BARfl/fl Hpb 1


title: P4_MN_ATAC_rep1


title: E13.5_MN_ATAC_rep2


title: P4_MN_ATAC_rep2


title: Sample22.Roe deer.204529320095_R04C02

value: Male


title: VillinCre-A2BARfl/fl Naïve 3


title: Sample21.Roe deer.204529320095_R03C02


title: VillinCre-A2BARfl/fl Naïve 2


title: SCFA - 2


title: Sample19.Roe deer.204529320095_R01C02


title: SCFA - 1


title: Sample20.Roe deer.204529320095_R02C02


title: E13.5_MN_ATAC_rep1


title: Sample18.Roe deer.204529320095_R06C01


title: Germ-free - 2

value: Germ-free


title: E10.5_MN_ATAC_rep2


title: Germ-free - 3


title: Germ-free - 1


title: Sample16.Roe deer.204529320095_R04C01


title: WT_blood, C17

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

data_processing:
Quality control of raw sequencing data was conducted using FastQC tool (Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were then mapped to the genome (Mus musculus genome GRCm38) using bowtie2 (version 2.2.2, (Langmead and Salzberg, 2012)). Reads that overlap with genes were then counted using HTSEQ tool (version 0.11.2, (Anders et al., 2015), -m intersection-nonempty -s no -i gene_id -t exon).
Expression values of protein coding genes were first normalized and differential expression analysis between the different groups was conducted using Deseq2 (Love et al., 2014)
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression_raw_counts.csv (file with HT-seq count output for all samples)

source_name: blood

growth_protocol: Female and male APP Swedish PS1 dE9 mice expressing a chimeric mouse/human mutant amyloid precursor protein (Mo/HuAPP695swe) and a mutant human presenilin 1 (PS1-dE9) both directed to CNS neurons under the prion protein promoter were used (available by Jackson Laboratory, http://www.jax.org/strain/005864). Mice were housed at the Paracelsus Medical University Salzburg in groups under standard conditions at a temperature of 22°C and a 12 h light/dark cycle with ad libitum access to standard food and water. Animal care, handling, genotyping and experiment were approved by local ethical committees (BMWFW-66.019/0011-WF/V/3b/2016). Animal breeding was done under special pathogen free (SPF) conditions and mice were transferred to non-SPF conditions a few days before the use in the experiment.

extract_protocol:
Brain: Brain samples were split in two hemispheres and both hemispheres per mouse were prepared. In short, each brain hemisphere (including brainstem and cerebellum) was mechanically chopped with a razor blade and homogenized in 2 mL ice cold HBSS with 15 mM HEPES (all from Thermofisher), 0.5% glucose (Sigma) and RNAsin (1:250, Promega) using a glass homogenizer. Cells were passed through a 100 µm cell strainer and rinsed two times with 2 mL ice cold HBSS (with 15 mM HEPES and 0.5% glucose). Cell suspensions were centrifuged at 340 g for 7 min. at 4°C. Myelin was removed by resuspending the cell pellet in 30% percoll (Sigma) solution and centrifuged at 950 g for 20 min. at 4°C. Supernatant was carefully removed and pellets containing cells of interest were diluted in HBSS followed by centrifugation at 300 g for 10 min at 4°C. Pellets were resuspended in PBS containing fixable viability dye eFlour780 (1:2000, eBioscience #65-0865) for 3-10 min. at RT and transferred to round-bottom polystyrene tubes (Corning). After centrifugation for 5 min. at 300 g, cell pellets were dissolved in FACS buffer (PBS with 2% BSA and 2 mM EDTA) containing Rat Anti-Mouse CD16/CD32 Fc-Block (1:100, BD Biosciences, #553141) for 5 min. at RT. Primary fluorescent-labeled antibodies were added and antibody incubation was performed for 45 min. at 4°C in the dark. Samples were washed in FACS buffer two times and centrifuged at 400 g for 5 min. Finally, cell pellets were resuspended in 800 µL FACS buffer with RNAsin (1:250, Promega #N2115) and filtered with a 30 µm cell strainer.  Blood:  Blood samples were incubated for 7-10 minutes with 1x RBC lysis buffer (eBiosciences, #00-4300) for lysis of red blood cells. Reaction was stopped with FACS buffer and samples were centrifuged for 5 min. at 500 g. Supernatant was removed and cell pellets resuspended in PBS containing fixable viability dye eFlour780 (1:2000, eBioscience #65-0865) for 3-10 min at RT. Samples were centrifuged for 5 min. at 500 g and supernatant was removed. Afterwards cell pellets were dissolved in FACS buffer containing Rat Anti-Mouse CD16/CD32 Fc-Block (1:100, BD Biosciences, #553141) for 5 min. Primary fluorescent-labeled antibodies were directly added to the samples and samples were incubated for 30 minutes at RT in the dark. Samples were washed with FACS buffer and filtered through a 30 µm cell strainer. After final centrifugation for 5 minutes at 500 g, cell pellets were dissolved in 800 µL FACS buffer with RNAsin (1:250, Promega #N2115). Samples were placed on 4 °C until they were analysed by flow cytometry. Following primary antibodies were used: CD3-PE (17A2) (1:100, BD Biosciences #555275), CD8a FITC (1:100, eBioscience #11-0081). Single stains and isotype controls were performed with PBMCs for compensation and verification of the signals. The following isotype control antibodies were used: PE IgG2b kappa (1:100, BDBiosciences #553989), FITC IgG2a kappa (1:100, eBioscience 11-4321-80). Single, living CD3 and CD8 double positive cells were gated (see, Figure 1D) and sorted from brain and blood samples via flow cytometry-based cell sorting (FACS sort) using the BD FACS Aria cell sorter (BD Biosciences) with BD FACS Diva software (8.0.1, BD Biosciences). In general about 104 CD3+/CD8+ T-cells were sorted from total brains or blood samples directly in RNA later (Sigma) and stored at -80°C. Sort purity was analyzed with sorted samples for every experiment day using LSR Fortessa flow cytometer (BD Biosciences). Sorted samples had a purity of about 97-100 %. RNeasy Micro Kit (Qiagen) was used to isolate the RNA from the sorted CD8+ T-cells. Isolation procedure was performed according to the manufacturer’s instructions using an elution volume of 14 µl. The elution step was carried out twice to increase the yield.
The mRNAseq was performed by Qiagen using QIAseq UPX 3’ Transcriptome analysis according to the companies protocols.
3’ Transcriptome analysis

