title: NSC_NRS_polysomal_rep3

status: Public on Aug 05 2021

city: Edinburgh

first: Magdalena

middle: Maria

last: Maslon

address: Crewe Road

institute: University of Edinburgh

data_processing:
Basecall data produced by the NextSeq 550
reads were mapped to the mouse genome sequence (mm10) by STAR
The PIs and associated polysomal shift ratios (PSRs) were calculated for each sample
The results were filtered by a minimum coverage of 10 reads per junction and replicate, dPSI>0.2 and FDR<0.05
Genome_build: mm10
Supplementary_files_format_and_content: excel file with TPM values, polysome index value (PI), and polysome shift ratio (PSR) with associated pvalues

source_name: mouse neural stem cells

growth_protocol: ESCs were grown on gelatin -coated plates in 2i media (1:1 Neurobasal and DMEM/F12, supplemented with 0.5X N2, 0.5x B27, 0.05% BSA, 1M PD0325901, 3M CHIR99021, 2mM L-glutamine, 0.15mM monothioglycerol, 100U/ml LIF). NSCs were grown on laminin-coated plates in DMEM/F12 medium supplemented with 2mM L-glutamine, 0.5x N2, B27, glucose, BSA, Hepes and 10ng/ml of both mouse EGF and human FGF-2. MEFs were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was extracted using Trizol standard protocol
Libraries were prepared from polysomal, subpolysomal and total samples TruSeq Stranded Total RNA library preparation kit

treatment_protocol: Cells were grown in 15 cm plates, followed by lysis using polysome extraction buffer. Lysates were loaded onto 10-45% sucrose gradient, fractions were collected and pooled into subpolysomal and polysomal. A fraction of cytoplasmic extract was retained to assess the expression changes.

value: mouse neural stem cells

value: SRSF1 NRS/NRS


title: KD1_1

status: Public on Aug 06 2021

type: SRA

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Louisville

description: PARP-1 knockdown low weight band, replicate 1.

library_source: transcriptomic

data_processing:
Library strategy: NET-seq
Analysis of the data followed previously published protocols from the Churchman lab.
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1). The FastQC results indicate the data is of a high quality value, meaning that trimming for sequence quality was not necessary.
The original fastq sequences were trimmed  using Trimmomatic v0.33 to remove potential sequencing primers and adapters.
The trimmed sequences were then collapsed to remove identical sequences which may be the result of PCR duplications using fastx_collapser v0.0.14 from the FASTX toolkit .
Sequences for rRNA genes were downloaded from SILVA 132 and tRNA genes were downloaded from GtRNAdb.  The rRNA genes were further filtered to include only Drosophila melanogaster sequences using a custom script. A star genome index was generated from the combined rRNA and tRNA sequences using STAR v20201.
The trimmed sequences for each of the eight samples were then mapped against the rRNA and tRNA database using star aligning RNA filtered reads that map to a single location in the genome.
After alignment, the resulting BAM files were split according to their strandedness using samtools v1.3.1.
The BED files were then converted to WIG files using a custom script, only accounting for the very first base in the read, which allows for a single-base resolution of the stopping point of the ribosome.
Genome_build: dm6
Supplementary_files_format_and_content: wig files representing number of unique reads beginning at each specified location on either the forward (FWD) or reverse (REV) strand

molecule: total RNA

organism: Drosophila melanogaster

growth_protocol: Drosophila melanogaster S2 cells (obtained from Thermo Fisher Scientific, Waltham, MA 02451), were cultured in Schneider’s Drosophila medium (Life Technologies, Austin, TX 78744 ) supplemented with 10%  heat activated fetal bovine serum  (Sigma, St Louis, MO 63146),  100 U/ml penicillin and 100 μg/ml streptomycin at 25oC.  All experimental samples and controls were growth time and cell-density matched.

extract_protocol:
Nascent RNA isolation was performed as described at Weber et al and cap selection was done using GFP-elF4E recombinant protein generously provided by Dr. G. Zentner, Indiana University. RNA:GFP-elF4E complexes were pulled by GFP-nAb Magnetic Agarose beads (Allele Biotech) according to manufacturer’s protocol.
Sequencing library preparation for nascent RNA samples was performed according Illumina Protocol with slight modification.  After 3’- SR adaptor ligation, RNA was fragmented to 30-100 nucleotides with the RNA Fragmentation Reagent (Albion, AM8740) and purified according to Mayer et al, 2015. In order to prevent RNA fragments ligation, we performed 3’-OH phosphorylation with T4 PNK (3’ phosphatase minus) before hybridization of reverse transcription primer and 5’-SR adaptor ligation. After reverse transcription with Superscript Reverse Transcriptase (Invitrogen) we purified cDNA on 15% polyacrylamide TBE-urea gel to avoid primer dimer formation, excised gel region between 50 and 300 nt and extracted cDNA. After PCR amplification we performed quality control (QC) and size selection. To be confident on PCR products we did cloning and sequencing by using Zero Blunt TOPO PCR Cloning kit (ThermoFisher Scientific). Positive colonies were harvested, plasmid DNA was purified with QIAprep Spin Miniprep kit (Qiagen) and digested with EcoR1.  Digested products were visualized on 1% agarose gel and sent to sequence (Eurofins Scientific).

treatment_protocol: siRNA mediated PARP1 knockdown was done as described previously.  Depletion of PARP1 was confirmed by western blot (protein level) and quantitative PCR (transcript level).

tag: cell type

tag: genotype/variation

value: PARP-1 knockdown


title: NSC_NRS_polysomal_rep2

country: United Kingdom

organism: Mus musculus

tag: genotype


title: NSC_NRS_subpolysomal_rep3


title: NSC_NRS_subpolysomal_rep2


title: NSC_NRS_polysomal_rep1


title: NSC_NRS_subpolysomal_rep1

value: SRSF1 WT/WT


title: NSC_NRS_total_rep1


title: NSC_WT_subpolysomal_rep2


title: NSC_WT_polysomal_rep2


title: NSC_WT_subpolysomal_rep1


title: NSC_WT_polysomal_rep3


title: NSC_NRS_total_rep2


title: NSC_WT_subpolysomal_rep3


title: hepar tissues  LncRNA of 12h after liver transplantation-2

type: RNA

city: Zhengzhou

first: chen

last: sanyang

state: erqi

address: No.1, East Jian She Road

department: Department of Hepatobiliary and Pancreatic Surgery

country: China

institute: The First Affiliated Hospital of Zhengzhou University

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Rat LncRNA Microarray V2.0, and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: 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, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

organism: Rattus norvegicus

source_name: hepar tissues 12h after liver transplantation

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

growth_protocol: Hepar tissues of 12h after brain death donor liver transplantation and  matched non-brain death donor liver transplantation

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

treatment_protocol: Tissues from liver transplantation and propmptly frozen in the liquid nitrogen

tag: strain

value: Lewis

tag: Sex

value: male

tag: tissur

value: hepar tissues

tag: time point

value: 12h after liver transplantation

tag: molecule subtype

value: LncRNA


title: hepar tissues  LncRNA of 12h after liver transplantation-3


title: MEF_NRS_polysomal_rep2

source_name: mouse fibroblasts

value: mouse fibroblasts


title: MEF_NRS_subpolysomal_rep3


title: NSC_WT_total_rep2


title: MEF_NRS_polysomal_rep1


title: hepar tissues  LncRNA of 12h after brain death donor liver transplantation-2

source_name: hepar tissues 12h after brain death donor liver transplantation


title: hepar tissues  LncRNA of 12h after brain death donor liver transplantation-3


title: hepar tissues  LncRNA of 12h after brain death donor liver transplantation-1


title: hepar tissues  LncRNA of 12h after liver transplantation-1


title: MEF_NRS_total_rep3


title: NSC_WT_total_rep1


title: MEF_NRS_total_rep2


title: NSC_WT_polysomal_rep1


title: MEF_NRS_polysomal_rep3


title: MEF_WT_subpolysomal_rep3


title: MEF_WT_subpolysomal_rep1


title: MEF_WT_polysomal_rep3


title: MEF_WT_subpolysomal_rep2


title: MEF_NRS_total_rep1


title: MEF_WT_polysomal_rep1


title: MEF_WT_total_rep3


title: MEF_NRS_subpolysomal_rep1


title: MEF_WT_total_rep1


title: MEF_WT_total_rep2


title: ESC_NRS_subpolysomal_rep1

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells


title: ESC_WT_polysomal_rep2


title: ESC_WT_polysomal_rep3


title: ESC_NRS_polysomal_rep2


title: ESC_NRS_total_rep1


title: ESC_NRS_total_rep2


title: MEF_NRS_subpolysomal_rep2


title: ESC_NRS_polysomal_rep3


title: ESC_NRS_subpolysomal_rep2


title: ESC_NRS_polysomal_rep1


title: ESC_WT_polysomal_rep1


title: ESC_NRS_subpolysomal_rep3


title: MEF_WT_polysomal_rep2


title: ESC_WT_subpolysomal_rep2


title: MEF HOM replicate 1

description: MEF HOM replicate 1

data_processing:
Basecall data produced by the NextSeq 550
Reads were mapped to the mouse (mm10) genome
Paired reads were pseudoaligned to the GRCm38 (mm10) Ensembl 87 transcriptome using salmon
Splicing changes were inferred from transcript TPMs using SUPPA2
Results were filtered on mean transcript expression (TPM>0.5)
Genome_build: mm10
Supplementary_files_format_and_content: excel files with TPM for expression
Supplementary_files_format_and_content: excel file with significant AS changes from SUPPA

growth_protocol: MEFs were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Cells were grown in 10 cm plates.

extract_protocol:
RNA was extracted using Trizol standard protocol,
Libraries were prepared from each total-RNA sample using the TruSeq Stranded Total RNA with Ribo-Zero kit

value: fibroblasts


title: MEF HET replicate 1

description: MEF HET replicate 1

value: SRSF1 NRS/WT


title: MEF WT replicate 3

description: MEF WT replicate 3


title: MEF HOM replicate 2

description: MEF HOM replicate 2


title: ESC_WT_total_rep1


title: ESC_WT_total_rep2


title: MEF HOM replicate 3

description: MEF HOM replicate 3


title: MEF WT replicate 1

description: MEF WT replicate 1


title: MEF HET replicate 2

description: MEF HET replicate 2


title: 96_hiPS_PCSK9_FL_p12_68

city: Nantes

first: Antoine

last: Rimbert

address: 8 quai moncousu

country: France

institute: Institut du thorax inserm-U1087

data_processing:
Pipeline details have been published by Charpentier E et al. 2018 (10.21203/rs.3.pex-1336/v1)
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

growth_protocol: iPS cells were cultured on mouse embryonic fibroblasts (MEFs) in hiPSC medium composed of DMEM/F12 (Life Technologies) supplemented with 20% Knockout Serum Replacer (Life Technologies), 0.5% L-Glutamine (Life Technologies) with 0.14% β-mercaptoethanol (Sigma), 1% NEAA and 5 ng/ml fibroblast growth factor 2 (FGF2, Miltenyi) in hypoxia (4% O2, 5% CO2).

