title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: 0dpc, biological replicate 2, technical replicate 1 and 2

status: Public on Mar 30 2024

city: Rockville

first: Fayna

last: Diaz San Segundo

state: MD

address: 5601 Fisher Ln

department: NIAID-DMID-OBRRTR

institute: NIH

data_processing: Matrix normalized and Fold Change sheets generated in separate excel analysis worksheets and then copied here. All data normalized by subtracting average CT of both replicates of the gene of interest from the average CT of the housekeeping gene GAPDH. For ISGs CCL2 through IFNb, GAPDH reps 1 and 2 were used to normalize. For the adaptive immunity genes CD40L through CXCR4, GAPDH reps 3 and 4 were used for normalization. In instances where the baseline CT values were Undetermined after two attempts to run the qPCR, the average was taken of the CT values of the other biological replicates in that treatment group.

label: FAM

organism: Bos taurus

source_name: PBMC

label_protocol: First DNA is digested using a Sigma kit (Sigma, cat# D5307-1000UN), then cDNA is synthesized using Invitrogen reagents (Cat#: 28025-13, Y00147, 48190-001, 10777-019). Thermocycler Set to 25°C for 10min for 1 cycle, then 45 cycles of 37°C and 95°C for 5min before holding at 4°C indefinitely.

extract_protocol: PBMCs were isolated by applying heparinized blood to a ficoll gradient, and lysing with RLT lysis buffer. Total RNA was extracted using Qiagen Rneasy kits.

treatment_protocol: Animals inoculated at either -5 or -3 days post-challenge (dpc) with 150ug/kg of PEGboIFN-lambda and/or 2.5x10^9 pfu Adt-O1M FMD vaccine. Animals were then challenged at 0dpc with 2x10^6 BID50 of FMDV O1Manisa

tag: Sex

value: Female

tag: breed

value: Holstein


title: PBMC, Control treatment group, timepoint: 21dpc, biological replicate 3, technical replicate 1 and 2

type: RNA

country: USA

molecule: total RNA


title: PBMC, Control treatment group, timepoint: 0dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: 0dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: 0dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: 0dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: 0dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: 21dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: 21dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: 21dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: 21dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: 21dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: 21dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: 21dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: 21dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: 21dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: 21dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: 21dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: 21dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: 14dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: 21dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: 14dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: 21dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: 21dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: 14dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: 14dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: 21dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: 14dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: 14dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: 14dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: 14dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: 14dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: 0dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: 14dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: 14dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: 14dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: 14dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: 0dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: 14dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -1dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: 14dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: 14dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: 0dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: 0dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: -1dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: 0dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: -1dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: 0dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: 0dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: 0dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -1dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: 14dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -1dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -2dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: 0dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: -2dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -2dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: -1dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: -2dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: 0dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: -1dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: 0dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: -1dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -2dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: -1dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: -1dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: -1dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: -3dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: -3dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: -1dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: -1dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: -1dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: -1dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -3dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: -1dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: -2dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: -1dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -3dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: -4dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: -4dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: -2dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: -2dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: -2dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: -2dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: -2dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: -2dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: -2dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: -2dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -4dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: -2dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -3dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -4dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -4dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: -3dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: -3dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: -3dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: -3dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, Control treatment group, timepoint: -3dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: -3dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: -3dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, Ad-O1M(-3dpc) treatment group, timepoint: -3dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: -3dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-3dpc) treatment group, timepoint: -2dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: -5dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: -3dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: -2dpc, biological replicate 1, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: -3dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-3dpc) treatment group, timepoint: -3dpc, biological replicate 3, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -5dpc, biological replicate 1, technical replicate 1 and 2


title: Kdm6a +/+ line 2, D14, exp2

type: SRA

city: Baltimore

first: Christine

middle: W

last: Gao

address: 733 N. Broadway, Rm 406

institute: Johns Hopkins University School of Medicine

library_source: transcriptomic

data_processing:
Reads were pseudoaligned to the GRCm38 transcriptome (Ensembl release 102) using Salmon 1.9.0 for paired-end reads, with selective alignment and GC bias correction enabled.
Raw transcript-level counts were imported and summarized to genes with tximeta 1.12.4.
Assembly: GRCm38.p6
Supplementary files format and content: Output from Salmon containing transcript-level quantification, in .sf format

molecule: polyA RNA

organism: Mus musculus

growth_protocol: CRISPR-Cas9 edited ATDC5 cells were maintained at 37°C, 5% CO2, with ATDC5 Complete Media (DMEM/F-12 supplemented with 5% heat-inactivated fetal bovine serum, 2 mM L-glutamine, 100 U/mL penicillin and 100 μg/mL streptomycin). To differentiate cells towards chondrocytes, media was exchanged for ATDC5 Complete Media supplemented with 0.05 mg/mL L-ascorbic acid, 10 mM β-glycerophosphoric acid, and 1x Insulin-Transferrin-Selenium (ITS-G). Cells were differrentiated for up to 7 or 14 days at 37°C, 5% CO2, with supplemented media changes every 48-72 hours.

extract_protocol:
Cells were homogenized with TRIzol reagent, followed by phenol-chloroform separation. Total RNA was purified from the aqueous phase using the Zymo RNA Clean and Concentrator-5 kit with DNase I treatment.
Library preparation was performed with the NEBNext Ultra II RNA Library Prep kit in conjunction with NEBNext Poly(A) mRNA Magnetic Isolation Module.

treatment_protocol: Cells were differentiated for either 7 or 14 days.

tag: cell line

tag: cell type

value: chondrocyte

tag: genotype

value: Kdm6a +/+

tag: line

value: line 2

tag: time

tag: group


title: Kdm6a +/+ line 4, D14, exp2

value: line 4


title: Kmt2d -/- line 1, D14, exp2

value: Kmt2d -/-

value: line 1


title: Kdm6a +/+ line 3, D14, exp2

value: line 3


title: Kmt2d +/+ line 3, D14, exp2

value: Kmt2d +/+


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -5dpc, biological replicate 2, technical replicate 1 and 2


title: PBMC, PEGboIFNλ3(-5dpc) treatment group, timepoint: -5dpc, biological replicate 1, technical replicate 1 and 2


title: Kmt2d +/+ line 2, D14, exp2


title: Kmt2d +/+ line 1, D14, exp2


title: Kdm6a -/- line 5, D14, exp2

value: Kdm6a -/-

value: line 5


title: Kdm6a -/- line 3, D14, exp2


title: Kdm6a -/- line 2, D14, exp2


title: Kdm6a +/+ line 4, D7, exp2


title: PBMC, PEGboIFNλ3+Ad-O1M(-5dpc) treatment group, timepoint: -5dpc, biological replicate 3, technical replicate 1 and 2


title: Kmt2d -/- line 1, D7, exp2


title: Kdm6a +/+ line 2, D7, exp2


title: Kmt2d -/- line 2, D7, exp2


title: Kmt2d +/+ line 2, D7, exp2


title: Kmt2d -/- line 2, D14, exp2


title: Kdm6a +/+ line 3, D7, exp2


title: Kdm6a -/- line 5, D7, exp2


title: Kdm6a -/- line 3, D7, exp2


title: Kdm6a -/- line 5, D14, exp1


title: Kdm6a -/- line 3, D14, exp1


title: Kdm6a -/- line 4, D14, exp1


title: Kdm6a +/+ line 4, D14, exp1


title: Kdm6a -/- line 2, D14, exp1


title: Kdm6a +/+ line 3, D14, exp1


title: Kdm6a -/- line 2, D7, exp2


title: Kmt2d +/+ line 3, D7, exp2


title: Kdm6a +/+ line 2, D14, exp1


title: Kmt2d +/+ line 1, D7, exp2


title: ARM_d3_3

city: Philadelphia

first: Ellen

last: White

state: PA

address: 421 Curie Blvd

department: Dermatology

institute: Perelman School of Medicine

data_processing:
Quality control was performed on the sequencing reads using FastQC (version 0.12.1)
Reads were mapped to the reference genome [Genome Reference Consortium Mouse Build 39 (GRCm39)] using kallisto (version 0.48.0)
Subsequent analysis was performed in the R computing environment (version 4.1.3) in RStudio (version 2022.02.1+461). Transcript-level abundances were imported with tximport (version 1.22.0) using the length scaled transcripts per million
Differential gene expression analysis was performed using the DESeq2 package (version 1.34.0)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: skin

growth_protocol: Full thickness punch biopsies were made in the dorsum of diabetic mouse skin, treated with bacteria, harvested and snap-frozen at day 3 post wounding.

extract_protocol:
Tissue was first cryo-pulverized using the CP02 CryoPrep automated dry pulverizer (Covaris). Trizol (Invitrogen) based phenol-chloroform extraction was then performed for RNA purification, followed by on-column DNase digestion (Qiagen).
Ribosomal RNA was depleted and libraries were constructed using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina) using 100 ng of RNA input. IDT for Illumina UD indexes were ligated to the libraries

treatment_protocol: For bacterial treatment of wounds, 2x108 CFU of A. faecalis or S. aureus in 10 mL of PBS was applied to each wound. For vehicle-control treatment, the same volume of PBS with 10% glycerol was applied to the wounds

tag: tissue

value: skin

tag: treatment

value: Staphylococcus aureus


title: AF_d3_2

value: Alcaligenes faecalis


title: AF_d3_4


title: ARM_d3_2


title: ARM_d3_4


title: AF_d3_3


title: ARM_d3_1


title: PBS_d3_4

value: vehicle


title: Kdm6a +/+ line 5, D14, exp1


title: PBS_d3_3


title: PBS_d3_1


title: mrna-78

city: WuHan

first: Qixiao

last: Jin

address: No. 1, Shizishan Street, Hongshan District, Wuhan City, Hubei Province

country: China

institute: Hua Zhong Agricultural University

description:
mrna_syn.txt
F1coexpression_mrna.txt

data_processing:
Quality control: CircRNA-Seq data were processed by FastUniq. RNA-Seq data were processed by samtools rmdup to remove the large number of duplicates introduced by PCR amplification during high-throughput sequencing.
Alignment: Clean reads were aligned to the B73 AGPv4 reference genome and the Mo17 CAU1.0 reference genome using the default parameters of HISAT and StringTie.
Identification of non-coding RNA:  Tophat-fusion was used to identify circRNAs by aligning them to the maize B73 AGPv4 reference genome and the Mo17 CAU1.0 reference genome.
Quantification of RNA: Stringtie was used quantify the expression levels of the mRNAs. CIRCexplorer2 v2.0.1 was used quantify the expression levels of the circRNAs. The expression of mRNA was calculated according to the TPM standard formula. The expression of mRNA was calculated according to the CPM standard formula.
Collinear analysis: To find out the co-existing genes and circRNAs in the B73 and Mo17 genomes, we performed collinearity analysis using Synmap in the COGE platform. CircRNAs which parental genes in the B73 and Mo17 genomes were colinear genes, and the sequence across the splicing site alignment scores were greater than 150, were considered co-existing in both genomes. We used BLAST for sequence alignment.
Assembly: Zea_mays.B73_RefGen_v4; Zm-Mo17-REFERENCE-CAU-1.0
Supplementary files format and content: tab-delimited text files named "TPM" or "CPM" include expression values for each samples.

