title: Imaginal wing discs, PCP, Rep5, NovaSeq X Plus

description:
Library name: PCP_NovaSeqXPlus_R5
Column name in McNeill_Ft_raw_gene_counts.txt: PCP_NovaSeqXPlus_R5

value: delta PCP


title: LN-CIS  mDC_2

status: Public on Jan 28 2025

type: SRA

city: Toronto

first: Tracy

last: McGaha

state: Ontario

address: 610 University Ave

department: Immunology

country: Canada

institute: University Health Network

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

library_source: transcriptomic

data_processing:
75b single-end reads were sequenced on a NextSeq 500 Desktop Sequencer
Reads were aligned using the STAR release102 aligner with the GRCm38 mouse genome
Count and TPM matrices were generated using RSEM v1.3.0 with the corresponding GTF file.
Raw reads were normalized using DESeq2 v1.38.3
Assembly: GRCm38, release102
Supplementary files format and content: RSEM created count and TPM matrices

molecule: polyA RNA

organism: Mus musculus

source_name: Lymph node

extract_protocol:
TDLN or LN were digested and myeloid cell were sorted
Libraries were prepared using TruSeq Stranded mRNA kit (Illumina).

tag: tissue

value: Lymph node

tag: cell line

value: tissue

tag: cell type

value: Migratory dendritic cells

tag: genotype

value: Wild type

tag: treatment

value: Cisplatin


title: Imaginal wing discs, PCP, Rep4, NovaSeq X Plus

city: St. Louis

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

country: USA

institute: Washington University School of Medicine in St. Louis

description:
Library name: PCP_NovaSeqXPlus_R4
Column name in McNeill_Ft_raw_gene_counts.txt: PCP_NovaSeqXPlus_R4

data_processing:
Quality control of reads was performed using FastQC v.0.10.
Sequence reads were trimmed for adapter sequence/low-quality sequence using Trimmomatic v.0.33.
Trimmed sequence reads were mapped to dm6 using Salmon v.1.80 with default parameters
Read count extraction and normalization were performed using edgeR.
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes raw gene counts for each Sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: imaginal wing discs

extract_protocol:
RNA was harvested using ReliaPrep RNA Tissue Miniprep System (Promega). RNA-Seq libraries were prepared with 10ng of total RNA
cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq X Plus for the functional domains and conserved region D, and NovaSeq 6000 for the conserved regions A, B, C, E, and F, using paired end reads extending 150 bases

value: imaginal wing discs


title: Flag-DET1 A375 cells #2

first: Neha

last: Rohatgi

address: Roche 7070

institute: Roche

data_processing:
Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. Supplementary files use Ensemble gene IDs, counts and RPKM statistics.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Homo sapiens

source_name: A375 human melanoma cell line

extract_protocol:
Total RNA was isolated from cells and purified using RNeasy mini kits and on-column DNAse digestion per manufacturer (Qiagen) protocol. 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million single end 50 bp reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: A375 human melanoma cell line

value: DET1 WT

tag: replicate

value: DMSO


title: LN-CIS  mDC_1

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: 760560_PBMC_unstim_HC

city: Tel Aviv

first: Rachel

last: Brandes Leibovitz

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

data_processing:
MMSEQ package was used to infer gene expression levels
we mapped clean reads to reference transcripts using Bowtie2 software
we calculated the gene  expression level (FPKM) for each sample with the RSEM software
Assembly: hg19
Supplementary files format and content: FPKM normalized reads

source_name: PBMC

extract_protocol: RNA was extracted using the RNEasy mini kit.

tag: disease state

value: Healthy control

value: PBMC


title: 760559_PBMC_unstim_HC


title: 760574_PBMC_unstim_HC


title: 760566_PBMC_unstim_HC


title: Flag-DET1 A375 cells + Cobimetinib #1

value: Cobimetinib


title: 760556_PBMC_unstim_HC


title: Imaginal wing discs, PCP, Rep3, NovaSeq X Plus

description:
Library name: PCP_NovaSeqXPlus_R3
Column name in McNeill_Ft_raw_gene_counts.txt: PCP_NovaSeqXPlus_R3


title: Imaginal wing discs, PCP, Rep2, NovaSeq X Plus

description:
Library name: PCP_NovaSeqXPlus_R2
Column name in McNeill_Ft_raw_gene_counts.txt: PCP_NovaSeqXPlus_R2


title: 760555_PBMC_unstim_HC


title: TDLN-PBS mDC_2

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

source_name: Tumor-draining lymph node

value: Tumor-draining lymph node

value: PBS


title: seedling, cpie35_3_rep3

city: Wuhan

first: Ying

last: Zhang

address: Shizishan

country: China

institute: Huazhong Agricultural University

data_processing:
RNA-seq reads with low sequencing quality or reads with sequencing adaptors were filtered from the raw data. The resulting clean reads were then aligned to the A. thaliana reference genome (TAIR10) using Hisat2 with default parameters. A GFF formatted gene model annotation file was provided for reads alignment. Following the alignments, transcriptome quantification based on gene level was performed by FeatureCounts 46 and then used DESeq2 to find the significant differential gene expression. Genes with expression fold change ≥ 2 and false discovery rate (FDR) < 0.05 were considered as significantly different between samples with and without flg22 treatment. The differentially expressed genes were chosen for the hierarchical clustering analysis. A clustering heat map was generated using the TBtools software. GO term enrichment in each gene list was identified using agriGO v2.0 with the latest A. thaliana GO term annotations. The cutoff for significant enrichment is P-value < 0.05. The fold enrichment was calculated based on the frequency of genes annotated to the term compared with their frequency in the genome.
Assembly: Arabidopsis genome (TAIR10) was obtained from Ensembl (http://plants.ensembl.org/).
Supplementary files format and content: *BIGWIG , the genome coverage of each sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Ten-day-old seedlings were cultured on half-strength Murashige and Skoog (1/2MS) plates containing 1% sucrose and 0.8% agar, and grown in a growth room at 21°C, 45% humidity, and 75 μE m-2 s-1 light with a 12-hr-light/12-hr-dark photoperiod.

extract_protocol:
Total RNA was extracted from 2-week-old A. thaliana seedlings by TRNzol reagent and quantified with NanoDrop. For each repeat, equal amounts of RNA from three biological replicates were pooled for RNA-seq library construction.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR (1.5 nM). The qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and data amount required.

treatment_protocol: Three replicates treated by  chitin.

value: seedling

value: chitin-3 h


title: Imaginal wing discs, PCP, Rep1, NovaSeq X Plus

description:
Library name: PCP_NovaSeqXPlus_R1
Column name in McNeill_Ft_raw_gene_counts.txt: PCP_NovaSeqXPlus_R1

value: delta PCP


title: 760551_PBMC_unstim_HC


title: TDLN-PBS mDC_1

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: Imaginal wing discs, HpoN+PH, Rep4, NovaSeq X Plus

description:
Library name: HpoNPH_NovaSeqXPlus_R4
Column name in McNeill_Ft_raw_gene_counts.txt: HpoNPH_NovaSeqXPlus_R4

value: delta HpoN+PH


title: seedling, cpie35_3_rep2


title: TDLN-CIS mDC_3

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

value: tissue


title: seedling, cpie35_3_rep1


title: Imaginal wing discs, HpoN+PH, Rep3, NovaSeq X Plus

description:
Library name: HpoNPH_NovaSeqXPlus_R3
Column name in McNeill_Ft_raw_gene_counts.txt: HpoNPH_NovaSeqXPlus_R3


title: 760549_PBMC_unstim_HC


title: TDLN-CIS mDC_2

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

value: Migratory dendritic cells


title: Imaginal wing discs, HpoN+PH, Rep2, NovaSeq X Plus

description:
Library name: HpoNPH_NovaSeqXPlus_R2
Column name in McNeill_Ft_raw_gene_counts.txt: HpoNPH_NovaSeqXPlus_R2


title: TDLN-CIS mDC_1

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

value: Wild type


title: Imaginal wing discs, HpoN+PH, Rep1, NovaSeq X Plus

description:
Library name: HpoNPH_NovaSeqXPlus_R1
Column name in McNeill_Ft_raw_gene_counts.txt: HpoNPH_NovaSeqXPlus_R1


title: 760548_PBMC_unstim_HC


title: seedling, cpie35_1_rep2

value: chitin-1 h


title: seedling, cpie35_1_rep3


title: TDLN-PBS SSM_3

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: Subcapsular sinus macrophage


title: TDLN-PBS mDC_3

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: 760547_PBMC_unstim_HC


title: Imaginal wing discs, HpoC, Rep5, NovaSeq X Plus

description:
Library name: HpoC_NovaSeqXPlus_R5
Column name in McNeill_Ft_raw_gene_counts.txt: HpoC_NovaSeqXPlus_R5

value: imaginal wing discs

value: delta HpoC


title: LN-PBS  mDC_1

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

value: Lymph node


title: seedling, cpie35_1_rep1


title: Imaginal wing discs, HpoC, Rep4, NovaSeq X Plus

description:
Library name: HpoC_NovaSeqXPlus_R4
Column name in McNeill_Ft_raw_gene_counts.txt: HpoC_NovaSeqXPlus_R4


title: TDLN-PBS SSM_1

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv


title: 760545_PBMC_unstim_HC

value: Healthy control


title: seedling, cpie35_0.5_rep2

value: chitin-0.5 h


title: Imaginal wing discs, HpoC, Rep3, NovaSeq X Plus

description:
Library name: HpoC_NovaSeqXPlus_R3
Column name in McNeill_Ft_raw_gene_counts.txt: HpoC_NovaSeqXPlus_R3


title: 760544_PBMC_unstim_HC

value: PBMC


title: seedling, cpie35_0.5_rep1


title: Imaginal wing discs, HpoC, Rep2, NovaSeq X Plus

description:
Library name: HpoC_NovaSeqXPlus_R2
Column name in McNeill_Ft_raw_gene_counts.txt: HpoC_NovaSeqXPlus_R2


title: 760543_PBMC_unstim_HC


title: TDLN-PBS MSM_2

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: Tumor-draining lymph node

value: Medullary sinus macrophage


title: Imaginal wing discs, HpoC, Rep1, NovaSeq X Plus

description:
Library name: HpoC_NovaSeqXPlus_R1
Column name in McNeill_Ft_raw_gene_counts.txt: HpoC_NovaSeqXPlus_R1


title: seedling, cpie35_0_rep3

value: seedling

value: mock


title: Imaginal wing discs, Fd5-5, Rep2, NovaSeq X Plus

description:
Library name: FD55_NovaSeqXPlus_R2
Column name in McNeill_Ft_raw_gene_counts.txt: FD55_NovaSeqXPlus_R2


title: TDLN-PBS MSM_1

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: PBS


title: seedling, cpie35_0_rep1


title: 760546_PBMC_unstim_HC


title: TDLN-CIS SSM 2

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: Cisplatin


title: 760541_PBMC_unstim_HC


title: seedling, cpie35_0.5_rep3


title: Imaginal wing discs, WT, Rep2, NovaSeq X Plus

description:
Library name: w1118.csvd111_NovaSeqXPlus_R2
Column name in McNeill_Ft_raw_gene_counts.txt: w1118.csvd111_NovaSeqXPlus_R2

value: WT


title: TDLN-CIS SSM 1

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: tissue


title: 760536_PBMC_unstim_HC


title: TDLN-PBS SSM_2

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: Wild type


title: 760537_PBMC_unstim_HC


title: seedling, Col-0_3_rep3

value: chitin-3 h


title: Imaginal wing discs, WT, Rep1, NovaSeq X Plus

description:
Library name: w1118.csvd111_NovaSeqXPlus_R1
Column name in McNeill_Ft_raw_gene_counts.txt: w1118.csvd111_NovaSeqXPlus_R1


title: TDLN-PBS MSM_3

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv


title: TDLN-CIS MSM_3

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv


title: 760535_PBMC_unstim_HC


title: 760534_PBMC_unstim_HC


title: TDLN-CIS MSM_2

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv


title: seedling, Col-0_1_rep3

value: chitin-1 h


title: seedling, cpie35_0_rep2


title: 760539_PBMC_unstim_HC


title: Imaginal wing discs, Fd5-5, Rep1, NovaSeq X Plus

description:
Library name: FD55_NovaSeqXPlus_R1
Column name in McNeill_Ft_raw_gene_counts.txt: FD55_NovaSeqXPlus_R1

value: imaginal wing discs


title: TDLN-CIS MSM_1

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv


title: 760533_PBMC_unstim_HC


title: A549_24hr_PR8_rep2

type: RNA

city: Changchun

first: Ming

last: Duan

state: Jilin

address: 5333 Xian Road

institute: Jiin Univiersity

description: circRNA expression data from PR8-infected A550 cells

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

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: A549 cells

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: The A549 cells were maintained in RPMI 1640 medium with 10% (v/v) fetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin and cultured at 37℃, 5% CO2 atmosphere.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: A549 cells were mock infected or virus infected with PR8 at a multiplicity of infection (MOI) of 2.

