title: RNA-seq Prrx1Cre conditional wildtype  replicate 3

description: Hic1 f/+ 3


title: p20 WT 1

status: Public on Apr 05 2023

type: SRA

city: Irvine

first: Jefferson

middle: K

last: Chen

address: UC Irvine

country: USA

institute: UC Irvine

description: p20 WT

library_source: transcriptomic

data_processing:
Deseq2 was used to identify differentially expressed genes. Gene ontology was conducted using Metascape
Assembly: mm10
Supplementary files format and content: TSV files containing Kallisto abundances

molecule: total RNA

organism: Mus musculus

source_name: hair follicle stem cell

extract_protocol:
P18 and P20 back skin was dissected and incubated in 0.25% trypsin (Invitrogen 1505-065) for 2hrs at 34C. The epidermal side was mechanically separated and resuspended in 2% FBS PBS. Debris was removed with 40uM and 70uM mesh filters. Whole epidermis samples were processed for bulk RNA-seq. For HFSC bulk RNAseq, cells were labeled with CD45f (eBioscience 12-0495), Ly-6A/E (eBioscience 45-5981-82), CD34 (eBioscience 50-0341-82), and DAPI.  Ly-6A/E- CD34+ CD45f+ HFSC were isolated for bulk RNAseq
RNA quality was determined with Aglient Bioanalyzer; only samples with RNA Integrity Number > 8 were used. Library preparation with Illumina TrueSeq library preparation kit
Single end Illumina HiSeq 2500 sequencing was performed at the University of California, Irvine High Throughput Genomics Facility. Read alignment was preformed using Kallisto/0.46.2

tag: tissue

value: hair follicle stem cell


title: RNA-seq Prrx1Cre conditional wildtype  replicate 2

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

country: Canada

institute: University of British Columbia

description: Hic1 f/+ 2

data_processing:
Basecalls were made using RTA v2.1.
Demultiplexing was achieved using bcl2fastq2.
Alignment was performed using Tophat 2 with Bowtie 2.
FPKM values were generated using Cufflinks.
Assembly: Ingenuity Pathway Analysis was run using a differential expression list generated by Cufflinks filtered for p < 0.05.
Supplementary files format and content: mm10
Supplementary files format and content: xlsx files include FPKM gene values for each Sample

molecule: polyA RNA

source_name: embryonic forelimb

growth_protocol: Mice were bred and raised using standard approved animal care committee methodology.

extract_protocol:
N/A
Forelimbs were homogenized in RNAzol lysis reagent and further processed as per manufacturer's instructions to obtain RNA for library preparation and subsequent NGS.
tru seq stranded mRNA

treatment_protocol: Adult dams >7 weeks of age were paired in timed matings and subsequently sacrificed at embryonic day thirteen and a half at which point forelimbs were dissected and RNA was isolated for interrogation.

value: embryonic forelimb

tag: genotype

value: WT

tag: developmental stage


title: GM21 fibroblasts, empty vector, biol rep 1, day 56

type: RNA

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

description: Gene expression profiling of time alone in GM21 fibroblasts

hyb_protocol: Hybridization cocktail of fragmented and labeled ss-cDNA were incubated 16hr, 60rpm at 45°C on Human Transcriptome Arrays 2.0. Genechips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip® Expression Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 scanner.

data_processing:
Raw Affymetrix HTA 2.0 array intensity data were analyzed using open-source Bioconductor packages on R. All the data were normalized all together using the robust multi-array average normalization approach implemented in the oligo package (Carvalho and Irizarry, 2010). Internal control probe sets were removed and average expression deciles over all treatment and time points. Probes whose average expression was lower than the 4th expression decile were removed for subsequent analyses.
To remove sources of experimental variation and consider batch effects, data were finally corrected with the sva package. Principal component analysis and bi-clustering based on Pearson’s correlation and Ward’s aggregation criterion were used to confirm consistency between biological replicates and experimental conditions at each step of the pre-processing.

label: biotin

organism: Homo sapiens

source_name: GM21 fibroblasts empty vector time-alone control at day 56 post-transduction

label_protocol: Fragmented and labeled DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol from 100 ng total RNA starting material and 5.5 µg single strand cDNA.

growth_protocol: Human somatic GM21 foreskin fibroblasts (Coriell Institute, Camden, NJ) and WI-38 human fetal lung fibroblasts (European Collection of Authenticated Cell Cultures, Porton Down, UK) were cultured in a DMEM medium containing 10% fetal bovine serum (FBS) and 1× penicillin/streptomycin (Corning) at 37 °C in a 2% oxygen atmosphere

extract_protocol: Macherey-Nagel RNA XS columns. At least 200 ng RNA with RIN number 9 were used for library construction.

treatment_protocol: GM21-RASV12 fibroblasts and their empty vector counterparts were generated by retroviral transduction. GM21 fibroblasts constitutively expressing non-targeting and POU2F2-targeting shRNAs (pLKO.1-Neo-CMV-tGFP, pLKO.1-Neo-CMV-tGFP-TRCN0000245324 and pLKO.1-Neo-CMV-tGFP-TRCN0000245325) (Millipore-Sigma, Saint Louis, MO) were generated by lentiviral transduction and selected with 400 µg/ml neomycin for seven days. Cells were subsequently retrovirally transduced with RASV12

tag: cell type

value: skin fibroblast


title: GM21 fibroblasts, RAS, biol rep 1, day 23

description: Gene expression profiling of the entry and exit from RAS-induced senescence in GM21 fibroblasts

source_name: GM21 fibroblasts at day 23 post-transduction with H-RAS-G12V


title: p20 Irx5KO 3

description: p20 Irx5KO


title: RNA-seq Prrx1Cre conditional heterozygous  replicate 5

description: PxCre; Hic1 f/+ 5

value: HET


title: p20 WT 4

description: p20 WT


title: p18 Irx5KO 3

description: p18 Irx5KO


title: m668

city: San Francisco

first: Qing

last: Dong

state: CA

institute: UCSF

data_processing:
Paired-end reads were mapped to mouse reference genome (mm10) by Hisat2 (v2.0.5).
Quantification of gene expression was analyzed by featureCounts (version 1.5.0-p3).
Differential gene expression levels in mutant and WT tissues were compared using the DESeq2 R package (version 1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: cortex

growth_protocol: All experimental animals were singly housed on a LD 12:12 cycle and given ad libitum access to food and water.

extract_protocol: Paried-end RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cortex

tag: strain

tag: age

value: 8 month


title: p20 Irx5KO 1

description: p20 Irx5KO


title: RNA-seq Prrx1Cre conditional wildtype  replicate 1

description: Hic1 f/+ 1


title: RNA-seq Prrx1Cre conditional heterozygous  replicate 4

description: PxCre; Hic1 f/+ 4


title: RNA-seq conventional knockout  replicate 2

description: Hic1 -/- 2

value: KO


title: p20 Irx5KO 2

description: p20 Irx5KO


title: RNA-seq conventional knockout  replicate 3

description: Hic1 -/- 3


title: p18 WT 3

description: p18 WT


title: p18 Irx5KO 2

description: p18 Irx5KO


title: p20 WT 2

description: p20 WT


title: m677


title: p20 WT 3

description: p20 WT


title: GM21 fibroblasts, empty vector, biol rep 1, day 32

source_name: GM21 fibroblasts empty vector time-alone control at day 32 post-transduction


title: RNA-seq Prrx1Cre conditional heterozygous  replicate 2

description: PxCre; Hic1 f/+ 2


title: RNA-seq conventional knockout  replicate 1

description: Hic1 -/- 1


title: p18 WT 2

description: p18 WT


title: RNA-seq Prrx1Cre conditional wildtype  replicate 5

description: Hic1 f/+ 5


title: p18 WT 1

description: p18 WT


title: p18 Irx5KO 1

description: p18 Irx5KO


title: GF3PH

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

country: Switzerland

institute: University of Bern

data_processing:
fastq files were aligned to the mouse reference genome with Hisat
sam files were sorted and converted to bam files with SAMtools
reads were counted with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with read per sample

source_name: 3h regenerating liver tissue from germ free mouse_3

extract_protocol:
total RNA was extracted with Trizol from whole liver tissue
Libraries were constructed using IlluminaTruSeq Stranded mRNA Prep kit according to the manufacture's protocol.

treatment_protocol: Mice underwent a standard two-thirds surgical hepatectomy. The resected liver tissue served as the baseline, non-regenerating control. The regeneratng liver tissue was harvested three hours post resection.

tag: Sex

value: male

value: liver

tag: timepoint

value: 3 hours post two-thirds hepatectomy


title: RNA-seq conventional heterozygous replicate 1

description: Hic1 +/- 1


title: RNA-seq conventional heterozygous replicate 2

description: Hic1 +/- 2


title: RNA-seq conventional wildtype replicate 3

description: Hic1 +/+ 3


title: GF4

source_name: baseline liver tissue from germ free mouse_4

value: baseline


title: GF1PH

source_name: 3h regenerating liver tissue from germ free mouse_2


title: RNA-seq conventional wildtype replicate 2

description: Hic1 +/+ 2


title: OS030_Mp

city: Kraków

first: Marcin

last: Czepiel

address: Anny 12

department: Clinical Immunology

country: Poland

institute: Jagiellonian University Medical College

data_processing:
After processing OpenArray miRNA Expression run, the data analysis was performed. Quality control images (QC Images) were exported and investigated to find potential loading errors. The result files created by QuantStudio Software v1.2.3 were uploaded to ThermoFisher Cloud and analyzed with Relative Quantification qPCR Application. miRNA Panel A and B were analyzed in separate analysis groups
The Processed (normalized) Data is organized in separate excel files - each file for each target (miRNA). This data has been normalised to U6 rRNA Ct values coming from the relevant Raw Data files namely: "Panel_A_Sample Results.csv" and "Panel_B_Sample Results.csv". In these raw data files you will find the Sample name, target name and Ct values in columns 1, 2 and 3 respectively (column names: Sample Name, Target Name, Mean Equivalent Cq).
The expression of each miRNA type was calculated using 2−ΔΔCT method and snRNa U6 was used as a control to all miRNA analysis

source_name: Axial SpA Patient 30 - Intermediate Monocytes

label_protocol: cDNA was pre‐amplified to increase its quantity before performing the OpenArray qPCR. Preamplification products were prepared in two separate reactions for Megaplex™ PreAmp Primers Pool A and Pool B, corresponding to the Megaplex™ RT Primers Pool used previously for reverse transcription. For each pre-amplification we used 2,5 µl cDNA and 22,5 μL of PreAmp Reaction Mix, containing Megaplex™ PreAmp Primers Pool A or Pool B (2,5 µl), 2x TaqMan® PreAmp Master Mix (12,5 µl) and nuclease-free water (all reagents by ThermoFisher Scientific, Waltham, MA, USA). Pre-amplification reaction tubes with reagents were incubated on ice for 5 minutes before performing RUN on SimplyAmp Thermal Cycler (Applied Biosystems by ThermoFisher Scientific, Waltham, MA, USA). The following thermal conditions were used to run pre-amplification: 95°C for 10 minutes, 55°C for 2 minutes, 72°C for 2 minutes, 12 cycles including 95°C for 15 seconds and 60°C for 4 minutes, hold step with 99,9°C for 10 minutes and final hold step 4°C. Negative control was used for each preamplification. Every single preamplification product was diluted 1:20 with nuclease-free water and used for the next step within 12 hours. For each sample, qPCR reaction was prepared by mixing 22,5 µl 2x TaqMan® OpenArray® Real‐Time PCR Master Mix and 22,5 µl pre-amplification product on 96-well plate. Next, the qPCR reaction mixes with samples (5 µl) were transferred by pipetting to 384-well plate according to protocol created in OpenArray Sample Tracker Software (ThermoFisher Scientific, Waltham, MA, USA) and loaded to OpenArray plates by OpenArray™ AccuFill™ System (ThermoFisher Scientific, Waltham, MA, USA). OpenArray cases were sealed according to guidelines within 90 seconds. Ready OpenArray Plates were put into the QuantStudio 12K Flex Real-time PCR System with OpenArray block and processed.

