title: Healthy_donor_01_T_cells, Gene expression (T43_GEX)

description: 10x Genomics

value: PBMC

value: Healthy control


title: Myeloma_patient_03_T_cells, T cell receptor (T4_TCR)

status: Public on Jul 29 2024

type: SRA

city: Seattle

first: Lawrence

last: Fong

state: Washington

address: 1100 Fairview Ave N

department: Immunotherapy Integrated Research Center, Translational Science and Therapeutics Division

country: USA

institute: Fred Hutch Cancer Center

description: 10x Genomics

library_source: transcriptomic

data_processing:
All sequencing was performed on an Illumina NovaSeq S4 sequencer with paired end 200 base pair read length and 25,000 reads per droplet for gene expression and 5,000 reads for TCR libraries.
CellRanger version 5 (10x Genomics, Genome Build: GRCh38 3.0.0) was used to align the raw sequencing data.
Doublet detection scoring was performed on the filtered gene expression matrices from Cell Ranger using DoubletDetection with default parameters, and then the combined gene expression matrix were analyzed by Scanpy pipeline. The following filters were set to retain high-quality cells: 1) cells with less than 10% mitochondrial transcripts, 2) number of detected genes per cell was above 100 but below 2,500 genes, 3) genes expressed in at least 3 cells were kept, 4) platelets (PF4 UMI>0), red blood cells (HBB UMI>1), and doublets were removed. We then used scanpy to normalize, logarithmize, and scale the data, identify highly variable genes, and perform principal component analysis. We used Combat and Harmony for batch correction prior to Leiden clustering and UMAP visualization
Assembly: GRCh38 3.0.0
Supplementary files format and content: 10x Genomics cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz; VDJ cellranger output: comma separated values files
Library strategy: scTCR-seq

molecule: polyA RNA

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
Bone marrow aspirates were diluted 1:1 in FACS buffer (PBS without magnesium or calcium, with 0.1% BSA and 2 mM EDTA). Peripheral blood samples were diluted 1:2 in FACS buffer. Mononuclear cell separation was performed by density centrifugation (Ficollpauqe, GE) with diluted bone marrow cells. Cells were manually aspirated and washed with FACS buffer. Red blood cells were lysed using RBC lysis buffer (Invitrogen) for 5 min at 4C. Within 1 hour of processing, cells were stained and sorted (Aria Fusion, BD) based on forward and side scatter, gated on CD45+ CD19- CD3+ (T cells) and CD45+ CD19- CD3- (nonB nonT cells).
Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x 5ʹ Reagent Kits version 1, according to manufacturer instructions. 10X 5’ kits for TCR amplification were used to generate libraries per manufacturer instructions.

tag: individual

tag: cell subtype

value: T cells

tag: cell type

value: Immune and tumor cells

tag: tissue

value: Bone Marrow

tag: timepoint

value: 270d post treatment

tag: library type

value: VDJ


title: 62y bone marrow scRNA-seq (GR94)

city: Cambridge

first: Hojun

last: Li

state: MA

address: 500 Main St

department: David H. Koch Institute for Integrative Cancer Research

institute: Massachusetts Institute of Technology

data_processing:
inDrop Pipeline:
Count normalization - Default parameters:  Seurat v3.0 NormalizeData function, normalization to 10^4 counts per cell, along with log transformation on each sample individually (default parameters).
Find variable features - Default parameters:  Seurat v3.0 FindVariableGenes function, vst method based on top 2000 features (default parameters).
Sample integration - Default parameters:  Seurat v3.0 IntegrateData function using 2000 anchors and 30 dimensions.
Filtering - Default parameters:  Iterative visualizations and plotting of QC metrics led to the exclusion of cells with low transcript and high mitochondrial content, as well as cells displaying endothelial and liver markers.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed count matrix, compressed MM and TXTs - Sparse matrix with normalized counts, feature names and cell identifiers in compressed TXTs
Supplementary_files_format_and_content: Cell metadata, compressed CSV -  Contains cell identifiers, sample of origin, cluster assignments, and cluster labels for all cells retained for downstream analysis.

molecule: total RNA

source_name: 62y bone marrow

growth_protocol: N/A, cells analyzed without being cultured

extract_protocol:
Cryopreserved bone marrow CD34-enriched cells were thawed and FACS-sorted for CD34+ cells. Sorted CD34+ cells were submitted for scRNA-seq analysis.
InDrop
InDrop protocol
InDrop scRNA-seq library prep (Illumina NextSeq500)

treatment_protocol: N/A, cells were not treated prior to analysis

value: 62y bone marrow

value: CD34+ Cells


title: Myeloma_patient_03_T_cells, Surface protein (T4_CSFL)

description:
10x Genomics
T4_barcodes.tsv.gz, T4_features.tsv.gz, T4_matrix.mtx.gz

library_source: other

data_processing:
All sequencing was performed on an Illumina NovaSeq S4 sequencer with paired end 200 base pair read length and 25,000 reads per droplet for gene expression and 5,000 reads for TCR libraries.
CellRanger version 5 (10x Genomics, Genome Build: GRCh38 3.0.0) was used to align the raw sequencing data.
Doublet detection scoring was performed on the filtered gene expression matrices from Cell Ranger using DoubletDetection with default parameters, and then the combined gene expression matrix were analyzed by Scanpy pipeline. The following filters were set to retain high-quality cells: 1) cells with less than 10% mitochondrial transcripts, 2) number of detected genes per cell was above 100 but below 2,500 genes, 3) genes expressed in at least 3 cells were kept, 4) platelets (PF4 UMI>0), red blood cells (HBB UMI>1), and doublets were removed. We then used scanpy to normalize, logarithmize, and scale the data, identify highly variable genes, and perform principal component analysis. We used Combat and Harmony for batch correction prior to Leiden clustering and UMAP visualization
Assembly: GRCh38 3.0.0
Supplementary files format and content: 10x Genomics cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz; VDJ cellranger output: comma separated values files

molecule: protein

value: Antibody-derived oligonucleotide (ADT)


title: HT29_BatchA_Vehicle(DMSO)_rep1

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description: sample HT29-A1-1-1

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: Human colorectal adenocarcinoma cell line, HT29 (HTB-38) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). HT29 cells were maintained in DMEM medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 5% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.Human astrocytoma cell line, SW1783 (HTB-13) was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). SW1783 cells were maintained in Leibovitz’s L-15 medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, without CO2 incubator. The cells were subcultured every 3 or 4 days, depending on the cell density.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: Dulbecco’s modified Eagle medium (DMEM), phosphate-buffered saline (PBS), TrypLE Express, penicillin–streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Leibovitz’s L-15 medium was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). The cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO) and wortmannin were purchased from Sigma-Aldrich (St. Louis, MO, USA), and QIAzol Lysis Reagent was purchased from Qiagen (Germany). The EZ-Cytox Cell Viability Assay Kit was purchased from DoGen Bio (Seoul, Republic of Korea). Dried ACD was supplied by Kwangmyungdang Medicinal Herbs Co. (Ulsan, Re-public of Korea) and its morphology was carefully validated by Dr. Goya Choi from the Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM), Republic of Korea. A voucher specimen (2-23-0011) was deposited in the Ko-rean Herbarium of Standard Herbal Resources of KIOM (Naju, Republic of Korea). The crushed material was extracted at 100 ± 3 °C for 3 h using a water reflux system (MS-DM609, Misung Scientific, Yangu, Republic of Korea) and filtered through a 5 µm cartridge filter (KOC Biotech, Daejeon, Republic of Korea). The filtrates were concen-trated at 40 °C using a rotary evaporator (Ev-1020t, SciLab, Seoul, Republic of Korea) and freeze-dried (LP20, ilShin Biobase, Dongducheon, Republic of Korea). The yield of water extract of ACD was 25.4%, and the final extracts were homogenized and stored in an airtight container in a cold room at 4 °C. For the in vitro investigation, homoge-nous ACD extract was vigorously vortexed for 30 min at room temperature in PBS (Thermo Fisher Scientific) containing 2% DMSO and then sterilized by filtering through a 0.22-µm membrane. The stock solution of ACD extracts (10 mg/mL) was al-iquoted in a 1.5 mL tube and stored at −80 °C until use.

tag: cell line

tag: treatment

value: 0.1% DMSO

tag: time


title: UNK 100vertRBNS, 100nM, rep1

city: Chapel Hill

first: Daniel

last: Dominguez

state: NC

address: 120 Mason farm

department: Pharmacology

institute: UNC Chapel Hill

data_processing:
Reads were trimmed using fastx_toolkit before mapping with STAR to generate counts
Counts were normalized for library size
Enrichments were calculated as the frequency of an oligo in the protein bound sample divided by the frequency in the input pool
Assembly: Custom genome (see supplementary files)
Supplementary files format and content: tab-delimited text file includes enrichment values for each sample

organism:
Pan troglodytes
Homo sapiens

source_name: in vitro large scale binding experiment

extract_protocol:
Bound RNA was eluted from streptavidin magnetic beads in 4 mM biotin (nsRBNS) or 0.1% SDS with 0.3 mg/mL proteinase K (100vertRBNS). RNA was concentrated via phenol-chloroform extraction
RNA libraries for sequencing were reverse transcribed with SuperScript IV following manufacturer's protocols, PCR amplified with Phusion DNA polymerase to attach Illumina TrueSeq Small RNA adapters, then agarose gel purified

value: UNK 100vertRBNS


title: 62y bone marrow scRNA-seq (GR91)


title: ForebrainOrganoid_WildType_Rep2

city: Ann Arbor

first: Charles

middle: William

last: Ryan

state: Michigan

address: 1241 Catherine St, 4909 Buhl Building

department: Human Genetics

institute: University of Michigan

description:
Illumina NextSeq 75 cycle instrument
Sequencing performed by University of Michigan Advanced Genomics Core

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to hg38 and processed to single cell gene expression matrices using the Drop-seq_tools-1.13 pipeline.
Assembly: hg38
Supplementary files format and content: Single cell reads per gene matrix output

source_name: Neural progenitor cell monolayer

growth_protocol: Dual SMAD inhibition neural differentiation protocol. After day 14, , maintained in N2/B27/FGF growth media at 37C 5%CO2 shaking in suspension at 95 rpm.

extract_protocol:
SEQWell Protocol
Prepped libraries with Nextera XT kit (illumina) and sequenced on  Illumina NextSeq 75 cycle instrument

treatment_protocol: CRISPR-cas9 genome editing was used to generate a RING1/RNF2 allelic series. Otherwise, organoids were cultivated to dat 42 of differentiation as described in the associated manuscript

value: Neural progenitor cell monolayer

value: H9 Human Embryonic Stem Cel (WiCell Lot#WB0090)

value: Forebrain organoid at day 42 of differentiation

tag: genotype

value: wild type

value: Normal growth conditions


title: 53y bone marrow scRNA-seq (Samp26)

source_name: 53y bone marrow

value: 53y bone marrow


title: hMDM_Ifn_B_Donor06_S24

type: RNA

city: Dublin

first: Gina

middle: R

last: Leisching

address: St James's Hospital

department: Clinical Medicine

country: Ireland

institute: Trinity College Dublin

data_processing: All data were analyzed using nSolver 4.0. Background was subtracted from negative controls and samples were normalized to the positive controls and housekeeping genes. Data were further analyzed by normalized count and fold difference, and differences were compared between the subtypes. Data visualisation was performed in Rstudio (R version 4.3.3) using packages EnhancedVolcano (version 1.10.0), ggplot2 (version 3.4.0), ggrepel(version 0.9.2), and pheatmap (version 1.0.12).

source_name: Human monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from the buffy coats of healthy donors, obtained with consent from the Irish Blood Transfusion Services, by density-gradient centrifugation over Lymphoprep (StemCell Technologies). Cells were washed, resuspended at 2.5x106 PBMC/ml in RPMI (Gibco) supplemented with 10% AB human serum (Sigma90 Aldrich), and plated onto non-treated tissue culture plates (Costar). Cells were maintained in humidified incubators for 7 days at 37°C and 5% CO2. Non-adherent cells were removed by washing every 2-3 days. The purities of MDM were assessed by flow cytometry and were routinely > 90% pure.