tag: tag

value: cell line


title: LN-PBS SSM 3

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: Lymph node

value: Subcapsular sinus macrophage


title: 760532_PBMC_unstim_HC

value: Healthy control


title: seedling, Col-0_1_rep1


title: seedling, Col-0_1_rep2


title: A549_24hr_PR8_rep3

description: circRNA expression data from PR8-infected A551 cells


title: A549_24hr_PR8_rep1

description: circRNA expression data from PR8-infected A549 cells


title: 760529_PBMC_unstim_HC

value: PBMC


title: LN-PBS SSM 2

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv


title: seedling, Col-0_3_rep2


title: seedling, Col-0_0.5_rep3

value: chitin-0.5 h


title: LN-PBS SSM 1

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv


title: 760527_PBMC_unstim_HC


title: seedling, Col-0_3_rep1


title: A549_24hr_mock_rep3

description: circRNA expression data from mock-infected A551 cells


title: seedling, Col-0_0.5_rep2


title: LN-PBS MSM_3

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: Medullary sinus macrophage


title: 760526_PBMC_unstim_HC


title: seedling, Col-0_0.5_rep1

value: seedling


title: A549_24hr_mock_rep2

description: circRNA expression data from mock-infected A550 cells


title: 760550_PBMC_unstim_HC


title: LN-PBS MSM_2

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv


title: seedling, Col-0_0_rep3

value: mock


title: MutuDC_OVA

city: Beijing

first: Zhongfei

last: Ma

address: DongDanSanTiao, DongCheng district

institute: Chinese Academy of Medical Sciences

description: Library name: Sample

data_processing:
Illumina CASAVA 1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genome (GRCm38/mm10).
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Excel file including the gene count

source_name: MutuDC

extract_protocol:
RNA was harvested using Trizol reagent. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Library was constructed by Novogene China Co. Ltd. Briefly, fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: MutuDC

value: murine dendritic cells

value: wild type

value: treated with 3 mg/ml OVA for 9 h


title: 760525_PBMC_unstim_HC


title: 760521_PBMC_unstim_HC


title: 760523_PBMC_unstim_HC


title: LN-PBS MSM_1

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: tissue

value: Wild type

value: PBS


title: seedling, Col-0_0_rep2


title: LN-CIS SSM 2

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: Cisplatin


title: Lung endothelial cells from mice4 under ND

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
Obtained reads were single-end 85bp. Clontech adapters were removed with cutadapt, and later the last 15bp were removed from reads. Reads were then analysed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19, allowing three mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1, using the mouse gene annotation from GENCODE (gencode.vM20.GRCm38.Ensembl95). Differential expression was performed with DESeq2, using a 0.05 FDR.  GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: GRCm38
Supplementary files format and content: Tabulated text file with DESeq2 normalized counts

source_name: Lung

extract_protocol:
Total RNA was extracted using the TRIzol Reagent (Invitrogen). After recovery of the aqueous phase using chloroform, DNase treatment and further purification were performed using the RNeasy Micro kit (Qiagen) following the manufacturer’s instructions.
500 cells per sample were were processed with the "NEBNext Single Cell/Low Input RNA Library Prep" kit (NEB #E6420) by following manufacturer instructions. Briefly, extracts obtained by sample suspension in cell lysis buffer were submitted to an oligo(dT) primed reverse transcription with a template switching reaction. Double stranded cDNA production was performed by limited-cycle PCR. Sequencing libraries were completed with the "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" (NEB #E7805) and subsequently analysed on anIllumina NextSeq 550 (with v2.5 reagent kits).

value: Lung

value: endothelial cell

value: ND for 3 months


title: Control, Tetramer and Anti-CD28, 24h, Rep 3

city: Baltimore

first: Joel

middle: L.

last: Pomerantz

state: MD

address: 733 N Broadway, Room 623

department: Department of Biological Chemistry and Institute for Cell Engineering

institute: Johns Hopkins University School of Medicine

data_processing:
FASTQ data were processed in fastp software to remove low quality reads and reads containing adapter and poly-N sequences.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the reads for each mapped gene.
Assembly: Mus Musculus(GRCm38.p6)
Supplementary files format and content: RawCounts_All.txt tab-delimited text file contains raw counts for each gene in each sample.
Supplementary files format and content: FPKM_All.txt tab delimited text file contains FPKM for each gene in each sample.

source_name: CD8+ T cells

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy Mini Kit with on-column DNase digestion according to the manufacturer’s instructions.
mRNA was purified from total RNA via polyA enrichment. Libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions.

treatment_protocol: OT-1 CD8+ T cells were harvested from the spleen using the Miltenyi CD8a+ T Cell Isolation Kit (Mouse) according to the manufacturer's instructions. Cells were either left unstimulated or treated for 4 or 24hrs with MHC Class I N4 Ova tetramer (1nM) with or without anti-CD28 co-stimulation (2µg/mL).

value: CD8+ T cells

value: QRICH1-fl/fl, OT-1/+

value: N4 Ova Tetramer and Anti-CD28, 24hrs


title: Control, Tetramer and Anti-CD28, 24h, Rep 1


title: 760524_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: LN-CIS SSM 3

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: Lymph node

value: Subcapsular sinus macrophage


title: 760520_PBMC_unstim_HC


title: Lung endothelial cells from mice3 under ND


title: 760519_PBMC_unstim_HC


title: LN-CIS SSM 1

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv


title: LN-CIS MSM_3

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: Medullary sinus macrophage


title: Control, Tetramer, 24h, Rep 3

value: N4 Ova Tetramer, 24hrs


title: Control, Tetramer, 24h, Rep 2


title: LN-CIS MSM_2

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv


title: 760518_PBMC_unstim_HC


title: Lung endothelial cells from mice5 under HFD

value: HFD for 3 months


title: Control, Tetramer, 24h, Rep 1


title: 760517_PBMC_unstim_HC


title: LN-CIS MSM_1

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

value: tissue


title: A549_24hr_mock_rep1

description: circRNA expression data from mock-infected A549 cells

value: cell line


title: Lung endothelial cells from mice4 under HFD


title: Control, Tetramer and Anti-CD28, 24h, Rep 2


title: seedling, Col-0_0_rep1

value: seedling

value: mock


title: 760515_PBMC_unstim_HC


title: Control, Tetramer and Anti-CD28, 4h, Rep 3

value: N4 Ova Tetramer and Anti-CD28, 4hrs


title: 760513_PBMC_unstim_HC


title: Flag-DET1 A375 cells #1

value: A375 human melanoma cell line

value: DET1 WT

value: DMSO


title: Control, Tetramer and Anti-CD28, 4h, Rep 2

value: CD8+ T cells

value: QRICH1-fl/fl, OT-1/+


title: Lung endothelial cells from mice2 under HFD

value: Lung

value: endothelial cell


title: Cpt1a KO, rep3

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V4.0.3, Rstudio V1.3.1093 and biomaRt V2.46.0
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Differential gene expression analysis was performed via limma (v.3.46.0) R package, after normalization via the trimmed mean of M-values (TMM) method
Assembly: mm10
Supplementary files format and content: tab-delimited text containing raw counts

source_name: Islet

growth_protocol: Islets were extracted from perfused pancreata, and cultured in RPMI 1640 with 10% FBS and Pen/Strep/Amphotericin for 48 hours.

extract_protocol:
RNA was extracted using a Qiagen RNeasy Kit
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: No treatment

tag: strain

value: Cpt1a knockout mice


title: Cpt1a KO, rep4


title: Lung endothelial cells from mice1 under ND

value: ND for 3 months


title: 760507_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: Top2HTP_wt_none_3a

city: Warsaw

first: Tomasz

middle: Wojciech

last: Turowski

address: Pawinskiego 5a

department: Laboratory of Transcription Mechanisms

country: Poland

institute: Insitute of Biochemistry and Biophysics PAS

description: RNA bound to Top2

data_processing:
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were kept. Barcode is always first segment of each name.
Collapsing reads: To remove PCR duplicates, reads were collapsed usinf fastx_collapser, part of FASTX Toolkit 0.0.14
Debrarcoding: The 5' barcodes were removed using FASTX-trimmer from FASTX toolkit v0.0.14
Filtering reads: Reads were trimmed using flexbar v3.5.0 to remove the 3’-linker sequence and were additionaly filtered and only 3'linker-containing reads were included to further analyses.
Reads alignment: Reads were aligned to the Saccharomyces cerevisiae genome sequence (Ensembl release EF4.74) by STAR v2.7.10a
Additional processing: novoalign SAM reads were modified using custom made script to keep only the 5' or 3' ends of reads. SAM files were converted to BAM format using samtools v1.15.1 and BigWig files were generated using using bamCoverage script from deepTools package v3.5.1 (reads) or trxtools v0.2.2 (5' ends, 3' ends and non-coded RNA on the 3' ends)
Assembly: sacCer3, EF4.74
Supplementary files format and content: Genomic coordinates of the 3' ends of mapped reads in BigWig format
Supplementary files format and content: Genomic coordinates of the non-coded polyA on the 3' ends of mapped reads in BigWig format
Supplementary files format and content: Genomic coordinates of the 5' ends of mapped reads in BigWig format
Supplementary files format and content: Genomic coordinates of mapped reads in BigWig format

organism: Saccharomyces cerevisiae

growth_protocol: S.cerevisiae strains expressing C-terminal HTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified using three step purification. Last purification was performed under denaturing conditions and RNAs associated with HTP tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking at 254 nm for 100s usnig Megatron.

