title: Retina Prss56-Mutant rep3

city: San Francisco

first: Swanand

last: Koli

address: 10 Koret Way RM K-110 # 0730

department: Ophthalmology

institute: UNIVERSITY OF CALIFORNIA SAN FRANCISCO

data_processing:
Data Analysis : Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Reads mapping to the reference genome : Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
Differential expression analysis (For DESeq2 with biological replicates) Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Correlations To allow for log adjustment, genes with 0 FPKM are assigned a value of 0.001. Correlation were determined using the cor test function in R with options set alternative =”greater” and method = “Spearman”.
GO and KEGG enrichment analysis of differentially expressed genes Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the cluster Profiler R package, in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). cluster Profiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways.
PPI analysis of differentially expressed genes PPI analysis of differentially expressed genes was based on the STRING database, which contained known and predicted Protein-Protein Interactions. For the species existing in the database(like human and mouse), the networks were constructed by extracting the target gene lists from the database.
Fusion gene analysis Fusion gene is refers to the two genes of all or part of the sequences perform fusion ,results of the chimeric gene, usually caused by reasons such as chromosome translocation and problem. Star-fusion(0.8.0) software was used for analysis and detection of fusion genes.
Alternative splicing analysis Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.1) software was used to analysis the ASevent.
SNP analysis We deal with the bam alignment results of each sample by using picard tools(v1.111) and samtools(v0.1.18), including reorder, sort, add head information, mark duplicates, local realignment around indels and base qulaity score recalibration. Then we call snp by the tool HaplotypeCaller in GATK3.4 version. Finally, we ues annovar to do SNP annotation against dbSNP database and some other database.
Differentially expressed gene annotation TFCat and Cosmic database were used to annotate the differential expressed gene. TFCat is a curated catalog of mouse and human transcription factors (TF) based on a reliable core collection of annotations obtained by expert review of the scientific literature. COSMIC is a database designed to store and display somatic mutation information and related details which contains information relating to human cancers
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: tab-delimited text files include read counts and FPKM values for all Mutants and controls

source_name: Retina

extract_protocol:
Briefly, retinas from P15 mice were extracted after enucleation, flash frozen on dry ice and RNA was isolated using Qiagen RNeasy Mini Kit as per manufacturers protocol. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: retina

tag: age

value: postnatal day 15


title: IN_ctr_1_1_II

status: Public on Mar 01 2021

type: SRA

city: Planegg-Martinsried

first: Martina

last: Peritore

state: Bayern

address: Am Klopferspitz 18

country: Germany

institute: MPIB

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
IN_517_1:1_I_AGGCGAAGATTACTCG

library_source: genomic

data_processing:
Sequecing reads were mapped to the S. cerevisiae genome using Bowtie2  (version 2.2.9) with default parameters
Multiple mapping reads were filtered with SAMtools.
Genome_build: LYZE00000000.1, sacCer3
Supplementary_files_format_and_content: All files were generated with R. Bed files contain aligned reads, bedGraph files represent read coverage

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Cells

growth_protocol: Cells were grown in YP-media containing 2% raffinose at 30°C. Exponentially  growing cells (OD600 0.5-0.7) were synchronized in M phase with 5 μg/ml  nocodazole for 2-3 hours. Cell cycle arrest was assessed via microscopy and  DNA content measured by flow cytometry.

extract_protocol:
Cells were mechanically lysed and chromatin was sheared by sonication to  fragments of 200-500 bp. 40% of the chromatin extract was used for  immunoprecipitation, the purified complexes were treated with proteinase K and crosslinks reversed. DNA was purified by phenol-chloroform extraction and ethanol  precipitation.
Strand-specific ChIP-seq libraries were prepared starting from 1-3 ng of DNA using Accel-NGS® 1S Plus Library Kit following manufacturer instructions and 10-12 cycles were used for library amplification. Clean-up steps were performed with SPRIselect beads.

treatment_protocol: Site-specific DSBs were introduced  inducing the HO endonuclease or the AsiSI restriction enzyme via the galactose  promoter, adding galactose to the cultures to a final concentration of 2%. Cells  were crosslinked at the indicated time points with 1% formaldehyde for 16  minutes at room temperature and the reaction quenched with glycine (final concentration 400 mM). Cells were harvested by centrifugation (3500xg at  4°C), washed with cold PBS and the pellet flash frozen in liquid nitrogen.

tag: strain

tag: genome used for alignment


title: Retina Prss56-Mutant rep2

state: CA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype


title: Retina Prss56-Mutant rep1


title: BR.b3

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Raw data obtained from the Illumina NextSeq 500 was trimmed and aligned as described in Yuan et al, Genome Medicine, 2018. For each read with a unique, strand specific alignment to exonic sequence, we constructed an address comprised of the sample barcode, unique molecular identifier (UMI) barcode, and gene identifier. The resulting address file only contained the addresses from reads with corresponding single index. We generated a digital gene expression matrix and filter sample barcodes as described previously (Yuan et al. 2018). Briefly, reads with the same sample barcode, UMI and aligned gene were collapsed and sequencing errors in the sample barcode and UMI were corrected to generate a  matrix of molecular counts for each cell.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file that contains the gene expression counts of each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: FAC-sorted pDCs from Donor 3

growth_protocol: PBMCs from donors' blood were isoalted by Ficoll gradient (GE Healthcare). pDCs and pan-DCs wre enriched from PBMCs by negative selection using EasySep Human Plasmacytoid DC Enrichment Kit and EasySep Human pan-DC Pre-Enrichment Kit (STEM CELL Technologies) with ~80-90% purity and cultured in RPMI-1640 complete medium with 2 mM L-gluatamine, 1 mM sodium pyruvate, 1x MEM non-essential amino acids, 100 U/mL penicillin-streptomycin, and 10% fetal bovine serum. MRC5 human lung fibroblasts were cultured under the same conditions. All cells were incubated at 37C with 5% carbon dioxide.

extract_protocol:
pDCs were detached from plates by gentle pipetting and stained for viability with the Zombie Aqua Fixable Vaiability Kit in PBS for 20 mins at 4C. Cells were washed in 4C medium and FAC-sorted to remove MRC5 cells based on forward and side-scatter using an SH800Z sorter (SONY Biotechnology). Total RNA from sorted live pDCs was isolated using an RNeasy Mini Kit (QIAGEN).
Pooled RNA-seq was performed using the low-input RNA-seq protocol reported in Snyder et al, Science Immunology, 2019. All of the steps prior below that  come before the barcoded cDNA libraries are pooled were performed using a BioMek  4000 automated liquid handling robot (Beckman). Briefly, we added deoxyribonucleotides  (dNTPs) (ThermoFisher) to a final concentration of 2 mM and reverse transcriptase primer  to 2 uM followed by primer annealing at 72C for 3 mins. We then added 7.5 uL of reverse  transcription mixture to each well comprised of 2M betaine (Affymetrix), 2x ProtoScript  Buffer (NEB), 12 mM MgCl2 (ThermoFisher), 10 mM dithiothreitol (ThermoFisher), 5.3 U  of Protoscript II reverse transcriptase (NEB), 0.53 U of SUPERaseIN (ThermoFisher), and  2 uM template-switching oligo. The reverse transcription reaction was incubated at 42C  for 90 mins followed by 10 cycles of 50C for 2 mins, 42C for 2 mins, and 70C for 10 mins.  Next, 2 uL of exonuclease I (ThermoFisher) was added to each well (1.875 U of  exonuclease I in water) and the resulting mixture was incubated at 37C for 30 mins, 85C  for 15 mins, and 75C for 30s.

treatment_protocol: Cells were stimulated or co-cultured with 2.5 uM CpG, IL-3, 10 MOI CMV, MRC5 cells, or CMV-infected MRC5 cells for 2, 4, 8, 16, or 32 hours.

tag: donor number

value: Donor 3

tag: cell type

value: pDCs

tag: treatment

value: CpG (2.5 uM)

tag: time

value: 4 hr


title: IN_ctr_1_1_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
IN_517_1:1_ATAGAGGCCGGCTATG


title: IN_ctr_1_1_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
IN_517_1:1_II_CAGGACGTATTCAGAA


title: BR.b1

source_name: FAC-sorted pDCs from Donor 1

value: Donor 1


title: SA04158

city: Los Angeles

first: Yu-Ling

last: Chang

state: California

address: 10833 Le Conte Ave

department: Pathology and Laboratory Medicine

institute: University of California, Los Angeles

data_processing:
Read quality was checked using FastQC (version 0.11.7)
Reads with the adaptors and the terminal CG were trimmed using the trimmomatic software (v0.38)
Reads aligned using BS-Seeker2 pipeline with the aligner bowtie (v1.2.2)
Genome_build: cohort1(Hg19); cohort2(Hg38)
Supplementary_files_format_and_content: [CGfinal files] chromosome, dinucleotide, position, methylated counts, total counts, methylation frequency, 95% confidence interval for methylation frequency

source_name: Peripheral blood

extract_protocol:
Genomic DNA was extracted from whole blood samples using QIAGEN’s QIAamp DNA Blood Midi/Maxi Kit, performed at Duke. The purified genomic DNA was shipped on ice to University of California, Los Angeles (UCLA) for RRBS library preparation. Genomic DNA was first quantified by Qubit dsDNA BR Assay Kit (ThermoFisher cat. Q32850). The RRBS libraries were prepared as described(52) with the following conditions. For each sample, 100 ng of purified genomic DNA was digested with 20 U of MspI (NEB, cat # R0106L) at 37°C o/n in the presence of RNase Cocktail Mix (Ambion, cat # AM2286). End-repair and adenylation tailing were performed by the addition of Klenow Fragment 3ʹ->5ʹ exo- (NEB, cat # M0212L) in the presence of dATP, dGTP, and d5meCTP (Fermentas). Adapter Ligation was performed by the addition of 0.3 µl of Illumina TruSeq methylated Adapters (Illumina, TruSeq Nano cat# FC-121-4001) and 1 µl of Quick T4 DNA Ligase (NEB cat# M2200L). Samples were pooled and purified using an equal volume of SPRI beads (Beckman Coulter, cat # B23318). Size-selection was performed using SPRI beads to enrich for fragments from 200 to 400 bp. Bisulfite treatment was performed using EpiTect Bisulfite kit (QIAGEN, cat # 59104) according to manufacturer’s protocol, except that two consecutive rounds of conversion were performed, for a total of 10 hr of incubation. Purified converted DNA was PCR amplified using MyTaq HS Mix (Bioline, cat# BIO-25045) and TruSeq PCR Primer Cocktail (Illumina, TruSeq Nano cat# FC-121-4001) according to the following protocol: initial denaturation at 98°C for 30 s; 12 cycles of 98°C for 15 s, 60°C for 30 s, 72°C for 30 s; final extension at 72°C for 5 min. Amplified libraries were purified twice with an equal amount of SPRI beads to remove primer and adapter dimers.
The sequencing data were first demultiplexed based on the barcodes of each sample pooled in the lanes. The data were subjected to a quality control step using FastQC (version 0.11.7), where the low quality reads were discarded from further analysis based on the per base sequence quality and per sequence quality score using the default criteria setting in FastQC(53). Sequencing data were trimmed to remove the adaptors and the terminal CG using the trimmomatic software (v0.38) (54). The reads were aligned to the human genome GRCh38/hg38 (release 93, downloaded from Ensembl) and DNA methylation levels were determined using the BS-Seeker2 pipeline(55) with the aligner bowtie (v1.2.2) and the default settings for the fragment length (20 for lower bound, 500 for upper bound). Samples with less than 5 M total raw reads (3 samples) were excluded from further analyses. On average each sample generated about 36 M total raw reads with 73.7% mappability. Within the study, sequencing data were generated from two sequencing runs, termed batch.