extract_protocol:
RNA was prepared using thethe RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).
the libraries was prepared from 10 ng of total RNA. 15 RNA samples were extracted from hiPS. The mRNA poly(A) tail was tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples were then pooled, amplified and tagmented using a transposon-fragmentation approach, which enriches for 3’ends of cDNA. 100ng of full-length cDNAs was used as input to the Nextera DNA Sample Prep kit (ref FC-121-1030, Illumina), which enriches for 3′ends of cDNA. Size library is controlled on 2200 Tape Station Sytem (Agilent Technologies). A library of 350-800bp was run on an Illumina HiSeq 2500 using a HiSeq Rapid SBS Kit v2 (50 cycles; FC-402-4022) and a HiSeq Rapid PE Cluster Kit v2 (PE-402-4002) according to manufacturer’s protocol (Denaturing and Diluting Libraries for the HiSeq® and GAIIx, Part # 15050107 v03 protocol, Illumina).

treatment_protocol: PCSK9 knockout in control hiPS cells was generated using the Alt-R™ CRISPR-Cas9 System (Integrated DNA Technologies) targeting the exon 7 of PCSK9 at both alleles. Briefly gRNA CCAGCGACTGCAGCACCTGC was first duplexed with the Alt-R® CRISPR-Cas9 tracrRNA, then complexed to the Alt-R® S.p. Cas9 Nuclease according to IDT recommandations.

value: Induced pluripotent stem cells

tag: gender

value: Female


title: ESC_WT_subpolysomal_rep3


title: ESC_WT_subpolysomal_rep1


title: 95_hiPS_PCSK9_FL_p12_67


title: 92_hiPS_PCSK9_KO_clG5_p62


title: 93_hiPS_PCSK9_KO_clG5_p59


title: 87_hiPS_PCSK9_KO_clC2_p72


title: 88_hiPS_PCSK9_KO_clC2_p65


title: 90_hiPS_PCSK9_KO_clG5_p73


title: 82_hiPS_PCSK9_KO_clB2_p67


title: 94_hiPS_PCSK9_FL_p12_66


title: 86_hiPS_PCSK9_KO_clC2_p73


title: 91_hiPS_PCSK9_KO_clG5_p72


title: 85_hiPS_PCSK9_KO_clB2_p59


title: 89_hiPS_PCSK9_KO_clC2_p61


title: input_clamp-RNAi_2-4_hr_3

city: Ithaca

first: Ellie

last: Duan

state: New York

address: 507 Tower Rd., Ithaca, NY 14853, Ithaca, NY 1485

department: Animal Science

institute: Cornell University

description: n.a.

library_source: genomic

data_processing:
We trimmed ChIP sequencing raw reads with Trim galore (v. 0.5.0, Krueger, 2017) with the minimal phred score 20, 36bp minimal read length and illumina adaptor removal. We then mapped cleaned reads to the D. melanogaster genome (UCSC dm6) with Bowtie2 (v. 2.3.0) with --very-sensitive-local flag. We used Picard tools (v. 2.9.2) and SAMtools (v.1.9, (Li et al., 2009) to remove the PCR duplicates. We used MACS2 (version 2.1.1, Zhang et al., 2008) to identify peaks with default parameters and MSPC (v.4.0.0, Jalili et al., 2015) to obtain consensus peaks from 3 replicates. ENCODE blacklist was used to filter out problematic regions in dm6 (Amemiya et al., 2019). We identified differential binding and non-differential binding using DiffBind with the DESeq2 method (v. 3.10, Stark and Brown, 2019). We used DeepTools (version 3.1.0, Ramírez et al., 2014) and Homer (v 4.11, Givler and Lilienthal, 2005) to generate enrichment heatmaps (SES normalization), average profiles, motif searches, peak overlaps and peak annotation. Visualizations and statistical tests were conducted in R (R Core Team, 2014).
Genome_build: dm6
Supplementary_files_format_and_content: Peak files: consensus peaks from 3 replicates, obtained using MSPC (v.4.0.0). Peak files are in bed format. The column 5 has X^2 of the p-values of all the peaks overlapping this peak (including the peak itself) with 2k degree of freedom, where k is the number of overlapping peaks. Bigwig files: generated using Deeptools (v.3.1.0) bamCompare tools. Each IP and coresponding input file were compared in bamCompare, -SES option was used to normalize the library size difference. Log2 ratio of (IP/input) Fold Change value was ouput from bamCompare in bigwig format.

molecule: genomic DNA

source_name: embryos 2-4hr

growth_protocol: To deplete maternally deposited clamp or zld mRNA throughout oogenesis, we crossed a maternal triple driver (MTD-GAL4, Bloomington, #31777) line with a Transgenic RNAi Project (TRiP) clamp RNAi line (Bloomington, #57008) or a TRiP zld RNAi line (from C. Rushlow lab, Sun et al., 2015). We used the MTD-GAL4 line alone as the control line.

extract_protocol: We performed ChIP-seq as previously described (Blythe and Wieschaus, 2015). We collected and fixed 200-400 embryos from each MTD-GAL4 and RNAi cross 0-2hr or 2-4hr after fertilization. We used 3 ul of rabbit anti-CLAMP (Soruco et al., 2013) and 2 ul rat anti-ZLD (from C. Rushlow lab) per sample. We performed three biological ChIP replicates for each protein (n=2), genotype (n=3)  and time point (n=2). In total, we prepared 36 libraries using the NEBNext Ultra ChIP-seq kit (New England Biolabs) and sequenced libraries on Illumina HiSeq 2500 sequencer in 2x150-bp mode.

tag: developmental stage

value: embryos 2-4hr

value: clamp-RNAi

tag: chip antibody

value: input


title: input_MTD_2-4_hr_3

description: n.a.

value: MTD


title: Zelda_clamp-RNAi_2-4_hr_3

description:
Zelda_clampRNAi_2-4hr_avg_SES.bw
Zelda_clampRNAi_2-4hr_C1_x2value_bl.bed

value: Zelda


title: CLAMP_Zelda-RNAi_2-4_hr_3

description:
CLAMP_ZeldaRNAi_2-4hr_avg_SES.bw
CLAMP_ZeldaRNAi_2-4hr_C1_x2value_bl.bed

value: Zelda-RNAi

value: CLAMP


title: Zelda_MTD_2-4_hr_3

description:
Zelda_MTD_2-4hr_avg_SES.bw
Zelda_MTD_2-4hr_C1_x2value_bl.bed


title: CLAMP_clamp-RNAi_2-4_hr_3

description:
CLAMP_clampRNAi_2-4hr_avg_SES.bw
CLAMP_clampRNAi_2-4hr_C1_x2value_bl.bed


title: Zelda_Zelda-RNAi_2-4_hr_3

description:
Zelda_ZeldaRNAi_2-4hr_avg_SES.bw
Zelda_ZeldaRNAi_2-4hr_C1_x2value_bl.bed


title: input_clamp-RNAi_0-2_hr_3

description: n.a.

source_name: embryos 0-2hr

value: embryos 0-2hr


title: MEF WT replicate 2

description: MEF WT replicate 2

value: SRSF1 WT/WT


title: CLAMP_MTD_2-4_hr_3

description:
CLAMP_MTD_2-4hr_avg_SES.bw
CLAMP_MTD_2-4hr_C1_x2value_bl.bed


title: Zelda_Zelda-RNAi_0-2_hr_3

description: n.a.


title: input_Zelda-RNAi_0-2_hr_3

description:
Zelda_ZeldaRNAi_0-2hr_avg_SES.bw
Zelda_ZeldaRNAi_0-2hr_C1_x2value_bl.bed


title: 83_hiPS_PCSK9_KO_clB2_p66


title: CLAMP_clamp-RNAi_0-2_hr_3

description:
CLAMP_clampRNAi_0-2hr_avg_SES.bw
CLAMP_clampRNAi_0-2hr_C1_x2value_bl.bed


title: CLAMP_Zelda-RNAi_0-2_hr_3

description:
CLAMP_ZeldaRNAi_0-2hr_avg_SES.bw
CLAMP_ZeldaRNAi_0-2hr_C1_x2value_bl.bed


title: Zelda_clamp-RNAi_0-2_hr_3

description:
Zelda_clampRNAi_0-2hr_avg_SES.bw
Zelda_clampRNAi_0-2hr_C1_x2value_bl.bed


title: CLAMP_MTD_0-2_hr_3

description:
CLAMP_MTD_0-2hr_avg_SES.bw
CLAMP_MTD_0-2hr_C1_x2value_bl.bed


title: input_Zelda-RNAi_2-4_hr_3

description: n.a.


title: input_Zelda-RNAi_2-4_hr_2


title: Zelda_clamp-RNAi_2-4_hr_2


title: Zelda_Zelda-RNAi_2-4_hr_2

description: n.a.


title: CLAMP_clamp-RNAi_2-4_hr_2


title: input_clamp-RNAi_2-4_hr_2

description: n.a.


title: Zelda_MTD_2-4_hr_2


title: input_MTD_2-4_hr_2

description: n.a.


title: input_MTD_0-2_hr_3

description: n.a.


title: CLAMP_MTD_2-4_hr_2


title: Zelda_Zelda-RNAi_0-2_hr_2

description: n.a.


title: input_clamp-RNAi_0-2_hr_2

description: n.a.


title: input_Zelda-RNAi_0-2_hr_2


title: CLAMP_Zelda-RNAi_0-2_hr_2


title: Zelda_MTD_0-2_hr_3

description:
Zelda_MTD_0-2hr_avg_SES.bw
Zelda_MTD_0-2hr_C1_x2value_bl.bed


title: input_MTD_0-2_hr_2

description: n.a.


title: input_Zelda-RNAi_2-4_hr_1

description: n.a.


title: CLAMP_MTD_0-2_hr_2


title: Zelda_MTD_0-2_hr_2


title: Zelda_clamp-RNAi_0-2_hr_2


title: CLAMP_Zelda-RNAi_2-4_hr_1


title: CLAMP_clamp-RNAi_0-2_hr_2


title: Zelda_Zelda-RNAi_2-4_hr_1


title: input_clamp-RNAi_2-4_hr_1

description: n.a.


title: Zelda_clamp-RNAi_2-4_hr_1


title: Zelda_Zelda-RNAi_0-2_hr_1


title: CLAMP_MTD_2-4_hr_1


title: input_MTD_2-4_hr_1

description: n.a.


title: Zelda_MTD_2-4_hr_1


title: input_Zelda-RNAi_0-2_hr_1

description: n.a.


