title: hiPSC-derived MGL, 127_CTM_01, IL-6

city: London

first: Amalie

middle: Charlotte Maria

address: 5 Cutcombe Road

department: Basic and Clinical Neuroscience

institute: King's College London

data_processing:
Paired-end fastq files were aligned to the human reference genome (GRCh38) with STAR (Dobin et al., 2013).
Read count extraction was prepared and filtered for counts ≥ 1 using featureCounts (Liao et al., 2014) from the Rsubread (Yang Liao et al., 2019) package, version 2.4.3.
Assembly: GRCh38 - hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for each Sample, plus annotation values for entrezgene IDs, ensembl IDs, HGNC symbols, chromosome location, start and end position, strand, band and gene biotype.

growth_protocol: hiPSC-derived MGLs were differentated to 14 days following the protocol published by Haenseler et al. (2017).

extract_protocol:
RNA was extracted using Trizol Reagent (Invitrogen; 15596026) following the manufacturers protocol.
Libraries were prepared using a polyA selection method using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Cells were treated for 3h with 100ng/ml IL-6 (Gibco; PHC0066) or 100pM Acetic Acid as per manufacturers instruction.

value: hiPSC-derived microglia-like cell

value: Control

value: 100ng/ml IL-6


title: GST scRNAseq

status: Public on Sep 30 2024

type: SRA

city: Marseille

first: Magali

last: Irla

address: 163 Av. de Luminy

country: France

institute: Centre d’Immunologie de Marseille-Luminy (CIML)

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw fastq files were processed using the Cell Ranger software (v6.0.1) from 10x Genomics. Alignment was done on the GRCm38 reference genome. All clustering analyses were performed using the Seurat v4.3.0 package in R v4.2.2.
Assembly: GRCm38
Supplementary files format and content: Gzipped tab separated value and matrix files containing the cellular barcodes (barcodes.tsv.gz), the list of features (features.tsv.gz) and the UMI matrix count (matrix.mtx.gz).

molecule: total RNA

organism: Mus musculus

source_name: Thymus

extract_protocol:
Thymic single cell suspensions were obtained by mechanical digestion in the presence of DNase I (100 µg/ml) and Liberase TM (50 µg/ml) for 40 min and washed PBS 5%BSA 1mM EDTA. Samples were enriched for CD45- cells using the autoMACS® Pro Separator with the Depletes program (Miltenyi). Viable CD31+ EC and EpCAM+ TEC were sorted using a BD FACSAriaIII cell sorter. Sorted EC and TEC from each sample were pooled and loaded in a single capture well for subsequent 10x Genomics Single Cell 5’ v32 workflow, targeting a capture of 10,000 cells.
Libraries were performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).  The resulting libraries containing distinct i5 and i7 indexes were pooled and sequenced together on an Illumina NextSeq2000 platform using a P2 flow cell (100 cycles).

treatment_protocol: Aged mice were treated for 3 consecutive days with GST (control) or RANKL proteins and thymi were withdrawn 21 days after the first injection.

tag: tissue

value: Thymus

tag: cell type

value: EpCAM+ thymic epithelial cells (TECs) and CD31+ endothelial cells (Ecs)

tag: genotype

value: C57BL/6 mice

tag: treatment

value: GST

tag: age

value: 10-12 months old


title: hiPSC-derived MGL, 014_CTM_02, IL-6

last: Couch

country: United Kingdom

library_source: transcriptomic

organism: Homo sapiens

tag: cell line


title: ST-00017449-T

city: Portland

first: Rosalie

last: Sears

state: OR

address: 2730 SW Moody Ave, CL4RS

department: Molecular and Medical Genetics

country: USA

institute: Oregon Health & Science University

description: Primary pancreas tumor

data_processing:
Paired-end fastq sequences were trimmed using trim-galore (ver 0.6.3) and default parameters.
Pseudoalignment was performed with kallisto (ver 0.44.0) using genome assembly GRCh38.p5 and gencode (ver 24) annotation using default parameters.
Bioconda package bioconductor-tximport (ver 1.12.1) was used to create gene level counts and abundances (TPMs).
Quality checks were assessed with FastQC (ver 0.11.8) and MultiQC (ver 1.7).
Assembly: GRCh38.p5
Supplementary files format and content: Gene level count estimates are provided as a matrix in tab delimited text format.  Feature annotations are provided in the first few columns.
Supplementary files format and content: Gene level TPM estimates are provided as a matrix in tab delimited text format.  Feature annotations are provided in the first few columns.
Supplementary files format and content: Per sample h5 file output from the kallisto pipeline is provided.
Supplementary files format and content: Gene level TMM normalized (edgeR method) estimates are provided as a matrix in tab delimited text format. Feature annotations are provided in the first few columns as well as a column with expression level filtering status. The TMM gene level estimates provided are not log scaled and are generated from the h5 files using general recommendations for importing from the kallisto method as given here: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto & https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#edgeR

source_name: Pancreas

extract_protocol:
Starting with sectioned FFPE PDAC specimen blocks, Clinical pathologists marked regions of high tumor content (>20% ratio of tumor to normal nuclei) on H&E stained slides for RNA extraction. Solid tumor total nucleic acid was extracted from these tumor regions on adjacent FFPE tissue sections using Chemagic 360 sample-specific extraction kits (Perkin Elmer) and digested by proteinase K. RNA was purified from the total nucleic acid by DNase-I digestion.
100ng of RNA for each tumor sample was heat fragmented in the presence of magnesium to an average size of 200 bp. Library preps were hybridized to the xGENExome Research Panel v1.0 (Integrated DNA Technologies) and target recovery was performed using Streptavidin-coated beads, followed by amplification with the KAPA HiFi Library Amplification Kit.

tag: tumor type

value: Primary

value: Pancreas

value: scraped tumor


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep1_DNA#03

city: SCOTTSDALE

first: Zong

last: Wei

state: Arizona

address: 13400 E Shea Blvd

institute: Mayo Clinic

library_source: genomic

data_processing:
Preprocessing of Paired-tag were carried out with the scripts available from GitHub (https://github.com/cxzhu/Paired-Tag).Cellular barcodes were extracted from Read2 and assigned to each sample barcodes (12 initial tubes for tagmentation and reverse transcription) and combination of ligated barcodes. The first base of BC#1, BC#2 and BC#3 should locate within 84-87th, 47-50th and 10-13th base of Read2. We identify the positions of barcodes by matching the linker sequences adjacent to the cellular barcodes.Cleaned reads were first mapped to a mouse GRCm38 genome reference genome with STAR (version: 2.7.3a) for RNA or bowtie2 for DNA. Duplicates were removed based on the mapped position, cellular barcode, PCR index and UMI.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include cell embeddings for each cell.

molecule: genomic DNA

source_name: Pancreatic Islet

extract_protocol:
Single-cell suspension were prepared from the pancreatic islet, Spin-down cells at 300 g for 5 mins, resuspended the cells in 1 mL 0.2% NIB-RPI(1 mL 0.2% NIB, 20 µL Protease Inhibitor (50X), 25 µL SUPERase IN and 12.5 µL RNaseOUT). Sit on ice for 5 min.Count the nuclei using cell counter.
Libraries were constructed by Paired-tag workflow, briefly: First, permeabilized nuclei were incubated with antibodies (H3K27ac, Cell Signaling #8173S, H3K4me1, Cell Signaling #5326S) targeting chromatin regions of interest to trigger the targeted binding of protein A-fused Tn5. Tagmentation reaction and reverse transcription (RT) were then sequentially performed: reactions were carried out in 12 different wells, with the same set of barcodes in transposase adaptors and RT primers, to label different samples or replicates (1st round of barcodes). Next, a ligation-based combinatorial barcoding strategy was used to introduce the 2nd and 3rd rounds of barcodes to nuclei, by sequential attaching well-specific DNA barcodes from 96-well plates to the 5’-end of both DNA fragments and cDNA from RT. Lastly, barcoded nuclei were divided into sub-libraries and lysed, the DNA/cDNA was purified to give rise DNA and RNA libraries for sequencing

treatment_protocol: Mice were maintained on chow or high fat diets for 8 or 16 weeks

value: Pancreatic Islet

tag: antibody

value: normal chow (NC)


title: 3T3-L1 maintained in Medium_rep3

type: RNA

city: TSUKUBA

first: ELDA NURAFNIE

last: IBNU RASID

state: IBARAKI

address: 1-1-1 TENNODAI

country: Japan

institute: UNIVERSITY OF TSUKUBA

description: Gene expression data without Tsuru treatment for 9 days

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S Array, Mouse; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files) filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space).
Signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4).

label: biotin

source_name: 3T3-L1  cells without treatment for 9 days

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: Mouse 3T3-L1 cells (Riken, Tsukuba, Japan) were cultured in DMEM (Sigma, Tokyo, Japan) supplemented with fetal bovine serum (FBS) (Gibco™) and 1% Penicillin-Streptomycin (Sigma-Aldrich, USA) at 37oC in a 5% CO2 humidified incubator.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: The 3T3-L1 was seeded at 3.0x104 cells/cm2 in preadipocytes medium (DMEM containing 10% FBS). After post confluence (DO), the medium was replaced with induction medium containing 1% of 1000x cell-based assay IBMX solution, 1000x insulin solution and 1000x adipogenesis assay dexamethasone solution with Tsuru treatment at 1/1000 and 1/100 of dilution of 100mg/ml Tsuru and without treatment (control) . At Day 3 (D3), the induction medium was replaced with insulin medium that is preadipocytes medium with 1% of 1000x Insulin Solution. The differentiation continued for 9 days (D9) and the differentiation medium was replaced every two days until D9.

value: Mouse fibroblast-like cell line

value: control


title: hiPSC-derived MGL, 014_CTM_02, Vehicle

value: 100pM Acetic Acid Vehicle


title: hiPSC-derived MGL, 127_CTM_01, Vehicle


title: hiPSC-derived MGL, M3_CTR_36S, IL-6


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep1_DNA#02


title: 3T3-L1 maintained in Medium_rep1


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep1_DNA#01


title: ST-00017310-T

description: Primary pancreas tumor


title: ST-00017340-T

description: Primary pancreas tumor


title: hiPSC-derived MGL, M3_CTR_36S, Vehicle


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep2_RNA#04

molecule: nuclear RNA


title: ST-00017804-T

description: Primary pancreas tumor


title: ST-00021355-T

description: Primary pancreas tumor


title: OCI-LY3 IP

city: Shanghai

first: JIAO

last: MA

address: Huangpu District

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
After passing Solexa CHASTITY quality filter, the clean reads were aligned to human reference genome UCSC HG19 using BOWTIE (V2.1.0). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-3. The peaks were annotated by the nearest gene using the newest UCSC RefSeq database.
Assembly: human reference genome UCSC HG19
Supplementary files format and content: LY3-IRF4_vs_LY3-input_1e-3_10_30_peaks.bed; Peak _Annotation. Xls

growth_protocol: OCI-LY3 cells were cultured in IMDM supplemented with 20% Fetal Bovine Serum (FBS) and 100g/mL penicillin/streptomycin.

extract_protocol:
OCI-LY3 cell pellet was wash twice with ice cold PBS and DNA was extracted using DNeasy Blood & Tissue Kit (#69504, Qiagen) per instruction manual DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina)
Sequencing library was prepared by converting 10 ng DNA of each sample to phosphorylated blunt-end fragment. An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments, and Illumina's genomic adapters were ligated to the A tailed DNA fragments prior to subject to PCR amplification to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads. The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using Cluster Kit.