tag: in line_barcode

value: NNNGACTTAGC


title: Control, Tetramer, 4h, Rep 3

value: N4 Ova Tetramer, 4hrs


title: Cpt1a KO, rep1


title: Cpt1a KO, rep2


title: 760508_PBMC_unstim_HC


title: Top2HTP_wt_none_3b

description: RNA bound to Top2

value: NNNAGAGC


title: Control, Tetramer, 4h, Rep 2


title: Control, Tetramer and Anti-CD28, 4h, Rep 1


title: Cpt1a WT, rep4

value: Wild-type mice


title: 760506_PBMC_unstim_HC


title: Top2HTP_wt_none_2a

description: RNA bound to Top2


title: 760504_PBMC_unstim_HC


title: Control, Tetramer, 4h, Rep 1


title: Top2HTP_wt_none_1

description: RNA bound to Top2

value: NNNGCGCAGC


title: Control, Unstim, Rep 3

value: Unstim


title: 760502_PBMC_unstim_HC


title: Top2HTP_wt_none_2b

description: RNA bound to Top2


title: Cpt1a WT, rep2


title: Rpa135HTP_wt_none_6b

description: nascent RNA covalently attached to RNAPI

value: NNNCTAGC


title: Control, Unstim, Rep 2


title: 760501_PBMC_unstim_HC


title: Cpt1a WT, rep1


title: 760499_PBMC_unstim_HC


title: Rpa135HTP_wt_none_6a

value: NNNATTAGC


title: QRICH1 KO, Tetramer and Anti-CD28, 24h, Rep 1

value: QRICH1-fl/fl, OT-1/CD4-Cre

value: N4 Ova Tetramer and Anti-CD28, 24hrs


title: Rpa135HTP_Rpa12dC-nsi1d_none_2a

value: Rpa135-HTP Rpa12dC nsi1d

value: NNNGTGAGC


title: Hy5-3

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
Illumina bcl2fastq software (v.2.20.0) used for basecalling.
Sequenced reads were mapped to Phytozome v13 CreinhardtiiCC_4532_707_v6.1 whole genome using STAR v. 2.7.10b with default parameters
Raw counts are produced by htseq-count (HTSeq v. 0.11.3)
Normalization and differential expression analysis were performed with edgeR v3.42.4
Assembly: Phytozome v13 CreinhardtiiCC_4532_707_v6.1
Supplementary files format and content: rawcounts.txt = tab-delimited text files include rawcount values for each Sample

organism: Chlamydomonas reinhardtii

growth_protocol: Algae cells were grown in the Tris Acetate Phosphate (TAP) growth medium under continuous light (20 µmol photons m-2 s-1, from LED panels) and shaking (110 rpm). Cells were harvested during the exponential phase (2-3 x 106 cells per mL), washed, and resuspended in High Salt Medium (HSM) minimal growth medium at 4.5 x 106 cells per mL. They were placed for at least 1 h under dim light (20 µmol photons m-2 s-1) before applying specific light treatments.

extract_protocol:
20 million cells were pelleted and frozen in liquid nitrogen. RNA were extracted using the RNeasy Plant Mini Kit (Qiagen) including a DNase treatment to remove residual genomic DNA (RNase-Free DNase Set, Qiagen).
Illumina TruSeq HT stranded mRNA

treatment_protocol: UV-B-exposed samples (+ UV-B) were treated by Philips TL20W/01S narrowband UV-B tubes filtered with a WG filter (Schott Glaswerke) with half-maximal transmission at 311 nm (0.2 mW cm2). Control (-UV-B) samples were placed under a WG filter with half-maximal transmission at 360 nm to block UV-B. In both conditions, samples were concomitantly exposed to dim light (20 µmol photons m-² s-1) provided by fluorescent white light tubes (Osram Dulux L).


title: Rpa135HTP_Rpa12dC-nsi1d_none_1b

value: NNNACTCAGC


title: 760498_PBMC_unstim_HC


title: QRICH1 KO, Tetramer and Anti-CD28, 24h, Rep 3

value: CD8+ T cells


title: 760496_PBMC_unstim_HC


title: Rpa135HTP_Rpa12dC-nsi1d_none_2b


title: Cpt1a WT, rep3


title: 760497_PBMC_unstim_HC


title: QRICH1 KO, Tetramer and Anti-CD28, 24h, Rep 2


title: QRICH1 KO, Tetramer, 24h, Rep 3

value: N4 Ova Tetramer, 24hrs


title: CO-3

value: co


title: Rpa135HTP_Rpa12dC-nsi1d_none_1a


title: uvr8+3

value: UVB


title: CO+3


title: Rpa135HTP_Rpa12dC_none_5b

value: Rpa135-HTP Rpa12dC

value: NNNTGGAGC


title: uvr8-3


title: 760492_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: QRICH1 KO, Tetramer, 24h, Rep 2


title: 760495_PBMC_unstim_HC


title: Control, Unstim, Rep 1

value: QRICH1-fl/fl, OT-1/+


title: Hy5+3


title: 760490_PBMC_unstim_HC


title: WT+3

value: WT


title: Rpa135HTP_Rpa12dC_none_5a

value: NNNGCGCAGC


title: QRICH1 KO, Tetramer, 24h, Rep 1


title: Rpa135HTP_nsi1d_none_2b

value: Rpa135-HTP nsi1d

value: NNNTAGTGC


title: QRICH1 KO, Tetramer and Anti-CD28, 4h, Rep 3

value: QRICH1-fl/fl, OT-1/CD4-Cre

value: N4 Ova Tetramer and Anti-CD28, 4hrs


title: 760489_PBMC_unstim_HC


title: 760486_PBMC_unstim_HC


title: WT-3


title: Rpa135HTP_nsi1d_none_1b

value: NNNGCACTA


title: QRICH1 KO, Tetramer and Anti-CD28, 4h, Rep 2


title: Hy5+2


title: Rpa135HTP_nsi1d_none_2a

value: NNNTCTCTAGC


title: QRICH1 KO, Tetramer and Anti-CD28, 4h, Rep 1

value: CD8+ T cells


title: QRICH1 KO, Tetramer, 4h, Rep 2

value: N4 Ova Tetramer, 4hrs


title: Hy5-2


title: 760485_PBMC_unstim_HC


title: 760483_PBMC_unstim_HC


title: 760484_PBMC_unstim_HC


title: QRICH1 KO, Tetramer, 4h, Rep 3


title: QRICH1 KO, Tetramer, 4h, Rep 1


title: Rpa135HTP_Rpa12dC_none_1


title: 760482_PBMC_unstim_HC


title: CO-2

value: co


title: Rpa135HTP_wt_none_5

value: NNNATTAGC


title: uvr8+2

value: UVB


title: Rpa135HTP_wt_none_4

value: NNNGTGAGC


title: QRICH1 KO, Unstim, Rep 3

value: Unstim


title: 760479_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: WT+2

value: WT


title: uvr8-2


title: Rpa135HTP_Rpa12dC_none_4

value: Rpa135-HTP Rpa12dC


title: 760478_PBMC_unstim_HC


title: QRICH1 KO, Unstim, Rep 2


title: Rpa135HTP_Rpa12dC_none_3

value: NNNCACTAGC


title: Rpa135HTP_nsi1d_none_1a

value: Rpa135-HTP nsi1d


title: 760477_PBMC_unstim_HC


title: QRICH1 KO, Unstim, Rep 1

value: QRICH1-fl/fl, OT-1/CD4-Cre


title: CO+2


title: WT-2


title: Rpa135HTP_Rpa12dC_none_2

value: NNNGACTTAGC


title: Rpa135HTP_wt_none_3

value: NNNACTCAGC


title: Hy5+1


title: 760476_PBMC_unstim_HC


title: CO+1


title: 760473_PBMC_unstim_HC


title: 760481_PBMC_unstim_HC


title: WT, E62, biol rep2

city: Minneapolis

first: Daniel

last: Garry

state: Minnesota

address: 2231 6th Street SE, Suite 4-156

department: Lillehei Heart Institute

institute: University of Minnesota

description: Library name: WT62_0987-4_RHL_S10_L001

data_processing:
Sequencing reads were aligned to the Sus scrofa (pig) genome assembly Sscrofa11.1 (susScr11) using kallisto.
Using tximport to determine the read count for each transcript and quantified transcript abundance as transcripts per kilobase per million reads mapped
The read counts data were normalized by DESeq2, followed by differential expression analysis
Assembly: Sscrofa11.1
Supplementary files format and content: raw counts for each Smaple

organism: Sus scrofa

source_name: Limb muscle tssue

growth_protocol: Tissue harvested from E41 and E60 stages

extract_protocol:
Qiagen Rneasy mini kit
Illumina’s TruSeq RNA Sample Preparation Kit (Cat. # RS-122-2001 or RS-122-2002) or Stranded mRNA Sample Preparation Kit (Cat. # RS-122-2101)

value: Limb muscle tssue

tag: developmental stage


title: 760472_PBMC_unstim_HC


title: CO-1


title: WT, E62, biol rep1

description: Library name: WT62_0987-3_RHL_S9_L001


title: 760471_PBMC_unstim_HC


title: Hy5-1


title: MYF5/MYOD/MYF6 knockout, E62, biol rep2

description: Library name: 212-4281_E62SKM_RHL_Emb4_S2

value: MYF5/MYOD/MYF6 knockout


title: uvr8+1


title: MYF5/MYOD/MYF6 knockout, E62, biol rep1

description: Library name: 212-4281_E62SKM_RHL_Emb1_S1


title: uvr8-1


title: 760468_PBMC_unstim_HC


title: WT-1


title: WT, E41, biol rep2

description: Library name: 181-0991-3_LHL_S2_L001


title: 760465_PBMC_unstim_HC


title: 760466_PBMC_unstim_HC


title: MYF5/MYOD/MYF6 knockout, E41, biol rep2

description: Library name: SKM_0923-3_RHL_S6_L001


title: P2S5_kidney_tumor_8_(240201_SH_Hs_P2S5_KiT4_0128)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Library name: P2S5_kidney_tumor_8
Human Kidney Tumor RNAPIIS5p

library_source: genomic

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments.
4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg19 track which is the fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw)
Assembly: hg19
Supplementary files format and content: bw
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Kidney

extract_protocol:
https://www.protocols.io/edit/cutac-for-ffpes-c5huy36w
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: Kidney

tag: group

value: Tumor

value: Human Kidney Normal/Tumor Biochain T823514PT

tag: antibody

value: RNAP2Ser5P Cell Signaling Technology cat# 13523


title: 760463_PBMC_unstim_HC


title: MYF5/MYOD/MYF6 knockout, E41, biol rep1

description: Library name: SKM_0923-1_RHL_S5_L001


title: E16,cWT,rep3

city: Ann Arbor

first: Shigeki

last: Iwase

state: Michigan

address: 1241 E. Catherine St.

department: Human Genetics

institute: University of Michigan

description: Library name: E16,cWT,rep3

data_processing:
Read quality was determined using FastQC (v0.11.8).
Reads were mapped to the mm10 genome using STAR (v2.6.1). Count files were generated by FeatureCounts (SubRead v1.5.0).
BAM files were converted to bigwigs using deepTools2 (v.3.2.0). The computational workflow was managed by Snakemake (v.5.4.0).
DESeq2 (v.1.24.0)75 was used for differential gene expression analysis. Differentially expressed genes (DEGs) were identified with a q-value <0 (p-adjusted via FDR/Benjamini-Hochberg correction), and the log2 fold changes were calculated using lfcShrink with the default apeglm package.
Assembly: mm10
Supplementary files format and content: fastq

source_name: cortex

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Kit (Zymo Research) according to the manufacturer’s protocol.
Samples were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina(catalog number E7760L) Ribo depletion Module NEBNext rRNA Human/Mouse/Rat (catalog number E6310X) and NEBNext Multiplex Oligos for Illumina Unique dual (catalog number E6440L) (NEB, Ipswich, MA). Total RNA (375 ng) was treated with the rRNA Depletion module. The rRNA-depleted RNAs were then fragmented for 10 min, determined by the RIN (RNA Integrity Number) of input RNA as per protocol, and subjected to the first-strand cDNA synthesis dUTP mix. Samples undergo end repair and dA-Tailing step followed by ligation of NEBNext adapters. The libraries were PCR-amplified and checked for quality and quantity by TapeStation (Agilent). The samples were pooled and sequenced on the Illumina NovaSeq S4 Paired-end 150bp, according to manufacturer’s recommended protocols.