extract_protocol: RNAs were isolated using miRVana microRNA isolation kit (Thermo Fisher Scientific) and transcripted into cDNA using Megaplex™ RT Primers and TaqMan® MicroRNA Reverse Transcription Kit

value: Intermediate Monocytes

value: peripheral blood

tag: disease state

value: Axial SpA Patient


title: RNA-seq conventional wildtype replicate 1

description: Hic1 +/+ 1


title: GF3

source_name: baseline liver tissue from germ free mouse_3


title: OS028_Mp

source_name: Axial SpA Patient 28 - Intermediate Monocytes


title: GF1

source_name: baseline liver tissue from germ free mouse_2


title: RNA-seq conventional heterozygous replicate 3

description: Hic1 +/- 3


title: ASF2PH

source_name: 3h regenerating liver tissue from ASF colonized mouse_2


title: ASF4PH

source_name: 3h regenerating liver tissue from ASF colonized mouse_4


title: OS024_Mp

source_name: Axial SpA Patient 24 - Intermediate Monocytes


title: OS027_Mp

source_name: Axial SpA Patient 27 - Intermediate Monocytes


title: OS022_Mp

source_name: Axial SpA Patient 22 - Intermediate Monocytes


title: ASF4

source_name: baseline liver tissue from ASF colonized mouse_4


title: OS021_Mp

source_name: Axial SpA Patient 21 - Intermediate Monocytes


title: ASF2

source_name: baseline liver tissue from ASF colonized mouse_2


title: ASF3PH

source_name: 3h regenerating liver tissue from ASF colonized mouse_3


title: OS020_Mp

source_name: Axial SpA Patient 20 - Intermediate Monocytes


title: OS025_Mp

source_name: Axial SpA Patient 25 - Intermediate Monocytes


title: ASF3

source_name: baseline liver tissue from ASF colonized mouse_3


title: GF4PH

source_name: 3h regenerating liver tissue from germ free mouse_4


title: OS019_Mp

source_name: Axial SpA Patient 19 - Intermediate Monocytes


title: DU4475 - suspension, matrigel, soft fibrin, stiff fibrin

city: Espoo

first: Maria

last: Heilala

address: Puumiehenkuja 2

country: Finland

institute: Aalto University

data_processing:
Sequencing with 75 cycles produced 20 bp Read 1 (bases 1-12 sample barcode, bases 13-20 UMI) and 55 bp Read 2 (sequence derived from the mRNA).
Raw sequence data was inspected using FastQC and multiQC to ensure the quality of sequencing results (Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc; Ewels P. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016).  Subsequently, reads were filtered to remove low quality reads and reads shorter than 20 bp using Trimmomatic (Bolgeret al. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics. 2014).
Reads passing the filter were then processed further using Drop-seq tools and the pipeline originally suggested in Drop-seq paper (v. 2.3.0,Macoskoet al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015). In brief, the raw, filtered read libraries were converted to sorted BAM files using Picard tools (http://broadinstitute.github.io/picard). This was followed by tagging reads with sample specific barcodes and unique molecular identifiers (UMIs). Tagged reads were then trimmed for 5’ adapters and 3’ poly A tails. Alignment ready reads were converted from BAM formatted files to fastq files that were used as an input for STAR aligner (Dobin A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013).
Alignments were done using data from GENCODE Release 40 human genome (GRCh38.p13) and comprehensive gene annotation files (Frankish A. et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 2019) with default STAR settings. Following the alignment, the uniquely aligned reads were sorted and merged with previous unaligned tagged BAM file to regain barcodes and UMI’s lost during the alignment step. Next, annotation tags are added to aligned and barcode tagged BAM files to complete the alignment process. Finally, Drop-seq tools are used to detect and correct systematic synthesis errors present in sample barcode sequences. Digital expression matrices are then created by counting the total number of unique UMI sequences (UMI sequences that differ only by a single base are merged together) for each transcript.
Assembly: GENCODE Release 40 human genome (GRCh38.p13) and comprehensive gene annotation files.
Supplementary files format and content: csv-file includes UMI read counts for each sample

source_name: breast

growth_protocol: DU4475 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine and 1% penicillin-streptomycin. The cells were maintained in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen) and purified with RNA Clean and Concentrator kit together with DNAse treatment (Zymo).
The library was contructed using the bulk RNA barcoding (BRB) sequencing method. Total RNA (10 ng) was barcoded, converted to cDNA, and amplified by PCR. The PCR products were pooled together, purified with 0.6X Agencourt AMPure XP Beads (Beckman Coulter) and tagmented using the Nextera kit (Illumina). Library quantity was assessed using a Qubit 2 fluorometer (Invitrogen) and the Qubit DNA HS Assay Kit (ThermoFisher Scientific) and library quality using the LabChip GXII Touch HT (PerkinElmer), with the DNA High Sensitivity Assay (PerkinElmer) and the DNA 5 K / RNA / Charge Variant Assay LabChip (PerkinElmer). The libraries were then sequenced using Illumina NextSeq 500 (Illumina).
3' RNA-Seq (Drop-seq-like)

value: breast

tag: disease

value: carcinoma

tag: cell line

value: epithelial


title: OS018_Mp

source_name: Axial SpA Patient 18 - Intermediate Monocytes


title: Healthy control activated naïve B cells 48 hours [HD 4]

city: Vienna

first: Ola

last: Grimsholm

address: Wahringer Gurtel 18-20

department: Pathophysiology and Allergy Research

country: Austria

institute: Medical University of Vienna

data_processing:
Quality control of the FASTQ files using FastQC High Throughput Sequence QC Report version 0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequences using Trimmomatic tool version 0.39 (Phred score:20, SLIDINGWINDOW:4:20)
Assembly: Trimmed reads were aligned to the human reference genome (GRCh38/hg38) with Gencode 29 annotations using STAR aligner v. 2.6.1a in 2-pass mode
Supplementary files format and content: Raw reads per gene were counted by STAR
Supplementary files format and content: Normalization and Differential gene expression analysis was conducted by using the featureCounts and DESeq2 packages version 1.38.3 in R respectively
Supplementary files format and content: Other analysis and visualisation techniques were performed in R using different packages such as ggplot2, pheatmap, biomaRt, edgeR, org.Hs.eg.db, and GO.db

source_name: Peripheral blood

growth_protocol: Complete RPMI medium

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.5-1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina® Stranded mRNA Prep, Ligation (16 Samples) following manufacturer's protocols.

treatment_protocol: Naïve B cells were activated with anti-Ig (10 ug/ml )+ CD40L (1ug/ml) + IL-21 (20ng/ml) for 48 hours

value: Peripheral blood

value: Healthy control

value: Naive B cells

tag: time

value: 48 hours

tag: treatment

value: In vitro actvation:anti-Ig+CD40L+IL-25


title: OS016_Mp

source_name: Axial SpA Patient 16 - Intermediate Monocytes


title: Healthy control activated naïve B cells 48 hours [HD 2]


title: OS015_Mp

source_name: Axial SpA Patient 15 - Intermediate Monocytes


title: Healthy control activated naïve B cells 48 hours [HD 1]


title: OS012_Mp

source_name: Axial SpA Patient 12 - Intermediate Monocytes


title: OS010_Mp

source_name: Axial SpA Patient 10 - Intermediate Monocytes


title: OS013_Mp

source_name: Axial SpA Patient 13 - Intermediate Monocytes


title: OS011_Mp

source_name: Axial SpA Patient 11 - Intermediate Monocytes


title: OS009_Mp

source_name: Axial SpA Patient 9 - Intermediate Monocytes


title: CVID activated naïve B cells 48 hours [CVID 53]

value: CVID


title: CVID activated naïve B cells 48 hours [CVID 52]


title: CVID activated naïve B cells 48 hours [CVID 45]


title: OS008_Mp

source_name: Axial SpA Patient 8 - Intermediate Monocytes


title: OS004_Mp

source_name: Axial SpA Patient 4 - Intermediate Monocytes


title: OS005_Mp

source_name: Axial SpA Patient 5 - Intermediate Monocytes


title: CVID activated naïve B cells 48 hours [CVID 51]


title: CVID activated naïve B cells 48 hours [CVID 47]


title: CVID activated naïve B cells 48 hours [CVID 50]


title: OS003_Mp

source_name: Axial SpA Patient 3 - Intermediate Monocytes


title: CVID activated naïve B cells 48 hours [CVID 49]


title: OS006_Mp

source_name: Axial SpA Patient 6 - Intermediate Monocytes


title: Healthy control activated naïve B cells 48 hours [HD 3]


title: CVID activated naïve B cells 48 hours [CVID 41]


title: OS001_Mp

source_name: Axial SpA Patient 1 - Intermediate Monocytes


title: CVID activated naïve B cells 48 hours [CVID 48]


title: CVID activated naïve B cells 48 hours [CVID 40]


title: KIT_D816V_clone_30_2_S10

city: Aachen

first: Mirle

last: Schemionek

state: NRW

address: Pauwelsstr. 30

department: Hematology, Oncology, Hemostaseology and SCT

country: Germany

institute: University Hospital RWTH Aachen

data_processing:
Files were processed with the RNAseq pipeline (v1.4.2) from NextFlow (v20.01.0).  Briefly, this includes the following steps: assessing read quality with FastQC (v0.11.8); removal of adapter contamination and low quality regions with TrimGalore (v0.6.4) and Cutadapt (v2.9); removal of rRNA with SortMeRNA (v2.1b); read alignment with STAR (vSTAR_2.6.1d); assessing RNAseq data quality with RSeQC (v3.0.1), Qualimap (v.2.2.2-dev), dupRadar (v1.14.0), Preseq (v2.0.3), and visualization through MultiQC (v1.7). Finally, gene count extraction and quantification with featureCount (v1.6.4).
Assembly: GRCh38.p13
Supplementary files format and content: *.featureCounts.txt: tab-delimited text files include probe IDs, location, gene names and read counts for each gene/probe
Supplementary files format and content: *merged_gene_counts.txt: tab-delimited text files include probe IDs, gene names and read counts for each gene/probe for all samples

source_name: iPS cell-derived mast cells

growth_protocol: iPS cell-derived mast cells were cultivated in serum-free medium (SFM) with SCF and hyper-IL-6.