value: Diffuse Large B cell lymphoma cells


title: ST-00017804-M

description: Metastisis to the Lung

source_name: Lung

value: Met

value: Lung


title: ST-00017297-T

description: Primary pancreas tumor


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep2_RNA#02


title: OCI-LY3 Input DNA


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep1_RNA#03


title: ST-00017261-T

description: Primary pancreas tumor


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep1_RNA#02


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep1_RNA#01


title: 3T3-L1 treated with Tsuru_rep1

description: Gene expression data from 3T3-L1 treated with Tsuru for 9 days

source_name: 3T3-L1 cells were treated with Tsuru for 9 days

value: Tsuru


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep1_RNA#04


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep2_DNA#04


title: ST-00020153-T

description: Primary pancreas tumor


title: ST-00020089-M

description: Metastisis to the Liver

source_name: Liver

value: Liver


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep1_DNA#04


title: ST-00017080-T

description: Primary pancreas tumor


title: AZ.7

city: Chicago

first: Azzurra

last: Zicarelli

state: illinois

address: 929 E 57th St

institute: University of Chicago

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification. After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After the extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Assembly: Homo sapiens
Supplementary files format and content: tab-delimited includes raw counts for each sample

source_name: Xenograft

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen).
RNA sequencing (RNA-seq) libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina. Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation and quantified by using Qubit 2.0 Fluorometer as well as by quantitative PCR

value: Xenograft

value: Epithelial cells

value: ERa Y537S Heterozygous

value: Lasofoxifene


title: AZ.12

value: Niraparib + Lasofoxifene


title: AZ.10


title: AZ.8


title: AZ.9


title: AZ.11


title: ST-00021358-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: KPC_45_Sphere

city: Madrid

first: Susana

last: García-Silva

state: madrid

address: Melchor Fernandez Alamgro

department: Molecular Oncology

country: Spain

institute: Spanish national Cancer Research Centre

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: ~250 ng. Volume: 40 uL. Temperature (ºC): 65. Duration: 24 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

data_processing: Images were quantified using Agilent Feature Extraction Software (ver. 10.1.1). Microarray background subtraction was carried out using the normexp method. Quantiles were used to perform normalization. Filtered data were tested for differential expression applying R limma package (Bioconductor project, http://www.bioconductor.org).

label_protocol: Amount of nucleic acid labeled: 250ng. Recommendations from Sigma-Aldrich for the integration of TransPlex WTA with the Agilent microarray workflow were followed, such as the omission of Cot-1 DNA. Briefly, cDNA is non-enzymatically labeled with ULS technology (Kreatech), in which a platinum dye complexed with Cy3 fluorophor couples preferentially with guanine molecules of the sample. Labeled samples are purified with gel filtration columns.

growth_protocol: For Adherent samples, cells were grown for 4 days in RPMI medium with 10%fetal bovine serum and 50units/ml penicillin/streptomycin in regular culture dishes. For Sphere samples, cells were grown for 4 days in ultra-low attachment plates using serum-free RPMI supplemented with B27 1:50, 20 ng/mL bFGF, L-Glutamine and 50 units/ml penicillin/streptomycin.

extract_protocol: Total RNA fraction. RNA Integrity Numbers were in the range 8,5 to 9,8 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer. Available RNA amounts in the range of 1-2 ng were subjected to a preliminary amplification step with a TransPlex Whole Transcriptome Amplification WTA2 kit (Sigma-Aldrich). Optimal cycle number was set at 18, by proceeding 2–4 cycles beyond the amplification “plateau” as observed with real-time qPCR.

value: tissue:Primary tumor cells from pancreatic tumors in KPC mice growing in non adherent/sphere conditions

value: Pancreatic tumoral tissue


title: AZ.6

value: Niraparib


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep1_DNA#03

value: Pancreatic Islet

value: normal chow (NC)


title: ST-00020093-T

description: Primary pancreas tumor

value: scraped tumor


title: KPC_6_Sphere

description: Primary tumor cells from pancreatic tumors in KPC mice growing in non adherent/sphere conditions


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep2_DNA#02


title: KPC_1_Sphere


title: ST-00017074-T

description: Primary pancreas tumor


title: KPC_45_Adherent

value: tissue:Primary tumor cells from pancreatic tumors in KPC mice growing in adherent conditions


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep1_DNA#02


title: AZ.3

value: Vehicle


title: ST-00017967-T

description: Primary pancreas tumor


title: AZ.4


title: Paired_tag_islet_H3K4me1_0week_B6_sub_library_rep1_DNA#01


title: KPC_1_Adherent

description: Primary tumor cells from pancreatic tumors in KPC mice growing in adherent conditions


title: Paired_tag_islet_H3K4me1_0week_B5_sub_library_rep1_RNA#04


title: AZ.2


title: ST-00017381-T

description: Primary pancreas tumor


title: KPC_6_Adherent


title: AZ.5


title: Paired_tag_islet_H3K4me1_0week_B5_sub_library_rep1_RNA#03


title: AZ.1


title: C replicate 2

source_name: EpCAM+Sca1+CD133- cells

extract_protocol: Total RNA fraction from sorted cells from freshly isolated pancreatic tumors. RNA Integrity Numbers were in the range 7,3 to 8,2 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer. Available RNA amounts in the range of 1-2 ng were subjected to a preliminary amplification step with a TransPlex Whole Transcriptome Amplification WTA2 kit (Sigma-Aldrich). Optimal cycle number was set at 18, by proceeding 2–4 cycles beyond the amplification “plateau” as observed with real-time qPCR.

value: EpCAM+Sca1+CD133- cells

tag: tissue of origin

value: KPC mouse pancreatic tumor


title: D replicate 3

source_name: EpCMA+Sca-1+CD133+ cells

value: EpCMA+Sca-1+CD133+ cells


title: H replicate 3

source_name: EpCAM+Sca1-CD133+ cells

value: EpCAM+Sca1-CD133+ cells

value: Control pancreas


title: D replicate 2


title: G replicate 2

source_name: EpCAM+Sca1+CD133-  cells

value: EpCAM+Sca1+CD133-  cells


title: Paired_tag_islet_H3K4me1_0week_B5_sub_library_rep1_RNA#02


title: B replicate 2


title: G replicate 1


title: ST-00017078-T

description: Primary pancreas tumor


title: B replicate 3


title: A replicate 3

source_name: EpCAM+Sca1-CD133-  cells

value: EpCAM+Sca1-CD133-  cells


title: C replicate 1


title: H replicate 2


title: D replicate 1


title: Paired_tag_islet_H3K4me1_0week_B5_sub_library_rep1_RNA#01


title: A replicate 1


title: ST-00017003-M

description: Metastisis to the Liver

value: Met

value: Liver


title: ST-00020133-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: H replicate 1


title: Paired_tag_islet_H3K4me1_0week_B5_sub_library_rep1_DNA#04


title: ST-00017041-T

description: Primary pancreas tumor


title: Paired_tag_islet_H3K4me1_0week_B5_sub_library_rep1_DNA#03


title: PolyA_RNAseq_Patient_1_PB_Cycle2_Day1

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
Prior to mapping, raw FASTQ files were trimmed using Trim_galore (v0.6.4) to remove residual Illumina adapter and/or low quality (Q<15) sequences. Trimmed sequencing reads were then aligned to the human Hg19 reference genome (GENCODE, GRCh37.p13) using STAR (v2.7.5).
Samtools (v1.9) was used to convert SAM files to BAM files, as well as sorting, and indexing.
Sorted BAM files were used for read counting across genomic features (exons) with featureCounts (part of the subread package; v1.5.0) (Liao et al., 2014) using the following parameters: -p -T 20 -O -F GTF -t exon.
The resultant counts file was used as input for differential gene expression analysis, which was performed using the edgeR (v3.32.1), DESeq2 (v1.30.1) (Love et al., 2014), and limma voom (v3.46.0) (Law et al., 2014) R packages.
Differential alternative splicing events were detected using Multivariate Analysis of Transcript Splicing (rMATS, v4.1.1) using the GENCODE (v19) GTF annotation for GRCh37.
Assembly: Hg19
Supplementary files format and content: CSV file of raw (non-normalized) gene expression counts produced by featureCounts.

molecule: polyA RNA

source_name: Peripheral blood

growth_protocol: K562 cells wild-type for SF3B1/SRSF2 or with knock-in of a single allele mutation in SF3B1-K700E, SF3B1-K666N, or SRSF2-P95H or NKM1 cells (which harbor a naturaly occurring U2AF1-Q157P mutation) were cultured under standard in vitro culture conditions reccomended by vendors.

extract_protocol:
RNA was extracted using the Qiagen RNeasy extraction kit, according to the manufacturer’s instructions.
A minimum of 500 ng of high-quality RNA (as determined by Agilent Bioanalyzer) per replicate was used as input for library preparation. Poly(A)-selected, strand-specific (dUTP method) Illumina libraries were prepared by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center (MSKCC) with a modified TruSeq protocol.
Libraries were sequenced on the Illumina HiSeq 2000 to obtain ∼100M 2x101 bp paired-end reads per sample.

treatment_protocol: K562 cells wild-type for SF3B1/SRSF2 or with knock-in of a single allele mutation in SF3B1-K700E, SF3B1-K666N, or SRSF2-P95H or NKM1 cells (which harbor a naturaly occurring U2AF1-Q157P mutation) were treated for 24 hours with DMSO vehicle or E7820 (1uM) treatment .

value: Peripheral blood

value: AML Patient 1

value: Haematopoietic

value: E7820 (Cycle 2, Day 1)


title: ST-00016213-T

description: Primary pancreas tumor

value: scraped tumor


title: HPV-KER cells, Candida parapsilosis-treated, 12 hours, replicate 2

city: Szeged

first: Marton

last: Horvath

state: Csongrád

address: Közép fasor 52.

department: Microbiology

country: Hungary

institute: University of Szeged

description:
cell_raw_counts.csv
HK_Cp_2

data_processing:
Human sequenced reads were trimmed for standard Illumina adaptor sequences / low-quality sequences using trim-galore (v0.6.4) (parameters: -q 20 --length 36 --paired --illumina). Fungal sequenced reads were trimmed for specified adaptor sequences using Cutadapt (v2.8) (parameters: (-a CGTATGCCGTCTTCTGCTTG$ -A GCATACGGCAGAAGACGAAC$ -g ^AATGATACGGCGACCACCGAGA -G ^TTACTATGCCGCTGGTGGCTCT).
Processed human- and fungal reads were aligned using Hisat2 (v2.1.0)  (parameter: --phred33 --dta --non-deterministic --rna-strandness "RF")
The resulting alignment files were sorted and indexed via Samtools (v1.15), and fungal reads were quantified with featureCounts (v2.0.1) (parameters: -p --countReadPairs -s 2 -f -O -M).
Assembly: GRCh38 (release 96) from ENSEMBL, C. parapsilosis CDC317 and C. albicans SC5314 (Assembly21) from the Candida Genome Database
Supplementary files format and content: Sorted bam files containing aligned human reads ordered by their alignment positions on the reference genome.
Supplementary files format and content: Sorted bam files containing aligned fungal reads ordered by their alignment positions on the reference genome.