treatment_protocol: RNAs from E16 cortices, 3 embryos per genotype (WT or Phf21a−/−, the sex was balanced between genotypes), was assessed for quality using the TapeStation (Agilent, Santa Clara, CA).

value: cortex


title: 760462_PBMC_unstim_HC


title: 760461_PBMC_unstim_HC


title: E16,cWT,rep2

description: Library name: E16,cWT,rep2


title: H69AR, doxorubicin, rep2

city: Guangzhou

first: Qiong

last: Lyu

state: Guang Dong

address: 253 GongYe Road

department: Oncology

institute: Zhujiang Hospital, Southern Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt.
Sequencing reads were mapped to the human reference genome (NCBI38/hg38).
The RNA-seq data was mapped to the human reference annotation (NCBI38/hg38)  by HISAT2, and the read counts at the gene level were aggregated by HTSeq.
Assembly: hg38
Supplementary files format and content: The comma-separated file includes normalized values for each sample and the output data from differential expression analysis.

source_name: Pleural effusion

growth_protocol: All cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS) and antibiotics in an incubator at 37˚C with 5% CO2. The chemoresistant cell lines H69AR were cultured with addional adriamycin necessary to maintain their chemoresistance.

extract_protocol:
Qiagen Rneasy total RNA extraction
RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina following manufacturer's protocols.

value: Pleural effusion

value: Small cell lung cancer

value: RPMI-1640 medium containing 10% fetal calf serum,doxorubicin


title: E16,cWT,rep1

description: Library name: E16,cWT,rep1

value: WT


title: H69AR, doxorubicin, rep1


title: 760459_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: 760458_PBMC_unstim_HC


title: E16,cKO,rep3

description: Library name: E16,cKO,rep3


title: E16,cKO,rep2

description: Library name: E16,cKO,rep2


title: 760457_PBMC_unstim_HC


title: H69, parental, rep2

value: RPMI-1640 medium containing 10% fetal calf serum


title: WT+1

value: UVB


title: WT, E41, biol rep1

description: Library name: 181-0991-1_LHL_S1_L001


title: E16,cKO,rep1

description: Library name: E16,cKO,rep1


title: 760456_PBMC_unstim_HC


title: H69, parental, rep1


title: Ion_024

city: Valencia

first: Joaquin

last: Panadero

state: Valencia

address: Avenida Fernando Abril Martorell, 106 Torre A

department: Genomics

institute: Instituto Investigación Sanitaria La Fe

data_processing:
fastq alignment against miRBase “has” reference
read counts obtained from BAM/SAM files using htseqCount
Assembly: GRCh38
Supplementary files format and content: Tabular delimited text file containing read counts

source_name: Ovary

growth_protocol: Not applicable

extract_protocol:
Fresh tissues were fragmented with a scalpel and homogenised using the Fisherbrand™ 150 handheld homogenizer (Fisherbrand™). RNA was extracted from 25 mg of fresh tissue using the mirVana miRNA Isolation Kit (Ambion), following manufacturer’s recommendations.
The RNA integrity of the extracted total RNA was analysed using the Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer (Agilent Technologies) and assessed by the RNA integrity number (RIN). A RIN cut-off value of ≥6.0 was considered for subsequent miRNA library preparation. Library preparation was performed using the CleanTag Small RNA Library Preparation Kit (TriLink Biotechnologies®) following manufacturer’s protocol. Briefly, 100 ng of the isolated total RNA were employed and sequential steps of 3’ and 5’ adapter ligation, reverse transcription (RT) reaction of tagged RNA library and PCR amplification were performed from each RNA sample. PCR products were purified following a 2-step protocol with the Agencourt AMPure XP Beads (Beckman Coulter™), yielding a total of 15 μL of purified library. Then, library preparation efficacy was evaluated using the Agilent DNA 1000 Kit on an Agilent 2100 Bioanalyzer (Agilent Technologies). A 142pb peak, representing tagged small RNA of ~21nt in the small RNA libraries, was considered suitable. Finally, miRNA sequencing was performed on an Ion GeneStudio™ S5 Systems (Ion Torrent™), using an Ion 540™ Chip (Ion Torrent™) with appropriate reagents.

treatment_protocol: Fresh tissue samples were preserved in RNAlater® (Applied Biosystems) and stored at - 80 ºC until processed.

value: Ovary

tag: sample type


title: H69, parental, rep3


title: Cdh2fl/+-SMAA Cre Af-challenged_4

city: Boston

first: Zheming

last: An

state: Massachusetts

address: 3 Blackfan Street

department: Division of Genetics and Genomics

institute: Boston Children's Hospital

data_processing:
Raw fastq files were trimmed for quality and adapter contamination using Trimmomatic 0.38. Trimmed reads were mapped to a reference genome (UCSC mm10) with HISAT2 V2.1.0. StringTie V2.1.3b was used for transcript assembly. The expression profile was calculated for each sample and transcript/gene as a read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million). Genes with fewer than 10 counts in at least two samples were removed from the dataset, across a total of 8 samples
Assembly: GRCm39

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions. RNA samples were reverse transcribed to cDNA and libraries constructed using the TruSeq DNA Library Preparation Kit (Illumina
TruSeq DNA Library standard protocol

value: Lung

value: Cdh2fl/+-SMAA Cre


title: Cdh2fl/+-SMAA Cre Af-challenged_3


title: Ion_024_1


title: P2S5_kidney_tumor_7_(240118_SH_Hs_P2S5_KT2_0113)

description:
Library name: P2S5_kidney_tumor_7
Human Kidney Tumor RNAPIIS5p


title: 760454_PBMC_unstim_HC


title: H69AR, doxorubicin, rep3


title: Cdh2fl/+-SMAA Cre Af-challenged_2


title: 760464_PBMC_unstim_HC


title: Ion_023

value: Control


title: 760450_PBMC_unstim_HC


title: Cdh2fl/+-SMAA Cre Af-challenged_1


title: 760449_PBMC_unstim_HC


title: Ion_023_1


title: WT Af-challenged_4


title: Ion_022


title: 760446_PBMC_unstim_HC


title: 760448_PBMC_unstim_HC


title: 760455_PBMC_unstim_HC


title: 760444_PBMC_unstim_HC


title: WT Af-challenged_2


title: Ion_021


title: WT Af-challenged_3


title: Ion_022_1


title: WT Af-challenged_1


title: 760443_PBMC_unstim_HC


title: 760442_PBMC_unstim_HC


title: HFD6Right

city: Salt Lake City

first: Natalia

middle: Sara

last: Harasymowicz

state: UT

address: 26 Medical Dr N

department: Orthopaedics

institute: University of Utah

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The obtained reads were aligned to the mouse UCSC mm10 reference genome. The alignment results were used to quantify the gene expression level and to generate a gene-barcode matrix. Based on mitochondrial genes, the number of genes and UMIs expressed in each cell, low-quality cells, and potentially dead cells were removed.
Assembly: mm10
Supplementary files format and content: fastq.gz
Supplementary files format and content: mtx tsv

source_name: synovial capsule

extract_protocol:
Single, live synovial CD45+ cells were isolated by flow cytometry sorting and subsequently analyzed by scRNA-seq.
Approximately 1000 cells/µL were loaded into an eight-channel microfluidic chip, which encapsulated them with gel beads (GEMs) and barcoded with a unique molecular identifier (UMI) using 10xGenomics Single Cell 3′ reagent kit following manufacturer instructions (10xGenomics, Pleasanton, CA).
A single-cell RNA-seq library from each biological replicate was run independently on Illumina NovaSeq flow cell with 26x98 bp reads and generated approximately 38,000-1,000,000 mean reads per library capturing 700-16000 cells per mice (see details in sTable 3).

value: synovial capsule

value: sorted CD45 cells

tag: Sex

value: Male

value: HFD


title: 760441_PBMC_unstim_HC


title: Ion_019


title: HFD6Left

description: 10x Genomics


title: Ion_018

value: Tumor


title: HFD5Right

description: 10x Genomics


title: 760440_PBMC_unstim_HC


title: Ion_017


title: HFD5Left

description: 10x Genomics


title: 760438_PBMC_unstim_HC


title: Ion_016


title: HFD4Right

description: 10x Genomics


title: 760439_PBMC_unstim_HC


title: 760437_PBMC_unstim_HC


title: Ion_016_1


title: HFD4Left

description: 10x Genomics


title: Control6Right

description: 10x Genomics

value: Control Diet


title: Ion_021_1


title: △Xist-R2

city: Bangalore

first: SRIMONTA

last: GAYEN

state: Karnataka

address: GE14, new biological science building, Indian institute of Science

department: Department of Developmental biology and Genetics

country: India

institute: Indian Institute of Science, Bangalore, India

data_processing:
Quality of RNA-seq reads was checked using FastQC
Reads were mapped to the mouse genome GRCm38 (mm10) using STAR (2.7.9a)
Read counting was done using featureCounts (2.0.1)
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each samples

source_name: EpiSC

growth_protocol: XEN cells were cultured in DMEM supplemented with FBS, L-glutamine, Pen-strep, NEAA etc. EpiSC were cultured on matrigel using knockout DMEM supplemented with KO FBS, FGF2, Activin

extract_protocol:
Total RNA was extracted from XEN and EpiSC cells following the Trizol RNA extraction method
RNA-seq library was prepared following the manufacturer’s guidelines using the NEBNext Ultra/Tru-seq stranded RNA library preparation kit for Illumina.

treatment_protocol: Cells were treated with 20uM 5-Aza 2 -deoxy-cytidine

value: Female

value: EpiSC

value: Epiblast Stem cells (EpiSC)

value: Heterozygous Xist deletion


title: Ion_014


title: Control6Left

description: 10x Genomics


title: Control5Right

description: 10x Genomics


title: Ion_015


title: 760436_PBMC_unstim_HC

city: Tel Aviv

first: Rachel

last: Brandes Leibovitz

address: Ramat Aviv

institute: Tel Aviv University

data_processing:
MMSEQ package was used to infer gene expression levels
we mapped clean reads to reference transcripts using Bowtie2 software
we calculated the gene  expression level (FPKM) for each sample with the RSEM software
Assembly: hg19
Supplementary files format and content: FPKM normalized reads

extract_protocol: RNA was extracted using the RNEasy mini kit.

value: Healthy control

value: PBMC


title: Ion_0151


title: 760435_PBMC_unstim_HC


title: 760430_PBMC_unstim_HC


title: Ion_029


title: Ion_014_1


title: 760428_PBMC_unstim_HC


title: Control4Right

description: 10x Genomics


title: Control4Left

description: 10x Genomics


title: Ion_013


title: Control5Left

description: 10x Genomics


title: WT-AZA-R1

source_name: XEN

value: XEN

value: Extra-embryonic endoderm stem cell (XEN)

value: WT-Aza treated


title: WT EPI R2

value: WT


title: 760429_PBMC_unstim_HC


title: TDLN-CIS SSM 3

city: Toronto

first: Tracy

last: McGaha

address: 610 University Ave

institute: University Health Network

description:
msm_ssm_counts.csv
msm_ssm_tpm.csv

data_processing:
75b single-end reads were sequenced on a NextSeq 500 Desktop Sequencer
Reads were aligned using the STAR release102 aligner with the GRCm38 mouse genome
Count and TPM matrices were generated using RSEM v1.3.0 with the corresponding GTF file.
Raw reads were normalized using DESeq2 v1.38.3
Assembly: GRCm38, release102
Supplementary files format and content: RSEM created count and TPM matrices

extract_protocol:
TDLN or LN were digested and myeloid cell were sorted
Libraries were prepared using TruSeq Stranded mRNA kit (Illumina).