title: CLAMP_clamp-RNAi_2-4_hr_1


title: 84_hiPS_PCSK9_KO_clB2_p62


title: CLAMP_Zelda-RNAi_0-2_hr_1


title: input_clamp-RNAi_0-2_hr_1

description: n.a.


title: CLAMP_clamp-RNAi_0-2_hr_1


title: Zelda_clamp-RNAi_0-2_hr_1


title: input_MTD_0-2_hr_1

description: n.a.


title: CLAMP_MTD_0-2_hr_1


title: Zelda_MTD_0-2_hr_1


title: 3032_CAP_D0 [RNA-seq]

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description:
CAP_D0
day0
count.3032

data_processing:
Read alignment done by HISAT2 version 2.1.0.
Reads were trimmed using Trimmomatic version 0.36.
Count data were generated by means of the HTSeq method.
Genome_build: GRCh38
Supplementary_files_format_and_content: *txt: Text files include counts.

source_name: CD14+ monocytes

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized-blood by density-gradient centrifugation (1700 RPM for 30 min at 21°C, acceleration 1, breaks 0) using Ficoll-Paque PLUS. PMBCs were resuspended in MACS buffer (phosphate-buffered saline (PBS) having endotoxin-free 0.5% bovine serum albumin (BSA), 2mM ethylenediaminetetraacetic acid (EDTA)), containing magnetic beads coated with anti-CD14 antibodies (Miltenyi Biotec, 130-050-201), and incubated for 15 minutes on a roller bank kept at 4C. CD14+ monocytes were purified using a LS MACS column (Miltenyi Biotec, QuadroMACS) and magnetic separator (Miltenyi Biotec). Monocyte purity (CD14+ purity > 80%) was assessed by flow cytometry (FACS Canto II with FACSDiva Software; BD Biosciences). For RNA-sequencing, 1 x 10^6 purified monocytes were resuspended in 350ul RNA cell protect buffer (Qiagen), and stored at -80C.

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA mini kit according to the manufacturer’s instructions (Qiagen). RNA quality was assessed by bioanalysis (Agilent), with all samples having RNA integrity numbers > 9.
Libraries were prepared from 200ng total RNA using KAPA RNA Hyperprep with RiboErase (Roche) kits.

tag: diagnosis

value: Community-acquired pneumonia

value: Hospital admission

value: CD14+ monocytes


title: 3030_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3030D28

value: After 1 month recovery


title: 3031_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3031


title: 3032_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3032D28


title: 3029_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3029


title: 3028_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3028


title: 3023_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3023D28


title: 3028_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3028D28


title: 3020_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3020


title: 3018_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3018


title: 3019_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3019


title: 3019_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3019D28


title: 3018_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3018D28


title: 3012_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3012D28


title: 3015_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3015


title: 3009_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3009D28


title: 3012_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3012


title: H1299 cells_no daidzein_rep 2

city: Jiujiang

first: FANG

middle: LAI

last: LI

address: 57 Xunyang East Road

institute: Jiujiang University

hyb_protocol: DNA in hybridization solution was denatured at 95C for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: lung adenocarcinoma H1299 cells, no daidzein, replicate 2

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: The cells were maintained in high-glucose medium supplemented with 10% fetal bovine serum (Haoyang Biological Products Technology Co., Ltd.) and 1% penicillin/streptomycin (Beijing Solarbio Science & Technology Co., Ltd.), at 37˚C in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: A total of 4 ml medium, supplemented with dimethyl sulfoxide (Beijing Solarbio Science & Technology Co., Ltd.) was added to the cells in the control group for 24 h at 37˚C, while 4 ml 10 μM daidzein (Shanxi Huike Plant Development Co., Ltd.) was added to the cells in the treatment group for 24 h at 37˚C.

tag: cell line

value: H1299 cells

tag: treatment

value: not treated with daidzein


title: 3015_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3015D28


title: H1299 cells_daizein_rep 2

source_name: lung adenocarcinoma H1299 cells, daizein, replicate 2

value: treated with daidzein


title: 3013_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3013


title: H1299 cells_no daidzein_rep 3

source_name: lung adenocarcinoma H1299 cells, no daidzein, replicate 3


title: H1299 cells_no daidzein_rep 1

source_name: lung adenocarcinoma H1299 cells, no daidzein, replicate 1


title: H1299 cells_daizein_rep 1

source_name: lung adenocarcinoma H1299 cells, daizein, replicate 1


title: H1299 cells_daizein_rep 3

source_name: lung adenocarcinoma H1299 cells, daizein, replicate 3


title: 3009_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3009


title: 3008_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3008D28


title: 3006_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3006D28


title: 3001_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3001D28


title: 3007_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3007


title: 3007_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3007D28


title: 3002_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3002


title: 3008_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3008


title: 3006_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3006


title: 3005_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3005


title: 3002_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3002D28


title: 2048_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2048

value: Healthy control


title: 3005_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.3005D28


title: 2046_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2046


title: 2040_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2040


title: 2039_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2039


title: 2042_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2042


title: 2031_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2031


title: 2030_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2030


title: 2049_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2049


title: 2047_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2047


title: 2043_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2043


title: 3001_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3001


title: 2032_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2032


title: 2045_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2045


title: 2028_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2028


title: 2034_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2034


title: 2036_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2036


title: 2027_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2027


title: 2026_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2026


title: 2038_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2038


title: 2029_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2029


title: 2020_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2020


title: 2019_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2019


title: 2021_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2021


title: 2024_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2024


title: 2022_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2022


title: 2015_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2015


title: 2013_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2013


title: 2011_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2011


title: 2012_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2012


title: 2010_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2010


title: 2014_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2014


title: 2008_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2008


title: 2018_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2018


title: 2025_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2025


title: CLAMP_Zelda-RNAi_2-4_hr_2

value: embryos 2-4hr


title: 2005_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2005


title: 2007_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2007


title: 2006_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2006


title: 2004_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2004


title: 2002_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2002


title: 2003_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2003


title: 1093_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1093D28


title: 2044_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2044


title: 2009_HV [RNA-seq]

description:
Healthy_Volunteer
day0
count.2009


title: 1090_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1090


title: 1086_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1086


title: 1086_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1086D28


title: 1085_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1085


title: 1091_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1091


title: 1079_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1079


title: 1084_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1084


title: 1092_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1092


title: 1080_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1080


title: 1075_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1075


title: 3016_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.3016


title: 1093_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1093


title: 1074_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1074


title: 1091_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1091D28


title: 1073_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1073


title: 1075_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1075D28


title: 1074_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1074D28


title: 1090_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1090D28


title: 1077_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1077


title: 12_NP_TonEBP+/-_(Clariom_S_Mouse)

city: Philadelphia

first: Steven

last: Tessier

state: Pennsylvania

address: 3700 Gateway Dr., Apt 622

department: Orthopedic Surgery

institute: Thomas Jefferson

description: Gene expression data from lumbar NP tissue of 12-month-old TonEBP +/- mouse.

hyb_protocol: GeneChips (Mouse Clariom S) were hybridized with fragmented and biotin-labeled cDNA. Arrays were washed and stained with GeneChip hybridization wash & stain kit.

scan_protocol: Scanned on an Affymetrix GeneChip Scanner 3000 7G, using Command Console Software.

data_processing: CHP files were generated by sst-rma normalization from Affymetrix CEL files using Expression Console Software. Experimental group was compared with control group by using Transcriptome array console 4.0 software. The SST-RMA algorithm was used for data normalization.

label: biotin

source_name: Lumbar NP tissue, TonEBP +/-

label_protocol: Fragmented biotin labeled cDNA was synthesized using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: AF and NP tissue were dissected from lumbar discs (L1-S1) of 12-month-old TonEBP haploinsufficient and wild-type mice (n=3).

extract_protocol: Pooled tissue from single animal served as an individual sample. Samples were homogenized and total RNA was extracted using RNeasy® Mini kit (Qiagen).

tag: tissue

value: Nucleus Pulposus

value: TonEBP +/-

tag: strain/background

tag: age


title: 08_NP_C57BL6_(Clariom_S_Mouse)

description: Gene expression data from lumbar NP tissue of 12-month-old C57BL/6 mouse.

source_name: Lumbar NP tissue, WT

value: WT


title: 06_AF_TonEBP+/-_(Clariom_S_Mouse)

description: Gene expression data from lumbar AF tissue of 12-month-old TonEBP +/- mouse.

source_name: Lumbar AF tissue, TonEBP +/-

value: Annulus Fibrosus


title: 1071_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1071

tag: cell type


title: 04_AF_TonEBP+/-_(Clariom_S_Mouse)

tag: genotype/variation


title: 07_NP_C57BL6_(Clariom_S_Mouse)


title: 05_AF_TonEBP+/-_(Clariom_S_Mouse)


title: 11_NP_TonEBP+/-_(Clariom_S_Mouse)


title: 1070_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1070D28


title: 02_AF_C57BL6_(Clariom_S_Mouse)

description: Gene expression data from lumbar AF tissue of 12-month-old C57BL/6 mouse.

source_name: Lumbar AF tissue, WT


title: 1070_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1070


title: CVID 2 21low

city: Freiburg

first: Baerbel

last: Keller

department: Department of Rheumatology and clinical immunology

country: Germany

institute: University Medical Center Freiburg

data_processing:
Alignments and gene count tables were obtained for each sample using STAR (version 2.4.2a) on GRCh38 genome and annotation (GRCh38.p7).
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file includes reads per gene

source_name: primary cells

extract_protocol:
Total RNA was purified from sorted B cell subpopulations using the Qiagen Rneasy Microkit according to the manufacturer’s instructions (Qiagen)
Samples were processed using the NEBNext Directional Ultra RNA 2 (NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina, cat # E7760L) protocol from NEB, with 10 ng of input total RNA and with 15 PCR cycles. Samples were sequenced 84-bases long on 2 lanes of NextSeq® 550 with high output flowcell (NextSeq® 500/550 High Output Kit v2).