source_name: HPV-KER

growth_protocol: HPV-KER cells were maintained in K-SFM medium supplemented with 1% L-glutamine, 1% penicillin-streptomycin, 0.05mg/ml BPE and 0.005 μg/ml rEGF and HaCaT keratinocytes in DMEM medium supplemented with 10% FBS, 1% penicillin-streptomycin and 1% L-glutamine at 37 °C, in the presence of 5% CO2, until 80% confluency.

extract_protocol:
Fungal transcriptome: Total RNA was isolated from C. albicans cells after their coincubation with HaCaT epithelial cells (MOI 10:1) for 4 hours at 37C, in the presence of 5% CO2. MOI = pathogen : host.
Total RNA was isolated from cell lines using the RNeasy® Plus Mini Kit, according to the manufacturer’s suggestions. Total RNA was isolated from yeast cells with the RiboPure Yeast Kit according to the manufacturer’s suggestions.
mRNA sequencing library preparation and mRNA sequencing (Illumina) was performed by specialists at Novogene according to their standard library preparation protocols.

treatment_protocol: Host transcriptome: After reaching 80% confluency, total RNA was isolated from HPV-KER / HaCaT epithelial cells after stimuli with either C. albicans (MOI of 1:25) or C. parapsilosis (MOI of 1:1) cells for 12 hours at 37C, in the presence of 5% CO2. MOI = pathogen : host.

value: HPV-KER

value: keratinocyte

tag: time

value: C.parapsilosis MOI1(host):1(patogen)


title: HPV-KER cells, Candida albicans-treated, 12 hours, replicate 3

description:
cell_raw_counts.csv
HK_Ca_3

value: C.albicans MOI25(host):1(patogen)


title: HPV-KER cells, Candida parapsilosis-treated, 12 hours, replicate 3

description:
cell_raw_counts.csv
HK_Cp_3


title: HPV-KER cells, Candida parapsilosis-treated, 12 hours, replicate 1

description:
cell_raw_counts.csv
HK_Cp_1


title: PolyA_RNAseq_Patient_4_PB_Cycle1_Day15

value: AML Patient 4


title: ST-00016968-T

description: Primary pancreas tumor


title: A replicate 2

value: KPC mouse pancreatic tumor


title: Paired_tag_islet_H3K4me1_0week_B5_sub_library_rep1_DNA#02

value: Pancreatic Islet

value: normal chow (NC)


title: ST-00016911-T

description: Primary pancreas tumor


title: PolyA_RNAseq_Patient_4_PB_Cycle2_Day1


title: HPV-KER cells, Candida albicans-treated, 12 hours, replicate 2

description:
cell_raw_counts.csv
HK_Ca_2


title: PolyA_RNAseq_Patient_3_PB_Cycle2_Day1

value: AML Patient 3


title: HPV-KER cells, Candida albicans-treated, 12 hours, replicate 1

description:
cell_raw_counts.csv
HK_Ca_1


title: ST-00020131-M

description: Metastisis to the Peritoneum

source_name: Peritoneum

value: Met

value: Peritoneum


title: Paired_tag_islet_H3K4me1_0week_B5_sub_library_rep1_DNA#01


title: PolyA_RNAseq_Patient_2_PB_Cycle2_Day1

value: AML Patient 2


title: B replicate 1

value: EpCAM+Sca1-CD133+ cells


title: PU.1_KO_24_hrs

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA 3.4.4 software (for NovaSeq 6000) was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: skin

extract_protocol:
Harvested skin wound tissues were homogenized using TissueLyzer II (Qiagen). Total RNA was harvested using miRNeasy Tissue/Cells Advanced mini kit (Qiagen) according to manufacturer’s guide.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: skin

tag: disease state

value: wound

tag: strain


title: ST-00020126-M

description: Metastisis to the Peritoneum


title: ST-00020127-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: WT_24_hrs

value: WT


title: HPV-KER cells, non-treated control, 12 hours, replicate 3

description:
cell_raw_counts.csv
HK_C_3

value: HPV-KER

value: keratinocyte

value: untreated control


title: HPV-KER cells, non-treated control, 12 hours, replicate 2

description:
cell_raw_counts.csv
HK_C_2


title: PolyA_RNAseq_Patient_2_PB_Cycle1_Day15

value: Peripheral blood

value: Haematopoietic


title: PolyA_RNAseq_Patient_2_BM_Cycle2_Day1

source_name: Bone marrow

value: Bone marrow

value: E7820 (Cycle 2, Day 1)


title: ST-00016806-T

description: Primary pancreas tumor

source_name: Pancreas

value: scraped tumor


title: MAFb KO 3

city: Nice

first: Filippo

last: Massa

state: Provence-Alpes-Cote d'Azur

address: 28, Avenue de Valombrose

institute: CNRS

description: MAFB deletion

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina)
Paired-end clean reads were mapped to the reference genome using HISAT2 software
For samples with biological replicates, differential expression analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). It provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. Therefore, if the readcount of the i-th gene in j-th sample is Kij, there is: Kij ～ NB(μij,σij2) And the resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Assembly: GRCm38/mm10
Supplementary files format and content: Differential Expression Analysis (tab delimited)

source_name: kidney

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's protocols.

treatment_protocol: Podocytes were isolated by FACS sorting (based on mTmG reporter gene) 72 hours after Cre mediated gene recombination (Mafb gene deletion)

value: kidney

value: isolated renal podocytes

value: WT1-CreErt2; Rosa26R mTmG; Mafb LoxP/LoxP

value: Tamoxifen induction

value: 72hours post induction


title: HPV-KER cells, non-treated control, 12 hours, replicate 1

description:
cell_raw_counts.csv
HK_C_1


title: PolyA_RNAseq_Patient_4_BM_Cycle2_Day1

value: AML Patient 4


title: ST-00020123-T

description: Primary pancreas tumor

value: Primary


title: HaCaT cells, Candida parapsilosis-treated, 12 hours, replicate 3

description:
cell_raw_counts.csv
HC_Cp_3

source_name: HaCaT

value: HaCaT

value: C.parapsilosis MOI1(host):1(patogen)


title: MAFb KO 2

description: MAFB deletion


title: PolyA_RNAseq_Patient_1_BM_Cycle4_Day1

value: AML Patient 1

value: E7820 (Cycle 4, Day 1)


title: PolyA_RNAseq_Patient_3_BM_Cycle2_Day1

value: AML Patient 3


title: MAFb KO 1

description: MAFB deletion


title: ST-00016499-T

description: Primary pancreas tumor

value: Pancreas


title: HaCaT cells, Candida parapsilosis-treated, 12 hours, replicate 2

description:
cell_raw_counts.csv
HC_Cp_2

value: keratinocyte


title: ST-00016742-T

description: Primary pancreas tumor


title: HaCaT cells, Candida parapsilosis-treated, 12 hours, replicate 1

description:
cell_raw_counts.csv
HC_Cp_1


title: PolyA_RNAseq_Patient_1_PB_Cycle1_Day15

value: Peripheral blood

value: Haematopoietic


title: WT ctrl 3

description: control

value: WT1-CreErt2; Rosa26R mTmG; Mafb LoxP/wt


title: PolyA_RNAseq_Patient_4_BM_pretreatment

value: Bone marrow

value: Pre-treatment


title: WT ctrl 4

description: control

value: kidney

value: isolated renal podocytes


title: HaCaT cells, Candida albicans-treated, 12 hours, replicate 3

description:
cell_raw_counts.csv
HC_Ca_3

value: C.albicans MOI25(host):1(patogen)


title: ST-00016289-T

description: Primary pancreas tumor

value: scraped tumor


title: ST-00016257-T

description: Primary pancreas tumor

value: Primary


title: HaCaT cells, Candida albicans-treated, 12 hours, replicate 2

description:
cell_raw_counts.csv
HC_Ca_2

value: HaCaT


title: PolyA_RNAseq_Patient_3_BM_pretreatment


title: MAFb KO 4

description: MAFB deletion

value: WT1-CreErt2; Rosa26R mTmG; Mafb LoxP/LoxP

value: Tamoxifen induction

value: 72hours post induction


title: WT ctrl 2

description: control


title: PolyA_RNAseq_Patient_2_BM_pretreatment

value: AML Patient 2


title: HaCaT cells, Candida albicans-treated, 12 hours, replicate 1

description:
cell_raw_counts.csv
HC_Ca_1


title: ST-00020118-M

description: Metastisis to the Liver

value: Met

value: Liver


title: ST-00015973-T

description: Primary pancreas tumor

value: Pancreas


title: HaCaT cells, non-treated control, 12 hours, replicate 3

description:
cell_raw_counts.csv
HC_C_3

value: keratinocyte

value: untreated control


title: PolyA_RNAseq_Patient_1_BM_pretreatment

value: Bone marrow

value: AML Patient 1

value: Haematopoietic


title: ST-00020117-T

description: Primary pancreas tumor


title: PolyA_RNAseq_Patient_4_PB_pretreatment

value: Peripheral blood

value: AML Patient 4

value: Pre-treatment


title: Pituitary_TpitKO

city: Montreal

first: Arthur

middle: Jules

last: Gouhier

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

description:
Normalized_Counts.tsv
CellRanger_Aggregate.cloupe
CellBarcode_UMAPCoordinates_ClusterID.tsv
Raw_Counts.tsv

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5 (10x Genomics). Sequences were aligned on the mm10 mouse reference genome on which lacZ sequence was added.
Data filtering, normalization and scaling, dimensionality reduction, standard unsupervised clustering algorithms and identification of cluster “signature” genes were performed using the Seurat R package v3.1. The following parameters were used to exclude low quality cells: 200 > nFeature counts > 4000; nCount RNA > 10,000; 5 > % mitochondrial DNA > 0.5. The three samples were combined using the merge function in Seurat. Cell clusters were identified by principal component analysis and visualized by uniform manifold approximation and projection (UMAP) embedding and unsupervised graph-based clustering with the Louvain algorithm with a resolution of 0.3. UMAP identified cell clusters were annotated based on differential expression of key pituitary marker genes.
Doublets were removed with the DoubletFinder using the default parameters, resulting in a total of 37,474 cells (11,222 WT, 12,839 Tpit+/- and 13,413 Tpit-/-).
UMAP and gene expression were visualized on 10x Genomics Loupe Browser v 6.0.
CellPhoneDB v2.0 (publicly available from https://www.cellphonedb.org/) was used with the default parameters to predict putative ligand-receptor pairs mediating cell-cell interactions. The study was limited to corticotropes, gonadotropes and somatotropes and ligand-receptor interaction pairs with a mean ≥ 0.35 and a P value ≤ 1e-10 were retained as significant.
For the differential gene expression analysis, sequenced reads were first associated to their respective cell using the cellular barcode sequence. Single-cell gene expression was quantified using Ensembl GRCm38 annotations and summing all reads mapped to any exon in the same direction as transcription. Cluster gene expression was computed as the total gene expression of all cells in the cluster and normalized using the median of ratios method (as in DESeq2) across all clusters from all samples. Normalized single-cell gene expression per cluster was computed by applying the previously computed normalization factor. Differential expression was computed using normalized cluster gene expression with two-sided Mann-Whitney U test on normalized single-cell gene expression within the cluster. Genes were considered differentially expressed if -1 ≥ log2FC ≥ 1 and –log10P > 4.
Assembly: mm10
Supplementary files format and content: Loupe Browser file from Cell Ranger Aggregate
Supplementary files format and content: Association of unique cell barcode with UMAP coordinates and cluster ID
Supplementary files format and content: Gene expression (raw count)
Supplementary files format and content: Gene expression (normalized)