value: Tumor-draining lymph node

value: tissue

value: Subcapsular sinus macrophage

value: Wild type

value: Cisplatin


title: Ion_013_1

value: Ovary

value: Control


title: Ion_012

value: Tumor


title: 760424_PBMC_unstim_HC


title: hff_48hpi_b

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

institute: Weizmann Institute

description:
Library name: Sample 2
cd14_hff_processed.csv

data_processing:
For the time course libraries, raw sequences were first trimmed at their 3′ end, removing the illumina adapter and polyA tail.
Alignment was performed using Bowtie (allowing up to 2 mismatches) and reads were aligned to concatenation of the human (hg19) and the viral genomes (NCBI EF999921.1). Reads aligned to ribosomal RNA were removed.
Reads that were not aligned to the genome were then aligned to the transcriptome.
Analysis of libraries generated with the MARS-seq protocol was done as previously described . Briefly, 37-bp reads were aligned using Bowtie (allowing up to 2 mismatches) to concatenation of the human (hg19) and the viral genomes (NCBI EF999921.1). Counting of reads per gene was done based on unique molecular identifiers (UMIs) (8 bp).
The transcription units of the virus were based on NCBI annotations, with some changes, including merging several transcripts (considering that the library maps only the 3’ ends of transcripts) and adding some antisense transcripts.
Genome_build: human (hg19) and the viral genomes (NCBI EF999921.1)
Supplementary files format and content: All processed files are comma delimited files with the number of reads on the transcripts

organism:
Homo sapiens
Human betaherpesvirus 5

growth_protocol: Human foreskin fibroblasts (ATCC CRL-1634) were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, and 100 units/ml penicillin and streptomycin (Beit-Haemek, Israel) and maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
for cd14 and hff time course experiment RNA was extracted using Tri-Reagent (Sigma-Aldrich), total RNA was extracted. poly-A selection was performed using Dynabeads mRNA DIRECT. For MARseq libraries epigenetic treatments RNA was extracted directly from cells using Dynabeads mRNA DIRECT.
Briefly, mRNA samples of ~4ng were subjected to DNaseI treatment and 3′ dephosphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3′ adaptor ligation using T4 ligase (NEB). The ligated products were used for reverse transcription with SSIII (Invitrogen) for first-strand cDNA synthesis. The cDNA products were 3′ ligated with a second adaptor using T4 ligase and amplified with 8 cycles of PCR for final library products of 200–300 base pairs. For epigenetic drug-treated CD14+ monocyte samples, RNA libraries were generated from samples of ~100,000 cells according to the MARS-seq protocol

treatment_protocol: For the time course analysis fibroblasts and CD14+ monocytes were infected with the same stock of HCMV strain TB40E-GFP at a multiplicity of infection (MOI) of 1 and 10, respectively. For all other experiments CD14+ monocytes or THP1 cells were infected with HCMV strain TB40E-GFP at an MOI of 5. Cells were incubated with the virus for 2h, washed, and supplemented with fresh medium. CHX was added to infected fibroblasts and CD14+ monocytes immediately after infection at a final concentration of 100 ug/ml and 200 ug/ml or at 100 ug/ml, respectively. PFA was added to fibroblasts and CD14+ monocytes immediately after infection at a final concentration of 400 ug/ml. for epigenetic drug treatments - 48 hpi, TB40-infected CD14+ monocytes were divided into 1.2 ml tubes containing ~100,000 cells per tube and inhibitors or DMSO for negative control were added to a final concentration of 1uM for 24 hours

tag: virus strain

value: HFF

tag: time course


title: 760420_PBMC_unstim_HC


title: 7DPI_C2

city: seoul

first: hyewon

last: chung

address: Seoul National University College of Medicine

country: South Korea

institute: seoul national university

description: Library name: 7DPI_C2

data_processing:
Illumina bcl2fastq 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 Genome assembly Macaca_fascicularis_5.0 whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: Genome assembly Macaca_fascicularis_5.0
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Macaca fascicularis

source_name: Blood

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: We isolated circulating endothelial cells at 7 days post infection (DPI) with SARS-CoV-2, comparing unvaccinated and vaccinated groups, where C represents the control group and G represents the vaccinated group.

tag: tissue

value: Blood

value: Circulating endothelial cells

tag: time

value: 7 DPI

value: not vaccinated


title: 760423_PBMC_unstim_HC

source_name: PBMC

value: Healthy control

tag: cell type

value: PBMC


title: KO, LPS+IFNG, Rep4

first: Matthew

middle: D

last: Smith

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

data_processing:
Raw sequencing files were processed by Salmon (v1.7.0) for transcript quantification using GRCm39 transcriptome reference using selective alignment with whole genome as decoy.
Salmon quantifications were imported into R with tximport (v1.30.0) and the length scaled counts were converted to a DGEList object. Low expression genes were filtered out by limma (v3.58.1) function filterByExpr with group size of 4 and then TMM scaling factors were generated using calcNormFactors function. Counts Per Million and log Counts Per Million were generated with limma function cpm, normalized argument set to TRUE, and log argument set to FALSE (cpm) or TRUE (lcpm) respectively.
Assembly: GRCm39
Supplementary files format and content: sf files: Tab seperated files with transcript name (RefSeq), Transcript Length, Effective Length, TPM, and NumReads for each sample generated by Salmon
Supplementary files format and content: cpm.csv and lcpm.csv: comma seperated spreadsheets where column is sample and row is gene. Both are post-normalization performed by limma. cpm is not log scale, lcpm is log scale (with auto-calculated prior added to avoid logarithm of 0)

source_name: p6 neonatal murine brain

growth_protocol: P6 mouse pups were euthanized, meninges removed, then dissociated with mechanical and enzymatic trituration (Papain 20U/ml, DNAse 100U/mL) for 30 minutes at 37c. They were then diluted with equal volume of 1% BSA in HBSS, centrifuged, and resuspended in 0.02% BSA in HBSS and filtered over 100μM strainer. Cells were Fc blocked and positively selected with anti-mouse ACSA2 MicroBeads and LS Columns (Miltenyi Biotec) per manufacturer's recommendations then seeded onto poly-D-lysine-coated 6 well plates at density of 5e5 cells/well. Cells were cultured in serum free media containing 50% DMEM, 50% Neurobasal, 1% pen/strep, N-acetyl cysteine (5μg/mL), and 1xSATO and supplemented with heparin-binding EGF (5ng/mL). Purify was confirmed by ICC (GFAP+, Sox9+, Iba1-). Astrocytes were grown for approximately 10 days until cultures reached a desired density with media changes every 2 days.

extract_protocol:
Cells were lysed in RLT Buffer and RNA extracted using the Rneasy Plus Mini Kit (Qiagen)
RNA was submitted to NovoGene who performed poly-A capture based RNA-seq followed by library sequencing

treatment_protocol: Cells were treated with vehicle (H2O) or 500ng/mL lipopolysacharide (LPS, Cell Signaling) and 10ng/mL IFNγ (Peprotech) for 24 hours.

value: p6 neonatal murine brain

tag: cell line

value: ACSA2 positive selection primary culture

value: Astrocyte

tag: genotype

value: LPS+IFNG


title: hff_48hpi_a

description:
Library name: Sample 1
cd14_hff_processed.csv

source_name: Human foreskin fibroblasts (ATCC CRL-1634)


title: KO, Vehicle, Rep4

tag: treatment

value: Vehicle


title: Ion_011_1


title: Ion_012_1


title: 0DPI_C2

description: Library name: 0DPI_C2

value: 0 DPI


title: Ion_011


title: KO, LPS+IFNG, Rep1


title: KO, Vehicle, Rep3


title: KO, LPS+IFNG, Rep3


title: 7DPI_G2

description: Library name: 7DPI_G2

value: vaccinated against COVID


title: WT-AZA-R2

value: Female

value: XEN

value: Extra-embryonic endoderm stem cell (XEN)

value: WT-Aza treated


title: 760418_PBMC_unstim_HC

tag: disease state


title: Ion_010_1

value: Ovary

value: Tumor


title: 7DPI_G1

description: Library name: 7DPI_G1

value: Blood

value: Circulating endothelial cells

value: 7 DPI


title: KO, LPS+IFNG, Rep2


title: PBS_negative control for serum

type: protein

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

description:
raw data files: MCF_SSK_546_Slide2_532.gpr/MCF_SSK_546_Slide2_635.gpr
IgG/IgA

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
NFI were normalized by robust linear model using build-in Ig control with various dilutions
Submission data have been preprocessed, for example, average the duplicated sopts, PBS subtracted and normalized by robost linear model using internal positive controls, values will set as 0.001 if signal intensity are less than 0

molecule: protein

organism: blank sample

label_protocol: Mouse serum /tesr samples were first treated with DNAse I to remove free-DNA and then applied onto antoantigen arrays with 1:50 dilution. The autoantibodies binding to the antigens on the array were detected with cy3-labeled anti-human IgG  and the array slides were scanned with Genepix 4400A scanner with laser wavelengths 532nm for cy3 and 635nm for cy5 to generate Tiff images.  Genepix Pro 7.0 software is used to analyze the image and generate the Genepix report (GPR) files (Molecular Devices, Sunnyvale, California, USA). The net fluorescent intensity (NFI) of each antigen was generated by subtracting the local background and negative control (Phosphate buffered saline or simplified as PBS) signal.

extract_protocol:
Serum/tear  samples from recipients collected as per routine protocol as defined above were procured from histocompatibility lab after IRB approval. All subjects were aliquoted and stored at -80ºC.
8  positive controls (anti-IgG and IgG control) were also imprinted on the arrays as positive controls.

tag: slide

tag: block

value: Negative control


title: WT, LPS+IFNG, Rep4

city: Baltimore

value: p6 neonatal murine brain

value: WT


title: KO, Vehicle, Rep1

value: ACSA2 positive selection primary culture

value: Astrocyte


title: Ion_010


title: KO, Vehicle, Rep2

value: Vehicle


title: 760416_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: 760415_PBMC_unstim_HC


title: Ion_009

value: Control


title: 760411_PBMC_unstim_HC


title: Ion_009_1


title: 0DPI_G1

description: Library name: 0DPI_G1

value: 0 DPI

value: vaccinated against COVID


title: 760413_PBMC_unstim_HC


title: BALBc_M4_serum

source_name: Serum

tag: strain

value: BALB/c


title: Ion_007

value: Ovary


title: 760417_PBMC_unstim_HC


title: Ion_008_1

value: Tumor


title: WT, Vehicle, Rep3


title: 760409_PBMC_unstim_HC


title: Ion_008


title: 0DPI_C1

description: Library name: 0DPI_C1

value: Blood

value: not vaccinated


title: BALBc_M5_serum


title: WT, LPS+IFNG, Rep3

value: LPS+IFNG


title: 760410_PBMC_unstim_HC


title: 760414_PBMC_unstim_HC


title: WT, Vehicle, Rep4


title: Ion_007_1


title: BALBc_M1_serum


title: Ion_006_1


title: BALBc_M3_serum


title: 760412_PBMC_unstim_HC


title: Ion_005


title: BALBc_M2_serum


title: BALBc_M6_serum


title: WT, Vehicle, Rep1


title: NOR_M3_serum

value: NOR


title: Ion_006


title: 760407_PBMC_unstim_HC


title: WT, LPS+IFNG, Rep2

value: p6 neonatal murine brain


title: WT, Vehicle, Rep2

value: WT


title: Ion_005_1


title: NOR_M4_serum


title: 760405_PBMC_unstim_HC


title: WT, LPS+IFNG, Rep1

value: ACSA2 positive selection primary culture


title: Ion_004_1


title: Tumor_WT_Un_Tx1

description:
ST2_Tumor_cnts.csv
ST2_Tumor_meta.csv

data_processing:
Demultiplxing, alignment, feature counting and filtering was performed with the 10x Genomics Cell Ranger v7.0.0 against reference transcriptome mm10-2020-A.
Count matrices were analyzed using Seurat v5.0.0 using Log normalization
Samples were integrated using the fast MNN approach implemented in Batchelor v1.18.1 prior to UMAP dimensional reduction
Upon subsetting for specific cell-types, the data was re-integrated prior to UMAP dimensional reduction
Assembly: mm10-2020-A
Supplementary files format and content: Raw count matrices and cellular annotation with UMAP reductions

source_name: Tumor

extract_protocol:
Tumor or matched TDLN were digested and cells sorted
Libraries were prepared using TruSeq Stranded mRNA kit (Illumina).

