title: CMEC-B-3

first: Jessica

last: Garbern

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: CM+EC co-culture

data_processing:
Raw Illumina NovaSeq sequence data (.bcl) files were de-multiplexed and converted into fastq.gz files using the -mkfastq command in cellranger v6.1.1 from 10X Genomics.
Fastq.gz files were processed using 10X Genomics cellranger v6.1.1 to produce UMI matrix (matrix.mtx.gz) and cell (barcode.tsv.gz) and gene (features.tsv.gz) files.
Processed files were converted into Seurat objects using Seurat v4.0.5, then data were filtered and normalized using SCTransform in Seurat.
Normalized data were used to perform principal component analysis and gene expression analysis.
Note that names of cellranger output files have been changed for clarity. Prior to input into Seurat, organize files into sample-specific folders then change names of processed files to “matrix.mtx.gz”, “barcodes.tsv.gz” and “features.tsv.gz” to allow Seurat to read files.
Assembly: GRCH38 (hg38)
Supplementary files format and content: matrix table with raw gene counts for every gene and every cell

source_name: iPSC-derived cardiac organoids

extract_protocol:
iPSC-CMs +/- iPSC-ECs were dissociated using the STEMDiff Cardiomyocyte Dissociation Kit (Stem Cell Technologies) then filtered through a 70 µm strainer. Single cells were washed then resuspended in phosphate buffered saline (PBS) containing 0.04% bovine serum albumin (BSA) at a concentration of 1000 cells/µL. Single cells were prepared with the 10X Genomics Chromium Single Cell 3’ v3 Reagent Kit according to the 10X Genomics Single Cell Protocols Cell Preparation Guide. 10,000 cells per sample were used for loading into a single lane of a NovaSeq S4 flow cell.
Library construction was performed using the 10x Chromium single cell 3' v3 kit according to the manufacturer's instructions.

value: iPSC-derived cardiac organoids

value: iPSC-derived cardiomyocytes and endothelial cells

value: WT

value: CM+EC co-culture


title: CNT_F5_P1_F5

status: Public on Mar 08 2023

type: SRA

city: Cambridge

first: Matthew

middle: R

last: Brown

state: MA

address: 75 Ames St

country: USA

institute: Broad Institute

library_source: transcriptomic

data_processing:
Alignment was performed with STAR, reads were counted with HTSeq and QC metrics were generated with RNA-SeQC.
The resulting count matrix was filtered by column for samples with more than 10^3 detected genes (counts > 0) and by row for coding genes (as defined by the MGI database) with a row sum across all samples > 500 counts (with a total number of 500 samples). The resulting normalized and filtered count matrix was then variance stabilized using the vst method from the DESeq2 R package. Surrogate variable analysis (SVA, R package) was performed on the vst count matrix to account for linear batch effects.
Assembly: mm10

molecule: total RNA

organism: Mus musculus

source_name: Mouse INsulinoma 6

extract_protocol:
RNA was extracted from cells using TCL buffer (#1031576, Qiagen) with 1% beta-mercaptoethanol followed by an RNA clean-up with Agencourt RNA cleanup XP (#A63987, Beckman Coulter).
Bulk RNA (1 μl) was added to a 3 step cDNA synthesis reaction with 3’RT (5’- AGCAGTGGTATCAACGCAGAGTAC(T30)VN-3’, IDT), template switching (5’-AAGCAGTGGTATCAACGCAGAGTACrGrG+G-3’, Qiagen), and ISPCR (5’-AAGCAGTGGTATCAACGCAGAGT-3’, IDT) oligos from the SMART-seq2 protocol 139. cDNA was purified using AMPure XP Agencourt (#100609, Beckman Coulter) and quantified using Qubit dsDNA High Sensitivity (#102689, Life Technologies). Samples were diluted to 0.2 ng/ul in TE and tagmented (Nextera XT DNA Library Preparation Kit (#FC-131-1096, Illumina). Indexing was performed using the Nextera XT Index Kit (#FC-131-1001, Illumina). Final libraries were QCed using the Qubit dsDNA High Sensitivity kit and Bioanalyzer High Sensitivity DNA Kit (#5067-4627, Agilent).

treatment_protocol: 40,000 MIN6 cells/well were seeded in 96-well plates 24 h prior to treatment in three replicates. FFA library compound plates were transferred into assay plates which were then incubated for 24 h (n=6).

tag: cell line

value: Mouse INsulinoma 6 (MIN6)

tag: treatment

value: 24h 0.5mM BSA


title: KO1 input

city: Hangzhou

first: Rifeng

last: Gao

state: Zhejiang

address: No. 88 Jiefang Road

country: China

institute: Zhejiang University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction:
Read count extraction and normalization were performed using CC genomic benchwork
Assembly: GRCm38.p6
Supplementary files format and content: bigwig files for each samples

source_name: ALKBH5flox/flox, αMyHC-Cre-DOX-1

growth_protocol: Myocardial tissues of ALKBH5-Control(WT, ALKBH5flox/flox) mice and ALKBH5 myocardial-specific knockout(KO, ALKBH5flox/flox, αMyHC-Cre) mice were methylated RNA immunoprecipitation sequencing (MeRIP-seq) and MeRIP-seq-qPCR

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Oiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and MeRIP-seq-qPCR

treatment_protocol: Mice were intraperitoneally injected with 20mg/kg doxorubicin.

tag: tissue

value: Heart

tag: rip antibody

value: input

tag: genotype

value: ALKBH5flox/flox, {alpha}MyHC-Cre-DOX-1

value: Doxorubicin


title: Con-myo-4

city: Shanghai

first: Shang

last: Li

address: 845 Lingshan Road

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

data_processing:
Raw reads were trimmed to remove the poor-quality reads, the adapters, and the polluted reads using Seqtk.
The trimmed reads were mapped to the reference genome using Hisat2 (2.0.4).
The fragments per kilobase of exon model per million mapped reads (FPKM) values were calculated.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Myometrium

extract_protocol:
Full thickness uterine specimens (including endometrium and myometrium) from 6  women with adenomyosis and 5 controls were collected and snap frozen using liquid nitrogen. Endometrium and myometrium were dissected from the frozen full thickness tissue using surgical blade. RNA was harvested using NuleoSpin RNA isolation Kit (MACHEREY-NAGEL, PA, USA) and llumina TruSeq RNA Library Prep Kit (Illumina, CA, USA) was used for the preparation of mRNA-seq library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: control

value: myometrium

tag: phase

value: proliferative phase of the menstrual cycle

tag: participant

value: participant 10


title: CMEC-B-2

description: CM+EC co-culture

library_source: transcriptomic single cell

tag: cell type


title: Con-myo-5

value: participant 11


title: CM-B-3

description: CMs alone

value: iPSC-derived cardiomyocytes

value: CMs alone (control)


title: KO2 input

source_name: ALKBH5flox/flox, αMyHC-Cre-DOX-2

value: ALKBH5flox/flox, {alpha}MyHC-Cre-DOX-2


title: CMEC-B-1

description: CM+EC co-culture

value: iPSC-derived cardiac organoids

value: iPSC-derived cardiomyocytes and endothelial cells


title: Con-myo-3

value: participant 9


title: Con-myo-2

value: participant 8


title: K65207153_P1_F4

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 5(Z),8(Z)-7Dimethyleicosadienoic acid


title: K95656032_P1_F2

value: 24h 0.5mM 7(E)-Nonadecenoic acid


title: siFBLN4-3

city: Tsukuba

first: Hiromi

last: Yanagisawa

state: Ibaraki

address: 1-1-1 Tennodai

department: TARA Center

country: Japan

institute: University of Tsukuba

data_processing:
sequencing was performed with NovaSeq/HiSeq (illumina) to generate 6 gz fastq files per treatment.
FASTQ files were analyzed using CLC Genomics Workbench (Version 22.0, QIAGEN). Sequences were mapped to human genome (GRCh38.105) and quantified annotated genes on CLC Genomics Workbench.
Gene expression values were presented in RPKM values.
Differentially expressed genes were analyzed using the statistical analysis tool  in Microarray analysis on CLC Genomics Workbench.
Assembly: GRCh38.105
Supplementary files format and content: tab-delimited text files include gene name (no identifier); fold change and p value for differential expressed genes comparison of siFBLN4 to CTRL;and RPKM values in each sample.

source_name: Human aortic endothelial cells

growth_protocol: Human aortic EC (HAEC; Lonza, CC-2535; lot#18TL099141 and 18TL177324) was grown in EGMTM-2 BulletKitTM (Lonza, CC-3162) supplemented with 2% (v/v) fetal bovine serum and growth factors. HAEC was used between passage 6 and 10.

extract_protocol:
After 4 days transfection, total RNA was extracted using RNeasy mini kit (QIAGEN) according to the manufacture’s protocol and quantified RNA concentration by Nanodrop One (Thermo Fisher).
An amount of 500 ng total RNA was used for RNA-seq library preparation and sequencing was performed with NovaSeq/HiSeq (illumina) by Azenta Japan Corp.

treatment_protocol: HAECs were transiently transfected with 10 pmol for a final concentration of scramble (non-target) siRNA (Invitrogen, #12935110) and FBLN4-siRNA (EFEMP2HSS121198) using Lipofectamine RNAiMAX transfection reagent (Thermo Fisher Scientific, #13778075) according to the manufacturer’s instruction.

value: HAEC

value: endothelial cells

value: FBLN4 siRNA


title: Con-endo-5

source_name: Endometrium

value: control

value: eutopic endometrium


title: Ctr1

city: Jena

first: Leijie

last: Jia

address: Adolf-Reichwein-Straße 23

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

data_processing:
HISAT2
StringTie v2.2.1 (parameter-merge -F 0.1 -T 0.1)
gffcompare 0.12.6 (parameter- default)
Assembly: Version information of the reference genome is: Homo_sapiens.GRCh37_release87.genome.fa.
Supplementary files format and content: xlsx file include reads count and FPKM values for each Sample

source_name: Lung

growth_protocol: H441 cells were co-incubated with A. fumigatus conidia with MOI = 10 for 4 hours at 37°C and 5% (v/v) CO2.

extract_protocol:
RNA isolation from cells was performed using the Universal RNA purification Kit (Roboklon GmbH, Berlin, Germany)
Qualified RNA were processed for library construction. The procedures are described as follow: (1) mRNA was isolated by Oligo(dT)-attached magnetic beads. (2) mRNA was then randomly fragmented in fragmentation buffer. (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp. (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.

value: Lung

value: Epithelial

value: WT

value: No treatment


title: WT3 input

value: Heart

value: input

value: Doxorubicin


title: K07992496_P1_F3

value: 24h 0.5mM 9(E)-Tetradecenoic acid


title: KO3 IP

source_name: ALKBH5flox/flox, αMyHC-Cre-DOX-3

value: Anti-m6A (Synaptic Systems, Cat. No 202 003)

value: ALKBH5flox/flox, {alpha}MyHC-Cre-DOX-3


title: Con-endo-4

value: proliferative phase of the menstrual cycle

value: participant 10


title: CM-B-1

description: CMs alone

value: iPSC-derived cardiac organoids

value: iPSC-derived cardiomyocytes

value: CMs alone (control)


title: WT2 input


title: WT1 input


title: MCF-7 cells treated with MYCMI-7, mycmi_1

city: Stockholm

first: Lars-Gunnar

last: Larsson

address: Solnavagen 9

department: Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institute

data_processing:
Demultiplexed .fastq files were aligned to the human GRCh37 reference genome using Tophat v 2.0. After alignment, .bam files from two separate flowcell lanes were merged using samtools. Raw read counts per gene were then generated using htseq-count v0.6.1.
Genome_build: GRCh37
Supplementary_files_format_and_content: CSV file with raw read counts per gene per sample

source_name: Breast carcinoma cell line

extract_protocol: Libraries for RNA sequencing were prepared using the TruSeq Stranded Total RNA kit with RiboZero (Illumina) and sequenced on two lanes of the HiSeq 2500 platform with a single-end 1x51 setup and the HiSeq Rapid SBS v2 chemistry.