source_name: Pituitary

extract_protocol:
Freshly dissected  pituitaries from Tpit-WT, Tpit-HT and Tpit-KO mice were cut in pieces using a scalpel to facilitate tissue dissociation and kept during the dissections in 1 ml of dissection buffer (DMEM - 10% FBS – 10 mM HEPES, pH 7.4 – 100 U/ml DNase). Pituitaries were then digested in 500 µl of the digestion medium (DMEM – 10 mM HEPES, pH 7.4 - 0.3% BSA – 0.25% trypsin – 100 U/ml DNase) at 37 °C for 10 min. 2 mM EDTA were then added and cells were dissociated by 20-30 ups and downs with a P1000 pipetman homogenizer, following a 5 min incubation at  37 °C. Trypsin was neutralized by adding 10% of FBS (55 µl) and cell dissociation was completed with 10-20 additional ups and downs. Cells were filtered using a 40 µM cell strainer (BF Falcone 352340), centrifuged for 5 min at 400 g and resuspended in 120 µl of FACS buffer (1xPBS - 0.8% BSA – 10% FBS - 10 mM HEPES, pH 7.4 - 100 U/ml DNase) complemented with propidium iodide (1 µg/106 cells) to exclude dead cells and sorted using a FACSAria SORP sorter (BD).
Dissociated pituitary cells were processed using Chromium Single Cell 3′ v3 Reagent (10x Genomics) following the manufacturer’s instructions. Briefly, 16,000 cells were passed on the channel to recover 10,000 cells. Pituitary cells were partitioned into gel beads in emulsion for cell lysis and barcoded with oligo-dT priming and reverse transcribed. cDNA library was amplified, fragmented and size selected. Samples were controlled at multiple steps during the procedure by running on BioAnalyzer. Resulting libraries were sequenced on Illumina NovaSeq 6000 S1 PE28x91 generating ≈300x106 reads/sample.

value: Pituitary

value: TpitKO


title: ST-00020119-M

description: Metastisis to the Lymph Node

source_name: Lymph Node

value: Lymph Node

value: scraped tumor


title: HaCaT cells, non-treated control, 12 hours, replicate 1

description:
cell_raw_counts.csv
HC_C_1

value: HaCaT


title: Pituitary_TpitHT

value: TpitHT


title: HaCaT cells, non-treated control, 12 hours, replicate 2

description:
cell_raw_counts.csv
HC_C_2


title: PolyA_RNAseq_Patient_3_PB_pretreatment

value: AML Patient 3


title: tumor 59

first: Shejuan

last: An

state: IL

address: 303 East Superior Street

institute: Northwestern University

library_source: other

data_processing:
Sequencing read adapters were removed by cutadapt (version 4.8), and low-quality trim was performed by trimmomatic (version 0.39) with paired-end trimming mode. Sequencing reads were aligned with the human reference genome hg38 using Bowtie2(version 2.5.3) in paired mode. Reads were sorted and indexed using SAMtools (version 1.19). Data was reduced to 300 bp genomic windows with the MEDIPS (1.54.0) package .
Sequences mapping to chromosomes X, Y or the mitochondrial genome were excluded.
Count per million (CPM) values were calculated for these windows (edgeR, version 4.0.16), with windows < 1 CPM filtered out across all samples.
CPM was normalized with log2(1000*CPM + 2) (R4.3.3) transformation
Assembly: hg38
Supplementary files format and content: comma delimited .csv

molecule: other

source_name: Glioneuronal tumor rep 13

extract_protocol:
Cell-free DNA (cfDNA) was extracted from 1-4 ml of plasma using QIAamp Circulating Nucleic Acid Kit (Qiagen, 55114). All of the cfDNA were performed Right Side Size Selection (0.95X) by using SPRIselect beads (Beckman Coulter, B23317) immediately after the DNA extraction to eliminate genomic DNA contamination.
cfDNA libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems, CN: KK8502).
End-repair, A-tailing, and adaptor ligation of NEBNext adaptors (NEBNext Multiplex Oligos for Illumina kit (index primer set I), E7335L) were performed.

value: Glioneuronal tumor rep 13


title: C57BL6 Control macropahges stimulated with RANKL rep2

city: New York

first: Kyung-Hyun

last: Park-Min

email: ParkminK@HSS.EDU, parkmink@gmail.com

state: NY

address: 535 East 70th Street

institute: Hospital for Special Surgery

description:
WT.RL72_WT_MCSF.RANKL_rep2
GEO_edgeR_counts_IRFKO_2021-01-15.xlsx

data_processing:
Basecalling was performed using bcl2fastq (version bcl2fastq-1.8.4)
Sequenced reads were preprocessed with fastp (with parameters fastp -q 15 -n 10 -l 20)
After preprocessing, sequenced reads were mapped to mm10 whole genome using STAR v2.7.3a (with parameters --outFilterMultimapNmax 1  --outSAMstrandField intronMotif --quantMode GeneCounts), using gencode mm10 annotation
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts, filtered gene counts (min expression cutoff of 5 CPM) and log CPMs from edgeR for every gene and every sample

source_name: Bone marrow-derived macrophages

growth_protocol: For the generation BMDMs, bone marrow cells were flushed from femurs and tibias of mice and cultured at 37oC, 5% CO2 in complete α-MEM medium (10% heat-inactivated defined FBS (HyClone Fisher), penicillin-streptomycin (Invitrogen), and L-glutamine (Invitrogen)) with 5% L929 cell supernatant as conditioned medium (CM) as a source of M-CSF (Englen et al., 1995) after lysis of RBCs using ACK lysis buffer (Invitrogen). Then, the non-adherent cell population was recovered the next day and cultured for three additional days. Final concentration of M-CSF in our culture was 23.3 ng/ml. Cells that remained in suspension were removed by aspiration and attached cells were washed twice with PBS, then re-plated and cultured with complete α-MEM medium with M-CSF containing conditionaed media.

extract_protocol:
RNA from the cultures was extracted using a RNeasy Plus Mini Kit (Qiagen) according to the manufacturers instructions.
Libraries were prepared following the manufacturer's procotols for the Illumina TruSeq Stranded mRNA library preparation kit (part # 20020595). Purified mRNA was isolated from total RNA using oligo-dT beads then converted into double stranded cDNA. Fragmented cDNA libraries were individually indexed and properly ligated molecules were PCR enriched to generate final library.

treatment_protocol: Cells were stimulated with or without RANKL (40ng/ml) for additional  3days

value: Bone marrow-derived macrophages

value: WT

value: MCSF+RANKL

tag: Sex

value: female


title: ST-00020092-M

description: Metastisis to the NA

value: Met


title: Pituitary_TpitWT

value: TpitWT


title: PolyA_RNAseq_Patient_2_PB_pretreatment

value: Peripheral blood

value: AML Patient 2

value: Haematopoietic


title: tumor 58

source_name: Embryonal tumor rep 9

value: Embryonal tumor rep 9


title: ST-00017227-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: ST-00015839-T

description: Primary pancreas tumor

value: scraped tumor


title: WT ctrl 1

description: control

value: kidney

value: isolated renal podocytes

value: WT1-CreErt2; Rosa26R mTmG; Mafb LoxP/wt

value: Tamoxifen induction

value: 72hours post induction


title: tumor 57

source_name: Pediatric type diffuse high grade glioma rep 5


title: C57BL6 Control macropahges stimulated with RANKL rep1

description:
WT.RL72_WT_MCSF.RANKL_rep1
GEO_edgeR_counts_IRFKO_2021-01-15.xlsx

value: Bone marrow-derived macrophages

value: WT


title: PolyA_RNAseq_Patient_1_PB_Cycle4_Day1

value: AML Patient 1

value: E7820 (Cycle 4, Day 1)


title: C57BL6 Control macrophages rep2

description:
WT_WT_MCSF_rep2
GEO_edgeR_counts_IRFKO_2021-01-15.xlsx

value: MCSF

value: female


title: tumor 56

source_name: Glioma NOS rep 4

value: Glioma NOS rep 4


title: PolyA_RNAseq_NKM1_parental_E7820_24hours

value: Peripheral blood

value: Haematopoietic

value: Parental


title: PolyA_RNAseq_NKM1_parental_DMSO_24hours

value: DMSO (24 hours)


title: ST-00015777-T

description: Primary pancreas tumor

value: Primary

value: Pancreas

value: scraped tumor


title: ST-00015839-M

description: Metastisis to the Ovary

source_name: Ovary

value: Met

value: Ovary


title: C57BL6 Control macrophages rep1

description:
WT_WT_MCSF_rep1
GEO_edgeR_counts_IRFKO_2021-01-15.xlsx


title: tumor 55

source_name: Glioma NOS rep 3

value: Glioma NOS rep 3


title: PolyA_RNAseq_K562_SRSF2-P95H_E7820_24hours

value: Bone marrow


title: ST-00015760-T

description: Primary pancreas tumor


title: IRF7 deficient macrophages stimulated with RANKL  rep2

description:
IRf7KO.RL72_IRF7KO_MCSF.RANKL_rep2
GEO_edgeR_counts_IRFKO_2021-01-15.xlsx

value: IRF7 deficient mice

value: Bone marrow-derived macrophages

value: IRF7 KO

value: MCSF+RANKL


title: IRF7 deficient macrophages stimulated with RANKL  rep1

description:
IRf7KO.RL72_IRF7KO_MCSF.RANKL_rep1
GEO_edgeR_counts_IRFKO_2021-01-15.xlsx

value: female


title: ST-00020112-M

description: Metastisis to the Liver

source_name: Liver

value: Liver


title: IRF7 deficient macrophages rep2

description:
IRf7KO_IRF7KO_MCSF_rep2
GEO_edgeR_counts_IRFKO_2021-01-15.xlsx

value: MCSF


title: tumor 53

source_name: Ependymal tumor rep 3

value: Ependymal tumor rep 3


title: PolyA_RNAseq_K562_SRSF2-P95H_DMSO_24hours

value: Haematopoietic


title: ST-00020106-M

description: Metastisis to the Liver


title: IRF7 deficient macrophages rep1

description:
IRf7KO_IRF7KO_MCSF_rep1
GEO_edgeR_counts_IRFKO_2021-01-15.xlsx


title: PolyA_RNAseq_K562_SF3B1-K666N_E7820_24hours


title: tumor 52

source_name: Circumscribed astrocytic glioma rep 14

value: Circumscribed astrocytic glioma rep 14


title: LysM cre Control macropahges stimulated with RANKL rep2

description:
WTLysMcre.RL72_WTLysMcre_MCSF.RANKL_rep2
GEO_edgeR_counts_SREBP2KO_2021-01-15.xlsx

value: LysM cre

value: WT


title: ST-00020109-T

description: Primary pancreas tumor

value: Primary

value: Pancreas

value: scraped tumor


title: PolyA_RNAseq_K562_SF3B1-K700E_DMSO_24hours

value: DMSO (24 hours)


title: PolyA_RNAseq_K562_SF3B1-K700E_E7820_24hours

value: Bone marrow


title: tumor 49

source_name: Glioneuronal tumor rep 11

value: Glioneuronal tumor rep 11


title: PolyA_RNAseq_K562_parental_E7820_24hours

source_name: Bone marrow

value: Parental


title: LysM cre Control macropahges stimulated with RANKL rep1

description:
WTLysMcre.RL72_WTLysMcre_MCSF.RANKL_rep1
GEO_edgeR_counts_SREBP2KO_2021-01-15.xlsx

value: Bone marrow-derived macrophages


title: non tumor 9

source_name: Non-neoplastic rep 5

value: Non-neoplastic rep 5


title: LysM cre Control macrophages rep2

description:
WTLysMcre_WTLysMcre_MCSF_rep2
GEO_edgeR_counts_SREBP2KO_2021-01-15.xlsx

value: female


title: ST-00015163-T

description: Primary pancreas tumor

source_name: Pancreas


title: ST-00015184-T

description: Primary pancreas tumor


title: tumor 54

source_name: Embryonal tumor rep 8

value: Embryonal tumor rep 8


title: PolyA_RNAseq_K562_parental_DMSO_24hours


title: tumor 48

source_name: Circumscribed astrocytic glioma rep 13

value: Circumscribed astrocytic glioma rep 13


title: ST-00020105-M

description: Metastisis to the Liver

value: Met

value: Liver


title: tumor 47

source_name: Pediatric type diffuse high grade glioma rep 4


title: Input for THP-1

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
THP-1 input
ChIPmentation

data_processing:
Alignment to hg19 using Bowtie v1.1 Parameters -n 1 -k 1 -m 1 -l 32 -t -q best
Peak calling using MACS2, parameters bw 150 min peak 3 max peak 50
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: _sequence.n1_m1_k1.tdf: tdf files
Supplementary_files_format_and_content: *txt: Tab-delimited text files

source_name: Culture

growth_protocol: THP-1 cells were grown in RPMI 1640 medium, supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin at 37°C.

