title: BCBL-1_Mutant_peptide_2

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Illimuna next-generation sequencing (100bp, single read)

data_processing:
Library strategy: SLAM-seq
SLAM-Seq datasets were analyzed using the T>C conversion-aware SLAM-DUNK (Digital Unmasking of Nucleotide conversion-containing k-mers) pipeline utilizing the default parameters (DOI: 10.1038/nmeth.4435, DOI: 10.1186/s12859-019-2849-7). Briefly, nucleotide conversion-aware read mapping of adapter- and poly(A)-trimmed sequences to the human GRCh38/hg38 reference genome assembly was performed with NextGenMap (DOI:10.1093/bioinformatics/btt468). Alignments were filtered for those with a minimum identity of 95% and minimum of 50% of the read bases mapped. For multi-mappers, ambiguous reads and non-3' UTR alignments were discarded, while one read was randomly selected from multimappers aligned to the same 3’ UTR. SNP calling (coverage cut-off of 10X and variant fraction cut-off of 0.8) with VarScan2 (DOI: 10.1101/gr.129684.111) was performed in order to mask actual T>C SNPs prior. Non-SNP T>C conversion events were then counted and the fraction of labeled transcripts determined. All output is contained in tcount files.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: The processed data is contained in the tcount file, which are the central output of slamdunk. These contain all results, conversion rates, and other statistics for each UTR. Tcount files are tab-separated text files containing one line entry per annotated 3’ UTR. Each entry contains the following columns: "chromosome, start end, name, length, strand, conversionRate, readsCPM, Tcontent, coverageOnTs, conversionsOnTs, readCount, tcReadCount, and multimapCount.

source_name: human primary effusion lymphoma

growth_protocol: BCBL-1 and BC-1, and BC-3 cell lines were cultured in RPMI 1640 medium supplemented with 15% FBS. The cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 (v/v). Mycoplasma contamination was routinely tested by using a PCR-based assay.

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen).
Total RNA was isolated from cells following incubation with 4-Thiouridine (s4U; 300 uM). Subsequently, the 4-thiol groups in the s4Uracil-labeled transcripts were alkylated with iodoacetamide (IAA). QuantSeq 3’ mRNA-Seq (FWD) (Lexogen, Inc.) Illumina-compatible, indexed sequencing libraries were then prepared from the alkylated RNA samples (100 ng) according to the manufacturer’s protocol for oligo(dT)-primed first strand cDNA synthesis, random-primed second strand synthesis, and library amplification.

treatment_protocol: BCBL-1 and BC-1 cell cultures (two cultures per treatment) were incubated with wild type peptide (24 uM), mutant peptide (24 uM), or vehicle control for 30 minutes. Subsequently, 4-Thiouridine (s4U; 300 uM) was added to the culture media and the cells treated for 1 hour in order to label newly synthesized RNA.

value: Mutant peptide (24uM) for 90 minutes

tag: labeling treatment

value: 4-Thiouridine (s4U; 300 uM) for 1 hour


title: BCBL-1_Wt_peptide_1

status: Public on Dec 01 2021

type: SRA

state: CA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: treatment

value: Wild type peptide (24uM) for 90 minutes


title: MDF104_r1: Dural cells MDF 104 rep 1

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
salmon (v0.13.1) was used to map the paired-end reads to the human transcriptome (gencode.v28). --validateMappings and -l ISR flags were used.
tximport (v1.14.0) was used to import the salmon quantification files to R (3.6.1)
DESeq2 (v1.26.0) was used to gene expression changes.
Genome_build: hg38
Supplementary_files_format_and_content: tsv (transcript abundance)

source_name: Dural cells

growth_protocol: DMEM high glucose with Sodium pyruvate, FBS, and PenStrep

extract_protocol:
Quick rna microprep kit from Zymo Research #R1051
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (#634413 Takara)

tag: cell type

value: Dural cells

tag: tissue collection

value: Postmortem

tag: tissue storage

value: Frozen (no cryoprotectant)


title: BCBL-1_Control_1

value: No treatment for 90 minutes


title: BC-1_Mutant_peptide_2


title: BCBL-1_Control_2


title: GFI1KO_G2ECs_1

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

description: GATA2+_ECs derived in GFI1KO

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptors were cut from reads using cutadapt (v1.13), and reads were aligned to human genome (UCSC hg38) using bowtie2 (v2.2.5).
Duplicates were removed using samtools (v1.3.1) and Picard Tools (v1.90). Signals were pileupped using MACS2 callpeak and bdgcmp, and differential open peaks were called using MACS2 bdgdiff
Signal density heatmap and profile were plotted using deeptools (v2.4.2), and motifs were found using homer.
Peaks were annotated with gene annotation using ChIPpeakAnno (v3.12.7) and gene ontology analysis was performed using clusterProfiler (v3.6.0).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bed

molecule: genomic DNA

source_name: Endothelial cells

extract_protocol:
In brief, 5×104 cells of each sample were processed for ATAC-seq.
DNA libraries were prepared for sequencing using standard Illumina protocols.

value: hESCs derived Endothelial cells

tag: genotype


title: WM278_E+B_RES

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

data_processing:
Raw sequencing data (fastq) were aligned to human reference genome version GRCh38 using HISAT2 algorithm and BAM files were generated. Downstream analysis was performed using StrandNGS software (www.strand-ngs.com).
BAM files were imported into the software DESeq1 algorithm was used for normalization.
To identify differentially expressed genes between conditions Moderated T-Test with Benjamini-Hochberg FDR for multiple testing correction was used.
Genome_build: hg38
Supplementary_files_format_and_content: normalized abundance measurements

source_name: melanoma cell line

growth_protocol: The cells were cultured in RPMI-1640 medium (Lonza Group Ltd., Basel, Switzerland) and supplemented with 10 % foetal bovine serum (Gibco, CA, USA), 2 mmol/L glutamine, and antibiotics at 37°C.

extract_protocol:
RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) was used to isolate total RNA from the melanoma cell lines.
cDNA libraries for RNA-Seq analyses were prepared from 1 μg total RNA using Ultra II RNA Sample Prep kit (New England BioLabs Inc., USA) according to the manufacturer’s protocol.

treatment_protocol: Resistant cell lines were generated through long-term high-dose treatment using in-creasing concentrations of ENCO+BINI in every passage. The concentration of the drug combination at the beginning of treatment was 1 nmol/l for each cell line and increased up to 200 nmol/l. To reach the maximum concen-tration of the drug combination, the time window varied between 3 and 5 months. Re-sistant cells were maintained in complete medium supplemented with a 200 nmol/l com-bination of encorafenib + binimetinib.

value: melanoma cell line

tag: tumor stage

value: primary

tag: condition

value: encorafenib and binimetinib resistant cell line


title: BC-1_Mutant_peptide_1


title: WM902B

value: original WM902B cell line


title: BC188_S10

city: Los Angeles

first: Ahmad

last: Besaratinia

address: 1450 Biggy Street, NRT building, First Floor, Office No: 1509A, M/C 9603