organism: Zea mays

growth_protocol: Twenty-six tissues or stages were sampled from B73, Mo17 and the F1 of B73xMo17 maize plants in a greenhouse. The plants were cultivated under a 12-h light/12-h dark cycle at 25 ℃.

extract_protocol:
Three replicates were prepared per tissue. RNA was extracted from 5–10 individual plants per replicate. The three replicates were extracted separately and then mixed in equal amounts for sequencing. Total RNA was isolated from 1cm ear using a Direct-zol RNA Microprep kit (Zymo Research) following the manufacturer’s guidelines.
RNA libraries were prepared for sequencing using corresponding standard protocols.

treatment_protocol: No special treatment.

tag: Stage

tag: age


title: total rna-1

description:
mrna_syn.txt
F1coexpression_mrna.txt


title: mrna-77

description:
mrna_syn.txt
F1coexpression_mrna.txt


title: PBS_d3_2


title: Kdm6a -/- line 1, D14, exp1


title: mrna-76

description:
mrna_syn.txt
F1coexpression_mrna.txt


title: mrna-75

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: 2mm tassel

value: 2mm tassel


title: mrna-74

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Inflorescence

value: Inflorescence


title: mrna-73

description:
mrna_syn.txt
F1coexpression_mrna.txt


title: Kdm6a +/+ line 1, D14, exp1


title: mrna-72

description:
mrna_syn.txt
F1coexpression_mrna.txt


title: mrna-71

description:
mrna_syn.txt
F1coexpression_mrna.txt


title: mrna-69

description:
mrna_syn.txt
F1coexpression_mrna.txt


title: mrna-70

description:
mrna_syn.txt
F1coexpression_mrna.txt


title: AF_d3_1


title: mrna-67

description:
mrna_syn.txt
F1coexpression_mrna.txt


title: mrna-61

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Tip of Stage 2 Leaf-N(V5)

value: Tip of Stage 2 Leaf-N(V5)


title: mrna-60

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Third Leaf(V3)

value: Third Leaf(V3)


title: mrna-62

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Tip of Stage 2 leaf-L(V5)

value: Tip of Stage 2 leaf-L(V5)


title: mrna-64

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Base of Stage 2 leaf-L(V5)

value: Base of Stage 2 leaf-L(V5)


title: mrna-63

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Base of Stage 2 Leaf-N(V5)

value: Base of Stage 2 Leaf-N(V5)


title: mrna-65

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Ear-leaf

value: Ear-leaf


title: mrna-59

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: First Leaf-N(V3)

value: First Leaf-N(V3)


title: mrna-58

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: First Leaf-L(V3)

value: First Leaf-L(V3)


title: mrna-52

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-49

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-66

description:
mrna_syn.txt
F1coexpression_mrna.txt


title: mrna-50

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-68

description:
mrna_syn.txt
F1coexpression_mrna.txt


title: mrna-53

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Primary Root(V1)

value: Primary Root(V1)


title: mrna-57

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Topmost Leaf-N(V3)

value: Topmost Leaf-N(V3)


title: mrna-43

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-45

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-41

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-40

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-47

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-48

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-56

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Topmost Leaf-L(V3)

value: Topmost Leaf-L(V3)


title: mrna-54

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Primary Root(6DAS)

value: Primary Root(6DAS)


title: mrna-46

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-44

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-51

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-39

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-37

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-36

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-38

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-42

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-35

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-32

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-31

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-55

description:
mrna_syn.txt
F1coexpression_mrna.txt

source_name: Husk leaf

value: Husk leaf


title: mrna-34

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-28

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-24

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-25

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-21

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-30

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-22

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-29

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-20

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-19

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-17

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-16

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-15

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-23

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-13

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-18

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-14

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-33

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-12

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-11

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-26

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-6

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-8

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-4

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-9

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-7

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-10

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-27

description:
mrna_syn.txt
Mo17coexpression_mrna.txt


title: mrna-2

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-3

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: circ-78

description:
B73circ.gff3
Mo17circ.gff3
circRNA_syn.txt
F1coexpression_circRNA.txt

tag: molecule

value: circular RNA


title: mrna-5

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: mrna-1

description:
mrna_syn.txt
B73coexpression_mrna.txt


title: circ-75


title: circ-74


title: circ-73


title: circ-72


title: circ-70


title: circ-71


title: circ-69


title: circ-67


title: circ-66


title: circ-63


title: circ-62


title: circ-61


title: circ-65


title: circ-60


title: circ-58


title: circ-77


title: circ-59


title: circ-76


title: circ-52

description:
Mo17circ.gff3
circRNA_syn.txt
Mo17coexpression_circRNA.txt


title: circ-53


title: circ-56


title: circ-51


title: circ-48


title: circ-50


title: circ-49


title: circ-68


title: circ-46


title: circ-64


title: circ-42


title: circ-47


title: circ-41


title: circ-43


title: circ-44


title: circ-39


title: circ-57


title: circ-37


title: circ-38


title: circ-35


title: circ-54


title: circ-36


title: circ-55


title: circ-34


title: circ-32


title: circ-33


title: circ-30


title: circ-31


title: circ-29


title: circ-28


title: circ-27


title: circ-26

description:
B73circ.gff3
circRNA_syn.txt
B73coexpression_circRNA.txt


title: circ-25


title: circ-45


title: circ-23


title: circ-21


title: circ-20


title: circ-19


title: Hp_TFS-MPA_3

city: CDMX

first: Iris

middle: Angélica

last: Feria

state: CDMX

address: Cuauhtemoc 330, Doctores

department: UIMEN

country: Mexico

institute: Instituto Mexicano del Seguro Social

hyb_protocol: Hybridization was performed according to the manufacturer's recommendations in the GeneChip WT Plus Reagent Kit.

scan_protocol: The chips were scanned with a GeneChip Scanner Affymetrix 3000 7G

data_processing: Data normalization and statistical analyzes were performed in R (Bioconductor). Two main packages were used: affy and limma. Raw microarray data were normalized using the robust multichip average (RMA) normalization method. For differential gene expression, general linear models and empirical Bayes statistics were used. An absolute logarithmic fold change in expression greater than 1 and an unadjusted P-value lower than 0.05 were thresholds used for gene selection.

label: biotin

organism: Rattus norvegicus

source_name: transcranial focal stimulation and single seizure

label_protocol: Label was performed according to the manufacturer's recommendations in the GeneChip WT Plus Reagent Kit.

extract_protocol: rats were sacrificied by decapitation and the brain was dissected immediately after in cold conditions. All samples were stores at -70°C until use.

treatment_protocol: tfs-mpa rats received tfs (300Hz, 50mA) for 5 minutes, 5 minutes after they received an injection with 3-mercaptopropionic acid (37.5 mg/kg, i.p.). Four hours after the sample was collected. Rats in the mpa groups only received the dose of the proconvulsant. Rats in the tfs group only received the stimulation.

value: bilateral hippocampus

value: male

value: tfs-mpa


title: Hp_TFS-MPA_2


title: Hp_TFS-MPA_1


title: Hp_TFS_3

source_name: transcranial focal stimulation

extract_protocol: rats were sacrficied by decapitation and the brain was dissected immediately after in cold conditions. All samples were stores at -70°C until use.

treatment_protocol: tfs rats received tfs (300Hz, 50mA) for 5 minutes. Four hours after the sample was collected. Sham rats consisted in the same manipulation as tfs rats but no stimulation was applied

value: tfs


title: circ-18


title: primary rat astrocytes + H2O 3

city: Düsseldorf

first: Joel

last: Gruchot

address: Moorenstraße 5

department: Neurology

country: Germany

institute: Heinrich-Heine-University

data_processing:
raw data in FASTQ format were adapter- and quality trimmed.
Mapping was performed against the Rattus norvegicus (mRatBN7.2.1110; January 05, 2024) genome sequence using Hisat2 alignment method.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach
Assembly: mRatBN7.2.1110
Supplementary files format and content: raw counts as .txt

source_name: cortical

growth_protocol: Briefly, dissociated P1 Wister rat cortices were cultured on T-75 cell culture flasks in Dulbecco′s Modified Eagle′s Medium (DMEM) substituted with 10% fetal calf serum (FCS) and 4 mM L-glutamine, 50 U/ml penicillin/streptomycin. After 10 days, flasks were shaken at 180 rpm/min at 37 °C and microglia-containing supernatants were collected after 2 and 24 h. To further purify the primary rat microglia, cells were sorted using MACS against CD11b/c microbeads.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) and 150 ng of total RNA was used for the library construction
RNA libraries for RNA-Seq were prepared according to the manifacturers protocol using the VAHTS™ Universal RNA-Seq Library Prep Kit for Illumina® V6 with mRNA capture module

treatment_protocol: One day after microglial isolation or 3 days after astroglial isolation, cells were stimulated with with 1 µg/ml recombinant HERV-W ENV protein or with 100 ng/ml LPS in glial media (10% FCS, 2 mM L-glutamine, 50 U/ml penicillin/streptomycin in DMEM).