extract_protocol:
Cells were grown in culture as mentioned above, after which they were crosslinked with formaldehyde, lysed and the DNA was extracted. Then, ChIPmentation was performed.
The library was created using NEBNext Ultra II DNA Library Prep Kit for Illumina and the samples were barcoded using Nextera sequencing primers. The pooled libraries were sequenced on an Illumina HiSeq2000.

treatment_protocol: Cells were treated with either 100 nM of 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% ethanol).

tag: chip antibody


title: ST-00015332-T

description: Primary pancreas tumor


title: SREBP2 deficient macrophages stimulated with RANKL  rep2

description:
SREBP2KO.RL72_SREBP2KO_MCSF.RANKL_rep2
GEO_edgeR_counts_SREBP2KO_2021-01-15.xlsx

source_name: Bone marrow-derived macrophages

value: SREBP2floxflox LysM cre

value: SREBP2 KO

value: MCSF+RANKL


title: PolyA_RNAseq_K562_SF3B1-K666N_DMSO_24hours

value: Haematopoietic


title: non tumor 8

source_name: Non-neoplastic rep 4

value: Non-neoplastic rep 4


title: ST-00020108-T

description: Primary pancreas tumor

value: Primary

value: Pancreas

value: scraped tumor


title: tumor 51

source_name: Glioneuronal tumor rep 12

value: Glioneuronal tumor rep 12


title: ST-00015136-T

description: Primary pancreas tumor


title: THP-1 8 h after 1,25D treatment, 3rd replicate VDR

description:
VDR VD 8 N3
ChIPmentation

tag: time point

value: VDR (Cell Signaling Technology, #12550)


title: SREBP2 deficient macrophages stimulated with RANKL  rep1

description:
SREBP2KO.RL72_SREBP2KO_MCSF.RANKL_rep1
GEO_edgeR_counts_SREBP2KO_2021-01-15.xlsx

value: Bone marrow-derived macrophages


title: THP-1 8 h after EtOH treatment, 3rd replicate VDR

description:
VDR EtOH 8 N3
ChIPmentation

value: EtOH


title: SREBP2 deficient macrophages rep2

description:
SREBP2KO_SREBP2KO_MCSF_rep2
GEO_edgeR_counts_SREBP2KO_2021-01-15.xlsx

value: MCSF

value: female


title: tumor 46

source_name: Circumscribed astrocytic glioma rep 12

value: Circumscribed astrocytic glioma rep 12


title: THP-1 8 h after 1,25D treatment, 2nd replicate VDR

description:
VDR VD 8 N2
ChIPmentation


title: SREBP2 deficient macrophages rep1

description:
SREBP2KO_SREBP2KO_MCSF_rep1
GEO_edgeR_counts_SREBP2KO_2021-01-15.xlsx


title: tumor 45

source_name: Circumscribed astrocytic glioma rep 11

value: Circumscribed astrocytic glioma rep 11


title: THP-1 8 h after EtOH treatment, 2nd replicate VDR

description:
VDR EtOH 8 N2
ChIPmentation


title: tumor 44

source_name: Embryonal tumor rep 7

value: Embryonal tumor rep 7


title: ST-00020102-T

description: Primary pancreas tumor


title: tumor 41

source_name: Circumscribed astrocytic glioma rep 10

value: Circumscribed astrocytic glioma rep 10


title: PA4

city: League city

first: Hui

last: Wang

state: Texas

address: 301 University Blvd.

institute: UTMB

description: 2×150bp paired-endsequencing (PE150)

data_processing:
Data were analyzed and visualized by NovoMagic, including GO, KEGG pathway analysis. Ingenuity Pathway Analysis (IPA) (Qiagen, Valencia, CA) was used to analyze the most significant pathways and molecules from the Qiagen IPA library that were relevant to the dataset
Assembly: mm10
Supplementary files format and content: tab-delimited text files include DESeq2-normalized counts, fpkm

source_name: kidney

growth_protocol: Kidney tissues were from mice treated with propionate at 200mM for 6 weeks.

extract_protocol:
RNA was purified from kidney tissues using the RNeasy Mini kit (Qiagen).
Preparation of RNA library and transcriptome sequencing were conducted by Novogene (Sacramento, CA). Qualified libraries were sequenced using NovaSeq X Plus Series (PE150) (Illumina, San Diego, CA). Data were analyzed and visualized by NovoMagic, including GO, KEGG pathway analysis.

treatment_protocol: MRL-lpr mice were treated with PA at 200mM in drinking water for 6 weeks.

value: kidney

value: MRL-lpr mice

value: 12 weeks

value: propionate

tag: treatment time

tag: sample id


title: ST-00015114-T

description: Primary pancreas tumor

value: Primary

tag: tissue


title: PA3

description: 2×150bp paired-endsequencing (PE150)


title: LysM cre Control macrophages rep1

description:
WTLysMcre_WTLysMcre_MCSF_rep1
GEO_edgeR_counts_SREBP2KO_2021-01-15.xlsx

value: LysM cre

value: WT


title: ST-00020104-M

description: Metastisis to the Peritoneum

source_name: Peritoneum

value: Met

value: Peritoneum

tag: cell type

value: scraped tumor


title: THP-1 8 h after 1,25D treatment, 1st replicate VDR

description:
VDR VD 8 N1
ChIPmentation

value: VDR (Cell Signaling Technology, #12550)


title: THP-1 8 h after EtOH treatment, 1st replicate VDR

description:
VDR EtOH 8 N1
ChIPmentation

value: EtOH


title: ST-00016028-T

description: Primary pancreas tumor

value: Pancreas


title: tumor 39

source_name: Circumscribed astrocytic glioma rep 9

value: Circumscribed astrocytic glioma rep 9


title: PA2

description: 2×150bp paired-endsequencing (PE150)


title: ST-00014575-T

description: Primary pancreas tumor


title: Donor BHum, infected, Ifenprodil

city: Bochum

first: Eike

last: Steinmann

state: NRW

address: Universitätsstr. 150

department: Molecular Medical Virology

country: Germany

institute: Ruhr-University Bochum

data_processing:
CLC Genomics Workbench (Qiagen, Aarhaus)
Paired reads were mapped to the Hg38 genome scaffold, with gene and transcript annotations. For HEV infected samples, unmapped reads were saved
For HEV infected samples, unmapped reads were mapped to HEVp6 genome to determine HEV infection levels
For each sample, read counts for each human gene were normalised (RPKM, TPM)
Hg38 mappings were used in to identify differentialy expressed genes (DEGs) between conditions (FDR <0.05)
Assembly: Hg38
Supplementary files format and content: Each sample has a .xlsx file containing processed data. This includes gene name, ENSEMBL ID, reads counts, RPKM, TPM

source_name: liver

growth_protocol: Primary human hepatocytes (PHHs) were procured as cryopreserved cells from Primacyt (Schwerin, Germany), thawed according to the manufacturer’s guidelines and cultured in 24-well plates using Human Hepatocyte Maintenance Medium (HHMM, Primacyt). Cells were cultivated on type I collagen-coated plasticware and maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was then extracted using the NucleoSpin RNA kit (Macherey-Nagel) according to manufacturer’s instructions. RNA quality and quantity were analyzed using the NanoDrop One (Thermo Scientific).
Sequencing libraries were generated using a NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

value: liver

tag: agent

value: hepatitis E virus

value: primary human hepatocytes

tag: genotype

value: Ifenprodil


title: tumor 38

source_name: Circumscribed astrocytic glioma rep 8

value: Circumscribed astrocytic glioma rep 8


title: Donor BHum, uninfected, Ifenprodil

tag: treatment


title: PA1

description: 2×150bp paired-endsequencing (PE150)

value: kidney

value: MRL-lpr mice

tag: age

value: 12 weeks


title: ST-00020098-T

description: Primary pancreas tumor

source_name: Pancreas

extract_protocol:
Starting with sectioned FFPE PDAC specimen blocks, Clinical pathologists marked regions of high tumor content (>20% ratio of tumor to normal nuclei) on H&E stained slides for RNA extraction. Solid tumor total nucleic acid was extracted from these tumor regions on adjacent FFPE tissue sections using Chemagic 360 sample-specific extraction kits (Perkin Elmer) and digested by proteinase K. RNA was purified from the total nucleic acid by DNase-I digestion.
100ng of RNA for each tumor sample was heat fragmented in the presence of magnesium to an average size of 200 bp. Library preps were hybridized to the xGENExome Research Panel v1.0 (Integrated DNA Technologies) and target recovery was performed using Streptavidin-coated beads, followed by amplification with the KAPA HiFi Library Amplification Kit.