department: Preventive Medicine

institute: University of Southern California

data_processing:
Sequencing was performed on Illumina Nextseq 500 for a single-end read for 75 cycles. Data quality check was done by Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v2.17 program. RNA-seq data were trimmed, aligned, and quantified using Partek® Flow® version 8.0.19.1027 (Partek® Inc., St. Louis, MO). Raw sequencing reads were trimmed from both ends (Phred QC score > 20, minimum read length = 25 nt). To align trimmed reads to the human reference genome hg38, STAR version 2.6.1d was used with default parameter settings. Mapped reads were quantified using Partek E/M, Partek’s optimization of the expectation-maximization algorithm for transcript abundance estimation with Gencode 27 annotation. Post-alignment processing, quantification, and all downstream differential expression (DE) analysis were performed in R, a programming language and environment for statistical computing. To establish quality control, we applied the following criteria: samples were included in the analysis if they had high sequencing depth (> 30 million reads/sample) and high percentage reads aligned (> 50% reads aligned). All samples passed the quality control and met the above criteria. Furthermore, we excluded genes with less than 1 count per million (cpm) in at least 23 samples, where 23 was the sample size of our control group, against which the vaping and smoking groups were contrasted.
Differential expression analysis | Primary model: We used the limmaVoom with quality weights method to transform the RNA-seq data and account for the mean-variance relationship of counts prior to linear modeling in limma. We performed group comparison of DEGs in vapers and smokers relative to controls using linear contrasts defined a priori as follows: tested features were considered differentially expressed (DE) if they possessed an absolute fold change (FC) of greater than 1.5 and a false discovery rate (FDR) below 10%: yi j= αi + βiClassificationj + δiAgej + μiSexj + εij . We used the above formula for transcript feature i and donor j and Classificationj (levels: controls, vapers, and smokers), adjusting for subject’s age and sex. After fitting the linear model to RNA-seq data, we applied Empirical Bayes smoothing to the standard errors, borrowing information from all genes. The normalized expression data were analyzed in two contrasts relative to control group (i.e., vapers vs. controls and smokers vs. controls) in such way that regression coefficients represent log-fold changes between comparison groups. We corrected for multiple testing and obtained adjusted P-values (FDR, or q) by applying the Benjamini and Hochberg procedure.
Ordinal sensitivity analysis | Sensitivity model: We performed a posthoc ordinal sensitivity analysis to seek the relationship between DEGs in vapers and smokers and exposure indices, including cumulative e-liquid consumption and pack year. To tease out the influence of e-cig use in vapers with and without a history of smoking, we stratified vapers into three categories based on pack years (PY) smoked: (1) No smoking history [PY = 0; n = 7]; (2) Light smoking history [PY < 7; n = 15]; and (3) Heavy smoking history [PY > 7; n = 15]. To assess dose-dependent effects of e-cig use in vapers, we also divided vapers in two categories based on cumulative e-liquid (cum e-liq) consumed: (1) Light vapers [cum e-liq < 5000 ml; n = 18]; (2) Heavy vapers [cum e-liq > 5000 ml; n = 19]. To evaluate dose-dependent effects of cigarette smoking in smokers, we similarly divided smokers in two categories based on PY smoked: 1) Light smokers [PY < 7; n = 7]; (2) Heavy smokers [PY > 7; n = 15]. In all analyses, we included controls [PY = 0, cum e-liq = 0; n = 23] to improve statistical power. Testing of the ordinal variables for differential gene expression was performed as described above for the primary DE analysis, while adjusting for age and sex. We applied two sensitivity models for vapers, including cum e-liq sensitivity and PY sensitivity models, and one sensitivity model for smokers, including PY sensitivity model. In vapers, we tested whether each DEG identified in our primary analysis remained differentially expressed, at a statistically significant level, in the cum e-liq- and PY sensitivity analyses. Consistent differential expression of the tested DEG in the cum e-liq sensitivity model and failure to remain significantly differentially expressed in the PY sensitivity model indicate that vaping, but not past smoking, contributes to the differential expression of the DEG, as detected in the primary analysis. In other words, consistency between the results of our primary analysis and the cum e-liq sensitivity analysis, but not the PY sensitivity analysis, supports that past smoking in vapers ex-smokers has little to no impact on differential expression of the tested genes. At the same time, it reaffirms that exposure to e-cigs influences differential expression of the tested DEG in vapers, irrespective of past smoking history. Likewise, in smokers, reproducibility of the expression results between our primary analysis and the PY sensitivity analysis reassures that exposure to cigarette smoke modulates differential expression of the tested DEG.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Peripheral blood leukocytes

extract_protocol:
Peripheral blood (30 ml) was drawn from the study subjects by venipuncture. Plasma was collected by centrifugation, and subsequently leukocytes and erythrocytes were separated using LeucosepTM tubes according to the manufacturer’s instructions (Greiner Bio-One Inc., Monroe, NC). The collected plasma, and leukocyte and erythrocyte fractions were aliquoted into multiple microtubes (Eppendorf, Inc., San Diego, CA), snap frozen, and preserved at -80° C until further analysis. An aliquot of the thawed leukocyte samples from each subject was used for total RNA isolation using the RNeasy Mini Kit (Qiagen, Valencia, CA).
Libraries for RNA-seq were prepared from total RNA (300 ng per sample) using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Inc. acquired by Roche). The workflow consisted of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming, followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (ds cDNA), and incorporation of dUTP into the second cDNA strand. cDNA generation was followed by end repair to generate blunt ends, A-tailing, adaptor ligation, and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

value: Leukocytes

tag: vapers/smokers/controls

value: Vaper


title: BC183_S9


title: BC164_S7

value: Smoker


title: BC162_S5


title: BC159_S3


title: BC158_S2


title: BC-1_Wt_peptide_1


title: BCBL-1_Wt_peptide_2


title: BC-1_Control_2


title: BC-1_Control_1


title: BC156_S4


title: control6

city: Ji Nan

first: Xiangyu

last: Zhai

state: China

address: Department of general surgery, Qilu hospital of Shandong University，Wenhuaxi Road

institute: Qilu hospital of Shandong University

description:
circRNA
N6

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
After image recognition and base recognition, the original reads were harvested from the Illumina HiSeq sequencer. Use cutadapt software to remove joints, remove low-quality reads, and obtain high-quality clean reads. Use the STAR software to compare clean reads to the human reference genome (UCSC hg19), and use the Ensembl transcriptome (v75) gtf file as a guide, and use the DCC software for circular RNA detection.
We divide the circular RNA into exon circular RNA, intron circular RNA or intergenic circular RNA based on the alignment position of the two ends of the circular RNA. Then according to the genomic position of the circular RNA, the circular RNA identified by the circBase database and the circ2Trait circular RNA-disease database link. The newly identified circular RNAs are labeled novel.
Supplementary_files_format_and_content: Number of raw junction read

source_name: plasma exosome

growth_protocol: Transcriptome high throughput sequencing was performed by CloudSeq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs with NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.

extract_protocol:
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs
The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.

treatment_protocol: Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.

tag: tissue

value: plasma exosome

tag: disease state

value: healthy control


title: BC149_S14


title: BC148_S1


title: control5

description:
circRNA
N5


title: control2

description:
circRNA
N2


title: BC147_S13


title: control1

description:
circRNA
N1


title: control3

description:
circRNA
N3


title: BC174_S8


title: BC138_S12


title: BC-1_Wt_peptide_2


title: Hepatocellular carcinoma5

description:
circRNA
C5

value: Hepatocellular carcinoma


title: Hepatocellular carcinoma4

description:
circRNA
C4


title: BC-196_S24


title: BC-201_S28


title: BC-198_S26


title: Hepatocellular carcinoma6

description:
circRNA
C6


title: BC123_S11


title: Hepatocellular carcinoma3

description:
circRNA
C3


title: BC163_S6


title: Hepatocellular carcinoma2

description:
circRNA
C2


title: BC-195_S23


title: Hepatocellular carcinoma1

description:
circRNA
C1


title: Day 5 JQ1 rep1

city: Chicago

first: Lucy

last: Godley

state: IL

address: 5841 S. Maryland Ave. MC 2115

institute: University of Chicago

data_processing:
Sequence reads aligned to reference genome and transcriptome by HISAT2
Initial quantification by Cufflinks
Statistical test by Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing genes and FPKM quantification

source_name: K562 cells

growth_protocol: K562 cells were cultured in RPMI 1640 with 10% FBS. The cells were grown at 37 degree celcius with 5% CO2.

extract_protocol:
RNA was extracted by RNAzol following manufactor's instruction.
mRNA library was prepared by KAPA mRNA HyperPrep Kit.

tag: time point

value: Day 5

value: 200nM JQ1


title: control4

description:
circRNA
N4


title: Day 5 DMSO rep 2


title: BC-194_S22


title: BC-193_S21


title: BC-191_S19


title: Day 5 DMSO rep 1


title: BC-192_S20


title: BC-186_S17


title: BCBL-1_Mutant_peptide_1

value: Mutant peptide (24uM) for 90 minutes

value: 4-Thiouridine (s4U; 300 uM) for 1 hour


title: Day 3 JQ1 rep2

value: Day 3


title: BC-185_S16


title: BC-184_S15


title: BC-181_S14


title: Day 3 DMSO rep 2


title: Day 3 JQ1 rep1


title: Day 3 DMSO rep 1


title: BC-179_S12


title: BC-180_S13


title: Day 0 rep2 (No treatment control)

value: Day 0

value: No treatment


title: BC-177_S11


title: iHiC2_CM

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Straße 40

department: Institut für Pathologie

country: Germany

institute: Universitätsmedizin Göttingen

data_processing:
Raw reads were mapped, annotated, and corrected for biases using the Juicer suite 1.5 with default parameters with the exception of "-r 0" (comprehensive alignment was performed) and "-t 32" (parallelization was performed using 8 processes running in 4 CPUs).
Compartment analysis was performed using the signal of the first principal component of the Pearson's Hi-C contact matrices.
TAD boundaries were identified using rGMAP v.1.4 on contact maps with a resolution of 10 kbp and the following parameters: logt = TRUE, dom_order = 2, maxDistInBin = 80, min_d = 25, max_d = 100, min_dp = 5, max_dp = 10, hthr = 0.99, t1thr = 0.75.
Chromatin contacts (loops) were called using the proposed method Bloom and multiple loop callers (see main manuscript).
Genome_build: NCBI37 (mm9) and GRCh37 (hg19)
Supplementary_files_format_and_content: Juicer suite's .hic contact matrices

source_name: iPS-derived cardiomyocytes cells (hIPSC-CM)

growth_protocol: mESC were cultured in Knockout-DMEM medium containing 15% FBS and LIF on gelatin-coated plates. hiPSC-CMs were thawed in iCell Cardiomyocyte Plating Medium and plated on a ﬁbronectin-coated plates while after 2nd day they were maintained in iCell Cardiomyocyte Maintenance Medium

extract_protocol:
Standard DNA isolation
Hi-C performed for mESC according to the iHi-C published protocol DOI:10.15252/msb.20167311 and for hiPSC-CM according to the modified iHi-C 2.0 protocol DOI: 10.1016/j.ymeth.2019.07.003

value: human induced pluripotent stem cell-derived cardiomyocytes

value: wt

tag: library id


title: BC-172_S8


title: BC-175_S10


title: Day 5 JQ1 rep2


title: BC-173_S9


title: DB4-A_4F-A

city: New Haven

first: Elena

last: Tarabra

state: Connecticut

address: 330 cedar street

department: Endocrinology/Pediatrics

institute: Yale University - School of Medicine

data_processing:
RNA-seq reads were aligned to the human reference genome (hg38) using the HISAT2.
Gene models were downloaded from the GENCODE project (v27).
Read counts were extracted from StringTie output using the prepDE.py script (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq).
DESeq2 was used to determine differentially expressed genes.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *csv: Comma-separated gene expression values.