tag: disease state

value: APMB

tag: batch


title: BR.a9

value: CMV-infected MRC5 cells

value: 2 hr


title: SA04137


title: IN_ctr_1_0_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
IN_517_10h_II_CAGGACGTTCCGCGAA


title: Retina Prss56-Control rep3


title: BR.b2

source_name: FAC-sorted pDCs from Donor 2

value: Donor 2


title: IN_ctr_1_0_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
IN_517_10h_I_AGGCGAAGGAATTCGT


title: SA04228

value: ARMB


title: BR.a8


title: IN_ctr_1_0_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
IN_517_10h_CCTATCCTTCCGGAGA


title: IN_ctr_1_8_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
IN_517_1:8_I_AGGCGAAGATTCAGAA


title: Retina Prss56-Control rep2


title: Retina Prss56-Control rep1


title: SA04096


title: BR.a7


title: IN_ctr_0_1_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
IN_517_0h_II_CAGGACGTGAGATTCC


title: BR.a6

value: uninfected MRC5 cells


title: SA04059


title: SA03567


title: Lung at DPI 8 27

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description: RNA extracted from untreated mouse with no SARS2 infection

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the mouse Ensembl GRCh38.76 primary assembly and SARS-CoV-2 NCBI NC_045512 Wuhan-Hu-1 genome with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in at least four samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights
Genome_build: mouse Ensembl GRCh38.76 primary assembly
Supplementary_files_format_and_content: text file and raw gene counts

source_name: lung

extract_protocol:
Total RNAs were extracted with the MagMax mirVana Total RNA isolation kit (Thermo Scientific) on the Kingfisher Flex extraction robot (Thermo Scientific).
cDNA libraries were constructed from 10 ng of total RNA from lung tissues of mice. Library construction was performed using 100 ng of cDNA undergoing end repair, A tailing, ligation of universal TruSeq adapters and amplification of 8 cycles to incorporate unique dual index sequences. Libraries were sequenced on the NovaSeq 6000 (Illumina, San Diego, CA) targeting 40 million read pairs and extending 150 cycles with paired end reads.

treatment_protocol: Eight-week-old mice of both sexes were administered 2.5 x 10^4 PFU of SARS-CoV-2 via intranasal administration.

tag: infection

value: Naïve


title: IN_ctr_0_1_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
IN_517_0h_ATAGAGGCTAATGCGC


title: SA03505


title: BR.a4


title: SA03469


title: HO_RPA_3_4h

tag: chip antibody

value: anti-RFA antibody (Cat# AS07-214, Agrisera)


title: Lung at DPI 8 26


title: Lung at DPI 8 25

description: RNA extracted from mouse with SARS2 infection but treated with human monoclonal antibody (COV2-2050 with genetic variation "LALA-PG") at DPI 2

value: LALA-PG D+2


title: BR.a3


title: Lung at DPI 8 24


title: BR.a2


title: Lung at DPI 8 23


title: HO_RPA_3_0h


title: FOXK2 knockout K562 cell pool 1

city: Shanghai

first: Yu-Kun

last: Xia

address: Room 812, 131 Dongan Rd.

country: China

institute: Fudan University

description:
sgFOXK2_1
sgFOXK2_vs_sgSCR.xlsx

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep ) and Sickle (https://github.com/najoshi/sickle ) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using TopHat (http://tophat.cbcb.umd.edu/，version2.0.0)[1] software. The mapping criteria of bowtie was as follows: sequencing reads should be uniquely matched to the genome allowing up to 2 mismatches, without insertions or deletions. Then the region of gene were expanded following depths of sites and the operon was obtained. In addition, the whole genome was split into multiple 15kbp windows that share 5kbp. New transcribed regions were defined as more than 2 consecutive windows without overlapped region of gene, where at least 2 reads mapped per window in the same orientation.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/)  was used to quantify gene abundances. R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
The TopHat-Cufflinks pipeline was used to predict gene isoforms from our RNA-seq data. In TopHat (http://tophat.cbcb.umd.edu/，version2.0.0), the option ‘‘min-isoform-fraction’’ was disabled, instead ‘‘coverage-search,’’“butterfly-search,’’ and ‘‘microexon-search’’ were used. The expected fragment length was set to 200 bp and the ‘‘small-anchor-fraction’’ was set to 0.08, which requires at least 8 bp on each side of an exon junction for our 100-bp RNA-seq data. Cuffcompare was used to compare and merge the reference annotation and the isoform predictions.
All the alternative splice events that occurred in our sample were identified by using recently releases program Multivariate Analysis of Transcript Splicing (MATS, http://rnaseq-mats.sourceforge.net/). Only the isoforms that were similar to the reference or comprised novel splice junctions were considered, and the splicing differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention events.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Excel format, fpkm, differentially expressed genes of different groups

source_name: K562 cell line

growth_protocol: K562 (CCL-243, ATCC) cells were cultured in RPMI-1640 medium supplemented with 10% FBS, penicillin, and streptomycin

extract_protocol:
Total RNA was extracted from cultured cells by Trizol reagent (Invitrogen) following the manufacturer’s instruction.
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 5μg of total RNA. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq 4000 (2×150bp read length).

treatment_protocol: Mutant ASXL1 or FOXK1/FOXK1 was knockout

tag: cell line

value: FOXK2 knockout


title: HO_RPA_2_4h


title: FOXK2 knockout K562 cell pool 2

description:
sgFOXK2_2
sgFOXK2_vs_sgSCR.xlsx


title: SA04095


title: FOXK1 knockout K562 cell pool 2

description:
sgFOXK1_2
sgFOXK1_vs_sgSCR.xlsx

value: FOXK1 knockout


title: HO_RPA_2_0h


title: Lung at DPI 8 21


title: Lung at DPI 8 22


title: IN_ctr_0_1_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
IN_517_0h_I_GGCTCTGAAGCGATAG


title: control 966 (9421) iPSCs

city: Jerusalem

first: Israel

last: Ben-Dor

state: Israel

address: Ein-Kerem

department: Gene Therapy

country: Israel

institute: Hadassah university hospital

description: iPSCs.xlsx

data_processing:
Raw reads were quality-trimmed at both ends with a quality threshold of 32. Adapter sequences were removed with Cutadapt, version 1.9.1, using parameters -m 15, -O 1 and --match-read-wildcards. Remaining reads were filtered by quality with fastq_quality_filter, FASTX-toolkit version 0.0.13, using parameters –q20 –p90.
Processed reads were aligned with TopHat, version 2.0.14, using parameters -G genes.gtf, -N 5, --read-gap-length 5, --read-edit-dist 10, --segment-length 20, and --read-realign-edit-dist 1.
Htseq-count, version 0.6.0, was used with the C9orf72 portion of the alignment results and special annotations to count raw number of reads in specific areas of the gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: Both processed data files (for fibroblasts and iPSCs samples) are Excel tables that show the number of raw counts in specific areas of the C9orf72 gene. The counted areas are listed as column headers, while rows are for each relevant sample, followed by a row with average values per condition (Control or C9-ALS, as indicated). The last columns show normalized values, relative to a consensus area (exons 2-5).

source_name: fibroblast derived iPSCs

growth_protocol: Human skin fibroblast cultures were established from punch biopsies. Cells were cultured in high-glucose DMEM supplemented with 15% fetal calf serum, 2 mM l-glutamine, 50 U/ml penicillin, and 50 μg/ml streptomycin. iPSC lines were maintained on MMC-treated human foreskin fibroblasts in gelatin-coated 6-well plates (3 × 105 feeders/well) cultured in hESC medium, which consisted of Knockout DMEM supplemented with 16% KnockOut SR, 2 mM l-glutamine, 1% nonessential amino acids, 0.1 mM b-mercaptoethanol, 50 U/ml penicillin, 50 μg/ml streptomycin, and 5 ng/ml bFGF in a 5% O2 incubator. iPSCs were passaged weekly by mechanical dissection or dissociation with 1 mg/ml collagenase IV.

extract_protocol:
Total fibroblast and iPSC RNA was isolated from cells using a PerfectPure RNA Cultured Cell Kit following the manufacturer's protocol, including on-column DNase treatment. RNA integrity was confirmed on the 2200 TapeStation and quantified with Qubit RNA HS Assay Kit. Only  RIN ≥ 9.4 was used for RNA-seq. Before library preparation, rRNA was depleted from 1 ug of total RNA using the Ribo-Zero rRNA Removal.
Libraries were constructed using the KAPA Stranded mRNA-Seq Kit, according to the manufacturer protocol.

tag: Sex

value: female

tag: race

value: Caucasian

value: no

tag: cells

value: iPSCs


title: HO_RPA_1_4h


title: FOXK1 knockout K562 cell pool 1

description:
sgFOXK1_1
sgFOXK1_vs_sgSCR.xlsx


title: BR.a5

value: pDCs


title: HO_RPA_1_2h


title: SCR knockout K562 cell pool 2

description:
sgSCR_2
sgFOXK1_vs_sgSCR.xlsx
sgFOXK2_vs_sgSCR.xlsx

value: SCR knockout


title: Lung at DPI 8 19

description: RNA extracted from mouse with SARS2 infection but treated with human monoclonal antibody (COV2-2050 with genetic variation "LALA-PG") at DPI 1

value: LALA-PG D+1


title: control 351 (3441) iPSCs

description: iPSCs.xlsx

value: male

tag: age


title: HO_RPA_1_0h

tag: strain


title: Lung at DPI 8 18


title: BR.a1

value: Donor 1

value: CpG (2.5 uM)

value: 2 hr


title: Mutant ASXL1 knockout K562 clone 3

description:
mutant_KO_3
KO_mutant_vs_parental.xlsx

value: Mutant ASXL1 knockout


title: C9-ALS 883 (8231) iPSCs

description: iPSCs.xlsx

value: yes


title: C9-ALS 540 (5134) iPSCs

description: iPSCs.xlsx


title: HO_Rad51_2_0h

value: anti-Rad51 antibody (RRID:AB_655028)

tag: genome used for alignment


title: Mutant ASXL1 knockout K562 clone 2

description:
mutant_KO_2
KO_mutant_vs_parental.xlsx


title: HO_Rad51_1_4h


title: Lung at DPI 8 17


title: Mutant ASXL1 knockout K562 clone 1

description:
mutant_KO_1
KO_mutant_vs_parental.xlsx


title: control 1143 fibroblasts

description: Fibroblasts.xlsx

source_name: skin fibroblasts from biopsies

value: primary skin fibroblasts


title: Lung at DPI 8 15

description: RNA extracted from mouse with SARS2 infection but treated with human monoclonal antibody (COV2-2050 with FcR intact) at DPI 2


title: C9-ALS 312 (3751) iPSCs

description: iPSCs.xlsx


title: Lung at DPI 8 20


title: control 70 (7511) iPSCs

description: iPSCs.xlsx


title: parental K562 clone 3

description:
parental_3
KO_mutant_vs_parental.xlsx

value: parental


title: Lung at DPI 8 16


title: parental K562 clone 2

description:
parental_2
KO_mutant_vs_parental.xlsx


title: HO_long_H3_4h

value: anti-H3 antibody (RRID:AB_2687473)


title: Lung at DPI 8 14


title: Lung at DPI 8 13


title: C9-ALS 883 fibroblasts

description: Fibroblasts.xlsx


title: parental K562 clone 1

description:
parental_1
KO_mutant_vs_parental.xlsx


title: HO_Rad51_2_4h


title: Lung at DPI 8 12


title: C9-ALS 312 fibroblasts

description: Fibroblasts.xlsx


title: C9-ALS 184 fibroblasts

description: Fibroblasts.xlsx

value: female


title: HO_IN_2_4h


title: C666-1 KOa

city: Changsha

first: zhenqi

last: qin

address: 87 Xiangya Road

institute: Xiangya Hospital, Central South University

description: knockouting tp53 in C666-1 by using the CRISPR-Cas9 gene editing system

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,Bowtie/Bowtie2 was used for building the genome index,  and Clean Data was mapped to the reference genome using TopHat v2.0.12.
Fragments Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM(Fragments Per Kilobase Per Million Mapped Fragments) was then calculated to estimate the expression level of genes in each sample
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HumanC666-1 and KO cell lines were cultured and maintained in Dulbecco's modified RPMI-1640 medium containing 10% (v/v) fetal bovine serum (FBS) (Life Technologies) at 37℃.