tag: tumor type

value: Primary


title: tumor 36

source_name: Glioneuronal tumor rep 10

value: Glioneuronal tumor rep 10


title: ST-00014550-T

description: Primary pancreas tumor


title: CON4

description: 2×150bp paired-endsequencing (PE150)

value: control


title: tumor 35

source_name: Circumscribed astrocytic glioma rep 7

value: Circumscribed astrocytic glioma rep 7


title: Donor BHum, infected, DMSO

value: WT

value: DMSO


title: CON2

description: 2×150bp paired-endsequencing (PE150)


title: ST-00014537-T

description: Primary pancreas tumor

value: scraped tumor


title: Donor BHum, uninfected, DMSO


title: Donor CHM2221, infected, Ifenprodil


title: CON1

description: 2×150bp paired-endsequencing (PE150)


title: tumor 33

source_name: Glioneuronal tumor rep 9

value: Glioneuronal tumor rep 9


title: ST-00003635-T

description: Primary pancreas tumor

value: Pancreas


title: Donor CHM2221, uninfected, Ifenprodil

value: liver


title: tumor 31

source_name: Glioneuronal tumor rep 8

value: Glioneuronal tumor rep 8


title: Donor CHM2221, infected, DMSO

value: hepatitis E virus

value: primary human hepatocytes


title: Donor CHM2221, uninfected, DMSO


title: ST-00014494-T

description: Primary pancreas tumor


title: ST-00014391-T

description: Primary pancreas tumor


title: tumor 29

source_name: Circumscribed astrocytic glioma rep 6

value: Circumscribed astrocytic glioma rep 6


title: Donor CHM2225, infected, Ifenprodil

value: Ifenprodil


title: ST-00014104-T

description: Primary pancreas tumor


title: ST-00014524-A-T

description: Primary pancreas tumor


title: ST-00014023-T

description: Primary pancreas tumor


title: Donor CHM2225, uninfected, Ifenprodil


title: tumor 34

source_name: Meningioma rep 1

value: Meningioma rep 1


title: ST-00014524-M

description: Metastisis to the Liver

source_name: Liver

value: Met

value: Liver


title: non tumor 5

source_name: Non-neoplastic rep 3

value: Non-neoplastic rep 3


title: tumor 32

source_name: Mesenchymal tumor rep 4

value: Mesenchymal tumor rep 4


title: serum_automation_healthy_20

city: Cambridge

first: Josephine

middle: Yen

last: Fang

state: MA

address: 40 Landsdowne Street

department: DMPK

institute: Takeda Pharmaceuticals

hyb_protocol: NanoString protocol

scan_protocol: The miRNA expressions were profiled using NanoString nCounter® with the Human v3 miRNA CodeSet kit (CSO-MMIR15-12) with nCounter® miRNA Sample Prep (Mu-MIRTAG-12). The codeset consists of 827 unique miRNAs barcodes, including six positive controls, eight negative controls, six ligation controls, five spike-in controls (ath-miR-159a, cel-miR-248, miR-254, and osa-miR-414 and 442). Additionally, five reference controls (housekeeping mRNAs: RPL10, ACTB, B2M, GAPDH, and RPL19) were included. Input material comprised 5 µL of concentrated RNA, and the experiment was run according to the manufacturer’s protocol. All hybridizations were carried out for 19 hours, and data counts were obtained by scanning on the MAX model for 555 fields of view (FOV) per sample.

data_processing:
The normalization of data (RCC file) was performed using nSolver Analysis Software v4.0 (NanoString Technologies, https://nanostring.com/products/analysis-solutions/ncounter-analysis-solutions/). Background correction was performed by subtracting the geometric mean of negative control counts by sample within NanoString nSolver™. Positive control and CodeSet normalization utilized the geometric mean of positive controls and the top 100 highly expressed miRNAs probe set according to nSolver™ guidelines.
The processed data in "FinalProcessFabryDiffIsoMethod" is obtained as following:
Fold change expression differences were calculated using nSolver Ratio data based on normalized count data. The data was further filtered for miRNA measured above detection levels in at least 15% of samples. Subsequent data analysis was performed using Rosalind (https://nanostring.rosalind.bio/login). Rosalind conducts differential expression analysis using the R package limma to obtain fold change values and p-values. The comparison of disease and healthy controls was performed within samples in either one of the isolation methods (manual or automated isolation). In this step, we could receive output datasheets:  "FabryManualNormalizedExpression,"  "FabryAutoNuomalizedExpression, "VolcanoManualFvH," "VolcanoAutoFvH, " "heatmapFabryHealthyManualOnly," and HeatmapFvHAutoOnly" from Rosaline processed result. According to the method section from Rosaline's website, Heatmaps of differentially expressed miRNAs from Rosalind were scaled and generated using Ward's hierarchical agglomerative clustering method with the fpc R package. Then I used p<0.05 as threshold to select miRNAs from "VolcanoManualFvH" and "VolcanoAutoFvH" to generate sheets "HighDeFvHManual" and" HighDeFvHAutomated". " Sequentially, the highly differential candidates from "HighDeFvHManual" and" HighDeFvHAutomated" were sorted into ERT treated and non-treated samples for comparison. The results were recorded in "HighDEFvHERTimpact" and "HighlyDEFvHAutoERTimpact" datasheet.
To predict and validate the miRNA-target interactions of the highly differential miRNAs(listed in heatmap) between Fabry and healthy control groups, we used MiRWalk (http://mirwalk.umm.uni-heidelberg.de). We employed the following default parameters: species human, miRNAID, GeneSymbol, Statistic power: 0.95, Position: 3UTR. The databases used for prediction were TargetScan, miRDB, and miRTarBase, and only interactions listed in all three (plus miRWalk's own database) were included. The results are recorded in "miRWalk_miRNA_TargetsManual" and "miRWalk_miRNA_TargetsAuto."
Gene set enrichment analysis (GSEA) was performed to identify significantly enriched functions of the predicted target genes. System analysis, annotation, and visualization of gene function were conducted using the Reactome, the Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene ontology enrichment analysis. The results are recorded in datasheet: ReactomeManual, ReactomeAuto, KEGGMaual, KEGGAutomated, GO_BPManual, GO_BPAutomated, GO_CCManual, GO_CCAutomated, GO_MFManual, GO_MFAutomated. The last two datasheets are the pathyways achieving and FDR(False Discovery Rate)-corrected p<0.05 from Reactome, KEGG, and GO_BP, GO_CC, and GO_MF.

source_name: serum, healthy control, Discovery Life Sciences

extract_protocol: Serum samples were thawed on ice and 200 µL of each sample was transferred into new tubes. miRNAs were isolated using miRNeasy Serum/Plasma Kit (cat. no. 217184, Qiagen, MD). Some samples were alternatively extracted using KingFisher™ Flex Magnetic Particle Processor 96DW with MagMAX mirVana™ Total RNA Isolation Kit (cat. no. 5400630 and A2728, both from ThermoFisher Scientific, MA), following the manufacturer’s protocol. For comparison purposes, eight samples were proceeded using both manual and machine-based methods. The miRNA concentrations were quantified using Qubit™ microRNA assay Kits (ThermoFisher Scientific, MA) with Qubit™ Flex Fluorometers.

treatment_protocol: Serum samples were derived from healthy and Fabry Disease patients.

tag: patientid

value: Male

tag: isolation

value: automation

tag: race

value: Caucasian

value: serum


title: serum_automation_healthy_17

value: Asian


title: serum_automation_healthy_16

value: Female


title: serum_automation_healthy_19


title: serum_automation_healthy_18


title: Donor CHM2225, uninfected, DMSO

value: liver

value: WT

value: DMSO


title: ST-00020085-T

first: Rosalie

last: Sears

address: 2730 SW Moody Ave, CL4RS

institute: Oregon Health & Science University

description: Primary pancreas tumor

data_processing:
Paired-end fastq sequences were trimmed using trim-galore (ver 0.6.3) and default parameters.
Pseudoalignment was performed with kallisto (ver 0.44.0) using genome assembly GRCh38.p5 and gencode (ver 24) annotation using default parameters.
Bioconda package bioconductor-tximport (ver 1.12.1) was used to create gene level counts and abundances (TPMs).
Quality checks were assessed with FastQC (ver 0.11.8) and MultiQC (ver 1.7).
Assembly: GRCh38.p5
Supplementary files format and content: Gene level count estimates are provided as a matrix in tab delimited text format.  Feature annotations are provided in the first few columns.
Supplementary files format and content: Gene level TPM estimates are provided as a matrix in tab delimited text format.  Feature annotations are provided in the first few columns.
Supplementary files format and content: Per sample h5 file output from the kallisto pipeline is provided.
Supplementary files format and content: Gene level TMM normalized (edgeR method) estimates are provided as a matrix in tab delimited text format. Feature annotations are provided in the first few columns as well as a column with expression level filtering status. The TMM gene level estimates provided are not log scaled and are generated from the h5 files using general recommendations for importing from the kallisto method as given here: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto & https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#edgeR

value: Primary

value: Pancreas

value: scraped tumor


title: tumor 27

source_name: Circumscribed astrocytic glioma rep 5

value: Circumscribed astrocytic glioma rep 5


title: ST-00013971-T

description: Primary pancreas tumor


title: CON3

description: 2×150bp paired-endsequencing (PE150)

source_name: kidney

value: kidney

value: MRL-lpr mice

value: 12 weeks

value: control


title: tumor 25

source_name: Pediatric type diffuse high grade glioma rep 3


title: B5.R, mRNA-seq

city: Cádiz

first: Fernando

last: Bonet

address: Plaza Falla 9

institute: University of Cádiz

description: AAC553CM5_B5R_22s002836-1-1_TORO_lane122s002836_sequence.txt.gz

data_processing:
European version of the Galaxy platform (https://usegalaxy.eu/)
Reads were trimmed with the Trim Galore software (Galaxy Version 0.6.7+galaxy0)
Trimmed sequences reads were aligned to the built-in human reference genome Dec. 2013 (GRCh38/hg38) with the RNA STAR Gapped-read mapper (Galaxy Version 2.7.10b+galaxy3)
For gene expression analyses, bam files were downloaded from the Galaxy server and further analyzed with the different RStudio packages downloaded from the Bioconductor website (http://bioconductor. org).
Reads were assigned to genes by means of the “featureCounts” function of the “Rsubread” package, version 2.10.5. and annotation files human release 43 (GRCh38.p13) (https://www.gencodegenes.org/human/release_43.html)
Assembly: hg38
Supplementary files format and content: Excel file contents RAW counts for each sample

source_name: Myocardium

extract_protocol:
RNA was isolated using Trizol and RNA Clean & Concentrator Kits (Zymo Research). 1.5 ug of total RNA was used for the construction of sequencing libraries
Standard specific mRNA-sequencing (mRNA-seq) libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA), and single-end libraries were sequenced on an Illumina SE100 Platform with an output of ~680M reads per sample.

value: Myocardium

value: ACM


title: tumor 26

source_name: Adult-type diffuse glioma

value: Adult-type diffuse glioma


title: serum_automation_healthy_14

value: automation

value: African American

value: serum


title: tumor 30

source_name: Glioneuronal tumor rep 7

value: Glioneuronal tumor rep 7


title: ST-00013861-T

city: Portland

description: Primary pancreas tumor

source_name: Pancreas


title: tumor 24

source_name: Ependymal tumor rep 2

value: Ependymal tumor rep 2


title: B3.R, mRNA-seq

description: AAC553CM5_B3R_22s002835-1-1_TORO_lane122s002835_sequence.txt.gz


title: ST-00020077-T

description: Primary pancreas tumor


title: serum_automation_healthy_13

value: Female

value: Asian


title: B2.R, mRNA-seq

description: AAC553CM5_B2R_22s002834-1-1_TORO_lane122s002834_sequence.txt.gz


title: tumor 23

source_name: Embryonal tumor rep 6

value: Embryonal tumor rep 6


title: ST-00013526-M

description: Metastisis to the Lung

source_name: Lung

value: Met

value: Lung

value: scraped tumor


title: serum_automation_healthy_12

description:
H12
serum from the same patient used in H7 and H12


title: Donor CHM2225, infected, DMSO

source_name: liver

value: liver

value: hepatitis E virus

value: primary human hepatocytes

value: WT

value: DMSO


title: tumor 22

source_name: Germ cell tumor

value: Germ cell tumor


title: B1.R, mRNA-seq

description: AAC553CM5_B1R_22s002833-1-1_TORO_lane122s002833_sequence.txt.gz

value: Myocardium

value: ACM


title: tumor 21

source_name: Glioneuronal tumor rep 6

value: Glioneuronal tumor rep 6


title: A6.R, mRNA-seq

description: AAC553CM5_A6R_22s002832-1-1_TORO_lane122s002832_sequence.txt.gz

value: Control


title: ST-00013496-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: serum_automation_healthy_11