source_name: adipose tissue

extract_protocol:
SAT were removed, and homogenized into QIAzol Lysis Reagent. Total RNA was isolated using RNeasy Mini kit. Ribosomal depletion. Illumina HI-Seq 4000 was used to sequencing 0.5 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: phenotype

value: Obese

tag: gender

value: Female

tag: tissue depot

value: abdominal subcutaneous adipose tissue

value: biopsy


title: DB3-A_3F-A


title: BC-171_S7

value: Leukocytes

value: Smoker


title: BC-168_S5


title: DB7-A_6F-A


title: DB-34-A


title: BC-167_S4


title: Baseline 3


title: Follow-up 3

value: biopsy during follow-up visit after gaining weight


title: Follow-up 2


title: BC-169_S6


title: BC-165_S3

value: Control


title: BC-160_S1


title: BC-189_S18


title: Baseline 2


title: DB28-A_19F-A


title: BC-157_S28


title: DB26-A_18F-A


title: BC-161_S2


title: DB29-A_20F-A


title: DB-30-A


title: BC-155_S27

value: Vaper


title: BC-153_S25


title: BC-154_S26


title: Day 0 rep1 (No treatment control)


title: Follow-up 1


title: BC-152_S24


title: DB23-A_17F-A


title: DB22-A_16F-A


title: BC-151_S23


title: BC-150_S22


title: Baseline 1


title: DB20-A_14F-A


title: DB18-A_12F-A


title: BC-144_S19


title: BC-146_S21


title: BC-141_S17


title: BC-145_S20


title: DB12-A_9F-A


title: BC-142_S18


title: DB11-A_8F-A


title: m6A-IP

city: Chongqing

first: Huang

last: Wu

address: 10 Changjiang Access Road

department: Department of Blood Transfusion

institute: Daping Hospital, Army Medical University

data_processing:
Basecalls performed using CASAVA(version 1.8).
MeRIP-seq reads were  processed using FastP (version 0.19.11) and mapped to hg38 using BWA (version0.7.12).
m6A peak identification used exomePeak (version 2.16.0). m6A-enriched motifs identified by HOMER (version 4.9.1).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: Human Umbilical Vein Endothelial Cell

growth_protocol: HUVECs were cultured in  Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10%  fetal bovine serum (FBS). HUVECs were incubated at 37°C in 5% CO2 incubator with the humidified environment.

extract_protocol:
Total RNAs were extracted using Trizol Reagent. RNA fragmented  to 200 nts long size. Fragmented mRNA was subjected to IP using anti-m6A antibodies (ab151230; abcam).After  stringent washing, enriched RNA  eluted by RLT buffer (1015762; QIAGEN) .
Library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN) according to the manufacturer's instructions.

value: HUVEC

tag: rip antibody

value: anti-m6A (ab151230; abcam)


title: BC-140_S16


title: Input

value: none (input)


title: BC-139_S15


title: HUVEC shMETTL3 replicate3

data_processing:
Basecalls performed using CASAVA(version 1.8).
RNA-seq reads were  processed using FastP (version 0.20.0) and mapped to hg38 using HISAT2 (version 2.0.5).
FPKM (fragments per kilobase of transcript per million mapped reads)  were used for estimating gene expression levels.
Differential expression analysis was performed using the DESeq2 R package (version 1.16.1).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

extract_protocol:
Total RNAs were extracted using Trizol Reagent. PolyA RNA was isolated with oligo dT magnetic beads and fragmented with divalent cations.
RNA-Seq libraries preparation with NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB #E7770) according to the manufacturer's instructions.

treatment_protocol: HUVEC cells were infected with lentiviruses expressing scramble  or METTL3 shRNA vector  and selected using 1 μg/ml puromycin.

tag: cell line

value: Human Umbilical Vein Endothelial Cell


title: BC-137_S14


title: BC-136_S13


title: HUVEC shMETTL3 replicate2


title: HUVEC scramble  replicate3


title: BC-135_S12


title: HUVEC shMETTL3 replicate1


title: HUVEC scramble  replicate2


title: BC-133_S10


title: BC-132_S14


title: DB15-A_F10-A


title: HUVEC scramble  replicate1


title: BC-131_S13


title: BC-130_S12


title: BC-126_S9


title: BC-125_S9


title: BC-127_S10


title: BC-128_S11


title: BC-124_S8


title: BC-134_S11


title: BC-121_S6


title: BC-122_S7


title: BC-120_S5


title: si-Atf3  rep1

city: Shanghai

first: Hongjie

last: Zhang

address: Siping Road

institute: Tongji University

data_processing:
For RNAseq, sequenced reads were trimmed for adaptor sequence, then mapped to rn6 whole genome using hisat2 v2.1.0 with parameters -p 8 --dta -x -1 -2 -S. Raw transcripts were assembled using the StringTie (v1.3.4). Counts per million (cpm) were calculated by the edgeR (v3.20.9).
For scRNAseq, raw sequencing data were processed using Cell Ranger (version 3.1.0, 10X Genomics). Aligned sequencing reads were mapped to the rat transcriptome (rn6) using STAR aligner, gene expressions of each cell were quantified using cell barcodes.
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Neoatal Rat Ventricular Cardiomyocytes

growth_protocol: For RNA-seq, Neonatal rat’s hearts were harvested from 1-day old SD rats. Next, the ventricles were separated and cut into pieces (1–3 mm2), then they were dissociated in 0.25% trypsin (Gibco, 15090046) at 4 °C overnight. Then the tissue was transferred to 0.1% collagenase type Ⅱ (Worthington, LS004176) to further digest at 37°C at 145 rpm, and the supernatant was collected into DMEM medium containing 10% FBS every 5 min. The digestion procedure was repeated 3-4 times. When the tissue was completely digested, the supernatant was centrifuged at 1500 rpm for 6 min. Then, the cells were plated in DMEM medium which containing 10% FBS, 100 unit/ml penicillin and 100 mg/ml streptomycin at 15 cm dishes at an atmosphere of 5% CO2 at 37℃ for 90 min, to remove cells that are easier attached the dishes than cardiomyocytes. Finally, the culture supernatant was collected, plated in the plates which were coated with collagen and then incubated 24 h in an atmosphere of 5% CO2 at 37 ℃ with the same medium. After 24 h, the medium was changed to cardiomyocyte medium: DMEM: F12 (1:1) medium containing 0.25% FBS, 3 mM sodium pyruvate, 0.1 mM Vitamin C and 2 mM L-Glu.

extract_protocol:
For RNA-seq, The total RNA was extracted by TRIzol extraction reagent (Invitrogen, 15596018). Furthermore, the purity and concentration of RNA were examined by measuring the absorbance value at 260 and 280 nm.For single-cell RNA-seq, it performed by 10X genomics protocol.
For RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols; For single-cell RNA-seq, we performed according to 10X genomics protocols.

treatment_protocol: For RNA-seq, NRVCs were transfected with 50 nM si-Atf3 or si-Jun and si-control for 36h.

value: cardiomyocytes


title: si-Jun  rep1


title: BC-119_S4


title: si-Control  rep2


title: BC-118_S3


title: db-3

type: RNA

city: Beijing

first: huimin

last: liu

state: Beijing

address: 38 Xueyuan Rd , Haidian District

department: Peking University Health Science Center

institute: Peking University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

organism: Mus musculus

source_name: db/db

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The submandibular glands of mice are preserved at -80 degrees Celsius.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: submandibular gland

value: male

tag: age

tag: Sex


title: db-5


title: db-1


title: m-1

source_name: db/m


title: BC-116_S1

tag: cell type


title: RRBS ER-Hoxa9-Lys-GFP (-) E2 120h rep 2

city: Philadelphia

first: Andres

last: Blanco

state: PA

address: 380 S. University Avenue, Hill Pavillion Room 414

department: Biomedical Sciences

institute: University of Pennsylvania

data_processing:
Reads were aligned to build mm9 of the mouse genome with MAQ in bisulfite alignment mode.
For each CpG, the methylation level was computed as the number of reads with unconverted cytosines divided by the number of total reads covering that CpG. Mean methylation for each genomic feature was calculated as the mean methylation level of the CpGs within the feature weighted by the sequence coverage at each CpG, and only CpGs covered at 5x or higher were used in this calculation.
Differentially methylation testing was performed by using methylation levels of CpGs covered at 5X or higher in a two-sample weighted coverage t-test. FDR q-values were calculated from the t-test p-values using the R q-value package. Differentially methylated features were required to have a methylation difference of 0.2 at a FDR q-value threshold of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Peak coordinate BED files (Rep 1 and Rep 2 samples merged for a given timepoint)

source_name: ER-Hoxa9-Lys-GFP cells

growth_protocol: Cell culturing in RPMI + 10% FBS + 1%SCF conditioned media + 1% pen/strp (+) or (-) E2

extract_protocol:
Genomic DNA from 1x10^6 cells per sample was purified using a PureLink genomic DNA kit following the manufacturer's recommendation.
Illumina TruSeq adapters were ligated on to purified DNA, bisulphite conversions were performed, and DNA was amplified with primers for multiplexing. DNA from transposed nuclei was isolated and PCR-amplified using barcoded Nexteral primers (Illumina). Library QC was carried out using a high sensitivity DNA bioanalyzer assay and quibit measurement.