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

value: nasopharyngeal carcinoma cell line

value: tp53 KO


title: control 351 fibroblasts

description: Fibroblasts.xlsx

value: Caucasian

value: no


title: HO_IN_2_0h


title: HO_Rad51_1_0h


title: Donor3-NorINF-sEVs_rep2

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

data_processing:
Base calling was performed with default Illumina NextSeq500 workflow
Reads are first processed by trimming off the 3’ adapter and low-quality bases using cutadapt (cutadapt.readthedocs.io/en/stable/guide.html). Reads with no adapter sequence are tallied (no_adapter_reads).Following trimming, the insert sequences and UMI sequences are identified. Reads with less than 16 bp insert sequences (too_short_reads) or less than 10 bp UMI sequences (UMI_defective_reads) are discarded.
To annotate the insert sequences, a unique sequence set is made for all readsets/samples in a submitted job. Following this, reads were alligned miRBase mature, using bowtie (bowtiebio.sourceforge.net/index.shtml). miRBase V21 is used for miRNA, and piRNABank is used for piRNA.
For each sample in a submitted job, all reads assigned to a particular miRNA or piRNA ID are counted, and the associated UMIs are aggregated to count unique molecules. Only UMI counts are presented in the output CSV file
Genome_build: miRBase 21 - Genome Reference Consortium GRCh38
Supplementary_files_format_and_content: hAD_MSC_EVmiRNA_Profile_UMIcounts.csv presents UMI counts for each miRNA in miRBase21  in each sample
Supplementary_files_format_and_content: EVhAD_MSC_RNA_Type_Reads.csv presents the total reads distribution over RNA types in each sample

source_name: EVs obtained from Mesenchymal stromal cells

growth_protocol: MSCs were obtained from subcutaneous adipose liposuction aspirates from human healthy donors after informed consent. Adipose tissue was extensively washed with PBS and digested in 0.1% type I Collagenase in PBS at 37°C for 60 minutes. The resulting stromal vascular fraction (SVF) pellet was rinsed, plated and cultured in Dulbecco's MEM  supplemented with 10% fetal bovine serum , 2mM of l-glutamine, and 50 mg/ml penicillin/streptomycin, 1 ng/ml of fibroblast growth factor-2(standard condition). Medium was changed every 3 days and cells expanded after reaching about 85% confluence using 0.05% trypsin-EDTA. All cultures were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
mEVs and sEVs isolated from MSC were suspended in 700 µL of Qiazol reagent (Qiagen,). EV RNA was extracted with the miRNeasy Micro Kit (Qiagen) according to the manufacturer's instructions. miRNA content was assessed by performing the Qubit microRNA Assay Kit and RNA quality and sizes were checked with Agilent 2100 Bioanalyzer using the Agilent Small RNA chip according to manufacturer’s protocol. Each sequencing library was constructed from 9.2ng of isolated miRNA.
Small RNA libraries were prepared and amplified using QIAseq miRNA Library kit (Qiagen), following manufacturer's instructions. Libraries were pooled after quality check and quantification by TapeStation (Agilent Technologies) using Agilent High Sensitivity D1000 ScreenTape. Pooled libraries were quantified by real-time qPCR following “Sequencing Library qPCR Quantification” Guide (Illumina Inc.) and sequenced by Illumina NextSeq platform using the 75 cycles high output kit (Illumina Inc.).

tag: extracellular vesicle subfraction

value: small-sized EVs

tag: preconditioning of ev releasing cells

value: Normoxia and inflammatory stimuli


title: HO_long_H3_0h


title: C666-1 KOc

tag: genotype


title: C666-1 KOb

tag: cell type


title: C666-1 WTc

description: nasopharyngeal carcinoma cell line

value: WT


title: Lung at DPI 8 8

description: RNA extracted from mouse with SARS2 infection but treated with human monoclonal antibody (COV2-2050 with FcR intact) at DPI 1

tag: treatment


title: HO_IN_1_2h


title: HO_IN_1_4h


title: Donor1-HypINF-sEVs_rep2

value: Hypoxia and inflammatory stimuli


title: Donor2-NorINF-sEVs_rep2


title: Donor1-NorINF-sEVs_rep2


title: C666-1 WTb

description: nasopharyngeal carcinoma cell line


title: HO_IN_1_0h


title: HO_long_H3_10h


title: Lung at DPI 8 7


title: C666-1 WTa

description: nasopharyngeal carcinoma cell line


title: SCR knockout K562 cell pool 1

description:
sgSCR_1
sgFOXK1_vs_sgSCR.xlsx
sgFOXK2_vs_sgSCR.xlsx

value: SCR knockout


title: Lung at DPI 8 6


title: Donor1-Nor-sEVs_rep2

value: Normoxia


title: HO_H3_FLAG_2_4h

value: anti-FLAG beads (RRID:AB_2637089)


title: C666-1-KOc

data_processing:
Raw Data was processed with in-house scripts. The filtering criteria was as follows:1) Remove the reads without 3’adapter; 2) Remove the reads without insert fragment; 3) Remove the reads contain too much A/T; 4) Remove the reads which length is out of range; 5) Remove the low-quality reads. Using Bowtie1 to build the reference genome index, and then mapping the clean reads to the genome. Mapping reads to mature miRNA and hairping which recorded in miRbase (release 21) to identiy known-miRNA. After got the count of mature miRNA in miRDeeo2, TPM (Transcripts Per Million) was used for estimation and normalization.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

extract_protocol:
total RNA was harvested using Trizol reagent from NPC cells ,Small RNA Sample Preparation Kit (Illumina, RS-200-0048) was used with 1 ug of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols


title: Lung at DPI 8 10


title: Lung at DPI 8 11


title: Lung at DPI 8 9


title: Lung at DPI 8 5

description: RNA extracted from isotype antibody-treated mouse with SARS2 infection

value: Isotype


title: C666-1-KOb


title: Donor3-NorINF-sEVs_rep1


title: HO_H3_FLAG_2_0h


title: HO_H3_FLAG_1_0h


title: Donor1-Hyp-sEVs_rep2

value: Hypoxia


title: HO_H3_FLAG_1_4h


title: Donor3-NorINF-mEVs_rep1

value: mid-sized EVs


title: Lung at DPI 8 2


title: Lung at DPI 8 3


title: C666-1-WTb

description: nasopharyngeal carcinoma cell line

value: wild type


title: Lung at DPI 8 1


title: HO_H3_2_0h

value: anti-H3 antibody (RRID:AB_2687473)


title: HO_H3_2_4h


title: HO_H3_1_4h


title: Donor2-NorINF-sEVs_rep1


title: exp2_control_homecage_4

city: Iowa City

first: Ethan

last: Bahl

state: IA

address: 25 S Grand Ave

institute: University of Iowa

description:
total RNA (Ribo-Zero gold)
sample18

data_processing:
Reads were aligned to the mm10 genome build using STAR version 020201, with default parameters from bcbio-nextgen version 1.0.7
BAM files were indexed and sorted using SAMtools version 1.6, with default parameters from bcbio-nextgen version 1.0.7
Gene-level counts were quantified using featureCounts version 1.4.4, with default parameters from bcbio-nextgen version 1.0.7
Genome_build: mm10, GENCODE release M14
Supplementary_files_format_and_content: CSV text file containing gene-level counts for all samples

source_name: dorsal hippocampus

extract_protocol:
Dorsal hippocampus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Ribo-zero gold) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: dorsal hippocampus

tag: experiment

value: tTA+/DN-

tag: dn genotype

value: DN-

tag: tta genotype

value: tTA+

tag: exposure

value: homecage


title: exp2_control_SOR_4

description:
total RNA (Ribo-Zero gold)
sample19

value: SOR


title: exp2_control_SOR_3

description:
total RNA (Ribo-Zero gold)
sample17


title: Donor2-NorINF-mEVs_rep1

value: Normoxia and inflammatory stimuli


title: Donor2-HypINF-sEVs_rep1

value: small-sized EVs


title: exp2_control_homecage_3

description:
total RNA (Ribo-Zero gold)
sample16


title: TCPOBOP_Female_2 [G178-M11]

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: polyA-selected RNA, stranded library

data_processing:
RNA-seq data was processed using a custom pipeline, as described in Connerney et al., 2017 (PMID: 28323953)
Custom GTF files previously used to count sequence reads mapping to 24,195 RefSeq genes and 15,558 liver-expressed lncRNA genes (Melia et al., 2019; PMID: 30840070) were combined into single GTF file, after removing 852 non-coding RefSeq genes that significantly matched one of the 15,558 lncRNA structures (combined total of 38,901 genes). The GTF file entry for each gene is comprised of the union of all exonic regions for all isoforms of each gene ('Exon Collapsed' counting).
Reads were mapped using TopHat (v2.0.13), and multi-mapped reads were removed from the BAM files, leaving only singly mapped reads, which were counted by featureCounts (1.4.6-p5) using the MultiOverlap funtion (-O).
Differential expression analysis was performed with edgeR as described in Robinson et al., 2010 (PMID: 19910308)
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel files contain differential expression data (FPKM, fold-change, adjusted p-value) for 3 pairwise comparisons: Vehicle-treated Male vs Vehicle-treated Female, Vehicle-treated Male vs TCPOBOP-treated Male, and Vehicle-treated Female vs TCPOBOP-treated Female liver.