value: cortical

value: Postnatal day 1

value: astrocytes

tag: strain

value: Wistar


title: primary rat astrocytes + LPS 4

value: LPS (100ng/ml)


title: circ-17


title: primary rat astrocytes + H2O 4


title: primary rat astrocytes + LPS 3


title: primary rat astrocytes + H2O 2


title: primary rat astrocytes + LPS 2


title: Hp_Sham_2

source_name: sham manipulation

value: sham


title: Hp_Sham_3


title: Hp_Sham_1


title: circ-24


title: Hp_TFS_1


title: Hp_TFS_2


title: primary rat astrocytes + LPS 1


title: Cx_Sham_2

value: bilateral parietotemporal cortex


title: Cx_Sham_1


title: Hp_MPA_3

source_name: single seizure

value: mpa


title: circ-22

source_name: Inflorescence

value: Inflorescence


title: circ-40


title: circ-16


title: primary rat astrocytes + buffer 4

value: buffer


title: primary rat astrocytes + HERV-W ENV 3

value: HERV-W ENV (1µg/ml)


title: primary rat astrocytes + HERV-W ENV 4


title: Hp_MPA_2


title: primary rat astrocytes + H2O 1


title: Hp_MPA_1


title: Cx_TFS-MPA_3


title: circ-14


title: primary rat astrocytes + buffer 2


title: circ-13

value: Ear-leaf


title: primary rat astrocytes + HERV-W ENV 2


title: circ-15

value: circular RNA


title: primary rat astrocytes + HERV-W ENV 1


title: Cx_TFS-MPA_2


title: primary rat astrocytes + buffer 1


title: circ-12

value: Base of Stage 2 leaf-L(V5)


title: Cx_Sham_3

value: male


title: Cx_TFS-MPA_1

value: tfs-mpa


title: Epimedium pubescens leaves,+P,90d,rep C [miRNA]

city: 北京

first: 尚年

last: 刘

state: 北京

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

data_processing:
To obtain clean reads from raw data in fastq format, custom Perl and Python scripts are employed for processing.
Bowtie is utilized to align small RNA tags against a reference sequence without mismatches. Using miRBase20.0 as the reference, modified versions of the software mirdeep2 and srna-tools-cli are applied to identify potential miRNAs and generate secondary structures.
To predict novel miRNAs, the available software miREvo (Wen et al., 2012) and mirdeep2 (Friedlander et al., 2011) are integrated. These tools explore the secondary structures, Dicer cleavage sites, and minimum free energy of unannotated small RNA tags from previous steps.
Known and novel miRNAs in each sample are normalized for expression levels using TPM. Differential expression analysis is performed using DESeq2.
Assembly: IMPLAD_EP_1.0
Supplementary files format and content: XLS file includes raw counts for each Sample
Supplementary files format and content: XLS file includes TPM values for each Sample

organism: Epimedium pubescens

source_name: leaves

growth_protocol: The plants were cultivated in sand, under 2000 lux light for 14 hours daily, at 22 ± 2 ℃ in a controlled environment.

extract_protocol:
The total RNA of leaves was extracted using the RNAprep Pure Polysaccharide Polyphenol Plant Total RNA Extraction Kit (QIAGEN, Germany).2 ug of total RNA was used for the construction sequencing library.
Sequencing libraries were generated using NEB Next® Multiplex Small RNA Library Prep Set for Illumina® (NEB E7300L). Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridazition with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment.

treatment_protocol: Irrigation was treated with adjusted Hogland's nutrient solution of 0 mmol/L and 1 mmol/L Pi.

value: leaves

value: Normal


title: Cx_MPA_3


title: Epimedium pubescens leaves,+P,90d,rep B [miRNA]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: circ-11

value: Base of Stage 2 Leaf-N(V5)


title: Epimedium pubescens leaves,-P,90d,rep C [miRNA]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: Phosphorus deficiency


title: Epimedium pubescens leaves,+P,90d,rep A [miRNA]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: Epimedium pubescens leaves,-P,90d,rep B [miRNA]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: Cx_MPA_2


title: Epimedium pubescens leaves,-P,90d,rep A [miRNA]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: circ-9

source_name: Tip of Stage 2 Leaf-N(V5)

value: Tip of Stage 2 Leaf-N(V5)


title: circ-10

source_name: Tip of Stage 2 leaf-L(V5)

value: Tip of Stage 2 leaf-L(V5)


title: Cx_MPA_1


title: Epimedium pubescens leaves,+P,30d,rep B [miRNA]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: Epimedium pubescens leaves,+P,30d,rep A [miRNA]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: primary rat astrocytes + buffer 3

value: cortical

value: Postnatal day 1

value: astrocytes

value: Wistar


title: circ-8

source_name: Third Leaf(V3)

value: Third Leaf(V3)


title: Epimedium pubescens leaves,+P,30d,rep C [miRNA]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: Cx_TFS_3

value: bilateral parietotemporal cortex

value: tfs


title: Epimedium pubescens leaves,-P,30d,rep C [miRNA]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: Epimedium pubescens leaves,-P,30d,rep A [miRNA]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: circ-6

value: First Leaf-L(V3)

value: circular RNA


title: circ-7

source_name: First Leaf-N(V3)

value: First Leaf-N(V3)


title: Epimedium pubescens leaves,+P,90d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

data_processing:
Raw data in FASTQ format (raw reads) is processed using FASTP software and low-quality reads are filtered.
Align the obtained clean data to the reference genome using HISAT2 v2.0.5.
StringTie (1.3.3b) was used for new gene prediction.
featureCounts (1.5.0-p3) is used to calculate the reads mapped to each gene.
Assembly: IMPLAD_EP_1.0
Supplementary files format and content: XLS file includes raw counts for each Sample
Supplementary files format and content: XLS file includes FPKM values for each Sample

extract_protocol:
The total RNA of leaves was extracted using the RNAprep Pure Polysaccharide Polyphenol Plant Total RNA Extraction Kit (QIAGEN, Germany).0.4 ug of total RNA was used for the construction sequencing library.
RNA libraries for RNA-seq were prepared using the NEBNext® Ultra RNA Library Prep Kit for Illumina® according to the manufacturer's protocol.


title: Epimedium pubescens leaves,+P,90d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: Cx_TFS_2

value: male


title: Epimedium pubescens leaves,-P,30d,rep B [miRNA]

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: leaves


title: circ-4

value: Topmost Leaf-L(V3)


title: circ-5

value: Topmost Leaf-N(V3)


title: Epimedium pubescens leaves,-P,90d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: Phosphorus deficiency


title: Epimedium pubescens leaves,+P,90d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: Normal


title: PATIENT_#21'S_MOTHER

city: Nantes

first: Frédéric

last: Ebstein

address: IRS-UN - 8 quai Moncousu - BP 70721

department: L'unité de recherche de l'institut du thorax, Inserm UMR 1087

country: France

institute: French Institute of Health and Medical Research (Inserm)

hyb_protocol: One hundred nanograms total RNA was hybridized with the nCounter Autoimmune Profiling panel CodeSets for 16 hours at 65°C.

scan_protocol: Hybridized probes were immobilized on streptavidin-coated cartridges for digital counting by a nCounter™ Digital Analyzer.

data_processing: RCC files were analysed using nSolver 4.0. Normalization of RNA loading was performed using the geometric mean of a unique housekeeping gene.

label: NanoString CodSets

organism: Homo sapiens

source_name: Stimulated T cells

label_protocol: Labelling was performed using gene-specific biotin-tagged molecular barcodes (CodeSets) designed and provided by the manufacturer.

growth_protocol: PBMC were cultured in U-bottom 96-well plates together with irradiated feeder cells using RPMI 1640 medium supplemented with 10% human AB serum.

extract_protocol: Total RNA was isolated from resting T cells using the kit from Analytic Jena AG following the manufacturer’s instructions.

treatment_protocol: PBMC were stimulated with 1 µg/µl L-PHA (Sigma) and 150 U/ml IL-2 (Miltenyi Biotec) for three weeks to expand naive T cells following the procedure of Fonteneau et al.

tag: gender

value: female

value: PSMC3 +/+ (wild-type)

tag: phenotype

value: Clinically healthy


title: ENDSEQ-VABL-NC1

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

library_source: genomic

data_processing:
END-seq reads were aligned to the mouse (mm10) genome using Bowtie (version 1.1.2) with the options–best–all –strata –l 50. 3 mismatches were allowed while keepinng the best strata for tags with multiple alignments (-n 3 –k 1).
MACS 1.4.3 was used for peak calling of H.pylori-infected data, with default parameters (p value cutoff for peak detection = 1x10E-5;–keep-dup = auto). Uninfected cells were used as control, keeping > 10-fold-enriched peaks.
For genome browser tracks visualization, aligned bed files were converted into bedgraph using bedtools genomecov, following by bedGraphToBigWig to make a bigwig file. Values were normalized to reads per million. Visualization of genomic profiles was done by the Integrative Genomic Viewer (IGV) browser.
Assembly: mm10
Supplementary files format and content: bigwig file
Library strategy: END-seq

molecule: genomic DNA

source_name: vAbl cell line

growth_protocol: RAG1-/- preB vAbl cells - generously contributed by Dr. Andre Nussenzweig, National Cancer Institute, NIH -were cultured in RPMI supplemented with 15% FBS (Gibco), penicillin streptomycin, L-Glutamine and Sodium Pyruvate (Gibco) at 37 °C.