value: breast carcinoma cells


title: siFBLN4-2

value: HAEC

value: endothelial cells

value: FBLN4 siRNA


title: CNT_F1_P1_F1

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM BSA


title: KO2 IP

value: Heart

value: ALKBH5flox/flox, {alpha}MyHC-Cre-DOX-2


title: BSA_M_P1_E12

value: #N/A


title: Con-endo-3

value: control

value: eutopic endometrium

value: participant 9


title: K18059238_P1_E11

value: 24h 0.5mM 6(Z), 9(Z), 12(Z)-Octadecatrienoic Acid


title: Con-endo-2

value: proliferative phase of the menstrual cycle

value: participant 8


title: CM-B-2

description: CMs alone

value: iPSC-derived cardiac organoids

value: iPSC-derived cardiomyocytes

value: WT


title: Con-endo-1

value: participant 7


title: K72611551_P1_E10

value: 24h 0.5mM 13(Z)-Docosenoic acid


title: siFBLN4-1

value: HAEC

value: endothelial cells

value: FBLN4 siRNA


title: CTRL-3

value: scramble siRNA


title: Con-myo-1

value: myometrium


title: KO1 IP

value: Heart

value: Anti-m6A (Synaptic Systems, Cat. No 202 003)

value: ALKBH5flox/flox, {alpha}MyHC-Cre-DOX-1

value: Doxorubicin


title: K04565634_P1_E9

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Octadecanoic acid


title: CTRL-2


title: WT2 IP


title: WT3 IP


title: CTRL-1


title: Ade-myo-6

value: adenomyosis

value: proliferative phase of the menstrual cycle

value: participant 6


title: WT1 IP


title: TUN_3_P1_E8

value: 24h 50ng/ml Tunicamycin


title: human ventricular cardiac organoid chamber [COC-W-4_S52_L004]

city: Sha Tin

first: Shangli

last: Cheng

address: No. 15 Science Park West Avenue

department: Ming Wai Lau Centre for Reparative Medicine

country: Hong Kong

institute: Karolinska Institutet

description:
hvCOC-02
hESC_UMIcounts.txt

data_processing:
The unique molecular identifier (UMI) counts of each barcode were analysed by using Cell Ranger following the pipeline with default parameters..
The low-quality cells with total UMI counts of less than 1,000 or more than 50,000 or with mitochondrial genes accounting for more than 15% out of the total UMI counts were excluded from the analysis. The cells expressing less than 1,000 or more than 7,500 features were also disregarded.
All analyses were carried out with R (version 4.1.1).
The analysis of maturation state was carried out by using Cellular Trajectory Reconstruction Analysis (CytoTRACE, version 0.3.3).
The differentially expressed genes were calculated using the DESeq2 (version 1.32.0).
Assembly: hg38
Supplementary files format and content: UMI count matrices of hPSCs with sample information in the column names.

source_name: hPSC

growth_protocol: All hPSCs were cultured in a 6-well tissue culture plate coated with Matrigel, using mTeSR1 medium

extract_protocol:
All tissue constructs were washed with PBS without Ca2+ and Mg2+ and incubated in a solution containing 10 unit/mL of papain (Sigma, 76220) and 1 mM of EDTA (Roth, 8043.2) for 45 min at 37°C. The cells were then gently triturated for ~1 min until a single-cell suspension was obtained. Medium with 10% fetal calf serum (FCS, Merck-Milipore, S 0615) was added to inhibit the digestion process. The cells were then washed in PBS and counted.
Single Cell 3’ Reagent Kit v2 (Chromium Single Cell 3’ Library & Gel Bead Kit v2, Chromium Single Cell A Chip Kit, 48 runs, 10x Genomics) and Chromium Controller (10x Genomics)

treatment_protocol: All hPSCs were differentiated in a 6-well low-attachment culture plate using the embryoid body suspension method in two induction stages: stage 1 with the addition of BMP4 and Activin A for mesodermal induction and stage 2 with the addition of IWR-1 to inhibit Wnt signaling pathways for cardiac specification.

tag: batch

value: hESC

tag: tissue configuration

value: hvCOC


title: K39965020_P1_E7


title: Ade-myo-5

value: participant 5


title: Ade-myo-4

value: participant 4


title: human ventricular cardiac organoid chamber [COC-W-3_S51_L004]

description:
hvCOC-02
hESC_UMIcounts.txt


title: K07624241_P1_E6

value: 24h 0.5mM 13(E)-Docosenoic acid


title: 21102-0008

city: Muenchen

first: Noushafarin

last: Khajavi

state: Bavaria

address: Goethestr. 33

department: Walther-Straub-Institut für Pharmakologie und Toxikologie

institute: LMU

data_processing:
NovaSeq Control Software (NVCS) v1.6.0.
The P-value of a pairwise comparison was derived from the Wald test. To control the false positive rate, FDR-corrected and Bonferroni-corrected p-values were calculated.
A gene or transcript is classified as upregulated or downregulated in a specific comparison if its FDR-corrected P value is ≤ 0.05 and its fold change is ≥ 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary cells

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

extract_protocol:
Islets were isolated and purified from the WT and Trpm7R/R mice. Islets pellets lysed in NEBNext Lysis Buffer.
Library preparation was performed with the NEBNext® Single Cell / Low Input RNA technology (New England Biolabs), according to the manufacturer´s protocol.

treatment_protocol:
Mice were fed diabetogenic diet (Research Diets, D12451), containing 45% kcal from fat, beginning at 8 weeks of age. Mice recieved this diet for 16 weeks.
Mice were single- or group-housed on a 12-h/12-h light-dark cycle at 22 °C with free access to food and water.

value: primary cells

value: Pancreatic islet cells

value: Obesogenic diet

tag: time

value: 16 weeks


title: 21102-0006


title: THP_3_P1_E5

value: 24h 0.00001mM Thapsigargin


title: Ade-myo-3

value: myometrium

value: participant 3


title: human ventricular cardiac organoid chamber [COC-W-2_S50_L004]

description:
hvCOC-02
hESC_UMIcounts.txt


title: Ade-myo-2

value: participant 2


title: Ade-endo-6

value: adenomyosis

value: eutopic endometrium


title: 21102-0002

value: WT


title: K48097184_P1_E3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 11(E)-Octadecenoic acid


title: 21102-0003


title: human ventricular cardiac organoid chamber [COC-W-1_S49_L004]

description:
hvCOC-02
hESC_UMIcounts.txt

value: hESC

value: hvCOC


title: human ventricular cardiac organoid chamber [COC-3_S35_L004]

description:
hvCOC-01
hESC_UMIcounts.txt


title: K81456670_P1_E2

value: 24h 0.5mM 11(Z)-Eicosenoic acid


title: Ade-endo-5

value: proliferative phase of the menstrual cycle

value: participant 5


title: 21102-0001

value: primary cells

value: Pancreatic islet cells


title: CNT_E1_P1_E1

value: 24h 0.5mM BSA


title: human ventricular cardiac organoid chamber [COC-2_S34_L004]

description:
hvCOC-01
hESC_UMIcounts.txt


title: Ade-endo-4

value: participant 4


title: CNT_D12_P1_D12


title: Ade-endo-3


title: human ventricular cardiac organoid chamber [COC-1_S33_L004]

description:
hvCOC-01
hESC_UMIcounts.txt


title: human ventricular cardiac tissue strip [Coll2-4_S36_L002]

description:
hvCTS-03
hESC_UMIcounts.txt

value: hvCTS


title: 21102-0004

value: Obesogenic diet

value: 16 weeks


title: M5215-3

city: Yinchuan

first: Jianwen

last: Wu

address: victory street

institute: Ningxia Medical University

description: 10x Genomics

data_processing:
Cell Ranger software (https://support.10xgenomics.com/single-cell-geneexpression/ software/overview/welcome) was used to perform data quality statistics on raw data and to match the reference genome.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMCs

extract_protocol:
Mice PBMCs and spleen single cell suspension were extracted, and the dead cells were removed before sequencing
Cells from the spleen and PBMCs of infected (3 mice pooled) and uninfected (3 mice pooled) mice were washed once in PBS with 0.04% BSA and loaded to the 10X Genomics Chromium to capture single cells for scRNA-seq following the manufacturer's instructions of 10X Genomics Chromium Single-Cell 5' kit (V2.0). In brief, gel beads containing barcode information were combined with a mixture of cells and enzymes and then encapsulated by droplets of oil surfactant in a microfluidic "double-cross" system to form gel beads-in-emulsions (GEMs), which flowed into a reservoir and were collected. The gel beads were lysed to release the barcode sequence, cDNA fragments were reversed transcribed, and the sample was labeled. After breaking the gel beads and oil droplets, cDNA was broken into fragments of about 200-300 bp using enzymes, and sequencing connectors and primers were added. Finally, polymerase chain reaction (PCR) amplification was performed to obtain the DNA library. Libraries were sequenced on an Illumina NovaSeq 6000 (LC-Bio Technology Co. Ltd., HangZhou, China) sequencing system using a 150 bp paired-end multiplexing run.

value: PBMCs

tag: Sex

value: female

value: normal mice

tag: age

value: 6-8 weeks old

value: PBS treatment


title: M5215-2

description: 10x Genomics

source_name: spleen

value: spleen

value: Middle and late stage of infection

value: Echinococcus granulosus infection


title: K39534559_P1_D10

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Decanoic acid


title: Ade-endo-2

value: adenomyosis

value: eutopic endometrium

value: proliferative phase of the menstrual cycle

value: participant 2


title: human ventricular cardiac tissue strip [Coll2-3_S35_L002]

description:
hvCTS-03
hESC_UMIcounts.txt

value: hESC

value: hvCTS


title: K00392230_P1_D11

value: 24h 0.5mM BSA


title: M5215-4

description: 10x Genomics


title: Ade-myo-1

value: myometrium

value: participant 1


title: human ventricular cardiac organoid chamber [COC-4_S36_L004]

description:
hvCOC-01
hESC_UMIcounts.txt

value: hvCOC


title: human ventricular cardiac tissue strip [Coll2-2_S34_L002]

description:
hvCTS-03
hESC_UMIcounts.txt


title: human ventricular cardiac tissue strip [Coll2-1_S33_L002]

description:
hvCTS-03
hESC_UMIcounts.txt


title: HeLa_C7_72_2

city: Yokohama

first: Yuki

last: Yamaguchi

address: 4259 Nagatsuta

department: Life Science and Technology

institute: Institute of Science Tokyo

data_processing:
Sequenced reads were trimmed for adaptor sequences and low QV region using cutadapt and Trimmomatic.
Trimmed read data were mapped to the reference genome using TopHat (Bowtie 1).
Expression analysis was carried out using Cufflinks (Cuffdiff).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table containing raw counts and FPKM values for all the samples

source_name: HeLa cells

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS and 1% Pen Strep.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) in accordance with the manufacturer’s instructions. Concentration and purity of isolated RNA was evaluated using a NanoDrop LITE (Thermo Fisher Scientific). Integrity of the RNA samples was analyzed using Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Seeded in 24-well plates 2 days before transfection, HeLa cells at a cell confluency of 50–70% were transfected with 50 µL of Opti-MEM I containing 5 pmol of siRNA specific for C7orf26 (C7 siRNA) or negative control siRNA with scrambled sequences (NS siRNA) using Lipofectamine RNAiMAX Transfection Reagent in accordance with the manufacturer’s instructions. Cells were treated for 6 h before harvest with 30 µg/mL cycloheximide and harvested 48 or 72 h after transfection.