treatment_protocol: (-) E2 treatment: 3X wash in PBS, change to media (-) E2

tag: strain

tag: treatment

value: (-) E2 for 120 hours

value: cells culture in vitro

value: ER-Hoxa9-Lys-GFP cells


title: RRBS ER-Hoxa9-Lys-GFP (-) E2 72h rep 2

value: (-) E2 for 72 hours then +E2 add-back for 48 hours


title: RRBS ER-Hoxa9-Lys-GFP (-) E2 56h rep 2

value: (-) E2 for 56 hours then +E2 add-back for 64 hours


title: postnatal day7 rat heart

source_name: Neoatal Rat Heart

value: heart

value: cardiomyocytes and non-myocytes


title: postnatal day1 rat heart


title: m-2


title: BC-115_S8

value: Leukocytes

value: Smoker


title: RRBS ER-Hoxa9-Lys-GFP (-) E2 40h rep 2

value: (-) E2 for 40 hours then +E2 add-back for 80 hours


title: RRBS ER-Hoxa9-Lys-GFP (-) E2 24h rep 2

value: (-) E2 for 24 hours then +E2 add-back for 96 hours


title: db-4


title: si-Jun  rep2


title: si-Atf3  rep2


title: WT.MEF.GS.12hr

city: Dongjak-Gu

first: Junil

last: Kim

state: Seoul

address: 369 Sangdo-Ro

department: Department of Bioinformatics

country: South Korea

institute: SOONGSIL UNIVERSITY

data_processing:
Sequences were mapped to mouse mm10 genome, de-multiplexed and filtered using 10X Genomics Cell Ranger Software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes UMI values for each cell.

source_name: mouse embryonic fibroblasts (MEFs)

extract_protocol:
At the end of starvation, MEFs were collected using trypsin EDTA and resuspended in freezing media (10% DMSO + 90% dialyzed FBS). The control sample (0 hour starvation) was collected and resuspended in freezing media composed of 90% FBS instead of dialyzed FBS. Vials containing each sample were stored in a deep freezer before proceeding to sequencing. The viability of samples was checked using Countess and 5,000 cells from each sample were used for single cell isolation, library preparation and sequencing performed by Theragenetex.
MEFs in starvation condition were collected using trypsin EDTA and resuspended in freezing media (10% DMSO + 90% dialyzed FBS). The control sample (0 hour starvation) was collected and resuspended in freezing media composed of 90% FBS instead of dialyzed FBS.
All scRNAseq libraries were prepared using Single Cell 3’ v2 chemistry 10X chromium Kit and sequenced using Illumina HiSeq 4000.

treatment_protocol: MEF cells (MEFs) were cultured at 37 °C in Dulbecco’s modified Eagle’s medium (DMEM) containing 10 % fetal bovine serum (FBS) and antibiotics in a humidified incubator with 5 % CO2. MEFs used in the study was regularly tested for mycoplasma contamination. For glucose/amino acid starvation, cells were washed with PBS, then incubated with glucose/amino acid-free DMEM supplemented with 10 % dialyzed FBS. Transfection was performed with Lipofectamine 3000 (Invitrogen). 500000 of MEFs were plated on culture dish containing high glucose DMEM (Cat. SH30243.01) with FBS and were stabilized for one day. After stabilization, the cells were washed with either glucose starvation media (Cat. LM001-56) or amino acid starvation media (Cat. LM001-90) containing dialyzed FBS. Subsequently, the normal media was changed with appropriate starvation media and cells were incubated in the cell incubator for different duration of time according to starvation signal (amino acid starvation 3 and 6 hours, glucose starvation 6 and 12 hours).

value: mouse embryonic fibroblasts (MEFs)

tag: genotype

value: WT


title: BC-113_S6

value: Control


title: si-Control  rep1

value: cardiomyocytes


title: m-4

value: submandibular gland


title: RRBS ER-Hoxa9-Lys-GFP (-) E2 72h Rep 1


title: m-3

value: male


title: Wild type, biological rep2

city: Hangzhou

first: Yongbo

last: Hong

address: No.28 Shuidaosuo Rd. Fuyang distract

institute: China National Rice Research Institute

description: Gene expression data from 3-week-old WT leaf

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Oryza sativa

source_name: rice leaf

label_protocol: Biotin-tagged cRNA was prepared using a MessageAmp II cRNA Amplification Kit

growth_protocol: Rice plants were grown in a growth room under 28°C 14 h light/26°C 10 h dark cycle, and 80-85% relative humidity.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen, Shanghai, China). Two micrograms of total RNA were used for synthesis of double-stranded cDNA

treatment_protocol: At normal growth condition

tag: developmental stage

value: 3-week-old leaf

value: Wild type


title: OsBIERF3-OE, biological rep2

description: Gene expression data from 3-week-old OsBIERF3-OE leaf


title: BC-111_S5

tag: vapers/smokers/controls


title: Wild type, biological rep1


title: WT.MEF.GS.6hr


title: OsBIERF3-OE, biological rep1


title: RRBS ER-Hoxa9-Lys-GFP (-) E2 56h Rep 1

tag: tissue

value: cells culture in vitro

value: ER-Hoxa9-Lys-GFP cells


title: BC-108_S4

value: Vaper


title: BC-114_S7


title: RRBS ER-Hoxa9-Lys-GFP (+) E2 (untreated)

value: (+) E2 (untreated)


title: RRBS ER-Hoxa9-Lys-GFP (-) E2 40h Rep 1


title: Testis Ppp2ca-cKO rep2

city: Changzhou

first: Wenbin

last: Wang

address: NO.188, Gehu Street, Changzhou

institute: Nanjing Medical University

data_processing:
Sequencing was carried out using a 2x150 paired-end (PE) configuration.
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Rsem software (V1.2.6) with a protocol from Mortazavi et al, 2008.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Testis

extract_protocol:
Left testis 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: testis

value: post natal day 56


title: WT.MEF.AAS.3hr


title: Testis WT rep2

value: wild type


title: RRBS ER-Hoxa9-Lys-GFP (-) E2 120h Rep 1

value: (-) E2 for 120 hours


title: BC-107_S3

value: Leukocytes


title: Testis Ppp2ca-cKO rep1


title: BC-105_S2


title: Left ventricle 3 [LV_3]

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: left ventricle cardiomyocyte nuclei

data_processing:
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: mm10
Supplementary_files_format_and_content: RNA_seq_counts_BZ_RM_LV.xlsx (Excel file with normalized (DESeq2) count data per gene).

source_name: cardiac tissue left ventricle

growth_protocol: The border zone, remote myocardium or left ventricle was isolated from 8 week old mice

extract_protocol:
cardiac nuclei were isolated, stained with PCM1 and sorted by FACS, RNA was isolated with the Rneasy plus micro kit (Quiagen)
Ovation RNA-seq V2, UltraLow V2 kit

treatment_protocol: tissue was snap frozen and stored at -80 degree celcius

value: FVB

value: 8 weeks

value: wildtype

tag: tissue subtype

value: left ventricle cardiomyocyte nuclei


title: BC-104_S1

value: Control


title: Testis WT rep1


title: BC-117_S2


title: pMEF72_HAT1_KO

city: Columbus

first: Mark

middle: R

last: Parthun

state: OH

address: 1060 Carmack Rd.

department: Biological Chemistry and Pharmacology

institute: The Ohio State University

data_processing:
Data were collected using HCS (v2.0.12) software.
Differential expression was calculated using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: csv file contains edgeR output
Supplementary_files_format_and_content: bigwig files

source_name: HAT1 KO_pMEFs

growth_protocol: Cells were grown in DMEM media (Sigma) supplemented with 10% FBS (Sigma) and 1X Penicillin/Streptomycin antibiotics (Gibco).

extract_protocol: Total RNA was extracted from primary mouse embryonic fibroblasts using Total RNA purification plus kit (Norgen Biotek Corp.) according to the manufacturer's instructions. The RNA quality was tested using Agilent 2,100 Bioanalyzer, and RNA libraries were prepared using 200 ng total RNA as per manufacturer's instructions for the TruSeq RNA Sample Prep Kit (v2, Illumina). Concentration and size distribution of completed libraries was determined using an Agilent Bioanalyzer.