extract_protocol:
single-cell suspensions of vAbl cells (40 million cells for STI-treated and 20 million cells for untreated), were washed with PBS, and resuspended in cell suspension buffer (Bio-Rad), embedded in agarose, and transferred into plug molds (Bio-Rad). Plugs were allowed to solidify at 4°C and were then incubated with Proteinase K solution (Puregene, QIAGEN) for 1 hr at 50°C and then for ON at 37°C, followed by consecutive washes in a wash buffer containing 10 mM Tris-HCl (pH 8.0) and 50 mM EDTA (Wash Buffer) and then in a TE Buffer containing (10 mM Tris (pH 8.0) and 1 mM EDTA). Washed plugs were subsequently treated with RNaseA (Puregene, QIAGEN), washed again in Wash Buffer, and stored at 4°C (up to 2-4 days).
Blunting, A-tailing, and ligation to END-seq hairpin adaptor 1 were done at 37°C, 4°C respectively. DNA recovered from melted plugs was sheared to a length between 150 and 200 bp by sonication (Covaris), and biotinylated DNA fragments were purified using streptavidin beads (MyOne C1, Invitrogen). Following streptavidin capture, the newly generated ends were end repaired using T4 DNA polymerase (15 U), Klenow fragment (5 U), and T4 polynucleotide kinase (15 U); A-tailed with Klenow exo-fragment (15 U); and finally ligated to END-seq hairpin adaptor 2 using the NEB Quick ligation kit. After the second adaptor ligation, libraries were prepared by first digesting the hairpins on both adapters with USER enzyme (NEB) and PCR amplified for 16 cycles using TruSeq index adapters. PCR reactions were run on a 2% agarose gel and a smear of 200-400bp was cut and gel purified using MACHEREY-NAGEL extraction Kit (740609.50S).  Quantification of the library was performed by KAPA Library Quantification Kit for Illumina Platforms (Roche) and using dsDNA HS Assay Kit and QUBIT (Molecular Probes, Life Technologies) and qualification was done using the Agilent HS DNA Kit and Bioanalyzer 2100.  10nM of each library was pooled together and was diluted to 4nM according to NextSeq manufacturer’s instructions. 1.7pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced by Illumina NextSeq 500 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

value: vAbl cell line

value: pre-B

value: untreated


title: PATIENT_#21'S_FATHER


title: ENDSEQ-VABL-NC2


title: Epimedium pubescens leaves,-P,90d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: circ-2

value: Primary Root(6DAS)


title: circ-1

source_name: Primary Root(V1)

value: Primary Root(V1)


title: ENDSEQ-VABL-STI2

value: STI


title: circ-3

value: Husk leaf

value: circular RNA


title: Epimedium pubescens leaves,+P,30d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: Epimedium pubescens leaves,-P,90d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: ENDSEQ-VABL-STI1


title: PATIENT_#21

value: PSMC3 +/E305D

value: Neurodevelopmental disorder


title: PATIENT_#18'S_FATHER

value: male


title: ENDSEQ-VABL-HP_STI2

value: H.pylori infection+STI


title: Epimedium pubescens leaves,+P,30d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: leaves


title: Epimedium pubescens leaves,+P,30d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: Normal


title: PATIENT_#18

value: female

value: PSMC3 +/R304W


title: ENDSEQ-VABL-HP1

value: H.pylori infection


title: Epimedium pubescens leaves,-P,30d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: Phosphorus deficiency


title: Cx_TFS_1

value: bilateral parietotemporal cortex

value: tfs


title: PATIENT_#17'S_MOTHER

value: PSMC3 +/+ (wild-type)

value: Clinically healthy


title: Uterus, RNA, month 6, individual 3

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

data_processing:
The raw reads were filtered using fastp 0.23.1. Next, clean reads were aligned to the reference genome (Capra hircus, ARS1.2) using Hisat2.
Transcript were assembled and quantified were utilized using StringTie 1.3.3b.
Transcipts expression levels were normalized to FPKM (Fragments Per Kilobase of transcript per Million mapped reads) to facilitate accurate quantification with RSEM 1.3.0.
Assembly: Capra hircus, ARS1.2
Supplementary files format and content: Excel files includes read counts of all samples.

organism: Capra hircus

source_name: Uterus

growth_protocol: Not Applicable

extract_protocol:
Total RNA was isolated from 20 uterine tissue and 20 ovarian tissues samples with TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The RNA concentration, purity and integrity were calculated and checked by a NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and an Agilent 5400 Bioanalyzer (Agilent, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Not Applicable

value: Uterus

tag: timepoint

value: month 6


title: Uterus, RNA, month 6, individual 4


title: Uterus, RNA, month 6, individual 2


title: Uterus, RNA, month 6, individual 1


title: PATIENT_#17


title: Epimedium pubescens leaves,-P,30d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: PATIENT_#13'S_FATHER


title: Epimedium pubescens leaves,-P,30d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: Uterus, RNA, month 4, individual 5

value: month 4


title: PATIENT_#13

value: PSMC3 +/G262R


title: Uterus, RNA, month 4, individual 4


title: capture-DENND1A-STARR-seq-Output-3

city: Durham

first: Timothy

middle: E

last: Reddy

state: NC

address: 101 Science Dr

institute: Duke University

data_processing:
STARR-seq: Sequencing data quality was assessed with FastQC, and adapters were trimmed with Trimmomatic.) . STARR-seq input and output libraries were aligned to the human genome assembly hg38 with Bowtie2 (version 2.2.4)32, using the following parameters: bowtie2 -X 2000 --sensitive. Samtools was used to process alignments.Only properly-paired alignments with a MAPQ score ≥ 30 outside hg38 centromeres, gap and blacklist regions were were retained in downstream analyses. We used CRADLE (Kim et al., 2021) package to correct biases and call peaks with the following options. We then estimated differential STARR-seq activity across the regions as fold change using DESeq (Love et al., 2014).
ATAC-seq: ATAC-seq libraries for H295R and COV434 cell lines were individually aligned to the human genome (hg38). Each cell line had 2 biological replicates, and >40 million reads were generated per sample. Sequencing data quality was assessed with FastQC, and adapters were trimmed with Trimmomatic. Trimmed reads were aligned to the GRCh38 genome using Bowtie94 reporting only alignments having no more than two mismatches, discarding multi-mapping reads(-v 2 --best --strata -m 1). Reads mapping to the ENCODE hg38 blacklisted regions (https://www.encodeproject.org/files/ENCFF356LFX; manually curated regions with anomalous signal across multiple genomic assays and cell types) were removed using bedtools2 intersect (v2.25.0). Properly paired reads were then filtered to exclude presumed PCR duplicates using Picard MarkDuplicates (v1.130; http://broadinstitute.github.io/picard/). Reads were then used to generate reads per million (RPM) counts of bigWig files for visualization using deeptools bamCoverage (v3.0.1). Peaks were called using MACS2 with an FDR cutoff 0.1.
Assembly: hg38
Supplementary files format and content: STARR-seq: Input files were processed as described. RPKM normalized files are submitted Output files were processed as described above. UMIs were used for deduplication and RPKM normalized files are submitted
Supplementary files format and content: ATAC-seq: ATAC-seq libraries were processed as described above. The RPKM normalized, deduplicated files are submitted

source_name: Adrenal

growth_protocol: NCI-H295R  cells were cultured in DMEM/F-12 medium (Gibco #21041025) supplemented with 2.5% Nu-Serum (Corning #355100) and 1% ITS+Premix (Corning #354352) and grown as a monolayer at 37 °C, 5%CO2.  COV434  cells were cultured in DMEM (Gibco #11965092) supplemented with 2 mM Glutamine and 10% Foetal Bovine Serum (FBS) and grown as a monolayer at 37 °C, 5%CO2. All experiments were performed between passages 5 and 12.

extract_protocol:
The custom locus enrichedSTARR-seq plasmid Library was transfected into H295R cells with Lonza Nucleofector™ X Kit (SF-DN-100 ) according to the manufacturer’s protocol. At 6 hours post-transfection, the media was removed and cells were washed with, washed with PBS, and total RNAs harvested using the Qiagen RNeasy system
STARR-seq : Each washed cell pellet harvested from a 500 cm2 plate was lysed in a 50 mL conical tube with 5 mL of a 1:10 mixture of β-mercaptoethanol and Qiagen Buffer RLT. The lysates were vortexed, snap frozen, and stored at -80°C. Lysates were thawed on ice and passed through a 20-guage needle 10x. Total RNAs were purified with the Qiagen RNeasy midi-columns performing the on-column DNase step. The amount of purified RNA was quantified using a Nanodrop instrument, and RNA quality was assessed using an Agilent TapeStation 2200 with RNA ScreenTape. After adding 1 ul RNase Block (Agilent) samples were stored at -80. Total RNAs harvested from H295R or COV434 cells transfected with the custome STARR-seq plasmid library were subjected to poly-A enrichment, DNase digestion, reporter-specific reverse transcription, and PCR enrichment. ATAC-seq: Omni-ATAC protocol (Corces et al., 2017) was used, with the inclusion of the DNase treatment for COV434 cells.

treatment_protocol: The custom STARR-seq plasmid Library was transfected into H295R or COV434 cells with Lonza Nucleofector™ X Kit (SF-CM-138 or SF-DN-100 respectively ) according to the manufacturer’s protocol. At 6 hours post-transfection, the media was removed and cells were washed with, washed with PBS, and total RNAs harvested using the Qiagen RNeasy system

value: Adrenal


title: capture-DENND1A-STARR-seq-Output-2


title: HCC827OR-2

city: wuhan

first: wei

last: lin

state: 否

address: Luo Yu Road 1037，Hongshan District

institute: Huazhong University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
TPM were calculated using a protocol. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: lung