value: CD21low naive B cells

tag: health status

value: CVID patient


title: 09_NP_C57BL6_(Clariom_S_Mouse)


title: CVID 3 21low


title: 01_AF_C57BL6_(Clariom_S_Mouse)


title: HD1 21pos

value: CD21pos naive B cells

value: healthy


title: 10_NP_TonEBP+/-_(Clariom_S_Mouse)


title: 1068_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1068D28

value: Community-acquired pneumonia


title: CVID 2 21pos


title: mESC purified eccDNA RCA nanopore

city: Boston

first: Yi

last: Zhang

state: MA

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

description: eccDNA

data_processing:
Nanopore base calling and reads mapping:   The fast5 files generated by Nanopore MinION sequencer were fed to Guppy (version 3.5.2) for base calling. The parameters used for Guppy were: --flowcell FLO-MIN106 --kit SQK-LSK109 --qscore_filtering --calib_detect --trim_barcodes --trim_strategy dna --disable_pings --device auto --num_callers 16. The generated reads in fastq format were further processed by porechop (version 0.2.4) to remove adaptor sequences for each read with parameters: --extra_end_trim 0 --discard_middle. To reduce artifacts due to misalignment during reads mapping, we compiled a customized reference mouse genome (mm10combine) based on mm10 reference sequences. Then the cleaned reads were aligned to mm10combine using minimap2 (version 2.17) with parameters: -x map-ont -c --secondary=no -t 16. The alignments for each read were stored in PAF format.
Consensus eccDNA generation:   To obtain the consensus boundary and sequence of each eccDNA from the mapped RCA long reads, we developed a tool (https://github.com/icebert/eccDNA_RCA_nanopore) that uses the alignments in PAF file as input and outputs eccDNA fragments composition (chromosome, genomic start and end positions of each fragment), successive fragments coverage (number of passes) and consensus sequence derived from each RCA long read. The sub-reads of each RCA long read could be mapped to one genomic location or multiple locations. The sub-reads with mapping quality lower than 30 were discarded. This tool performed bootstrapping of successive sub-reads in each RCA long read to checks whether the order of the mapped genomic locations for each sub-read is concordant with their order in the RCA long read. Due to the inaccuracy and gap-prone property of Nanopore reads, we allowed a maximum of 20bp offset of the mapped genomic positions (start and end position, respectively) between two sub-reads to be considered as mapping to the same location. Reads with discordant sub-reads order and locations would be discarded. The exact boundaries of eccDNA fragments were determined by voting from the sub-reads’ start and end positions, respectively. The boundary positions were further refined by threading the sub-reads to ensure no gaps or overlaps between any successive sub-reads. The number of passes for each eccDNA fragment was calculated as the number of concordant sub-reads mapped to that location. Only eccDNA with at least 2 passes was kept for downstream analysis. Each eccDNA sequence was derived from the reference genome sequence where it mapped to, with sequence variants incorporated. The sequence variants were called from sub-reads mapped to the corresponding location, requiring minimum depth of 4 and minimum allele frequency of 0.75.
Genomic distribution of eccDNA:   The eccDNA fragments were piled up across the genome. To remove PCR duplicates, eccDNA fragments with the same chromosome, start and end positions were treated as duplicates and only one was retained. The coverage of unique eccDNA fragments at each base of the genome was obtained using bedtools (version 2.29.2) and stored in bigwig file.
Mapping of Illumina sequencing reads:   Raw Illumina sequence reads were preprocessed by Trimmomatic (version 0.39) to remove sequencing adaptors and low-quality reads, using parameters: ILLUMINACLIP:adapters/NexteraPE-PE.fa:2:30:10:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:75 TOPHRED33. BWA MEM (version 0.7.17) with default parameters were used to map the reads to our customized mm10combine reference genome. Duplicated reads were removed by Picard (version 2.23.4). Reads with mapping quality of at least 60 were considered as unique mapped and used for downstream analysis. The genomic coverage was calculated using bamCoverage from deeptools (version 3.5.0) with binSize 1.
Genome_build: mm10
Supplementary_files_format_and_content: For the Nanopore sequencing, the bigwig file contains the coverage of unique eccDNAs across the genome. For the Illumina sequencing, the bigwig file contains the read depth of purified eccDNA at each base of the genome.

growth_protocol: Mouse ES-E14 cells were cultured on dishes coated with 0.1% gelatin in standard LIF/serum medium containing mouse LIF (1000U/ml), 15% fetal bovine serum (FBS), 0.1 mM nonessential amino acids, 0.055mM β-mercaptoethanol (BME), 2 mM GlutaMax, 1mM sodium pyruvate and penicillin-streptomycin (PS).

extract_protocol:
Nanopore sequencing library for eccDNA was prepared by following Ligation Sequencing Kit (Oxford Nanopore) according to manufactory’s instruction after rolling cycle amplification and debranching. RCA were performed with phi29 DNA polymerase (NEB) with some modification to ensure efficient amplification from 100 pg template per reaction. Briefly, in a 20 μl reaction mixture: 2 μl 10X phi29 DNA polymerase buffer (NEB), 2 μl 25 mM dNTPs, 1 μl Exo Resistant Random Primer (Thermo Fisher), and eccDNA >=100 pg, were added with ultra-pure H2O to 17.6 μl, mixed and incubated at 95 ˚C for 5 minutes before being ramped to 30 ˚C at 1% Ramp Rate. Then, 1 μl phi29 DNA polymerase, 0.6 μl Pyrophosphatase Inorganic (yeast, NEB), 0.4 μl 0.1M DTT (NEB), 0.4 μl 20 mg/ml BSA (NEB) were added. The reaction mixture was incubated at 30 ˚C for 10-16 hours. Since high branch structure of RCA products could block nanopore to abolish sequencing, RCA products of eccDNAs were further debranched with T7 Endonuclease I (NEB) before being used for sequencing library construction with Ligation Sequencing Kit (Oxford Nanopore, SQK-LSK109). The library was sequenced in Flow cell (R9.4.1, FL-MIN106D) on MinION according to manufactory’s instruction.
To purify eccDNAs, cells were first dehydrate in >90% methanol before crude extrachromosomal DNA were extracted in an alkaline lysis buffer at pH11.8. After neutralization and precipitation, crude extrachromosomal DNA were bound in silica column (Qiagen) in binding buffer. Bound DNAs were eluted and digested with PacI (NEB) and Plasmid Safe ATP-dependent DNase (Lucigen) for 4-16 hours. Undigested eccDNA is then extracted with Phenol/chloroform/isoamyl alcohol (PCI) solution (25:24:1) in a Phase Lock Gel tube (QuantaBio) to minimize DNA loss. After precipitation with carrier glycogen (Roche) and 1/10 V 3M NaOAc (pH 5.5), the precipitated crude eccDNAs were resuspended in Solution P and further purified by magnetic silica beads that selectively bind to eccDNAs. The eccDNAs were then eluted with 0.1X Elution buffer (1mM Tris-HCl pH8.0) and the concentration is measured by Qubit dsDNA HS Assay kit (Thermo Fisher).
purified eccDNA seq

value: mESC

tag: genotype


title: 1067_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1067D28

value: CD14+ monocytes


title: 1064_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1064

value: Hospital admission


title: 1068_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1068


title: positive3

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

data_processing:
Adapter seqeucnes were trimmed by using cutadapt
Clean reads were mapped to genome by using STAR v2.7.5a
Reads counts were calculated using featureCounts v2.0.1. The number of reads falling in the exons were counted.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Reads counts for each Sample

source_name: white blood cell

extract_protocol:
RNA were extracted from white blood cells using Direct-zol RNA Miniprep Kits (Zymo Research, R2050). The eluted product was incubated with DNase I (ThermoFisher Scientific, RNase-free, EN0521) at 37 °C for 30 min to further remove the DNA and then fragmented with RNA Fragmentation Reagents (Invitrogen, AM8740) at 70 °C for 15 min. Finally, the RNA was purified with RNA Clean and ConcentratorTM-5 kits
The RNA without enrichment and the m6A-enriched RNA were used for library preparation performed with SMARTer® Stranded Total RNA-Seq Kit v2 (Takara Bio USA, Inc., 634411). All of the quality-ensured libraries were sequenced on the Illumina hiseq Xten platform in 150 bp paired-end mode (sequenced by Genewiz).

value: white blood cell

tag: disease state

value: SFTSV infection


title: 1071_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1071D28

value: After 1 month recovery


title: 1061_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1061


title: CVID 3 21pos


title: patient3_time_5 (negative3)

description: patient3_time_5 is also named as negative3

value: Infection with SFTSV turned negative


title: 1060_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1060D28


title: 1067_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1067


title: 1062_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1062D28


title: 1063_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1063


title: positive2


title: CVID 1 21pos


title: 1062_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1062


title: Whole fruit 68 DAA rep2

city: Hermosillo

first: A.

middle: Corina

last: Hayano-Kanashiro

state: Sonora

address: Avenida Luis Donaldo Colosio s/n Edificio 7G, Colonia Centro

department: Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora

country: Mexico

institute: Universidad de Sonora

description: Whole fruits of Chiltepin peppers (Capsicum annuum var. glabriusculum) at 68 Days After Anthesis. Biological replicate R2.

data_processing:
Raw reads were processed with Trimmomatic V. 0.36 to remove Illumina sequencing adapters, a sliding window filter with 4base pairs and phred quality value <15 was used and reads with a final length < 50 base pairs were removed.
Clean reads were aligned to the Capsicum annuum reference genome ( cv. CM334 V. 1.6) with Hisat2 V. 2.1.0 using known splice sites extracted from the Capsicum annuum cv. CM334 annotation V. 2.0 file. Gene raw counts were estimated using HTseq-count V. 0.11.0 with the 'union' option.
Genome_build: Capsicum annuum  cv. 'Criollo de Morelos'  (CM334) V. 1.6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Capsicum annuum

source_name: Chiltepin

growth_protocol: Collected seeds of Chiltepin were sterilized with a 70% ethanol solution, followed by six rinses with distilled water. Seeds were germinated in plastic trays with a mixture of peat moss, perlite and vermiculite. Seedlings were tranfered into 5L pots with the soil mixture described before. The seedlings cultivated under greenhouse conditions. Fruits at 20 and 68 days after anthesis (DAA) were randomly collected, cleaned with ethanol and stored at 80°C.

extract_protocol:
6 fruits at 20 and 68 DAA stages were randomly selected. Whole fruits were ground using a TissueLyser system (QIAGEN) with beads at intervals of 1 min at 30 freq/s. A NucleoSpin RNA Plant kit (Macherey-Nagel) was used for total RNA extraction (following the manufacturer's recommendations) from each fruit separately and 100mg aliquots were measured from each RNA extraction and then pooled. The process was repeated with a different collection of fruits in order to obtain an independent biological replicate. RNA concentration was quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Scientific Nanodrop), RNA integrity was evaluated by electrophoresis on a 1.0\% agarose gel and aliquots of RNA were run an Agilent 2100 Bioanalyzer. Sequencing of the RNA samples was performed in the Servicios Genómicos (CINVESTAV-LANGEBIO, Irapuato, México) using a Illumina NextSeq 500 to obtain at least 37 million raw paired-end reads of 150 pb per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatments were employed.

tag: collection time

value: 68 Days After Anthesis (DAA)

value: Whole fruit

value: Wild type


title: HD2 21pos


title: patient3_time_4


title: 03_AF_C57BL6_(Clariom_S_Mouse)

value: WT


title: 1063_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1063D28

tag: time point


title: 1060_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1060


title: patient4_IP


title: patient3_time_2


title: 1061_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1061D28


title: patient3_time_3


title: Whole fruit 68 DAA rep1

description: Whole fruits of Chiltepin peppers (Capsicum annuum var. glabriusculum) at 68 Days After Anthesis. Biological replicate R1.