tag: strain background

value: HAT1 KO

value: primary mouse embryonic fibroblasts (pMEFs)


title: pMEF41_HAT1_KO


title: Left ventricle 2 [LV_2]

description: left ventricle cardiomyocyte nuclei


title: pMEF33_HAT1_KO


title: Left ventricle 1 [LV_1]

description: left ventricle cardiomyocyte nuclei


title: pMEF78_HAT1_WT

source_name: HAT1 WT_pMEFs

value: HAT1 WT


title: RRBS ER-Hoxa9-Lys-GFP (-) E2 24h Rep 1

value: (-) E2 for 24 hours then +E2 add-back for 96 hours

value: cells culture in vitro


title: APL1

city: Bologna

first: Valentina

last: Indio

state: Bologna

address: via Giuseppe Massarenti,11

country: Italy

institute: University of Bologna

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using TopHat v.2.0.9
Count per million (CPM) were calculated using htseq-count version 0.6.1p1 using the annotation from Ensembl v.81.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count per million (CPM) values

source_name: bone marrow

extract_protocol:
RNA was extracted from bone marrow using the RNeasy Mini Kit (Qiagen), and cDNA libraries were synthesized from 500ng total RNA using the TruSeq Stranded mRNA kit (Illumina). Whole transcriptome sequencing was carried out at paired end mode on a Illumina platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age (months)

value: F

tag: disease state

value: acute promyelocytic leukemia lacking PML/RARA fusion


title: pMEF47_HAT1_WT


title: I9-OC-BA-dent_S15

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing: The counts matrix was analysed for differential expression using DESeq2 (v 3.5)

source_name: Peripheral blood mononuclear cells

growth_protocol: Cells were culture in alpha-MEM supplemented with M-CSF and RANKL as described in Knowles et al. (PMID22782381)

extract_protocol: Total RNA was extracted using Trizol/phenol/chloroform method and Dnase-treated

value: Osteoclasts

tag: culture surface

value: dentine


title: I8-OC-BE-no-sub-_S19

value: No-substrate


title: WT.MEF.GS.AAS.0hr

value: mouse embryonic fibroblasts (MEFs)

value: WT


title: Remote myocardium_197 [RM_197]

description: left ventricle cardiomyocyte nuclei remote myocardium

source_name: cardiac tissue left ventricle myocardial infarction

value: FVB


title: I7-OC-BK-no-sub-_S12


title: I6-OC-BJ-no-sub-_S5


title: Border zone_197 [BZ_197]

description: left ventricle cardiomyocyte nuclei border zone

value: 8 weeks


title: Border zone_206 [BZ_206]

value: wildtype

value: left ventricle cardiomyocyte nuclei border zone


title: Dhcr24TG XZ14

first: Xinbo

address: Rm320, 10 Amistad St

department: Comparative Medicine

institute: Yale University

data_processing:
Using the PartekFlow® software, version 8.0.19.0405 (Partek, Inc., St. Louis, MO) the reads were aligned with the STAR algorithm to the mouse genome mmu10.
To estimate the transcript expression abundance we used Quantify to annotation model (Partek E/M) algorithm.
Genome_build: mmu10
Supplementary_files_format_and_content: quantification matrix

source_name: WD macrophage

growth_protocol: WT and Dhcr24TG mice (8 weeks old, male) were i.p injected with PCSK9 adeno-associated virus (AAV8-Pcsk9) at 1.0x1011 vector genome copies per mouse.

extract_protocol:
Mice were injected intraperitoneally with 3% thioglycollate broth to elicit peritoneal macrophages after 16 weeks on CD or WD diet. Thioglycollate-elicited macrophages were allowed to attach on 6-well plates for 2 hrs and washed twice with PBS to remove unattached cells. The cells were collected immediately after PBS wash for CD/WD group or cultured in 10% lipoprotein-deficient serum for 48 hrs for resting macrophage group. Total RNA was extracted and purified using a RNA isolation Kit (Qiagen) followed by DNAse treatment to remove genomic contamination using RNA MinElute Cleanup (Qiagen).
rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina). RNA libraries from WT BMDMs were performed TrueSeq Small RNA Library preparation (Illumina).
RNA libraries were sequenced for 45 cycles on Illumina HiSeq 2000 platform (1 x 75bp read length).

treatment_protocol: Two weeks after AAV8-Pcsk9 injection, animals were maintained in a chow diet or Western-type diet for 16 weeks.

value: C57 BL/6J

value: Abdominal Cavity

tag: genetype

value: AAV8-Pcsk9 +Western diet for 16 weeks

value: macrophage


title: I5-OC-BI-no-sub-_S7


title: Dhcr24TG XZ15

value: AAV8-Pcsk9 + Western diet for 16  weeks


title: Dhcr24TG XZ16


title: WT XZ13

description: WT


title: I3-OC-BF-no-sub-_S11


title: WT.MEF.AAS.6hr


title: I4-OC-BH-no-sub-_S22


title: Border Zone mouse 40 [BZ-40], reanalyzed

description: nuclear RNA

source_name: Cardiomyocytes border zone

value: 7 days after LAD

value: infarcted myocardium


title: Dhcr24TG XZ10

source_name: CD macrophage

value: AAV8-Pcsk9 + chow diet for 16  weeks


title: WT XZ11

description: WT


title: WT XZ12

description: WT


title: Border Zone mouse 32 [BZ-32], reanalyzed

description: nuclear RNA


title: WT XZ7

description: WT


title: I2-OC-BB-no-sub-_S21

value: Osteoclasts


title: Dhcr24TG XZ9


title: Dhcr24TG XZ8


title: Remote Myocardium mouse 43 [RM-43], reanalyzed

description: nuclear RNA

source_name: Cardiomyocytes remote myocardium


title: pMEF36_HAT1_WT

value: HAT1 WT

value: primary mouse embryonic fibroblasts (pMEFs)


title: WT XZ5

description: WT


title: WT XZ6

description: WT


title: Dhcr24TG XZ4

source_name: Resting PMs

value: AAV8-Pcsk9 + chow diet for 16  weeks+resting for 48 hrs


title: WT XZ2

description: WT

value: WT


title: I23-OC-BK-cart_S20

value: cartilage from OA patient


title: I22-OC-BJ-cart_S2


title: Border Zone mouse 34 [BZ-34], reanalyzed

description: nuclear RNA

value: FVB

value: 8 weeks


title: WT XZ1

description: WT


title: LV3

description:
left ventricle cardiomyocyte nuclei left ventricle
nuclear RNA PCM-1+ nuclei

data_processing:
Library strategy: Cut & Run
The BEDTools suite was used to distribute the genome wide signal into bins of 500 bp. The background read level was determined per sample per 500 bp by taking the average read count in bins with less than 20 tags. The background level of tags was subtracted per bin per sample.
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
To allow for differential peak calling between datasets, quantile normalization was applied using the deepTools2 suite (Ramirez et al., 2016).
Differential acetylation was assessed using the DESeq2 package based on a model using the negative binomial distribution (Love et al., 2014). P-values were corrected for multiple testing using the false discovery rate (FDR) method of Benjamini-Hochberg. We have used 0.05 as FDR control level. Continuous bins with differential signal were subsequently merged together using the BEDTools suite
Genome_build: mm10
Supplementary_files_format_and_content: BZ_CUTRUN_BZ_vs_LV_DESEQ2_diff_acetyl_MGU.xlsx

growth_protocol: The border zone or left ventricle was isolated from 8 week old mice, with and without myocardial infarction

extract_protocol:
cardiac nuclei were isolated, stained with PCM1 and sorted by FACS, CUT&RUN-sequencing was performed according to Hainer et al 2019
NEBNext Ultra 2 ( E7645S, E7335S)

value: wildtype


title: fl/fl

city: Atlanta

first: Bingzhong

last: Xue

state: Georgia

address: 50 Decatur St SE

department: Biology

institute: Georgia State University

data_processing:
raw reads are filtered into clean reads which will be aligned to the reference sequences.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio.
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). FPKM method is used in calculated expression level
Genome_build: mm10

source_name: Brown adipose tissue

extract_protocol:
Brown adipose tissue were removed, flash frozen in liquid nitrogen, and RNA was harvested using Tri-reagent.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary

value: fl/fl

value: Brown adipose tissue

tag: diet

value: 60% High Fat Diet (20 weeks)


title: I21-OC-BI-cart_S6


title: 3bKO


title: WT-1

first: Guan

last: Guiwen

address: 38 Xueyuan Road, Haidian District

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were mapped to GRCm38 whole genome using tophat2 with default settings.
Htseq2 was used to caculate gene expression level, and TPM was used to express expression level.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with TPM for every gene for this sample.