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

value: lung

value: non-small cell lung cancer cells

value: osimeitinib resistant


title: ENDSEQ-VABL-HP2

value: vAbl cell line

value: pre-B


title: capture-DENND1A-STARR-seq-Input3


title: HCC827OR-3


title: HCC827OR-1


title: Uterus, RNA, month 4, individual 3


title: HCC827-3

value: osimeitinib sensitive


title: female_5

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website 2 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: reference genome was built using Hisat2 v2.0.5 a
Supplementary files format and content: excel file with FPKM

source_name: Kidney

extract_protocol:
RNA was extracted using the Trizol reagent according to the manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification). The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Kidney

tag: cell line:

value: Tissue

tag: Sex

value: female


title: HCC827-2

tag: cell line


title: Uterus, RNA, month 4, individual 1


title: female_4

tag: cell type


title: ExVivoArtery(puncture site)_Exosealrep3

city: guangzhou

first: wenxuan

last: Wu

state: Guangdong

address: xiaoguwei Street

institute: South China University of Technology

description: Gene expression after 6hr in 0Gy-irradiated human blood

hyb_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

organism: Sus scrofa

source_name: ExVivoArtery(puncture site)_Exosealrep3

label_protocol: Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

extract_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology).

tag: puncture site

value: Left

tag: ttrated methods

value: Exoseal


title: ExVivoArtery(puncture site)_Exosealrep1

source_name: ExVivoArtery(puncture site)_Exosealrep1

value: TAG


title: ExVivoArtery(puncture site)_Exosealrep2

source_name: ExVivoArtery(puncture site)_Exosealrep2


title: ExVivoArtery(puncture site)_TAGrep1

source_name: ExVivoArtery(puncture site)_TAGrep1


title: ExVivoArtery(puncture site)_TAGrep2

source_name: ExVivoArtery(puncture site)_TAGrep2


title: female_3


title: capture-DENND1A-STARR-seq-Output-1


title: ExVivoArtery(puncture site)_TAGrep3

source_name: ExVivoArtery(puncture site)_TAGrep3


title: H295R-STARR-seq-Output-2

description: Total RNAs harvested from H295R cells transfected with the a custom plasmid STARR-seq library were subjected to poly-A enrichment, DNase digestion, reporter-specific reverse transcription, and PCR enrichment. Input library referes to the DNA from the plasmid pool. Output librraies refer to the reporter RNA librray

data_processing:
STARR-seq: Sequencing data quality was assessed with FastQC, and adapters were trimmed with Trimmomatic.) . STARR-seq input and output libraries were aligned to the human genome assembly hg38 with Bowtie2 (version 2.2.4)32, using the following parameters: bowtie2 -X 2000 --sensitive. Samtools was used to process alignments.Only properly-paired alignments with a MAPQ score ≥ 30 outside hg38 centromeres, gap and blacklist regions were were retained in downstream analyses. We used CRADLE (Kim et al., 2021) package to correct biases and call peaks with the following options. We then estimated differential STARR-seq activity across the regions as fold change using DESeq (Love et al., 2014).
ATAC-seq: ATAC-seq libraries for H295R and COV434 cell lines were individually aligned to the human genome (hg38). Each cell line had 2 biological replicates, and >40 million reads were generated per sample. Sequencing data quality was assessed with FastQC, and adapters were trimmed with Trimmomatic. Trimmed reads were aligned to the GRCh38 genome using Bowtie94 reporting only alignments having no more than two mismatches, discarding multi-mapping reads(-v 2 --best --strata -m 1). Reads mapping to the ENCODE hg38 blacklisted regions (https://www.encodeproject.org/files/ENCFF356LFX; manually curated regions with anomalous signal across multiple genomic assays and cell types) were removed using bedtools2 intersect (v2.25.0). Properly paired reads were then filtered to exclude presumed PCR duplicates using Picard MarkDuplicates (v1.130; http://broadinstitute.github.io/picard/). Reads were then used to generate reads per million (RPM) counts of bigWig files for visualization using deeptools bamCoverage (v3.0.1). Peaks were called using MACS2 with an FDR cutoff 0.1.
Assembly: hg38
Supplementary files format and content: STARR-seq: Input files were processed as described. RPKM normalized files are submitted Output files were processed as described above. UMIs were used for deduplication and RPKM normalized files are submitted
Supplementary files format and content: ATAC-seq: ATAC-seq libraries were processed as described above. The RPKM normalized, deduplicated files are submitted
Library strategy: STARR-seq

extract_protocol:
The custom STARR-seq plasmid Library was transfected into H295R cells with Lonza Nucleofector™ X Kit (SF-DN-100 ) according to the manufacturer’s protocol. At 6 hours post-transfection, the media was removed and cells were washed with, washed with PBS, and total RNAs harvested using the Qiagen RNeasy system
STARR-seq : Each washed cell pellet harvested from a 500 cm2 plate was lysed in a 50 mL conical tube with 5 mL of a 1:10 mixture of β-mercaptoethanol and Qiagen Buffer RLT. The lysates were vortexed, snap frozen, and stored at -80°C. Lysates were thawed on ice and passed through a 20-guage needle 10x. Total RNAs were purified with the Qiagen RNeasy midi-columns performing the on-column DNase step. The amount of purified RNA was quantified using a Nanodrop instrument, and RNA quality was assessed using an Agilent TapeStation 2200 with RNA ScreenTape. After adding 1 ul RNase Block (Agilent) samples were stored at -80. Total RNAs harvested from H295R or COV434 cells transfected with the custome STARR-seq plasmid library were subjected to poly-A enrichment, DNase digestion, reporter-specific reverse transcription, and PCR enrichment. ATAC-seq: Omni-ATAC protocol (Corces et al., 2017) was used, with the inclusion of the DNase treatment for COV434 cells.


title: HCC827-1


title: Uterus, RNA, month 2, individual 5

value: Uterus

value: month 2


title: H295R-STARR-seq-Output-1


title: Uterus, RNA, month 2, individual 2


title: Uterus, RNA, month 2, individual 4


title: female_1


title: Donor 09-9-6 MDM, TT genotype, Uninfected

city: Boston

first: Xin

last: Wang

address: 677 Huntington Ave

institute: Harvard University School of Public Health

data_processing:
1.8.0 - RTA, STAR, RSEM
The single-end raw reads were filtered by Trimmomatic version 0.39 to remove the adaptors and low-quality bases.
We used STAR version 2.6.0c and RSEM version 1.2.29 to quantify gene expression using human genome primary assembly (GRCh38) and its basic gene annotation from gencode human release 43 (GRCh38.p13).
The pipeline generates expected counts and transcripts per million (TPM) for each gene.
Assembly: human genome primary assembly (GRCh38)
Supplementary files format and content: Comma-separated values (csv) file format of TPM values of each sample

source_name: hMDM

growth_protocol: Mammalian cells were cultured in RPMI 1640 with 10% fetal bovine serum (FBS), 10 mM HEPES, and 2mM L-glutamine

extract_protocol:
RNA was extracted using the Zymo Direct-Zol kit.
The library was prepared using the KAPA mRNA HyperPrep kit (Roche)

treatment_protocol: hMDMs were infected by Mtb strains

value: hMDM

value: human monocyte-derived macrophage

tag: genotype

value: FLOT1 TT

value: Uninfected


title: Donor 09-9-6 MDM, TT genotype, Infected by strain 7944 (Non-G2G)

value: Infected


title: Uterus, RNA, day1, individual 5


title: Uterus, RNA, month 2, individual 3


title: Donor 09-9-6 MDM, TT genotype, Infected by strain 5209 (G2G)


title: female_2


title: Uterus, RNA, month 4, individual 2

value: month 4


title: Uterus, RNA, day1, individual 4


title: H295R-STARR-Seq-Input-1

description: A custom plasmid STARR-seq library was generated for the targeted regions. Input library refers to the targeted genomic regions sequenced from the plasmid library pool.

value: Adrenal


title: Donor 09-9-6 MDM, TT genotype, Infected by strain 7822 (Non-G2G)


title: capture-DENND1A-STARR-seq-Input1


title: H295R-STARR-seq-Output-3


title: H295R-STARR-Seq-Input-3


title: male_5

value: male


title: Donor 09-9-6 MDM, TT genotype, Infected by strain 8165 (G2G)


title: male_3


title: Donor 09-9-6 MDM, TT genotype, Infected by strain 8152 (G2G)


title: H295R-STARR-Seq-Input-2


title: Uterus, RNA, month 2, individual 1


title: Uterus, RNA, day1, individual 3


title: COV434-STARR-seq-Output-3

description: Total RNAs harvested from COV434 cells transfected with the a custom plasmid STARR-seq library were subjected to poly-A enrichment, DNase digestion, reporter-specific reverse transcription, and PCR enrichment. Input library referes to the DNA from the plasmid pool. Output librraies refer to the reporter RNA librray

source_name: Ovary

extract_protocol:
The custom STARR-seq plasmid Library was transfected into COV434 cells with Lonza Nucleofector™ X Kit (SF-CM-138 ) according to the manufacturer’s protocol. At 6 hours post-transfection, the media was removed and cells were washed with, washed with PBS, and total RNAs harvested using the Qiagen RNeasy system
STARR-seq : Each washed cell pellet harvested from a 500 cm2 plate was lysed in a 50 mL conical tube with 5 mL of a 1:10 mixture of β-mercaptoethanol and Qiagen Buffer RLT. The lysates were vortexed, snap frozen, and stored at -80°C. Lysates were thawed on ice and passed through a 20-guage needle 10x. Total RNAs were purified with the Qiagen RNeasy midi-columns performing the on-column DNase step. The amount of purified RNA was quantified using a Nanodrop instrument, and RNA quality was assessed using an Agilent TapeStation 2200 with RNA ScreenTape. After adding 1 ul RNase Block (Agilent) samples were stored at -80. Total RNAs harvested from H295R or COV434 cells transfected with the custome STARR-seq plasmid library were subjected to poly-A enrichment, DNase digestion, reporter-specific reverse transcription, and PCR enrichment. ATAC-seq: Omni-ATAC protocol (Corces et al., 2017) was used, with the inclusion of the DNase treatment for COV434 cells.