value: CD45 ST2-sorted

value: Untreated


title: NOR_M2_serum


title: 760404_PBMC_unstim_HC

value: Healthy control


title: 760408_PBMC_unstim_HC

value: PBMC


title: NOR_M1_serum


title: Tumor_WT_Tx1

description:
ST2_Tumor_cnts.csv
ST2_Tumor_meta.csv

value: PLX4720 Tx1


title: Tumor_KO_Un_Tx1

description:
ST2_Tumor_cnts.csv
ST2_Tumor_meta.csv


title: 760403_PBMC_unstim_HC


title: Ion_003_1

value: Control


title: Ion_002_1


title: NOD_M6_serum

value: NOD


title: Tumor_KO_Tx1

description:
ST2_Tumor_cnts.csv
ST2_Tumor_meta.csv


title: 760402_PBMC_unstim_HC


title: 760401_PBMC_unstim_HC


title: 760406_PBMC_unstim_HC


title: Ion_001_1


title: NOD_M5_serum


title: Tumor_WT_Un_Tx7

description:
ST2_Tumor_cnts.csv
ST2_Tumor_meta.csv


title: WT mouse 3

city: New York

first: Anqi

last: Wang

state: NY

address: 530 West 166th Street

department: Systems Biology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm10) using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes FPKMs for each sample

source_name: Bone marrow

extract_protocol:
RNA was extracted using AllPrep RNA kit (Qiagen)
Total RNA libraries were prepared using Illumina TruSeq Stranded Total RNA kit  with a modified protocol  replacing the Illumina TruSeq PCR reaction with KAPA HiFi HotStart Ready Mix for the final PCR step

value: Bone marrow

value: LSK cells


title: Tumor_WT_Tx7

description:
ST2_Tumor_cnts.csv
ST2_Tumor_meta.csv

value: Tumor

value: PLX4720 Tx7


title: NOD_M4_serum


title: WT mouse 2


title: 760399_PBMC_unstim_HC


title: NOD_M3_serum


title: Tumor_KO_Un_Tx7

description:
ST2_Tumor_cnts.csv
ST2_Tumor_meta.csv


title: 760398_PBMC_unstim_HC


title: WT mouse 1


title: 760397_PBMC_unstim_HC


title: NOD_M1_serum


title: TDLN_WT_Un_Tx7

description:
ST2_LN_cnts.csv
ST2_LN_meta.csv

source_name: Tumor-draining lymph node

value: Tumor-draining lymph node


title: Tumor_KO_Tx7

description:
ST2_Tumor_cnts.csv
ST2_Tumor_meta.csv


title: 760396_PBMC_unstim_HC


title: bcat(ex3)osb mouse 3


title: BALBc_M6_Tears

description:
raw data files: MCF_SSK_546_Slide1_532.gpr/MCF_SSK_546_Slide1_635.gpr
IgG/IgA

source_name: Tears

value: BALB/c


title: TDLN_WT_Tx7

description:
ST2_LN_cnts.csv
ST2_LN_meta.csv


title: bcat(ex3)osb mouse 1


title: bcat(ex3)osb mouse 2


title: BALBc_M5_Tears


title: 760394_PBMC_unstim_HC


title: TDLN_KO_Un_Tx7

description:
ST2_LN_cnts.csv
ST2_LN_meta.csv


title: 760395_PBMC_unstim_HC


title: 760400_PBMC_unstim_HC


title: BALBc_M4_Tears


title: BALBc_M3_Tears


title: TDLN_KO_Tx7

description:
ST2_LN_cnts.csv
ST2_LN_meta.csv


title: PBS_negative control for Tears

value: Negative control


title: 760392_PBMC_unstim_HC


title: TDLN_WT_Un_Tx1

description:
ST2_LN_cnts.csv
ST2_LN_meta.csv


title: TDLN_WT_Tx1

description:
ST2_LN_cnts.csv
ST2_LN_meta.csv


title: TDLN_KO_Un_Tx1

description:
ST2_LN_cnts.csv
ST2_LN_meta.csv


title: 760393_PBMC_unstim_HC


title: WT EPI R1

value: Female

value: EpiSC

value: Epiblast Stem cells (EpiSC)


title: △Xist-Pat-1-AZA

value: XEN

value: Extra-embryonic endoderm stem cell (XEN)

value: Paternal Xist deletion-AZA treated


title: △Xist-Pat-2-AZA

value: Paternal Xist deletion-aZA treated


title: 760391_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: BALBc_M1_Tears


title: 760390_PBMC_unstim_HC


title: NOR_M4_Tears

value: NOR


title: △Xist-Pat-2

value: Paternal Xist deletion


title: NOR_M3_Tears


title: △Xist-Pat-3


title: △Xist-Pat-1


title: CD45_Tumor_WT_PLX4720

description:
CD45_Tumor_cnts.csv
CD45_Tumor_meta.csv


title: 760388_PBMC_unstim_HC


title: WT XEN R2

value: WT


title: △Xist-R1

value: Heterozygous Xist deletion


title: 760387_PBMC_unstim_HC


title: 760389_PBMC_unstim_HC


title: TDLN_KO_Tx1

description:
ST2_LN_cnts.csv
ST2_LN_meta.csv

value: CD45 ST2-sorted

value: PLX4720 Tx1


title: BALBc_M2_Tears

value: BALB/c


title: CD45_Tumor_WT_Un

description:
CD45_Tumor_cnts.csv
CD45_Tumor_meta.csv

value: Tumor

value: Untreated


title: NOR_M2_SSK_Tears


title: NOR_M1_Tears


title: 760386_PBMC_unstim_HC


title: WT XEN R1

value: Female


title: NOD_M5_Tear

value: NOD


title: 760385_PBMC_unstim_HC


title: NOD_M6_Tear


title: RBPJ KO_Td2_rep2

first: Baohong

last: Zhao

address: 535 E70th ST

institute: Hospital for Special Surgery

data_processing:
fastp(https://github.com/OpenGene/fastp) was used to evaluate quality of sequenced reads and trim contaminated adaptor portions of sequenced reads. RNA-seq reads were aligned to the the mouse genome (mm10) using HISAT2. HTseq was subsequently used to count reads in features and then edgeR was used to estimate the transcript abundances as CPM (counts per million) values.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for all Samples

source_name: Bone marrow macrophages

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) was used to purify poly-A+ transcripts and generate libraries with multiplexed barcode adaptors following the manufacturer’s instructions.

value: Bone marrow macrophages

value: RBPJ KO

value: TNF d2


title: 760317_PBMC_unstim_HC


title: RBPJ KO_d0_rep2

value: No TNF


title: CD45_Tumor_KO_Un

description:
CD45_Tumor_cnts.csv
CD45_Tumor_meta.csv


title: NOD_M3_Tears


title: WT_Td2_rep2


title: CD45_Tumor_KO_PLX4720

description:
CD45_Tumor_cnts.csv
CD45_Tumor_meta.csv


title: WT_d0_rep2


title: ScRNA, Combination

city: Wuhan

first: Canhui

last: Cao

state: China

address: Jiefang Road 1095

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

data_processing:
The single-cell transcriptome data underwent a comprehensive preprocessing workflow. Initially, cell barcodes and unique molecular identifiers (UMIs) were identified using UMI-tools (Smith et al., 2017) and then attached to read names for distinguishing different cells and RNA molecules. Read adapters were removed with cutadapt (Kechin et al., 2017), and the high-quality reads were mapped to the GRCm39 mouse reference genome. FeatureCount (Liao et al., 2014) was employed to count the reads mapped to each genomic gene, and Samtools (Li, 2011) organized and indexed the BAM files for efficient storage of mapped reads. Subsequently, UMI-tools were used for UMI-corrected molecular counts. Finally, a unified gene expression matrix, encompassing all sequenced samples, was generated through a local Perl script, ensuring the dataset's readiness for downstream analysis
Assembly: GRCm39
Supplementary files format and content: Matrix files

extract_protocol:
Single-cell 5′ and V(D)J libraries of the T-cell receptor (TCR) were prepared in accordance with the protocol provided by the 10x Genomics Chromium Single Cell Gene Expression platform.
Cell suspensions containing 700-1,200 viable cells per microliter (with a viability of at least 85%, as determined by CounterStar) were loaded onto a Chromium Single Cell Controller (10× Genomics). This step facilitated the generation of single-cell gel beads in emulsion (GEMs) by employing Chromium Single Cell V(D)J Reagent Kits. After the cells were captured, they underwent lysis, and the resulting RNAs were barcoded via reverse transcription, all within individual GEMs. Subsequently, each single-cell 5′ and V(D)J library was subjected to sequencing using the Illumina Novaseq 6000, employing 150 paired-end reads for comprehensive analysis

value: Cervical cancer

value: Combination


title: NOD_M1_Tears


title: 760312_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: ScRNA, anti-PD-1


title: 760311_PBMC_unstim_HC


title: PBS_negative_control

description:
raw data file: MCF_SH_179_Slide1_532.gpr
IgG

data_processing:
NFI were normalized  by scaling method using build-in Ig control
Submission data have been preprocessed, for example, average the duplicated spots, PBS subtracted and normalized by scaling method using internal positive controls, values will be set as 0.001 if signal intensity are less than 0

label_protocol: Mouse serum samples were first treated with DNAse I to remove free-DNA and then applied onto antoantigen arrays with 1:50 dilution. The autoantibodies binding to the antigens on the array were detected with cy3-labeled anti-human IgG  and the array slides were scanned with Genepix 4400A scanner with laser wavelengths 532nm for cy3  to generate Tiff images.  Genepix Pro 7.0 software is used to analyze the image and generate the Genepix report (GPR) files (Molecular Devices, Sunnyvale, California, USA). The net fluorescent intensity (NFI) of each antigen was generated by subtracting the local background and negative control (Phosphate buffered saline or simplified as PBS) signal.

extract_protocol:
Mouse serum samples from recipients collected as per routine protocol as defined above were procured from histocompatibility lab after IRB approval. serum of all subjects were aliquoted and stored at -80ºC.
2 positive controls (anti-IgG and IgG control) were also imprinted on the arrays as positive controls.