extract_protocol: On day 5 of CT1E, RNA from each treatment group was extracted using the RNeasy® Plus Mini Kit (Cat. No. 74134, Qiagen, Limburg, Netherlands) according to the manufacturer’s instructions. The ‘gDNA eliminator’ column included in this kit removed genomic DNA in all  107 samples. For each experiment, RNA quality and quantity was assessed and only RNA with a RNA integrity Number (RIN) above 9.0 was used for Nanostring analysis. The NanoString nCounter Human Metabolic Pathways Panel (Cat # XT-CSO-HMP1-12, N = 6 per IFN sub110 type), which detects transcripts of 768 metabolic genes.

treatment_protocol: Human IFNβ (IF014, Merck, KGaA, Darmstadt), IFNα2a (11100-1, PBL assay science, NJ, USA), and IFN IFNα2b (11105-1, PBL assay science, NJ, USA) concentrations were determined through a dose response curve, where expression of ISG15 was used as a marker for activation of the type I IFN pathway (Supplementary figure 1). As described previously (Buang, N. et al., Nature Comms, 1980), IFN α2a, α2b, and β were added at a concentration of 1000U/ml for 5 days before analysis. This concentration of IFNs increased ISG expression to the same degree seen in IFN-High SLE patients and was therefore used in all subsequent experiments. No evidence of cell death was detected after the 5-day period (Supplementary figure 1).

value: IFN beta, 1000U/ml for 5 days

tag: condition

value: Healthy


title: Myeloma_patient_02_T_cells, T cell receptor (T3_TCR)

description: 10x Genomics

value: T cells

value: Immune and tumor cells

value: 180d post treatment


title: hMDM_Ifn_B_Donor05_S23


title: 45y bone marrow scRNA-seq (Samp25)

source_name: 45y bone marrow

value: 45y bone marrow


title: HT29_BatchA_Vehicle(DMSO)_rep2

description: sample HT29-A1-2-1


title: Myeloma_patient_02_T_cells, Surface protein (T3_CSFL)

description:
10x Genomics
T3_barcodes.tsv.gz, T3_features.tsv.gz, T3_matrix.mtx.gz

value: Bone Marrow


title: hMDM_Ifn_B_Donor04_S22


title: Myeloma_patient_02_T_cells, Gene expression (T3_GEX)

value: Gene expression


title: hMDM_Ifn_B_Donor03_S21


title: 32y bone marrow scRNA-seq (BM2)

source_name: 32y bone marrow

value: 32y bone marrow

value: CD34+ Cells


title: Myeloma_patient_01_T_cells, T cell receptor (T2_TCR)

description: 10x Genomics

source_name: PBMC

value: PBMC

value: Baseline

value: VDJ


title: hMDM_Ifn_B_Donor02_S20


title: Myeloma_patient_01_T_cells, Gene expression (T2_GEX)

description: 10x Genomics


title: 25y bone marrow scRNA-seq (BM3)

source_name: 25y bone marrow

value: 25y bone marrow


title: Myeloma_patient_01_T_cells, T cell receptor (T1_TCR)

description: 10x Genomics


title: 25y bone marrow scRNA-seq (BM1)


title: hMDM_Ifn_B_Donor01_S19


title: Myeloma_patient_03_T_cells, Gene expression (T4_GEX)

value: 270d post treatment


title: hMDM_Ifn_A2B_Donor06_S18

value: IFN alpha2b, 1000U/ml for 5 days


title: hMDM_Ifn_A2B_Donor05_S17


title: 5555-mEGFP_PLX [B5]

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description:
replicate 2
B5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was transformed using variance-stabilizing transformation before quantile normalisation using the lumi package in R.

label: biotin

organism: Mus musculus

source_name: 5555 melanoma cell line

label_protocol: Standard Illumina biotin labelling protocol

growth_protocol: Melanoma cells were maintained in DMEM (Invitrogen) with 10% fetal bovine serum/1% PenStrep (GIBCO).

extract_protocol: RNA was extracted using a Qiagen RNA extraction kit. The RNA was amplified using an Ambion Illumina TotalPrep RNA Amplification Kit.

treatment_protocol: MAF2-mCherry and 5555-mEGFP co-cultures were treated with DMSO (0.1%) or PLX4720 (1 mM) for 24 hours. mEGFP-positive fraction (5555-mEGFP) were FACS-sorted.

tag: tag


title: Mixed_5555-mEGFP_PLX [B7]

description:
replicate 2
B7


title: Mixed_5555-mEGFP_PLX [A7]

description:
replicate 1
A7


title: 35y bone marrow scRNA-seq (Samp24)

source_name: 35y bone marrow

value: 35y bone marrow


title: 17y bone marrow scRNA-seq (GR90)

source_name: 17y bone marrow

value: 17y bone marrow


title: 12y bone marrow scRNA-seq (Samp43)

source_name: 12y bone marrow

value: 12y bone marrow


title: JC73-RK100 I-BET-762 + RK-582 3 µM (2)

city: Tokyo

first: Shun

last: Morino

address: 3-8-31, Ariake, Koto-ku

country: Japan

institute: JFCR

description:
raw_count_JC73RK100_BET.csv
CPM_JC73RK100_BET.csv

data_processing:
Raw FASTQ file were checked quality using FastQC (version 0.11.9) and removed adapters using Trimmomatic (version 0.39).
The reads were aligned to hg38 using STAR (version 2.7.9a).
Gene expression was quantified using FeatureCounts of Subread package (version 2.0.1).
Filtering low expression genes and normalization were performed using edgeR.
To exclude contaminated RNA such as rRNA, we extracted and analyzed protein coding genes. Expression of each RNA was transformed to CPM.
Assembly: hg38
Supplementary files format and content: csv file include raw counts for each sample.
Supplementary files format and content: csv file includes CPM values for each sample after protein coding gene extraction.

growth_protocol: JC73 and JC73-RK100 cells were maintained in StemProTM hESC SFM supplemented with 10 µM Y-27632 and Antibiotic-Antimycotic Solution in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
(1) JC73 and JC73-RK100 cells were treated with 0, 30 nM, 3 µM tankyrase inhibitor RK-582 for 120h, and (2) JC73-RK100 cells were treated with 0, 30 nM, 3 µM  RK-582 with or without 10 µM BET inhibitor I-BET-762 for 120 h. RNA was extracted using FastGene RNA Basic Kit (Nippon Genetics Co., Ltd, Tokyo, Japan) according to the manufacturer’s instructions.
Sequence libraries were constructed with TruSeq stranded mRNA library preparation kit(Illumina) according to the manufacture's instructions.

treatment_protocol: (1) JC73 and JC73-RK100 cells were treated with the indicated concentration of tankyrase inhibitor RK-582 for 120h, and (2) JC73-RK100 cells were treated with the indicated concentration of RK-582 with or without BET inhibitor I-BET-762 for 120 h.

value: colorectal cancer patient-derived cells

value: Combination of 10 µM I-BET-762 and 3 µM RK-582 for 120 h


title: Tomato root, galls, Day21, RNA_rep 3

city: Knoxville

first: Tarek

last: Hewezi

state: TN

address: 2431 Joe Johnson Drive

department: Plant Sciences

institute: University of Tennessee

data_processing:
Quality assessment was performed on fastq raw data files using FASTQC.
Paired-end RNA-seq reads were mapped to the  Solanum lycopersicum reference genome (SL4.0) with STAR (v2.7.9a)
Uniquely mapped paired-end reads were counted using Htseq (v0.13.5).
Assembly: Solanum lycopersicum  Heinz1706 assembly 4.0
Supplementary files format and content: Read count text files were generated using Htseq.

organism: Solanum lycopersicum

source_name: Root

growth_protocol: The susceptible tomato Heinz1706 seeds were germinated in top soil and grown at 26°C under long day conditions.

extract_protocol:
Root tissues of 14-day-old (non-infected) and 4 dpi (M. incognita infected) plants were collected and frozen immediately in liquid nitrogen. Total RNA was extracted using Direct-zol TM RNA Miniprep Plus (R2070S). Same protocol was repeated for 11 dpi infected and non-infected replicates.
For the construction of a stranded and ribosomal depleted library, mature mRNAs were processed and captured using oligo(dT) beads following the addition of a 3' poly(A) tail.

treatment_protocol: Replicates of each plant were inoculated with 1000 freshly-hatched J2 M. incognita at 10 days old. Inoculated replicates were grown in light conditions as previously described until 5 and 11 days post inoculation (dpi).

value: Root

value: Galls

value: Heinz1706 susceptible

value: inoculated with 1000 J2 M. incognita per plant at 10 days old

tag: developmental stage

value: 11 days post inoculation


title: 5555-mEGFP_DMSO [B1]

description:
replicate 2
B1

value: DMSO


title: 5555-mEGFP_PLX [A5]

description:
replicate 1
A5


title: hMDM_Ifn_A2B_Donor04_S16

value: Healthy


title: Mixed_5555-mEGFP_DMSO [B3]

description:
replicate 2
B3


title: Mixed_5555-mEGFP_DMSO [A3]

description:
replicate 1
A3


title: Tomato root, galls, Day21, RNA_rep 2


title: JC73-RK100 I-BET-762 + RK-582 30 nM (2)

value: Combination of 10 µM I-BET-762 and 30 nM RK-582 for 120 h


title: Tomato root, galls, Day21, RNA_rep 1


title: 5555-mEGFP_DMSO [A1]

description:
replicate 1
A1


title: 4y bone marrow scRNA-seq (Samp44)

source_name: 4y bone marrow

value: 4y bone marrow

value: CD34+ Cells


title: 2y bone marrow scRNA-seq (GR95)

source_name: 2y bone marrow

value: 2y bone marrow


title: JC73-RK100 I-BET-762 (2)

value: 10 µM I-BET-762 for 120 h


title: hMDM_Ifn_A2B_Donor02_S14

value: IFN alpha2b, 1000U/ml for 5 days


title: JC73-RK100 RK-582 3 µM (2)

value: 3 µM RK-582 for 120 h


title: Cord blood scRNA-seq (CB2)

source_name: Cord blood

extract_protocol:
Cryopreserved cord blood CD34-enriched cells were thawed and FACS-sorted for CD34+ cells. Sorted CD34+ cells were submitted for scRNA-seq analysis.
InDrop
InDrop protocol
InDrop scRNA-seq library prep (Illumina NextSeq500)

value: Cord blood


title: Tomato root, neighboring region, Day21, RNA_rep 2

value: Neighboring Region


title: hMDM_Ifn_A2B_Donor01_S13


title: Myeloma_patient_01_T_cells, Gene expression (T1_GEX)

description: 10x Genomics

source_name: Bone Marrow

value: T cells

value: Immune and tumor cells

value: Bone Marrow

value: Baseline

value: Gene expression


title: JC73-RK100 RK-582 30 nM (2)

value: colorectal cancer patient-derived cells


title: Tomato root, neighboring region, Day21, RNA_rep 1

value: Root

value: Heinz1706 susceptible

value: inoculated with 1000 J2 M. incognita per plant at 10 days old

value: 11 days post inoculation


title: Cord blood scRNA-seq (CB1)

value: CD34+ Cells


title: JC73-RK100 DMSO (2)

value: DMSO for 120 h


title: hMDM_Ifn_A2A_Donor06_S12

value: IFN alpha2a, 1000U/ml for 5 days

value: Healthy


title: Tomato root, non-infected whole root, Day21, RNA_rep 3

value: Whole Root

value: non-infected

value: 21 days old


title: 23w fetal liver scRNA-seq (GR74)

source_name: 23w fetal liver

extract_protocol:
Cryopreserved fetal liver CD34-enriched cells were thawed and FACS-sorted for CD34+ cells. Sorted CD34+ cells were submitted for scRNA-seq analysis.
InDrop
InDrop protocol
InDrop scRNA-seq library prep (Illumina NextSeq500)