tag: sirna target

tag: time after sirna transfection


title: CNT_D8_P1_D8


title: K84290455_P1_D9

value: 24h 0.5mM 5(Z)-Eicosenoic acid


title: HeLa_NS_72_2

value: non-specific


title: Infected with Hu-1 strain, 4 dpi

city: Iksan

first: Gun-Hee

last: Lee

address: 820-120 Hana-ro, Iksan, Jeonbuk

country: South Korea

institute: Korea zoonosis research institute, Jeonbuk National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Brain

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: Brain

value: Total brain cells

tag: infection

value: Hu-1 strain

value: 4 dpi


title: Infected with B1.617.2 variant, 4 dpi

value: B1.617.2 variant


title: M5215-1

description: 10x Genomics

value: PBMCs

value: female

value: Middle and late stage of infection

value: 6-8 weeks old

value: Echinococcus granulosus infection


title: human ventricular cardiac tissue strip [Coll1-4_S32_L002]

description:
hvCTS-02
hESC_UMIcounts.txt

tag: cell line

value: hESC

value: hvCTS


title: K18478158_P1_E4

value: Mouse INsulinoma 6 (MIN6)

tag: treatment

value: 24h 0.5mM 6(Z), 9(Z), 12(Z), 15(Z)-Octadecatetraenoic acid


title: human ventricular cardiac tissue strip [Coll1-3_S31_L002]

description:
hvCTS-02
hESC_UMIcounts.txt


title: K83944490_P1_D6

value: 24h 0.5mM 14(E)-Tricosenoic acid


title: K57491984_P1_D7

value: 24h 0.5mM 6(Z)-Octadecenoic acid


title: Infected with B1.617.2 variant, 3 dpi

tag: tissue

value: 3 dpi


title: HeLa_NS_72_1

value: non-specific


title: Negative control, 4 dpi

value: Brain

value: Total brain cells

value: Negative control


title: Ade-endo-1

value: adenomyosis

value: eutopic endometrium

value: proliferative phase of the menstrual cycle

value: participant 1


title: human ventricular cardiac tissue strip [Coll1-2_S30_L002]

description:
hvCTS-02
hESC_UMIcounts.txt


title: CNT_D5_P1_D5

value: 24h 0.5mM BSA


title: Infected with Hu-1 strain, 3 dpi

value: Hu-1 strain


title: human ventricular cardiac tissue strip [Coll1-1_S29_L002]

description:
hvCTS-02
hESC_UMIcounts.txt

value: hESC


title: HeLa_C7_48_2


title: HeLa_NS_48_2


title: K77749911_P1_D4

value: 24h 0.5mM 11-Dodecenoic acid


title: Negative control, 3 dpi


title: K17709609_P1_D3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 10(Z)-Pentadecenoic acid


title: HeLa_C7_48_1


title: Douglas-4p38i2R11

city: Saint Louis

first: Douglas

middle: V.

last: Faget

state: MO

address: 660 S. Euclid Ave, Box 8228

institute: Washington University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4/v5 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone metastases

extract_protocol:
After 13 days, femurs were harvested and cells were isolated by digestion and sorted following the parameters below.
Immune Stroma: Calcein/Blue+ Live/DEAD- CD45+ mCherry± cells were sorted; Non-Immune Stroma: Samples underwent negative selection for CD45 using MACS column. Calcein/Blue+ Live/DEAD- CD45- CD71- Ter119- GFP- mCherry± cells were sorted.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: Non-immune stromal cells

value: Bone metastases

tag: strain

value: Albino B6

value: 6-8 weeks old


title: human ventricular cardiac tissue strip [CTS-4_S40_L004]

description:
hvCTS-01
hESC_UMIcounts.txt

value: hvCTS


title: human ventricular cardiac tissue strip [CTS-3_S39_L004]

description:
hvCTS-01
hESC_UMIcounts.txt


title: K29160692_P1_D2

value: 24h 0.5mM 9(E)-Hexadecenoic acid


title: human ventricular cardiac tissue strip [CTS-2_S38_L004]

description:
hvCTS-01
hESC_UMIcounts.txt


title: HeLa_NS_48_1

value: non-specific


title: CNT_D1_P1_D1


title: OA_M_P1_C12

value: 24h 0.5mM 9(Z)-Octadecenoic acid


title: human ventricular cardiac tissue strip [CTS-1_S37_L004]

description:
hvCTS-01
hESC_UMIcounts.txt


title: HeLa_C7_72_1


title: Douglas-2Veh2R11

description: 10x Genomics


title: Douglas-1Veh2R10

description: 10x Genomics


title: human ventricular cardiac anisotropic sheet  [CAS-4_S44_L004]

description:
hvCAS-01
hESC_UMIcounts.txt

value: hvCAS


title: E233S_1-5

city: Qingdao

first: yunfeng

last: Yang

state: Shandong

address: 72 Binhaidadao, Aoshanwei, Jimo

institute: Shandong University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: REY15A(E233S)
Supplementary files format and content: tab-delimited text file includes count and FPKM values for each Sample

organism: Saccharolobus islandicus

source_name: bacterial cells

growth_protocol: S. islandicus REY15A(E233S) was cultured in STV(U) medium

extract_protocol:
Centrifugation at 10,000 rpm for 10 minutes to collect the cells, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For transcriptomic analysis,Briefly, S. islandicus REY15A(E233S) was first grown aerobically at 75°C with shaking (145 rpm) in 30 ml of STV(U) medium. When the OD600 reached 0.6-0.8, the cells were transferred into 300 ml STV medium with an initial estimated OD600 of 0.05. When the OD600 reached 0.15-0.2, acetic acid was added at a final concentration of 6 mM and the cells were blocked at G2 phase of the cell cycle after 6h treatment.

value: bacterial cells

value: 5 hours after synchronization

value: Acetic acid treatment


title: E233S_3-5


title: E233S_2-5


title: human ventricular cardiac anisotropic sheet  [CAS-3_S43_L004]

description:
hvCAS-01
hESC_UMIcounts.txt


title: E233S_2-4

value: 4 hours after synchronization


title: K80025777_P1_C11

source_name: Mouse INsulinoma 6

value: 24h 0.5mM 9(Z), 11(E)-octadecadienoic acid


title: TUN_2_P1_C8

value: 24h 500ng/ml Tunicamycin


title: human ventricular cardiac anisotropic sheet  [CAS-1_S41_L004]

description:
hvCAS-01
hESC_UMIcounts.txt

value: hESC


title: Douglas-5p38i45R7

description: 10x Genomics

value: Immune Cells


title: E233S_3-4


title: Douglas-2Veh45R8

description: 10x Genomics


title: human ventricular cardiac anisotropic sheet  [CAS-2_S42_L004]

description:
hvCAS-01
hESC_UMIcounts.txt


title: Douglas-3p38i2R10

description: 10x Genomics

value: Non-immune stromal cells


title: cardiac spheroid aggregates [EB-4_S28_L002]

description:
CS-02
hESC_UMIcounts.txt

value: CS


title: K57347788_P1_C7

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Heneicosanoic acid


title: E233S_1-4


title: Douglas-6p38i45R8

description: 10x Genomics

value: Bone metastases

value: Albino B6

value: 6-8 weeks old


title: NoEp biol rep 2

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

country: Spain

institute: FIMA

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm39 whole genome using STAR v2.7.9
Read summarization were obtained using featureCounts.
Normalization were performed in R statistical environment with edgeR package, then log2CPM was calculated using voom
Assembly: mm39
Supplementary files format and content: tab-delimited text files include log2CPM values for each Sample
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Spleen

growth_protocol: Pmel-1 spleen cells were extracted, activated 48h with hgp100 and mantained another 48h with hIL-2

extract_protocol:
RNA was extracted using RNA Easy Mini Kit (Qiagen)
TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: pmel-1 T cells were elecrtoporated with the corresponding mRNA and cultured 24h before RNA extraction

value: Spleen

value: pmel-1 lymphocytes

tag: genotype

value: WT


title: cardiac spheroid aggregates [EB-3_S27_L002]

description:
CS-02
hESC_UMIcounts.txt


title: NoEp biol rep 1


title: Mock biol rep 1

value: Mock

value: mRNA electroporated


title: Mock biol rep 2


title: cardiac spheroid aggregates [EB-2_S26_L002]

description:
CS-02
hESC_UMIcounts.txt


title: K57739283_P1_C6

value: 24h 0.5mM 12-Tridecenoic acid


title: E233S_3-2

value: bacterial cells

value: 2 hours after synchronization

value: Acetic acid treatment


title: IL12/DRIL18 biol rep 2

value: mixtures of scIL12/DRIL18 mRNA transfected


title: cardiac spheroid aggregates [EB-4_S48_L004]

description:
CS-01
hESC_UMIcounts.txt

value: hESC


title: cardiac spheroid aggregates [EB-3_S47_L004]

description:
CS-01
hESC_UMIcounts.txt

value: CS


title: K47192521_P1_C3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z), 17(Z)-Eicosapentaenoic acid


title: IL12/DRIL18 biol rep1


title: E233S_1-2


title: K51131535_P1_C2

value: 24h 0.5mM 9(Z), 12(Z)-Octadecadienoic acid


title: E233S_3-3

value: 3 hours after synchronization


title: cardiac spheroid aggregates [EB-1_S25_L002]

description:
CS-02
hESC_UMIcounts.txt


title: cardiac spheroid aggregates [EB-2_S46_L004]

description:
CS-01
hESC_UMIcounts.txt


title: E233S_2-2


title: K57135146_P1_B11

value: 24h 0.5mM 15(Z)-Tetracosenoic acid


title: K06914719_P1_B10

value: 24h 0.5mM 10(E)-Heptadecenoic acid


title: cardiac spheroid aggregates [EB-1_S45_L004]

description:
CS-01
hESC_UMIcounts.txt


title: THP_2_P1_C5

value: 24h 0.0001mM Thapsigargin


title: E233S_3-1

value: 1 hours after synchronization


title: IL-12 biol rep 2

value: Spleen

value: pmel-1 lymphocytes

value: scIL-12 mRNA transfected


title: K98002709_P1_C10

value: 24h 0.5mM 10(E)-Nonadecenoic acid


title: E233S_1-3

value: bacterial cells


title: IL-12 biol rep 1

value: mRNA electroporated


title: E233S_2-1

value: Acetic acid treatment


title: Douglas-1Veh45R7

description: 10x Genomics

value: Immune Cells

value: Bone metastases

value: Albino B6

value: 6-8 weeks old


title: K33223064_P1_B9

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Pentadecanoic acid


title: DRIL18 biol rep 2

value: DRIL18 mRNA transfected


title: A4_control

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

data_processing:
mapping to Ensembl human genome, Icell8 ranger and illumina software (bclConvert v3.7.5.)
The number of read counts in the sequenced libraries were 1,718,425, 12,372,392, 13,206,940 and 3,351,685. There were 6,223 barcodes for sample 1, 6,262 for sample 2 3,538 for sample 3 5,332 barcodes and for sample 4, 10,952. Number of features: A1-A4 33,538 each.
filtering to reads with count > 10 , differential gene expression analysis including FDR calculation
hirerchical clustering, scatter plot
network generation, Cell harmonhy analysis (www.altanalyze.org)
UMAP/scatter plot, hirerchical clustering gene set enrichment analysis (ICG8 bimarker analysis, bclConvert v3.7.5. )
Genome_build: Ensembl GRCh38.p13
Supplementary_files_format_and_content: Filteered files (matrix, barcode and features file content: count data, sequencing barcodes, ensenbl gene IDs)
Supplementary_files_format_and_content: * There was still over 1.6Bn clusters generated though, which is within the specification for an S1 flow-cell, and base call quality was excellent : 97% >Q30. The occupancy rate was also low (63-81%).