value: Negative control


title: CD45+ Cells, ADT/HTO

city: Grand Rapids

first: Brandon

last: Oswald

state: MI

address: 333 Bostwick Ave NE

department: Metabolism

institute: Van Andel Institute

description:
Antibody-derived oligonucleotide (ADT) / hashtag-derived oligonucleotide (HTO)
ADT: read1 file contains cell barcode and UMI; read 2 file contains ADT reads. HTO library: read1 file contains cell barcode and UMI; read2 file contains HTO tag reads
Files contain all ADT and HTO data. Refer to .csv file in supplemental files for clarity
CD45HTO_S1 (S1, S2, S3, S4, S6)

library_source: other

data_processing:
*library strategy: CITE-seq
CellRanger-7.0.1 functions used to generate the following files: barcode.tsv.gz, features.tsv.gz, matrix.mtx.gz  (GEX, ADT, HTO information combined)
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output files: barcode.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
CD45+ Cells were obtained from the subq tumors of 4 AL mice and 4 DR mice. Vability was assess and proper hashing (HTO) and Staining (ADT) was conducted on those live cells. This was done in accordance with Biolegenends total seq protocol: https://www.biolegend.com/Files/Images/media_assets/support_protocol/20-0014-01_TotalSeq-UC_8x11.pdf
Libraries were generated and sequenced by the Van Andel Institute Genomics Core. Cells were processed with 10X Chromium Next GEM Single Cell 5ʹ GEM kit v1.1 (10X Genomics, Pleasanton, CA) according to the manufacturer’s instruction to target an output of 13,000 cells per sample using a 10X Genomics Chromium Controller. Briefly, single cell suspensions in PBS + 0.04% BSA were assessed for quantity and viability on the CytoFLEX S (Beckman Coulter, Indianapolis, IN), then 20,000 cells per sample were loaded onto the Chromium Controller. Single cells were captured in gel beads in emulsion (GEMs) where they were lysed and released RNA was barcoded then converted to cDNA. Using beads, cDNA was separated from the hashtag oligos (HTO) and each were used to generate adapter ligated libraries. Quality and quantity of the finished gene expression and HTO libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA). 2 x 100 bp, paired end sequencing was performed on an Illumina NovaSeq 6000 sequencer (Illumina Inc., San Diego, CA, USA) using an S2, 200 cycle sequencing kit (v1.5) to a minimum depth of 20K reads per cell.  Base calling was done by Illumina RTA3 and output was demultiplexed and converted to FastQ format with Cell Ranger (10X Genomics, v3.1.0).

tag: library type

value: mixed (HTO/ADT)

value: mixed sample (DR, AL)

tag: hto

tag: adt


title: 760314_PBMC_unstim_HC


title: ScRNA, Plerixafor

value: Plerixafor


title: Ribotag_PV+_VEH-treated_rep3

city: London

first: Martijn

last: Selten

address: 4th Floor, New Hunt's House, 18-20 Newcomen Street

department: CDN

country: United Kingdom

institute: King's College London

data_processing:
High-throughput sequencing data from PV+ interneurons-derived ribosome-associated mRNAs were processed using the community-curated Nextflow (version 21.03.0.edge, build 5518 (05-03-2021 10:52 UTC)) RNA-seq pipeline (version 3.0) . Specifically, sequencing reads were quality-controlled by FastQC and quality-trimmed by Trim Galore!. Mouse GRCm38/mm10 genome annotation was accessed from Illumina’s iGenomes repository and used as reference for read alignment by STAR and for gene abundance quantification by Salmon.
Assembly: GRCm38/mm10
Supplementary files format and content: Selten_gene_counts.tsv – TSV file containing aligned read counts for all samples
Supplementary files format and content: Selten_gene_id_names.tsv -TSV file containing list of gene identifiers and names
Supplementary files format and content: Selten_gene_normalised_TpM.tsv - TSV file containing normalised read counts for all samples

source_name: Brain

extract_protocol:
RNA purification of immunoprecipitated RNA was performed using the RNeasy Plus Micro kit (Qiagen) following the manufacturer’s protocol. RNA quality was checked on a Bioanalyzer instrument (Agilent Technologies) using a RNA 6000 Pico Chip and only RNA samples with RNA integrity number (RIN) values higher than 9 were used for library preparation and sequencing.
Library preparation and RNA sequencing experiments were performed by the Genomic Unit of the Centre for Genomic Regulation (CRG, Barcelona, Spain). Library preparation for all samples was performed using the SMARTer Ultra Low RNAkit and samples were then sequenced paired-end using an Illumina HiSeq 2500 platform to a mean of approximately 60 million mapped reads per sample.

treatment_protocol: mice were treated with vehicle or CNO (1mg/kg) for ~48h via 5 injections. Injections were administered starting 2 days before the experimental day and took place in the morning (between 8.00h and 10.00h) and in the evening (between 18.00h and 21.00h). A fifth injection was administered on the experimental day between 8.00 and 10.00h.

value: Brain

value: PV+ interneurons

tag: aav treatment

value: VEH


title: 760310_PBMC_unstim_HC


title: ScRNA, Solution

value: Tumor

value: Solution


title: M15_NOD_33wks

value: NOD


title: Ribotag_PV+_VEH-treated_rep2


title: 760298_PBMC_unstim_HC


title: NOD_M4_Tears


title: ScATAC, cKO

library_source: genomic single cell

data_processing:
The raw sequencing reads underwent demultiplexing and were aligned to the reference genome using the 10X Genomics Cell Ranger (v7.1.0) pipeline, with default parameters. Raw sequencing reads were first subjected to demultiplexing and alignment to the reference genome using the 10X Genomics Cell Ranger pipeline with default parameters. Subsequent single-cell analyses, unless stated otherwise, were carried out using Cell Ranger (v7.1.0), Seurat t (v3.1.4), and Signac (v0.2.5) (Stuart et al., 2019). To summarize, in the context of gene expression data, unique molecule identifiers were counted for each gene and each cell barcode (filtered by CellRanger-arc), resulting in the creation of digital expression matrices. For ATAC data, the raw sequencing data were aligned to the reference genome, followed by read filtering, detection of accessible chromatin peaks, dimensionality reduction, cell clustering, and differential accessibility analyses.The Cell Ranger-ATAC (v2.1.0) count module processed FASTQ files and performed alignment, filtering, barcode counting, and UMI counting. It utilized Chromium cellular barcodes to generate feature barcode matrices, which were subsequently used in dimensionality reduction, clustering, feature linkage, and transcription factor analysis, all following the default parameter settings of cellranger-arc. For secondary analysis involving ATAC and gene expression data, we utilized Seurat and Signac. The Signac package was specifically employed for data normalization, dimensionality reduction, clustering, and feature linkage. We employed a data integration algorithm implemented in Seurat3 to identify 'integration anchors,' allowing us to effectively integrate all the samples and mitigate batch effects. Subsequently, we conducted UMAP dimensional reduction on the scaled data using the RunUMAP function provided by Seurat. To delineate distinct cell populations, we utilized the FindClusters function in Seurat. Following cluster identification, we further eliminated a few clusters that consisted of only a small number of cells and lacked enrichment in positive marker genes, indicating a potential presence of cell-cell multiplets. Next, we employed the Seurat function FindAllMarkers to identify open chromatin peaks that were specific to individual cell clusters. Additionally, we calculated differentially accessible peaks using the Seurat function FindMarkers.
Assembly: GRCm39
Supplementary files format and content: Matrix files

source_name: Spleen

extract_protocol:
Single-cell RNA-seq libraries were prepared following the protocols outlined in the Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics) in accordance with the manufacturer's instructions. For the isolation of nuclei required for single cell ATAC Sequencing (scATAC-seq), the 10x Genomics Nuclei Isolation protocol (CG000169) was followed.
Subsequently, scATAC-seq library construction and sequencing were initiated by incubating the prepared nuclei with Tn5 transposase. The nuclei suspension was then loaded into the Chromium microfluidic chip E, using 10x reagents, and barcoded through the 10x Chromium Controller (10x Genomics, Pleasanton, CA). DNA fragments from the barcoded cells were subsequently amplified, and sequencing libraries were constructed employing reagents from a Chromium Single Cell ATAC reagent kit (10x Genomics; PN-1000110, PN-1000156, PN-1000084), following the manufacturer's instructions as outlined in the Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics). DNA fragments from the barcoded cells were subsequently amplified, and sequencing libraries were constructed employing reagents from a Chromium Single Cell ATAC reagent kit (10x Genomics; PN-1000110, PN-1000156, PN-1000084), following the manufacturer's instructions as outlined in the Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics). Post-library construction, preliminary quantification was performed using Qubit 2.0, followed by quality inspection of the Insert DNA of the library using the Fragment Analyzer (FA). Once the Insert size met the expected criteria, qPCR was employed to accurately quantify the effective library concentration at 2 nM. Subsequently, the libraries were pooled and loaded onto an Illumina NovaSeq platform for sequencing.

value: Spleen

value: cKO


title: Ribotag_PV+_VEH-treated_rep1


title: CD45+ Cells, GEX

description:
polyA RNA
5' (mRNA) library: read1 file contains cell barcode and UMI, read2 file contains transcript
File contains all GEX data for all samples
CD45GEX_S1 (S1, S2, S3)

value: mRNA


title: M14_NOD_33wks


title: 760292_PBMC_unstim_HC


title: ScATAC, control

value: con


title: Ribotag_PV+_CNO-treated_rep4

value: CNO


title: ScRNA, cKO

value: cKO Cxcr4


title: 760240_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: 760289_PBMC_unstim_HC


title: ScRNA, control

value: control


title: M13_NOD_24wks


title: Ribotag_PV+_CNO-treated_rep3


title: M16_NOD_33wks


title: M11_NOD_24wks


title: 760236_PBMC_unstim_HC


title: Combination, replication5

data_processing:
RNA-seq datasets were processed using HISAT2 (v.2.1.0) (32), and then calculated the number of reads per gene by HTSeq (v.0.11.2) (33). StringTie (v.2.1.4) (34) was used to calculated fragments per kilobase of exon model per million mapped reads (FPKM) with default parameters. DESeq2 (v.1.28.1) (35) was used to identify differentially expressed genes (DEGs). We deemed genes to be significant if they exhibited an FDR (False Discovery Rate) < 0.01 and an absolute log2 (fold-change) > 1.
Assembly: GRCm39
Supplementary files format and content: Matrix files

extract_protocol:
Purified total RNA from tumors was extracted by total RNA extraction kit (TIANGEN, Cat. No. DP419) according to the manufacturer’s instructions and analyzed by an Agilent Bioanalyzer to assess RNA integrity.
Sequencing libraries were prepared using a VAHTS Stranded mRNA-seq Library Pre Kit (Vazyme, NR602-02) as the manufacturer’s protocol. RNA Sequencing was performed on the Illumina NovaSeq 6000 platform.

value: Cervical cancer

value: Combination, replication5


title: Ribotag_PV+_CNO-treated_rep1

value: Brain


title: M10_NOD_8wks


title: Ribotag_PV+_CNO-treated_rep2

value: PV+ interneurons


title: M9_NOD_8wks


title: BC932_CD14_S16

city: Manchester

first: Kiran

last: Batta

address: Paterson Building

department: Division of cancer Sciences

institute: The University of Manchester

description: Library name: KB15_16_932_CD14_S16

data_processing:
Quality control of fastq files was performed using FastQC6 (v0.11.7) and multiQC7 (v1.7). BBDuk (BBTools suite8, v38.23) was used to trim low-quality reads.
Adapters were trimmed with BBDuk’s default list of adapters.
Reads were aligned to the hg38 reference genome with STAR20 (v2.7.1) with flag --twopassMode Basic set to account for the potential occurrence of novel splice junctions
Assembly: hg38
Supplementary files format and content: tab limited text file to include FPKM value for each sample

source_name: PBMNCs

growth_protocol: CD14+ monocytes were enriched from cryopreserved PBMNC samples by MACS for use in RNA-seq.