extract_protocol:
RNA was extracted using RNeasy Kit from Qiagen following the manufactor's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols with rRNA depletion (NEBNext rRNA Depletion Kit), NEBNext Ultra II Directional RNA Library Prep Kit and NextSeq 500/550 Mid Output Kit v2.5

value: iPS cell-derived mast cells

value: KIT D816V


title: CVID activated naïve B cells 48 hours [CVID 46]


title: OB021_Mp

source_name: Peripheral SpA Patient 21 - Intermediate Monocytes

value: Peripheral SpA Patient


title: OS002_Mp

source_name: Axial SpA Patient 2 - Intermediate Monocytes


title: OB019_Mp

source_name: Peripheral SpA Patient 19 - Intermediate Monocytes


title: KIT_D816V_clone_30_1_S9


title: OB018_Mp

source_name: Peripheral SpA Patient 18 - Intermediate Monocytes


title: WT_clone_8_1_S8

value: control (WT)


title: dialout MOLM13_RNAseq_combo_3

city: Boston

first: Oana

last: Ursu

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
demultiplex: cellranger mkfastq. Cellranger 6.1.2
alignment and counts: cellranger count. Cellranger 6.1.2. This results in the deposited files (genes.tsv, cells.tsv, matrix.mtx and protospacer_calls.csv), quantifying the number of UMIs/gene/cell, and assigning each cell to the perturbation(s) it received.
Assembly: "single" and "combo" experiments: human transcriptome version GRCh38. SHARE-seq: hg19
Supplementary files format and content: Perturb-seq experiments: Processed expression matrices (matrix.mtx files) containing raw UMI counts are provided in mtx (Market Exchange) format, as produced by the cellranger software. Each line represents the counts (third column) for a given gene (second column) in a given cell (first column). The cells and genes are represented as their indices in the files (cells.tsv and genes.tsv, respectively).   NOTE: this expression matrix includes the number of UMIs recorded for each perturbation in each cell, in addition to the number of UMIs for each gene's expression. It is recommended to remove these perturbation UMI counts from the expression matrix before normalization of expression data, and treat them as a separate entity.    The assignments of cells to specific perturbations are provided in the protospacer_calls.csv files. The first column provides the name of the cell, the second specifies how many distinct perturbations were found in that cell, the third column specifies the names of the perturbations found in the cell, separated by “|” and the fourth column notes the number of UMIs supporting the presence of each perturbation in the cell, in the order provided in the third column, again separated by “|”.    SHARE-seq experiment: For SHARE-seq, the expression data are provided as described for the Perturb-seq experiments, in mtx format, consisting of the files (MOLM13_SHAREseq_RNA.cells.tsv, MOLM13_SHAREseq_RNA.genes.tsv and MOLM13_SHAREseq_RNA.matrix.mtx). In addition, for the ATAC-seq measurements in SHARE-seq, we identify peaks of chromatin accessibility and provide the counts recorded for each peak in each cell in mtx format in the files MOLM13_SHAREseq_ATAC.cells.tsv, MOLM13_SHAREseq_ATAC.peaks.tsv.

source_name: MOLM13 AML cell line

growth_protocol: MOLM-13 cells were grown in RMPI 1640 medium (no glutamine) supplemented with 10% FBS (Omega), 1% Penicillin-Streptomycin (Gibco), and 1% GlutaMax (Gibco).  Cells were maintained in an incubator at 37 degrees Celsius with 5% Carbon Dioxide.

extract_protocol:
We used 6000 cells per channel, for 15 channels for the "single" experiment, and 3 channels for the "combo" experiment.
The “single” and “combo” experiments were profiled with 15 and 3 channels, respectively, and were sequenced paired-end on an Illumina Hi-Seq instrument at a ratio of 3 channels of 10x to 1 lane of sequencing (5 for the “single” experiment, and 1 for the “combo” experiment), using paired end reads as follows.     For the “single” experiment, read 1 is 28 bases long (16 for cell barcode, 12 for UMI), read 2 is 91 bases long and sample index read is 8 bases long.     For the “combo” experiment, read 1 is 28 bases long (16 for cell barcode, 12 for UMI), read 2 is 91 bases long and sample index read is 8 bases long.     Perturbations were assigned to cells using dial-out PCR. Dial-out PCR products were sequenced on an Illumina Mi-seq, paired-end (for all experiments, read 1 is 28 bases and read 2 is 60 bases long), with read 1 having the same structure as in the high-throughput sequencing of the libraries described above. Each experiment required only one Mi-Seq run to process the dial-out libraries.

treatment_protocol: 1. Perturb-seq experiments: We performed Perturb-seq on MOLM13 cells, following either individual perturbation of subunits (“single” experiment) or combinatorial perturbation of selected subunit combinations (“combo” experiment).     2. SHARE-seq experiment: We performed SHARE-seq on MOLM13 cells following CRISPR-mediated knockout of specific mSWI/SNF subunits, obtaining both RNA-seq and ATAC-seq readouts in the same single cell. We performed SHARE-seq for 5 conditions: control guide, ARID1A, SMARCD2, SMARCA4 and BRD9, each with 2 replicate wells in an arrayed format.

tag: experiment type

value: combinatorial perturbation

tag: readout

value: 3' sc-RNAseq


title: WT_clone_8_1_S7


title: MCF7 cells, 3D-Igen-SM, R3

city: Rome, RM

first: Alice

last: Massacci

address: Via Elio Chianesi, 53, 00128 Rome RM

country: Italy

institute: IRCSS Regina Elena National Cancer Institute, Rome

data_processing:
The libraries were quantified by qPCR and sequenced in paired-end mode (2x75 bp) with NextSeq 500 (Illumina, CA).
Primary analysis was carried out with Nextflow nf-core/rnaseq pipeline.
Secondary analysis, including differential expression analysis, functional enrichment and inter-comparison GO data visualization were entirely carried out with an in-house package, auto-GO (https://www.biorxiv.org/content/10.1101/2022.02.25.482003v1), which makes use of the DeSeq2, Enrichr and tidyverse.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains raw counts values for each Sample
Supplementary files format and content: tab-delimited text file contains TPM values for each Sample

growth_protocol: For 2D culture conditions, H460 cells were grown in RPMI1640 medium (Sigma-Aldrich, St. Louis, MO, USA) while MCF7 were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) medium (Sigma-Aldrich, St. Louis, MO, USA). Both media were supplemented with 10% fetal bovine serum (FBS) (Invitrogen, San Diego, CA) and 1% (v/v) penicillin and streptomycin (Sigma-Aldrich, St. Louis, MO, USA). All cell lines were maintained at 37°C in humidified 5% CO2 atmosphere. Cells were passed twice per week using trypsin, thus leading gentle cell detachment. Cell lines were tested for mycoplasma contamination and STR profiled for authentication. 3D tumor spheroids were grown in two different culture conditions: i) a customized nutrient-rich spheroid medium (3D_SM), consisting of DMEM/F-12 (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 0.5% Glucose (Sigma-Aldrich, St. Louis, MO, USA), 2.5mM L-Glutamine (Thermo Fisher Scientiﬁc, Waltham, MA, USA), 2% B-27, 5μg/ml Heparin, 20μg/ml Insulin (Thermo Fisher Scientiﬁc, Waltham, MA, USA), 20ng/ml EGF (Thermo Fisher Scientiﬁc, Waltham, MA, USA), 20ng/ml Recombinant Human bFGF (Thermo Fisher Scientiﬁc, Waltham, MA, USA), 0.1% Bovine Serum Albumin (BSA) (Sigma-Aldrich, St. Louis, MO, USA) and 1% (v/v) of penicillin/streptomycin 100U/ml; ii) customized nutrient-restricted RPMI or DMEM culture media supplemented with only 2% FBS (3D_FBSlow).

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, IT), purified from DNA contamination through a DNase I (Qiagen, IT) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen, IT). Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and by Agilent 2100 Bioanalyzer (Agilent Technologies, CA), respectively.
RNA libraries for sequencing were generated in triplicate using the same amount of RNA for each sample according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, CA).

value: breast cancer cell line

value: wild type

value: cultured in nutrient-rich culture conditions


title: dialout MOLM13_RNAseq_single_15

value: single perturbation


title: dialout MOLM13_RNAseq_combo_2


title: dialout MOLM13_RNAseq_combo_1


title: dialout MOLM13_RNAseq_single_13


title: dialout MOLM13_RNAseq_single_11


title: dialout MOLM13_RNAseq_single_9


title: dialout MOLM13_RNAseq_single_14


title: dialout MOLM13_RNAseq_single_10


title: OB014_Mp

source_name: Peripheral SpA Patient 14 - Intermediate Monocytes

value: Intermediate Monocytes

value: peripheral blood


title: OB013_Mp

source_name: Peripheral SpA Patient 13 - Intermediate Monocytes


title: MCF7 cells, 3D-Igen-SM, R1


title: MCF7 cells, 3D-Igen-2p, R3

value: cultured in nutrient-restricted culture conditions


title: MCF7 cells, 3D-Igen-SM, R2


title: MCF7 cells, 3D-Igen-2p, R2


title: OB017_Mp

source_name: Peripheral SpA Patient 17 - Intermediate Monocytes


title: OB016_Mp

source_name: Peripheral SpA Patient 16 - Intermediate Monocytes


title: OB015_Mp

source_name: Peripheral SpA Patient 15 - Intermediate Monocytes


title: dialout MOLM13_RNAseq_single_7


title: OB012_Mp

source_name: Peripheral SpA Patient 12 - Intermediate Monocytes


title: MCF7 cells, 3D-Igen-2p, R1


title: OB011_Mp

source_name: Peripheral SpA Patient 11 - Intermediate Monocytes


title: dialout MOLM13_RNAseq_single_12


title: dialout MOLM13_RNAseq_single_6


title: OB010_Mp

source_name: Peripheral SpA Patient 10 - Intermediate Monocytes


title: dialout MOLM13_RNAseq_single_4


title: dialout MOLM13_RNAseq_single_5


title: dialout MOLM13_RNAseq_single_3


title: MCF7 cells, 2D, R2

value: control


title: MCF7 cells, 2D, R1


title: dialout MOLM13_RNAseq_single_1


title: dialout MOLM13_RNAseq_single_8


title: OB007_Mp

source_name: Peripheral SpA Patient 7 - Intermediate Monocytes


title: dialout MOLM13_RNAseq_single_2


title: OB006_Mp

source_name: Peripheral SpA Patient 6 - Intermediate Monocytes


title: OB009_Mp

source_name: Peripheral SpA Patient 9 - Intermediate Monocytes


title: MCF7 cells, 2D, R3


title: HAM821_MEMTIC

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

institute: McGill University

data_processing:
Canadian Center for Computational Genomic's pipeline GenPipes (Bourgey et al., 2019) was used to analyze the data.
Raw fastq reads were trimmed for adaptor sequence/low-quality using trimmomatic tool and were aligned to the GRCh38 genome reference using STAR aligner with default parameters.
HTseq count tool was used to quantify the number of reads
Read counts were used for differential expression gene (DEG) analysis with the edgeR package
Assembly: GRCh38
Supplementary files format and content: one excel file including TPM values of all samples

source_name: Brain

extract_protocol:
Qiagen Rneasy mini kit
mRNA stranded

value: Brain

value: Microglia

value: Abud medium+FBS


title: iMGL_11

source_name: DYR0100 (ATCC)

value: DYR0100 (ATCC)

value: iPSC-derived microglia


title: H460 cells, 3D-Igen-SM, R3

value: lung adenocarcinoma (LUAD) cell line


title: iMGL_10


title: iMGL_12


title: HAM821_MEMFBS

value: Abud medium+TIC


title: H460 cells, 3D-Igen-SM, R2


title: H460 cells, 3D-Igen-SM, R1


title: HAM821_MEM

value: Abud medium


title: iMGL_9


title: HAM821_ex vivo

value: MEM+FBS


title: H460 cells, 3D-Igen-2p, R3


title: OB005_Mp

source_name: Peripheral SpA Patient 5 - Intermediate Monocytes

value: Peripheral SpA Patient


title: OB004_Mp

source_name: Peripheral SpA Patient 4 - Intermediate Monocytes


title: HAM821_Diff_mediaTIC

value: MEM+TIC


title: OB002_Mp

source_name: Peripheral SpA Patient 2 - Intermediate Monocytes


title: OB001_Mp

source_name: Peripheral SpA Patient 1 - Intermediate Monocytes


title: GK022_Mp

source_name: Healthy Control 22 - Intermediate Monocytes

value: Healthy Control


title: HAM821_Diff_media

value: ex vivo


title: HAM816_MEMFBS


title: H460 cells, 3D-Igen-2p, R1

value: wild type


title: H460 cells, 3D-Igen-2p, R2


title: HAM816_ex vivo


title: GK021_Mp

source_name: Healthy Control 21 - Intermediate Monocytes

value: Intermediate Monocytes

value: peripheral blood


title: HAM816_Diff_mediaTIC


title: H460 cells, 2D, R3

value: control


title: HAM816_Diff_mediaFBS

value: Brain


title: HAM816_Diff_media

value: Microglia


title: GK020_Mp

source_name: Healthy Control 20 - Intermediate Monocytes


title: H460 cells, 2D, R2


title: HAM815_MEMTIC

value: Abud medium+FBS


title: HAM815_MEMFBS


title: GK019_Mp

source_name: Healthy Control 19 - Intermediate Monocytes


title: HAM821_Diff_mediaFBS

value: MEM


title: HAM815_ex_vivo


title: H460 cells, 2D, R1


title: extracellular vesicle from wjMSC-3

city: Seoul

first: Donghyun

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University College of Medicine

description:
wj_sg MSC-EV miRNAseq.xlsx
wjMSC_EV_3

data_processing:
Sequence reads were aligned using Bowtie2.
Differentially expressed genes were determined using coverage in Bedtools.
The read counts were processed based on TMM+CPM normalization method using EdgeR in R environment.
Assembly: hg19 for RNAseq, mirBase for miRNA
Supplementary files format and content: wj_sg MSC RNAseq.xlsx / Excel datasheet including gene symbol, Normalized values, Fold changes, and p-values
Supplementary files format and content: wj_sg MSC-EV miRNAseq.xlsx / Excel datasheet including miRNA symbol, Normalized values, Fold changes, and p-values

source_name: umbilical cord

growth_protocol: 2 MSCs were maintained in αMEM supplemented with 10% FBS and 1% P/S and incubated at 37℃ with 5% CO2.