extract_protocol:
single nuclei were isolated from the brain samples
The RNA was sequenced on a Chromium machine
3' seq, using the Library & Gel Bead Kit v3, 16 rxns PN-1000075 and machine chemistry - paired-end sequencing on a NovaSeq 6000

value: Brain tissue


title: DRIL18 biol rep 1


title: CNT_B8_P1_B8

value: 24h 0.5mM BSA


title: E233S_1-1

value: 1 hours after synchronization


title: A3_AD Braak stage III/IV

value: BA41/42, BA 6/8, anterior hippocampal cortex

tag: Stage

value: Braak stage III-IV


title: E233S_3-0

value: 0 hours after synchronization


title: K14557781_P1_B7

value: 24h 0.5mM 9(Z)-Octadecenoic acid


title: K96144918_P1_B6

value: 24h 0.5mM 5(Z), 8(Z), 11(Z)-Eicosatrienoic Acid


title: E233S_1-0

value: bacterial cells


title: E233S_2-0

value: Acetic acid treatment


title: A2_control brain


title: psesd_aCcr1_3

description: aCcr1 overexpressed

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: REY15A
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: cells

growth_protocol: Strains of Sis/pSeSD and Sis/pSeSD-aCcr1 were cultured in ATV medium

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For transcriptomic analysis, culture was inoculated with an initial OD600 of 0.05. The cells were pelleted at 6,000 g for 10 min after 12 h of cultivation when the OD600 reached approximately 0.2. The pellet was resuspended in 1 ml PBS buffer. The cells were pelleted again and stored at -80°C.

value: cells

value: strain

value: aCcr1 overexpressed strain

value: Arabinose induction


title: K32862852_P1_B4

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 12-Methoxydodecanoic acid


title: K01624546_P1_C4

value: 24h 0.5mM 13(Z), 16(Z), 19(Z)-Docosatrienoic acid


title: psesd_aCcr1_2

description: aCcr1 overexpressed


title: A1_AD Braak stage III/IV


title: E233S_2-3

value: 3 hours after synchronization


title: OGD-treated BMECs exosomes,biological rep1

type: RNA

city: Changsha

first: Mengqi

last: Zhang

address: 87 Xiangya Road

institute: Xiangya Hospital

description: miRNA expression data from OGD-treated BMECs exosomes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000(Affymetrix).

data_processing:
Image analysis was performed using Affymetrix GeneChip Command Console Software ver. 3.2.4. Data analysis was performed using Expression ConsoleTM Software ver. 1.4.1.46 (Affymetrix).
The algorithms were RMA and DABG.

label: biotin

source_name: oxygen-glucose deprivation (OGD)-cultured human brain microvascular endothelial cell exosomes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 130 ng total RNA.

growth_protocol: BMECs with or without OGD exposure were stored in a CO2 incubator at 37 °C for 4 h.

extract_protocol: Total RNA extractions from EVs were performed using the miRNeasy Mini Kit, according to the manufacturer's protocol (Qiagen GmbH, Hilden, Germany）

treatment_protocol: To pellet EVs from the collected supernatant, ultracentrifugation was performed using an Optima XE-100 (Beckman Coulter, Brea, CA, USA), SW41 T1 (Beckman Coulter), and Ultra-Clear tube (Beckman Coulter) at 100,000 g for 70 min

tag: culture method

value: OGD-cultured BMECs

value: BMEC exosome


title: normal BMECs exosomes,biological rep3

description: miRNA expression data from normal BMECs exosomes

source_name: human brain microvascular endothelial cell exosomes

value: normal cultured human BMECs


title: K63913457_P1_B3

data_processing:
Alignment was performed with STAR, reads were counted with HTSeq and QC metrics were generated with RNA-SeQC.
The resulting count matrix was filtered by column for samples with more than 10^3 detected genes (counts > 0) and by row for coding genes (as defined by the MGI database) with a row sum across all samples > 500 counts (with a total number of 500 samples). The resulting normalized and filtered count matrix was then variance stabilized using the vst method from the DESeq2 R package. Surrogate variable analysis (SVA, R package) was performed on the vst count matrix to account for linear batch effects.
Assembly: mm10

extract_protocol:
RNA was extracted from cells using TCL buffer (#1031576, Qiagen) with 1% beta-mercaptoethanol followed by an RNA clean-up with Agencourt RNA cleanup XP (#A63987, Beckman Coulter).
Bulk RNA (1 μl) was added to a 3 step cDNA synthesis reaction with 3’RT (5’- AGCAGTGGTATCAACGCAGAGTAC(T30)VN-3’, IDT), template switching (5’-AAGCAGTGGTATCAACGCAGAGTACrGrG+G-3’, Qiagen), and ISPCR (5’-AAGCAGTGGTATCAACGCAGAGT-3’, IDT) oligos from the SMART-seq2 protocol 139. cDNA was purified using AMPure XP Agencourt (#100609, Beckman Coulter) and quantified using Qubit dsDNA High Sensitivity (#102689, Life Technologies). Samples were diluted to 0.2 ng/ul in TE and tagmented (Nextera XT DNA Library Preparation Kit (#FC-131-1096, Illumina). Indexing was performed using the Nextera XT Index Kit (#FC-131-1001, Illumina). Final libraries were QCed using the Qubit dsDNA High Sensitivity kit and Bioanalyzer High Sensitivity DNA Kit (#5067-4627, Agilent).

value: 24h 0.5mM 11(Z), 14(Z), 17(Z)-Eicosatrienoic Acid


title: OGD-treated BMECs exosomes,biological rep2


title: psesd_aCcr1_1

description: aCcr1 overexpressed


title: YDFR CB3 DIMER EXP1

type: protein

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.  Each slide was probed with one antibody.  The detection system used was a GenPoint-based staining kit from Agilent.

scan_protocol: Array-Pro Analyzer

data_processing: Relative protein levels for each sample were determined by interpolation of each dilution curve from the “standard curve” (supercurve) of the slide (Ab). Supercurve is constructed by a script in R written by Bioinformatics (“Supercurve Fitting” developed by the Department of Bioinformatics and Computational Biology in MD Anderson Cancer Center, http://bioinformatics.mdanderson.org/Software/supercurve). The raw spot intensity data were adjusted to correct spatial bias before model fitting. The protein concentrations of each set of slides were then normalized by median polish, which was corrected across samples by the linear expression values using the median expression levels of all Ab experiments to calculate a loading correction factor for each sample. These values (given as log2 values) are defined as Supercurve Log2 (Raw) values. All the data points were normalized for protein loading and transformed to linear values.

label: DAB

molecule: protein

source_name: YDFR CB3 DIMER

label_protocol: Samples were probed with Ab by CSA amplification approach and visualized by DAB colorimetric reaction.

growth_protocol: Melanoma cells were maintained in RPMI-1640 medium (Biological Industries, Kibbutz Beit Haemek, Israel) supplemented with 10% fetal bovine serum (FBS), 2 mmol/ml L-glutamine, 100 units/ml penicillin, 0.1 mg/ml streptomycin, and 12.5 units/ml nystatin. 0.5% FBS supplemented medium was used for starvation in all the experiments. Cells were cultured in an incubator with humidified air with 5% CO2 at 37°C.

extract_protocol: cell lysate was extracted using RIPA buffer (Sigma-Aldrich).

treatment_protocol: 1×106 melanoma cells were seeded for 24 hrs. Then cells were harvested by Trypsin EDTA (Biological Industries). Cell pellet was washed twice with phosphate-buffered saline (PBS) and lysed (1% Triton X-100, 50mM HEPES, pH 7.4, 150mM NaCl, 1.5mM MgCl2, 1mM EGTA, 100mM NaF, 10mM Na pyrophosphate, 1mM Na3VO4, 10% glycerol, protease and phosphatase inhibitors). Protein concentration was adjusted to 1-1.5µg/µl and denatured by 1% SDS. Cell lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slides in 11×11 format.

value: Human melanoma-brain metastases (MBM) cell line


title: YDFR CB3 DIMER EXP2


title: psesd_3

description: empty plasmid

value: control


title: HBMEC_8

city: Cardiff

first: Frank

last: Wessely

address: Maindy Road

department: UK DRI

institute: Cardiff University

data_processing:
Salmon (v0.13.1) was used to map raw sequencing reads to a human reference transcriptome combining cDNA plus ncRNA and for which alternative sequences were removed before mapping (ensembl GRCh38 version 98). The Salmon index was generated with k-mer length -k 23 due to shorter read length. Default Salmon mapping options were applied including the additional option --validateMappings.
Salmon quantification data were imported and summarised on the gene level using the tximeta R package (v1.4.5).
Assembly: GRCh38
Supplementary files format and content: TAB-delimited text files contain Salmon output providing transcript quantifiaction (Name, ensembl transcript ID; Length, length of transcript; EffectiveLength, effective length of transcript; TPM, Salmon-computed transcripts per million; NumReads, number of mapped reads)

growth_protocol: Passage one of human brain microvascular endothelial cells (HBMEC), human pulmonary microvascular endothelial cells (HPMEC) and human hepatic sinusoidal endothelial cells (HHSEC) were collectively purchased from ScienCell Research Laboratories (Carlsbad, CA, USA) and Innoprot (Derio, Biskaia, Spain). Each vial contained approximately 5x10^5 cells at passage one, which were cultured in the conditions provided by ScienCell Research Laboratories. Cells were grown in a fibronectin-coated T-75 flask at 37C with 5% CO2 in endothelial media comprising Endothelial Cell Medium (ScienCell Research laboratories), supplemented with 10% fetal bovine serum (FBS, ScienCell Research laboratories) and Endothelial Cell Growth Supplement (ScienCell Research laboratories). Cells were harvested after two passages to achieve the quantity of material necessary for bulk RNA-sequencing.

extract_protocol:
Total RNA was individually extracted using the Ambion MagMAX-96 total RNA isolation kit (Life Sciences) according to the manufacturer’s instructions. Briefly, cells were lysed using RLT buffer from QIAGEN. Nucleic acids were captured onto magnetic beads, washed and treated with DNase. Total RNA was then eluted in 50μl elution buffer. RNA quality and concentration was measured using the Fragment Analyzer (AATI).
Sequencing library preparation was done using 200ng of total RNA input with the TruSeq RNA Sample Prep Kit Set B (RS-122-2102, Illumina Inc, San Diego, CA) producing 275bp fragments including adapters on average size. In the final step before sequencing, individual libraries were normalized and pooled together using the adapter indices supplied by the manufacturer. Pooled libraries were clustered on the cBot instrument from Illumina using the HS 3000/4000 SR Cluster Kit - cBot - HS (GD-410-1001, Illumina Inc, San Diego, CA).