title: patient3_time_1


title: Whole fruit 20 DAA rep1

description: Whole fruits of Chiltepin peppers (Capsicum annuum var. glabriusculum) at 20 Days After Anthesis. Biological replicate R1.

value: 20 Days After Anthesis (DAA)


title: patient4_IN (positive4)

description: patient4_IN is also named as positive4


title: Whole fruit 20 DAA rep2

description: Whole fruits of Chiltepin peppers (Capsicum annuum var. glabriusculum) at 20 Days After Anthesis. Biological replicate R2.


title: positive1


title: 1058_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1058


title: 1058_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1058D28


title: patient3_IP


title: Cerebellum_M_KO_5

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description:
Sample_60
counts.txt
voom_cpm.txt
voom_weights.txt

data_processing:
The reads were aligned against the Genecode M23 trranscriptome using the Salmon aligner (Patro et al., 2015) to generate estimated counts for each transcript. Transcript counts were summarized to gene counts using the Bioconductor tximport package (Soneson et al., 2015).
The reads were normalized using the trimmed-means of M-values (TMM) method, and then filtered using the edgeR filterByExpr function, based on the group size (5 per group).
Reads were converted to logCPM and array weights were estimated using the limma voomWithQualityWeights function. The comparisons were made by fitting a weighted analysis of variance (ANOVA) model using lmFit and then computing empirical Bayes weighted contrasts.
Genome_build: BRCm38.p6
Supplementary_files_format_and_content: The counts.txt file contains the counts/gene estimated using the Bioconductor tximport function. The files voom_cpm.txt and voom_weights.txt contain the voom logCPM and voom weights data, which can be used to generate an EList object similar to what we used.

source_name: Cerebellum

extract_protocol:
RNA was extracted from 30 – 50 mg of pulverized brain tissue utilizing a Qiagen RNeasy kit (Qiagen, Hilden, Germany) performed by the Functional Genomics, Proteomics & Metabolomics Facility Core at the University of Washington.
Samples were commercially sequenced by Beijing Genomics Inc. (BGI, Shenzen, China) using their proprietary sequencer which generates 150 nt paired-end sequences.

tag: Sex

value: Male

value: PON2 deficient

value: Cerebellum


title: Cerebellum_M_KO_3

description:
Sample_58
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cerebellum_M_KO_2

description:
Sample_57
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1054_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1054D28


title: patient2_time_3


title: Cerebellum_F_KO_4

description:
Sample_54
counts.txt
voom_cpm.txt
voom_weights.txt

value: Female


title: patient2_time_2


title: Cerebellum_F_KO_2

description:
Sample_52
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cerebellum_F_KO_5

description:
Sample_55
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cerebellum_M_KO_1

description:
Sample_56
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cerebellum_F_KO_1

description:
Sample_51
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cerebellum_M_WT_5

description:
Sample_50
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1055_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1055

value: Community-acquired pneumonia


title: patient3_IN


title: Cerebellum_M_WT_4

description:
Sample_49
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1055_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1055D28


title: patient2_IP


title: 1053_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1053D28


title: Cerebellum_M_WT_1

description:
Sample_46
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cerebellum_M_WT_2

description:
Sample_47
counts.txt
voom_cpm.txt
voom_weights.txt


title: patient2_time_1 (positive5)

description: patient2_time_1 is also named as positive5


title: Cerebellum_M_KO_4

description:
Sample_59
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1053_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1053


title: 1054_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1054


title: Cerebellum_F_WT_4

description:
Sample_44
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cerebellum_F_KO_3

description:
Sample_53
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cerebellum_F_WT_2

description:
Sample_42
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cerebellum_M_WT_3

description:
Sample_48
counts.txt
voom_cpm.txt
voom_weights.txt


title: patient1_time_4


title: patient2_time_4


title: Striatum_M_KO_5

description:
Sample_40
counts.txt
voom_cpm.txt
voom_weights.txt

source_name: Striatum

value: Striatum


title: 1049_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1049

value: CD14+ monocytes


title: 1056_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1056

value: Hospital admission


title: 1052_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1052D28


title: Cerebellum_F_WT_3

description:
Sample_43
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1051_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1051D28


title: 1047_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1047


title: Striatum_M_KO_1

description:
Sample_36
counts.txt
voom_cpm.txt
voom_weights.txt


title: patient2_IN

value: white blood cell


title: Striatum_M_KO_4

description:
Sample_39
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1047_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1047D28


title: Striatum_M_KO_2

description:
Sample_37
counts.txt
voom_cpm.txt
voom_weights.txt


title: Striatum_M_KO_3

description:
Sample_38
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1049_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1049D28


title: Cerebellum_F_WT_5

description:
Sample_45
counts.txt
voom_cpm.txt
voom_weights.txt


title: Striatum_F_KO_4

description:
Sample_34
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cerebellum_F_WT_1

description:
Sample_41
counts.txt
voom_cpm.txt
voom_weights.txt


title: patient1_time_1 (positive6)

description: patient1_time_1 is also named as positive6

value: SFTSV infection


title: patient1_IN


title: 1051_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1051


title: 1045_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1045D28

value: After 1 month recovery


title: Striatum_F_KO_5

description:
Sample_35
counts.txt
voom_cpm.txt
voom_weights.txt


title: patient1_time_2 (positive7)

description: patient1_time_2 is also named as positive7


title: patient1_time_5 (negative4)

description: patient1_time_5 is also named as negative4

value: Infection with SFTSV turned negative


title: Striatum_F_KO_2

description:
Sample_32
counts.txt
voom_cpm.txt
voom_weights.txt


title: patient1_IP


title: patient1_time_3


title: Striatum_F_KO_3

description:
Sample_33
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1045_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1045


title: negative1


title: Striatum_M_WT_5

description:
Sample_30
counts.txt
voom_cpm.txt
voom_weights.txt


title: negative2


title: 1041_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1041


title: 1035_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1035D28


title: Striatum_M_WT_1

description:
Sample_26
counts.txt
voom_cpm.txt
voom_weights.txt


title: Striatum_M_WT_2

description:
Sample_27
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1035_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1035


title: Striatum_M_WT_4

description:
Sample_29
counts.txt
voom_cpm.txt
voom_weights.txt


title: control3_IP

value: healthy donors


title: control3_IN


title: 1034_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1034D28


title: Striatum_F_KO_1

description:
Sample_31
counts.txt
voom_cpm.txt
voom_weights.txt


title: Striatum_F_WT_2

description:
Sample_22
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cortex_M_KO_5

description:
Sample_20
counts.txt
voom_cpm.txt
voom_weights.txt

source_name: Cortex

value: Cortex


title: Striatum_F_WT_3

description:
Sample_23
counts.txt
voom_cpm.txt
voom_weights.txt

value: Wild type


title: control2_IP


title: 1034_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1034

source_name: CD14+ monocytes


title: Cortex_M_KO_3

description:
Sample_18
counts.txt
voom_cpm.txt
voom_weights.txt


title: Striatum_F_WT_5

description:
Sample_25
counts.txt
voom_cpm.txt
voom_weights.txt


title: Striatum_F_WT_1

description:
Sample_21
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cortex_M_KO_4

description:
Sample_19
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1032_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1032D28


title: Cortex_M_KO_2

description:
Sample_17
counts.txt
voom_cpm.txt
voom_weights.txt


title: control1_IP


title: Cortex_M_KO_1

description:
Sample_16
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1031_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1031D28


title: Cortex_F_KO_5

description:
Sample_15
counts.txt
voom_cpm.txt
voom_weights.txt


title: Striatum_M_WT_3

description:
Sample_28
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cortex_F_KO_4

description:
Sample_14
counts.txt
voom_cpm.txt
voom_weights.txt


title: Striatum_F_WT_4

description:
Sample_24
counts.txt
voom_cpm.txt
voom_weights.txt


title: control1_IN


title: Cortex_F_KO_3

description:
Sample_13
counts.txt
voom_cpm.txt
voom_weights.txt


title: control2_IN


title: Cortex_F_KO_2

description:
Sample_12
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1030_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1030D28


title: Cortex_F_KO_1

description:
Sample_11
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cortex_M_WT_5

description:
Sample_10
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1030_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1030


title: 1032_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1032


title: 1029_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1029


title: Cortex_M_WT_3

description:
Sample_8
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cortex_M_WT_4

description:
Sample_9
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cortex_M_WT_1

description:
Sample_6
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cortex_F_WT_4

description:
Sample_4
counts.txt
voom_cpm.txt
voom_weights.txt


title: Cortex_F_WT_5

description:
Sample_5
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1028_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1028D28


title: 1028_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1028


title: Cortex_M_WT_2

description:
Sample_7
counts.txt
voom_cpm.txt
voom_weights.txt


title: LQ50 group (Sample 156)

city: Falcon Heights

first: Ramya Lekha

last: Medida

state: MN

address: 1216 Fifield Ave

institute: University of Minnesota

data_processing:
Quality of reads was examined using FastQC tool kit.
Adapter and low-quality bases were trimmed using Trimmomatic.
Trimmed paired end sequences were mapped to pig reference genome Sscrofa 11.1 (Ensembl) using Kallisto.
Transcripts per million (TPM) values for each gene were used for downstream statistical analysis.
Genome_build: Sscrofa 11.2
Supplementary_files_format_and_content: Excel file includes TPM values for every gene and every sample.

organism: Sus scrofa

source_name: Ileum, LQ50 group

growth_protocol: Finisher pigs (77.5± 2.5 kg) were randomly assigned to one of the five diets: a diet without added zinc (ZnR), ZnR with either 50 ppm or 100 ppm of zinc supplemented from organic (LQ100, LQ50) and inorganic sources (ZnCl100, ZnCl50).

extract_protocol:
RNA was extracted from ileal samples Qiagen Rneasy Mini Kit (Qiagen, Germantown, MD, USA).
Libraries were prepared using Trueseq stranded RNA kit
RNA sequencing was run on Illumina HiSeq 2500 platform.

treatment_protocol: On day 32 of experminent, pigs were euthanized and ileal samples were collected and snap frozen and stored at -81C for further experiements.

tag: body weight

value: Ileum

tag: diet


title: LQ50 group (Sample 164)


title: LQ50 group (Sample 296)


title: LQ50 group (Sample 308)


title: LQ50 group (Sample 343)


title: LQ50 group (Sample 70)


title: Cortex_F_WT_1

description:
Sample_1
counts.txt
voom_cpm.txt
voom_weights.txt


title: 1026_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1026D28


title: Cortex_F_WT_3

description:
Sample_3
counts.txt
voom_cpm.txt
voom_weights.txt


title: LQ50 group (Sample 358)


title: SS_L3

city: Anyang

first: Qinqin

last: Wang

state: HeNan

address: 38 Huanghe Avenue

institute: Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan 455000 China.