extract_protocol:
Total RNA was extracted from MSCs using TRIzol or MSC-derived EVs using TRIzol LS reagents.
For RNAseq, library was constructed with the QuantSeq 3ʹ’ mRNA-Seq Library Prep Kit. For miRNAseq, NEBNext Multiplex Small RNA Library Prep kit was used according to manufacturers' instructions.

value: umbilical cord

value: mesenchymal stem cell


title: HAM815_Diff_MediaTIC


title: GK018_Mp

source_name: Healthy Control 18 - Intermediate Monocytes


title: GK017_Mp

source_name: Healthy Control 17 - Intermediate Monocytes


title: HAM815_Diff_Media


title: HAM814_ex vivo


title: extracellular vesicle from wjMSC-2

description:
wj_sg MSC-EV miRNAseq.xlsx
wjMSC_EV_2


title: HAM814_Diff_mediaTIC

value: Abud medium+TIC


title: extracellular vesicle from wjMSC-1

description:
wj_sg MSC-EV miRNAseq.xlsx
wjMSC_EV_1


title: GK016_Mp

source_name: Healthy Control 16 - Intermediate Monocytes


title: HAM814_Diff_mediaFBS

value: Abud medium


title: GK015_Mp

source_name: Healthy Control 15 - Intermediate Monocytes


title: HAM814_Diff_media


title: extracellular vesicle from sgMSC-3

description:
wj_sg MSC-EV miRNAseq.xlsx
sgMSC_EV_3

source_name: salivary gland

value: salivary gland


title: extracellular vesicle from sgMSC-2

description:
wj_sg MSC-EV miRNAseq.xlsx
sgMSC_EV_2


title: Primary ALL sample at diagnosis [GE9347]

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

institute: university of eastern finland

description: Bone marrow from diagnosis, B-cell acute lymphoblastic leukemia, ETV6-RUNX1

data_processing:
Nextflow-based (21.02.0.edge) nf-core/rnaseq (3.0) pipeline
Trimming of the paired-end reads by trimgalore (0.6.6)
Reads were aligned to human genome GRCh38 with ENSEMBL gene annotation GRCh38.103 using STAR (2.6.1d).
The aligned reads were quantified at the transcript level using Salmon (1.4.0)
Transcript level expression values were subsequently summarized to the gene level using the bioconductor package tximeta (1.8.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited raw count matrix

source_name: Bone marrow or Peripheral blood

extract_protocol:
NEBNext Ultra Directional RNA Library Prep Kit
Bone marrow or blood cells were collected and samples stored at -80C in PAX5gene Blood RNA tube, or in liquid nitrogen as viably frozen mononuclear cells (MNC) obtained using Ficoll extraction, or as RNA extracted using the Qiagen Allprep protocol, as indicated. Total RNA extracted was depleted of rRNA using the indicated kit.
Stranded total RNA libraries were prepared using the specified library preparation kit, following manufacturer instructions.

tag: sample preparation_and_storage_method

value: Qiagen Allprep DNA/RNA/miRNA Universal kit

tag: rna extraction_kit

value: TruSeq Stranded Total RNA Library Prep (Human/Mouse/Rat)

value: Bone marrow or Peripheral blood

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: female

tag: predicted subtype


title: Primary ALL sample at diagnosis [GE9336]

tag: tissue


title: Primary ALL sample at diagnosis [GE9344]


title: GK014_Mp

source_name: Healthy Control 14 - Intermediate Monocytes

value: Intermediate Monocytes

value: peripheral blood

value: Healthy Control


title: GK013_Mp

source_name: Healthy Control 13 - Intermediate Monocytes


title: Primary ALL sample at diagnosis [GE8321]


title: Primary ALL sample at diagnosis [GE8322]

value: male


title: Primary ALL sample at diagnosis [GE8329]


title: extracellular vesicle from sgMSC-1

description:
wj_sg MSC-EV miRNAseq.xlsx
sgMSC_EV_1


title: wharton's jelly mesenchymal stem cells-3

description:
wj_sg MSC RNAseq.xlsx
WJ_3


title: Primary ALL sample at diagnosis [GE8315]


title: HHL5

type: genomic

city: Newcastle

first: Gordon

last: Strathdee

address: Paul O'Gorman Building, Framlington Place

country: United Kingdom

institute: Newcastle University

hyb_protocol: X-stain and hybridisation to Infinium MethylationEPIC Bead chip v1 carried out on a Tecan Freedom Evo robotic workstation.

scan_protocol: Arrays were imaged using iScan BeadArray Reader using standard recommended Illumina scanner settings.

data_processing: BeadStudio software v3.2

label: cy3, cy5

molecule: genomic DNA

source_name: immortalised normal hepatocyte cell line

label_protocol: DNA bisulphite converted by EZ Zymo methylation kit (Zymo kit D5004) - this includes Illumina specific variations to the protocol. Standard Illumina Infinium HD Methylation Protocol (#1501951 v07).

growth_protocol: Hepatocellular carcinoma (HCC) cell lines HepG2, Huh-7, PLC/PRF-5 were cultured with Dulbecco's modified Eagle's /Ham F12 medium (Sigma, UK). Hepatocellular carci-noma SNU182 cell line was cultured with RPMI-1640 and the immortalised hepatocyte cell line HHL5, was propagated in Dulbecco's modified Eagle's medium/high glucose supplemented with 1% non-essential amino acid (Sigma, UK). All mediums were sup-plemented with 10% fetal bovine serum (Gibco, UK), 100 U/ml penicillin and 100 µg/ml streptomycin (Sigma), and 1% L-glutamine (Sigma).

extract_protocol: DNA extraction was performed with the PureLink® Genomic DNA Mini Kit (Thermo Fisher)

treatment_protocol: Cells were untreated

value: Normal Hepaocyte cell line


title: GK012_Mp

source_name: Healthy Control 12 - Intermediate Monocytes


title: Primary ALL sample at diagnosis [GE3317]


title: GK011_Mp

source_name: Healthy Control 11 - Intermediate Monocytes


title: HUH-7

source_name: HCC cell line

value: HCC tumour cell line


title: HepG2


title: SKHEP1

source_name: liver cancer cell line


title: SNU182


title: salivary gland mesenchymal stem cells-3

description:
wj_sg MSC RNAseq.xlsx
SG_3


title: Primary ALL sample at diagnosis [GE2328]


title: Primary ALL sample at diagnosis [GE1329]


title: wharton's jelly mesenchymal stem cells-2

description:
wj_sg MSC RNAseq.xlsx
WJ_2

value: umbilical cord


title: GK010_Mp

source_name: Healthy Control 10 - Intermediate Monocytes


title: Primary ALL sample at diagnosis [GE1312]


title: GK009_Mp

source_name: Healthy Control 9 - Intermediate Monocytes


title: PLC5


title: Primary ALL sample at diagnosis [GE0335]


title: GK008_Mp

source_name: Healthy Control 8 - Intermediate Monocytes


title: salivary gland mesenchymal stem cells-2

description:
wj_sg MSC RNAseq.xlsx
SG_2

value: mesenchymal stem cell


title: GK007_Mp

source_name: Healthy Control 7 - Intermediate Monocytes


title: wharton's jelly mesenchymal stem cells-1

description:
wj_sg MSC RNAseq.xlsx
WJ_1

source_name: umbilical cord


title: salivary gland mesenchymal stem cells-1

description:
wj_sg MSC RNAseq.xlsx
SG_1


title: Primary ALL sample at diagnosis [ALLT-379]

description: Bone marrow from diagnosis, T-cell acute lymphoblastic leukemia

source_name: Bone marrow

value: MNC extraction, viably frozen cells

value: Bone marrow

value: childhood T acute lymphoblastic leukemia

value: T-ALL


title: Primary ALL sample at diagnosis [ALLT-380]

value: TruSeq Stranded Total RNA Library Prep (Human/Mouse/Rat)


title: Primary ALL sample at diagnosis [GE0310]

value: Qiagen Allprep DNA/RNA/miRNA Universal kit

value: Bone marrow or Peripheral blood


title: Primary ALL sample at diagnosis [GE3320]

value: childhood B acute lymphoblastic leukemia

value: diagnosis


title: Primary ALL sample at diagnosis [GE3309]

value: female


title: HAM815_Diff_MediaFBS

source_name: Brain

value: Brain

value: Microglia

value: MEM+TIC


title: set2_starved_8

city: Tel Aviv

first: Karen

last: Avraham

country: Israel

institute: TAU

data_processing:
Sequenced reads were mapped to the homo sapians genome (hg38), using STAR v2.5.3a_modified
Genes were identified using a .gtf obtained from GENCODE release 27. Per gene reads were counted using HTSeq.
Normalization and detection of differentially expressed genes were done using DEseq2
Assembly: hg38
Supplementary files format and content: Text file with a gene count table

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in a humidified incubator with 5% CO2 at 37°C in DMEM (01-052-1A, Biological industry) supplemented with 10% heat-inactivated bovine serum (FBS) (04-007-1A, Biological Industries), penicillin/ streptomycin (15240-062, Gibco), and L-Glutamine (G7513, Sigma)

extract_protocol:
Total RNA was extracted from HeLa cells using Trizol (009010233100 Bio-Lab)
Sequencing libraries were prepared using the INCPM mRNA protocol

treatment_protocol: For nutrient starvation experiments, cells were washed with PBS and treated with HBSS (14025092, Gibco) for 4 h. Control cells were kept in the nutrient-rich/growth media. The cells were next harvested for RNA isolation

value: HeLa cells from ATCC (CCL-2)

tag: media type

value: starved


title: GK006_Mp

source_name: Healthy Control 6 - Intermediate Monocytes

tag: cell type

value: Intermediate Monocytes

value: peripheral blood

value: Healthy Control


title: Primary ALL sample at diagnosis [ALLT-378]

description: Bone marrow from diagnosis, B-cell acute lymphoblastic leukemia, B-other

value: MNC extraction, viably frozen cells

value: Bone marrow

value: male


title: GK005_Mp

source_name: Healthy Control 5 - Intermediate Monocytes


title: Primary ALL sample at diagnosis [ALLT-377]

description: Bone marrow from diagnosis, B-cell acute lymphoblastic leukemia, high hyperdiploid karyotype

value: TruSeq Stranded Total RNA Library Prep (Human/Mouse/Rat)

value: HeH


title: Primary ALL sample at diagnosis [ALLT-375]

description: Bone marrow from diagnosis, B-cell acute lymphoblastic leukemia, KMT2A-rearranged


title: Primary ALL sample at diagnosis [GE0325]

source_name: Bone marrow or Peripheral blood

value: Qiagen Allprep DNA/RNA/miRNA Universal kit

value: Bone marrow or Peripheral blood


title: set2_starved_4


title: GK004_Mp

source_name: Healthy Control 4 - Intermediate Monocytes


title: set2_starved_12


title: set2_nutrient_rich_2

value: rich


title: set2_nutrient_rich_6


title: Primary ALL sample at diagnosis [ALLT-371]