value: Female

value: automation

value: Caucasian

value: serum


title: A4.R, mRNA-seq

description: AAC553CM5_A4R_22s002831-1-1_TORO_lane122s002831_sequence.txt.gz


title: ST-00013415-T

description: Primary pancreas tumor

value: scraped tumor


title: tumor 19

source_name: Pediatric type diffuse high grade glioma rep 2


title: A2.R, mRNA-seq

description: AAC553CM5_A2R_22s002830-1-1_TORO_lane122s002830_sequence.txt.gz


title: serum_automation_healthy_21

description:
H21
serum from the same patient used in H5 and H21


title: A1.R, mRNA-seq

description: AAC553CM5_A1R_22s002829-1-1_TORO_lane122s002829_sequence.txt.gz


title: serum_automation_healthy_22

description:
H22
serum from the same patient used in H6 and H22


title: ST-00013291-T

description: Primary pancreas tumor


title: non tumor 3

source_name: Non-neoplastic rep 2

value: Non-neoplastic rep 2


title: serum_automation_fabry_25

source_name: serum, Fabry Disease, Sanguine Bioscience

value: Male


title: serum_automation_fabry_24


title: serum_automation_fabry_23


title: tumor 17

source_name: Circumscribed astrocytic glioma rep 4

value: Circumscribed astrocytic glioma rep 4


title: ST-00020072-M

description: Metastisis to the Omentum

source_name: Omentum

value: Met

value: Omentum


title: ST-00013253-T

description: Primary pancreas tumor


title: tumor 20

source_name: Glioneuronal tumor rep 5

value: Glioneuronal tumor rep 5


title: A549 Cells, TC 3, Day7

city: Denton

first: Brian

last: Meckes

email: brian.meckes@unt.edu, bmeckes@gmail.com

state: TX

address: 3940 N Elm St

department: Biomedical Engineering

institute: University of North Texas

data_processing:
Galaxy.org
Concatenated files were trimmed for low-quality sequence using trimmomatic function in Galaxy  (parameter- Average quality required: 20)
Trimmed sequences were mapped to Hg38 genome using HISAT2 function in Galaxy
Read counts extracted using FeatureCounts function in Galaxy
Read counts were normalized and compared for each group using edegR function in Galaxy
Assembly: Hg38
Supplementary files format and content: Tabular file includes raw counts for each sample (paired ends)
Supplementary files format and content: Normalized counts for all treatments
Supplementary files format and content: Text file format of differentially expressed genes compared in different conditions

growth_protocol: A549 cells were maintained in  DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using PureLink RNA Mini Kit (ThermoFisher). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Standard Total RNA library Prep kit (Illumina) following manufacturer's protocols.

treatment_protocol: Cells were grown in 3 conditions Stiff, Soft and TC plates for 7 days

tag: cell line

value: Lung Cancer

tag: time

value: 7 days

value: Tissue Culture Plastic, 7 days


title: tumor 16

source_name: Ependymal tumor rep 1

value: Ependymal tumor rep 1


title: A549 Cells, TC 2, Day7


title: serum_automation_fabry_22

tag: Sex


title: ST-00020069-M

description: Metastisis to the Peritoneum

source_name: Peritoneum

value: Peritoneum


title: A549 Cells, TC 1, Day7


title: tumor 15

source_name: Mesenchymal tumor rep 2

value: Mesenchymal tumor rep 2


title: A549 Cells, Soft 3, Day7

value: Cyclic stretch for 7 days on 5 kPa substrates


title: tumor 14

source_name: Embryonal tumor rep 5

value: Embryonal tumor rep 5


title: tumor 18

source_name: Mesenchymal tumor rep 3

value: Mesenchymal tumor rep 3


title: ST-00013160-T

description: Primary pancreas tumor

source_name: Pancreas

value: Primary

value: Pancreas


title: A549 Cells, Soft 2, Day7


title: serum_automation_fabry_21

value: automation

value: Caucasian

value: serum


title: ST-00020070-M

description: Metastisis to the Liver

source_name: Liver

value: Met

value: Liver

value: scraped tumor


title: serum_automation_fabry_20

description:
F20
serum from the same patient used in F12 and F20

value: Male


title: ST-00020081-T

description: Primary pancreas tumor


title: tumor 12

source_name: Glioneuronal tumor rep 4

value: Glioneuronal tumor rep 4


title: A549 Cells, Soft 1, Day7

value: Lung Cancer

value: 7 days


title: ST-00013091-T

description: Primary pancreas tumor


title: serum_automation_fabry_18

description:
F18
serum from the same patient used in F10 and F18


title: tumor 11

source_name: Circumscribed astrocytic glioma rep 3

value: Circumscribed astrocytic glioma rep 3


title: A549 Cells, Stiff 3, Day7

value: Cyclic stretch for 7 days on 50 kPa substrates


title: serum_automation_fabry_17

description:
F17
serum from the same patient used in F9 and F17


title: tumor 10

source_name: Glioma NOS rep 2

value: Glioma NOS rep 2


title: ST-00013084-T

description: Primary pancreas tumor


title: ST-00013158-T

description: Primary pancreas tumor


title: non tumor 1

source_name: Non-neoplastic rep 1

value: Non-neoplastic rep 1


title: ST-00013013-T

description: Primary pancreas tumor


title: tumor 9

source_name: Glioneuronal tumor rep 3

value: Glioneuronal tumor rep 3


title: A549 Cells, Stiff 2, Day7


title: serum_automation_fabry_19

description:
F19
serum from the same patient used in F11 and F19


title: serum_automation_fabry_16

description:
F16
serum from the same patient used in F6 and F16

value: Female


title: ST-00020064-M

description: Metastisis to the Pancreas

value: Pancreas


title: ST-00012931-T

description: Primary pancreas tumor

value: Primary


title: Ad3 Sasai Day 180 SC 4W SD-3

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

data_processing:
quality control was carrried out with FastQC v0.11.9 and MultiQC v1.14
Low quality bases at position 1 were trimmed with Cutadapt v3.5, removing all bases with Phred scores < 20
Reads were mapped to hg38 with salmon v1.9.0 using transcriptome from Gencode, v42
transcript level counts were read into R v4.4.2 and aggregated to gene level with tximport v 1.26.1
Differential expression analysis was carried out with DESeq2 v 1.38.2
Assembly: hg38
Supplementary files format and content: tab-delimited text files of raw (unnormalized) gene-level counts for each sample

source_name: retina

growth_protocol: ROs were cultured in 6-well low attachment plates (Corning) and maintained in  differentiation medium supplemented with IGF-1 10 ng/mL in 5% CO2 at 37 °C.

extract_protocol:
RNA isolation was performed using the ReliaPrep™ RNA Cell Miniprep System kit (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using the Illumina Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Exon 4 skipping was induced with 10uM of PROM1-PMO (PMO1) and 6 μM EndoPorter PEG solution (GeneTools) in ROs at day 180 of differentiation. Scrambled-PMO was used as a negative control.

value: retina

value: WT2 (iPSCs)

value: whole retinal organoids RNAseq

value: Scrambled PMO SD replicate 3


title: tumor 8

source_name: Pediatric type diffuse high grade glioma rep 1


title: serum_manual_fabry_14

source_name: serum, Fabry Disease, Sanguine Bioscience

value: manual

value: Caucasian

value: serum


title: serum_automation_fabry_15

description:
F15
serum from the same patient used in F4 and F15

value: automation


title: ST-00012908-T

description: Primary pancreas tumor

value: scraped tumor


title: Ad3 Sasai Day 180 SC 4W SD-1

value: Scrambled PMO SD replicate 1


title: tumor 7

source_name: Circumscribed astrocytic glioma rep 2

value: Circumscribed astrocytic glioma rep 2


title: ST-00012878-T

description: Primary pancreas tumor


title: tumor 6

source_name: Glioma NOS rep 1

value: Glioma NOS rep 1


title: Ad3 Sasai Day 180 PMO1 4W SD-3

value: PROM1 PMO SD replicate 3


title: ST-00012890-T

description: Primary pancreas tumor


title: serum_manual_fabry_12

description:
F12
serum from the same patient used in F12 and F20

value: Male


title: serum_manual_fabry_13


title: tumor 5

source_name: Mesenchymal tumor rep 1

value: Mesenchymal tumor rep 1


title: A549 Cells, Stiff 1, Day7

value: Lung Cancer

value: 7 days

value: Cyclic stretch for 7 days on 50 kPa substrates


title: serum_manual_fabry_11

description:
F11
serum from the same patient used in F11 and F19

value: Asian/Pacific Islander


title: serum_manual_fabry_10

description:
F10
serum from the same patient used in F10 and F18


title: tumor 4

source_name: High grade glioma NOS rep 1

value: High grade glioma NOS rep 1


title: ST-00012818-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: Ad3 Sasai Day 180 PMO1 4W SD-2

value: retina

value: WT2 (iPSCs)

value: whole retinal organoids RNAseq

value: PROM1 PMO SD replicate 2


title: Ad3 Sasai Day 180 SC 4W SD-2

value: Scrambled PMO SD replicate 2


title: Ad3 Sasai Day 180 PMO1 4W SD-1

value: PROM1 PMO SD replicate 1


title: tumor 2

source_name: Circumscribed astrocytic glioma rep 1

value: Circumscribed astrocytic glioma rep 1


title: ST-00012742-T

description: Primary pancreas tumor

value: scraped tumor


title: tumor 3

source_name: Glioneuronal tumor rep 2

value: Glioneuronal tumor rep 2


title: ST-00020057-M

description: Metastisis to the Peritoneum

source_name: Peritoneum

value: Met

value: Peritoneum


title: serum_manual_fabry_9

description:
F9
serum from the same patient used in F9 and F17

value: Male

value: manual

value: Caucasian

value: serum


title: Male, Donor 5, Outgrowth

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

institute: University of Alberta

data_processing:
Partek Flow: Trim bases Trim based on quality score (Phred score minimum of 20, Trim from 3-prime end, min read length of 25)
Partek Flow: Alignment (STAR 2.7.3a) Default settings from Partek Flow
Partek Flow: Quantify to annotation model (Partek E/M) Transcript model: hg38-RefSeq Transcripts 94 - 2020-05-01
Partek Flow: Filter features Exclude features where maximum ≤ 50.0. Processed data file included with filtered raw gene counts
Partek Flow: Normalize counts Normalization methods: Add 1.0, TMM, Log 2.0. Processed data file included with normalized gene counts for differential expression analysis
Partek Flow: ANOVA for DEGs Experiment I: Factors: Oxygen + TGF-B3 + Donor(Random) + Oxygen*TGF-B3. Shrinkage of error term variance: Limma-trend. Experiment II:  Factors: Loading + TGF-B3 + Donor(Random) + Loading*TGF-B3. Shrinkage of error term variance: Limma-trend
Assembly: hg38
Supplementary files format and content: .txt Normalized count

source_name: Meniscus

growth_protocol: Meniscus samples were cut into small approximately 1mm³ pieces using a scalpel and divided into 2 portions: ⅓ to be used for digestion method (d), ⅔ for outgrowth (og) and digestion after outgrowth (dog). Wet weights of meniscus tissue were recorded prior to isolation by digestion and remnant tissue wet weighed after outgrowth.

extract_protocol:
The constructs collected were immediately preserved in Trizol reagent (Life Technologies, United States) and stored at -80°C until RNA extraction. The PuroSPIN Total RNA Purification KIT (Luna Nanotech, Canada) was used for RNA extraction and purification according to the manufacturer's instructions.
Raw input reads were trimmed and aligned to the reference human genome hg38 using the STAR 2.7.3a aligner. Genes with maximum read counts below 50 were filtered out, and normalization was performed using the Add 1.0, TMM, and Log 2.0 parameters. Statistical analysis was conducted using ANOVA with biological sex and time points as factors.