extract_protocol:
RNA was isolated using the RNeasy Micro or Mini kit (QIAGEN), according to manufacturer’s instructions
Library preparation was performed using a SureSelect polyA kit (Agilent).

value: PBMNCs

value: Monocytes

tag: individual

value: CMML Patient


title: 760235_PBMC_unstim_HC


title: BC822_CD14_S15

description: Library name: KB15_15_822_CD14_S15


title: 760233_PBMC_unstim_HC


title: Combination, replication3

value: Tumor

value: Combination, replication3


title: Combination, replication4

value: Combination, replication4


title: 760232_PBMC_unstim_HC


title: BC786_CD14_S14

description: Library name: KB15_14_786_CD14_S14


title: M6 Balb_c_28wks

value: BALB/c


title: Combination, replication1

value: Combination, replication1


title: Combination, replication2

value: Combination, replication2


title: M12_NOD_24wks

value: NOD


title: M5 Balb_c_28wks


title: HV2_CD14_S13

description: Library name: KB15_13_HV2_CD14_S13

value: Healthy volunteer


title: 760231_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: anti-PD-1, replication5

value: Cervical cancer

value: anti-PD-1, replication5


title: BC201_CD14_S12

description: Library name: KB15_12_201_CD14_S12


title: 760238_PBMC_unstim_HC


title: 760229_PBMC_unstim_HC


title: BC572_CD14_S11

description: Library name: KB15_11_572_CD14_S11


title: HV3_CD14_S10

description: Library name: KB15_10_HV3_CD14_S10


title: M4 Balb_c_28wks


title: anti-PD-1, replication3

value: anti-PD-1, replication3


title: 760230_PBMC_unstim_HC


title: M3 Balb_c_8wks


title: Ribotag_PV+_VEH-treated_rep4

value: Brain

value: PV+ interneurons

value: VEH


title: anti-PD-1, replication4

value: anti-PD-1, replication4


title: 760227_PBMC_unstim_HC


title: 760226_PBMC_unstim_HC


title: M8_NOD_8wks


title: M2 Balb_c_8wks


title: anti-PD-1, replication2

value: Tumor

value: anti-PD-1, replication2


title: HV4_CD14_S9

description: Library name: KB15_09_HV4_CD14_S9

value: PBMNCs

value: Monocytes


title: M1 Balb_c_8wks

value: BALB/c


title: anti-PD-1, replication1

value: anti-PD-1, replication1


title: PBS_negative control

description:
raw data file: MCF_SH_292_Slide1_532.gpr
IgG

label_protocol: Mouse serum/rear  samples were first treated with DNAse I to remove free-DNA and then applied onto antoantigen arrays with 1:50 dilution. The autoantibodies binding to the antigens on the array were detected with cy3-labeled anti-human IgG  and the array slides were scanned with Genepix 4400A scanner with laser wavelengths 532nm for cy3  to generate Tiff images.  Genepix Pro 7.0 software is used to analyze the image and generate the Genepix report (GPR) files (Molecular Devices, Sunnyvale, California, USA). The net fluorescent intensity (NFI) of each antigen was generated by subtracting the local background and negative control (Phosphate buffered saline or simplified as PBS) signal.

extract_protocol:
Serum/tear samples from recipients collected as per routine protocol as defined above were procured from histocompatibility lab after IRB approval. All subjects were aliquoted and stored at -80ºC.
2 positive controls (anti-IgG and IgG control) were also imprinted on the arrays as positive controls.

tag: sample type

value: Negative control


title: BC666_CD14_S8

description: Library name: KB15_08_666_CD14_S8

value: CMML Patient


title: 760223_PBMC_unstim_HC

extract_protocol: RNA was extracted using the RNEasy mini kit.

value: Healthy control


title: BC776_CD14_S7

description: Library name: KB15_07_776_CD14_S7


title: 760222_PBMC_unstim_HC

value: PBMC


title: SeB3


title: Plerixafor, replication5

value: Cervical cancer

value: Plerixafor, replication5


title: Plerixafor, replication4

value: Plerixafor, replication4


title: BC872_CD14_S6

description: Library name: KB15_06_872_CD14_S6


title: BC665_CD14_S5

description: Library name: KB15_05_665_CD14_S5


title: SeB1


title: SeB2


title: 760221_PBMC_unstim_HC


title: 760218_PBMC_unstim_HC


title: SeN6

value: NOR


title: Plerixafor, replication2

value: Plerixafor, replication2


title: BC812_CD14_S3

description: Library name: KB15_03_812_CD14_S3


title: 760216_PBMC_unstim_HC


title: Plerixafor, replication1

value: Plerixafor, replication1


title: SeN4


title: Solution, replication5

value: Solution, replication5


title: 760215_PBMC_unstim_HC


title: BC796_CD14_S2

description: Library name: KB15_02_796_CD14_S2


title: Solution, replication4

value: Tumor

value: Solution, replication4


title: SeN3


title: BC830_CD14_S1

description: Library name: KB15_01_830_CD14_S1

value: PBMNCs


title: 760214_PBMC_unstim_HC


title: Solution, replication3

value: Solution, replication3


title: 760213_PBMC_unstim_HC


title: SeN2


title: 760211_PBMC_unstim_HC


title: Solution, replication2

value: Solution, replication2


title: BC872_CD14_pos

description: Library name: KB13_15_872_CD14_pos

data_processing:
Quality control of fastq files was performed using FastQC and multiQC. BBDuk was used to trim low quality reads.  Y-chromosomal and mitochondrial reads were removed from ATAC-seq data using Samtools
For differential accessibility analysis, DiffBind16 (v2.14; R v3.6.2) was used. DiffBind was also used to calculate fractions of reads in peaks. To annotate differentially accessible regions as identified by DiffBind to genes, Homer (v 4.10) annotatePeaks.pl was used, again with the hg38 assembly of the human reference genome. Normalisation was done by fraction of reads in peaks.
Assembly: HG38
Supplementary files format and content: bigwig

growth_protocol: CD14+ monocytes were enriched from cryopreserved PBMNC samples by MACS for use in fast-ATAC-seq. 5000 cells were used per reaction.

extract_protocol:
Fast-ATAC preparation was done based on Croces et al. Nature methods 2017
Library preparation was performed as per Buenrostro et al. Curr. Protoc. Mol. Biol. 2015

value: Monocytes


title: Plerixafor, replication3

value: Plerixafor, replication3


title: BC763_CD14_S4

description: Library name: KB15_04_763_CD14_S4

value: CMML Patient


title: SeN5


title: Solution, replication1

value: Solution, replication1


title: BC812_CD14_pos

description: Library name: KB13_14_812_CD14_pos


title: 760208_PBMC_unstim_HC

data_processing:
MMSEQ package was used to infer gene expression levels
we mapped clean reads to reference transcripts using Bowtie2 software
we calculated the gene  expression level (FPKM) for each sample with the RSEM software
Assembly: hg19
Supplementary files format and content: FPKM normalized reads

value: Healthy control

value: PBMC


title: 760217_PBMC_unstim_HC


title: BC572_CD14_pos

description: Library name: KB13_13_572_CD14_pos


title: Mouse T cell_plerixafor_pstat3_1

data_processing:
Basecalls were performed using bcl2fastaV217 for Novaseg output.
ChlP-seq reads were trimmed from 3' end until the final base had a quality score>30, using Trimmomatic v0.33, discarding reads left with <20bp
ChlP-seq reads were aligned to the hg38/GRCm38.p6  genome usina Bowtie version 1.1.2.
To create ChlP-seq coverage plots, the locations of the mapped ChlP-seg 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 <=0.0
Assembly: hg38/GRCm38.p6
Supplementary files format and content: none

growth_protocol: Jurkat cells were cultured in Roswell Park Memorial Institute (RPMI)-1640 medium (Gibco, Cat. No. 11875093). U14, TC-1 and ID8 were grown in Dulbecco’s Modification of Eagle’s Medium (DMEM) medium (Gibco, Cat. No. 11966025).  All mediums contain 10% fetal bovine serum (FBS, Thermo Fisher Scientific, Cat. No. A4766801) and 1% Penicillin/streptomycin (Servicebio, Cat. No. G4003). Cells were kept at 5% CO2 and at 37 ℃. T cells were cultured in RPMI 1640 Medium (Gibco, Cat. No. 11875093) supplementing with 10% FBS (Thermo Fisher Scientific, Cat. No. A4766801), 1% penicillin/streptomycin (Servicebio, Cat. No. G4003), interleukin-2 (IL-2) at a concentration of 150 U/mL (Thermo Fisher Scientific, Cat. No. PMC0025), 50 mmol/L of β-mercaptoethanol (Gibco, Cat. No.21985023), and 2 mmol/L of GlutaMAXTM (Gibco, Cat. No. 35050061). T cells were maintained in a controlled environment with 20% O2, 5% CO2, and a temperature of 37 °C.

extract_protocol:
The Chromatin immunoprecipitation (ChIP) assay was performed according to manufacturer instructions with SimpleChip Plus sonication chromatin IP kit (Cell Signaling Technology (CST), Cat. No. 56383) in Jurkat T cells or mouse T cells after treatment with DMSO or plerixafor for 48h, and T cells isolated from the spleens of tumor-bearing mice as described above. For each ChIP, 5106 cells were used. Briefly, cells were cross-linked with 1% methanol-free formaldehyde and quenched by 125mM glycine, and then the chromatin was sonicated to generate 500-800bp DNA fragments. The DNA-protein supernatant was used for immunoprecipitation by incubating with TOX (CST, Cat. No. 5638336778) or p-STAT3 (CST, Cat. No. 9145). Subsequently, the chromatin was eluted and the cross-link was reversed
The DNA libraries were prepared using TruSeq ChIP library preparation kit (Illumina) and sequenced on NovaSeq 6000

value: Spleen

value: Mouse T cell

value: Mouse spleen T cell

value: Plerixafor


title: BC763_CD14_pos

description: Library name: KB13_12_763_CD14_pos


title: T_B3

source_name: tear

value: BALB/c


title: T_B1


title: T_B2


title: 760206_PBMC_unstim_HC


title: T_N3

value: NOR


title: BC201_CD14_pos

description: Library name: KB13_11_201_CD14_pos


title: Mouse T cell_plerixafor_pstat3_2


title: 760207_PBMC_unstim_HC


title: BC776_CD14_pos

description: Library name: KB13_16_776_CD14_pos


title: 760205_PBMC_unstim_HC


title: Mouse T cell_control_pstat3_2

value: Control


title: Mouse T cell_control_pstat3_1


title: 760203_PBMC_unstim_HC


title: T_N2


title: BC822_CD14_pos

description: Library name: KB13_10_822_CD14_pos


title: SeN1


title: Mouse T cell_plerixafor_tox_2


title: 760202_PBMC_unstim_HC


title: T_N1


title: BC830_CD14_pos

description: Library name: KB13_09_830_CD14_pos


title: Mouse T cell_plerixafor_tox_1


title: 760200_PBMC_unstim_HC


title: BC666_CD14_pos

description: Library name: KB13_08_666_CD14_pos


title: Mouse T cell_control_tox_2