value: 23w fetal liver


title: hMDM_Ifn_A2B_Donor03_S15

value: IFN alpha2b, 1000U/ml for 5 days


title: 10y bone marrow scRNA-seq (GR96)

source_name: 10y bone marrow

value: 10y bone marrow


title: JC73-RK100 RK-582 3 µM (1)

description:
raw_count_JC73andJC73_RK100.csv
CPM_JC73andJC73_RK100.csv

value: 3 µM RK-582 for 120 h


title: 23w fetal liver scRNA-seq (GR73)


title: Tomato root, non-infected whole root, Day21, RNA_rep 2


title: JC73-RK100 RK-582 30 nM (1)


title: hMDM_Ifn_A2A_Donor04_S10


title: Tomato root, non-infected whole root, Day21, RNA_rep 1


title: Tomato root, neighboring region, Day21, RNA_rep 3

value: Neighboring Region


title: hMDM_Ifn_A2A_Donor02_S08


title: JC73 RK-582 3 µM (1)

value: colorectal cancer patient-derived cells


title: Tomato root, galls, Day14, RNA_rep 3

value: Root

value: Galls

value: 4 days post inoculation


title: hMDM_Ifn_A2A_Donor03_S09


title: Tomato root, galls, Day14, RNA_rep 2

value: Heinz1706 susceptible

value: inoculated with 1000 J2 M. incognita per plant at 10 days old


title: 20w fetal liver scRNA-seq (Samp42)

source_name: 20w fetal liver

value: 20w fetal liver

value: CD34+ Cells


title: 15w fetal liver scRNA-seq (Samp41)

source_name: 15w fetal liver

value: 15w fetal liver


title: 22w fetal liver scRNA-seq (GR72)

source_name: 22w fetal liver

value: 22w fetal liver


title: hMDM_Ifn_A2A_Donor01_S07

source_name: Human monocyte-derived macrophages

value: IFN alpha2a, 1000U/ml for 5 days

value: Healthy


title: hMDM_control_Donor06_S06

value: Untreated


title: JC73 RK-582 30 nM (1)


title: JC73-RK100 DMSO (1)

value: DMSO for 120 h


title: 14w fetal liver scRNA-seq (Samp23)

source_name: 14w fetal liver

value: 14w fetal liver


title: Tomato root, galls, Day14, RNA_rep 1


title: JC73 DMSO (1)


title: hMDM_Ifn_A2A_Donor05_S11


title: Tomato root, neighboring region, Day14, RNA_rep 3


title: JC21 RK-582 3 µM H3K27ac

library_source: genomic

data_processing:
Raw FASTQ file were checked quality using FastQC (version 0.11.9) and removed adapters using Trimmomatic (version 0.39).
The reads were aligned to hg38 and sacCer3 using STAR (version 2.7.9a).
Normalization using spike-in yeast DNA were performed by bedtools genomecov function.
Peak calling was performed using SEACR (version 1.3) with stringent mode.
Normalized CUT&RUN data was converted to bigwig file format using ucsc-bedgraphtobigwig (version 445).
Assembly: hg38
Supplementary files format and content: Bigwig files
Library strategy: CUT&RUN

molecule: genomic DNA

growth_protocol: JC73, JC73-RK100 and JC21 cells were maintained in StemProTM hESC SFM supplemented with 10 µM Y-27632 and Antibiotic-Antimycotic Solution in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
JC73, JC73-RK100 and JC21 cells were treated with 0, 30 nM, 3 µM tankyrase inhibitor RK-582 for 120h. CUT&RUN was performed using CUT&RUN Assay Kit (Cell Signaling Technology) according to the manufacturer’s instructions.
Sequence libraries were constructed with NEBNest UltraⅡ DNA library Prep Kit for Illumina (New England Biolabs, Inc.) according to the manufacture's instructions.

treatment_protocol: JC73, JC73-RK100 and JC21 cells were treated with the indicated concentration of tankyrase inhibitor RK-582 for 120h.

tag: cut&run antibody

value: H3K27ac (#8173, Cell Signaling Technology)

value: 3 µM RK-582 for 120 h


title: 11w fetal liver scRNA-seq (GR97)

source_name: 11w fetal liver

value: 11w fetal liver


title: 13w fetal liver scRNA-seq (Samp22)

source_name: 13w fetal liver

value: 13w fetal liver


title: Tomato root, neighboring region, Day14, RNA_rep 2

value: Root

value: Neighboring Region


title: JC21 RK-582 30 nM H3K27ac

value: colorectal cancer patient-derived cells


title: hMDM_control_Donor05_S05


title: hMDM_control_Donor04_S04


title: Tomato root, neighboring region, Day14, RNA_rep 1

value: Heinz1706 susceptible

value: inoculated with 1000 J2 M. incognita per plant at 10 days old

value: 4 days post inoculation


title: hMDM_control_Donor03_S03


title: 10w fetal liver scRNA-seq (Samp21)

source_name: 10w fetal liver

value: 10w fetal liver

value: CD34+ Cells


title: hMDM_control_Donor02_S02


title: JC21 DMSO H3K27ac


title: Tomato root, non-infected whole root, Day14, RNA_rep 3

value: Whole Root

value: non-infected

value: 14 days old


title: hMDM_control_Donor01_S01

value: Untreated

value: Healthy


title: Tomato root, non-infected whole root, Day14, RNA_rep 2


title: leaf potassium starvation day6d

city: Valencia

first: Eduardo

last: Bueso

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: IBMCP

country: Spain

institute: Universitat Politècnica de València

data_processing:
Read quality analysis with FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read quality trimming and adaptor removal using cutadapt v.4.1 (http://dx.doi.org/10.14806/ej.17.1.200)
Clean mapping to reference genome with STAR 2.7.10a (https://doi.org/10.1093/bioinformatics/bts635)
Differential gene expression using DESeq2 (https://doi.org/10.1186/s13059-014-0550-8)
Assembly: Brassica oleracea reference genome EnsemblPlants release 54
Supplementary files format and content: tab-delimited text file including gene TPMs for each sample

organism: Brassica oleracea var. italica

source_name: leaf

growth_protocol: Broccoli seeds were sown on MS plates for 6 days. Seedlings were transferred to hydroponic culture in a medium with 2 mM K2SO4 for 7 days in long day conditions (16 h light/8 h darkness).

extract_protocol:
Rneasy Plant Mini Kit (Qiagen, Germantown, MD, USA) following the manufacturer’s instructions and treated to remove the remaining genomic DNA with the Rnase-Free Dnase Set (Qiagen, USA).
DNBseq™ eukaryotic transcriptome resequencing

treatment_protocol: Half of the plants were transferred to potassium-free medium and samples were collected at days 1, 3 and 6.

value: leaf

tag: time point

value: day 6

value: WT

value: potassium starvation


title: leaf potassium starvation day6c


title: Tomato root, non-infected whole root, Day14, RNA_rep 1

value: Root


title: leaf potassium starvation day6b


title: JC21 DMSO BRD4

value: BRD4 (#13440, Cell Signaling Technology)

value: DMSO for 120 h


title: PBMCs, conA-treated, 24 h, biol. rep. 6

city: Berlin

first: Filip

last: Larsberg

address: Unter den Linden 6

department: Crop and Animal Sciences

country: Germany

institute: Humboldt-Universität zu Berlin

data_processing:
Demultiplexing of sequencing reads of different samples was performed with Illumina bcl2fastq (version 2.20).
Adaptors were trimmed with Skewer (version 0.2.2).
Trimmed raw reads were aligned to GRCg6a (GCA_000002315.5) using STAR (version 2.7.3).
The quality of the FASTQ files was analyzed with FastQC (version 0.11.5).
Differential gene expression between treatment and control groups was analyzed using DESeq2 (version 1.24.0) in R (version 3.6.1).
Assembly: GRCg6a (GCA_000002315.5)
Supplementary files format and content: tab-separated value (tsv) file includes raw counts for each Sample
Supplementary files format and content: tab-separated value (tsv) file includes normalized counts for each Sample

organism: Gallus gallus

source_name: Blood

growth_protocol: All experiments were performed in RPMI 1640 medium containing 10% chicken serum without Pen/Strep at 41°C with 5% CO2.

extract_protocol:
Total RNA was isolated from PBMCs from six different chickens (biological replicates) of pooled experimental (technical) duplicates from each chicken after treatment with either BS, BV or conA or untreated samples (medium) according to the manufacturer’s total RNA isolation protocol (NucleoSpin RNA Plus XS, Macherey & Nagel)
Libraries were prepared from 10 ng of total RNA using the SMARTSeq Stranded Kit (Takara Bio Inc.)

treatment_protocol: Co-culture experiments were conducted using probiotic bacterial strains and 1x10^6 PBMCs with either BS or BV in a ratio of 1:3 (PBMC: Bacillus) in 24- well plates for 24 h. ConA (10 µg/mL) was used as a positive control.

value: Blood

value: PBMC

value: conA

tag: treatment (condition)

value: 10 µg/mL


title: PBMCs, conA-treated, 24 h, biol. rep. 5


title: DG24

city: Lund

first: Henrik

last: Ahlenius

address: Sölvegatan 19

department: Department of Experimental Medical Science

country: Sweden

institute: Lund University

description: 10x Genomics

data_processing:
Raw data from single cell RNA sequencing were run through the Cell Ranger pipeline to generate count matrices
Assembly: mm10
Supplementary files format and content: Tab-separeted values files and matrix files

source_name: Dentate gyrus

extract_protocol:
Tissue from 4-5 mice were pooled in ice-cold L-15 medium, for each region respectively, and dissociated into a single cell suspension using the adult brain dissociation kit, mouse and rat (Miltenyi Biotech, 130-107-677) following manufacturer's guidelines. Cells were then purified through a two-step gradient and resuspended in FACS medium (4% BSA (W/V), 2% 2M HEPES (V/V) & 0.1% sodium azide (V/V) in HBSS). To enrich for neural progenitors, dissociated cells from Dcx-GFP mice were separated with fluorescence-activated cell sorting (FACS) (supplementary figure 1a) based on endogenous GFP using a FACSARIAII/III (BD Biosciences) and collected into PBS with 2% FBS
libraries were generated from FACS sorted cells expressing endogenous GFP (Dcx-GFP) for each experimental group separately using a Chromium system (10x genomics) according to manufacturer’s guidelines (Single Cell 3’ Reagent Kits v2 User Guide (CG00052)) with 12-13 cDNA amplification cycles and 14 sample index cycles.

value: Dentate gyrus

tag: strain

value: Dcx-GFP

value: GFP+

value: Heterozygote

tag: age

value: 24 months


title: JC21 RK-582 30 nM BRD3

value: BRD3 (#61489, Active motif)

value: colorectal cancer patient-derived cells


title: JC21 RK-582 3 µM BRD3

value: 3 µM RK-582 for 120 h


title: leaf potassium starvation day6a

value: leaf

value: day 6

value: WT


title: leaf control day6d

value: control


title: PBMCs, conA-treated, 24 h, biol. rep. 4


title: DG14

description: 10x Genomics

value: 14 months


title: JC21 RK-582 3 µM Input


title: JC21 RK-582 3 µM BRD4

value: BRD4 (#13440, Cell Signaling Technology)


title: PBMCs, conA-treated, 24 h, biol. rep. 3

value: Blood

value: PBMC


title: leaf control day6b


title: JC21 DMSO BRD3

value: DMSO for 120 h


title: DG3

description: 10x Genomics

value: Dentate gyrus

value: 3 months


title: PBMCs, conA-treated, 24 h, biol. rep. 2

value: conA

value: 10 µg/mL


title: Saline_ZT14

city: 福岡市

first: Yuya

last: Yoshida

state: 福岡県

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

institute: Kyushu-university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: saline injected at ZT14

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using ReliaPrep TM  RNA Cell Miniprep System (Promega) according to the manufacturer's instructions.

treatment_protocol: The kidney was prepared from mice at 1 day after injection.