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: female


title: GK003_Mp

source_name: Healthy Control 3 - Intermediate Monocytes


title: GK002_Mp

source_name: Healthy Control 2 - Intermediate Monocytes


title: GK001_Mp

source_name: Healthy Control 1 - Intermediate Monocytes


title: Primary ALL sample at diagnosis [ALLT-369]


title: Primary ALL sample at diagnosis [ALLT-368]

source_name: Peripheral blood

value: Peripheral blood


title: set2_nutrient_rich_10

value: HeLa cells from ATCC (CCL-2)


title: OS028_Mn

source_name: Axial SpA Patient 28 - Non-classical Monocytes

value: Non-Classical Monocytes

value: Axial SpA Patient


title: Primary ALL sample at diagnosis [ALLT-367]


title: set1_starved_3

value: starved


title: Primary ALL sample at diagnosis [ALLT-376]

description: Bone marrow from diagnosis, B-cell acute lymphoblastic leukemia, TCF3-PBX1


title: OS027_Mn

source_name: Axial SpA Patient 27 - Non-classical Monocytes

value: peripheral blood


title: Primary ALL sample at diagnosis [ALLT-366]


title: Primary ALL sample at diagnosis [ALLT-373]

value: MNC extraction, viably frozen cells

value: childhood T acute lymphoblastic leukemia

value: T-ALL


title: Primary ALL sample at diagnosis [ALLT-372]

value: TruSeq Stranded Total RNA Library Prep (Human/Mouse/Rat)

value: Bone marrow

value: male


title: Primary ALL sample at diagnosis [ALLT-364]

value: HeH


title: set1_nutrient_rich_9

value: rich


title: OS026_Mn

source_name: Axial SpA Patient 26 - Non-classical Monocytes


title: set1_starved_11


title: OS025_Mn

source_name: Axial SpA Patient 25 - Non-classical Monocytes


title: set1_nutrient_rich_5


title: Primary ALL sample at diagnosis [ALLT-362]

value: Qiagen Allprep DNA/RNA/miRNA Universal kit

value: Bone marrow or Peripheral blood

value: childhood B acute lymphoblastic leukemia


title: OS024_Mn

source_name: Axial SpA Patient 24 - Non-classical Monocytes


title: Primary ALL sample at diagnosis [ALLT-363]

value: diagnosis

value: female


title: set1_starved_7

value: HeLa cells from ATCC (CCL-2)


title: hiHep-BAL-Day4

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

country: China

institute: CEMCS, CAS

data_processing:
All sequencing reads from RNA-seq were mapped to the porcine reference genome sequence (Sscrofa11.1) using hisat2-2.104. FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks v.2.2.15 using default parameters for gene expression levels. We used htseq-count6 to count reads on genes. Differential expression analysis was performed using DESeq27. Genes were considered differentially expressed if FPKM>1 in all sample and | log2(fold changes) | >= 1, q-value<=0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: Liver

extract_protocol:
Total RNA was extracted from pig livers using Trizol (Invitrogen) according to the manufacturer’s instructions.
Sequencing library was prepared from one microgram of total RNA using Illumina TruSeq RNA Sample Prep Kit. Paired-end 150 bp read length sequencing was performed on Illumina Hiseq 4000 sequencer.

value: Liver

value: hepatocyte

tag: genotype

value: WT


title: hiHep-BAL-Day8-2


title: hiHep-BAL-Day8


title: Primary ALL sample at diagnosis [ALLT-361]

source_name: Bone marrow

value: PAXgene Blood RNA Tube

value: Ribo-Zero Magnetic Kit


title: OS022_Mn

source_name: Axial SpA Patient 22 - Non-classical Monocytes

value: Non-Classical Monocytes

value: peripheral blood

value: Axial SpA Patient


title: Smoke exposed 3

city: Erie

first: Ashley

middle: E

last: Russell

state: PA

address: 4205 College Dr.

department: Department of Biology

institute: Penn State Erie School of Science, The Behrend College

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The microarray slides were scanned with an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

label_protocol: Total RNA from each sample was treated with RNase R to enrich circular RNA. The enriched circular RNA was reverse transcribed with random primers containing a T7 promoter. The cRNA was linearly amplified and Cy3 labeled by in vitro T7 polymerase transcription using Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

growth_protocol: Approximately 400,000 cells/mL of H9 cells were passaged into 6 T75 flasks in 25 mL of media.

extract_protocol: Invitrogen mirVana miRNA Isolation Kit (ThermoFisher Scientific, Cat. No. AM1560) was used as directed to isolate total RNA from the cells. Briefly, approximately 105 cells from each flask were lysed with 600 µL lysis buffer. Then, 750 µL 100% ethanol was added and centrifuged at RCF 10,000x g for 15 seconds. The filters containing RNA were washed and total RNA was then eluted by adding 100 µL pre-heated nuclease-free water and centrifuging at maximum speed for 25 seconds. RNA quality was checked using an Agilent Fragment Analyzer. 5,000 ng of RNA from each sample was then shipped to Arraystar for a Human Circular RNA Array.

treatment_protocol: One Spectrum research-grade cigarette was smoked continuously by peristaltic pump into 25 mL of R10 media to make 100% cigarette smoke exposure media. The media was then diluted to form 50% CSEM and approximately 400,000 cells/mL of H9 cells were grown in either 50% CSEM of 0% CSEM for 24 hours.

value: Lymphocytic T cells


title: Smoke exposed 2


title: THP-1, ∆lphD∆romA infected, 7h, rep3

city: Paris

first: Christophe

last: Rusniok

address: 25, 28 rue du Docteur Roux

department: Genomes et Genetique

country: France

institute: Institut Pasteur

data_processing:
RNA isolation, library preparation, RNAseq, and data analysis performed by Active Motif.
The paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the STAR algorithm with default settings. Alignment information for each read is stored in the BAM format.
The number of fragments overlapping predefined genomic features of interest (e.g. genes) are counted. Only read pairs that have both ends aligned are counted. Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands are discarded. The gene annotations we use were obtained from Subread package. These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene.
Data Normalization: DESeq2 expects un-normalized count matrix of sequencing fragments. The DESeq2 model internally corrects for library size using their median-of-ratios method. The gene table obtained from the previous step is used as input to perform the DESeq2’s differential test.
After a differential test has been applied to each gene except the ones with zero counts, the p-value of each gene is calculated and adjusted to control the number of false positives among all discoveries at a proper level. This procedure is known as multiple testing adjustment. During this process, DESeq2 by default filters out statistical tests (i.e. genes) that have low counts by a statistical technique called independent filtering. It uses the average counts of each gene (i.e. baseMean), across all samples, as its filter criterion, and it omits all genes with average normalized counts below a filtering threshold from multiple testing adjustment. This filtering threshold is automatically determined to maximize detection power (i.e. maximize the number of differential genes detected) at a specified false discovery rate (FDR).
Gene Set Enrichment Analysis (GSEA): Using DESeq2 normalized gene counts, we perform GSEA with default settings to determine whether members of a priori defined gene set based on biological knowledge (e.g. genes sharing the same GO category) are enriched. Before running GSEA, we add a small pseudo-count to the normalized counts to avoid divide by zero errors. Our standard GSEA analysis uses MSigDB’s C5 (GO gene set) collection.
Softwares used: STAR (v2.5.2b), featureCounts in Subread software packages (v1.5.2), DESeq2 (v1.14.1), GSEA (v4.0.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text files with Gene ids and read count values for each gene

growth_protocol: THP-1 monocytes were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
 Total RNA was isolated from samples using the Qiagen RNeasy Mini Kit
 1 ug of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit

treatment_protocol: Cells were infected with the different L. pneumophila strains expressing GFP with MOI=50. After 30 minutes, Gentamycin (100µg/ml) was added to kill extracellular bacteria. After 7 hours of infection, cells were sorted based on GFP signal using the BioRad S3e cell sorter.

value: Peripheral blood

value: monocyte

value: L. pneumophila deltalphDdeltaromA infected


title: Empty-BAL-2


title: Control 2


title: OS021_Mn

source_name: Axial SpA Patient 21 - Non-classical Monocytes


title: Control 3


title: Control 1


title: Smoke exposed 1


title: Primary ALL sample at diagnosis [ALLT-360]

value: Bone marrow

value: male


title: Primary ALL sample at diagnosis [ALLT-358]

value: childhood B acute lymphoblastic leukemia

value: diagnosis


title: OS020_Mn

source_name: Axial SpA Patient 20 - Non-classical Monocytes


title: Primary ALL sample at diagnosis [ALLT-357]


title: THP-1, ∆lphD∆romA infected, 7h, rep1


title: set1_nutrient_rich_1

source_name: HeLa cells

value: HeLa cells from ATCC (CCL-2)

value: rich


title: No-BAL-2

value: Liver

value: hepatocyte


title: OS019_Mn

source_name: Axial SpA Patient 19 - Non-classical Monocytes


title: THP-1, ∆lphD∆romA infected, 7h, rep2

value: WT


title: THP-1, ∆romA infected, 7h, rep2

value: L. pneumophila deltaromA infected


title: THP-1, ∆romA infected, 7h, rep3


title: No-BAL-1


title: OS017_Mn

source_name: Axial SpA Patient 17 - Non-classical Monocytes

value: Non-Classical Monocytes


title: Control-3 (BAL)


title: Control-2 (BAL)


title: OS016_Mn

source_name: Axial SpA Patient 16 - Non-classical Monocytes

value: peripheral blood


title: Primary ALL sample at diagnosis [ALLT-354]

value: PAXgene Blood RNA Tube

value: Ribo-Zero Magnetic Kit

value: childhood T acute lymphoblastic leukemia

value: female

value: T-ALL


title: OS015_Mn

source_name: Axial SpA Patient 15 - Non-classical Monocytes

value: Axial SpA Patient


title: Primary ALL sample at diagnosis [ALLT-351]

description: Bone marrow from diagnosis, B-cell acute lymphoblastic leukemia, hypodiploid karyotype

value: Bone marrow

value: male


title: Control-1 (BAL)


title: Empty-BAL-1


title: RNA_seq_tdTomato_positive_ILC2_rp4

city: Akita City

first: Takashi

last: Ebihara

address: 1-1-1 Hondo

department: Department of Medical Biology

country: Japan

institute: Akita University Graduate School of Medicine

data_processing:
Alingnment by STAR with standard input parameters after quality check by FASTP for RNA-seq and ATAC-seq.
Transcript counts were produced using featureCounts (subread package) with the Ensembl annotation (release 104) for RNA-seq data.
EdgeR to calculate differentially expressed genes from RNA-seq deata.
HOMER to call peaks from ATAC-seq data.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include TPM values for each Sample of RNA-seq data after EdgeR (FDR < 0.05, LogCPM > 5.0)
Supplementary files format and content: bedGraph.tdf from ATAC-seq data

source_name: Lung

extract_protocol: RNA-seq libraries were prepared by SMARTer® Stranded RNA-Seq Kit. ATAC-seq libraries were prepared with the protocol of Illumina Tagment DNA TDE1 Enzyme and Buffer Kits.