value: blood

tag: disease state

value: control

value: female

value: CD8+ T cells


title: WT_brain, C5

source_name: brain

value: brain


title: Sample13.Roe deer.204529320095_R01C01


title: Sample14.Roe deer.204529320095_R02C01


title: Sample15.Roe deer.204529320095_R03C01


title: WT_blood, C88


title: Sample12.Roe deer.204529320094_R06C02


title: uw_batch2_aged_v3

city: Irvine

first: Remy

last: Vu

address: D288 Med Sci I Health Sciences Rd

institute: University of California, Irvine

description:
chromium kit version Cell barcode suffix for aggr file:
-6
young+aged_v3_batch2_matrix.mtx.gz
young+aged_v3_batch2_barcodes.tsv.gz
young+aged_v3_batch2_features.tsv.gz
uw_batch2_aged_v3_possorted_genome_bam.bam

data_processing:
FASTQ files were aligned utilizing 10x Genomics Cell Ranger 3.1.0.
Each library was aligned to an indexed mm10 genome using Cell Ranger Count.
Cell Ranger Aggr function was used to normalize the number of mapped reads per cells across the libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output

source_name: Mouse back skin

growth_protocol: All mice were purchased from Jax

extract_protocol: FACS-sorted cells were washed in PBS containing 0.04% BSA and resuspended at a concentration of approximately 1,000 cell/mL. Library generation was performed following the Chromium Single Cell 3ʹ Reagents Kits v2 or v3 (following the CG00052 Rev B. user guide) where we target 10,000 cells per sample for capture. Additional reagents included: nuclease-free water (Thermo Fisher Scientific; AM9937), low TE buffer (Thermo Fisher Scientific; 12090-015), ethanol (Millipore Sigma; E7023-500ML), SPRIselect Reagent Kit (Beckman Coulter; B23318), 10% Tween 20 (Bio-Rad; 1662404), glycerin (Ricca Chemical Company; 3290-32), QIAGEN Buffer EB (QIAGEN; 19086). Each library was sequenced on the Illumina HiSeq 4000 platform to achieve an average of approximately 50,000 reads per cell

value: dorsal skin

value: Aged

tag: wound timepoint

value: Unwounded skin

tag: chromium kit version


title: 4dpw_batch2_aged_v3

description:
chromium kit version Cell barcode suffix for aggr file:
-4
young+aged_v3_batch2_matrix.mtx.gz
young+aged_v3_batch2_barcodes.tsv.gz
young+aged_v3_batch2_features.tsv.gz
4dpw_batch2_aged_v3_possorted_genome_bam.bam