value: icr

value: kidney


title: OB24

description: 10x Genomics

source_name: Olfactory bulb

value: Olfactory bulb

value: Dcx-GFP

value: GFP+

value: Heterozygote

value: 24 months


title: Saline_ZT2

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

source_name: saline injected at zeitgeber time (ZT) 2


title: JC21 RK-582 30 nM Input

value: colorectal cancer patient-derived cells


title: JC21 RK-582 30 nM BRD4


title: leaf control day6a

value: leaf

value: day 6

value: WT

value: control


title: VCM_ZT14

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

source_name: vancomycin-injected at ZT14


title: VCM_ZT2

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

source_name: vancomycin-injected at ZT2


title: PBMCs, conA-treated, 24 h, biol. rep. 1

value: Blood

value: PBMC


title: OB14

description: 10x Genomics

value: 14 months


title: leaf potassium starvation day3d

value: day 3

value: potassium starvation


title: PBMCs, BV-treated, 24 h, biol. rep. 6

value: BV

value: 1:3 (PBMCs:Bacillus)


title: JC21 DMSO Input

value: DMSO for 120 h


title: JC73-RK100 RK-582 3 µM H3K27ac

value: H3K27ac (#8173, Cell Signaling Technology)

value: 3 µM RK-582 for 120 h


title: leaf potassium starvation day3c


title: SVZ24

description: 10x Genomics

source_name: Subventricular zone

value: Subventricular zone

value: Dcx-GFP

value: GFP+

value: Heterozygote


title: leaf control day6c

value: leaf

value: day 6


title: OB3

description: 10x Genomics

value: Olfactory bulb

value: 3 months


title: JC73-RK100 RK-582 30 nM H3K27ac

value: colorectal cancer patient-derived cells


title: PBMCs, BV-treated, 24 h, biol. rep. 4

value: Blood

value: PBMC


title: PBMCs, BV-treated, 24 h, biol. rep. 5


title: leaf potassium starvation day3b

value: day 3

value: WT

value: potassium starvation


title: JC73-RK100 DMSO H3K27ac

value: DMSO for 120 h


title: leaf potassium starvation day3a


title: leaf control day3d

value: control


title: SVZ3

description: 10x Genomics


title: PBMCs, BV-treated, 24 h, biol. rep. 2

value: BV

value: 1:3 (PBMCs:Bacillus)


title: JC73-RK100 RK-582 3 µM BRD4

value: BRD4 (#13440, Cell Signaling Technology)

value: 3 µM RK-582 for 120 h


title: JC73-RK100 RK-582 30 nM BRD4


title: PBMCs, BV-treated, 24 h, biol. rep. 1


title: leaf control day3b


title: leaf control day3c


title: DG_O8

description: 10x Genomics

data_processing:
Read Mapping: alignment of reads to a specified reference genome. This task was performed using the HISAT2 software, and the reference genome sequence was from the Ensemble database, and the mouse assembly was GRCm38.
Expression counts: assembly of the alignments into full transcripts and quantification of the expression levels of each gene and transcript. This task was performed using the StringTie software.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw read counts of all genes and samples

extract_protocol:
Tissue from 4-5 mice were pooled in ice-cold L-15 medium, for each sample respectively, and dissociated into a single cell suspension using the adult brain dissociation kit, mouse and rat (Miltenyi Biotech, 130-107-677) following manufacturer's guidelines. Cells were then purified through a two-step gradient and resuspended in FACS medium (4% BSA (W/V), 2% 2M HEPES (V/V) & 0.1% sodium azide (V/V) in HBSS). To enrich for neural progenitors, dissociated cells from Dcx-GFP mice were separated with fluorescence-activated cell sorting (FACS) (supplementary figure 1a) based on endogenous GFP using a FACSARIAII/III (BD Biosciences) and collected into PBS with 2% FBS
libraries were generated from FACS sorted cells expressing endogenous GFP (Dcx-GFP) for 2ng of each sample separately using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio USA, Inc.) following manufacturers manual (063017) with 4min fragmentation time and 14 PCR cycles amplification of final library.

value: Dentate gyrus

value: Dcx-GFP

value: GFP+

value: Heterozygote

value: 24 months


title: PBMCs, BS-treated, 24 h, biol. rep. 6

value: BS


title: JC73-RK100 RK-582 3 µM BRD3

value: BRD3 (#61489, Active motif)

value: colorectal cancer patient-derived cells


title: DG_O7

description: 10x Genomics


title: PBMCs, BS-treated, 24 h, biol. rep. 5

value: Blood

value: PBMC


title: leaf control day3a

value: leaf

value: day 3

value: WT


title: DG_O5

description: 10x Genomics


title: JC73-RK100 RK-582 30 nM BRD3


title: leaf potassium starvation day1d

value: day 1

value: potassium starvation


title: PBMCs, BS-treated, 24 h, biol. rep. 3

value: 1:3 (PBMCs:Bacillus)


title: PBMCs, BS-treated, 24 h, biol. rep. 4


title: DG_M5

description: 10x Genomics

value: 14 months


title: SVZ14

description: 10x Genomics

value: Subventricular zone


title: PBMCs, BV-treated, 24 h, biol. rep. 3

value: BV


title: DG_M4

description: 10x Genomics

value: Dentate gyrus

value: Dcx-GFP

value: GFP+


title: leaf potassium starvation day1c


title: JC73-RK100 DMSO BRD3

value: DMSO for 120 h


title: PBMCs, BS-treated, 24 h, biol. rep. 2

value: BS


title: JC73-RK100 RK-582 3 µM Input

value: colorectal cancer patient-derived cells

value: 3 µM RK-582 for 120 h


title: DG_O9

description: 10x Genomics

value: Heterozygote

value: 24 months


title: JC73-RK100 RK-582 30 nM Input


title: leaf potassium starvation day1b

value: leaf


title: DG_M3

description: 10x Genomics


title: PBMCs, BS-treated, 24 h, biol. rep. 1

value: Blood

value: PBMC


title: leaf potassium starvation day1a

value: day 1

value: WT

value: potassium starvation


title: JC73-RK100 DMSO BRD4

value: BRD4 (#13440, Cell Signaling Technology)


title: DG_M2

description: 10x Genomics

value: 14 months


title: JC73-RK100 DMSO Input


title: PBMCs, Control, 24 h, biol. rep. 6

value: Control

value: medium


title: leaf control day1d

value: control


title: DG_Y5

description: 10x Genomics

value: Dentate gyrus

value: Dcx-GFP

value: GFP+

value: 3 months


title: JC73 RK-582 3 µM H3K27ac

value: H3K27ac (#8173, Cell Signaling Technology)

value: colorectal cancer patient-derived cells

value: 3 µM RK-582 for 120 h


title: DG_Y3

description: 10x Genomics

value: Heterozygote


title: JC73 RK-582 30 nM H3K27ac


title: PBMCs, Control, 24 h, biol. rep. 4

value: Blood

value: PBMC


title: leaf control day1c

value: leaf

value: day 1

value: WT


title: DG_Y1

description: 10x Genomics


title: PBMCs, Control, 24 h, biol. rep. 3


title: JC73 DMSO H3K27ac

value: DMSO for 120 h


title: JC73 RK-582 3 µM BRD4

value: BRD4 (#13440, Cell Signaling Technology)


title: root potassium starvation day6d

source_name: root

value: root

value: day 6

value: potassium starvation


title: PBMCs, Control, 24 h, biol. rep. 2

value: Control

value: medium


title: leaf control day1a

value: control


title: root potassium starvation day6c


title: JC73 RK-582 30 nM BRD4


title: PBMCs, Control, 24 h, biol. rep. 1


title: OB_O8

description: 10x Genomics

value: Olfactory bulb

value: Dcx-GFP

value: GFP+

value: 24 months


title: JC73 DMSO BRD4

value: colorectal cancer patient-derived cells


title: root potassium starvation day6b


title: JC73 RK-582 3 µM BRD3

value: BRD3 (#61489, Active motif)

value: 3 µM RK-582 for 120 h


title: root potassium starvation day6a


title: Crtc-RNAi (KK) 7

city: La Jolla

first: Georg

last: Vogler

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
RNA-Seq Alignment (BaseSpace Workflow) 1.1.0
Isis (Analysis Software) 2.6.25.18
STAR (Aligner) STAR_2.5.0b
Isaac Variant Caller 2.3.13-31-g3c98c29-dirty
BEDTools 2.17.0, Cufflinks 2.2.1, BLAST 2.2.26+
Assembly: dm3
Supplementary files format and content: tab-delimited text file with raw counts

organism: Drosophila melanogaster

source_name: heart

growth_protocol: Flies were were reared at 25°C on a standard laboratory diet consisting of yeast, corn starch, and molasses.

extract_protocol:
RNA was extracted from the hearts of either one-week old or three-week old female flies using the miRNAeasy Mini Kit (QIAGEN, Germantown, MD, USA) as per manufacturer’s protocol. Hearts from 15 female flies were dissected as described previously, removed with fine forceps and pooled as a single sample. RNA was extracted using the Qiagen RNAeasy mini kit (QIAGEN, Germantown, MD, USA).
Barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA)
Libraries were pooled and paired-end sequenced (2X75) on the Illumina NextSeq 500 using the High output V2.5 kit

value: heart

value: cardiac; primary cells

value: tinCdelta4 x Crtc RNAi

value: RNAi


title: Crtc-RNAi (KK) 6


title: OB_O2

description: 10x Genomics

value: Heterozygote


title: PBMCs, Control, 24 h, biol. rep. 5

value: Blood

value: PBMC


title: root control day6d

value: root

value: day 6

value: WT


title: JC73 RK-582 30 nM BRD3


title: leaf control day1b

value: leaf

value: day 1

value: control


title: Crtc-RNAi (KK) 5


title: DG_Y2

description: 10x Genomics

value: Dentate gyrus

value: Dcx-GFP

value: GFP+

value: 3 months


title: OB_M5

description: 10x Genomics

value: Olfactory bulb

value: 14 months


title: JC73 DMSO BRD3

value: BRD3 (#61489, Active motif)

value: colorectal cancer patient-derived cells

value: DMSO for 120 h


title: root control day6c


title: OB_O9

description: 10x Genomics

value: Heterozygote

value: 24 months


title: root control day6b

value: root


title: JC73 RK-582 3 µM Input

value: 3 µM RK-582 for 120 h


title: OB_M4

description: 10x Genomics


title: OB_O4

description: 10x Genomics


title: JC73 RK-582 30 nM Input


title: Crtc-RNAi (KK) 2

value: heart

value: cardiac; primary cells

value: tinCdelta4 x Crtc RNAi

value: RNAi


title: root control day6a

value: day 6

value: WT

value: control


title: Crtc-RNAi (KK) 3


title: root potassium starvation day3d

value: day 3

value: potassium starvation


title: OB_M2

description: 10x Genomics

value: Olfactory bulb

value: Dcx-GFP

value: GFP+

value: 14 months


title: JC73 DMSO Input

value: colorectal cancer patient-derived cells

value: DMSO for 120 h


title: OB_M1

description: 10x Genomics

value: Heterozygote


title: LN229, replicate 3, 24 hours

city: Zurich

first: Berend

last: Snijder

address: Otto-Stern-Weg 3, HPM building

country: Switzerland

institute: ETH Zurich

data_processing:
Reads were mapped to GRCh38.p13 using STAR/2.7.8a (parameters--sjdbOverhang 150 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 100000 --alignMatesGapMax 100000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --alignEndsProtrude 3 ConcordantPair)
Read count extraction was performed using FeatureCounts and normalization was performed using the R package DESeq2
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include DESeq2 vsd-normalized count values and raw counts for each sample

source_name: Brain; Right frontal parieto-occipital cortex

growth_protocol: LN-229 glioblastoma cells were maintained in DMEM supplemented with 2% fetal bovine serum (FBS), 1% Pen-strep, and 25mM HEPES in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Direct-zol MicroPrep kit (Zymo). 400ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Truseq stranded mRNA Library Prep Kit following manufacturers protocols.