value: Brain

value: brain microvascular endothelial cells

tag: vendor

value: Innoprot

tag: catalogue no

tag: rin

value: F


title: PA_M_P1_A12

city: Cambridge

first: Matthew

last: Brown

address: 75 Ames St

institute: Broad Institute

value: 24h 0.5mM Hexadecanoic acid


title: YDFR CB3 CONTROL EXP3

source_name: YDFR CB3 CONTROL

tag: cell type


title: normal BMECs exosomes,biological rep2


title: normal BMECs exosomes,biological rep1


title: OGD-treated BMECs exosomes,biological rep3


title: HBMEC_7


title: CNT_B5_P1_B5

value: 24h 0.5mM BSA


title: aCcr1

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: REY15A
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: Strains  were cultured in MTSV medium

extract_protocol:
The cells were then resuspended in TBS-TT buffer (20 mM Tris, 150 mM NaCl, 0.1% Tween-20, 0.1% Triton X-100, pH 7.5) and fragmented by sonication until the DNA fragments were of 200-500 bp. After centrifugation (10,000 g for 15 minutes), a 100 µl aliquot of the DNA-containing supernatant was kept apart to be uses as an input control and the remaining sample was divided into two aliquots. One aliquot was incubated with anti-aCcr1 antibody-coated protein A beads (Cytiva) and the other was incubated with pre-immune serum-coated protein A beads, which served as a nonspecific binding control (Mock control). After incubation at 60 °C for 10 hrs, the samples were collected and the captured DNA was purified by using the DNA Cycle-Pure Kit (Omega) according to the manufacturer's instruction. The input samples were treated as above without the addition of antiserum and beads. The purified DNA was used for ChIP-Seq library preparation.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: the cells were collected 3 hours after synchronization, cross-linked by adding 1% formaldehyde for 15 minutes, and quenched with a final concentration of 125 mM glycine.

value: cells

tag: sample type

tag: antibody


title: K18766551_P1_A11

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 11(Z)-Octadecenoic acid


title: psesd_1

description: empty plasmid

value: strain

value: Arabinose induction


title: HBMEC_6

value: ScienCell

tag: Sex


title: K56767655_P1_A10

value: 24h 0.5mM Eicosanoic acid


title: K35238727_P1_B2

value: 24h 0.5mM 12(Z) Heneicosenoic acid


title: Mock

value: mock

value: pre-immune serum-coated protein A beads


title: DP CB2 DIMER EXP3

source_name: DP CB2 DIMER

value: Human melanoma-brain metastases (MBM) cell line


title: DP CB2 DIMER EXP2


title: HHSEC_6

source_name: Liver

value: Liver

value: hepatic sinusoidal endothelial cells

value: M


title: K25847431_P1_A9

value: 24h 0.5mM 9(E), 12(E)-Octadecadienoic acid


title: YDFR CB3 CONTROL EXP2


title: TUN_1_P1_A8

value: 24h 5000ng/ml Tunicamycin


title: HPMEC_6

source_name: Lung

value: Lung

value: pulmonary microvascular endothelial cells

value: F


title: psesd_2

description: empty plasmid

value: cells

value: control


title: HBMEC_5

value: Brain

value: brain microvascular endothelial cells


title: YDFR CB3 CONTROL EXP1


title: Input

value: Input

value: DNA-containing supernatant was kept apart to be uses as an input control


title: K04327383_P1_A6

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Hexadecanoic acid


title: K66986518_P1_A7

value: 24h 0.5mM 8(Z)-Eicosenoic acid


title: DP CB2 CONTROL EXP3

source_name: DP CB2 CONTROL

value: Human melanoma-brain metastases (MBM) cell line


title: DP CB2 DIMER EXP1


title: HHSEC_5

value: Liver

value: hepatic sinusoidal endothelial cells

value: Innoprot


title: THP_1_P1_A5

value: 24h 0.001mM Thapsigargin


title: HHSEC_4

value: M


title: HHSEC_3


title: F. pennsylvanica, low infestation, biol 3

city: Québec

first: Christine

last: Chiu

state: QC

country: Canada

institute: Laurentian Forestry Centre

data_processing:
CLC Genomic Workbench, version 11.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to the Fraxinus pennsylvanica 120313 transcriptome (BioProject PRJNA273266, downloaded at hardwoodgenomics.org ) using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Fraxinus pennsylvanica 120313

organism: Fraxinus pennsylvanica

source_name: phloem and xylem

extract_protocol:
RNA was extracted using RNeasy Plant Mini kit with DNase treatments according manufacturer’s instructions
RNA libraries for RNA-seq were prepared using Illumina NeoPrep Library Prep System following manufacturer's protocols.

tag: infestation level

value: Low

value: phloem and xylem


title: F. pennsylvanica, low infestation, biol 5


title: F. pennsylvanica, low infestation, biol 4


title: K99906572_P1_A3

value: 24h 0.5mM 10(E)-Pentadecenoic acid


title: HPMEC_5

value: Lung

value: pulmonary microvascular endothelial cells

value: F


title: F. pennsylvanica, low infestation, biol 2


title: F. pennsylvanica, low infestation, biol 1


title: F. pennsylvanica, med infestation, biol 5

value: Medium


title: MCNT_P1_A1

value: 24h Media


title: HPMEC_4


title: HPMEC_3


title: M16 CB3 DIMER EXP2

source_name: M16 CB3 DIMER


title: F. pennsylvanica, med infestation, biol 4


title: M16 CB3 DIMER EXP1


title: DP CB2 CONTROL EXP2


title: M16 CB3 CONTROL EXP3

source_name: M16 CB3 CONTROL


title: F. pennsylvanica, med infestation, biol 3


title: K16120488_P1_A4

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Tridecanoic acid


title: K08446574_P1_A2

value: 24h 0.5mM Nonadecanoic acid


title: HBMEC_4

source_name: Brain

value: Brain

value: brain microvascular endothelial cells


title: DP CB2 CONTROL EXP1

value: Human melanoma-brain metastases (MBM) cell line


title: Mut34-35

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

data_processing:
All analysis performed with CORALL Data Analysis Pipeline on the BlueBee® Genomics Platform
The UMI sequence for each read is added to the read identifier
FASTQC report of raw reads
Trimming of low quality tails, poly(A)read-through and  adapter contamination. 2nd FASTQC report of trimmed reads
STAR Aligner with modifi_x001E_ed ENCODE settings
Reads with identical mapping coordinates and UMI sequences are collapsed to remove PCR duplicates
Aligned BAM _x001E_le of UMI-collapsed, uniquely mapping reads
RSEQC report of the distribution of the reads on the annotation features
Gene reads count. HTSeq-count
Assembly: mm10
Supplementary files format and content: count tables (tab delimited tables)

source_name: Mutant mice

growth_protocol: No treatment

extract_protocol:
Trizol extraction followed by Qiagen RNeasy microkit.
kit CORALL RNA-Seq Library Prep (Lexogen)  Lexogen
Includes Unique Molecular Identifiers(UMI)  to correct for amplification biases.

value: TRalpha1 Mut34-35

tag: age

value: Post-natal day 14 mice

value: Inner ear


title: HBMEC_3

value: Innoprot


title: HHSEC_2

value: Liver

value: hepatic sinusoidal endothelial cells

value: ScienCell

value: M


title: Mut25-26

value: TRalpha1 Mut25-26


title: Mut21

value: TRalpha1 Mut21


title: F. pennsylvanica, med infestation, biol 2

value: Medium

value: phloem and xylem


title: Mut39

value: TRalpha1 Mut39


title: M12 CB3 DIMER EXP3

source_name: M12 CB3 DIMER


title: K20152659_P1_C9

source_name: Mouse INsulinoma 6

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 8(Z), 11(Z), 14(Z)-Eicosatrienoic Acid


title: F. pennsylvanica, high infestation, biol rep 5

value: High


title: HHSEC_1


title: M12 CB3 DIMER EXP2

value: Human melanoma-brain metastases (MBM) cell line


title: F. pennsylvanica, high infestation, biol rep 4


title: HPMEC_1

value: Lung

value: pulmonary microvascular endothelial cells

value: F


title: HPMEC_2


title: M16 CB3 CONTROL EXP2


title: M16 CB3 DIMER EXP3


title: M16 CB3 CONTROL EXP1


title: M12 CB3 DIMER EXP1


title: F. pennsylvanica, high infestation, biol rep 2


title: M12 CB3 CONTROL EXP3

source_name: M12 CB3 CONTROL


title: HBMEC_2

value: Brain

value: brain microvascular endothelial cells


title: WT19

source_name: Ctrl mice

value: Post-natal day 14 mice

value: Inner ear


title: M12 CB3 CONTROL EXP2


title: WT22-23


title: M12 CB3 CONTROL EXP1


title: F. pennsylvanica, med infestation, biol 1


title: F. pennsylvanica, high infestation, biol rep 3


title: Prefrontal_Cortex_NoRetrieval_Rep3

status: Public on Mar 07 2023

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

data_processing:
Full length reads were mapped to mm9 using Bowtie2. Only uniquely mapping reads were analyzed further.
Featurecounts was run to attribute reads to annotated genes
DESeq2 was used to call differential gene expression (model built incorporating biological replicate effect; beta prior=true; alpha=0.05).
Assembly: mm9

source_name: mouse medial prefrontal cortex

growth_protocol: Mice were raised 3-4 animals/cage in 12 hr light-dark cycle with food and water ad libidum

extract_protocol:
Dorsal hippocampi and prefrontal cortices were dissected from each mouse and snap-frozen in liquid nitrogen. Tissue was homogenized in Trizol reagent and total RNA purified.
Library preparation was derived from an adaptation of the Truseq protocol.

treatment_protocol: Mice were treated with an alcohol place conditioning protocol

value: mouse medial prefrontal cortex

value: brain tissue, neurons and glia

value: brief handling


title: Prefrontal_Cortex_Retrieval_Rep2

value: return to alcohol-paired context


title: F. pennsylvanica, high infestation, biol rep 1

value: phloem and xylem


title: Prefrontal_Cortex_NoRetrieval_Rep1


title: HBMEC_1

value: Innoprot


title: Dorsal_Hippocampus_NoRetrieval_Rep3

source_name: mouse dorsal hippocampus

value: mouse dorsal hippocampus


title: Dorsal_Hippocampus_Retrieval_Rep1


title: Prefrontal_Cortex_NoRetrieval_Rep2


title: WT31-33


title: Dorsal_Hippocampus_NoRetrieval_Rep1


title: WT38


title: Dorsal_Hippocampus_NoRetrieval_Rep2


title: Dorsal_Hippocampus_Retrieval_Rep2


title: Prefrontal_Cortex_Retrieval_Rep1


title: PPTumor_Vehicle2

city: Boston

first: Jean

last: Zhao

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description:
PP tumor cells isolated from tumor in vivo, vehicle control, biol rep 2
Column names: Gene,PPTumor_Vehicle1,PPTumor_Vehicle2,PPTumor_Vehicle3,PPTumor_AZD1,PPTumor_AZD2,PPTumor_AZD3

data_processing:
For mouse samples, data processing used the ampliSeqRNA plugin v5.12.0.1 available inside the Ion Torrent suite 5.12 for Ion torrent sequencing platform with default settings for all steps
For human PDX samples, RNA-Seq was performed by Novogene. Original image data file was transformed to sequenced reads by CASAVA base recognition. Alignments were performed with HISAT2 to reference genome.
Assembly: Mouse 4.6K: WG00278_Reference, (WG00278_Designed2.bed); Mouse 3.8K , Dana_Farbers_081215_Reference.fasta (Dana_Farbers_081215_Designed.bed); Human: hg38
Supplementary files format and content: xls: Tab-separated values and matrix file

source_name: Primary tumor cells

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN, # 74134).
RNA libraries for mouse samples were prepared using Ampliseq Library Prep Kit following manufacturer's protocols for targeted amplicon amplification
For mouse samples, other: Ion AmpliSeq Panels Mouse  3.8K (PP tumors_AZD6482-PD1) and 4.6K (all other mouse data sets) genes
For PDX samples, RNA-Seq