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the (http://mascotton.njau.edu.cn/info/1054/1118.htm) TM-1 reference genome using HISAT package
StringTie and edger was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with Fold Change ≥2 and FDR (false discovery rate) < 0.01 and statistical significance (p value < 0.05) by R package – edger.
Genome_build: TM-1 (http://mascotton.njau.edu.cn/info/1054/1118.htm)
Supplementary_files_format_and_content: 4_genes_fpkm_expression.xlsx

organism: Gossypium hirsutum

source_name: leaf, SS

growth_protocol: The cotton seedlings  grew in normal sand, then transferred to Na2SO4 solution and water solution.

extract_protocol:
Total RNA was extracted using TRlzol Reagent(Life technologies, California, USA) following the manufacturer's procedure. The integrity and concentration of total RNA was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). The isolated mRNA by NEB Next Poly (A) mRNA Magnetic Isolation Module (NEB, E7490) were used for constructing cDNA library through the manufacturer’s instructions of NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530) and NEB Next Multiplex Oligos for Illumina (NEB, E7500).
Approximately 200nt RNA inserts were used to synthesize the first-strand cDNA and the second cDNA, according to the fragmented mRNA. In the next step, the end-repair / dA-tail and adaptor ligation were performed for double-stranded cDNA, which is to form the cDNA library by Agencourt AMPure XP beads (Beckman Coulter, Inc.) and PCR amplification. Finally, the constructed cDNA libraries of the different samples were sequenced on a flow cell using an Illumina Novaseq 6000 platform.
The paired-end libraries was 300 bp ( ± 50 bp)

treatment_protocol: 300mM  Na2SO4 and water at three true leaf stage for 12 h

value: SS

value: leaf


title: 1026_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1026


title: LQ50 group (Sample 68)


title: SS_L1


title: SS_L2


title: SS_S2

source_name: stem, SS

value: stem


title: SS_R1

source_name: root, SS

value: root


title: SS_S1


title: SS_R2


title: 1018_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1018D28


title: Cortex_F_WT_2

description:
Sample_2
counts.txt
voom_cpm.txt
voom_weights.txt

value: Female


title: SS_S3


title: 1021_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1021D28

value: Community-acquired pneumonia


title: 1018_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1018


title: CK_L2

source_name: leaf, control


title: CK_L1


title: CK_S2

source_name: stem, control


title: LQ100 group (Sample 213)

source_name: Ileum, LQ100 group


title: CK_S3


title: LQ100 group (Sample 121)


title: LQ100 group (Sample 78)


title: 1017_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1017


title: SS_R3


title: LQ100 group (Sample 211)


title: 1016_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1016D28


title: LQ100 group (Sample 207)


title: 1017_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1017D28


title: 1021_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1021


title: CK_R2

source_name: root, control


title: LQ100 group (Sample 379)


title: 1025_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1025


title: LQ50 group (Sample 62)


title: CK_L3


title: LQ100 group (Sample 59)


title: retina, CTRL

city: guangzhou

first: yuhua

last: xiao

state: guangdong province

address: jinsui load

department: zhongshan Ophthalmic  center

institute: Sun Yat-sen University

data_processing:
Cellranger v3.1 was used for demultiplexing, aligment and quantification.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: h5 file

molecule: polyA RNA

organism: Macaca fascicularis

source_name: retina

extract_protocol:
All retina tissues were digested at 37℃, and were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in PBS solution. Single cell suspensions were diluted at a concentration of 500-1800 cells/uL in 0.04% BSA/Ames.
10x Genomics Chromium single cell system with v2

value: control

value: retina


title: retina, DM

value: diabetes mellitus


title: CK_S1


title: CK_R1


title: ZnCl50 group (Sample 320)

source_name: Ileum, ZnCl50 group


title: CK_R3


title: 1015_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1015

value: Hospital admission

value: CD14+ monocytes


title: 1016_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1016


title: ZnCl50 group (Sample 209)


title: 1015_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1015D28

value: After 1 month recovery


title: ZnCl50 group (Sample 270)


title: LQ100 group (Sample 54)


title: 1014_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1014


title: ZnCl50 group (Sample 146)


title: 1012_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1012D28


title: ZnCl50 group (Sample 94)


title: 1010_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1010D28


title: ZnCl50 group (Sample 39)


title: 1014_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1014D28


title: ZnCl50 group (Sample 66)


title: 1010_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1010


title: MTD 2-4hr #2

data_processing:
Demultiplexed reads were trimmed of adapters using TrimGalore (Krueger, 2017) and mapped to the Drosophila genome dm6 using Bowtie2 (v. 2.3.0) with option -X 2000. We used Picard tools (v. 2.9.2) and SAMtools (v.1.9, Li et al., 2009) to remove the reads that are unmapped, not primary alignment, or duplicated (-F 1804), and retain properly paired reads (-f 2) with MAPQ >30. Peak regions for accessible regions were called using HMMRATAC (v1.2.10, Tarbell and Liu, 2019). DiffBind with the DESeq2 method (v. 3.10, Stark and Brown, 2019) was used to identify differentially accessible regions. We used DeepTools (version 3.1.0, Ramírez et al., 2014) and Homer (v 4.11, Givler and Lilienthal, 2005) to generate enrichment heatmaps (CPM normalization), average profiles, motif searches, peak overlap and peak annotation. Visualizations and statistical tests were conducted in R (R Core Team, 2014).
Genome_build: dm6
Supplementary_files_format_and_content: peak: peaks were called using HMMRATAC (v.1.2.10); bigWig files were generated using Deeptools bamCoverage, normalized by CPM.

source_name: embryos 2-4hr

growth_protocol: To deplete maternal deposited clamp or zld mRNA throughout oogenesis, we crossed a maternal triple driver (MTD-GAL4, Bloomington, #31777) line with a Transgenic RNAi Project (TRiP) clamp RNAi line (Bloomington, #57008) or a TRiP zld RNAi line (from C. Rushlow lab, Sun et al., 2015). We used the MTD-GAL4 line alone as the control line.

extract_protocol: We conducted ATAC-seq following the protocol from Blythe and Wieschaus (2016). 0-2hr or 2-4hr embryos were collected from grape agar plates, dechorionated by 1min exposure to 6% bleach (Clorox) and then washed 3 times in deionized water. We homogenized 10 embryos and lysed each in 50ul lysis buffer (10mM Tris 7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40). We collected nuclei by centrifuging at 500g at 4°C and resuspended nuclei in 5ul TD buffer with 2.5ul Tn5 enzyme (Illumina Tagment DNA TDE1 Enzyme and Buffer Kits). We incubated samples at 37°C for 30min at 800 rpm (Eppendorf Thermomixer) for fragmentation, and then purified with Qiagen Minelute columns before PCR amplification. We amplified libraries by adding 10ul transposed DNA to 25ul NEBNext HiFi 2x PCR mix (New England Biolabs) and 2.5ul of 25uM each of Ad1 and Ad2 primers. We used 13 PCR cycles to amplify samples from 0-2hr embryos and 12 PCR cycles to amplify samples from 2-4hr embryos. Next, we purified libraries with 1.2x Ampure SPRI beads. We performed three biological replicates for each genotype (n=2) and time point (n=2). We measured the concentrations of 12 ATAC-seq libraries by Qubit and determined library quality by Bioanalyzer. We sequenced libraries on an Illumina Hi-seq 4000 sequencer at GeneWiz (South Plainfield, NJ) in 2x150-bp mode.

tag: developmental stage

value: embryos 2-4hr

value: MTD control


title: MTD 2-4hr #3


title: 1005_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1005

tag: diagnosis


title: ZnCl50 group (Sample 35)


title: MTD 2-4hr #1


title: 1004_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1004


title: RDES_shPRC1_utr_dox-, 1 biologial Rep, 60h

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Clariom D™ Arrays. Microarrays were washed and stained with Affymetrix GeneChip® 3000 Fluidics Station.

scan_protocol: Microarrays were scanned with Affymetrix GeneChip® 3000 Scanner.

data_processing:
The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
annotation file: Clariom_D_Human.r1.na36.hg38.a1.transcript.csv

label: Biotin

label_protocol: Biotinylated cRNA were prepared using Affymetrix GeneChip® WT PLUS Reagent Kit according to its manufacture's instruction from 6 μg total RNA.

growth_protocol: 700.000 cells per flask/T25 flask were cultured for 60h with/without addition of dox (1μg/ml).

extract_protocol: RNA was extracted by using RNA isolation kit from Macherey-Nagel.

treatment_protocol: Cells were treated with/without dox (1μg/ml) for 60h, with a refreshment after 48h.

tag: cell line

value: RDES

value: Ewing sarcoma cell line

value: shRNA against PRC1 3'UTR region


title: CLAMP-i 2-4hr #3

value: CLAMP RNAi


title: SK-N-MC_shPRC1_utr_dox+, 1 biologial Rep, 60h

value: SK-N-MC

tag: treatment

value: dox (1μg/ml)


title: RDES_shPRC1_utr_dox+, 1 biologial Rep, 60h


title: RDES_shPRC1_cds_dox+, 1 biologial Rep, 60h

value: shRNA against PRC1 CDS region


title: ZnCl100 group (Sample 357)

source_name: Ileum, ZnCl100 group

tag: tissue

value: Ileum


title: ZnCl100 group (Sample 380)


title: CLAMP-i 2-4hr #1


title: SK-N-MC_shPRC1_cds_dox+, 1 biologial Rep, 60h


title: SK-N-MC_shControl_dox+, 1 biologial Rep, 60h

value: shRNA Control


title: 1002_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1002

value: Community-acquired pneumonia


title: 1003_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1003D28


title: SK-N-MC_shPRC1_utr_dox-, 1 biologial Rep, 60h


title: RDES_shControl_dox-, 1 biologial Rep, 60h


title: ZnCl100 group (Sample 317)


title: CLAMP-i 2-4hr #2


title: 1001_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1001D28


title: MTD 0-2hr #2

source_name: embryos 0-2hr

value: embryos 0-2hr


title: SK-N-MC_shPRC1_cds_dox-, 1 biologial Rep, 60h


title: RDES_shPRC1_cds_dox-, 1 biologial Rep, 60h


title: SK-N-MC_shControl_dox-, 1 biologial Rep, 60h


title: CLAMP-i 0-2hr #2


title: 1002_CAP_D28 [RNA-seq]

description:
CAP_D28
one_month
count.1002D28


title: RDES_shControl_dox+, 1 biologial Rep, 60h


title: ZnCl100 group (Sample 268)


title: MTD 0-2hr #1


title: MTD 0-2hr #3


title: CLAMP-i 0-2hr #3


title: G54_2_ACT

city: Atlanta

first: Haydn

last: Kissick

address: 1462 Clifton Rd.