source_name: C57BL/6 mice

extract_protocol:
Total RNA was extracted from fetus mice liver tissue using TRIzol reagent (Invitrogen) according to the standard method and three biological repeats were performed for each group. RNA sequencing was completed on Illumina Hiseq2000 platform by Shanghai Majorbio Bio-pharm Technology Co.,Ltd.
After the samples pass the test, use the Ribo-zero kit to remove rRNA. Subsequently, high temperature and metal ions are used to achieve RNA fragmentation. Using Ribosomal-depleted RNA as a template, use six-base random primers (random hexamers) to synthesize one-strand cDNA, then add buffer, dNTPs (dUTP, dATP, dGTP and dCTP) and enzymes to synthesize two-strand cDNA, and then use VAHTSTM DNA Clean Beads purify double-stranded cDNA. The purified double-stranded cDNA is first repaired, A-tailed and connected to a sequencing adapter. VAHTSTM DNA Clean Beads are used for fragment size sorting. Then, UDG enzyme is used to degrade the cDNA chain containing U, and finally PCR enrichment is performed, and the PCR product is purified with VAHTSTM DNA Clean Beads to obtain the final chain-specific cDNA library. After the library is constructed, Qubit 3.0 is used to initially determine the concentration, and then the Agilent 2100 Bioanalyzer is used to detect the inserted fragments in the library. After this item meets expectations, the ABI Step One Plus Real-Time PCR system is used to accurately quantify the effective concentration of the library.

tag: strain/genotype

value: C57BL/6 WT

value: liver

value: fetal


title: Border Zone 3

description:
left ventricle cardiomyocyte nuclei border zone
nuclear RNA PCM-1+ nuclei

tag: age


title: WT-3


title: I1-OC-BA-no-sub-_S3

value: No-substrate


title: WT-2


title: I20-OC-BH-cart_S16


title: EXP-2

source_name: C57BL/6-Tg (HBV Alb-1) Bri44 HBV transgenic mice


title: EXP-3

value: C57BL/6-Tg (HBV Alb-1) Bri44 HBV transgenic


title: I19-OC-BF-cart_S23

value: Osteoclasts


title: Remote myocardium_206 [RM_206]

value: left ventricle cardiomyocyte nuclei remote myocardium


title: EXP-1


title: Border Zone 1


title: Remote Myocardium mouse 40 [RM-40], reanalyzed

description: nuclear RNA

value: 7 days after LAD

value: infarcted myocardium


title: Dhcr24TG XZ3

value: C57 BL/6J

value: Abdominal Cavity

value: AAV8-Pcsk9 + chow diet for 16  weeks+resting for 48 hrs

value: macrophage


title: I18-OC-BB-cart_S13

value: cartilage from OA patient


title: I17-OC-BA-cart_S24


title: LV2

value: FVB

value: 8 weeks

value: wildtype


title: Cherry_Positive

city: London

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

institute: The Francis Crick Institute

data_processing:
cellranger count (v2.1.1)
Filtering and re-clustering using the Seurat package (version 4.0.2) in R (version 4.0.3)
Tagging of clusters with marker genes and extraction of co-expressed genes (see methods for details)
Genome_build: mm10
Supplementary_files_format_and_content: Gzipped Tab delimted text file containing raw count data for each cell and annotated gene after primary filtering.

extract_protocol: Lung tissues were dissociated as described in Malanchi I., et al., Nature, 2011. Library generation for Genomics were performed following the Chromium Single Cell 3ʹ Reagents Kits and sequenced on an Hiseq4000 (Illumina), to achieve an average of 50,000 reads per cell.

value: Lung


title: I16-OC-BE-dent_S18

value: dentine


title: I15-OC-BK-dent_S1


title: I14-OC-BJ-dent_S4


title: 2547 f_ko_hfd_rep3

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were demultiplexed and converted from the native Illumina BCL format to fastq format using an in-house python wrapper to Illumina’s ‘bcl2fastq’ conversion utility.
FASTQ data were processed with ‘bcbio’ (v. 1.2.2), a best-practices pipeline available at the open-source ‘bcbio-nextgen’ project
Reads were aligned against the reference genome ‘mm10'  and counted with FeatureCounts using the mm10 Ensembl GTF
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

growth_protocol: All mice were fed ad libitum for the duration of the study.  Upon weaning all mice were fed a standard vivarium provided chow diet.   At 8 weeks of age a subset of mice were switched to a 45% (lard source) high fat diet.  Gastrocnemius tissue was collected at 30 weeks of age.

extract_protocol:
The gastrocnemius muscle was frozen in liquid nitrogen cooled isopentane immediately upon collection.  The frozen muscle tissue was powdered using a mortar and pestle.  Twenty-five to forty mg of frozen powdered gastrocnemius was homogenized in 600 µL RNAzol reagent in a Bullet Blender Storm 24 homogenizer (Next Advance; Troy, NY) at power setting #8 for a total of 12 minutes.  Total RNA was isolated using RNAzol RT Reagent (Cat. # R4533, Sigma-Aldrich) according to manufacturer’s protocol.  RNA was eluted in RNase-free water and column purified using the RNeasy Mini Kit (Cat. #74104, Qiagen) with RNase-Free DNase Kit (Cat. #79254, Qiagen) according to manufacturer’s protocol.   Purified RNA was eluted in 30 µL of RNase-free water.   Samples were stored at -80°C until further use.  Samples were quantified using fluorimetry and RNA quality was assessed using the Agilent BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA), generating an RNA Integrity Number (RIN).  Useable samples were required to have a mass ≥ 1 µg, with a RIN > 8.  Next, 500 ng of the DNase I-treated total RNA was used to enrich for polyA containing transcripts using oligo(dT) primers bound to beads.
The poly A enriched RNA was fragmented, converted to cDNA and ligated to sequencing adaptors containing indexes using the Illumina TruSeq stranded mRNA sample preparation kit (Cat. #RS-122-2101, Illumina, Inc., San Diego, CA).  The molar concentrations of the indexed libraries were measured using the 2100 Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) and combined equally into pools for sequencing.  The concentration of the pools was measured using the Illumina Library Quantification Kit (KAPA Biosystems, Wilmington, MA) and sequenced on the Illumina HiSeq 4000 genome sequencer using 150 bp paired-end SBS chemistry.

tag: Sex

value: female

value: MuRF1 -/-

value: HFD

value: gastrocnemius muscle


title: 2468 f_ko_hfd_rep4


title: Border Zone 2


title: 2459 f_ko_hfd_rep2


title: 2455 f_ko_hfd_rep1


title: 2513 f_wt_hfd_rep4

value: wild type


title: I10-OC-BB-dent_S14

tag: cell type

value: Osteoclasts


title: 2448 f_wt_hfd_rep2


title: Mut_24h_b (WT)

city: Bethesda

first: Alexander

middle: T

last: Bell

state: Maryland

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
HISAT2 was used for read mapping
samtools sort was used to convert SAM to BAM format
featureCounts from the Subread package was used to obtain raw gene counts
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text files containing raw gene counts for every gene and sample

source_name: HEK-Blue™ ISG Cells

growth_protocol: HEK-Blue™ ISG Cells and HEK-Blue™ ISG-KO-STING Cells were grown in DMEM with 10% fetal bovine serum, and supplemented with Zeocin™ (Invivogen) at 100ug/mL

extract_protocol:
RNA was isolated from transfected cells using Qiagen’s RNeasy Mini Kit (Qiagen 74104).
Paired-end RNA sequencing was performed with the NextSeq 500 Sequencing System from Illumina

treatment_protocol: We cloned the dacA gene (Uniprot:Q8Y5E4) and a catalytically inactivated mutant (D171N) into pcLucF (Plasmid #37328) using XbaI and XmaI restriction enzymes. We transfected the resulting product into our cells using Lipofectamine 2000 Transfection Reagent from Thermo Fisher according to the manufacturers protocol

value: HEK-Blue ISG Cells

tag: transfection

value: DLM D171N

tag: transfection time

value: 24 hours

tag: sting status

value: WT


title: Mut_24h_a (WT)


title: 2410 f_ko_chow_rep3

tag: genotype

value: chow


title: Cherry_Negative


title: I11-OC-BF-dent_S17


title: 2413 f_ko_chow_rep4


title: Mut_24h_c (WT)


title: I12-OC-BH-dent_S10


title: 2446 f_wt_hfd_rep1


title: SBA10-2

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with  SBA10_2 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPSM (Reads Per Silo bases per Million reads), and then differently expressed genes were identified by the DEGseq pacSage using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10

extract_protocol:
spleen tissues were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

tag: strain

value: IRC mouse

value: Cells

tag: treatment


title: SBA10-1

description: The group information is prefixed with  SBA10_1 in the column of processed data file

tag: tissue


title: SBA10-3

description: The group information is prefixed with  SBA10_3 in the column of processed data file


title: 2409 f_ko_chow_rep2


title: SBA0-3

description: The group information is prefixed with  SBA0_3 in the column of processed data file


title: DLM_24h_b (WT)

value: DLM


title: 2406 f_ko_chow_rep1


title: DLM_24h_c (WT)


title: 2478 f_wt_chow_rep4


title: SBA0-1

description: The group information is prefixed with  SBA0_1 in the column of processed data file


title: DLM_24h_a (WT)


title: Mut_12h_c (WT)

value: 12 hours


title: SA10-3

description: The group information is prefixed with  SA10_3 in the column of processed data file


title: SA10-2

description: The group information is prefixed with  SA10_2 in the column of processed data file


title: SA10-1

description: The group information is prefixed with  SA10_1 in the column of processed data file


title: Mut_12h_b (WT)


title: Mut_12h_a (WT)


title: SA0-3

description: The group information is prefixed with SA0_3 in the column of processed data file


title: 2421 f_wt_chow_rep2


title: SA0-2

description: The group information is prefixed with  SA0_2 in the column of processed data file


title: SA0-1

description: The group information is prefixed with SA0_1 in the column of processed data file


title: LungBA10-3

description: The group information is prefixed with  LungBA10_3 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPLungM (Reads Per Lungilo bases per Million reads), and then differently expressed genes were identified by the DEGseq pacLungage using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10

extract_protocol:
lung tissues were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.