source_name: liver tissue_chromatin bound fraction

extract_protocol:
The following buffers were prepared fresh daily and kept on ice for up to 2 hours: Base Solution, 10 mM Tris-Cl, pH 7.4, 146 mM NaCl, 1 mM CaCl2 21 mM MgCl2; Lysis Buffer, Base Solution containing 0.1% Triton X-100 (Cat. #T8787, Sigma), with 80 U/mL Protector RNase Inhibitor (Cat # 3335402001, Roche) added just prior to use; ST Nuclei Wash Buffer (ST Buffer), Base Solution containing 0.01% BSA (Cat. #SRE0036, Sigma), with 80 U/mL Protector RNAse Inhibitor added just prior to use; BSA Wash Buffer, 1X PBS containing 2% BSA and 0.02% Tween-20, with 80 U/mL Protector RNase Inhibitor added just prior to use. To minimize premature tissue thawing and RNA degradation, a ~250 mg piece of each liver was placed on dry ice and then cut into 2-3 smaller pieces, and stored in an Eppendorf tube on dry ice until ready for further processing. For this protocol, all pipette tips used were RNase-free and DNase-free (Cat. #76322 series, VWR). Each pre-cut liver sample was transferred to a 3 mL glass-on-glass dounce homogenizer with 1 mL of Lysis Buffer, on ice. Keeping the homogenizer on ice, the sample was dounced for 10 strokes with pestle A (loose fit) followed by ~10 strokes with pestle B (tight fit) until fully homogenized. Homogenization was performed in under one minute, while avoiding foaming and splattering of the sample. ST Buffer (1 ml) was then added, pipetted up and down a few times to mix, and the sample was then passed through a 40 µm cell strainer (Cat. # 10199-655, VWR) into a 50 mL conical tube on ice. A second 1 ml of ST Buffer was used to rinse the homogenizer and pestles, passed through the same 40 µm cell strainer and then combined with the homogenized sample. The homogenizer and pestles were then washed with Milli-Q water three times before being used to process the next sample. Homogenized samples were kept on ice until all samples were ready to proceed to the next stage. Each homogenized sample was divided into two 1.5 ml Eppendorf tubes, which were centrifuged at 500g in a swinging bucket centrifuge (Dynac Centrifuge, Clay Adams) for 5 min at 4° C to pellet the lysed cells. To avoid damage to the nuclei, a swinging bucket rotor was used to minimize the shear forces generated using a fixed-angle rotor. The supernatant was removed from the pelleted nuclei and the pelleted nuclei were gently resuspended in 1 ml BSA Wash Buffer while pooling the two tubes back into one sample, and then centrifuged at 500g in a swinging bucket rotor for 5 min at 4° C. The supernatant was discarded and the pellet was resuspended in 1 mL BSA Wash Buffer then passed through a 20 µm cell strainer (Cat # 43-50020-03, PluriSelect).  667 µl of strained sample was transferred to a LoBind 1.5 mL Eppendorf tube (Cat # 022431021, Eppendorf) on ice. Fractionation Buffer (1% Triton X-100, 20 mM HEPES (pH 7.5), 300 mM NaCl, 2 M Urea [Cat #5505UA, LifeTech], 0.2 mM EDTA, 1 mM DTT, with 250 U/mL Protector RNase Inhibitor) was prepared fresh each day. The nuclei were re-pelleted at 500g in a swinging bucket rotor for 5 min at 4° C, and the supernatant was discarded. The nuclear pellet was resuspended by gently pipetting in 200 µl Fractionation Buffer, incubated on ice for 10 min, and then centrifuged at 3000 g for 2 min at 4° C. All of the supernatant was carefully removed without disturbing the pellet and discarded. The pellet (chromatin bound (CB) fraction) was gently washed twice with 100 µl Fractionation Buffer, taking care to not disturb the pellet, and then centrifuged at 3000 g for 2 min at 4° C. The CB fraction was then incubated in 50 µl DNase I solution (1X DNase I buffer containing 0.2 U/µl DNase I [Cat #M6101, Promega] and 0.25 U/µl Protector RNase Inhibitor) for 30 min at 37° C, with gentle mixing via pipetting every 10 min. The final volume was brought to 250 µl with Milli-Q water. 750 µl Trizol LS was then added, the sample was vortexed briefly and stored at -20 °C. Frozen samples were thawed on ice, and vortexed for 10 s to fully resuspend each sample. Chloroform (isoamyl alcohol free, 0.2 ml) was then added, followed by vortexing vigorously for 15 s. The sample was allowed to sit for 2-3 min at room temperature and then spun at 12,000 x g for 15 min at 4° C. The clear upper, aqueous phase was carefully transferred to a new centrifuge tube, being careful not to disturb the genomic DNA-containing interface. Isopropanol (0.5 ml) was added to each sample followed by vortexing for 10 s. Glycogen (Cat. #AM9510, ThermoFisher) was then added to each sample (1 µg per 20 µl reaction). Samples were vortexed and then incubated for 10 min at room temperature. Samples were centrifuged at 12,000 x g for 20 min at 4° C, and the supernatant was discarded. The RNA pellet was washed with 1 mL of 75% ethanol by vortexing, and followed by centrifugation at 7,500 x g for 5 min at 4° C. The ethanol wash was removed and sample left to air dry for 5-10 min. Final RNA pellets were resuspended in 20 µl Milli-Q water, quantified on a Qubit instrument using Qubit RNA HS Assay (Cat. #Q32852, Invitrogen) and stored at -20° C.
Illumina sequencing libraries were prepared by poly(A) selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat #E7490L) using 0.5 µg of input RNA, followed by cDNA synthesis and library preparation using the NEBNext Ultra Directional RNA Sequencing for Illumina kit (Cat #E7420L).

treatment_protocol: TCPOBOP (1,4-bis(2-(3,5-dichloropyridyloxy))benzene) (Santa Cruz Biotechnology; Chem Cruze, Cat. #SC-203291) was dissolved in DMSO at 7.5 mg/ml, and then diluted 10-fold into corn oil, followed by IP injection at 4 µl per gram body weights (final dose: 3 mg TCPOBOP and 4 µl of 10% DMSO in corn oil, per kg body weight). Injections were performed at 8 AM; and 27 hr later, at 11 AM, mice were euthanized under CO2 followed by cervical dislocation (Boston University animal facility light cycle: 7:30 AM to 7:30 PM). Livers were excised and flash frozen in liquid nitrogen then stored at -80° C.

value: Female

value: 7-8 weeks

value: TCPOBOP (3 mg/kg) for 27 hrs

value: liver

tag: fraction

value: Chromatin RNA_polyA-selected


title: TCPOBOP_Female_3 [G178-M12]

description: polyA-selected RNA, stranded library

tag: Sex


title: Lung at DPI 8 4

tag: infection

value: Isotype


title: C666-1-WTc

description: nasopharyngeal carcinoma cell line

tag: cell line

value: nasopharyngeal carcinoma cell line


title: Donor3-HypINF-sEVs_rep1

value: Hypoxia and inflammatory stimuli


title: exp2_control_SOR_2

description:
total RNA (Ribo-Zero gold)
sample15


title: TCPOBOP_Female_1 [G178-M10]

description: polyA-selected RNA, stranded library

tag: age


title: HO_H3_1_0h

tag: strain

tag: chip antibody

value: anti-H3 antibody (RRID:AB_2687473)


title: Donor2-HypINF-mEVs_rep1

tag: extracellular vesicle subfraction

value: mid-sized EVs


title: exp2_control_homecage_2

description:
total RNA (Ribo-Zero gold)
sample14

value: dorsal hippocampus

value: tTA-/DN-

value: tTA-


title: Donor3-HypINF-mEVs_rep1

tag: preconditioning of ev releasing cells


title: HO_H2B_FLAG_2_4h

value: anti-FLAG beads (RRID:AB_2637089)

tag: genome used for alignment


title: HO_H2B_FLAG_2_0h


title: Vehicle_Female_3 [G178-M9]

description: polyA-selected RNA, stranded library

value: Vehicle


title: exp2_control_SOR_1

description:
total RNA (Ribo-Zero gold)
sample13

tag: genotype

value: DN-

value: SOR


title: Donor1-NorINF-mEVs_rep1

value: Normoxia and inflammatory stimuli


title: TCPOBOP_Female_4 [G178-M13]

description: polyA-selected RNA, stranded library

value: Female

value: 7-8 weeks

tag: treatment


title: Vehicle_Female_2 [G178-M8]

description: polyA-selected RNA, stranded library

tag: tissue

value: liver


title: exp2_control_homecage_1

description:
total RNA (Ribo-Zero gold)
sample12

tag: experiment

value: homecage


title: HO_H2B_FLAG_1_4h


title: Vehicle_Female_1 [G178-M7]

description: polyA-selected RNA, stranded library

value: Chromatin RNA_polyA-selected


title: HO_H3_1_2h


title: exp1_DN_SOR_5

description:
total RNA (Ribo-Zero gold)
sample11

value: tTA+/DN+

tag: dn genotype

value: DN+

value: tTA+


title: TCPOBOP_Male_3 [G178-M6]

description: polyA-selected RNA, stranded library

value: Male

value: TCPOBOP (3 mg/kg) for 27 hrs


title: HO_H2B_FLAG_1_0h


title: Donor1-HypINF-sEVs_rep1

value: small-sized EVs

value: Hypoxia and inflammatory stimuli


title: Donor1-HypINF-mEVs_rep1

value: mid-sized EVs


title: exp1_DN_SOR_4

description:
total RNA (Ribo-Zero gold)
sample10

value: dorsal hippocampus

tag: tta genotype


title: HO_gH2A_2_4h

value: anti-H2A phospho Ser129 antibody (RRID:AB_492642)


title: HO_gH2A_2_0h


title: exp1_control_SOR_6

description:
total RNA (Ribo-Zero gold)
sample09

value: tTA+/DN-

value: DN-

tag: exposure

value: SOR


title: Donor3-Nor-sEVs_rep1

value: Normoxia


title: TCPOBOP_Male_2 [G178-M5]

description: polyA-selected RNA, stranded library

value: 7-8 weeks

value: liver

tag: fraction


title: Donor1-NorINF-sEVs_rep1

value: Normoxia and inflammatory stimuli


title: HO_gH2A_1_4h


title: Donor3-Nor-mEVs_rep1


title: TCPOBOP_Male_1 [G178-M4]

description: polyA-selected RNA, stranded library

tag: Sex

value: Chromatin RNA_polyA-selected


title: HO_gH2A_1_2h


title: exp1_control_SOR_4

description:
total RNA (Ribo-Zero gold)
sample07


title: Vehicle_Male_3 [G178-M3]

description: polyA-selected RNA, stranded library

value: Vehicle


title: exp1_control_SOR_5

description:
total RNA (Ribo-Zero gold)
sample08

value: tTA+


title: Donor3-Hyp-sEVs_rep1

value: Hypoxia


title: exp1_DN_SOR_3

description:
total RNA (Ribo-Zero gold)
sample06

value: tTA+/DN+

value: DN+


title: HO_gH2A_1_0h


title: Donor2-Nor-sEVs_rep1

value: small-sized EVs


title: Vehicle_Male_1 [G178-M1]

description: polyA-selected RNA, stranded library

value: Male


title: Donor3-Hyp-mEVs_rep1

value: mid-sized EVs


title: exp1_control_SOR_3

description:
total RNA (Ribo-Zero gold)
sample05

value: dorsal hippocampus


title: HO_Dpb11_2_4h

value: anti-FLAG beads (RRID:AB_2637089)


title: TCPOBOP_Female_4 [G177-M13]