value: Lung

value: Papain and tamoxifen


title: Primary ALL sample at diagnosis [ALLT-347]

value: Globin-Zero Gold rRNA Removal Kit

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: HeH


title: OS012_Mn

source_name: Axial SpA Patient 12 - Non-classical Monocytes


title: OS013_Mn

source_name: Axial SpA Patient 13 - Non-classical Monocytes


title: Primary ALL sample at diagnosis [ALLT-356]


title: OS011_Mn

source_name: Axial SpA Patient 11 - Non-classical Monocytes


title: OS018_Mn

source_name: Axial SpA Patient 18 - Non-classical Monocytes


title: Primary ALL sample at diagnosis [ALLT-355]

source_name: Peripheral blood

value: Peripheral blood


title: Primary ALL sample at diagnosis [ALLT-343]

description: Bone marrow from diagnosis, B-cell acute lymphoblastic leukemia, BCR-ABL1


title: THP-1, wild type infected, 7h, rep3

value: monocyte

value: WT

value: L. pneumophila WT infected


title: Primary ALL sample at diagnosis [ALLT-346]

value: PAXgene Blood RNA Tube


title: THP-1, ∆romA infected, 7h, rep1

value: L. pneumophila deltaromA infected


title: OS010_Mn

source_name: Axial SpA Patient 10 - Non-classical Monocytes

value: Non-Classical Monocytes

value: peripheral blood


title: THP-1, wild type infected, 7h, rep1


title: Primary ALL sample at diagnosis [ALLT-342]

source_name: Bone marrow or Peripheral blood

value: Bone marrow or Peripheral blood


title: OS009_Mn

source_name: Axial SpA Patient 9 - Non-classical Monocytes

value: Axial SpA Patient


title: ATAC_seq_tdTomato_negative_ILC2_rp2

library_source: genomic


title: ATAC_seq_tdTomato_positive_ILC2_rp2


title: THP-1, ∆lphD infected, 7h, rep2

value: L. pneumophila deltalphD infected


title: OS008_Mn

source_name: Axial SpA Patient 8 - Non-classical Monocytes


title: Primary ALL sample at diagnosis [ALLT-339]

source_name: Bone marrow

value: Bone marrow

value: female


title: ATAC_seq_tdTomato_negative_ILC2_rp1

value: Lung

value: Papain and tamoxifen


title: RNA_seq_tdTomato_positive_ILC2_rp3


title: Primary ALL sample at diagnosis [ALLT-338]

value: Globin-Zero Gold rRNA Removal Kit

value: childhood B acute lymphoblastic leukemia

value: diagnosis


title: OS006_Mn

source_name: Axial SpA Patient 6 - Non-classical Monocytes


title: THP-1, non-infected, rep3

value: Peripheral blood

value: monocyte

value: non-infected


title: THP-1, non-infected, rep2

value: WT


title: Primary ALL sample at diagnosis [ALLT-337]

value: PAXgene Blood RNA Tube


title: OS005_Mn

source_name: Axial SpA Patient 5 - Non-classical Monocytes

value: Non-Classical Monocytes


title: ATAC_seq_tdTomato_positive_ILC2_rp1


title: RNA_seq_tdTomato_positive_ILC2_rp2


title: OS003_Mn

source_name: Axial SpA Patient 3 - Non-classical Monocytes

value: peripheral blood


title: RNA_seq_tdTomato_positive_ILC2_rp1


title: THP-1, wild type infected, 7h, rep2

value: L. pneumophila WT infected


title: THP-1, non-infected, rep1


title: MOLM13_SHAREseq_1 ATAC

source_name: MOLM13 AML cell line

value: single perturbation

value: SHARE-seq (ATAC)


title: Primary ALL sample at diagnosis [ALLT-340]

value: Bone marrow


title: Primary ALL sample at diagnosis [ALLT-335]

value: Bone marrow or Peripheral blood

value: female


title: OS002_Mn

source_name: Axial SpA Patient 2 - Non-classical Monocytes

value: Axial SpA Patient


title: RNA_seq_tdTomato_negative_ILC2_rp3

value: Lung

value: Papain and tamoxifen


title: THP-1, non-infected, rep4


title: OS001_Mn

source_name: Axial SpA Patient 1 - Non-classical Monocytes


title: Primary ALL sample at diagnosis [ALLT-334]

value: Globin-Zero Gold rRNA Removal Kit

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: male


title: RNA_seq_tdTomato_negative_ILC2_rp2

source_name: Lung


title: MOLM13_SHAREseq_1 RNA

value: SHARE-seq (RNA)


title: RNA_seq_tdTomato_negative_ILC2_rp1


title: OB021_Mn

source_name: Peripheral SpA Patient 21 - Non-classical Monocytes

value: Peripheral SpA Patient


title: Primary ALL sample at diagnosis [ALLT-333]

value: PAXgene Blood RNA Tube


title: Primary ALL sample at diagnosis [ALLT-331]


title: Primary ALL sample at diagnosis [ALLT-330]


title: UCD52PR, Hi-C seq

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description: primary tumor

data_processing:
The data was processed using the Juicer v.1.6 pipeline outlined in Durand NC. Et al. Methods 2016 (PMID: 27467249).
The Python implementation of HiCRep was used at 1Mb resolution to estimate reproducibility.
Multi-dimensional scaling and hierarchical clustering were performed on the matrix of pairwise chromosome-averaged HiCRep measures.
Data resolution was esimated using the pipeline described in Rao SSP. Et al. Methods 2014 (PMID: 25497547).
Assembly: hg38
Supplementary files format and content: HiC file

organism:
Homo sapiens
Mus musculus

source_name: Basal-like triple-negative breast cancer patient-derived xenograft; UCD52

growth_protocol: UCD52 PDX cells were grown in mammary fat pads of female NSG mice. Tumors were harvested when ~ 10mm x 10mm in size and 500K cells were injected into the right mammary gland of female NGS mice.

extract_protocol:
Hi-C sequencing was performed according to the expirimental procedure described in Dozmorov MG. Et al. Methods 2021 (PMID: 33880552).
Libraries were constructed according to the protocol described in Dozmorov MG. Et al. Methods 2021 (PMID: 33880552).

treatment_protocol: Once tumors reached 25-50 mm^2 in size, carboplatin resistance was induced by administering three intraparitoneal 40mg/kg doses of carboplatin spaced out over four days. Tumors were harvested once growth resumed and serially passaged into new recipient NGS mice, and was repeated until the tumor was unresponsive to carploplatin treatments. The carboplatin-resistant phenotype was maintained by continuing the carboplatin treatment regimen.

value: primary tumor from UCD52 PDX model

value: untreated


title: OB018_Mn

source_name: Peripheral SpA Patient 18 - Non-classical Monocytes

value: Non-Classical Monocytes

value: peripheral blood


title: OB017_Mn

source_name: Peripheral SpA Patient 17 - Non-classical Monocytes


title: scRNA-seq_Patient HP01 PDAC

city: Loma Linda

first: Charles

last: Wang

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

description: scRNA-seq 10x filtered matrix

library_source: transcriptomic single cell

data_processing:
Illumina RTA v2.4.11 software was used for basecalling and bcl2fastq v2.17.14 was used for generating fastq files.
RNA-seq reads were trimmed for adaptor sequence and low quality, then mapped to GRCh38 whole genome using STAR v2.6.1a with parameters with default settings. Reads mapped to annotated genes were counted and aggregated using HTSeq_count v0.6.1.
miRNA-seq reads were mapped and counted using the primary analysis procedure of Qiagen online miRNA-seq analysis software (https://geneglobe.qiagen.com/sg/analyze).
Single cell data was mapped and counted using Cellranger (v5.0.1) and the filtered feature matrix was used in Seurat analysis (v3.0).
Differential gene expression was analyzed using R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw gene count values for each gene.

source_name: Pancreas

extract_protocol:
Total RNA was extracted with Qiagen AllPrep DNA/RNA/miRNA Universal kit.
RNA-seq libraries were prepared for sequencing using Tecan Universal NuQuant Kit, miRNA-seq libraries were prepared using QIAseq miRNA kit, and single cell RNA-seq library was constructed using 10x Genomics 5' GXE kit.

value: Pancreatic tumor

tag: age


title: Primary ALL sample at diagnosis [ALLT-329]

value: Bone marrow or Peripheral blood

tag: Sex

value: HeH


title: OB016_Mn

city: Kraków

first: Marcin

last: Czepiel

institute: Jagiellonian University Medical College

data_processing:
After processing OpenArray miRNA Expression run, the data analysis was performed. Quality control images (QC Images) were exported and investigated to find potential loading errors. The result files created by QuantStudio Software v1.2.3 were uploaded to ThermoFisher Cloud and analyzed with Relative Quantification qPCR Application. miRNA Panel A and B were analyzed in separate analysis groups
The Processed (normalized) Data is organized in separate excel files - each file for each target (miRNA). This data has been normalised to U6 rRNA Ct values coming from the relevant Raw Data files namely: "Panel_A_Sample Results.csv" and "Panel_B_Sample Results.csv". In these raw data files you will find the Sample name, target name and Ct values in columns 1, 2 and 3 respectively (column names: Sample Name, Target Name, Mean Equivalent Cq).
The expression of each miRNA type was calculated using 2−ΔΔCT method and snRNa U6 was used as a control to all miRNA analysis

source_name: Peripheral SpA Patient 16 - Non-classical Monocytes

extract_protocol: RNAs were isolated using miRVana microRNA isolation kit (Thermo Fisher Scientific) and transcripted into cDNA using Megaplex™ RT Primers and TaqMan® MicroRNA Reverse Transcription Kit


title: Primary ALL sample at diagnosis [ALLT-327]

value: Bone marrow

value: female


title: miRNA_Patient HP05 plasma

description:
miRNAseq_countmatrix.csv
Plasma_HP05_T

source_name: Plasma

value: Peripheral blood

value: not collected


title: OC4_R1_oxWGBS

city: Hengyang

first: Zhengqing

last: Wan

address: 28 West Changsheng Road

institute: University of South China

description: Whole-genome oxidative bisulfite sequencing (oxWGBS‑seq)

data_processing:
Adapter and low‑quality reads were first trimmed using Trim Galore (version 0.4.4) in paired‑end mode with default parameters.
Cleaned reads were mapped to the hg38 reference genome using BSMAP software (version 2.73)
Methylation levels at specific single cytosine site (β value) were extracted from mapping results using a Python script (methratio.py) embedded in BSMAP.
Hydroxymethylation levels were calculated by MLML algorithm based on WGBS-seq and oxWGBS-seq results.
Assembly: hg38
Supplementary files format and content: Methylation and hydroxymethylation levels (beta value) of each CpG site with coverage larger than 10-fold

source_name: patient-4 tumor

extract_protocol:
Tissue blocks of about 30 mg were further dissected out and used for extraction of DNA and total RNA following the manufacturer’s instruction of the AllPrep DNA/RNA/miRNA Universal Kit (80224, Qiagen, USA).
1 μg of DNA were used for WGBS-seq and oxWGBS-seq library preparation. Lambda DNA spike-in with artificial methylation and hydroxymethylation modification were using as bisulfite and oxidation control.
Individual RNA libraries were pooled and sequenced using paired‑end sequencing with 150 bp reads on an Illumina HiSeq3000 instrument.