value: Ovary


title: Donor 17-6-6 MDM, TT genotype, Uninfected


title: male_4

value: Kidney


title: Uterus, RNA, day1, individual 1


title: male_2

value: Tissue


title: Uterus, RNA, month 6, individual 5

value: month 6


title: COV434-STARR-seq-Output-1


title: Donor 79-1-5 MDM, TT genotype, Uninfected


title: Donor 79-1-5 MDM, TT genotype, Infected by strain 7944 (Non-G2G)


title: Ovary, RNA, month 6, individual 5


title: COV434-STARR-Seq-Input-3


title: OCCS3, visium

city: Tokyo

first: Yutaro

last: Mori

address: 2-21-1 Kaga, Itabashi-ku

department: Advanced Comprehensive Research Organization

country: Japan

institute: Teikyo University

description: 10x Genomics

data_processing:
library strategy: spatial transcriptomics
Sequencing was performed on a HiSeq 2500 (Illumina).
Raw sequencing data was processed with the spaceranger pipeline (version 1.1.0., 10X Genomics) and mapped to the GRCh38 genome assembly.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: OCCC tumor

growth_protocol: All procedures were performed using protocols approved by the Ethics Committee of Teikyo University, Niigata University and the National Cancer Center. Informed consent was obtained from all patients. Surgical specimens of ovarian clear cell carcinoma tissues were excised from patients, washed with PBS, snap frozen in liquid nitrogen and stored in at −80°C until use.

extract_protocol:
For spatial transcriptomics, frozen tissue samples were embedded in pre-chilled OCT compound (#25608-930, Sakura Finetechnical). OCT-embedded samples were frozen on dry ice, and then stored at −80°C until use. Optimal parameters for tissue permeabilization for OCCC tissue were determined using the Visium Spatial Tissue Optimization Kit (PN-1000193, 10x Genomics). Visium Spatial Gene Expression was performed according to the manufacturer’s instructions (10x Genomics) with the following parameters: 10 mm thick sections of OCCC tissue were used. Permeabilization was carried out for 20 min.
Sequencing libraries were prepared per manufacturer’s protocol.

value: tumor cells

value: OCCC tumor


title: Donor 79-1-5 MDM, TT genotype, Infected by strain 7826 (Non-G2G)


title: COV434-STARR-seq-Output-2


title: Ovary, RNA, month 6, individual 4


title: COV434-STARR-Seq-Input-2


title: Donor 79-1-5 MDM, TT genotype, Infected by strain 7822 (Non-G2G)


title: Ovary, RNA, month 6, individual 3


title: OCCS5, snRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on a HiSeq 2500 (Illumina).
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38 (version 3.0.0 for premRNA)
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101, Sigma-Aldrich). Frozen tissue samples were homogenized using a KIMBLE Dounce tissue grinder set (D8938, Sigma-Aldrich) in 500 ml of ice-cold Nuclei EZ Lysis buffer, and they were incubated on ice for 5 minutes with an additional 1 ml of lysis buffer. The homogenate was filtered through a 70-mm cell strainer (#352350, Corning) and then centrifuged at 500×g for 1 minutes at 4°C. The pellet was resuspended and washed with 1 ml of Nuclei EZ Lysis buffer, and then, it was incubated on ice for 5 minutes. After another centrifugation, the pellet was subsequently washed twice in 1 ml of Nuclei Suspension Buffer (1× PBS, 1% BSA, and 0.2% RNase inhibitor (2313A, Clontech/TaKaRa)). The washed nuclear pellet was resuspended in 1 ml of Nuclei Suspension Buffer, filtered through a 35-mm cell strainer (#352235, Corning) for two times, and counted for snRNA-seq. snRNA-seq was performed after nucleus isolation with the 10X Chromium system using the Single Cell 3′ Reagent Kit v3 (PN-1000075, 10X Genomics) following the manufacturer’s protocol.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).


title: Donor 79-1-5 MDM, TT genotype, Infected by strain 8165 (G2G)


title: Ovary, RNA, month 6, individual 2


title: male_1


title: OCCR2, visium

description: 10x Genomics


title: Streptococcus pneumoniae-infected adult mice at 3 days post-infection, sample 5

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

description: Adult

data_processing:
The raw fastq reads were aligned to mm10 mouse references genome using STAR aligner.
Fastq Screen was used to check for any contamination in the samples and Picard RNA-seq Metrics was used to obtain the metrics of all aligned RNA-seq reads.
featureCounts was used to quantify the gene expression levels and raw gene counts were used for differential expression analysis.
A DESeq2 R package was used to identify DEGs.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Nasal lavage

growth_protocol: Mice were bred and housed in a conventional, SPF animal facility. Animals were kept on a 12-hour light cycle with a temperature in the animal facility of 70°F (±2°F). Mice were given food and water ad libitum. Infant mice remained with dam until weaning at 21 days of age.

extract_protocol:
Total RNA was extracted from a 600ul RLT lysis buffer (Qiagen) nasal lavage using a QIAshredder kit followed by an RNeasy minikit (Qiagen) according to the manufacturer's protocol.
The Illumina TruSeq Stranded mRNA Library 132 Prep Kit (Illumina) was used according to the manufacturer’s protocol.A total of 350ng RNA/sample with 11 cycles for final amplification was performed.

treatment_protocol: Four day old infant mice were treated with 3ul of PBS (mock-infected) or 3ul of 10^3 CFU of Streptococcus pneumoniae diluted in PBS. Adult mice were either treated with 10ul of PBS (mock-infected) or 10ul of 10^5 CFU of Streptococcus pneumoniae diluted in PBS.

value: Nasal lavage

value: Nasal mucosa

value: Wild-type

value: 10 ul of 10^5 CFU of Streptococcus pneumoniae serotype 23F


title: Ovary, RNA, month 6, individual 1


title: Donor 79-1-5 MDM, TT genotype, Infected by strain 8152 (G2G)

value: hMDM

value: human monocyte-derived macrophage


title: COV434-STARR-Seq-Input-1


title: Donor 79-1-5 MDM, TT genotype, Infected by strain 5209 (G2G)

value: FLOT1 TT


title: OCCS3, snRNAseq

description: 10x Genomics


title: OCCS4, snRNAseq

description: 10x Genomics


title: OCCS1, snRNAseq

description: 10x Genomics


title: OCCS2, snRNAseq

description: 10x Genomics


title: Streptococcus pneumoniae-infected adult mice at 3 days post-infection, sample 2

description: Adult


title: Streptococcus pneumoniae-infected adult mice at 3 days post-infection, sample 4

description: Adult


title: Donor 67-4-3 MDM, TT genotype, Uninfected

value: Uninfected


title: Donor 67-4-3 MDM, TT genotype, Infected by strain 7944 (Non-G2G)

value: Infected


title: Uterus, RNA, day1, individual 2

value: Uterus


title: Ovary, RNA, month 4, individual 4

value: month 4


title: Ovary, RNA, month 4, individual 3

value: Ovary


title: Donor 67-4-3 MDM, TT genotype, Infected by strain 7822 (Non-G2G)


title: Donor 67-4-3 MDM, TT genotype, Infected by strain 7826 (Non-G2G)


title: OCCR4, snRNAseq

description: 10x Genomics


title: OCCR5, snRNAseq

description: 10x Genomics


title: Streptococcus pneumoniae-infected adult mice at 3 days post-infection, sample 1

description: Adult


title: Streptococcus pneumoniae-infected adult mice at 3 days post-infection, sample 3

description: Adult


title: Ovary, RNA, month 4, individual 2


title: Streptococcus pneumoniae-infected 4 day old infant mice at 3 days post-infection, sample 4

description: Infant

value: 3 ul of 10^3 CFU of Streptococcus pneumoniae serotype 23F


title: Streptococcus pneumoniae-infected 4 day old infant mice at 3 days post-infection, sample 5

description: Infant


title: OCCR3, snRNAseq

description: 10x Genomics


title: Streptococcus pneumoniae-infected 4 day old infant mice at 3 days post-infection, sample 2

description: Infant


title: Streptococcus pneumoniae-infected 4 day old infant mice at 3 days post-infection, sample 1

description: Infant


title: capture-DENND1A-STARR-seq-Input2

value: Adrenal


title: Donor 21-1-5 MDM, AT genotype, Uninfected

value: FLOT1 AT


title: Ovary, RNA, month 4, individual 1


title: Donor 21-1-5 MDM, AT genotype, Infected by strain 7944 (Non-G2G)


title: Mock (PBS)-infected adult mice at 3 days post-treatment, sample 5

description: Adult

value: 10 ul of PBS administered intranasally


title: Donor 67-4-3 MDM, TT genotype, Infected by strain 8165 (G2G)


title: OCCR2, snRNAseq

description: 10x Genomics

value: tumor cells

value: OCCC tumor


title: Ovary, RNA, month 4, individual 5


title: Ovary, RNA, month 2, individual 5

value: month 2


title: Streptococcus pneumoniae-infected 4 day old infant mice at 3 days post-infection, sample 3

description: Infant

value: Nasal lavage

value: Nasal mucosa

value: Wild-type


title: OCCR1, snRNAseq

description: 10x Genomics


title: Ovary, RNA, month 2, individual 4


title: Donor 67-4-3 MDM, TT genotype, Infected by strain 5209 (G2G)

value: hMDM

value: human monocyte-derived macrophage


title: Ovary, RNA, month 2, individual 3


title: Mono_Cancer_scRNAseq

description: 10x Genomics

data_processing:
Sequencing was performed on a HiSeq 2500 (Illumina).
Raw sequencing data was processed with the cellranger pipeline (version 6.1.2, 10X Genomics) using the command “cellranger multi” and mapped to the GRCh38 reference genome to generate matrices of gene counts by cell barcodes. Expression data of three types of cells (Co-culture cells, Monoculture CAFs and Monoculture cancer cells) were obtained from one set of raw fastq files.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: All procedures were performed using protocols approved by the Ethics Committee of Teikyo University, Niigata University and the National Cancer Center. Informed consent was obtained from all patients. OCCC tissues were collected from patients with primary clear cell carcinoma within 30 min of surgical excision. The samples were washed with PBS and mechanically cut into small pieces using a scalpel, followed by dissociation with Collagenase/hyaluronidase (#7912, Stemcell Technologies) for 2 h at 37°C. Dissociated cells were sequentially ﬁltered through 100- and 70-μm cell strainers (352350, BD Falcon). Collected cells were isolated through density gradient centrifugal purification in PBS containing 30% Histodenz (D2158, Sigma). After lysis of red blood cells with ACK Lysing Buffer (A1049201, Thermo Fisher Scientific), the half of remaining cells were grown on ultra-low-attachment culture dishes (#3471 or #3262, Corning) in STEMPRO hESC SFM (A1000701, Thermo Fisher Scientific) supplemented with 8 ng/mL basic fibroblast growth factor (#AA10-155, Thermo Fisher Scientific) and penicillin/streptomycin (37°C, 5% CO2). For serial passaging, spheroid cells were dissociated with Accumax (AM105, Innovative Cell Technologies) once every 14 days. And the half of remaining cells were grown on attachment culture dishes (#35003, Corning) in MEM-α (#12561-05, Thermo Fisher Scientific) containing 10% FBS (#10270106, Thermo Fisher Scientific) and penicillin/streptomycin (37°C, 5% CO2). For serial passaging, CAFs were dissociated with TripLE Express Enzyme (#12604013, Thermo Fisher Scientific) once every 14 days.