value: FVB/NJ

value: Primary tumor cells

value: PP cells

value: Mammary tumor

value: Pten/Trp53 double KO

value: Tumor cells isolated from tumor treated with vehicle control in vivo


title: PPTumor_Vehicle1

description:
PP tumor cells isolated from tumor in vivo, vehicle control, biol rep 1
Column names: Gene,PPTumor_Vehicle1,PPTumor_Vehicle2,PPTumor_Vehicle3,PPTumor_AZD1,PPTumor_AZD2,PPTumor_AZD3


title: PPBTumor3

description:
PPB tumor cells isolated from tumor in vivo, biol rep 3
Column names: Gene,PPTumor1,PPTumor2,PPTumor3,PPBTumor1,PPBTumor2,PPBTumor3

value: PPB cells

value: Pten/Trp53/Pik3cb triple KO

value: Tumor cells isolated from tumor in vivo


title: PPTumor_AZD3

description:
PP tumor cells isolated from tumor in vivo, AZD6482 treatment, biol rep 3
Column names: Gene,PPTumor_Vehicle1,PPTumor_Vehicle2,PPTumor_Vehicle3,PPTumor_AZD1,PPTumor_AZD2,PPTumor_AZD3

value: Tumor cells isolated from tumor treated with AZD6482 in vivo


title: PPTumor3

description:
PP tumor cells isolated from tumor in vivo, biol rep 3
Column names: Gene,PPTumor1,PPTumor2,PPTumor3,PPBTumor1,PPBTumor2,PPBTumor3


title: PPTumor_AZD1

description:
PP tumor cells isolated from tumor in vivo, AZD6482 treatment, biol rep 1
Column names: Gene,PPTumor_Vehicle1,PPTumor_Vehicle2,PPTumor_Vehicle3,PPTumor_AZD1,PPTumor_AZD2,PPTumor_AZD3


title: PPB_EV_3

description:
PPB-EV cells in vitro, biol rep 3
Column names: Gene,PPB_EV_1,PPB_EV_2,PPB_EV_3,PPB_STAT3_CA_1,PPB_STAT3_CA_2,PPB_STAT3_CA_3

source_name: Cell line

value: Cell line

value: PPB cells stably expressing an empty vector

value: In vitro growth


title: PPTumor_AZD2

description:
PP tumor cells isolated from tumor in vivo, AZD6482 treatment, biol rep 2
Column names: Gene,PPTumor_Vehicle1,PPTumor_Vehicle2,PPTumor_Vehicle3,PPTumor_AZD1,PPTumor_AZD2,PPTumor_AZD3


title: PPBTumor1

description:
PPB tumor cells isolated from tumor in vivo, biol rep 1
Column names: Gene,PPTumor1,PPTumor2,PPTumor3,PPBTumor1,PPBTumor2,PPBTumor3


title: PPB_STAT3_CA_1

description:
PPB-STAT3-CA cells in vitro, biol rep 1
Column names: Gene,PPB_EV_1,PPB_EV_2,PPB_EV_3,PPB_STAT3_CA_1,PPB_STAT3_CA_2,PPB_STAT3_CA_3

value: PPB cells stably expressing constitutively active mutant STAT3


title: PPB_STAT3_CA_2

description:
PPB-STAT3-CA cells in vitro, biol rep 2
Column names: Gene,PPB_EV_1,PPB_EV_2,PPB_EV_3,PPB_STAT3_CA_1,PPB_STAT3_CA_2,PPB_STAT3_CA_3


title: PPTumor1

description:
PP tumor cells isolated from tumor in vivo, biol rep 1
Column names: Gene,PPTumor1,PPTumor2,PPTumor3,PPBTumor1,PPBTumor2,PPBTumor3


title: PPBTumor2

description:
PPB tumor cells isolated from tumor in vivo, biol rep 2
Column names: Gene,PPTumor1,PPTumor2,PPTumor3,PPBTumor1,PPBTumor2,PPBTumor3


title: PPB_EV_2

description:
PPB-EV cells in vitro, biol rep 2
Column names: Gene,PPB_EV_1,PPB_EV_2,PPB_EV_3,PPB_STAT3_CA_1,PPB_STAT3_CA_2,PPB_STAT3_CA_3


title: PPTumor2

description:
PP tumor cells isolated from tumor in vivo, biol rep 2
Column names: Gene,PPTumor1,PPTumor2,PPTumor3,PPBTumor1,PPBTumor2,PPBTumor3


title: PPB_EV_1

description:
PPB-EV cells in vitro, biol rep 1
Column names: Gene,PPB_EV_1,PPB_EV_2,PPB_EV_3,PPB_STAT3_CA_1,PPB_STAT3_CA_2,PPB_STAT3_CA_3


title: PPB_STAT3_CA_3

description:
PPB-STAT3-CA cells in vitro, biol rep 3
Column names: Gene,PPB_EV_1,PPB_EV_2,PPB_EV_3,PPB_STAT3_CA_1,PPB_STAT3_CA_2,PPB_STAT3_CA_3


title: PP_shStat3_2_2

description:
PP-shStat3(2) cells in vitro, biol rep 2
Column names: Gene,PP_shGFP_1,PP_shGFP_2,PP_shGFP_3,PP_shStat3-1_1,PP_shStat3-1_2,PP_shStat3-1_3,PP_shStat3-2_1,PP_shStat3-2_2,PP_shStat3-2_3

value: PP cells stably expressing shStat3(2)


title: PPTumor_Vehicle3

description:
PP tumor cells isolated from tumor in vivo, vehicle control, biol rep 3
Column names: Gene,PPTumor_Vehicle1,PPTumor_Vehicle2,PPTumor_Vehicle3,PPTumor_AZD1,PPTumor_AZD2,PPTumor_AZD3


title: PP_shStat3_2_1

description:
PP-shStat3(2) cells in vitro, biol rep 1
Column names: Gene,PP_shGFP_1,PP_shGFP_2,PP_shGFP_3,PP_shStat3-1_1,PP_shStat3-1_2,PP_shStat3-1_3,PP_shStat3-2_1,PP_shStat3-2_2,PP_shStat3-2_3


title: PP_shStat3_1_2

description:
PP-shStat3(1) cells in vitro, biol rep 2
Column names: Gene,PP_shGFP_1,PP_shGFP_2,PP_shGFP_3,PP_shStat3-1_1,PP_shStat3-1_2,PP_shStat3-1_3,PP_shStat3-2_1,PP_shStat3-2_2,PP_shStat3-2_3

value: PP cells stably expressing shStat3(1)


title: PP_shStat3_1_1

description:
PP-shStat3(1) cells in vitro, biol rep 1
Column names: Gene,PP_shGFP_1,PP_shGFP_2,PP_shGFP_3,PP_shStat3-1_1,PP_shStat3-1_2,PP_shStat3-1_3,PP_shStat3-2_1,PP_shStat3-2_2,PP_shStat3-2_3


title: PP_shGFP_3

description:
PP-shGFP cells in vitro, biol rep 3
Column names: Gene,PP_shGFP_1,PP_shGFP_2,PP_shGFP_3,PP_shStat3-1_1,PP_shStat3-1_2,PP_shStat3-1_3,PP_shStat3-2_1,PP_shStat3-2_2,PP_shStat3-2_3

value: PP cells stably expressing shGFP


title: PP_shGFP_1

description:
PP-shGFP cells in vitro, biol rep 1
Column names: Gene,PP_shGFP_1,PP_shGFP_2,PP_shGFP_3,PP_shStat3-1_1,PP_shStat3-1_2,PP_shStat3-1_3,PP_shStat3-2_1,PP_shStat3-2_2,PP_shStat3-2_3

value: FVB/NJ


title: PP_shGFP_2

description:
PP-shGFP cells in vitro, biol rep 2
Column names: Gene,PP_shGFP_1,PP_shGFP_2,PP_shGFP_3,PP_shStat3-1_1,PP_shStat3-1_2,PP_shStat3-1_3,PP_shStat3-2_1,PP_shStat3-2_2,PP_shStat3-2_3


title: PD1_2

description:
Bulk PP tumor, anti-PD-1 treatment, biol rep 2
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6

source_name: Bulk tumor

value: Bulk tumor

value: PP tumor

value: Bulk PP tumor treated with anti-PD-1 in vivo


title: COMBO6

description:
Bulk PP tumor, AZD6482 + anti-PD-1 treatment, biol rep 6
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6

value: Mammary tumor

value: Pten/Trp53 double KO

value: Bulk PP tumor treated with AZD6482 + anti-PD-1 in vivo


title: PD1_6

description:
Bulk PP tumor, anti-PD-1 treatment, biol rep 6
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: AZD6

description:
Bulk PP tumor, AZD6482 treatment, biol rep 6
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6

value: Bulk PP tumor treated with AZD6482 in vivo


title: COMBO3

description:
Bulk PP tumor, AZD6482 + anti-PD-1 treatment, biol rep 3
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: COMBO4

description:
Bulk PP tumor, AZD6482 + anti-PD-1 treatment, biol rep 4
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: PP_shStat3_2_3

description:
PP-shStat3(2) cells in vitro, biol rep 3
Column names: Gene,PP_shGFP_1,PP_shGFP_2,PP_shGFP_3,PP_shStat3-1_1,PP_shStat3-1_2,PP_shStat3-1_3,PP_shStat3-2_1,PP_shStat3-2_2,PP_shStat3-2_3


title: COMBO1

description:
Bulk PP tumor, AZD6482 + anti-PD-1 treatment, biol rep 1
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: PD1_1

description:
Bulk PP tumor, anti-PD-1 treatment, biol rep 1
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: CTRL6

description:
Bulk PP tumor, vehicle control, biol rep 6
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6

value: Bulk PP tumor treated with vehicle control in vivo


title: AZD3

description:
Bulk PP tumor, AZD6482 treatment, biol rep 3
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: PD1_3

description:
Bulk PP tumor, anti-PD-1 treatment, biol rep 3
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: PD1_5

description:
Bulk PP tumor, anti-PD-1 treatment, biol rep 5
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: CTRL5

description:
Bulk PP tumor, vehicle control, biol rep 5
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: CTRL4

description:
Bulk PP tumor, vehicle control, biol rep 4
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: PP_shStat3_1_3

description:
PP-shStat3(1) cells in vitro, biol rep 3
Column names: Gene,PP_shGFP_1,PP_shGFP_2,PP_shGFP_3,PP_shStat3-1_1,PP_shStat3-1_2,PP_shStat3-1_3,PP_shStat3-2_1,PP_shStat3-2_2,PP_shStat3-2_3


title: CTRL3

description:
Bulk PP tumor, vehicle control, biol rep 3
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: AZD1

description:
Bulk PP tumor, AZD6482 treatment, biol rep 1
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: CTRL2

description:
Bulk PP tumor, vehicle control, biol rep 2
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: CTRL1

description:
Bulk PP tumor, vehicle control, biol rep 1
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: AZD5

description:
Bulk PP tumor, AZD6482 treatment, biol rep 5
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: AZD2

description:
Bulk PP tumor, AZD6482 treatment, biol rep 2
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: COMBO5

description:
Bulk PP tumor, AZD6482 + anti-PD-1 treatment, biol rep 5
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: PP_AZD6482_3

description:
PP cells in vitro, AZD6482, biol rep 3
Colume names: Gene, PP_DMSO_1, PP_DMSO_2, PP_DMSO_3,PP_AZD6482_1,PP_AZD6482_2,PP_AZD6482_3

value: PP cells


title: PP_AZD6482_1

description:
PP cells in vitro, AZD6482, biol rep 1
Colume names: Gene, PP_DMSO_1, PP_DMSO_2, PP_DMSO_3,PP_AZD6482_1,PP_AZD6482_2,PP_AZD6482_3