description: non polyA-selected RNA, stranded library

source_name: liver tissue_chromatin bound (non-polyA selected) fraction

extract_protocol:
The following buffers were prepared fresh daily and kept on ice for up to 2 hours: Base Solution, 10 mM Tris-Cl, pH 7.4, 146 mM NaCl, 1 mM CaCl2 21 mM MgCl2; Lysis Buffer, Base Solution containing 0.1% Triton X-100 (Cat. #T8787, Sigma), with 80 U/mL Protector RNase Inhibitor (Cat # 3335402001, Roche) added just prior to use; ST Nuclei Wash Buffer (ST Buffer), Base Solution containing 0.01% BSA (Cat. #SRE0036, Sigma), with 80 U/mL Protector RNAse Inhibitor added just prior to use; BSA Wash Buffer, 1X PBS containing 2% BSA and 0.02% Tween-20, with 80 U/mL Protector RNase Inhibitor added just prior to use. To minimize premature tissue thawing and RNA degradation, a ~250 mg piece of each liver was placed on dry ice and then cut into 2-3 smaller pieces, and stored in an Eppendorf tube on dry ice until ready for further processing. For this protocol, all pipette tips used were RNase-free and DNase-free (Cat. #76322 series, VWR). Each pre-cut liver sample was transferred to a 3 mL glass-on-glass dounce homogenizer with 1 mL of Lysis Buffer, on ice. Keeping the homogenizer on ice, the sample was dounced for 10 strokes with pestle A (loose fit) followed by ~10 strokes with pestle B (tight fit) until fully homogenized. Homogenization was performed in under one minute, while avoiding foaming and splattering of the sample. ST Buffer (1 ml) was then added, pipetted up and down a few times to mix, and the sample was then passed through a 40 µm cell strainer (Cat. # 10199-655, VWR) into a 50 mL conical tube on ice. A second 1 ml of ST Buffer was used to rinse the homogenizer and pestles, passed through the same 40 µm cell strainer and then combined with the homogenized sample. The homogenizer and pestles were then washed with Milli-Q water three times before being used to process the next sample. Homogenized samples were kept on ice until all samples were ready to proceed to the next stage. Each homogenized sample was divided into two 1.5 ml Eppendorf tubes, which were centrifuged at 500g in a swinging bucket centrifuge (Dynac Centrifuge, Clay Adams) for 5 min at 4° C to pellet the lysed cells. To avoid damage to the nuclei, a swinging bucket rotor was used to minimize the shear forces generated using a fixed-angle rotor. The supernatant was removed from the pelleted nuclei and the pelleted nuclei were gently resuspended in 1 ml BSA Wash Buffer while pooling the two tubes back into one sample, and then centrifuged at 500g in a swinging bucket rotor for 5 min at 4° C. The supernatant was discarded and the pellet was resuspended in 1 mL BSA Wash Buffer then passed through a 20 µm cell strainer (Cat # 43-50020-03, PluriSelect).  667 µl of strained sample was transferred to a LoBind 1.5 mL Eppendorf tube (Cat # 022431021, Eppendorf) on ice. Fractionation Buffer (1% Triton X-100, 20 mM HEPES (pH 7.5), 300 mM NaCl, 2 M Urea [Cat #5505UA, LifeTech], 0.2 mM EDTA, 1 mM DTT, with 250 U/mL Protector RNase Inhibitor) was prepared fresh each day. The nuclei were re-pelleted at 500g in a swinging bucket rotor for 5 min at 4° C, and the supernatant was discarded. The nuclear pellet was resuspended by gently pipetting in 200 µl Fractionation Buffer, incubated on ice for 10 min, and then centrifuged at 3000 g for 2 min at 4° C. All of the supernatant was carefully removed without disturbing the pellet and discarded. The pellet (chromatin bound (CB) fraction) was gently washed twice with 100 µl Fractionation Buffer, taking care to not disturb the pellet, and then centrifuged at 3000 g for 2 min at 4° C. The CB fraction was then incubated in 50 µl DNase I solution (1X DNase I buffer containing 0.2 U/µl DNase I [Cat #M6101, Promega] and 0.25 U/µl Protector RNase Inhibitor) for 30 min at 37° C, with gentle mixing via pipetting every 10 min. The final volume was brought to 250 µl with Milli-Q water. 750 µl Trizol LS was then added, the sample was vortexed briefly and stored at -20 °C. Frozen samples were thawed on ice, and vortexed for 10 s to fully resuspend each sample. Chloroform (isoamyl alcohol free, 0.2 ml) was then added, followed by vortexing vigorously for 15 s. The sample was allowed to sit for 2-3 min at room temperature and then spun at 12,000 x g for 15 min at 4° C. The clear upper, aqueous phase was carefully transferred to a new centrifuge tube, being careful not to disturb the genomic DNA-containing interface. Isopropanol (0.5 ml) was added to each sample followed by vortexing for 10 s. Glycogen (Cat. #AM9510, ThermoFisher) was then added to each sample (1 µg per 20 µl reaction). Samples were vortexed and then incubated for 10 min at room temperature. Samples were centrifuged at 12,000 x g for 20 min at 4° C, and the supernatant was discarded. The RNA pellet was washed with 1 mL of 75% ethanol by vortexing, and followed by centrifugation at 7,500 x g for 5 min at 4° C. The ethanol wash was removed and sample left to air dry for 5-10 min. Final RNA pellets were resuspended in 20 µl Milli-Q water, quantified on a Qubit instrument using Qubit RNA HS Assay (Cat. #Q32852, Invitrogen) and stored at -20° C.
Sequencing libraries were prepared with 0.5 µg of input RNA using the NEBNext Ultra Directional RNA Sequencing for Illumina kit (Cat #E7420L).

value: Female

value: TCPOBOP (3 mg/kg) for 27 hrs

value: Chromatin-bound RNA_non polyA-selected


title: HO_Dpb11_2_2h


title: TCPOBOP_Female_3 [G177-M12]

value: 7-8 weeks


title: Donor2-Nor-mEVs_rep1

value: Normoxia


title: HO_Dpb11_2_0h


title: Donor2-Hyp-sEVs_rep1


title: exp1_control_SOR_2

description:
total RNA (Ribo-Zero gold)
sample03

value: tTA+/DN-

value: DN-

value: SOR


title: TCPOBOP_Female_2 [G177-M11]


title: HO_Ddc1_2_4h


title: Donor2-Hyp-mEVs_rep1


title: TCPOBOP_Female_1 [G177-M10]


title: Donor1-Nor-sEVs_rep1


title: exp1_control_SOR_1

description:
total RNA (Ribo-Zero gold)
sample02

value: tTA+


title: Vehicle_Male_2 [G178-M2]

description: polyA-selected RNA, stranded library

value: Vehicle

value: liver

value: Chromatin RNA_polyA-selected


title: exp1_DN_SOR_1

description:
total RNA (Ribo-Zero gold)
sample01

value: tTA+/DN+

value: DN+


title: HO_Ddc1_2_2h


title: Donor1-Nor-mEVs_rep1

value: mid-sized EVs


title: Vehicle_Female_3 [G177-M9]


title: Donor1-Hyp-sEVs_rep1

value: small-sized EVs

value: Hypoxia


title: SD9

description: total RNA (Ribo-Zero gold)

data_processing:
Reads were aligned to the mm10 genome build using STAR version 020201, with default parameters from bcbio-nextgen version 1.0.7
BAM files were indexed and sorted using SAMtools version 1.6, with default parameters from bcbio-nextgen version 1.0.7
Gene-level counts were quantified using featureCounts version 1.4.4, with default parameters from bcbio-nextgen version 1.0.7
Genome_build: mm10, GENCODE release M14
Supplementary_files_format_and_content: CSV text file containing gene-level counts for all samples
Supplementary_files_format_and_content: raw counts

source_name: Whole hippocampus

extract_protocol:
Whole hippocampi were removed and flash frozen on dry ice. Illumina TruSeq RNA Sample Prep Kit (Ribo-zero gold) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were either left undisturbed or sleep deprived using the gentle handling method (tapping and moving the cage).

value: Whole hippocampus

tag: batch

value: sleep deprived

tag: group

tag: group color


title: Vehicle_Female_1 [G177-M7]

tag: strain

value: Female

tag: age

value: Chromatin-bound RNA_non polyA-selected


title: fun30_mut_RPA_2_6h

tag: chip antibody

value: anti-RFA antibody (Cat# AS07-214, Agrisera)


title: SD7

description: total RNA (Ribo-Zero gold)


title: exp1_DN_SOR_2

description:
total RNA (Ribo-Zero gold)
sample04

value: dorsal hippocampus


title: HO_Ddc1_2_0h

value: anti-FLAG beads (RRID:AB_2637089)


title: Donor1-Hyp-mEVs_rep1

tag: extracellular vesicle subfraction

tag: preconditioning of ev releasing cells


title: fun30_mut_RPA_2_4h

tag: genome used for alignment


title: SD8

description: total RNA (Ribo-Zero gold)

tag: genotype


title: TCPOBOP_Male_3 [G177-M6]

value: Male

value: 7-8 weeks

tag: treatment

value: TCPOBOP (3 mg/kg) for 27 hrs


title: fun30_mut_RPA_2_2h


title: TCPOBOP_Male_2 [G177-M5]


title: fun30_mut_RPA_2_0h


title: SD6

description: total RNA (Ribo-Zero gold)

tag: tissue


title: SD5

description: total RNA (Ribo-Zero gold)


title: COPD 3

city: Lund

first: Mattias

last: Magnusson

address: BMC A12

department: Molecular Medicine and Gene Therapy

country: Sweden

institute: Lund university

data_processing:
Data sequenced on illumina  Nextseq 500
data procesing and analysis using Kallisto, version 0.46.0)
filtering seurat version 3.1.1, using function, sofiaK4 <- subset(sofiaK4, subset = nFeature_spliced > 200 & nFeature_spliced < 11000 & percent.mt < 22)
read alignment via kallisto version 0.46.0
Genome_build: Genome sequence, primary assembly (GRCh38)” file named GRCh38.primary_assembly.genome.fa.gz was attained from "https://notebook.community/linnarsson-lab/loompy/notebooks/build_index"
Genome_build: the comprehensive PRI gene annotation on the primary assembly GTF file named gencode.v31.primary_assembly.annotation.gtf  was attained from "https://notebook.community/linnarsson-lab/loompy/notebooks/build_index"
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Proximall lung cells after CD45 depletion

extract_protocol:
Total RNA was extracted from 2000 cells in nextseq1.Sample1, from 2000 cells in nextseq1.Sample2, and 1500 cells from nextseq3.Sample. This was after red blood cell lysis and CD45 depletion
cDNA Library constructed using Chromium system (10x Genomics)

treatment_protocol: Freshly isolated human lung cells from proximal tissue

tag: diagnosis

value: COPD GOLD IV

value: Biopsy


title: COPD 1


title: TCPOBOP_Male_1 [G177-M4]


title: fun30_mut_RPA_1_6h


title: Vehicle_Female_2 [G177-M8]

value: Vehicle


title: Healthy 1

value: Healthy


title: Vehicle_Male_3 [G177-M3]


title: Healthy 2

value: Proximal lung donor tissue


title: fun30_mut_RPA_1_4h


title: SD4

description: total RNA (Ribo-Zero gold)


title: fun30_mut_RPA_1_2h


title: SD3

description: total RNA (Ribo-Zero gold)


title: SD2

description: total RNA (Ribo-Zero gold)


title: Vehicle_Male_2 [G177-M2]


title: SD1

description: total RNA (Ribo-Zero gold)


title: HCC1433-2

city: Nutley

first: Kevin

last: Tong

state: NJ

address: 111 Ideation Way

department: CDI

institute: Hackensack Meridian Health

data_processing:
Read alignment and mapping done with Kallisto version v0.43.1 with 100 bootstraps for the expectation-maximization algorithm
Gene level summarization of Kallisto abundance (TPM) was established using the R package Tximport v1.0.3 and R v3.3.1
Genome_build: Ensembl human genome reference build 38
Supplementary_files_format_and_content: TPM, Excel Table

growth_protocol: Breast cancer cell lines were purchased from theAmerican Tissue Culture Collection (Manassas, VA, USA) and cultured according to thesuggested guidelines.

extract_protocol:
Total RNA was isolated using RNeasy plus Mini Kit (Qiagen)
NuGen Ovation Universal RNA-Seq System (Catalog # 0343-32)

treatment_protocol: Total RNA was extracted from HCC1143 cells treated with either siRNA targeting SOX4 or non-targeting control siRNA for 96 hours.