title: DLM_12h_c (WT)


title: LungBA10-1

description: The group information is prefixed with  LungBA10_1 in the column of processed data file


title: 2517 m_ko_hfd_rep3

source_name: male_MuRF1 -/-_HFD_gastrocnemius muscle

value: male


title: DLM_12h_a (WT)


title: LungBA0-3

description: The group information is prefixed with  LungBA0_3 in the column of processed data file


title: LungBA10-2

description: The group information is prefixed with  LungBA10_2 in the column of processed data file


title: LungBA0-2

description: The group information is prefixed with  LungBA0_2 in the column of processed data file


title: 2479 f_wt_chow_rep3


title: 2511 m_ko_hfd_rep2


title: LungA10-2

description: The group information is prefixed with  LungA10_2 in the column of processed data file


title: SBA0-2

description: The group information is prefixed with  SBA0_2 in the column of processed data file


title: 2510 m_ko_hfd_rep1


title: LungA10-1

description: The group information is prefixed with  LungA10_1 in the column of processed data file


title: control_b (WT)

value: Untransfected


title: control_c (WT)


title: 2515 m_wt_hfd_rep4

source_name: male_wild type_HFD_gastrocnemius muscle


title: LungA0-3

description: The group information is prefixed with LungA0_3 in the column of processed data file


title: LungA0-2

description: The group information is prefixed with  LungA0_2 in the column of processed data file


title: control_a (WT)


title: LungA0-1

description: The group information is prefixed with LungA0_1 in the column of processed data file


title: LBA10-3

description: The group information is prefixed with  LBA10_3 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPLM (Reads Per Lilo bases per Million reads), and then differently expressed genes were identified by the DEGseq pacLage using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10

extract_protocol:
liver tissues were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.


title: Mut_24h_c (KO)

source_name: HEK-Blue™ ISG-KO-STING Cells

value: HEK-Blue ISG-KO-STING Cells

value: KO


title: LBA10-2

description: The group information is prefixed with  LBA10_2 in the column of processed data file


title: 2453 m_wt_hfd_rep2

value: HFD


title: LBA10-1

description: The group information is prefixed with  LBA10_1 in the column of processed data file


title: LungA10-3

description: The group information is prefixed with  LungA10_3 in the column of processed data file


title: LBA0-3

description: The group information is prefixed with  LBA0_3 in the column of processed data file


title: Mut_24h_b (KO)


title: 2452 m_wt_hfd_rep1

value: gastrocnemius muscle


title: LBA0-2

description: The group information is prefixed with  LBA0_2 in the column of processed data file


title: LBA0-1

description: The group information is prefixed with  LBA0_1 in the column of processed data file


title: I24-OC-BE-cart_S8

value: cartilage from OA patient


title: LA10-3

description: The group information is prefixed with  LA10_3 in the column of processed data file


title: Mut_24h_a (KO)


title: LA10-2

description: The group information is prefixed with  LA10_2 in the column of processed data file


title: DLM_12h_b (WT)


title: LA10-1

description: The group information is prefixed with  LA10_1 in the column of processed data file


title: LungBA0-1

description: The group information is prefixed with  LungBA0_1 in the column of processed data file


title: 2594 m_ko_chow_rep4

value: MuRF1 -/-


title: 2428 m_ko_chow_rep2


title: 2559 m_ko_chow_rep3


title: LA0-3

description: The group information is prefixed with LA0_3 in the column of processed data file


title: Mut_12h_b (KO)


title: Mut_12h_a (KO)


title: LA0-2

description: The group information is prefixed with  LA0_2 in the column of processed data file


title: I13-OC-BI-dent_S9

value: Osteoclasts

value: dentine


title: KBA10-3

description: The group information is prefixed with  KBA10_3 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10

extract_protocol:
Kidney tissues were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.


title: LA0-1

description: The group information is prefixed with LA0_1 in the column of processed data file


title: DLM_24h_c (KO)

value: 24 hours


title: KBA10-2

description: The group information is prefixed with  KBA10_2 in the column of processed data file


title: KBA0-3

description: The group information is prefixed with  KBA0_3 in the column of processed data file


title: 2420 m_wt_chow_rep3

value: wild type


title: DLM_24h_b (KO)


title: Mut_12h_c (KO)

value: DLM D171N


title: DLM_24h_a (KO)


title: KBA0-2

description: The group information is prefixed with  KBA0_2 in the column of processed data file

value: IRC mouse


title: 2419 m_wt_chow_rep2

value: chow


title: ATAC_pMEF74_HAT1_KO

description: pMEF74_CKDL200146480-1a-N705_H75T7CCX2_L4

data_processing:
ATAC-seq reads were processed with the ENCODE ATAC-sequencing pipeline version 1.6.1. The reads were aligned to the mouse genome version mm10 using bowtie2.
Peaks were called using MACS2
Differential accessibility analysis was carried out in R using the DiffBind package version 2.14.0.
Genome_build: mm10
Supplementary_files_format_and_content: csv file contains results of differential accessibility analysis in Diffbind
Supplementary_files_format_and_content: bigwig files were generted using ENCODE ATAC-sequencing pipeline version 1.6.1.

source_name: HAT1 KO_pMEFs

extract_protocol:
Primary MEFs isolated from HAT1+/+ (n= 3) and HAT1-/- (n=3) embryos (5*10^4 cells) were collected, resuspended in cold PBS, and centrifuged for 5min at 500g at 4°C. Next, cells were washed with 1mL cold RSB buffer (10mM Tris-HCl, pH 7.4, 10 mM NaCl, and 3mM MgCl2). Cells were centrifuged at 500g for 10 min at 4°C, resuspended in 250µL of freshly made Lysis Buffer (250µL of RSB buffer and 2.5µL of 10% NP-40), and incubated for 5 minutes on ice. Cells were centrifuged at 500g for 10 min at 4°C to isolate the nuclei.
Isolated nuclei were resuspended in 50µL of the transposition mix (22.5µL of H2O, 25µL of the 2X Tagment DNA Buffer, 2.5µL of Tagment DNA Enzyme (both Illumina)) and incubated at 37°C for 30 min. Transposition reactions were purified with the MinElute PCR Purification Kit (Qiagen) and eluted in EB buffer. ATAC-seq libraries were amplified 23 with Nextera primers (Illumina) by PCR and purified with AMPure beads (Beckman Coulter).

tag: strain background

value: HAT1 KO

value: primary mouse embryonic fibroblasts (pMEFs)


title: KA10-1

description: The group information is prefixed with  KA10_1 in the column of processed data file

value: Cells


title: DLM_12h_c (KO)

value: DLM

value: 12 hours


title: KA10-2

description: The group information is prefixed with  KA10_2 in the column of processed data file


title: DLM_12h_b (KO)

value: HEK-Blue ISG-KO-STING Cells

value: KO


title: KA0-3

description: The group information is prefixed with KA0_3 in the column of processed data file


title: KBA0-1

description: The group information is prefixed with  KBA0_1 in the column of processed data file


title: 2434 m_ko_chow_rep1

value: male

value: gastrocnemius muscle


title: KA0-2

description: The group information is prefixed with  KA0_2 in the column of processed data file


title: DLM_12h_a (KO)


title: ATAC_pMEF643B_HAT1_KO

description: pMEF643B_CKDL200146480-1a-N701_H75T7CCX2_L4


title: KA0-1

description: The group information is prefixed with KA0_1 in the column of processed data file


title: HBA10-3

description: The group information is prefixed with  HBA10_3 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPHM (Reads Per Hilo bases per Million reads), and then differently expressed genes were identified by the DEGseq pacHage using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10

extract_protocol:
heart tissues were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.


title: KBA10-1

description: The group information is prefixed with  KBA10_1 in the column of processed data file


title: control_c (KO)

value: Untransfected


title: ATAC_pMEF41_HAT1_KO

description: pMEF41_CKDL200146480-1a-N704_H75T7CCX2_L4


title: HBA10-2

description: The group information is prefixed with  HBA10_2 in the column of processed data file


title: control_b (KO)


title: HBA10-1

description: The group information is prefixed with  HBA10_1 in the column of processed data file


title: 2418 m_wt_chow_rep1


title: HBA0-3

description: The group information is prefixed with  HBA0_3 in the column of processed data file


title: KA10-3

description: The group information is prefixed with  KA10_3 in the column of processed data file


title: 2427 m_wt_chow_rep4


title: ATAC_pMEF643C_HAT1_WT

description: pMEF643C_CKDL200146480-1a-N702_H75T7CCX2_L4

source_name: HAT1 WT_pMEFs

value: HAT1 WT


title: HBA0-1

description: The group information is prefixed with  HBA0_1 in the column of processed data file


title: HA10-3

description: The group information is prefixed with  HA10_3 in the column of processed data file


title: RNAseq RPMI-8226 carfilzomib resistant replicate-3

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

description:
8226.CR.rep3
Human myeloma cell line derived from human plasma cell myeloma and then cultured in carfilzomib until resistant.
Experiment performed on cell lines less than 1 month from resuscitation.