institute: Emory University

data_processing: Adapter trim with cutadapt, align with Hisat2, counts with subread-featurecount, differential expression between groups with DESeq2.

source_name: Blood

extract_protocol:
Cells were FACS sorted and used to generate single cell suspensions. RNA was extracted using qiagen all-prep kits.
Library construction was performed using clontech V4

value: HLADR+CD38+CD8+ T cells

value: cycle 2


title: 3032_CAPD28 [RRBS]

description:
3032_D28
RRBS
MspI digested and bisulfite sequencing.

data_processing:
Read alignment done by bs-seeker2 (version 2.1.8) and bowtie2 (version 2.3.4.3).
Methylation levels (number of C reads / [number of C + number of T]) were calculated by bs-seeker2 (version 2.1.8).
Methylation levels summarized by cgmaptools (version 0.1.8).
Genome_build: GRCh38
Supplementary_files_format_and_content: Cgmap methylation levels.

source_name: CD14+ monocyte

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized-blood by density-gradient centrifugation (1700 RPM for 30 min at 21°C, acceleration 1, breaks 0) using Ficoll-Paque PLUS. PMBCs were resuspended in MACS buffer (phosphate-buffered saline (PBS) having endotoxin-free 0.5% bovine serum albumin (BSA), 2mM ethylenediaminetetraacetic acid (EDTA)), containing magnetic beads coated with anti-CD14 antibodies (Miltenyi Biotec, 130-050-201), and incubated for 15 minutes on a roller bank kept at 4C. CD14+ monocytes were purified using a LS MACS column (Miltenyi Biotec, QuadroMACS) and magnetic separator (Miltenyi Biotec). Monocyte purity (CD14+ purity > 80%) was assessed by flow cytometry (FACS Canto II with FACSDiva Software; BD Biosciences). For reduced representation bisulfite sequencing (RRBS), 1 x 10^6 purified monocytes were resuspended in 350ul RNA cell protect buffer (Qiagen), and stored at -80C.

extract_protocol:
Genomic DNA was isolated using the AllPrep DNA/RNA mini kit according to the manufacturer’s instructions (Qiagen).
Libraries were prepared from 100ng genomic DNA using Diagenode Premium RRBS kits (Diagenode). Briefly, DNA was digested with the restriction enzyme MspI, which recognizes CCGG dinucleotides sites, and AMPpure XP kit (Beckman Coulter) for size selection. Samples were pooled based on concentrations (n=8 per pool) and treated with sodium bisulfite to convert the unmethylated cytosines to uracil leaving unmethylated cytosines unchanged. After bisulfite conversion samples were amplified by PCR using the following reaction setup: 20 minutes at 25°C, 10 minutes at 65°C, hold at 8°C. PCR products were cleaned using the AMPpure XP kit and sequenced on the Illumina HiSeq4000 (Illumina) instrument in single read (50) mode.

value: CD14+ monocytes

tag: gender

value: Female

tag: sequencing pool


title: ZnCl100 group (Sample 106)


title: ZnCl100 group (Sample 65)


title: CLAMP-i 0-2hr #1


title: ZnCl100 group (Sample 348)


title: ZnR group (Sample 354)

source_name: Ileum, ZnR group

value: ZnR


title: G56_1_ACT

value: cycle 1


title: 1001_CAP_D0 [RNA-seq]

description:
CAP_D0
day0
count.1001

source_name: CD14+ monocytes

value: Hospital admission

tag: cell type


title: G54_1_ACT


title: ZnCl100 group (Sample 261)


title: G56_B_ACT

value: baseline


title: G53_B_ACT


title: G54_B_ACT


title: G52_B_ACT


title: 3018_CAPD28 [RRBS]

description:
3018_D28
RRBS
MspI digested and bisulfite sequencing.

value: After 1 month recovery

tag: age


title: 3023_CAP [RRBS]

description:
3023
RRBS
MspI digested and bisulfite sequencing.

value: Male


title: G51_2_ACT


title: 3019_CAP [RRBS]

description:
3019
RRBS
MspI digested and bisulfite sequencing.


title: G52_1_ACT


title: G53_1_ACT


title: G50_1_ACT


title: ZnR group (Sample 378)


title: G50_2_ACT


title: G53_2_ACT


title: 3019_CAPD28 [RRBS]

description:
3019_D28
RRBS
MspI digested and bisulfite sequencing.


title: 3032_CAP [RRBS]

description:
3032
RRBS
MspI digested and bisulfite sequencing.


title: ZnR group (Sample 352)


title: 3018_CAP [RRBS]

description:
3018
RRBS
MspI digested and bisulfite sequencing.


title: G49_2_ACT


title: 3015_CAPD28 [RRBS]

description:
3015_D28
RRBS
MspI digested and bisulfite sequencing.


title: ZnR group (Sample 159)


title: ZnR group (Sample 315)


title: G52_2_ACT


title: G50_B_ACT


title: 3012_CAP [RRBS]

description:
3012
RRBS
MspI digested and bisulfite sequencing.


title: ZnR group (Sample 177)


title: ZnR group (Sample 83)


title: 3012_CAPD28 [RRBS]

description:
3012_D28
RRBS
MspI digested and bisulfite sequencing.


title: G46_2_ACT


title: G48_B_ACT


title: DAPI-, ITGA6bright EGFP+ and ITGA6bright EGFP- cells of skin epidermis of adult Troy-EGFP-IRES-CreERT2 mice, replicate 2

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

institute: University Hospital Würzburg

description: Adult murine skin epidermis

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Processed data file contains in the first three colums: DAPI- cells in column 1, ITGA6bright EGFP+ cells in column 2 and ITGA6bright EGFP- cells in column 3
Genome_build: mm10
Supplementary_files_format_and_content: coutb files contain UMI barcode normalised abundance counts

source_name: Murine skin epidermis

extract_protocol:
For bulk sequencing, mRNA was isolated from sorted primary epidermal cells using Qiagen's MicroRNA kit according to manufacter's protocol. RNA-sequencing libraries were prepared based on the DESeq2 method (Hashimshony et al., 2016; Love et al., 2014) with modifications (Kretzschmar et al., 2019)
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

value: Skin epidermis

tag: strain


title: Extracted RNA from EGFP+ and EGFP- cells of skin epidermis of adult Troy-EGFP-IRES-CreERT2 mice, replicate 4

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: coutt files contain UMI barcode normalised abundance counts

extract_protocol:
Live single cells were sorted in 384- well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: genotype

value: Adult


title: DAPI-, ITGA6bright EGFP+ and ITGA6bright EGFP- cells of skin epidermis of adult Troy-EGFP-IRES-CreERT2 mice, replicate 1

description: Adult murine skin epidermis


title: G46_1_ACT

tag: disease state


title: G49_1_ACT


title: 3005_CAPD28 [RRBS]

description:
3005_D28
RRBS
MspI digested and bisulfite sequencing.


title: G48_1_ACT


title: G45_B_ACT


title: G45_2_ACT


title: 3005_CAP [RRBS]

description:
3005
RRBS
MspI digested and bisulfite sequencing.


title: G46_B_ACT


title: 3007_CAP [RRBS]

description:
3007
RRBS
MspI digested and bisulfite sequencing.


title: 3001_CAP [RRBS]

description:
3001
RRBS
MspI digested and bisulfite sequencing.


title: G43_2_ACT


title: 3002_CAP [RRBS]

description:
3002
RRBS
MspI digested and bisulfite sequencing.


title: G42_2_ACT


title: Extracted RNA from EGFP+ and EGFP- cells of skin epidermis of adult Troy-EGFP-IRES-CreERT2 mice, replicate 2


title: G42_1_ACT


title: G42_B_ACT


title: G43_B_ACT


title: G38_2_ACT


title: RNA BMDC Myd88_KO eccDNA treated rep1

data_processing:
For RNA-seq data, adaptors and low-quality reads were trimmed using Trimmomatic1 (version 0.39) with parameters: ILLUMINACLIP:adapters/TruSeq3-PE.fa:2:30:10:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 TOPHRED33. The cleaned paired-end reads were aligned to mm10 reference genome with GENCODE2 mouse gene set M24, using STAR3 (version 2.7.6a) with parameters: --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD  --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM. RSEM4 (version 1.3.3) was used to quantify gene expression levels using the reads aligned to transcriptome in bam file as input, with parameters: --alignments --estimate-rspd --calc-ci --no-bam-output --seed 12345 --ci-memory 30000 --paired-end --strandedness reverse.
Genome_build: mm10
Supplementary_files_format_and_content: txt files with gene-level read counts derived from RSEM

source_name: RNA BMDC Myd88_KO eccDNA treated

growth_protocol: 8-12 weeks old male mice were used for preparing bone marrow cells (BMs) and all mice were from Jackson lab., including WT C57/BL6,  Sting-/- (Tmem173gt, Stock No: 017537), and Myd88-/-  (Myd88tm1.1Defr, Stock No: 009088). BMDC were differentiated in RPMI1640 medium supplemented with 10% heat inactivated FBS (Sigma), 10 mM HEPES, 1 mM sodium pyruvate, 100 U/ml PS, 2 mM GlutaMax and 20 ng/ml mouse GM-CSF (Peprotech). BMDM were differentiated in DMEM supplemented with 10% heat inactivated FBS, 100 U/ml PS, and 20% L929 conditioned medium. Half of the medium was replaced at day 3 and day 6. Identity of BMDCs were confirmed with CD11c+ and MHC II+ double positivity. Identity of BMDMs were confirmed with F4/80+ and CD11b+ double positivity. For cell stimulation, cells at day 7-9 were seeded in 96 wells-plates at 3.5×104 per well.

extract_protocol:
Cellular RNA was isolated with Zymo Direct-zol RNA Miniprep kit.
RNA-seq libraries were prepared by following the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, catalog no. E7420S).

treatment_protocol: DNA was transfected to cells with FuGENE HD (Promega) in Opti-MEM (Gibico) according to manufactory’s instructions after measuring their concentrations with Qubit dsDNA HS Assay kit (Thermo Fisher).

value: Bone Marrow-derived Dendritic Cells

value: treated with eccDNA


title: RNA BMDC STING_KO eccDNA treated rep2

source_name: RNA BMDC STING_KO eccDNA treated

value: STING -/-


title: RNA BMDC STING_KO eccDNA treated rep1


title: 2049_HV [RRBS]

description:
2049
RRBS
MspI digested and bisulfite sequencing.