tag: source

value: Oral cavity

value: OSCC tissue


title: OC4_R1_WGBS

description: Whole genome bisulfite sequencing (WGBS‑seq)


title: miRNA_Patient HP04 plasma

description:
miRNAseq_countmatrix.csv
Plasma_HP04_T


title: ON4_R1_oxWGBS

source_name: patient-4 NAT

value: normal adjacent tissue


title: ON4_R1_WGBS


title: OB015_Mn

address: Anny 12

source_name: Peripheral SpA Patient 15 - Non-classical Monocytes

tag: disease state


title: Primary ALL sample at diagnosis [ALLT-325]

source_name: Peripheral blood

value: Globin-Zero Gold rRNA Removal Kit

tag: disease

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: male


title: ON3_R1_oxWGBS

source_name: patient-3 NAT


title: UCD52CR, Hi-C seq

description: carboplatin-resistant

tag: cell line

value: Basal-like triple-negative breast cancer patient-derived xenograft; UCD52

value: carboplatin resistant tumor from UCD52 PDX model

value: carboplatin


title: OB014_Mn

source_name: Peripheral SpA Patient 14 - Non-classical Monocytes

value: Non-Classical Monocytes

value: peripheral blood

value: Peripheral SpA Patient


title: miRNA_Patient HP03 plasma

description:
miRNAseq_countmatrix.csv
Plasma_HP03_T


title: Primary ALL sample at diagnosis [ALLT-324]

source_name: Bone marrow

value: PAXgene Blood RNA Tube

value: Bone marrow


title: miRNA_Patient HP02 plasma

description:
miRNAseq_countmatrix.csv
Plasma_HP02_T

value: Peripheral blood


title: OB013_Mn

source_name: Peripheral SpA Patient 13 - Non-classical Monocytes


title: OC3_R1_oxWGBS

source_name: patient-3 tumor


title: Primary ALL sample at diagnosis [ALLT-323]

value: childhood T acute lymphoblastic leukemia

value: T-ALL


title: miRNA_Patient HP01 plasma

description:
miRNAseq_countmatrix.csv
Plasma_HP01_T


title: OB012_Mn

source_name: Peripheral SpA Patient 12 - Non-classical Monocytes


title: Primary ALL sample at diagnosis [ALLT-322]


title: miRNA_Healthy control plasma 6

description:
miRNAseq_countmatrix.csv
Plasma_C6

value: not collected


title: OB011_Mn

source_name: Peripheral SpA Patient 11 - Non-classical Monocytes


title: OC3_R1_WGBS

value: Oral cavity

value: OSCC tissue


title: Primary ALL sample at diagnosis [ALLT-320]

value: Globin-Zero Gold rRNA Removal Kit

value: childhood B acute lymphoblastic leukemia

value: HeH


title: miRNA_Healthy control plasma 5

description:
miRNAseq_countmatrix.csv
Plasma_C5


title: ON2_R1_oxWGBS

source_name: patient-2 NAT

value: normal adjacent tissue


title: miRNA_Healthy control plasma 4

description:
miRNAseq_countmatrix.csv
Plasma_C4


title: OB009_Mn

source_name: Peripheral SpA Patient 9 - Non-classical Monocytes


title: Primary ALL sample at diagnosis [ALLT-318]

value: diagnosis

value: male


title: OB007_Mn

source_name: Peripheral SpA Patient 7 - Non-classical Monocytes

value: Non-Classical Monocytes


title: Primary ALL sample at diagnosis [ALLT-315]

value: female


title: OB010_Mn

source_name: Peripheral SpA Patient 10 - Non-classical Monocytes

value: peripheral blood

value: Peripheral SpA Patient


title: Primary ALL sample at diagnosis [ALLT-314]

value: PAXgene Blood RNA Tube

value: Bone marrow


title: miRNA_Healthy control plasma 3

description:
miRNAseq_countmatrix.csv
Plasma_C3

value: Peripheral blood


title: OB008_Mn

source_name: Peripheral SpA Patient 8 - Non-classical Monocytes


title: miRNA_Healthy control plasma 2

description:
miRNAseq_countmatrix.csv
Plasma_C2

source_name: Plasma


title: miRNA_Healthy control plasma 1

description:
miRNAseq_countmatrix.csv
Plasma_C1


title: ON3_R1_WGBS


title: ON1_R1_oxWGBS

source_name: patient-1 NAT


title: OC2_R1_oxWGBS

source_name: patient-2 tumor


title: Primary ALL sample at diagnosis [ALLK-108]

value: Ribo-Zero Magnetic Kit


title: OB002_Mn

source_name: Peripheral SpA Patient 2 - Non-classical Monocytes


title: miRNA_Patient HP05 PDAC

description:
miRNAseq_countmatrix.csv
HP05_T

source_name: Pancreas

value: Pancreatic tumor

value: not collected


title: OB004_Mn

source_name: Peripheral SpA Patient 4 - Non-classical Monocytes


title: OC1_R1_oxWGBS

source_name: patient-1 tumor

value: Oral cavity

value: OSCC tissue


title: miRNA_Patient HP05 normal

description:
miRNAseq_countmatrix.csv
HP05_N

value: Duodenum Tissue


title: Primary ALL sample at diagnosis [ALLT-319]

source_name: Bone marrow

value: Globin-Zero Gold rRNA Removal Kit

value: childhood B acute lymphoblastic leukemia


title: ON1_R1_WGBS

value: normal adjacent tissue


title: OB001_Mn

source_name: Peripheral SpA Patient 1 - Non-classical Monocytes


title: ON2_R1_WGBS


title: OC2_R1_WGBS


title: miRNA_Patient HP04 PDAC

description:
miRNAseq_countmatrix.csv
HP04_T


title: LASCPC-01 cells, PP, Day3_1

first: Qi

state: Shanghai

address: Shanghai Pu Dong district, Dongfang Rd. No.1630

institute: Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: NEPC cells sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent 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 TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.

value: NEPC cells sample

value: NEPC cells

value: WT

value: Fluoxetine


title: OC1_R1_WGBS


title: LASCPC-01 cells, PBS, Day3_1

description: CtrlA

value: PBS


title: GK022_Mn

source_name: Healthy Control 22 - Non-classical Monocytes

value: Non-Classical Monocytes

value: peripheral blood

value: Healthy Control


title: miRNA_Patient HP03 PDAC

description:
miRNAseq_countmatrix.csv
HP03_T

value: female


title: GK021_Mn

source_name: Healthy Control 21 - Non-classical Monocytes


title: miRNA_Patient HP04 normal

description:
miRNAseq_countmatrix.csv
HP04_N

value: Pancreatic tumor


title: GK020_Mn

source_name: Healthy Control 20 - Non-classical Monocytes


title: miRNA_Patient HP03 normal

description:
miRNAseq_countmatrix.csv
HP03_N

value: Pancreatic benign tissue


title: RKO_f3

city: Guangzhou

first: Xiaoxia

last: Liu

state: Guangdong

address: 26 Yuancun Erheng Road

department: The Sixth Affiliated Hospital

institute: Sun Yat-sen University

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
UMI sequences on each read were identified with UMI-tools (1.0.0), and reads with UMIs were subjected to subsequent analysis.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1).

source_name: RKO

growth_protocol: RKO cells were maintained DMEM (high glucose, 4.5 g/L)  supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s

treatment_protocol: RKO cells were maintained DMEM (low glucose, 1g/L) supplemented with 1% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

value: RKO

value: Colorectal cancer (CRC) cells

value: fasting medium (1%FBS+1g/L glucose)


title: GK019_Mn

source_name: Healthy Control 19 - Non-classical Monocytes


title: RKO_f2


title: LASCPC-01 cells, PP, Day3_2


title: RKO_f1


title: miRNA_Patient HP01 PDAC

description:
miRNAseq_countmatrix.csv
HP01_T

value: male


title: GK017_Mn

source_name: Healthy Control 17 - Non-classical Monocytes


title: THP-1, ∆lphD infected, 7h, rep3

source_name: Peripheral blood

value: Peripheral blood

value: monocyte

value: L. pneumophila deltalphD infected


title: P19-331 Infarcted tissue

city: Cáceres

first: Esther

last: López Nieto

state: Cáceres

address: Carretera Nacional 521, Km 41.8 - 10071

department: Stem Cells Therapy

country: Spain

institute: jesús usón minimally invasive surgery centre

description: Gene expression data from remote and infarcted myocardium

hyb_protocol: RNA from tissue samples was hybridized using Affymetrix GeneChip WT Pico Reagent Kit according to the user guide.

scan_protocol: Scan protocol was assessed in a Gene Titan Affymetrix microarray platform.

data_processing: Data were processed using Transcriptome Analysis Console software.

label: Biotin

source_name: Infarcted myocardial tissue

label_protocol: RNA from tissue samples was labelled using Affymetrix GeneChip WT Pico Reagent Kit according to the user guide.

extract_protocol: RNA was isolated with PureLink RNA Mini Kit (Thermo Fisher Scientific, MA, USA) using TRIzol reagent.

treatment_protocol: Hearts were extracted by thoracotomy and washed with PBS. Infarcted tissue was minced and collected in Allprotect Tissue Reagent (Qiagen, Hilden, Germany) at -20 °C

tag: animal id

value: heart

tag: tissue region

value: Infarcted

tag: breed

value: Large White pigs


title: P19-328 Infarcted tissue


title: P19-366 Infarcted tissue


title: RKO_c3

value: WT

tag: treatment

value: control medium (10%FBS+4.5g/L glucose)


title: P19-708 Infarcted tissue


title: LASCPC-01 cells, PBS, Day3_2

description: CtrlB

value: NEPC cells sample

value: NEPC cells

value: PBS


title: miRNA_Patient HP01 normal

description:
miRNAseq_countmatrix.csv
HP01_N


title: GK018_Mn

source_name: Healthy Control 18 - Non-classical Monocytes

value: Non-Classical Monocytes

value: peripheral blood

value: Healthy Control


title: GK016_Mn

source_name: Healthy Control 16 - Non-classical Monocytes


title: GK015_Mn

source_name: Healthy Control 15 - Non-classical Monocytes


title: RKO_c1

value: RKO

value: Colorectal cancer (CRC) cells


title: miRNA_Patient HP02 PDAC

description:
miRNAseq_countmatrix.csv
HP02_T

source_name: Pancreas

value: Pancreatic tumor

value: male


title: P19-708 Remote tissue

source_name: Remote myocardial tissue

value: Remote


title: MQpool2-FB

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description:
Cell Hashing library
Hashtag-derived oligonucleotide (HTO)
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

library_source: other

data_processing:
Raw sequence data demultiplexing, barcode processing, alignment (GRCh38) and filtering for true cells were performed using the Cell Ranger Single-Cell Software Suite (v6.0.0)
Sample demultiplexing from hashtag feature barcoding (TotalSeq-C antibodies, BioLegend), subsequent filtering for high quality cells, and downstream analyses were performed using Seurat (v4)
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv
Library strategy: HTO

molecule: protein

source_name: PBMC

extract_protocol:
Single live CD45+CD19–CD3+CD56– cells were enriched from cryopreserved PBMC samples obtained pre-treatment and on-treatment at 3, 6, 9 weeks by flow cytometry sorting using a BD FACSAria II (BD Biosciences).
Cells were counted, hashed with TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253 and TotalSeq-C0254 anti-human antibodies, BioLegend) and pooled into 2 separate batchs (MQpool1, MQpool2).
The pooled cells were then counted again and immediately loaded onto the chromium chip G using the standard protocol for the Chromium single-cell 5’ kit v2 (10x Genomics, Inc).
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.
scRNA/VDJ-seq (5'GEX, VDJ, HTO)

value: PBMC

tag: cell type (sorted)

value: CD45+CD19-CD3+CD56- cells

value: NSCLC

tag: antibodies/tags

value: Dose_0--/TotalSeq-C0251 ; Dose_1--/TotalSeq-C0252 ; Dose_3--/TotalSeq-C0253 ; Dose_4--/TotalSeq-C0254

tag: library type

value: HTO


title: GK013_Mn

source_name: Healthy Control 13 - Non-classical Monocytes

tag: tissue


title: OG2 mESC, LSD1-KO, rep2 [none]

city: guangzhou

first: Xinjie

last: Li

address: gongming street 66

institute: sun yat-sen university

data_processing:
FastQC v 0.11.9 was used for qulity control.
ChIP-seq reads were trimmed for adaptor sequence/low-quality sequence using trim_galore v 0.0.1.
ChIP-seq reads were aligned to mm10 genome using Bowtie v 2.4.5. Only uniquely mapping reads were retained.
Peaks were called uing MACS v 2.2.7.1 the significance cut-off q-value <=0.05.
bigWig files were generated using deeptools v 3.5.1.  Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: mm10
Supplementary files format and content: bigWig (sample normalized coverage adjusted by input)

source_name: OG2 mESC

growth_protocol: OG2 mESC cells were maintained on gelatin-coated plate in DMEM supplemented with 15% fetal bovine serum (FBS) and 2iL in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a M220 focused-ultrasonicator (Covaris).
After the DNA samples quality control:(1) The DNA fragments are repaired, dA-tailed;(2) The DNA fragments with A tail are ligated to sequencing adaptors;(3) The final DNA library is obtained by size selection and PCR amplification.