title: TCPOBOP_Female_4 [G176-M13]

description: polyA-selected RNA, stranded library

source_name: liver tissue_nucleoplasmic fraction

extract_protocol:
The following buffers were prepared fresh daily and kept on ice for up to 2 hours: Base Solution, 10 mM Tris-Cl, pH 7.4, 146 mM NaCl, 1 mM CaCl2 21 mM MgCl2; Lysis Buffer, Base Solution containing 0.1% Triton X-100 (Cat. #T8787, Sigma), with 80 U/mL Protector RNase Inhibitor (Cat # 3335402001, Roche) added just prior to use; ST Nuclei Wash Buffer (ST Buffer), Base Solution containing 0.01% BSA (Cat. #SRE0036, Sigma), with 80 U/mL Protector RNAse Inhibitor added just prior to use; BSA Wash Buffer, 1X PBS containing 2% BSA and 0.02% Tween-20, with 80 U/mL Protector RNase Inhibitor added just prior to use. To minimize premature tissue thawing and RNA degradation, a ~250 mg piece of each liver was placed on dry ice and then cut into 2-3 smaller pieces, and stored in an Eppendorf tube on dry ice until ready for further processing. For this protocol, all pipette tips used were RNase-free and DNase-free (Cat. #76322 series, VWR). Each pre-cut liver sample was transferred to a 3 mL glass-on-glass dounce homogenizer with 1 mL of Lysis Buffer, on ice. Keeping the homogenizer on ice, the sample was dounced for 10 strokes with pestle A (loose fit) followed by ~10 strokes with pestle B (tight fit) until fully homogenized. Homogenization was performed in under one minute, while avoiding foaming and splattering of the sample. ST Buffer (1 ml) was then added, pipetted up and down a few times to mix, and the sample was then passed through a 40 µm cell strainer (Cat. # 10199-655, VWR) into a 50 mL conical tube on ice. A second 1 ml of ST Buffer was used to rinse the homogenizer and pestles, passed through the same 40 µm cell strainer and then combined with the homogenized sample. The homogenizer and pestles were then washed with Milli-Q water three times before being used to process the next sample. Homogenized samples were kept on ice until all samples were ready to proceed to the next stage. Each homogenized sample was divided into two 1.5 ml Eppendorf tubes, which were centrifuged at 500g in a swinging bucket centrifuge (Dynac Centrifuge, Clay Adams) for 5 min at 4° C to pellet the lysed cells. To avoid damage to the nuclei, a swinging bucket rotor was used to minimize the shear forces generated using a fixed-angle rotor. The supernatant was removed from the pelleted nuclei and the pelleted nuclei were gently resuspended in 1 ml BSA Wash Buffer while pooling the two tubes back into one sample, and then centrifuged at 500g in a swinging bucket rotor for 5 min at 4° C. The supernatant was discarded and the pellet was resuspended in 1 mL BSA Wash Buffer then passed through a 20 µm cell strainer (Cat # 43-50020-03, PluriSelect).  667 µl of strained sample was transferred to a LoBind 1.5 mL Eppendorf tube (Cat # 022431021, Eppendorf) on ice. Fractionation Buffer (1% Triton X-100, 20 mM HEPES (pH 7.5), 300 mM NaCl, 2 M Urea [Cat #5505UA, LifeTech], 0.2 mM EDTA, 1 mM DTT, with 250 U/mL Protector RNase Inhibitor) was prepared fresh each day. The nuclei were re-pelleted at 500g in a swinging bucket rotor for 5 min at 4° C, and the supernatant was discarded. The nuclear pellet was resuspended by gently pipetting in 200 µl Fractionation Buffer, incubated on ice for 10 min, and then centrifuged at 3000 g for 2 min at 4° C. A 180 µl aliquot of the supernatant, corresponding to the nucleoplasmic (NP) fraction, was removed and placed in a clean Eppendorf tube on ice. Immediately, the total volume was brought to 250 µl with Milli-Q water; 750 µl Trizol LS was then added followed by a few seconds of vortexing and storage at -20 °C. Frozen samples were thawed on ice, and vortexed for 10 s to fully resuspend each sample. Chloroform (isoamyl alcohol free, 0.2 ml) was then added, followed by vortexing vigorously for 15 s. The sample was allowed to sit for 2-3 min at room temperature and then spun at 12,000 x g for 15 min at 4° C. The clear upper, aqueous phase was carefully transferred to a new centrifuge tube, being careful not to disturb the genomic DNA-containing interface. Isopropanol (0.5 ml) was added to each sample followed by vortexing for 10 s. Glycogen (Cat. #AM9510, ThermoFisher) was then added to each sample (1 µg per 20 µl reaction). Samples were vortexed and then incubated for 10 min at room temperature. Samples were centrifuged at 12,000 x g for 20 min at 4° C, and the supernatant was discarded. The RNA pellet was washed with 1 mL of 75% ethanol by vortexing, and followed by centrifugation at 7,500 x g for 5 min at 4° C. The ethanol wash was removed and sample left to air dry for 5-10 min. Final RNA pellets were resuspended in 20 µl Milli-Q water, quantified on a Qubit instrument using Qubit RNA HS Assay (Cat. #Q32852, Invitrogen) and stored at -20° C.
Illumina sequencing libraries were prepared by poly(A) selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat #E7490L) using 0.5 µg of input RNA, followed by cDNA synthesis and library preparation using the NEBNext Ultra Directional RNA Sequencing for Illumina kit (Cat #E7420L).

value: Liver

value: nucleoplasmic RNA


title: fun30_mut_RPA_1_0h


title: COPD 2


title: Vehicle_Male_1 [G177-M1]


title: HCC1433-1


title: TCPOBOP_Female_3 [G176-M12]

description: polyA-selected RNA, stranded library


title: HCC1433_SIC-2

value: siControl


title: NSD8

description: total RNA (Ribo-Zero gold)

value: Whole hippocampus

value: non sleep deprived


title: fun30_mut_H3_2_4h

value: anti-H3 antibody (RRID:AB_2687473)


title: HCC1433_SIC-1


title: fun30_mut_H3_2_6h


title: fun30_mut_H3_2_2h


title: TCPOBOP_Female_2 [G176-M11]

description: polyA-selected RNA, stranded library

value: Female


title: NSD7

description: total RNA (Ribo-Zero gold)


title: TCPOBOP_Female_1 [G176-M10]

description: polyA-selected RNA, stranded library


title: RUES2 hESC-CMs

city: Seattle

first: Charles

middle: E

last: Murry

state: WA

address: 850 Republican Street

department: Pathology

institute: University of Washington

description: hESC-CMs analyed at day 30 of differentiation

data_processing:
base calling was done using cellranger mkfastq
alignment and gene expression in individual cells were done by cellranger count to get cell-gene count matrix
R package Seurat was used for data filtering, normallization, processing and plotting
Genome_build: GRCh38
Supplementary_files_format_and_content: the files that needed to construct the cell-gene count matrix

source_name: Cardiomyocytes

growth_protocol: RUES2 hESC-CMs were differentiated as previously described  (Bertero A. et al., Nature Communications 2019; PMID: 30948719), and cultured in RPMI-1640 supplemented with B-27 until day 30 of differentiation

extract_protocol:
10,000 intact single cells were loaded in a microfluidics channel of a Chromium Next GEM Chip G (10X Genomics) and processed with the Chromium Controller (10X Genomics) the to generate Gel bead-in-Emulsion (GEMs),  all according to the manufacturer's instructions for the Chromium NextGEM Single Cell 3’ kit (10X Genomics)
GEMs were processed to generate Illumina-compatible sequencing libraries, all according to the manufacturer's instructions for the Chromium NextGEM Single Cell 3’ kit (10X Genomics)

tag: cell type

value: hESC-derived cardiomyocytes

tag: cell line


title: NSD6

description: total RNA (Ribo-Zero gold)

tag: exposure


title: fun30_mut_H3_2_0h

source_name: Cells

extract_protocol:
Cells were mechanically lysed and chromatin was sheared by sonication to  fragments of 200-500 bp. 40% of the chromatin extract was used for  immunoprecipitation, the purified complexes were treated with proteinase K and crosslinks reversed. DNA was purified by phenol-chloroform extraction and ethanol  precipitation.
Strand-specific ChIP-seq libraries were prepared starting from 1-3 ng of DNA using Accel-NGS® 1S Plus Library Kit following manufacturer instructions and 10-12 cycles were used for library amplification. Clean-up steps were performed with SPRIselect beads.


title: NSD5

description: total RNA (Ribo-Zero gold)


title: BDM_K3-antimir_LPS2

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps-Universität Marburg

description: BDM_K3-anti-miR-155 inhibitor + LPS treatment, replicate 2

data_processing:
RTA version 1.18.66.4 was used for basecalling
bcl2fastq version 1.8.4. was used for demultiplexing
Reads were mapped using the CLC genomics workbench version 10.01 and the GRCh38 GENCODE human genome annotation with standard settings: mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8.
RPKMs were calculated based on uniqely mapped read numbers reported by the CLC genomics worbench version 10.01
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text-files including ENSEMBL gene ID, gene alias, chromosome, genomic position, unique gene reads, RPKM

source_name: Peripheral blood leukocytes

growth_protocol: U937 cell were cultivated in RPMI medium, supllemented wiht 10 % FCS, in cell culture multi-well plates (4*10e5 cell per 12-well, 1 ml of medium per well). Peripheral blood derived CD14+ monocytes (MACS enrichement from buffy coats) were differentiated in cell culture multi-well plates (4*10e5 cell per 12-well, 1 ml of medium per well) using X-Vivo-15 medium supplemented with 5 % FCS and 20 ng / ml of recombinant human GM-CSF for 8 days.

extract_protocol:
Cells were washed once with PBS and RNA was extracted with Trizol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit according to the manufacturer's protocol
poly(A) RNA-Seq

treatment_protocol: Cells were treated with PNA constructs (200 nM) for 24 hours, followed by LPS stimulation for 4 hours at a concentration of 100 ng / ml.

value: D8 GM-CSF macrophage

tag: precursor

value: CD14+ monocyte

tag: donor

value: healthy, caucasian


title: Vehicle_Female_2 [G176-M8]

description: polyA-selected RNA, stranded library

tag: Sex

value: 7-8 weeks

tag: fraction


title: Vehicle_Female_3 [G176-M9]

description: polyA-selected RNA, stranded library

tag: strain


title: fun30_mut_H3_1_6h


title: fun30_mut_H3_1_4h


title: NSD4

description: total RNA (Ribo-Zero gold)

tag: batch

tag: group

tag: group color


title: BDM_R8-antimir_LPS2

description: BDM_R8-anti-miR-155 inhibitor + LPS treatment, replicate 2


title: Vehicle_Female_1 [G176-M7]

description: polyA-selected RNA, stranded library

tag: age


title: NSD3

description: total RNA (Ribo-Zero gold)


title: BDM_R8-scrambled_LPS2

description: BDM_R8-scrambled inhibitor + LPS treatment, replicate 2


title: NSD9

description: total RNA (Ribo-Zero gold)


title: fun30_mut_H3_1_2h

tag: chip antibody

tag: genome used for alignment


title: fun30_mut_H3_1_0h


title: BDM_K3-antimir_LPS1

description: BDM_K3-anti-miR-155 inhibitor + LPS treatment, replicate 1


title: BDM_R8-scrambled_LPS1

description: BDM_R8-scrambled inhibitor + LPS treatment, replicate 1


title: BDM_R8-antimir_LPS1

description: BDM_R8-anti-miR-155 inhibitor + LPS treatment, replicate 1


title: NSD2

description: total RNA (Ribo-Zero gold)

tag: genotype


title: fun30_ctr_RPA_2_6h

value: anti-RFA antibody (Cat# AS07-214, Agrisera)


title: TCPOBOP_Male_2 [G176-M5]

description: polyA-selected RNA, stranded library

value: Male

tag: treatment

value: TCPOBOP (3 mg/kg) for 27 hrs

tag: tissue


title: TCPOBOP_Male_1 [G176-M4]

description: polyA-selected RNA, stranded library


title: U937_miR_KO_LPS2

description: U937_miR-155 KO cell-line_LPS treatment, replicate 2

tag: cell type

value: Myeloid leukemia cell line

value: Leukemia patient


title: Vehicle_Male_3 [G176-M3]

description: polyA-selected RNA, stranded library

value: Vehicle

value: Liver


title: Vehicle_Male_2 [G176-M2]

description: polyA-selected RNA, stranded library

value: nucleoplasmic RNA


title: U937_control_LPS2

description: U937_control cell-line_LPS treatment, replicate 2


title: fun30_ctr_RPA_2_4h


title: fun30_ctr_RPA_2_2h


title: Vehicle_Male_1 [G176-M1]