value: Cell line


title: PP_AZD6482_2

description:
PP cells in vitro, AZD6482, biol rep 2
Colume names: Gene, PP_DMSO_1, PP_DMSO_2, PP_DMSO_3,PP_AZD6482_1,PP_AZD6482_2,PP_AZD6482_3


title: AZD4

description:
Bulk PP tumor, AZD6482 treatment, biol rep 4
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: COMBO2

description:
Bulk PP tumor, AZD6482 + anti-PD-1 treatment, biol rep 2
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6


title: PP_DMSO_3

description:
PP cells in vitro, dmso, biol rep 3
Colume names: Gene, PP_DMSO_1, PP_DMSO_2, PP_DMSO_3,PP_AZD6482_1,PP_AZD6482_2,PP_AZD6482_3

value: DMSO


title: PP_3

description:
PP cells in vitro, biol rep 3
Colume names: Gene, PP_1, PP_2, PP_3, PPB_1, PPB_2, PPB_3

value: In vitro growth


title: PP_DMSO_1

description:
PP cells in vitro, dmso, biol rep 1
Colume names: Gene, PP_DMSO_1, PP_DMSO_2, PP_DMSO_3,PP_AZD6482_1,PP_AZD6482_2,PP_AZD6482_3


title: PP_DMSO_2

description:
PP cells in vitro, dmso, biol rep 2
Colume names: Gene, PP_DMSO_1, PP_DMSO_2, PP_DMSO_3,PP_AZD6482_1,PP_AZD6482_2,PP_AZD6482_3


title: PPB_1

description:
PPB cells in vitro, biol rep 1
Colume names: Gene, PP_1, PP_2, PP_3, PPB_1, PPB_2, PPB_3

value: PPB cells

value: Pten/Trp53/Pik3cb triple KO


title: PPB_3

description:
PPB cells in vitro, biol rep 3
Colume names: Gene, PP_1, PP_2, PP_3, PPB_1, PPB_2, PPB_3


title: YDFR CB3 DIMER EXP3

description: The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.  Each slide was probed with one antibody.  The detection system used was a GenPoint-based staining kit from Agilent.

source_name: YDFR CB3 DIMER

value: Human melanoma-brain metastases (MBM) cell line


title: PP_2

description:
PP cells in vitro, biol rep 2
Colume names: Gene, PP_1, PP_2, PP_3, PPB_1, PPB_2, PPB_3


title: PP_1

description:
PP cells in vitro, biol rep 1
Colume names: Gene, PP_1, PP_2, PP_3, PPB_1, PPB_2, PPB_3


title: CD10- PD1- PNT 2

city: Ghent

first: Laurenz

last: De Cock

address: Corneel Heymanslaan 10

department: Department of Diagnostic Sciences

country: Belgium

institute: Ghent University

description: PNT 3

data_processing:
Raw sequencing reads from fastq files were aligned to reference V, D and J genes from GenBank database specifically for ‘TRA’ or ‘TRB’ to build CDR3 sequences using the MiXCR software version 3.0.12
Following, the CDR3 sequences were analysed using VDJtools software version 1.2.1
Assembly: reference V, D and J genes from GenBank database
Supplementary files format and content: VDJ output files; tab-delimited tekst files
Library strategy: TCR sequencing

source_name: Thymus

extract_protocol:
RNA extraction was performed using the miRNeasy Micro kit (Qiagen) according to the manufacturer's protocol.
The first step in the library preparation is cDNA synthesis using template-switch anchored RT-PCR. The resulting cDNA is subsequently purified and amplified using either Cα or Cβ specific primers. The amplification product was then subject to an index PCR with Illumina sequencing adapters using the Nextera XT Index Kit.

value: Thymus

tag: population

value: T cells

value: WT

value: Untreated


title: CD10- PD1- PNT 1

description: PNT 1


title: CD3+ PD1- CB 6

description: LB 9

source_name: Cord blood

value: Cord blood

value: CD3+ PD1-


title: CD10+ PD1+ PNT 1

description: PNT 2


title: CD3low PD1+ CB 7

description: LB 12

value: CD3low PD1+


title: CD3low PD1+ CB 4

description: LB 6


title: CD3low PD1+ CB 6

description: LB 10


title: CD10+ PD1+ PNT 2

description: PNT 4


title: CD3+ PD1- CB 7

description: LB 11


title: CD3+ PD1- CB 2

description: LB 3


title: PPB_2

description:
PPB cells in vitro, biol rep 2
Colume names: Gene, PP_1, PP_2, PP_3, PPB_1, PPB_2, PPB_3

value: FVB/NJ

tag: cell line

value: Mammary tumor


title: CD3low PD1+ CB 5

description: LB 8

tag: treatment


title: CD3+ PD1- CB 4

description: LB 5

tag: tissue


title: npf8.4-1, Day 0, rep 3

city: Taipei

first: Yi-Fang

last: Tsay

address: 128 Academia Rd, Sec. 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
To obtain 150 bp paired-end reads, base-calling with bcl2fastq (version 2.17.1.14) Conversion Software was used to demultiplex data and convert BCL files to FASTQ.
All reads were trimmed and quality-filtered using CLC Genomics Workbench 12.0.3 (Qiagen), with settings of removal of low quality sequence (limit=0.05), no ambiguous nucleotides allowed, and removal of reads smaller than 25 nucleotides.
The trimmed reads were mapped to the TAIR10 genome using the RNA-seq mapping algorithm implemented in CLC Genomics Workbench 12.0.3 and allowing only unique mapping with a maximum of two mismatches.
Total exon reads were calculated as the expression value of each gene.
Assembly: TAIR10 genome
Supplementary files format and content: tab-delimited text files include Total exon reads, TPMs, and RPKM for each sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: young leaves

growth_protocol: Plants were grown hydroponically with 5 mM KNO3 for 15 days in a growth room (16-h light/8-h dark, light source: Philips Lifemax Cool White, 100 mmol m–2 s–1, 23° C).

extract_protocol:
Total RNA was extracted from the young leaves of plants using TRIzol reagent (Gibco BRL) and subjected to quality control with an Agilent 2100 Bioanalyzer.
Libraries were prepared using a TruSeq Stranded mRNA LT set A/B Sample Preparation kit

treatment_protocol: Plants grown with 5 mM KNO3 for 15 days were transferred to N-free medium for 2 days.

value: young leaves

value: 5 KN medium

tag: time

value: Day 0


title: npf8.4-1, Day 0, rep 1

tag: genotype


title: CD3low PD1+ CB 1

description: LB 2


title: CD3+ PD1- CB 1

description: LB 1


title: CD3low PD1+ CB 2

description: LB 4


title: npf8.4-1, Day 2, rep 3

value: N-free medium

value: Day 2


title: npf8.4-1, Day 2, rep 2


title: npf8.4-1, Day 2, rep 1


title: Col-0, Day 2, rep 3


title: Col-0, Day 2, rep 1


title: Col-0, Day 2, rep 2


title: A5

city: Wuxi

first: Wenjun

last: Zou

address: NO.68 Zhongshan Road

institute: Wuxi No.2 People’s Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg19 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: whole blood

extract_protocol:
RNA was harvested using TRIzol reagent(Beyotime, Nantong, China). Illumina TruSeq RNA Sample Prep Kit(Cat#FC-122-1001) was used with 1ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: whole blood

tag: condition


title: npf8.4-1, Day 0, rep 2


title: A3


title: Col-0, Day 0, rep 3


title: Col-0, Day 0, rep 2


title: CD3+ PD1- CB 5

description: LB 7


title: A1


title: H6

value: healthy control


title: Col-0, Day 0, rep 1


title: M8

value: MOG-ON


title: M7


title: M6


title: M5


title: H3


title: H2


title: M4


title: M3


title: M2


title: M1


title: A6


title: HUVECs, 8OH-G miR-483 overexpression, Rep 3

city: La Jolla

first: Ming

last: He

state: CA

address: 9500 Gilman Dr.

institute: UCSD

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt
Trimmed sequence reads were mapped to hg19 using RNA STAR
Read count extraction and normalization were performed using HTSeq-count
The differential gene expressions were identified using DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HUVECs

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were obtained from Cell Applications and cultured in M199 medium supplemented with 15% fetal bovine serum, 1 ng/mL recombinant human endothelial growth factor, 90 μg/mL heparin sodium, 100 U/mL streptomycin/penicillin, and 100 U/mL sodium pyruvate.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NovaSeq 6000 SP Reagent Kit v1.5 following manufacturer's protocols.

treatment_protocol: HUVECs were transfected with miR-483, 8OH-G miR-483, or scramble control (Ctrl) using Lipofectamine RNAi max. After 48 hr, total RNA was isolated for RNA-seq.

value: HUVECs

value: Human endothelial cells

value: 8OH-G miR-483 overexpression

value: Transfected with 8OH-G miR-483


title: A4


title: HUVECs, 8OH-G miR-483 overexpression, Rep 2


title: A2


title: H7


title: H5


title: AMA, replicate 2

city: Shenzhen

first: Bei

last: Wang

address: No.66,Gongchang Road,Guangming District

department: School of Pharmaceutical Sciences (Shenzhen)

institute: Sun Yat-sen University

data_processing:
Sequencing Data Filtering
Enrichment of sgRNAs and genes was analyzed using MAGeCK (Version 0.5.9.2)
Assembly: Brunello Library (#73179, Addgen)
Supplementary files format and content: tab-delimited text files include counts for each sgRNA

source_name: HAP1 cell

growth_protocol: HAP1 cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM; Gibco) supplemented with 10% Fetal Bovine Serum (FBS; NEWZERUM) and 1% penicillin-streptomycin (Hyclone).

extract_protocol:
Genomic DNA (gDNA) was isolated using TIANamp Genomic DNA kits (#DP304, TIANGEN) according to the manufacturer’s protocol. The sgRNA sequences were amplified using High-Fidelity 2X PCR Master Mix (#M0541L, NEB). PCR products were gel extracted, quantified, mixed and sequenced.
Genomic DNA was randomly interrupted by A Covaris ultrasonic breaker. After the end repair, addition of A tail, addition of sequencing adapter, purification, and PCR amplification, the DNA library was prepared.

value: HAP1 cell

value: near-haploid human cell line derived from the KBM-7 chronic myelogenous leukemia  cell line

value: AMA


title: Control, replicate 2

value: PBS


title: AMA, replicate 1


title: HUVECs, 8OH-G miR-483 overexpression, Rep 1


title: HUVECs, miR-483 overexpression, Rep 3

value: miR-483 overexpression

value: Transfected with hsa-miR-483


title: GM12878 WT UT RNA rep1

city: Boulder

first: Edward

last: Chuong

state: Colorado

address: 3415 Colorado Ave, JSCBB E251

institute: University of Colorado Boulder

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
reads were aligned using hisat2 and assigned to annotated genes using featureCounts. https://github.com/crmnbttlr/IFNAR1.L1M2a_2023
differential expression was performed using DESeq2. Pairwise analyses were conducted between wildtype and knockout datasets of the same timepoint, or between untreated and treated timepoints of the same genotype. Likelihood ratio tests were conducted to assess overall difference in interferon response of genes. https://github.com/crmnbttlr/IFNAR1.L1M2a_2023
Assembly: hg38
Supplementary files format and content: tab-delimited text files including normalized counts and DESeq output statistics

source_name: lymphoblastoid cell line

growth_protocol: Cells were grown at 37C in 5% CO2  in RPMI (Gibco (#72400-047) supplemented with 1X penicillin-streptomycin (Gibco #15140122), and 15% fetal bovine serum (Gibco #10437010).