value: OG2 mESC

value: mouse embryonic stem cells

tag: chip antibody


title: MQpool1-FB

tag: cell type

value: pre-treatment and on-treatment at 3, 6, 9 weeks


title: P19-366 Remote tissue

value: heart

value: Large White pigs


title: OG2 mESC, LSD1-KO, rep2 [H3K27me3 (Active Motif, 39055)]

value: H3K27me3 (Active Motif, 39055)


title: P19-331 Remote tissue


title: castration-resistant prostate cancer12

first: wen

last: tao

address: Tianhe Road 600

institute: The Third Affiliated Hospital, Sun Yat-sen University

description:
Ribosomal-depleted RNA
W3g
sample paired with:
W3

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw sequencing reads were subjected to trimming process with Trimmomatic (v.0.32)
High-quality reads were aligned to the Homo sapiens reference genome (GRCH37/hg19) by BWA (v.0.7.12). The resulted sequence alignment files (bam formatted file) were then sorted by reference position as required by SAMtools(v.2.6.2).
CircRNAs was identified and quantified by CIRI2
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: text file with abundance data, logFC,  logCPM,  Pvalue,  FDR. circRNAs are identified by their chromosome coordinates (chromosome:position1|position2).

source_name: plasma exosome

extract_protocol:
Isolation of exosomes using ExoQuick（SBI,Palo Alto,CA,US) according to the manufacturer's instructions.Exosomal RNA was isolated from samples using RNAiso Plus Total RNA extraction reagent (TAKARA, Dalian, China) according to the manufacturer's instructions and the RIN number was checked to detect RNA integrity by Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Further purification of qualified total RNA using RNAClean XP Kit (Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set(QIAGEN, GmBH, Germany).
The total RNA were treated with the RiboZero rRNA Removal Kit (Epicentre, WI, USA) to delete rRNA and digested linear RNA using RNase-R (Epicentre, WI, USA) according to the manufacturer’s instructions. Next, strand-specific libraries were constructed by using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, Nanjing, CHN) following the manufacturer’s instructions. In brief, The enriched circRNAs were fragmented using fragmentation buffer and then reverse transcribed into first-strand cDNA and second-strand cDNA in orderly. Then, the cDNA fragments were purified, subjected to end-repair, and modified to add poly (A) to the 3’ end. The sequencing adapters were ligated to the cDNA fragments. The double strand cDNA are digested by uracil-DNA glycosylase (UDG) (Cwbio, Beijing, CHN) to remove the second-strand cDNA before sequencing. The purified ligation products were performed 13-15 cycles of PCR amplification. The PCR amplification products of cDNA were purified with Agencourt AMPure XP Beads(Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and then sequenced by Illumina Hiseq X Ten system (Illumina, San Diego, CA, USA) on paired-end(PE) mode with length 150 bases following the vendor’s recommended protocol.

tag: subject id

value: plasma

tag: tissue compartment

value: exosome

tag: patient diagnosis

value: castration-resistant prostate cancer


title: castration-resistant prostate cancer15

description:
Ribosomal-depleted RNA
W6g
sample paired with:
W6

tag: Sex


title: castration-resistant prostate cancer13

description:
Ribosomal-depleted RNA
W4g
sample paired with:
W4


title: castration-resistant prostate cancer14

description:
Ribosomal-depleted RNA
W5g
sample paired with:
W5


title: P19-328 Remote tissue


title: GK011_Mn

source_name: Healthy Control 11 - Non-classical Monocytes

value: Non-Classical Monocytes

value: peripheral blood

tag: disease state

value: Healthy Control


title: RKO_c2

value: RKO

value: Colorectal cancer (CRC) cells

tag: genotype

value: WT

value: control medium (10%FBS+4.5g/L glucose)


title: GK010_Mn

source_name: Healthy Control 10 - Non-classical Monocytes


title: MQpool2-VDJ

description:
VDJ library
VDJ
filtered_contig_annotations.csv

data_processing:
Raw sequence data demultiplexing, barcode processing, alignment (GRCh38) and filtering for true cells were performed using the Cell Ranger Single-Cell Software Suite (v6.0.0)
Sample demultiplexing from hashtag feature barcoding (TotalSeq-C antibodies, BioLegend), subsequent filtering for high quality cells, and downstream analyses were performed using Seurat (v4)
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv
Library strategy: VDJ-seq

value: PBMC

value: CD45+CD19-CD3+CD56- cells

value: NSCLC

value: VDJ


title: castration-resistant prostate cancer11

description:
Ribosomal-depleted RNA
W2g
sample paired with:
W2

value: male


title: castration-resistant prostate cancer10

description:
Ribosomal-depleted RNA
W1g
sample paired with:
W1


title: MQpool1-VDJ

value: pre-treatment and on-treatment at 3, 6, 9 weeks


title: OG2 mESC, LSD1-KO, rep2 [H3K4me3 (abcam, ab8580)]

tag: cell line

value: OG2 mESC

value: mouse embryonic stem cells

value: H3K4me3 (abcam, ab8580)


title: MQpool2-GEX

description:
5' mRNA library
5'RNA
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
Raw sequence data demultiplexing, barcode processing, alignment (GRCh38) and filtering for true cells were performed using the Cell Ranger Single-Cell Software Suite (v6.0.0)
Sample demultiplexing from hashtag feature barcoding (TotalSeq-C antibodies, BioLegend), subsequent filtering for high quality cells, and downstream analyses were performed using Seurat (v4)
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv

value: mRNA


title: OG2 mESC, LSD1-KO, rep2 [H3K4me1(Abcam, #ab8895)]

value: H3K4me1(Abcam, #ab8895)


title: castration-resistant prostate cancer9

description:
Ribosomal-depleted RNA
X11
sample paired with:
X19

value: plasma

value: exosome

value: castration-resistant prostate cancer


title: GK009_Mn

source_name: Healthy Control 9 - Non-classical Monocytes

value: Non-Classical Monocytes

value: peripheral blood

value: Healthy Control


title: OG2 mESC, LSD1-KO [none]


title: MQpool1-GEX

value: PBMC


title: GK008_Mn

source_name: Healthy Control 8 - Non-classical Monocytes


title: GK014_Mn

source_name: Healthy Control 14 - Non-classical Monocytes


title: OG2 mESC, LSD1-KO [H3K27me3 (Active Motif, 39055)]

value: H3K27me3 (Active Motif, 39055)


title: castration-resistant prostate cancer8

description:
Ribosomal-depleted RNA
B8A
sample paired with:
B8


title: GK012_Mn

source_name: Healthy Control 12 - Non-classical Monocytes


title: H-CD161P-low2, HBV-infected patients, CD161+CD8+ non-MAIT cells, AST<40, biol rep2

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

data_processing:
Illumina novaseq 6000 platform used for basecalling.
Raw image Data files obtained by Illumina nova are analyzed by CASAVA Base Calling and converted into Raw Data of sequencing sequences，and the results are stored in FASTQ (.fq) file format. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
The clean reads obtained by filtering were compared to the reference sequence.Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, fusion gene detection and other analyses were performed.
HISAT was used to compare clean reads to reference genes. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads per Kilobase per Million Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Homo_sapiens.GRCh38.99.chr
Supplementary files format and content: Matrix table with read counts for every gene and every sample

source_name: Liver

extract_protocol:
Total RNAs were extracted from enriched cells using TRIzol Reagent (Invitrogen,cat. NO 15596026 ), following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
circulating CD161-CD8+ T cells(CD161N) from HD
circulating CD161+CD8+ non-MAIT cells(CD161P) from HD
circulating MAIT cells from HD
circulating CD161+CD8+ non-MAIT cells(CD161P) from HBV-infected patients
hepatic CD161+CD8+ non-MAIT cells from HBV-infected patients(AST>40 and AST<40)

value: Liver

value: hepatic CD161+CD8+ non-MAIT cells (H-CD161P-low)

tag: infection

value: HBV-infected

tag: ast


title: castration-resistant prostate cancer7

description:
Ribosomal-depleted RNA
B7A
sample paired with:
B7

value: male


title: RNA_seq_tdTomato_negative_ILC2_rp4

source_name: Lung

value: Lung

value: Papain and tamoxifen


title: GK007_Mn

source_name: Healthy Control 7 - Non-classical Monocytes


title: OG2 mESC, LSD1-KO [H3K4me3 (abcam, ab8580)]

value: OG2 mESC

value: mouse embryonic stem cells

value: H3K4me3 (abcam, ab8580)


title: GK006_Mn

source_name: Healthy Control 6 - Non-classical Monocytes


title: OG2 mESC, LSD1-KO [H3K4me1(Abcam, #ab8895)]

value: H3K4me1(Abcam, #ab8895)


title: THP-1, ∆lphD infected, 7h, rep1

source_name: Peripheral blood

value: Peripheral blood

value: monocyte

value: WT

value: L. pneumophila deltalphD infected


title: H-CD161P-low1, HBV-infected patients, CD161+CD8+ non-MAIT cells, AST<40, biol rep1


title: castration-resistant prostate cancer6

description:
Ribosomal-depleted RNA
B6A
sample paired with:
B6

value: plasma

value: exosome

value: castration-resistant prostate cancer


title: castration-resistant prostate cancer5

description:
Ribosomal-depleted RNA
B5A
sample paired with:
B5


title: H-CD161P-High2, HBV-infected patients, CD161+CD8+ non-MAIT cells, AST>40, biol rep2

value: Liver

value: hepatic CD161+CD8+ non-MAIT cells (H-CD161P-High)


title: OG2 mESC, LSD1-KO, rep2

data_processing:
FastQC v 0.11.9 was used for qulity control.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore v 0.0.1.
The remaining reads were mapped to the reference genome (mm10) with hisat2 v 2.2.1. Only uniquely mapping reads were retained.
Read count extraction and normalization were performed using HTSeq v 2.0.2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

growth_protocol: OG2 mESC cells were maintained on gelatin-coated plate in DMEM supplemented with 15% fetal bovine serum (FBS)and 2iL in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Total RNA Kit I (Omega Bio-Tek)  and then total RNA was used for the construction of sequencing libraries.
RNA libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: LSD1 knockdout


title: GK005_Mn

source_name: Healthy Control 5 - Non-classical Monocytes

value: Non-Classical Monocytes

value: peripheral blood

value: Healthy Control


title: CD161P-HBV, HBV-infected patients, CD161+CD8+ non-MAIT cells,  biol rep3

source_name: peripheral blood

value: circulating CD161+CD8+ non-MAIT cells (CD161P)

value: HBV-infected


title: H-CD161P-High1, HBV-infected patients, CD161+CD8+ non-MAIT cells, AST>40, biol rep1


title: GK003_Mn

source_name: Healthy Control 3 - Non-classical Monocytes


title: GK004_Mn

source_name: Healthy Control 4 - Non-classical Monocytes


title: castration-resistant prostate cancer3

description:
Ribosomal-depleted RNA
B3A
sample paired with:
B3

value: male


title: castration-resistant prostate cancer4

description:
Ribosomal-depleted RNA
B4A
sample paired with:
B4


title: castration-resistant prostate cancer2

description:
Ribosomal-depleted RNA
B2A
sample paired with:
B2


title: CD161P-HBV, HBV-infected patients, CD161+CD8+ non-MAIT cells,  biol rep2


title: OG2 mESC, LSD1-KO

source_name: OG2 mESC

value: OG2 mESC

value: mouse embryonic stem cells