description: polyA-selected RNA, stranded library


title: fun30_ctr_RPA_2_0h


title: U937_miR_KO_LPS1

description: U937_miR-155 KO cell-line_LPS treatment, replicate 1


title: LN-WT-153

city: Houston

first: Stephanie

middle: Lynn

last: Coffin

state: TX

address: 1250 Moursund St

institute: Baylor College of Medicine

description: Sample 22

data_processing:
Raw reads were trimmed before mapping by Trimmomatic-0.36 using the adapter reference TruSeq3-PE.fa.
STAR v2.7.2d was used to align trimmed reads to the Mus musculus genome (GRCm38.p6, https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26) and to obtain read counts with default parameters
Batch correction using ComBat_seq function in the SVA package v3.36.0 (Samples were sequenced in two batches, with samples 1-16 in the first batch and samples 17-24 in the second)
Differential gene expression analysis using DESeq2 package v1.28.1
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: Cerebellar tissue

extract_protocol:
Qiagen miRNeasy Kit
RNA libraries were prepared by Genewiz using standard Illumina protocols

value: Cerebellum

value: wt


title: TCPOBOP_Male_3 [G176-M6]

description: polyA-selected RNA, stranded library


title: LN-WT-154

description: Sample 23


title: TCPOBOP_Female_4 [G175-M13]

description: polyA-selected RNA, stranded library

source_name: liver tissue_nuclear fraction

extract_protocol:
The following buffers were prepared fresh daily and kept on ice for up to 2 hours: Base Solution, 10 mM Tris-Cl, pH 7.4, 146 mM NaCl, 1 mM CaCl2 21 mM MgCl2; Lysis Buffer, Base Solution containing 0.1% Triton X-100 (Cat. #T8787, Sigma), with 80 U/mL Protector RNase Inhibitor (Cat # 3335402001, Roche) added just prior to use; ST Nuclei Wash Buffer (ST Buffer), Base Solution containing 0.01% BSA (Cat. #SRE0036, Sigma), with 80 U/mL Protector RNAse Inhibitor added just prior to use; BSA Wash Buffer, 1X PBS containing 2% BSA and 0.02% Tween-20, with 80 U/mL Protector RNase Inhibitor added just prior to use. To minimize premature tissue thawing and RNA degradation, a ~250 mg piece of each liver was placed on dry ice and then cut into 2-3 smaller pieces, and stored in an Eppendorf tube on dry ice until ready for further processing. For this protocol, all pipette tips used were RNase-free and DNase-free (Cat. #76322 series, VWR). Each pre-cut liver sample was transferred to a 3 mL glass-on-glass dounce homogenizer with 1 mL of Lysis Buffer, on ice. Keeping the homogenizer on ice, the sample was dounced for 10 strokes with pestle A (loose fit) followed by ~10 strokes with pestle B (tight fit) until fully homogenized. Homogenization was performed in under one minute, while avoiding foaming and splattering of the sample. ST Buffer (1 ml) was then added, pipetted up and down a few times to mix, and the sample was then passed through a 40 µm cell strainer (Cat. # 10199-655, VWR) into a 50 mL conical tube on ice. A second 1 ml of ST Buffer was used to rinse the homogenizer and pestles, passed through the same 40 µm cell strainer and then combined with the homogenized sample. The homogenizer and pestles were then washed with Milli-Q water three times before being used to process the next sample. Homogenized samples were kept on ice until all samples were ready to proceed to the next stage. Each homogenized sample was divided into two 1.5 ml Eppendorf tubes, which were centrifuged at 500g in a swinging bucket centrifuge (Dynac Centrifuge, Clay Adams) for 5 min at 4° C to pellet the lysed cells. To avoid damage to the nuclei, a swinging bucket rotor was used to minimize the shear forces generated using a fixed-angle rotor. The supernatant was removed from the pelleted nuclei and the pelleted nuclei were gently resuspended in 1 ml BSA Wash Buffer while pooling the two tubes back into one sample, and then centrifuged at 500g in a swinging bucket rotor for 5 min at 4° C. The supernatant was discarded and the pellet was resuspended in 1 mL BSA Wash Buffer then passed through a 20 µm cell strainer (Cat # 43-50020-03, PluriSelect).  333 µl of strained sample was transferred to a LoBind 1.5 mL Eppendorf tube (Cat # 022431021, Eppendorf) on ice and 667 µl of Trizol LS reagent was immediately added to that tube, which was vortexed for a few seconds then stored at -20° C. Frozen samples were thawed on ice, and vortexed for 10 s to fully resuspend each sample. Chloroform (isoamyl alcohol free, 0.2 ml) was then added, followed by vortexing vigorously for 15 s. The sample was allowed to sit for 2-3 min at room temperature and then spun at 12,000 x g for 15 min at 4° C. The clear upper, aqueous phase was carefully transferred to a new centrifuge tube, being careful not to disturb the genomic DNA-containing interface. Isopropanol (0.5 ml) was added to each sample followed by vortexing for 10 s. Glycogen (Cat. #AM9510, ThermoFisher) was then added to each sample (1 µg per 20 µl reaction). Samples were vortexed and then incubated for 10 min at room temperature. Samples were centrifuged at 12,000 x g for 20 min at 4° C, and the supernatant was discarded. The RNA pellet was washed with 1 mL of 75% ethanol by vortexing, and followed by centrifugation at 7,500 x g for 5 min at 4° C. The ethanol wash was removed and sample left to air dry for 5-10 min. Final RNA pellets were resuspended in 20 µl Milli-Q water, quantified on a Qubit instrument using Qubit RNA HS Assay (Cat. #Q32852, Invitrogen) and stored at -20° C.
Illumina sequencing libraries were prepared by poly(A) selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat #E7490L) using 0.5 µg of input RNA, followed by cDNA synthesis and library preparation using the NEBNext Ultra Directional RNA Sequencing for Illumina kit (Cat #E7420L).

value: Liver nuclear RNA


title: U937_control_mock2

description: U937_control cell-line_mock treatment, replicate 2


title: fun30_ctr_RPA_1_6h

data_processing:
Sequecing reads were mapped to the S. cerevisiae genome using Bowtie2  (version 2.2.9) with default parameters
Multiple mapping reads were filtered with SAMtools.
Genome_build: LYZE00000000.1, sacCer3
Supplementary_files_format_and_content: All files were generated with R. Bed files contain aligned reads, bedGraph files represent read coverage


title: fun30_ctr_RPA_1_4h


title: NSD1

description: total RNA (Ribo-Zero gold)

value: Whole hippocampus

value: non sleep deprived


title: LN-2Q-S776A-152

description: Sample 20


title: TCPOBOP_Female_3 [G175-M12]

description: polyA-selected RNA, stranded library

value: Female


title: U937_control_LPS1

description: U937_control cell-line_LPS treatment, replicate 1

value: CD14+ monocyte


title: LN-2Q-S776A-151

description: Sample 19


title: fun30_ctr_RPA_1_2h


title: LN-WT-157

description: Sample 24


title: fun30_ctr_RPA_1_0h


title: TCPOBOP_Female_2 [G175-M11]

description: polyA-selected RNA, stranded library


title: LN-2Q-S776A-146

description: Sample 18


title: U937_control_mock1

description: U937_control cell-line_mock treatment, replicate 1


title: WT.2 female

city: London

first: Andrea

last: Cerase

address: Newark st

country: United Kingdom

institute: QMUL

data_processing:
Data QC and pre-processing : Quality control on the raw reads was performed using FastQC whereas quality trimming and adapter removal was carried out using cutadapt
Read Mapping: Trimmed reads were aligned to the reference genome using STAR v2.6.1a. FeatureCounts was used to count the reads on a gene basis
Genome_build: ENSEMBL Mus Musculus GRCm38.88
Supplementary_files_format_and_content: gene counts, csv format

source_name: Liver

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

value: post weaning

value: liver

value: WT


title: LN-2Q-S776A-140

description: Sample 17


title: TCPOBOP_Female_1 [G175-M10]

description: polyA-selected RNA, stranded library

value: 7-8 weeks


title: fun30_ctr_H3_2_6h

value: anti-H3 antibody (RRID:AB_2687473)


title: WT.1  Female


title: LN-WT-138

description: Sample 21


title: NT-KO.2 Female

value: KO


title: Vehicle_Female_3 [G175-M9]

description: polyA-selected RNA, stranded library


title: fun30_ctr_H3_2_4h


title: Vehicle_Female_2 [G175-M8]

description: polyA-selected RNA, stranded library


title: NT-KO.1 Female


title: Vehicle_Female_1 [G175-M7]

description: polyA-selected RNA, stranded library


title: LN-WT-134

description: Sample 15


title: fun30_ctr_H3_2_2h


title: fun30_ctr_H3_2_0h


title: WT.2 Male


title: fun30_ctr_H3_1_6h


title: NT-KO.2 Male


title: LN-SCA1-S776A-1272

description: Sample 11


title: WT.1 Male


title: TCPOBOP_Male_1 [G175-M4]

description: polyA-selected RNA, stranded library

value: Male

value: TCPOBOP (3 mg/kg) for 27 hrs


title: fun30_ctr_H3_1_0h


title: LN-SCA1-S776A-1120

description: Sample 10


title: LN-SCA1-S776A-584

description: Sample 12


title: LN-WT-1098

description: Sample 13


title: LN-WT-132

description: Sample 14


title: TCPOBOP_Male_2 [G175-M5]

description: polyA-selected RNA, stranded library


title: NT-KO.1 Male


title: TCPOBOP_Male_3 [G175-M6]

description: polyA-selected RNA, stranded library


title: fun30_ctr_H3_1_4h


title: LN-WT-142

description: Sample 16


title: Vehicle_Male_3 [G175-M3]

description: polyA-selected RNA, stranded library

value: Vehicle


title: Vehicle_Male_2 [G175-M2]

description: polyA-selected RNA, stranded library


title: LN-SCA1-S776A-1119

description: Sample 9


title: LN-SCA1-435

description: Sample 8


title: Vehicle_Male_1 [G175-M1]

description: polyA-selected RNA, stranded library


title: fun30_ctr_H3_1_2h


title: TCPOBOP_Female_4 [G174-M13]