treatment_protocol:
Low passage LN-229 cells were seeded at 2x10^5 cells/well into in 6-well multidishes and incubated overnight in culture media with 5% CO2 prior at 37C to drug treatment
The following day, Vortioxetine was manually added to each well at a final concentration of 20uM. At the start of the experiment, LN-229 cells that were not treated with Vortioxetine were collected as the 0 hour time point. After 3, 6, 9, 12, and 24 hours following Vortioxetine treatment, drug-containing media was removed and cells were collected in TRIzol™ Reagent.

value: Glioblastoma

value: Vortioxetine

value: 24 hours


title: RNAi control (KK) 7

value: heart

value: cardiac; primary cells

value: tinCdelta4 x KK control

value: RNAi control


title: OB_Y5

description: 10x Genomics

value: 3 months


title: LN229, replicate 2, 24 hours

value: Brain; Right frontal parieto-occipital cortex


title: root potassium starvation day3b

value: root

value: day 3

value: WT

value: potassium starvation


title: OB_Y3

description: 10x Genomics

value: Olfactory bulb

value: Dcx-GFP

value: GFP+


title: LN229, replicate 1, 24 hours


title: RNAi control (KK) 6


title: OB_Y2

description: 10x Genomics

value: Heterozygote


title: Crtc-RNAi (KK) 4

value: tinCdelta4 x Crtc RNAi

value: RNAi


title: OB_M3

description: 10x Genomics

value: 14 months


title: LN229, replicate 3, 12 hours

value: Glioblastoma

value: Vortioxetine

value: 12 hours


title: RNAi control (KK) 5

value: heart

value: cardiac; primary cells

value: tinCdelta4 x KK control

value: RNAi control


title: root control day3d

value: root

value: day 3

value: control


title: Crtc-RNAi (KK) 1


title: root control day3c

value: WT


title: RNAi control (KK) 4


title: LN229, replicate 2, 12 hours

value: Brain; Right frontal parieto-occipital cortex


title: OB_Y1

description: 10x Genomics

value: Olfactory bulb

value: Dcx-GFP

value: GFP+

value: 3 months


title: RNAi control (KK) 3


title: root control day3b


title: LN229, replicate 1, 12 hours


title: SVZ_O7

description: 10x Genomics

value: Subventricular zone

value: Heterozygote

value: 24 months


title: RNAi control (KK) 2


title: root control day3a


title: RNAi control (KK) 1


title: LN229, replicate 3, 9 hours

value: Glioblastoma

value: Vortioxetine

value: 9 hours


title: root potassium starvation day3c

value: potassium starvation


title: SVZ_M5

description: 10x Genomics

value: 14 months


title: LN229, replicate 2, 9 hours


title: root potassium starvation day3a

value: root


title: SVZ_Y5

description: 10x Genomics


title: LN229, replicate 1, 9 hours


title: root potassium starvation day1c

value: day 1


title: root potassium starvation day1d


title: Crtc knock-out 6

value: heart

value: cardiac; primary cells

value: Crtc[KO]

value: knock-out


title: Crtc knock-out 5


title: SVZ_O4

description: 10x Genomics

value: Dcx-GFP


title: root potassium starvation day1b

value: WT


title: Crtc knock-out 4


title: LN229, replicate 3, 6 hours

value: Brain; Right frontal parieto-occipital cortex

value: 6 hours


title: LN229, replicate 2, 6 hours


title: SVZ_O1

description: 10x Genomics

value: Subventricular zone

value: GFP+

value: Heterozygote


title: SVZ_O5

description: 10x Genomics

value: 24 months


title: LN229, replicate 1, 6 hours

value: Glioblastoma

value: Vortioxetine


title: Crtc knock-out 2


title: SVZ_M4

description: 10x Genomics

value: 14 months


title: root potassium starvation day1a

value: root

value: potassium starvation


title: LN229, replicate 3, 3 hours

value: 3 hours


title: Crtc knock-out 1

value: heart

value: cardiac; primary cells


title: SVZ_M3

description: 10x Genomics


title: root control day1c

value: day 1

value: control


title: background control 6


title: SVZ_O2

description: 10x Genomics

value: Dcx-GFP


title: LN229, replicate 1, 3 hours

value: Brain; Right frontal parieto-occipital cortex


title: LN229, replicate 2, 3 hours


title: Crtc knock-out 3

value: Crtc[KO]

value: knock-out


title: root control day1d

value: WT


title: root control day1a


title: background control 5


title: SVZ_M2

description: 10x Genomics

value: Subventricular zone

value: GFP+

value: Heterozygote


title: LN229, replicate 3, 0 hours

value: Glioblastoma

value: 0 hours


title: ssHi-C RE-deleted, DSB 2 hr

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

country: France

institute: ENS Lyon

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function with mapping quality set to 30 or 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
For ssHi-C, sparse matrices generated by hicstuff pipeline function were processed with the sshicstuff pipeline function to isolate fragments of interest
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz)
Supplementary files format and content: Hi-C and unfiltered ssHi-C contact data in cooler format, either per fragment (for ssHiC samples) or binned at 1kb (for HiC samples)
Supplementary files format and content: Unfiltered ssHi-C contact data in graal (sparse) format, per fragment
Supplementary files format and content: Tabulated ssHi-C contact data filtered with ssHiCstuff, binned at 1kb
Library strategy: ssHi-C

organism: Saccharomyces cerevisiae

source_name: RE-deleted, DSB 2 hr

growth_protocol: Cells were grown to exponential phase in YP-lactate media and synchronized in G1 with alpha-factor for 3 hours. Cells were washed 3 times in pre-warmed YP-lactate and released in S-phase in YP-lactate supplemented with 2% galactose. For Scc1-AID depletion experiment, 2 mM IAA were added at the time of release. For Pol3/Rfc1-AID depletion, 50 ug/mL doxycycline and  2 mM IAA were added 1 hour post-release.

extract_protocol:
Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm.
Hi-C and ssHi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells, with addition of the annealing oligonucleotide mix at 7 nM each in the lysis buffer prior to incubation at 62°C for 10 minutes.
DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions. For ssHi-C, two rounds of targeted capture using the IDT xGen Hybridization buffer and enhancer using biotinylated oligonucleotides at 0.6 uM each. The library was digested with MfeI and SspI in NEB cutsmart buffer prior to sequencing.

treatment_protocol: ~1.5x10^9 cells were crosslinked with 3% formaldehyde for 30 minutes at 120 rpm at room temperature, followed by quenching with 330 mM glycine for 30 minutes at 120 rpm.

value: S. cerevisiae culture


title: SVZ_Y4

description: 10x Genomics

value: 3 months


title: root control day1b

value: root


title: ssHi-C Pol3/Rfc1-depleted, DSB 4 hr

source_name: Pol3/Rfc1-depleted, DSB 4 hr


title: background control 3

value: heart


title: SVZ_Y3

description: 10x Genomics


title: LN229, replicate 1, 0 hours


title: ssHi-C Pol3-depleted, DSB 4 hr

source_name: Pol3-depleted, DSB 4 hr


title: SVZ_Y2

description: 10x Genomics


title: background control 2

value: cardiac; primary cells


title: Patient 24, P024, Vortioxetine treatment, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files provided per library. Aggregated count matrix for both libraries were provided as a 'count_matrix_scRNASeq_GBM_DMSO_VORT.txt' and associated a cell metadata table as 'cell_metadata_scRNASeq_GBM_DMSO_VORT.txt'.

source_name: Brain tumor, enzymatically dissociated

extract_protocol:
Cryopreserved single-cell suspensions of a glioblastoma patient sample were thawed in reduced serum media (DMEM containing 2% FBS) and used for single-cell RNA-Seq experiments. Viability markers SYTOX Blue and DRAQ5  were added to the cell suspension at least 15 minutes before sorting. FACS gates were set based on CD45, SYTOX Blue, and DRAQ5 intensities to isolate live CD45+ and CD45- populations.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

treatment_protocol: Three hours of Vortioxetine (20uM) or DMSO control treatment of isolated and FAC-sorted glioblastoma cells prior to scRNA-Seq library preparation.

value: Brain tumor, enzymatically dissociated

tag: tumor type

value: primary tumor

value: Vortioxetine treatment


title: background control 1

tag: cell type

value: control


title: ssHi-C rad51D DSB 2 hr replicate 2

source_name: rad51D DSB 2 hr

tag: tissue


title: Patient 24, P024, DMSO control, scRNAseq

description: 10x Genomics

value: DMSO control


title: LN229, replicate 2, 0 hours

value: Brain; Right frontal parieto-occipital cortex


title: NSCLC Plasma_Exo-miRNA_173_BASAL

status: Public on Jul 28 2024

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

hyb_protocol: After adding Hyb Spike-In, each sample was hybridized at 55°C for 20 hours on G4872A-070156 Human miRNA Microarray, Release 21.0, 8 x 60K (Agilent Technologies). The supplement of a commercial synthetic DNA poly-A oligonucleotide 3’ labeled pCp-Cy3, was added to the final hybridization mix. The 30-mer synthetic oligonucleotide (HPLC purified) was synthesized by TIB Molbiol s.r.l. (Genova, Italy). The lyophilized oligonucleotide was resuspended at a final concentration of 100 pmol/μL. Before use, an aliquot was taken and through serial dilutions brought to two final concentrations of 50 and 5 amol/μL.

scan_protocol: Microarrays were scanned (3 microns, 20 bit) on an Agilent microarray scanner (part number G2505C) and data extracted using Agilent feature extraction v.12.0.0.7. QC metrics from feature extraction were used to evaluate the success of the labeling and hybridization.

data_processing: Pre-processing, filtering and differential expression analysis were carried out using the Limma package, available within Bioconductor. Background correction and between array normalization were carried out using the normexp method, with an offset = 20, and the quantile method, respectively. Replicated probes were then averaged.

label: Cyanine 3-pCp

source_name: BASAL

label_protocol: Exosomal total RNA samples were processed using the Agilent miRNA complete labeling and hybridization kit (part number 5190-0456) and Agilent miRNA spike-in kit (part number 5190-1934). The Agilent miRNA microarray system was performed using 6 µl or 12 µl of purified total RNA  at unknown concentration, based on the plasma input (1 mL or 0.5 mL).

growth_protocol: No growth

extract_protocol: Exosomal total RNA  samples were purified from 0.5-1 mL of plasma using the  exoRNeasy Serum/Plasma Midi kit (Qiagen, Hilden, Germany)  according to manufacturer instructions.