extract_protocol:
After 3 days incubation, co-culture and monoculture cells were dissociated and scRNA-seq was performed using the Single Cell 3’ Reagent Kit v3 and 3’ CellPlex Kit Set A (10X Genomics) following the manufacturer’s protocol (single cell 3’ v3.1 with Feature Barcode technology for Cell Multiplexing protocol, 10x Genomics).
Library construction was performed according to the manufacter’s instructions.

treatment_protocol: Spheroid cells and CAFs were dissociated and mixed for co-culture at 1:1 ratio or unmixed for monoculture. The isolated cells were plated for 6 hrs on a plate containing growth factor reduced (GFR) Matrigel (#356231, Corning) with MEM-a supplemented with 10% FBS. After removing the floating dead cells, the cells were then overlaid onto GFR Matrigel and E medium (DMEM/F12-GlutaMAX (#10565-042, Thermo Fisher Scientific) supplemented with penicillin-streptomycin, 10 mM HEPES (#15630106, Thermo Fisher Scientific), N-2 Supplement (#17502-001, Thermo Fisher Scientific), B-27 supplement (#17504-001, Thermo Fisher Scientific), 1 mM N-acetylcysteine (A7250, Sigma-Aldrich), 50 ng/ml human EGF (PHG0313, Thermo Fisher Scientific)).

value: Cancer cells


title: Ovary, RNA, day1, individual 4


title: Sen_Rep_2

city: Nice

first: Julien

last: Cherfils-Vicini

address: 28 Avenue de Valombrose

institute: IRCAN - CNRS - INSERM

data_processing:
Low quality reads, adaptor contamination and excessively high levels of unknown base N reads were removed from the analysis with SOAPnuke. The reads were aligned to the GCF_000001405.39_GRCh38.p13 reference genome using HISAT2. After that, Ericscript (0.5.5-5) and rMATS (v4.1.1) were used to detect fusion genes and differential splicing genes. Bowtie2 was applied to align the clean reads to the gene set. Quantification was performed by RSEM (v1.2.28).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Counts and TPM

growth_protocol: All cells were cultured in DMEM 5% FBS with peni-streptomycin at 5% O2 at 37°C.

extract_protocol:
TRI reagent (Sigma-Aldrich) protocol.
Oligo dT Selection, random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP. The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase (UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer.

treatment_protocol: Primary human fibroblasts MRC5 were induced to senesce by exposure to Bleomycin (Sigma-Aldrich, ref#B8416-15UN) during 24h at 50 µg/mL. Replicative senescence was induced by continuous passaging of primary human fibroblasts MRC5 at 5% O2 until they reached a plateau in their growth curve. Oncogene-Induced senescence was induced in MRC5 fibroblasts transduced with a vector expressing H-RASG12V and treated with 4-Hydroxytamoxifen at 50nm every 48h for 5 or 8 days.

value: Fibroblasts


title: Mono_CAF_scRNAseq

description: 10x Genomics

value: CAFs


title: Ovary, RNA, month 2, individual 2


title: Donor 21-1-5 MDM, AT genotype, Infected by strain 8165 (G2G)

value: Infected


title: Coculture_cells_scRNAseq

description: 10x Genomics

value: Cancer cells and CAFs


title: Ovary, RNA, day1, individual 5

value: Ovary


title: Ovary, RNA, month 2, individual 1


title: Ovary, RNA, day1, individual 3


title: Sen_Rep_3


title: Donor 21-1-5 MDM, AT genotype, Infected by strain 7826 (Non-G2G)


title: Donor 21-1-5 MDM, AT genotype, Infected by strain 7822 (Non-G2G)


title: Sen_Rep_1


title: Mock (PBS)-infected adult mice at 3 days post-treatment, sample 3

description: Adult


title: Donor 67-4-3 MDM, TT genotype, Infected by strain 8152 (G2G)

value: FLOT1 TT


title: Mock (PBS)-infected 4 day old infant mice at 3 days post-treatment, sample 5

description: Infant

value: 3 ul of PBS administered intranasally


title: Mock (PBS)-infected 4 day old infant mice at 3 days post-treatment, sample 4

description: Infant


title: Donor 21-1-5 MDM, AT genotype, Infected by strain 8152 (G2G)

value: FLOT1 AT


title: Bleo_PDL30_1


title: Mock (PBS)-infected adult mice at 3 days post-treatment, sample 4

description: Adult

value: 10 ul of PBS administered intranasally


title: Bleo_PDL30_3


title: Bleo_PDL30_2


title: Ovary, RNA, day1, individual 1


title: Mock (PBS)-infected adult mice at 3 days post-treatment, sample 2

description: Adult


title: Donor 15-3-6 MDM, AT genotype, Uninfected

value: Uninfected


title: Bleo_pLVUT_RAS-ER_NI_3


title: Uterus, miRNA, month 6, individual 5

data_processing:
The raw reads were filtered using Cutadapt 1.16.
Using the Bowtie 1.0.1 filter out repeated sequences and ncRNAs based on RepeatMasker and Rfam. Next, clean reads were aligned to the reference genome (Capra hircus, ARS1.2) using BLAST 2.7.1.
MiRNAs were identified using miREvo 1.1 and miRDeep2 2.0.0.7.
MiRNA expression levels were normalized with RSEM 1.3.0
Assembly: Capra hircus, ARS1.2
Supplementary files format and content: Txt files includes read counts of all samples.

extract_protocol:
Total RNA was isolated from 20 uterine tissue and 20 ovarian tissues samples with TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The RNA concentration, purity and integrity were calculated and checked by a NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and an Agilent 5400 Bioanalyzer (Agilent, Santa Clara, CA).
miRNA sequencing libraries were prepared for sequencing using standard Illumina protocols.

value: Uterus

value: month 6


title: Donor 15-3-6 MDM, AT genotype, Infected by strain 7944 (Non-G2G)


title: Mock (PBS)-infected 4 day old infant mice at 3 days post-treatment, sample 1

description: Infant

value: Nasal lavage

value: Nasal mucosa


title: Uterus, miRNA, month 6, individual 3


title: Mock (PBS)-infected adult mice at 3 days post-treatment, sample 1

description: Adult

value: Wild-type


title: Uterus, miRNA, month 6, individual 4


title: Mock (PBS)-infected 4 day old infant mice at 3 days post-treatment, sample 2

description: Infant


title: Donor 21-1-5 MDM, AT genotype, Infected by strain 5209 (G2G)

value: hMDM

value: human monocyte-derived macrophage


title: Prolif_PDL30_3

value: Fibroblasts


title: Bleo_pLVUT_RAS-ER_NI_2


title: Ovary, RNA, day1, individual 2


title: Donor 09-9-6 MDM, TT genotype, Infected by strain 7826 (Non-G2G)


title: Donor 15-3-6 MDM, AT genotype, Infected by strain 8152 (G2G)


title: Prolif_PDL30_2


title: Donor 15-3-6 MDM, AT genotype, Infected by strain 7822 (Non-G2G)


title: Bleo_pLVUT_RAS-ER_NI_1


title: Donor 15-3-6 MDM, AT genotype, Infected by strain 5209 (G2G)


title: COV434-ATAC-seq-Rep2

description: Omni-ATAC protocol (Corces et al., 2017) was used to generate the ATAC-seq library in H295R cells.

extract_protocol:
Omni-ATAC protocol (Corces et al., 2017) was used to generate the ATAC-seq library in COV434 cells.
STARR-seq : Each washed cell pellet harvested from a 500 cm2 plate was lysed in a 50 mL conical tube with 5 mL of a 1:10 mixture of β-mercaptoethanol and Qiagen Buffer RLT. The lysates were vortexed, snap frozen, and stored at -80°C. Lysates were thawed on ice and passed through a 20-guage needle 10x. Total RNAs were purified with the Qiagen RNeasy midi-columns performing the on-column DNase step. The amount of purified RNA was quantified using a Nanodrop instrument, and RNA quality was assessed using an Agilent TapeStation 2200 with RNA ScreenTape. After adding 1 ul RNase Block (Agilent) samples were stored at -80. Total RNAs harvested from H295R or COV434 cells transfected with the custome STARR-seq plasmid library were subjected to poly-A enrichment, DNase digestion, reporter-specific reverse transcription, and PCR enrichment. ATAC-seq: Omni-ATAC protocol (Corces et al., 2017) was used, with the inclusion of the DNase treatment for COV434 cells.