source_name: Dorsal wound

value: Wound at 4dpw


title: WT_blood, C64

value: WT

tag: cell type


title: 7dpw_batch2_aged_v3

description:
chromium kit version Cell barcode suffix for aggr file:
-5
young+aged_v3_batch2_matrix.mtx.gz
young+aged_v3_batch2_barcodes.tsv.gz
young+aged_v3_batch2_features.tsv.gz
7dpw_batch2_aged_v3_possorted_genome_bam.bam

value: Wound at 7dpw


title: E10.5_MN_ATAC_rep1

value: C57BL/6- HB9-GFP

tag: treatment

value: mouse spinal cords

value: Tn5 Tagemented DNA


title: uw_batch1_aged_v3

description:
chromium kit version Cell barcode suffix for aggr file:
-3
aged_v3_batch1_matrix.mtx.gz
aged_v3_batch1_barcodes.tsv.gz
aged_v3_batch1_features.tsv.gz
uw_batch1_aged_v3_possorted_genome_bam.bam

tag: tissue


title: 4dpw_batch1_aged_v3

description:
chromium kit version Cell barcode suffix for aggr file:
-1
aged_v3_batch1_matrix.mtx.gz
aged_v3_batch1_barcodes.tsv.gz
aged_v3_batch1_features.tsv.gz
4dpw_batch1_aged_v3_possorted_genome_bam.bam


title: WT_brain, C76


title: WT_brain, C52


title: Sample11.Roe deer.204529320094_R05C02

description: genomic DNA methylation from tissue=Blood species=Roe deer

value: Female


title: 7dpw_batch2_young_v3

description:
chromium kit version Cell barcode suffix for aggr file:
-2
young+aged_v3_batch2_matrix.mtx.gz
young+aged_v3_batch2_barcodes.tsv.gz
young+aged_v3_batch2_features.tsv.gz
7dpw_batch2_young_v3_possorted_genome_bam.bam

value: Young


title: Sample9.Roe deer.204529320094_R03C02


title: WT_blood, C40


title: WT_brain, C29


title: Sample17.Roe deer.204529320095_R05C01

value: Male


title: Sample10.Roe deer.204529320094_R04C02


title: WT_blood, C16

value: blood


title: T4_Tx_Cur_1

city: Taoyuan

first: Nian Kang

last: Sun

address: No.261, Wenhua 1st Rd.Guishan Dist

department: Division of Biomedical Sciences

country: Taiwan

institute: Chang Gung University of Science and Technology

data_processing:
1. Illumina official tool, BCL2FASTQ conversion Software v2.20 was used to convert BCL files from the Illumina sequencing platform.
2. TRIMMOMATIC v0.36 was used to remove adaptors and trim low quality bases.
3. Trimmed reads were aligned to the reference genome sequence using HISAT2 v2.1.0 aligner to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
4. Differential expression analysis was performed using CUFFDIFF of CUFFLINKS package v2.2.1 to produce gene/transcript read count and FPKM profiles for each group of samples, then functional enrichment assay was performed using clusterProfiler v3.6.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: excel files include gene ID, gene type, gene name, EntrezGene ID, locus and FPKM values for each samples

source_name: Ovarian carcinoma

growth_protocol: SKOV3 cells were stably transfected with TLR4 expressing vector using blasticidin selection. Cells were maintained under standard cell culture conditions  (37ºC; 5% CO2) in DMEM/F12 nutrient medium (Life Technologies).

extract_protocol:
RNA were prepared with TRIzol Reagent (Thermo Fisher Scientific) according to the manufacturer's instruction. Purified RNA was qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA).
Agilent's SureSelect Strand-Specific RNA Library Preparation Kit was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

treatment_protocol: Cells were seeded at the day before treatment and treated with taxol (2 nM) alone or combined with curcumin (20 uM) for 24 hours.

tag: cell line

value: Ovarian carcinoma cell line

tag: genotype/variation

value: taxol+curcumin


title: T4_Tx_2

value: taxol


title: WT_brain, C28

value: brain

value: control

value: female

value: CD8+ T cells


title: 4dpw_batch2_young_v3

description:
chromium kit version Cell barcode suffix for aggr file:
-1
young+aged_v3_batch2_matrix.mtx.gz
young+aged_v3_batch2_barcodes.tsv.gz
young+aged_v3_batch2_features.tsv.gz
4dpw_batch2_young_v3_possorted_genome_bam.bam

value: dorsal skin

tag: age

value: Wound at 4dpw


title: T4_Tx_Cur_2