treatment_protocol: No treatment

tag: histotype

value: Adc

tag: gender

value: male

tag: smoke habit

value: Current smoker

value: Nivolumab

tag: # numer of metastatic sites

tag: # brain metastases

value: no

tag: # liver metastases

tag: # prior lines of treatment

tag: performance status

tag: basal or best response

value: Basal


title: NSCLC Plasma_Exo-miRNA_131_BR

source_name: BR

value: female

value: Former smoker

tag: treatment

value: Best Response


title: NSCLC Plasma_Exo-miRNA_127_BASAL


title: NSCLC Plasma_Exo-miRNA_127_BR


title: NSCLC Plasma_Exo-miRNA_173_BR


title: NSCLC Plasma_Exo-miRNA_117_BR


title: NSCLC Plasma_Exo-miRNA_129_BASAL

value: yes


title: NSCLC Plasma_Exo-miRNA_126_BASAL

value: Scc


title: NSCLC Plasma_Exo-miRNA_126_BR


title: SVZ_Y1_re

description: 10x Genomics

value: Subventricular zone

value: Dcx-GFP

value: GFP+

tag: genotype

value: Heterozygote

value: 3 months


title: NSCLC Plasma_Exo-miRNA_157_BASAL

value: Never smoker


title: EnhDel CD8+ T cells, Day 9, Slamf6+TIM3-, sample 22

city: Boston

first: Amy

last: Huang

address: 25 Shattuck St

department: Immunology

institute: Harvard Medical School

data_processing:
Quality of the bulk RNA-seq FASTQ files was determined using FastQC (v0.11.8) and MultiQC (v1.19), and low quality samples were removed (% duplicates > 60, % aligned < 67).
FASTQ preprocessing, including adapter sequence and low quality base trimming, was performed using fastp (v0.23.4).
Transcript-level quantification of gene expression was then performed using Kallisto (v0.50.1), with the Mus musculus cDNA FASTA (GRCm39) serving as input for generation of the index for pseudoalignment.
Counts normalization and downstream analysis performed in R using the DESeq2 package.
Assembly: GRCm39
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: spleen

extract_protocol:
After CD8+ T cells were isolated from spleen, cells were sorted: (1) live CD8b+ CD44+ CD45.1+ CD45.2- Slamf6+ TIM3-, (2) live CD8b+ CD44+ CD45.1+ CD45.2- Slamf6- TIM3+ CX3CR1-, (3) live CD8b+ CD44+ CD45.1+ CD45.2+ Slamf6+ TIM3-, (4) live CD8b+ CD44+ CD45.1+ CD45.2+ Slamf6- TIM3+ CX3CR1-. Samples from eight recipient mice were then pooled in pairs to create four biological replicate samples. Cells were stored at -80C, then cell lysates were thawed on ice.
RNA was purified using 2.2x volume of RNAClean XP beads (Beckman Coulter, A63987). Samples were incubated for 10 minutes at room temperature and then placed on a DynaMag-96 side skirted magnet (Invitrogen, 12027) for 5 minutes, followed by supernatant aspiration and two washes with 80% ethanol. Dried beads were resuspended in 4μL of Mix-1 containing 1μL (10 μM) primer (IDT, DNA oligo) 5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′, 1μL (10 mM) dNTPs (Thermo-Fisher, R0192), 1μL (4U/μL) Recombinant RNase Inhibitor (Takara Bio, 2313A), and 1μL nuclease-free water per sample, and plates were placed in a thermocycler for 3 minutes at 72°C for RNA denaturation. Samples were immediately placed on ice. Reverse transcription was performed by adding 7μL of Mix-2 containing 0.75μL nuclease-free water, 2μL 5X Maxima RT buffer (Thermo Scientific, EP0752), 2μL (5M) betaine (B0300-1VL), 0.9μL (100mM) MgCl2 (Thermo Scientific, AM9530G), 1μL (10μM) TSO primer (IDT, RNA oligo) 5′-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′, 0.25μL (40U/μL) Recombinant RNase Inhibitor (Takara Bio, 2313A), and 0.1μL (200U/μL) Maxima H Minus Reverse Transcriptase (Thermo Scientific, EP0752); plates were incubated in a thermocycler for 90 minutes at 50°C followed by 5 minutes at 85°C. PCR preamplification was performed next by adding 14μL of Mix-3 containing 1μL nuclease-free water, 0.5μL ISPCR primer (IDT, DNA oligo) 5′-AAGCAGTGGTATCAACGCAGAGT-3′, and 12.5μL 2X KAPA HiFi HotStart ReadyMix (Roche, 07958935001); whole-transcriptome amplification was done by incubating in a thermocycler for 3 minutes at 98°C followed by 17 to 20 cycles of [98°C for 15 seconds, 67°C for 20 seconds, 72°C for 6 minutes] depending on cell number input, followed by final extension at 72°C for 5 minutes. Reaction cleanup and primer dimer removal was performed by incubating samples with 20μL Agencourt AMPure XP beads (Beckman Coulter, A63881) for 5 minutes, placing the plate on a DynaMag-96 side skirted magnet for 5 minutes, followed by supernatant removal and two washes with 70% ethanol and resuspension of dried beads in 20μL of TE buffer (Tekanova, T0228). This step was repeated for complete primer dimer removal. cDNA concentration was determined using the Qubit dsDNA high sensitivity assay kit (Thermo Scientific, Q32854), and cDNA size distribution was evaluated via TapeStation using a High Sensitivity D5000 Screentape (Agilent, 5067-5592). Samples were diluted to a concentration of 0.1-0.2ng/μL. The cDNA library was generated using the Nextera XT Library prep kit (Illumina, FC-131-1096) according to the manufacturer's protocol using barcodes from the Nextera XT Index Kit v2 Set A (Illumina, FC-131-2001). Barcoded samples were pooled and cleaned using Agencourt AMPure XP beads (Beckman Coulter, A63881); concentration was determined using the Qubit dsDNA high sensitivity assay kit and size distribution was determined using the TapeStation High Sensitivity D5000 Screentape. The pooled library containing 36 samples was sequenced on a NextSeq 1000 sequencer (Illumina) using the P2 (100 cycle) v3 reagent kit (Illumina, 20046811) using paired-end 50-base reads.

treatment_protocol: CD8+ T cells were isolated from P14+ EnhDel and WT mice, then transferred to recipient mice prior to LCMV Clone 13 infection. Transferred cells were isolated from recipient spleens on day 9 of infection.

value: spleen

value: CD8+ T cells

value: B6.Cg-Pdcd1tm1.1Shr/J Tg(TcrLCMV)327Sdz

value: LCMV Clone 13


title: NSCLC Plasma_Exo-miRNA_129_BR

value: Adc

value: Nivolumab

value: no


title: NSCLC Plasma_Exo-miRNA_131_BASAL

value: female

value: Former smoker

value: Basal


title: WT CD8+ T cells, Day 9, Slamf6+TIM3-, sample 19


title: NSCLC Plasma_Exo-miRNA_157_BR

value: male

value: Best Response


title: WT CD8+ T cells, Day 9, Slamf6+TIM3-, sample 13


title: EnhDel CD8+ T cells, Day 9, Slamf6+TIM3-, sample 16


title: EnhDel CD8+ T cells, Day 9, Slamf6+TIM3-, sample 10


title: WT CD8+ T cells, Day 9, Slamf6+TIM3-, sample 7


title: WT CD8+ T cells, Day 9, Slamf6+TIM3-, sample 1


title: NSCLC Plasma_Exo-miRNA_117_BASAL

value: Current smoker


title: NSCLC Plasma_Exo-miRNA_112_BASAL


title: NSCLC Plasma_Exo-miRNA_112_BR


title: EnhDel CD8+ T cells, Day 9, Slamf6+TIM3-, sample 4


title: WT CD8+ T cells, Day 9, Slamf6-TIM3+CX3CR1-, sample 9


title: SVZ_M1

description: 10x Genomics

value: Subventricular zone

value: Dcx-GFP

value: GFP+

value: 14 months


title: WT CD8+ T cells, Day 9, Slamf6-TIM3+CX3CR1-, sample 15

value: spleen


title: WT CD8+ T cells, Day 9, Slamf6-TIM3+CX3CR1-, sample 21

value: CD8+ T cells


title: NSCLC Plasma_Exo-miRNA_115_BR


title: NSCLC Plasma_Exo-miRNA_115_BASAL


title: NSCLC Plasma_Exo-miRNA_110_BASAL


title: EnhDel CD8+ T cells, Day 9, Slamf6-TIM3+CX3CR1-, sample 25

value: B6.Cg-Pdcd1tm1.1Shr/J Tg(TcrLCMV)327Sdz


title: EnhDel CD8+ T cells, Day 9, Slamf6-TIM3+CX3CR1-, sample 12

value: LCMV Clone 13


title: WT CD8+ T cells, Day 9, Slamf6-TIM3+CX3CR1-, sample 3


title: background control 4

value: heart

value: cardiac; primary cells

value: control


title: EnhDel CD8+ T cells, Day 9, Slamf6-TIM3+CX3CR1-, sample 6


title: EnhDel CD8+ T cells, Day 9, Slamf6-TIM3+CX3CR1-, sample 18


title: NSCLC Plasma_Exo-miRNA_109_BR

value: Adc

value: female

value: Nivolumab

value: no


title: NSCLC Plasma_Exo-miRNA_110_BR

value: male

value: Former smoker

value: Best Response


title: NSCLC Plasma_Exo-miRNA_108_BASAL

value: Current smoker

value: Basal


title: BDE-47_10µM-4

city: Detroit

first: Brian

last: Cummings

state: MI

address: 259 Mack Avenue

department: College of Pharmacy and Health Sciences

institute: Wayne State University

data_processing:
RNA Bioinformatic analysis was performed using Galaxy
Low quality reads with < 20 nt and PHRED scores of < 20 were removed using Cutadapt
Quality checks were performed before and after trimming using FastQC
Results were mapped to the mouse genome (mm10) with splice junctions using RNA STAR
Mapping success was assessed using Read Distribution (in the RSeQC pipeline)
Reads were counted using FeatureCounts
Normalization and determination of differentially expressed genes were performed using DeSeq2
Assembly: mm10
Supplementary files format and content: tab delimited text files which include raw counts for each sample
Supplementary files format and content: tab delimited text files which include DeSeq2-determined differentially expressed genes, fold-changes, and adjusted p-values as compared to vehicle control for each tissue/cell treatment

growth_protocol: HT-22 cells were maintained at 37°C and 5% CO2 in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Cells above passage 25 were not utilized. Cells were seeded at 300,000 cells per well (6-well plate). Treatment proceeded after 24 hr cellular attachment.

extract_protocol:
Cells and tissues were collected in Trizol and frozen at -80°C. Upon thaw, tissues were homogenized. Total RNA was extracted using chloroform and purified using the RNEasy MiniKit according to the manufacturer's instructions.1.0 µg of total RNA was used for library preparation.
Libraries were generated using the Kapa Biosystems Stranded RNA-Seq kit following the manufacturer's instructions.

treatment_protocol: Cells were treated with DMSO (vehicle control) or brominated flame retardants TBBPA, HBCD, or BDE-47 at 10 nM or 10 µM for 48 hr. Mice were trained to consume peanut butter pellets, and were then provided peanut butter pellets only (vehicle control) or 1 mg/kg HBCD once every 3 days for 28 days (10 doses total).