title: Prolif_PDL30_1


title: Uterus, miRNA, month 6, individual 2


title: Donor 15-3-6 MDM, AT genotype, Infected by strain 8165 (G2G)


title: H295R-ATAC-seq-Rep1

extract_protocol:
Omni-ATAC protocol (Corces et al., 2017) was used to generate the ATAC-seq library in H295R cells.
STARR-seq : Each washed cell pellet harvested from a 500 cm2 plate was lysed in a 50 mL conical tube with 5 mL of a 1:10 mixture of β-mercaptoethanol and Qiagen Buffer RLT. The lysates were vortexed, snap frozen, and stored at -80°C. Lysates were thawed on ice and passed through a 20-guage needle 10x. Total RNAs were purified with the Qiagen RNeasy midi-columns performing the on-column DNase step. The amount of purified RNA was quantified using a Nanodrop instrument, and RNA quality was assessed using an Agilent TapeStation 2200 with RNA ScreenTape. After adding 1 ul RNase Block (Agilent) samples were stored at -80. Total RNAs harvested from H295R or COV434 cells transfected with the custome STARR-seq plasmid library were subjected to poly-A enrichment, DNase digestion, reporter-specific reverse transcription, and PCR enrichment. ATAC-seq: Omni-ATAC protocol (Corces et al., 2017) was used, with the inclusion of the DNase treatment for COV434 cells.

value: Adrenal


title: Uterus, miRNA, month 6, individual 1


title: Donor 09-9-3 MDM, AT genotype, Uninfected


title: H295R-ATAC-seq-Rep2


title: Mock (PBS)-infected 4 day old infant mice at 3 days post-treatment, sample 3

description: Infant


title: Uterus, miRNA, month 4, individual 4

value: month 4


title: pLVUT_RAS-ER_NI_2


title: COV434-ATAC-seq-Rep1


title: Donor 09-9-3 MDM, AT genotype, Infected by strain 7826 (Non-G2G)

value: Infected


title: pLVUT_RAS-ER_NI_1


title: Uterus, miRNA, month 4, individual 5


title: pLVUT_RAS-ER_NI_3


title: Donor 09-9-3 MDM, AT genotype, Infected by strain 7822 (Non-G2G)


title: Uterus, miRNA, month 4, individual 2


title: pLVUT_RAS-ER_D8_2


title: Uterus, miRNA, month 2, individual 4

value: month 2


title: pLVUT_RAS-ER_D8_1


title: Plasma, Diabetic normal renal function, rep12

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Raw read quality control was performed with FastQC
Adapters were trimmed with Trim Galore
Reads were collapsed with seqcluster and aligned with Bowtie1 against miRBase mature miRNA and miRBase hairpin (miRbase Ver 22, available athttp://mirbase.org)
Post-alignment processing of miRBase hairpin was performed using SAMtools and EdgeR (3.36.0) for miRBase analysis
Assembly: miRbase Ver 22
Supplementary files format and content: csv delimited text file containing raw counts of mature miRNAs

source_name: plasma

extract_protocol:
Whole blood was collected using a vacuette needle into an ethylenediaminetetraacetic acid (EDTA) collection tube for plasma isolation. Following centrifugation at 3,000 g for 10 minutes at 4°C, the supernatant was pipetted into 3 x 1 ml aliquots in RNase/DNase-free tubes and frozen at -80°C. RNA was extracted from 600 μl of plasma using the NextPrep™ MagnaZol™ cfRNA Isolation Kit (Bioo Scientific Corp, Texas, USA), following the manufacturer’s instructions, with purified RNA eluted in 16μl of nuclease-free water. RNA was quantified using the Qubit miRNA Assay kit (ThermoFisher Scientific, San Jose, USA).
miRNA libraries were prepared using QIAseq miRNA Library Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Library concentrations were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and quality control of library was performed using a High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, Santa Clara, CA, USA).

value: plasma

value: Diabetic normal renal function


title: Donor 09-9-3 MDM, AT genotype, Infected by strain 8152 (G2G)

value: FLOT1 AT


title: Plasma, Diabetic normal renal function, rep10


title: Donor 09-9-3 MDM, AT genotype, Infected by strain 7944 (Non-G2G)


title: Plasma, Diabetic normal renal function, rep13


title: pLVUT_RAS-ER_D8_3


title: Donor 09-9-3 MDM, AT genotype, Infected by strain 5209 (G2G)


title: Uterus, miRNA, month 4, individual 1


title: Plasma, Diabetic normal renal function, rep11


title: Uterus, miRNA, month 2, individual 5


title: Uterus, miRNA, month 2, individual 2


title: pLVUT_RAS-ER_D5_2


title: Uterus, miRNA, month 2, individual 1


title: Plasma, Diabetic normal renal function, rep9


title: WT typhoid toxin treated-3

city: Taipei

first: Po-Yo

last: Liu

address: No.1 Jen Ai road section 1 Taipei 100 Taiwan R.O.C.

department: Department and Graduate Institute of Medical Microbiology

country: Taiwan

institute: National Taiwan University College of Medicine

description: WT TT treated-3

data_processing:
Sequencing reads in fastq format were further analyzed with CLC Genomics Workbench 21 (version 21.0.1).
Reads were first trimmed for both adapter contamination and low-quality score trimming (Q<20)
Clean reads were mapped to the Homo sapiens (GRCh38) reference sequence with default parameters of the RNA Sequencing workflow for reads counting
The counting matrix were generated and used for differential expression analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: THP-1-derived macrophages

growth_protocol: THP-1 cells were cultured in Roswell Park Memorial Institute (RPMI)-1640 supplemented with 10% heat-inactivated fetal bovine serum (FBS), 4.5 g/L glucose, 10 mM HEPES and 10 mM sodium pyruvate. THP-1 cells were differentiated into macrophages by treating cells with 40 nM of phorbol 12-myristate 13- acetate (PMA) for 48 h, followed by overnight incubation in fresh medium before experiments.

extract_protocol:
Total RNAs from the cells were isolated using RNeasy purification kits (QIAGEN) following the manufacturer’s instructions. The concentration of RNA was measured by using Qubit RNA BR assay kit with Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, United States). RNA integrity Number (RIN) of RNA was assessed by using an RNA Nano 6000 assay kit and Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, United States). 100 ng of RNA with RIN ≧ 8 was used for library preparation with illumina stranded mRNA library prep Kit (Illumina, San Diego, CA , United States).
Briefly, messenger RNA (mRNA) with polyA tails was isolated by using oligo(dT) magnetic beads. Purified mRNA was fragmented into short segments and complementary DNA (cDNA) was synthesized with random hexamer primers. To achieve strand specificity, the deoxyuridine triphosphate (dUTP) was used for the replace of deoxythymidine triphosphate (dTTP) while performing second-strand cDNA synthesis. cDNA was clean up with AMPure XP beads (Beckman Coulter, Indianapolis, Indiana, United States) and followed by end repair, polyadenylation, and Illumina sequencing adapter ligation. After proper PCR amplification, final library was purified and paired-end 150 bp sequencing was performed with Illumina Novaseq to achieve 20 M reads per sample.

treatment_protocol: THP-1-derived macrophages were exposed to 160 rM of typhoid toxin at 37°C for 60 minutes and then changed to regular growth medium for 16 hours.

value: THP-1-derived macrophages

value: Human Monocytic Cell Line


title: Plasma, Diabetic normal renal function, rep8


title: pLVUT_RAS-ER_D5_3


title: Plasma, Diabetic normal renal function, rep7


title: Uterus, miRNA, month 2, individual 3

value: Uterus


title: Donor 06-8-5 MDM, AT genotype, Uninfected

value: Uninfected


title: Uterus, miRNA, month 4, individual 3


title: Plasma, Diabetic normal renal function, rep6


title: Donor 09-9-3 MDM, AT genotype, Infected by strain 8165 (G2G)


title: Uterus, miRNA, day1, individual 5


title: Uterus, miRNA, day1, individual 4


title: Plasma, Diabetic normal renal function, rep5


title: Uterus, miRNA, day1, individual 3


title: Uterus, miRNA, day1, individual 2


title: PltBS35A typhoid toxin treated-2

description: PltB mutant TT treated-2


title: WT typhoid toxin treated-2

description: WT TT treated-2


title: primary rat microglia + LPS 3

data_processing:
raw data in FASTQ format were adapter- and quality trimmed.
Mapping was performed against the Rattus norvegicus (mRatBN7.2.1110; January 05, 2024) genome sequence using Hisat2 alignment method.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach
Assembly: mRatBN7.2.1110
Supplementary files format and content: raw counts as .txt

source_name: cortical

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) and 150 ng of total RNA was used for the library construction
RNA libraries for RNA-Seq were prepared according to the manifacturers protocol using the VAHTS™ Universal RNA-Seq Library Prep Kit for Illumina® V6 with mRNA capture module

value: cortical

value: Postnatal day 1

value: microglia

value: Wistar

value: LPS (100ng/ml)


title: Plasma, Diabetic normal renal function, rep4


title: WT typhoid toxin treated-1

description: WT TT treated-1


title: primary rat microglia + H2O 3


title: Plasma, Diabetic normal renal function, rep3


title: pLVUT_RAS-ER_D5_1

value: Fibroblasts


title: primary rat microglia + LPS 2


title: Plasma, Diabetic normal renal function, rep2


title: Plasma, Diabetic kidney disease, rep9

value: Diabetic kidney disease


title: primary rat microglia + H2O 2


title: Ovary, miRNA, month 6, individual 4

value: Ovary

value: month 6


title: Ovary, miRNA, month 6, individual 5


title: Uterus, miRNA, day1, individual 1

source_name: Uterus


title: Mock-3


title: Mock-1


title: primary rat microglia + LPS 1


title: PltBS35A typhoid toxin treated-3

description: PltB mutant TT treated-3


title: Plasma, Diabetic normal renal function, rep1


title: primary rat microglia + buffer 3

value: buffer


title: Plasma, Diabetic kidney disease, rep8

value: plasma


title: Mock-2