description:
polyA-selected RNA, stranded library
G174-M13

source_name: liver tissue_cytoplasmic fraction

extract_protocol:
The following buffers were prepared fresh daily and kept on ice for up to 2 hours: Base Solution, 10 mM Tris-Cl, pH 7.4, 146 mM NaCl, 1 mM CaCl2 21 mM MgCl2; Lysis Buffer, Base Solution containing 0.1% Triton X-100 (Cat. #T8787, Sigma), with 80 U/mL Protector RNase Inhibitor (Cat # 3335402001, Roche) added just prior to use; ST Nuclei Wash Buffer (ST Buffer), Base Solution containing 0.01% BSA (Cat. #SRE0036, Sigma), with 80 U/mL Protector RNAse Inhibitor added just prior to use. To minimize premature tissue thawing and RNA degradation, a ~250 mg piece of each liver was placed on dry ice and then cut into 2-3 smaller pieces, and stored in an Eppendorf tube on dry ice until ready for further processing. For this protocol, all pipette tips used were RNase-free and DNase-free (Cat. #76322 series, VWR). Each pre-cut liver sample was transferred to a 3 mL glass-on-glass dounce homogenizer with 1 mL of Lysis Buffer, on ice. Keeping the homogenizer on ice, the sample was dounced for 10 strokes with pestle A (loose fit) followed by ~10 strokes with pestle B (tight fit) until fully homogenized. Homogenization was performed in under one minute, while avoiding foaming and splattering of the sample. ST Buffer (1 ml) was then added, pipetted up and down a few times to mix, and the sample was then passed through a 40 µm cell strainer (Cat. # 10199-655, VWR) into a 50 mL conical tube on ice. A second 1 ml of ST Buffer was used to rinse the homogenizer and pestles, passed through the same 40 µm cell strainer and then combined with the homogenized sample. The homogenizer and pestles were then washed with Milli-Q water three times before being used to process the next sample. Homogenized samples were kept on ice until all samples were ready to proceed to the next stage. Each homogenized sample was divided into two 1.5 ml Eppendorf tubes, which were centrifuged at 500g in a swinging bucket centrifuge (Dynac Centrifuge, Clay Adams) for 5 min at 4° C to pellet the lysed cells. To avoid damage to the nuclei, a swinging bucket rotor was used to minimize the shear forces generated using a fixed-angle rotor. The supernatant was removed from the pelleted nuclei, and 250 µl was placed in an Eppendorf tube to extract cytoplasmic RNA. To prevent RNA degradation, 750 µl of Trizol LS reagent was added immediately to the cytoplasmic fraction, which was vortexed for a few seconds, then stored at -20° C. Frozen samples were thawed on ice, and vortexed for 10 s to fully resuspend each sample. Chloroform (isoamyl alcohol free, 0.2 ml) was then added, followed by vortexing vigorously for 15 s. The sample was allowed to sit for 2-3 min at room temperature and then spun at 12,000 x g for 15 min at 4° C. The clear upper, aqueous phase was carefully transferred to a new centrifuge tube, being careful not to disturb the genomic DNA-containing interface. Isopropanol (0.5 ml) was added to each sample followed by vortexing for 10 s. Glycogen (Cat. #AM9510, ThermoFisher) was then added to each sample (1 µg per 20 µl reaction). Samples were vortexed and then incubated for 10 min at room temperature. Samples were centrifuged at 12,000 x g for 20 min at 4° C, and the supernatant was discarded. The RNA pellet was washed with 1 mL of 75% ethanol by vortexing, and followed by centrifugation at 7,500 x g for 5 min at 4° C. The ethanol wash was removed and sample left to air dry for 5-10 min. Final RNA pellets were resuspended in 20 µl Milli-Q water, quantified on a Qubit instrument using Qubit RNA HS Assay (Cat. #Q32852, Invitrogen) and stored at -20° C.
Illumina sequencing libraries were prepared by poly(A) selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat #E7490L) using 0.5 µg of input RNA, followed by cDNA synthesis and library preparation using the NEBNext Ultra Directional RNA Sequencing for Illumina kit (Cat #E7420L).


title: FLAG_H3flag_1_8_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
F_43_1:8_I_CAGGACGTTCCGGAGA

value: anti-FLAG beads (RRID:AB_2637089)


title: TCPOBOP_Female_3 [G174-M12]

description:
polyA-selected RNA, stranded library
G174-M12


title: FLAG_H3flag_1_6_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
F_43_1:6_II_TATAGCCTATTCAGAA


title: LN-SCA1-144

description: Sample 6

value: Cerebellum


title: FLAG_H3flag_1_8_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
F_43_1:8_II_TATAGCCTGAATTCGT


title: LN-SCA1-409

description: Sample 7


title: FLAG_H3flag_1_8_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
F_43_1:8_GGCTCTGATCCGCGAA


title: TCPOBOP_Female_2 [G174-M11]

description:
polyA-selected RNA, stranded library
G174-M11


title: LN-SCA1-135

description: Sample 5


title: FLAG_H3flag_1_6_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
F_43_1:6_I_CAGGACGTATTACTCG


title: TCPOBOP_Female_1 [G174-M10]

description:
polyA-selected RNA, stranded library
G174-M10


title: LN-Double-1249

description: Sample 4

value: double


title: Vehicle_Female_3 [G174-M9]

description:
polyA-selected RNA, stranded library
G174-M9


title: FLAG_H3flag_1_6_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
F_43_1:6_GGCTCTGACGGCTATG


title: FLAG_H3flag_1_4_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
F_43_1:4_II_TATAGCCTGAGATTCC


title: FLAG_H3flag_1_4_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
F_43_1:4_I_TAATCTTAAGCGATAG


title: LN-Double-1163

description: Sample 2


title: Vehicle_Female_1 [G174-M7]

description:
polyA-selected RNA, stranded library
G174-M7


title: LN-Double-1142

description: Sample 1


title: FLAG_H3flag_1_4_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
F_43_1:4_GGCTCTGATAATGCGC


title: TCPOBOP_Male_3 [G174-M6]

description:
polyA-selected RNA, stranded library
G174-M6


title: TCPOBOP_Male_2 [G174-M5]

description:
polyA-selected RNA, stranded library
G174-M5


title: TCPOBOP_Male_1 [G174-M4]

description:
polyA-selected RNA, stranded library
G174-M4


title: Control 6

first: Jinhang

last: Zhu

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

description: processed data file: circRNAs.SRPBM.txt

data_processing:
TrimGalore were trimmed for paired-end adaptor sequence.
Sequenced reads were mapped to mm10 whole genome using STAR software.
CIRI and CIRCexplorer software were used as the identified circRNA for subsequent analysis. CircBase and circ2Trait disease database was used to annotate the identification of circRNAs.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: circRNAs.SRPBM.txt: Tab-delimited text file includes SRPBM values for each Sample.

growth_protocol:
Control group (CCl4-induced): mice received 10% carbon tetrachloride (CCl4, 10 μl/10 g bodyweight) for 8 weeks (two times a week) injection to induce liver fibrosis.
Treatment group (PZH-treated): mice were injected by CCl4, and administered with PZH (25 mg/ml, once daily, weeks 2-8) dissolved by double distilled water under sonication. Six mice of each group were killed for collecting liver samples at 8th week for RNA-seq.

extract_protocol:
RNA from each hepatic fibrosis tissue sample was extracted using Trizol reagent (Invitrogen, CA, USA) and Illumina Hiseq 4000 was used for the construction of circRNA sequencing libraries.
RNA libraries were prepared for sequencing according to Illumina's instructions accompanying the TruSeqTM RNA sample prep Kit.

treatment_protocol: PZH medication.

value: Liver

tag: disease

value: carbon tetrachloride (CCl4)-induced liver fibrosis

value: Control


title: Control 4

description: processed data file: circRNAs.SRPBM.txt


title: Control 5

description: processed data file: circRNAs.SRPBM.txt


title: Vehicle_Male_3 [G174-M3]

description:
polyA-selected RNA, stranded library
G174-M3


title: FLAG_H3flag_1_1_III

first: Martina

last: Peritore

address: Am Klopferspitz 18

institute: MPIB

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
F_43_1:1_II_TATAGCCTTCCGGAGA


title: Control 3

description: processed data file: circRNAs.SRPBM.txt


title: FLAG_H3flag_1_2_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
F_43_1:2_I_TAATCTTATCTCGCGC


title: FLAG_H3flag_1_2_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
F_43_1:2_GGCTCTGACTGAAGCT


title: FLAG_H3flag_1_1_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
F_43_1:1_I_TAATCTTATCCGCGAA


title: Control 2

description: processed data file: circRNAs.SRPBM.txt


title: Vehicle_Male_1 [G174-M1]

description:
polyA-selected RNA, stranded library
G174-M1


title: Vehicle_Male_2 [G174-M2]

description:
polyA-selected RNA, stranded library
G174-M2


title: Control 1

description: processed data file: circRNAs.SRPBM.txt


title: FLAG_H3flag_1_0_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
F_43_10h_II_TATAGCCTCTGAAGCT


title: Gimap5-mutant homozygous (Gimap5sph/sph)

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Korea University College of Medicine

data_processing:
Cellranger (v3.0) count function with the default parameters was run to generate single cell feature counts from FASTQ files.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated file, feature counts amd indexes

source_name: liver endothelial cells

extract_protocol:
Liver endothelial cells (DAPI-CD45-CD31+) were isolated from one Gimap5sph/sph and one Gimap5sph/+ adult mice.
scRNA-Seq library was generated using Chromium Single Cell 3' Reagent Kits v3 (10x Genomics) following the manufacturer's protocol.

tag: strain background

tag: genotype/variation

value: sorted (CD45-CD31+) liver endothelial cells


title: Vehicle_Female_2 [G174-M8]

description:
polyA-selected RNA, stranded library
G174-M8

value: Female


title: Gimap5-mutant heterozygous (Gimap5sph/+)


title: PZH 6

description: processed data file: circRNAs.SRPBM.txt

value: Pien Tze Huang (PZH)


title: PZH 5

description: processed data file: circRNAs.SRPBM.txt


title: FLAG_H3flag_1_2_III

city: Planegg-Martinsried

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
F_43_1:2_II_TATAGCCTCGCTCATT


title: PZH 4

description: processed data file: circRNAs.SRPBM.txt


title: PZH 3

description: processed data file: circRNAs.SRPBM.txt


title: Inguinal adipose tissue, male sucrose (MS8369)

city: Downers Grove

first: Erin

middle: J

last: Stephenson

state: IL

address: 555 31st street

institute: Midwestern University

description: RNAseq performed by Novagene

data_processing:
Novogene transformed raw image data files to sequenced reads using CASAVA(1.8) base recognition and Qphred scores were used to determine the error rate distribution along reads. GC-content was used to detect potential AT/GC separation. To get clean reads, raw reads were filtered to remove reads containing adaptors, remove reads containing N>10%, and ensure the Qscore of over 50% of the read was <=5.
Novogene parsed alignments using Tophat and aligned paired-end clean reads to the reference genome using STAR (v2.5). HTSeq v0.6.1 was used to count the read numbers mapped to each gene
Investigators used DESeq2 (v1.24.0) to normalize counts and identify differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: matrixData_sucrose-iWAT.csv reports read counts

source_name: dorsolumbar-inguinal adipose tissue

growth_protocol: Temperature (~22 deg C) and humidity controlled rooms, ventilated cages with corn-cobb bedding

extract_protocol:
Total RNA was isolated using TRI reagent and purified using columns from a PureLink RNA isolation kit.
Total RNA samples were sent to Novogene where mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and NEB cDNA libraries were prepared. To construct libraries, first strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3'ends of DNA fragments, NEBNext Adaptor with hairpin look structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150-200 bp length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). The final library was constructed by PCR amplification and purification of PCR products by AMPure XP beads. Library quality was first determined by Qubit2.0 and the insert size was detected using Agilent 2100. Q-PCR was used to accurately quantify the library effective concentration (>2nM).

treatment_protocol: Beginning at 10 weeks of age, mice were either maintained on regular chow and plain drinking water, or began receiving drinking water supplemented with 10%w/v sucrose for 12 weeks. Mice were given an intraperitoneal injection of 0.9% saline prepared using 99% deuterium oxide 7 hours before tissues were collected

value: C57BL6/J x C57BL6/N

value: male

tag: diet

value: chow diet (Envigo #7912)

tag: drinking water

value: 10%w/v sucrose in water ad libitum

tag: treatment duration

value: 12 weeks

value: 22 weeks

value: dorsolumbar-inguinal adipose tissue


title: FLAG_H3flag_0_1_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
F_43_0h_I_TAATCTTACGGCTATG

tag: strain


title: FLAG_H3flag_0_1_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
F_43_0h_II_TATAGCCTATTACTCG


title: Inguinal adipose tissue, male sucrose (MS8222)

description: RNAseq performed by Novagene

tag: Sex


title: Inguinal adipose tissue, male sucrose (MS8289)

description: RNAseq performed by Novagene


title: LN-Double-1165

description: Sample 3


title: Inguinal adipose tissue, male sucrose (MS8393)

description: RNAseq performed by Novagene


title: Inguinal adipose tissue, male sucrose (MS8126)

description: RNAseq performed by Novagene


title: FLAG_H3flag_0_1_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
F_43_0h_GGCTCTGAATTCAGAA


title: FLAG_H3flag_1_1_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
F_43_1:1_GGCTCTGAGAATTCGT


title: FLAG_ctr_1_8_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
F_517_1:8_I_TAATCTTACTGAAGCT