tag: cell line

value: Hippocampal neural cells

tag: treatment duration

value: 48 hr


title: NSCLC Plasma_Exo-miRNA_109_BASAL

tag: age


title: BDE-47_10µM-3


title: NSCLC Plasma_Exo-miRNA_108_BR


title: BDE-47_10µM-2


title: NSCLC Plasma_Exo-miRNA_102_BASAL


title: NSCLC Plasma_Exo-miRNA_94_BASAL

value: yes


title: NSCLC Plasma_Exo-miRNA_90_BASAL


title: NSCLC Plasma_Exo-miRNA_90_BR


title: NSCLC Plasma_Exo-miRNA_94_BR


title: NSCLC Plasma_Exo-miRNA_85_BR


title: NSCLC Plasma_Exo-miRNA_102_BR


title: NSCLC Plasma_Exo-miRNA_85_BASAL


title: BDE-47_10nM-2


title: BDE-47_10µM-1


title: HBCD_10µM-4

value: HBCD, 10 uM


title: HBCD_10µM-3


title: BDE-47_10nM-1


title: NSCLC Plasma_Exo-miRNA_69_BASAL

value: Scc


title: HBCD_10µM-1


title: NSCLC Plasma_Exo-miRNA_83_BASAL


title: NSCLC Plasma_Exo-miRNA_83_BR


title: HBCD_10nM-4

value: HBCD, 10 nM


title: NSCLC Plasma_Exo-miRNA_69_BR


title: NSCLC Plasma_Exo-miRNA_60_BR

value: Never smoker


title: NSCLC Plasma_Exo-miRNA_58_BASAL


title: NSCLC Plasma_Exo-miRNA_53_BR


title: NSCLC Plasma_Exo-miRNA_58_BR


title: HBCD_10nM-2


title: NSCLC Plasma_Exo-miRNA_53_BASAL


title: BDE-47_10nM-4


title: HBCD_10nM-1


title: BDE-47_10nM-3


title: TBBPA_10µM-3

value: TBBPA, 10 uM


title: NSCLC Plasma_Exo-miRNA_52_BR

value: Adc


title: TBBPA_10µM-2


title: HBCD_10µM-2


title: NSCLC Plasma_Exo-miRNA_50_BASAL


title: NSCLC Plasma_Exo-miRNA_60_BASAL

value: female


title: NSCLC Plasma_Exo-miRNA_52_BASAL

value: Nivolumab


title: NSCLC Plasma_Exo-miRNA_50_BR

value: no


title: HBCD_10nM-3


title: TBBPA_10µM-1


title: TBBPA_10nM-4

value: TBBPA, 10 nM


title: NSCLC Plasma_Exo-miRNA_47_BR

value: male


title: TBBPA_10nM-1


title: TBBPA_10nM-3


title: NSCLC Plasma_Exo-miRNA_39_BR

value: Former smoker

value: Best Response


title: NSCLC Plasma_Exo-miRNA_40_BASAL

value: Current smoker

value: Basal


title: NSCLC Plasma_Exo-miRNA_40_BR


title: DMSO-4

value: Hippocampal neural cells

value: 48 hr


title: TBBPA_10µM-4


title: DMSO-3


title: DMSO-2


title: DMSO-1


title: NSCLC Plasma_Exo-miRNA_39_BASAL


title: NSCLC Plasma_Exo-miRNA_34_BR


title: Kidney_HBCD-4

description: treatment once every 3 days

source_name: Kidney cortex

value: Kidney cortex

value: 28 days

value: Vehicle


title: NSCLC Plasma_Exo-miRNA_34_BASAL


title: NSCLC Plasma_Exo-miRNA_47_BASAL


title: NSCLC Plasma_Exo-miRNA_10_BR

value: Never smoker

value: yes


title: NSCLC Plasma_Exo-miRNA_26_BR

value: Adc


title: Kidney_HBCD-1

description: treatment once every 3 days


title: Kidney_Vehicle-4

description: treatment once every 3 days

value: 1 mg/kg HBCD


title: Kidney_HBCD-3

description: treatment once every 3 days


title: Kidney_HBCD-2

description: treatment once every 3 days


title: Kidney_Vehicle-3

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_10_BASAL

value: female

value: Nivolumab


title: NSCLC Plasma_Exo-miRNA_3_BASAL

value: Other

value: no


title: Kidney_Vehicle-2

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_3_BR

value: male


title: NSCLC Plasma_Exo-miRNA_26_BASAL

value: Former smoker


title: NSCLC Plasma_Exo-miRNA_7_BR

value: Best Response


title: NSCLC Plasma_Exo-miRNA_7_BASAL

value: Basal


title: NSCLC Plasma_Exo-miRNA_178_BR

value: Current smoker


title: Kidney_Vehicle-1

description: treatment once every 3 days


title: Liver_HBCD-4

description: treatment once every 3 days

source_name: Liver

value: Liver


title: Liver_HBCD-3

description: treatment once every 3 days


title: Liver_HBCD-2

description: treatment once every 3 days


title: Liver_HBCD-1

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_178_BASAL


title: NSCLC Plasma_Exo-miRNA_150_BR


title: NSCLC Plasma_Exo-miRNA_145_BASAL


title: Liver_Vehicle-4

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_150_BASAL


title: Liver_Vehicle-3

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_124_BR


title: NSCLC Plasma_Exo-miRNA_145_BR


title: NSCLC Plasma_Exo-miRNA_116_BR

value: missed


title: Liver_Vehicle-1

description: treatment once every 3 days

value: 28 days


title: NSCLC Plasma_Exo-miRNA_124_BASAL


title: Ventral_Hippocampus_HBCD-1

description: treatment once every 3 days

source_name: Ventral Hippocampus

value: Ventral Hippocampus

value: Vehicle


title: Ventral_Hippocampus_HBCD-3

description: treatment once every 3 days


title: Ventral_Hippocampus_Vehicle-4

description: treatment once every 3 days


title: Ventral_Hippocampus_HBCD-2

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_114_BASAL


title: Ventral_Hippocampus_Vehicle-3

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_114_BR


title: Ventral_Hippocampus_Vehicle-2

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_116_BASAL


title: Ventral_Hippocampus_Vehicle-1

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_113_BR


title: NSCLC Plasma_Exo-miRNA_113_BASAL


title: NSCLC Plasma_Exo-miRNA_99_BR


title: Liver_Vehicle-2

description: treatment once every 3 days


title: Dorsal_Hippocampus_HBCD-4

description: treatment once every 3 days

source_name: Dorsal Hippocampus

value: Dorsal Hippocampus


title: NSCLC Plasma_Exo-miRNA_92_BR

value: Scc


title: Dorsal_Hippocampus_HBCD-3

description: treatment once every 3 days


title: Ventral_Hippocampus_HBCD-4

description: treatment once every 3 days


title: Dorsal_Hippocampus_HBCD-2

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_91_BR

value: Adc

value: yes


title: Dorsal_Hippocampus_HBCD-1

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_86_BR

value: Nivolumab


title: Dorsal_Hippocampus_Vehicle-3

description: treatment once every 3 days

value: 1 mg/kg HBCD


title: NSCLC Plasma_Exo-miRNA_91_BASAL

value: no


title: Dorsal_Hippocampus_Vehicle-2

description: treatment once every 3 days


title: Dorsal_Hippocampus_Vehicle-4

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_86_BASAL

value: male


title: NSCLC Plasma_Exo-miRNA_81_BR

value: Former smoker


title: Dorsal_Striatum_HBCD-4

description: treatment once every 3 days

source_name: Dorsal Striatum

value: Dorsal Striatum


title: NSCLC Plasma_Exo-miRNA_81_BASAL

value: Basal


title: Dorsal_Striatum_HBCD-3

description: treatment once every 3 days


title: Dorsal_Striatum_HBCD-2

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_76_BR

value: Best Response


title: Dorsal_Striatum_HBCD-1

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_99_BASAL

value: Current smoker


title: NSCLC Plasma_Exo-miRNA_92_BASAL

value: female


title: genomic DNA from LNP_mSTELLA-Swap1_rep1

type: genomic

city: Guangzhou

first: Wenbin

last: Gu

address: 190 Kaiyuan Avenue, Huangpu District, Guangzhou

department: Chinese Academy of Sciences

country: China

institute: Guangzhou Institutes of Biomedicine and Health

description: HCT116 xenograft tumor models treated by LNP-mSTELLA-Swap1

hyb_protocol: Bisulfite-converted DNA was analyzed using Illumina Infinium MethylationEPIC v2.0 BeadChip Kit by following manufacturer's manual. Beadchip contains more than 935,000 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

scan_protocol: Polymer-coated chips were image-processed in Illumina iScan scanner.

data_processing:
Data were extracted using Illumina GenomeStudio V2011.1 software. Methylation status of each CpG site was presented as beta value based on following definition: beta value = (signal intensity of methylation-detection probe)/(signal intensity of methylation- detection probe + signal intensity of non-methylation-detection probe + 100).
Matrix_processed.txt: Average Beta
Matrix_signal_intensities.txt: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: HCT116, LNP-mSTELLA-Swap1 treated HCT116 xenograft tumor tissue

label_protocol: DNA bisulfite conversion was carried out using EZ DNA Methylation Kit (Zymo Research) by following manufacturer's manual with modifications for Illumina Infinium Methylation Assay. Briefly, 0.5~1.0 ug of genomic DNA was first mixed with 5 ul of M-Dilution Buffer and incubate at 37C for 15 minutes and then mixed with 100 ul of CT Conversion Reagent prepared as instructed in the kit's manual. Mixtures were incubated in a thermocycler with 16 thermal cycles at 95C for 30 seconds and 50C for one hour. Bisulfite-converted DNA samples were loaded onto 96-column plates provided in the kit for desulphonation and purification. Concentration of eluted DNA was measured using Nanodrop-1000 spectrometer. Bisulfite-converted DNA was analyzed using Illumina Infinium MethylationEPIC v2.0 BeadChip Kit (20087708) by following manufacturer's manual. Beadchip contains more than 935,000 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

growth_protocol: A549 and MDA-MB-231 cells were maintained in DMEM complete medium.  The tumor tissues were isolated from the mice bearing HCT116 xenograft tumors.

extract_protocol: Genomic DNA was extracted and purified from cell pellets using the Promega Wizard Genomic DNA Purification Kit according to the manufacturer's instructions. Genomic DNA quality was assessed by low concentration agarose gel (0.6%) electrophoresis and spectrometry of OD260/280 and OD 260/230 ratio.

treatment_protocol: A549 and MDA-MB-231 cells with lentivirus-mediated stable overexpression of STELLA orthologs were harvested on Day 9 post virus-transduction. Mice with HCT116 xenograft tumors were peritumorally injected every other day by the indicated LNP formulations and the tumor tissues were isolated on Day 18.