extract_protocol:
Cells were lysed and RNA collected using Zymo Quick-RNA Miniprep Plus Kit (Zymo #R1057). Lysates were stored at -20°C prior to RNA extraction, and extracted RNA was stored at -20°C before library preparation.
Libraries preparation was performed using KAPA mRNA HyperPrep Kit (KAPA #KK8581) according to kit instructions.

treatment_protocol: Cells were resuspended in either untreated complete media or media treated with 10 units/mL of human IFNb (Proteintech #HZ-1298) and incubated at 37C for 4 hours, 12 hours, or 24 hours before lysing.

value: lymphoblastoid cell line

value: wildtype

value: untreated

tag: timepoint


title: GM12878 WT UT RNA rep2


title: HUVECs, miR-483 overexpression, Rep 2

value: Day 2


title: GM12878 WT 4hrIFNb RNA rep1

value: 10 U/ml hIFNb


title: GM12878 WT 4hrIFNb RNA rep2


title: GM12878 KO clone MN6.G11 UT RNA rep2

value: KO IFNAR1.L1M2a.enh clone MN6.G11


title: H1

value: whole blood

value: healthy control


title: GM12878 KO clone MN8.C12 UT RNA rep2

value: KO IFNAR1.L1M2a.enh clone MN8.C12


title: GM12878 KO clone MN6.G11 UT RNA rep1


title: GM12878 KO clone MN8.C12 UT RNA rep1


title: H4


title: HUVECs, miR-483 overexpression, Rep 1

value: HUVECs

value: Human endothelial cells


title: GM12878 KO clone MN8.C12 4hrIFNb RNA rep2


title: GM12878 KO clone L4.B6 24hrIFNb RNA rep2

value: KO IFNAR1.L1M2a.enh clone L4.B6


title: Control, replicate 1

value: HAP1 cell

value: near-haploid human cell line derived from the KBM-7 chronic myelogenous leukemia  cell line


title: GM12878 KO clone MN6.G11 4hrIFNb RNA rep1


title: GM12878 KO clone MN8.C12 4hrIFNb RNA rep1


title: GM12878 KO clone L4.B6 UT RNA rep2


title: GM12878 KO clone L4.B6 4hrIFNb RNA rep2


title: GM12878 KO clone L4.B6 12hrIFNb RNA rep1


title: GM12878 KO clone L4.B6 4hrIFNb RNA rep1


title: GM12878 KO clone L4.B6 12hrIFNb RNA rep2


title: GM12878 KO clone L4.B6 UT RNA rep1


title: GM12878 KO clone L3.E4 24hrIFNb RNA rep2

value: KO IFNAR1.L1M2a.enh clone L3.E4


title: GM12878 KO clone L3.E4 UT RNA rep2


title: GM12878 KO clone L4.B6 24hrIFNb RNA rep1


title: GM12878 KO clone L3.A4 24hrIFNb RNA rep2

value: KO IFNAR1.L1M2a.enh clone L3.A4


title: GM12878 KO clone L3.E4 4hrIFNb RNA rep2


title: GM12878 KO clone L3.A4 12hrIFNb RNA rep2


title: GM12878 WT clone 2F3 UT RNA rep1

value: wildtype clone 2F3


title: GM12878 WT clone 2F3 4hrIFNb RNA rep1

value: lymphoblastoid cell line


title: GM12878 WT clone 2F3 4hrIFNb RNA rep2


title: GM12878 WT clone 2D9 4hrIFNb RNA rep2

value: wildtype clone 2D9


title: GM12878 KO clone MN6.G11 4hrIFNb RNA rep2


title: GM12878 WT clone 2D9 4hrIFNb RNA rep1


title: GM12878 KO clone L3.E4 24hrIFNb RNA rep1


title: GM12878 KO clone L3.E4 4hrIFNb RNA rep1


title: GM12878 WT clone 2D3 UT RNA rep2

value: wildtype clone 2D3

value: untreated


title: GM12878 KO clone L3.A4 4hrIFNb RNA rep2

value: 10 U/ml hIFNb


title: GM12878 KO clone L3.E4 12hrIFNb RNA rep2


title: GM12878 KO clone L3.E4 UT RNA rep1


title: GM12878 WT clone 2D9 UT RNA rep2


title: GM12878 WT clone 2D9 UT RNA rep1


title: GM12878 WT clone 2D3 UT RNA rep1


title: GM12878 KO clone L3.A4 4hrIFNb RNA rep1


title: GM12878 WT clone 2F3 UT RNA rep2


title: GM12878 WT clone 2D3 4hrIFNb RNA rep2


title: GM12878 KO clone MN8.C12 24hrIFNb RNA rep1


title: GM12878 WT clone 2D3 4hrIFNb RNA rep1


title: GM12878 KO clone L3.A4 UT RNA rep1


title: GM12878 KO clone MN8.C12 12hrIFNb RNA rep1


title: GM12878 KO clone L3.A4 UT RNA rep2


title: GM12878 WT clone 2F3 24hrIFNb RNA rep2


title: GM12878 KO clone L3.A4 12hrIFNb RNA rep1


title: GM12878 WT clone 2D9 24hrIFNb RNA rep2


title: GM12878 WT clone 2D9 12hrIFNb RNA rep2


title: GM12878 WT clone 2D9 24hrIFNb RNA rep1


title: GM12878 WT clone 2D9 12hrIFNb RNA rep1


title: GM12878 KO clone MN8.C12 12hrIFNb RNA rep2


title: GM12878 KO clone L3.E4 12hrIFNb RNA rep1


title: GM12878 KO clone MN8.C12 24hrIFNb RNA rep2


title: GM12878 KO clone MN6.G11 24hrIFNb RNA rep2

value: KO IFNAR1.L1M2a.enh clone MN6.G11


title: GM12878 WT clone 2F3 12hrIFNb RNA rep2


title: GM12878 KO clone MN6.G11 12hrIFNb RNA rep1


title: GM12878 KO clone MN6.G11 12hrIFNb RNA rep2


title: GM12878 KO clone MN6.G11 24hrIFNb RNA rep1


title: GM12878 WT clone 2F3 24hrIFNb RNA rep1


title: GM12878 WT clone 2F3 12hrIFNb RNA rep1


title: GM12878 KO clone L3.A4 24hrIFNb RNA rep1


title: GM12878 WT clone 2D3 12hrIFNb RNA rep1


title: GM12878 WT clone 2D3 24hrIFNb RNA rep2


title: GM12878 WT 24hrIFNb RNA rep2

value: wildtype


title: GM12878 WT 24hrIFNb RNA rep1


title: GM12878 WT clone 2D3 24hrIFNb RNA rep1


title: GM12878 WT UT Pol2

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
adapter sequences were trimmed with bbduk and reads were aligned to hg38 using bwa mem. https://github.com/crmnbttlr/IFNAR1.L1M2a_2023
peaks were called using macs 2 and bigwigs were generated using BedGraphToBigWig. https://github.com/crmnbttlr/IFNAR1.L1M2a_2023
Assembly: hg38
Supplementary files format and content: bed files of narrow peaks called by macs2
Library strategy: CUT&Tag

growth_protocol: Cells were grown at 37C in 5% CO2  in RPMI media (Gibco (#72400-047) supplemented with 1X penicillin-streptomycin (Gibco #15140122), and 15% fetal bovine serum (Gibco #10437010).

extract_protocol:
Nuclei were isolated according to CUT&Tag protocol (https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3) with gentle fixing. Isolated nuclei were slow frozen and stored at approximately 3 milion per ml at -80C
CUT&Tag was performed according to protocol adapted from https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3. 500 thousand cells per sample were used as input. Both primary antibody and secondary antibody labeling were performed over night. pAG-Tn5 (EpiCypher #15-1017) was used at a 1:40 dilution.

treatment_protocol: Cells were resuspended in either untreated complete media or media treated with 10 units/mL of human IFNb (Proteintech #HZ-1298) and incubated at 37C for 4 hours before harvesting nuclei.


title: GM12878 WT IFNb IgG


title: GM12878 WT UT IgG


title: GM12878 WT IFNb H3K9me3


title: GM12878 WT UT H3K27ac


title: GM12878 WT UT H3K9me3


title: GM12878 WT IFNb H3K27ac


title: GM12878 WT 12hrIFNb RNA rep1


title: GM12878 KO clone MN8.C12 IFNb IgG


title: GM12878 WT clone 2D3 12hrIFNb RNA rep2


title: GM12878 KO clone MN6.G11 IFNb H3K27ac


title: GM12878 KO clone MN8.C12 IFNb H3K9me3


title: GM12878 KO clone L3.E4 UT Pol2


title: GM12878 KO clone MN6.G11 IFNb IgG


title: GM12878 KO clone MN8.C12 IFNb H3K27ac


title: PD1_4

description:
Bulk PP tumor, anti-PD-1 treatment, biol rep 4
Column names: Gene,CTRL1,CTRL2,CTRL3,CTRL4,CTRL5,CTRL6,AZD1,AZD2,AZD3,AZD4,AZD5,AZD6,PD1_1,PD1_2,PD1_3,PD1_4,PD1_5,PD1_6,COMBO1,COMBO2,COMBO3,COMBO4,COMBO5,COMBO6

tag: strain

value: FVB/NJ

value: Bulk tumor

value: PP tumor

value: Mammary tumor

value: Pten/Trp53 double KO

value: Bulk PP tumor treated with anti-PD-1 in vivo


title: GM12878 WT clone 2F3 IFNb H3K9me3


title: GM12878 KO clone L3.E4 UT H3K9me3


title: GM12878 WT clone 2F3 IFNb H3K27ac


title: GM12878 KO clone L3.E4 UT H3K27ac


title: GM12878 KO clone MN6.G11 IFNb H3K9me3


title: GM12878 WT clone 2D9 IFNb IgG


title: GM12878 KO clone L3.E4 UT IgG


title: GM12878 WT clone 2D9 IFNb H3K9me3


title: GM12878 WT 12hrIFNb RNA rep2


title: GM12878 WT clone 2F3 IFNb IgG


title: GM12878 WT clone 2D9 IFNb H3K27ac


title: GM12878 WT clone 2D3 IFNb H3K9me3


title: GM12878 WT clone 2D3 IFNb IgG


title: DF1807_AZD4

description:
PDX, AZD6482, biol rep 4
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4

value: PDX DFBC-1807

value: Breast cancer

value: Breast cancer PDX treated with AZD6482 in vivo


title: DF1807_AZD3

description:
PDX, AZD6482, biol rep 3
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4


title: DF1807_AZD2

description:
PDX, AZD6482, biol rep 2
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4


title: DF1807_V3

description:
PDX, vehicle control, biol rep 3
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4

value: Breast cancer PDX treated with vehicle control in vivo


title: DF1807_V2

description:
PDX, vehicle control, biol rep 2
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4


title: DF1807_V4

description:
PDX, vehicle control, biol rep 4
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4


title: DF1732_AZD3

value: PDX DFBC-1732


title: DF1807_V1

description:
PDX, vehicle control, biol rep 1
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4


title: DF1732_AZD4


title: DF1732_AZD2


title: DF1732_AZD1

description:
PDX, AZD6482, biol rep 1
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4


title: DF1732_V4


title: DF1732_V2


title: DF1732_V3


title: DF1637_AZD3

value: PDX DFBC-1637


title: DF1637_AZD4


title: DF1732_V1


title: GM12878 WT clone 2D3 IFNb H3K27ac

value: lymphoblastoid cell line

value: wildtype clone 2D3


title: DF1807_AZD1