value: Control


title: G43_1_ACT


title: G45_1_ACT


title: G35_2_ACT


title: 3001_CAPD28 [RRBS]

description:
3001_D28
RRBS
MspI digested and bisulfite sequencing.

value: Community-acquired pneumonia


title: Extracted RNA from EGFP+ and EGFP- cells of skin epidermis of adult Troy-EGFP-IRES-CreERT2 mice, replicate 1


title: G37_B_ACT

value: HLADR+CD38+CD8+ T cells


title: 2043_HV [RRBS]

description:
2043
RRBS
MspI digested and bisulfite sequencing.


title: G38_B_ACT


title: G38_1_ACT


title: G51_1_ACT


title: RNA BMDC Myd88_KO eccDNA treated rep2


title: 2040_HV [RRBS]

description:
2040
RRBS
MspI digested and bisulfite sequencing.


title: Extracted RNA from EGFP+ and EGFP- cells of skin epidermis of adult Troy-EGFP-IRES-CreERT2 mice, replicate 3


title: 2047_HV [RRBS]

description:
2047
RRBS
MspI digested and bisulfite sequencing.


title: G35_1_ACT


title: G37_1_ACT


title: 2046_HV [RRBS]

description:
2046
RRBS
MspI digested and bisulfite sequencing.


title: G36_B_ACT


title: RNA BMDC C200 treated rep1

source_name: RNA BMDC C200 treated

value: WT

value: treated with synthetic circular DNA (200bp)


title: 2036_HV [RRBS]

description:
2036
RRBS
MspI digested and bisulfite sequencing.

value: CD14+ monocytes


title: G33_2_ACT

value: cycle 2


title: G36_1_ACT

value: cycle 1


title: G35_B_ACT


title: G30_1_ACT


title: 2034_HV [RRBS]

description:
2034
RRBS
MspI digested and bisulfite sequencing.


title: RNA BMDC C200 treated rep2


title: RNA BMDM linearDNA treated rep3

source_name: RNA BMDM linearDNA treated

value: Bone Marrow-derived Macrophages

value: treated with linear DNA


title: RNA BMDM linearDNA treated rep2


title: G30_B_ACT

value: baseline


title: RNA BMDM linearDNA treated rep1


title: G29_1_ACT


title: 2031_HV [RRBS]

description:
2031
RRBS
MspI digested and bisulfite sequencing.

value: Male


title: RNA BMDM eccDNA treated rep3

source_name: RNA BMDM eccDNA treated


title: G28_1_ACT


title: RNA BMDM eccDNA treated rep2


title: 2029_HV [RRBS]

description:
2029
RRBS
MspI digested and bisulfite sequencing.


title: G28_B_ACT


title: G33_1_ACT


title: G33_B_ACT


title: G29_B_ACT


title: RNA BMDM eccDNA treated rep1


title: G26_1_ACT


title: G26_2_ACT


title: G26_B_ACT


title: G29_2_ACT


title: 2028_HV [RRBS]

description:
2028
RRBS
MspI digested and bisulfite sequencing.


title: 2032_HV [RRBS]

description:
2032
RRBS
MspI digested and bisulfite sequencing.

value: Female


title: 2027_HV [RRBS]

description:
2027
RRBS
MspI digested and bisulfite sequencing.


title: 2021_HV [RRBS]

description:
2021
RRBS
MspI digested and bisulfite sequencing.


title: G24_2_ACT


title: RNA BMDM mock treated rep2

source_name: RNA BMDM mock treated

value: mock treated


title: RNA BMDM mock treated rep1


title: G23_2_ACT


title: 2026_HV [RRBS]

description:
2026
RRBS
MspI digested and bisulfite sequencing.


title: G24_B_ACT


title: G28_2_ACT


title: G24_1_ACT


title: G22_1_ACT


title: G23_1_ACT


title: 2020_HV [RRBS]

description:
2020
RRBS
MspI digested and bisulfite sequencing.


title: G22_B_ACT


title: G23_B_ACT


title: RNA BMDM mock treated rep3


title: G21_2_ACT


title: RNA BMDC linearDNA treated rep3

source_name: RNA BMDC linearDNA treated

value: Bone Marrow-derived Dendritic Cells


title: 2019_HV [RRBS]

description:
2019
RRBS
MspI digested and bisulfite sequencing.


title: G21_B_ACT


title: 2014_HV [RRBS]

description:
2014
RRBS
MspI digested and bisulfite sequencing.


title: G21_1_ACT


title: RNA BMDC linearDNA treated rep1


title: RNA BMDC linearDNA treated rep2


title: RNA BMDC eccDNA treated rep3

source_name: RNA BMDC eccDNA treated

value: treated with eccDNA


title: 2012_HV [RRBS]

description:
2012
RRBS
MspI digested and bisulfite sequencing.


title: RNA BMDC eccDNA treated rep2


title: 2008_HV [RRBS]

description:
2008
RRBS
MspI digested and bisulfite sequencing.


title: RNA BMDC eccDNA treated rep1


title: 2005_HV [RRBS]

description:
2005
RRBS
MspI digested and bisulfite sequencing.


title: Delta-liaF replicate W

city: Houston

first: Anthony

last: Flores

state: TX

address: 6431 Fannin St., MSB 3.130

institute: UTHSC/McGovern Medical School

data_processing:
Base calls onboard Illumina HiSeq
Raw data files processed using CLC Genomics Workbench v20
Reads mapped to reference genome ABC25 (CP049696)
RPKM/TPM calculated using CLC Genomics Workbench v20
Genome_build: ABC25 (CP049696)
Supplementary_files_format_and_content: normalized read counts (TPM)

organism: Streptococcus pyogenes

source_name: Mutant

growth_protocol: GAS cells were grown in rich medium (Todd-Hewitt, 0.2% yeast extract) to an OD of 0.5 (mid-exponential phase)

extract_protocol:
Cells collected in RNA protect and total RNA extracted using Qiagen RNeasy protocol adapted for GAS as described in Methods
Libraries constructed using Illumina ScriptSeq Complete v3

treatment_protocol: No treatments

tag: replicate

value: replicate W

value: Delta-liaF

tag: growth condition

value: in vitro


title: RNA BMDC mock treated rep3

source_name: RNA BMDC mock treated


title: Delta-liaF replicate Y

value: replicate Y


title: RNA BMDC mock treated rep2

value: WT


title: Delta-liaR replicate X

value: replicate X

value: Delta-liaR


title: Delta-liaR replicate Y


title: 2013_HV [RRBS]

description:
2013
RRBS
MspI digested and bisulfite sequencing.

value: Control

value: CD14+ monocytes


title: Delta-liaF replicate Z

value: replicate Z


title: 2003_HV [RRBS]

description:
2003
RRBS
MspI digested and bisulfite sequencing.


title: 1086_CAP [RRBS]

description:
1086
RRBS
MspI digested and bisulfite sequencing.

value: Community-acquired pneumonia

tag: time point

value: Hospital admission


title: 1086_CAPD28 [RRBS]

description:
1086_D28
RRBS
MspI digested and bisulfite sequencing.

value: After 1 month recovery


title: RNA BMDC mock treated rep1


title: Delta-liaR replicate W


title: RNA from tdTomato+ and tdTomato- skin epidermis cells of adult Troy-EGFP-IRES-CreERT2 x Rosa26-LSL-tdTomato mice, rep2

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.coutt.csv: coutt files contain UMI barcode normalised abundance counts.

source_name: Adult skin epidermis

extract_protocol:
Live single cells were sorted in 384-well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

value: Adult

value: Skin epidermis


title: MGAS10870 replicate Y

source_name: Wild-type


title: 1070_CAP [RRBS]

description:
1070
RRBS
MspI digested and bisulfite sequencing.

value: Female


title: 1070_CAPD28 [RRBS]

description:
1070_D28
RRBS
MspI digested and bisulfite sequencing.


title: G48_2_ACT

source_name: Blood

value: HLADR+CD38+CD8+ T cells

value: cycle 2


title: MGAS10870 replicate W

value: replicate W


title: MGAS10870 replicate X

value: in vitro


title: 1068_CAPD28 [RRBS]

description:
1068_D28
RRBS
MspI digested and bisulfite sequencing.

source_name: CD14+ monocyte


title: 1068_CAP [RRBS]

description:
1068
RRBS
MspI digested and bisulfite sequencing.


title: RLHC6-DBS : umbilical cord blood from normal pregnancies

city: London

first: Ping

last: Yip

address: 4 Newark St

department: Blizard Institute

institute: Queen Mary University of London

data_processing:
Illumina miseq 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
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
mm9
Genome_build: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: newborn dried blood spot

extract_protocol:
Blood was placed onto protein saver cards. 2 x 6 mm chad was hol-punched out and extracted using the MirVana miRNA isolation kit
NEB_small RNA libraries were prepared for sequencing using standard Illumina protocols

value: dried blood


title: RLHC9-DBS : umbilical cord blood from normal pregnancies


title: RLHC5-DBS : umbilical cord blood from normal pregnancies


city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 3520E MSRB 1, 1150 W. Medical Center Dr.

institute: University of Michigan

description:
Wildtype_h3.3__Mouse_neuronal stem cell_Input
19_03DH_00F8Michigan_WT_Input

data_processing:
After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end). Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. For active histone marks (H3K4me3, H3K27Ac), peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7.
For H3K27me3 enriched regions were identified using the SICER algorithm at a cutoff of FDR 1E-10 and a max gap parameter of 600 bp.
Spike-in of Drosophila chromatin was performed and the number of test tags were normalized by the same number of spike-in Drosophila tags for each sample.
Genome_build: mm 10

source_name: mouse Neuronal stem cells (p16Ink4a - /p14Arf -) with stably transduced WTH3.3

growth_protocol: mNSC (mouse) cells were cultured in Neurobasal A supplemented with N2, B27, L-glutamine (2 mM), Pen/strep (1X), heparin (2 μg/mL), human-EGF (20 ng/mL), human-bFGF (20 ng/mL), and BSA (45 ng/ml)

extract_protocol:
H3.3WT and H3.3K27M mNSC cell lines were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara).

tag: chip antibody

value: neuronal stem cells

value: wildtype H3.3


title: RNA from tdTomato+ and tdTomato- skin epidermis cells of adult Troy-EGFP-IRES-CreERT2 x Rosa26-LSL-tdTomato mice, rep1


description:
H3.3K27M_Mouse_neuronal stem cell_H327me3
14_03N3_00F8Michigan_K27M_H3K27me3

source_name: mouse Neuronal stem cells (p16Ink4a - /p14Arf -) with stably transduced H3.3K27M

value: anti-H3K27me3 Chip-grade antibody (Active Motif cat#39155 Lot#31917019 4ul volume 30 ug chromatin)


description:
Wildtype_h3.3__Mouse_neuronal stem cell_H3K27me3
13_03N2_00F8Michigan_WT_H3K27me3