tag: tumor type

value: colorectal carcinoma

value: LNP-mSTELLA-Swap1 treated


title: Dorsal_Striatum_Vehicle-4

description: treatment once every 3 days

value: 28 days


title: genomic DNA from LNP_mSTELLA-Swap1_rep2


title: NSCLC Plasma_Exo-miRNA_74_BASAL


title: genomic DNA from LNP_mSTELLA_rep3

description: HCT116 xenograft tumor models treated by LNP-mSTELLA

source_name: HCT116, LNP-mSTELLA treated HCT116 xenograft tumor tissue

value: LNP-mSTELLA treated


title: genomic DNA from LNP_mSTELLA-Swap1_rep3


title: Dorsal_Striatum_Vehicle-3

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_59_BR

value: Scc


title: NSCLC Plasma_Exo-miRNA_59_BASAL


title: NSCLC Plasma_Exo-miRNA_76_BASAL


title: NSCLC Plasma_Exo-miRNA_56_BR

value: Adc


title: genomic DNA from LNP_mSTELLA_rep1


title: genomic DNA from LNP_mSTELLA_rep2


title: Dorsal_Hippocampus_Vehicle-1

description: treatment once every 3 days

value: Dorsal Hippocampus


title: NSCLC Plasma_Exo-miRNA_56_BASAL

value: Nivolumab


title: Dorsal_Striatum_Vehicle-2

description: treatment once every 3 days

value: 1 mg/kg HBCD


title: genomic DNA from LNP_rep3

description: HCT116 xenograft tumor models treated by LNP

source_name: HCT116, LNP treated HCT116 xenograft tumor tissue

value: LNP treated


title: genomic DNA from LNP_rep2


title: NSCLC Plasma_Exo-miRNA_51_BR

value: male

value: no


title: NSCLC Plasma_Exo-miRNA_74_BR

value: yes


title: Dorsal_Striatum_Vehicle-1

description: treatment once every 3 days

value: Dorsal Striatum


title: genomic DNA from MDA-MB-231_mSTELLA-OE

description: MDA-MB-231 cells stably expressing mSTELLA

source_name: MDA-MB-231, mSTELLA overexpression

value: breast carcinoma

value: mSTELLA overexpression


title: Frontal_cortex_HBCD-4

description: treatment once every 3 days

source_name: Frontal Cortex

value: Frontal Cortex

value: Vehicle


title: genomic DNA from LNP_rep1

value: colorectal carcinoma


title: genomic DNA from MDA-MB-231_EV

description: MDA-MB-231 cells stably expressing empty vector

source_name: MDA-MB-231, empty vector

value: empty vector


title: genomic DNA from MDA-MB-231_hSTELLA-OE

description: MDA-MB-231 cells stably expressing hSTELLA

source_name: MDA-MB-231, hSTELLA overexpression

value: hSTELLA overexpression


title: genomic DNA from A549_mSTELLA-OE

description: A549 cells stably expressing mSTELLA

source_name: A549, mSTELLA overexpression

value: lung carcinoma


title: Frontal_cortex_HBCD-3

description: treatment once every 3 days

value: 28 days


title: genomic DNA from A549_hSTELLA-OE

description: A549 cells stably expressing hSTELLA

source_name: A549, hSTELLA overexpression


title: NSCLC Plasma_Exo-miRNA_27_BR

value: Adc

value: female

value: Former smoker

value: Best Response


title: genomic DNA from A549_EV

description: A549 cells stably expressing empty vector

source_name: A549, empty vector


title: Frontal_cortex_HBCD-1

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_27_BASAL

source_name: BASAL

value: Nivolumab

value: Basal


title: Frontal_cortex_Vehicle-4

description: treatment once every 3 days

value: 1 mg/kg HBCD


title: NSCLC Plasma_Exo-miRNA_25_BR

source_name: BR

value: Never smoker

value: no


title: Frontal_cortex_Vehicle-3

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_25_BASAL


title: NSCLC Plasma_Exo-miRNA_51_BASAL

value: male

value: Current smoker


title: NSCLC Plasma_Exo-miRNA_12_BR


title: Frontal_cortex_Vehicle-2

description: treatment once every 3 days

value: Frontal Cortex


title: NSCLC Plasma_Exo-miRNA_12_BASAL


title: Frontal_cortex_HBCD-2

description: treatment once every 3 days

value: Vehicle


title: Frontal_cortex_Vehicle-1

description: treatment once every 3 days


title: NSCLC Plasma_Exo-miRNA_11_BR


title: TBBPA_10nM-2

tag: cell type

value: Hippocampal neural cells

value: 48 hr

value: TBBPA, 10 nM


title: NSCLC Plasma_Exo-miRNA_5_BR


title: mWTA Slide3 121422 DSP-1001660013725-A-C07

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

data_processing:
Raw basecall files were demultiplexed into individual fastqs corresponding to ROI, using bclconvert software
Fastqs were converted to Digital Count Conversion files using NanoString’s GeoMx NGS Pipeline v.2.3.0.
DCC files were processed using the GeoMX tools workflow. Probe data was filtered using a minProbeRatio value of 0.1 and a percentFailGrubbs value of 20. The background noise within the study is defined as the expression signal from negative control probes. ROIs with 2 geometric standard deviations above the background were kept along with those containing> 4% gene detection rate (51 ROIs). Genes detectedin 5% of ROIswere kept. Q3 normalization was then performed on the filtered data.
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx .pkc file.
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode).

source_name: brachiocephalic artery

extract_protocol:
The formalin-fixed, paraffin-embedded tissue blocks were cut at 5-μm thickness onto APEX treated slides to improve attachment.  After baking at 60°C overnight, deparaffinization and antigen retrieval was performed on Leica BOND RX autostainer using HIER2 (EDTA based antigen retrieval solution for 20 min) and proteinase K (15 min at 37°C, 1 μg/ml) following Nanostring’s recommendations.  The 6 slides were processed on 2 consecutive days, 2 slides (#1 and #3 on day 1 and #2, #4, #5 and #7 on day 2). RNA probes (NanoString GeoMx Whole Transcriptome Atlas Mouse RNA probes for NGS, item# 121401103) were added for hybridization at 37°C for 16 h. The slides were then washed 2X with stringent wash (50% formamide in 2XSSC for 25 min each) followed by 2X wash with 2XSSC (2 min each).  Slides were blocked with W buffer for 30 min and then incubated with anti CD31 primary antibody (1:50 dilution in W buffer) for 45 min. The slides were washed 2 times with 1X SSC (5 min each) followed by 20 min incubation with donkey anti-goat antibody conjugated to AF532 (1:100 dilution in W buffer). After 2X wash in SSC (5 min each), the slides were incubated for 60 min at RT with the antibody cocktail containing CD45-AF594 (1:40), aSMA-AF647(1:200) and Syto 83 (10 mM, nuclear stain).  The slides were washed with SSC buffer two times and scanned on the GeoMx DSP machine for selection of regions of interest (ROIs), using FITC/525 nm filter to detect CD31 (200 msec), Cy3/568 nm channel to detect nuclei (50 msec), Texas Red/615 nm to detect CD45 (200 msec) and Cy5/666 nm to detect aSMA (200 msec).  Based on the morphology of the tissues, ROIs for media, cap, core and normal wall were selected using polygons, with no masking, for a total of 83 ROIs.  The combined surface area of ROIs was 2989910.17 mm2 containing 8446 nuclei.  Oligonucleotide barcodes from each ROI were UV-photocleaved, collected into 96-well plates.
Library preparation and sequencing as recommended by the NanoString GeoMx protocol

tag: tissue

value: brachiocephalic artery

tag: roi

tag: segment

value: cap

value: Ldlr-/- +GCV

tag: Sex

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)

tag: nuclei count


title: mWTA Slide3 121422 DSP-1001660013725-A-C08

value: media


title: NSCLC Plasma_Exo-miRNA_5_BASAL

tag: histotype

value: Adc

tag: gender

tag: smoke habit

value: Former smoker

value: Nivolumab

tag: # numer of metastatic sites

tag: # brain metastases

tag: # liver metastases

tag: # prior lines of treatment

value: Basal


title: patient C4P5, before apheresis, T cells

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

description: Gene expression data for a patient with MS who underwent apheresis treatment

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D Arrays (Applied Biosystems). The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.3 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background reduction, intensity normalization, probe set summarization and log2 transformation. The TAC software was also utilized for the analysis of differential alternative splicing. Exon-level processed data are available on the Series record.

label: Biotin

source_name: T helper cells from the peripheral blood

label_protocol: According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Up to ~30 ml of peripheral blood were taken from MS patients in relapse immediately before and after therapeutic apheresis.

extract_protocol: The blood was collected in BD Vacutainer Glass Cell Preparation Tubes (Fisher Scientific). The tubes were centrifuged for the isolation of peripheral blood mononuclear cells (PBMC). B cells were positively selected from the PBMC using CD19 MicroBeads. T helper cells were obtained from the negative fraction of the B-cell separation by first removing non-T cells using the Pan T Cell Isolation Kit (Miltenyi Biotec) and then isolating CD4+ T cells using CD4 MicroBeads (Miltenyi Biotec). The RNA was isolated using the miRNeasy Mini Kit and the RNase-Free DNase Set (Qiagen).

treatment_protocol: The patients were treated according to the approved labels and the guidelines and recommendations of the German Society of Neurology.

tag: patient id

tag: time point

value: before

tag: cell population

value: CD4+ T cells

tag: purity (%)

tag: rna integrity number

tag: age (years)

value: female

tag: study center

value: Rostock

tag: current smoker

value: no

tag: body mass index

tag: course of disease

value: CIS/RRMS

tag: disease duration (years)

tag: comorbidities

tag: relapses in the past 2 years

tag: edss score

tag: relapse presentation

value: monosymptomatic

tag: symptomatic phenotype

value: new

tag: relapse therapy

value: immunoadsorption

tag: relapse therapy phase

value: initiation

tag: number of apheresis sessions

tag: clinical evaluation

value: non-responder


title: patient C4P4, after apheresis, T cells

tag: patient id

tag: time point

value: after

tag: cell population

tag: purity (%)

tag: Sex

value: yes

value: polysymptomatic

value: plasma exchange

value: escalation

value: responder


title: patient C4P5, after apheresis, T cells

tag: rna integrity number

tag: age (years)

tag: study center

tag: current smoker

tag: body mass index


title: NSCLC Plasma_Exo-miRNA_11_BASAL

tag: age

tag: histotype

value: Adc

tag: gender

value: male

tag: smoke habit

value: Former smoker

tag: treatment

value: Nivolumab

tag: # numer of metastatic sites

tag: # brain metastases

tag: # liver metastases

tag: # prior lines of treatment

tag: performance status

tag: basal or best response

value: Basal


title: patient C4P3, after apheresis, T cells

tag: patient id

tag: time point

tag: cell population

value: CD4+ T cells

tag: purity (%)

tag: Sex

value: female

value: Rostock

value: no

tag: course of disease

value: CIS/RRMS

tag: disease duration (years)

tag: comorbidities

tag: relapses in the past 2 years

tag: edss score

tag: relapse presentation

tag: symptomatic phenotype

tag: relapse therapy

tag: relapse therapy phase

tag: number of apheresis sessions

tag: clinical evaluation


title: patient C4P4, after apheresis, B cells

source_name: B cells from the peripheral blood

value: CD19+ B cells

tag: rna integrity number

tag: age (years)

tag: study center

tag: current smoker

tag: body mass index

value: new


title: mWTA Slide3 121422 DSP-1001660013725-A-C05

tag: tissue

value: brachiocephalic artery

tag: roi

tag: segment

value: cap

tag: genotype

value: Ldlr-/- +GCV

tag: Sex

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)

tag: nuclei count


title: NSCLC Plasma_Exo-miRNA_2_BASAL

tag: age

tag: histotype

value: Adc

tag: gender

tag: smoke habit

value: Current smoker

tag: treatment

tag: # numer of metastatic sites

tag: # brain metastases

value: yes

tag: # liver metastases

tag: # prior lines of treatment

tag: performance status

tag: basal or best response


title: patient C4P3, after apheresis, B cells

tag: patient id

tag: time point

value: after

tag: cell population

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: study center

tag: current smoker

tag: body mass index

tag: course of disease

tag: disease duration (years)

tag: comorbidities

tag: relapses in the past 2 years

tag: edss score

tag: relapse presentation

value: monosymptomatic

tag: symptomatic phenotype

tag: relapse therapy

value: immunoadsorption

tag: relapse therapy phase

value: escalation

tag: number of apheresis sessions

tag: clinical evaluation

value: responder


title: patient C4P4, before apheresis, B cells

tag: patient id

tag: time point

value: before

tag: cell population

tag: purity (%)

tag: Sex

value: female

value: Rostock

value: polysymptomatic

value: plasma exchange


title: Inflamed Colonic UC smRNA sample #43

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

state: NY

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

data_processing:
Sequencing was aligned and quantified using miRquant2.0. Sequence reads were trimmed for adaptors and low quality reads using Cutadapt.
Bowtie and SHRimp were used for alignment of the reads to hg19, allowing for perfect matches and isomiRs.
All annotation is provided by miRquant using TargetScan. The alignment was done to the human genome (hg19).
Assembly: hg19
Supplementary files format and content: tab deliminated file of raw counts for each Sample
Supplementary files format and content: tab deliminated file of normalized counts for each Sample

source_name: Colon Tissue

extract_protocol:
RNA was isolated from FFPE tissue using the Roche High Pure miRNA Isolation kit.
smRNA libraries were generated using the TruSeq Small RNA Sample Preparation Kit (Illumina).

tag: tissue

value: Colon Tissue

tag: inflammation

value: Inflamed

tag: disease status

value: UC


title: patient C2P9, after apheresis, T cells

value: CD4+ T cells

tag: rna integrity number

tag: age (years)

value: male

tag: study center

value: Greifswald

tag: current smoker

value: no

tag: body mass index

tag: course of disease

value: CIS/RRMS

tag: disease duration (years)

tag: comorbidities

value: new

value: non-responder


title: Non-inflamed Colonic UC smRNA sample #43

value: Non-Inflamed


title: mWTA Slide3 121422 DSP-1001660013725-A-C06

value: brachiocephalic artery

tag: roi

tag: segment

value: media

tag: genotype

value: Ldlr-/- +GCV

value: Female

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area area_(um^2)

tag: nuclei count


title: patient C4P3, before apheresis, B cells

tag: patient id

tag: time point

value: before

tag: cell population

value: CD19+ B cells

tag: purity (%)

tag: Sex

value: female

value: Rostock

value: yes

tag: relapses in the past 2 years

tag: edss score

tag: relapse presentation

value: monosymptomatic

tag: symptomatic phenotype

tag: relapse therapy

value: immunoadsorption

tag: relapse therapy phase

value: escalation

tag: number of apheresis sessions

tag: clinical evaluation

value: responder


title: TAMER-/-

city: Xiamen

first: Jing

last: Bi

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District, Xiamen, Fujian Province, China

institute: Xiamen University

data_processing:
Base-calling performed using CASAVA version 1.4
Reads were aligned using HISAT2 version2.0.4
Genome_build: GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: abundance measurements

source_name: breast cancer MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium with 10%FBS

extract_protocol:
RNA was harvested using TRIzol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard BGI protocols

tag: cell line

tag: genotype

value: TAMER-/-