treatment_protocol: Cells were expanded to P1 at a seeding density of 10,000 cells/cm². Media was changed every 3-4 days. Cells were then expanded to P2 at a 1:2 ratio. Passaging of adherent cells was done using trypsin-EDTA 0.05% (Cellgro, 25-052-CI). All cell expansion experiments were incubated under humidified hypoxic conditions (3% O₂, 5% CO₂, 37°C).

value: Meniscus

value: Primary cell

value: Outgrowth


title: Male, Donor 6, Outgrowth


title: serum_manual_fabry_8

value: Female


title: serum_manual_fabry_7


title: Male, Donor 4,  Outgrowth


title: ST-00012327-T

state: OR

description: Primary pancreas tumor

source_name: Pancreas

value: Primary

value: Pancreas


title: ST-00020051-A-T

description: Primary pancreas tumor


title: tumor 1

city: Chicago

source_name: Glioneuronal tumor rep 1

value: Glioneuronal tumor rep 1


title: Female, Donor 3, Outgrowth


title: serum_manual_fabry_6

description:
F6
serum from the same patient used in F6 and F16

value: Asian/Pacific Islander


title: ST-00020045-M

description: Metastisis to the Liver

source_name: Liver

value: Liver


title: Male, Donor 1, Outgrowth


title: ST-00011357-T

description: Primary pancreas tumor

value: scraped tumor


title: Male, Donor 6, Digestion after Outgrowth

value: Digestion after Outgrowth


title: ST-00012319-T

description: Primary pancreas tumor


title: HCT116 cells, ID3, ChIP

city: Fuzhou

first: Chuanzhong

last: Huang

state: Fujian

address: No. 420 Fuma Road

institute: Fujian Cancer Hospital

data_processing:
Sequence quality was examined using the FastQC software. The clean reads (trimmed 5’,3’-adaptor bases) were aligned to human reference genome UCSC HG19 using BOWTIE (V2.2.7).
Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2.
Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-3.
The peaks were annotated by the nearest gene using the newest UCSC RefSeq database.
Assembly: hg19
Supplementary files format and content: bed

growth_protocol: The HCT116 cells were maintained in 1640 culture medium (Hyclone) supplemented with 10% fetal calf serum (Gibco) and incubated in a 37°C, 5% CO2 incubator.

extract_protocol:
CRC cells were collected and treated with cell lysate. Ultrasonic disruption was performed, followed by centrifugation to remove sediment. ChIP dilution buffer and Protein A gel were added to the supernatant, and the mixture was incubated overnight at 4°C. Subsequently, ID3 (CST #9837) antibodies were added. The solution was inverted and mixed overnight, then centrifuged to remove the supernatant. The precipitated mixture was washed with a buffer, eluted with eluent, and treated with NaCl and proteinase K to dissolve the cross-linking.
ChIP-Sequencing library preparation was performed according to Illumina’s protocol Preparing Samples for ChIP Sequencing of DNA. 10 ng DNA of each sample was converted to phosphorylated blunt-ended; An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments; Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads.

value: Colorectal cancer cells

tag: chip antibody


title: T-shNC

city: Wuhan

first: Da

state: Hubei

address: 1095 Jiefang Avenue

department: Biliary-Pancreatic Surgery

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: TshNC

data_processing:
Raw data (raw reads) of fastq format were processed with fastp, an ultra-fast FASTQpreprocessor with useful quality. Clean data (clean reads) were obtained after quality control, adapter trimming, quality filtering and per-read quality cutting. All the downstreamanalyses werebased on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome websitedirectly. Paired-end clean reads were aligned to the reference genome using HISAT2 v2.1.0(hierarchical indexing for spliced alignment of transcripts), which is a highly efficient systemforaligning reads from RNA sequencing experiments
Featurecount was used to count the reads numbers mapped to each gene. And then TPMofeach gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates percondition) was performed using the DESeq R package (1.18.1). DESeq provide statistical routinesfor determining differential expression in digital gene expression data using a model based on thenegative binomial distribution. The resulting P-values were adjusted using the Benjamini andHochberg’s approach for controlling the false discovery rate. Genes with |log2(FoldChange)| >1and adjusted Pvalue <0.05 found by DESeq were assigned as differentially expressed.
Assembly: NCBI:GRCh38.p13
Supplementary files format and content: All.TPM.txt contains the TPM value of each sample (T-shNC and T-shMBD2).

source_name: Cholangiocarcinoma

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Cholangiocarcinoma

value: Cancer cell line

value: negative control

value: no


title: ST-00012975-M

description: Metastisis to the Liver

value: Met


title: HCT116 cells, sgCtrl, rep2

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5).
Assembly: Hg19
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.

extract_protocol:
Total RNA was isolated using the standard Trizol extraction method. In contrast to cells, tissues required repetitive grinding in a mortar with liquid nitrogen prior to RNA extraction, followed by lysis with trizol (Invitrogen).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). Firststrand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).

value: wildtype


title: serum_manual_fabry_3

value: Male

value: manual

value: Caucasian

value: serum


title: serum_manual_fabry_4

description:
F4
serum from the same patient used in F4 and F15

value: Female


title: Male, Donor 4, Digestion after Outgrowth

value: Meniscus

value: Primary cell


title: serum_manual_fabry_2


title: Male, Donor 5, Digestion after Outgrowth


title: HCT116 cells, sgCtrl, rep1


title: serum_manual_healthy_10

source_name: serum, healthy control, Discovery Life Sciences


title: T-shMBD2

value: knockdown of MBD2


title: serum_automation_healthy_15

value: automation


title: serum_manual_fabry_5


title: Female, Donor 2, Digestion after Outgrowth

value: Digestion after Outgrowth


title: ST-00011343-T

description: Primary pancreas tumor

value: Primary

value: Pancreas

value: scraped tumor


title: HCT116 cells, input

value: Colorectal cancer cells


title: ST-00011168-T

description: Primary pancreas tumor


title: HCT116 cells, sgID3, rep1

value: ID3 knockout


title: Female, Donor 3, Digestion after Outgrowth


title: Male, Donor 1, Digestion after Outgrowth


title: ST-00010984-T

description: Primary pancreas tumor


title: Male, Donor 6, Digestion

value: Digestion


title: Human induced Treg cells, transduced with shLACC1 (KD), donor 4

city: La Jolla

first: Gabriel

last: Ascui

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
FASTQ was merged and filtered using fastp (v0.23.3)
Reads were aligned with the STAR aligner (2.7.10b)
Samtools (v1.17) was used to index and sort BAM friles from STAR
QC report was performed with bamCoverage (v3.5.1), and Qualimap (v.2.2.2-dev)
Raw and transcripts per million reads (TPM) counts were taken from STAR’s BAM aligned output.
Assembly: hg19
Supplementary files format and content: LACC1_counts.txt.gz raw counts for 18 samples in TAB delimited TXT
Supplementary files format and content: LACC1_tpm.txt.gz transcripts per million reads (TPM) counts for 18 samples in TAB delimited TXT
Supplementary files format and content: LACC1_metadata.txt.gz metadata for 18 samples in TAB delimited TXT

source_name: PBMC

growth_protocol: Naïve CD4+ T cells were enriched from human PBMCs. 1 x 105 cells were seeded into each well of a 96-well plate pre-coated with 5 ug/mL purified anti-human CD3 antibody (Clone UCHT1, BioLegend) in 200 ul human T cell culture medium containing 2.5 ug/mL purified anti-human CD28 antibody (Clone CD28.2, BioLegend) and cytokine polarization cocktails. 24h after activation, the supernatant was replaced with medium containing shRNA-expressing lentivirus for transduction. After transduction, the virus medium was replaced by T cell culture medium containing anti-human CD28 antibody and cytokine polarization cocktails for another 48h. The cells were expanding in fresh T cell polarization medium for 4 days, and were split as needed every 2 days. Th0 cell polarization medium contained 5 ng/mL IL-2 (BioLegend). Treg cell polarization medium contained 5 ng/mL IL-2 (BioLegend), and doses of human TGFb from 0 to 5 ng/mL (R&D Systems).

extract_protocol:
Total RNA was purified using the miRNeasy Micro Kit (QIAGEN).
cDNA was reversely transcribed from total RNA with oligo-dT primer, random hexamers with SuperScript™ II Reverse Transcriptase (Invitrogen) and then amplified with IS PCR primers and Kapa HiFi Hotstart Ready Mix (Roche). Then the cDNA library was fragmented and tagged with sequencing adapters using Nextera XT DNA Library Preparation Kit (Illumina), and finally ~500 bp amplicons were got. Quality of library was assessed using the High Sensitivity RNA ScreenTape Kit (Agilent Life Sciences). DNA was quantified using Quant-iT PicoGreen dsDNA Assay Kits (Invitrogen) and purified using AMPure XP beads (Beckman Coulter). Libraries were subjected to 2 × 50-bp paired-end sequencing on an Illumina NovaSeq6000 (Illumina), generating at least 8 million uniquely mapped reads for each sample.

value: PBMC

value: CD4 T cells

value: KD

value: Transduced with shLACC1 (KD)


title: serum_manual_healthy_8

value: manual

value: Caucasian

value: serum


title: serum_manual_healthy_7

description:
H7
serum from the same patient used in H7 and H12

value: Female

value: African American


title: serum_manual_healthy_9

value: Male


title: serum_manual_fabry_1


title: ST-00012967-M

description: Metastisis to the Liver

value: Met

value: Liver


title: Human induced Treg cells, transduced with shLACC1 (KD), donor 2


title: Male, Donor 5, Digestion

value: Meniscus

value: Primary cell


title: serum_manual_healthy_6

description:
H6
serum from the same patient used in H6 and H22


title: Human induced Treg cells, transduced with shLACC1 (KD), donor 3


title: ST-00010924-T

description: Primary pancreas tumor

value: Primary

value: Pancreas

value: scraped tumor


title: Male, Donor 4, Digestion

value: Digestion


title: HCT116 cells, sgID3, rep2

value: Colorectal cancer cells

value: ID3 knockout


title: ST-00010919-T

description: Primary pancreas tumor


title: ST-00010984-M

description: Metastisis to the Peritoneum

value: Peritoneum


title: Female, Donor 3, Digestion


title: serum_manual_healthy_5

description:
H5
serum from the same patient used in H5 and H21

value: manual


title: Human induced Treg cells, transduced with shLACC1 (KD), donor 1

value: PBMC

value: CD4 T cells

value: KD

value: Transduced with shLACC1 (KD)


title: serum_manual_healthy_4

value: Male

value: Caucasian

value: serum


title: Human induced Treg cells, transduced with empty vector (EV), donor 4

value: EV

value: Transduced with empty vector (EV)


title: ST-00010889-T

description: Primary pancreas tumor

value: Primary


title: Female, Donor 2, Digestion

value: Meniscus

value: Female

value: Primary cell


title: Human induced Treg cells, transduced with empty vector (EV), donor 3


title: ST-00011356-M

description: Metastisis to the Liver

value: Met

value: Liver

value: scraped tumor


title: Male, Donor 1, Digestion

value: Digestion


title: ST-00009776-T

description: Primary pancreas tumor

value: Pancreas


title: serum_manual_healthy_2

value: manual

value: African American