data_processing:
Reads were mapped against the mouse (mm10) or human (hg19) reference genome using the STAR spliced alignment algorithm version 2.5.3a with default parameters and --chimSegmentMin 20, --quantMode GeneCounts
Genome_build: mm10 (GRCm38), hg19 (GRCh37)
Supplementary_files_format_and_content: *counts.tsv: Tab-delimited file of gene expression.

source_name: Cell line derived from human plasma cell myeloma

growth_protocol: All cell lines grown in IMDM media with 20% fetal bovine serum + penicillin-streptomycin + L-glutamine + sodium pyruvate + HEPES. 5TGM1.BR cells cultured in 20nM bortezomib, with media changed twice weekly. 8226.BR cells cultured in 10nM bortezomib, with media changed twice weekly. 8226.CR cells cultured in 10nM carfilzomib, with media changed twice weekly.

extract_protocol:
RNA was extracted from 1x10^7 cells using the Qiagen RNeasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cell lines were removed from drug five days before RNA extraction.

tag: cell line

value: Human myeloma cell line

tag: drug resistance

value: Carfilzomib


title: HBA0-2

description: The group information is prefixed with  HBA0_2 in the column of processed data file


title: ATAC_pMEF34_HAT1_WT

description: pMEF34_CKDL200146480-1a-N703_H75T7CCX2_L4


title: control_a (KO)


title: HA10-2

description: The group information is prefixed with  HA10_2 in the column of processed data file


title: HA0-2

description: The group information is prefixed with  HA0_2 in the column of processed data file


title: HA0-1

description: The group information is prefixed with HA0_1 in the column of processed data file


title: RNAseq RPMI-8226 carfilzomib resistant replicate-2

description:
8226.CR.rep2
Human myeloma cell line derived from human plasma cell myeloma and then cultured in carfilzomib until resistant.
Experiment performed on cell lines less than 1 month from resuscitation.


title: ATAC_imMEF78T_HAT1_WT

data_processing:
The reads were aligned to the mouse genome using bwa version 0.7.12 .
Peaks were called using MACS2 version 2.1.0.
Differential accessiblity analysis was carried out using DESeq2 in R.
Genome_build: mm10
Supplementary_files_format_and_content: csv file contains results of differential accessibility analysis in DESeq2; bigwig files

source_name: HAT1 WT_imMEFs

extract_protocol: Immortalized MEFs isolated from Hat1+/+ (n= 2) and Hat1-/- (n=2) (1*10^5 cells) were collected, nuclei were isolated from the cells and subjected to a transposition reaction  with Tn5 transposase by Novogene. Sequencing libraries were amplified by PCR.

value: immortalized mouse embryonic fibroblasts (imMEFs)


title: ATAC_imMEF41T_HAT1_KO

source_name: HAT1 KO_imMEFs


title: F1_8276OV_T3

description: The group information is prefixed with  F1_8276OV_T3 in the column of processed data file

extract_protocol:
F1 mouse testis were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: F1 mouse testes


title: ATAC_pMEF78_HAT1_WT

description: pMEF78_CKDL200146480-1a-N706_H75T7CCX2_L4


title: F1_8276OV_T1

description: The group information is prefixed with  F1_8276OV_T1 in the column of processed data file

value: IRC mouse


title: RNAseq RPMI-8226 carfilzomib resistant replicate-1

description:
8226.CR.rep1
Human myeloma cell line derived from human plasma cell myeloma and then cultured in carfilzomib until resistant.
Experiment performed on cell lines less than 1 month from resuscitation.


title: F1_8276KD_T3

description: The group information is prefixed with  F1_8276KD_T3 in the column of processed data file


title: F1_8276OV_T2

description: The group information is prefixed with  F1_8276OV_T2 in the column of processed data file


title: RNAseq RPMI-8226 bortezomib resistant replicate-3

description:
8226.BR.rep3
Human myeloma cell line derived from human plasma cell myeloma and then cultured in bortezomib until resistant.
Experiment performed on cell lines less than 1 month from resuscitation.

value: Bortezomib


title: RNAseq RPMI-8226 bortezomib resistant replicate-2

description:
8226.BR.rep2
Human myeloma cell line derived from human plasma cell myeloma and then cultured in bortezomib until resistant.
Experiment performed on cell lines less than 1 month from resuscitation.


title: WT2_me3

data_processing:
Reads were aligned to the mouse genome using BWA version 0.7.12.
Peaks were called using MACS2 version 2.1.0.
Differential accessibility analysis was carried out using the DiffBind package.
Genome_build: mm10
Supplementary_files_format_and_content: csv files contain Diffbind results; bigwig

source_name: HAT1 WT_imMEFs_H3K9me3

extract_protocol:
Immortalized MEFs isolated from HAT1+/+ (n= 2) and HAT1-/- (n=2) embryos were collected, washed with PBS, and resuspended in CiA fixing buffer (50 mM HEPES, pH 8, 1 mM EDTA, 100 mM NaCI, and 0.5 mM EGTA). Cells were fixed with 1% formaldehyde (Thermo Scientific) for 10 min at room temperature. Crosslinking reaction was quenched with 0.125M glycine. Cells were washed with PBS supplemented with 1X of Complete protease inhibitor cocktail (Roche), pelleted and frozen. The pellets were thawed and resuspended 0.8mL of ice-cold TE buffer (pH 8.0) supplemented with 1X of Complete protease inhibitor cocktail (Roche). Human Dbt immortalized myoblasts were 30 added to the mouse cells to be used as a spike-in control. Samples were sonicated with an Active Motif sonicator for 20 min at 30% amplitude using a 30sec on/off cycle. Sheared chromatin samples were adjusted to RIPA 200 mM NaCl buffer (final concentrations of 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, and 200 mM NaCl in 1X TE). Samples were incubated on ice for 5 minutes and centrifuged at 13,000 rpm for 10 min at 4°C. H3K9me2 and H3K9me3 antibodies (Abcam ab1220 and ab8898, respectively) were added to the supernatant, and the samples were incubated at 4°C with rotation for 2 hours. Next, pre-washed with RIPA 200mM NaCl buffer Dynabeads (Invitrogen) were added to the samples for overnight incubation. After incubation, Dynabeads were isolated and washed twice with RIPA buffer (0.1% SDS, 0.1% sodium deoxycholate, and 1% Triton X-100 in 1X TE), twice with RIPA 200 mM NaCl Buffer, twice with LiCl Buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate in 1X TE), and twice with TE buffer. Beads were isolated, sonicated DNA was decrosslinked overnight and eluted using the MinElute PCR kit (Qiagen).
Sequencing libraries were prepared by PCR amplification and sequenced with pairedend reads by Novogene.

tag: chip antibody


title: F1_8276KD_T2

description: The group information is prefixed with  F1_8276KD_T2 in the column of processed data file


title: F1_8276KD_T1

description: The group information is prefixed with  F1_8276KD_T1 in the column of processed data file


title: RNAseq RPMI-8226 bortezomib resistant replicate-1

description:
8226.BR.rep1
Human myeloma cell line derived from human plasma cell myeloma and then cultured in bortezomib until resistant.
Experiment performed on cell lines less than 1 month from resuscitation.


title: ATAC_imMEF643BT_HAT1_KO

value: HAT1 KO


title: F1_5NC_T3

description: The group information is prefixed with  F1_5NC_T3 in the column of processed data file


title: RNAseq RPMI-8226 wild type drug naïve replicate-3

description:
8226.wt.rep3
Human myeloma cell line derived from human plasma cell myeloma.
Experiment performed on cell lines less than 1 month from resuscitation.

value: Naive


title: HA0-3

description: The group information is prefixed with HA0_3 in the column of processed data file

value: Cells


title: F1_5NC_T2

description: The group information is prefixed with  F1_5NC_T2 in the column of processed data file


title: KO2_me3

source_name: HAT1 KO_imMEFs_H3K9me3


title: F1_5NC_T1

description: The group information is prefixed with  F1_5NC_T1 in the column of processed data file


title: 2400 f_wt_chow_rep1

value: female

value: wild type

value: chow


title: RNAseq RPMI-8226 wild type drug naïve replicate-2

description:
8226.wt.rep2
Human myeloma cell line derived from human plasma cell myeloma.
Experiment performed on cell lines less than 1 month from resuscitation.


title: F1_3NC_T2

description: The group information is prefixed with  F1_3NC_T2 in the column of processed data file


title: 2464 m_wt_hfd_rep3

value: HFD


title: F1_3NC_T3

description: The group information is prefixed with F1_3NC_T3 in the column of processed data file


title: 2462 f_wt_hfd_rep3


title: RNAseq RPMI-8226 wild type drug naïve replicate-1

description:
8226.wt.rep1
Human myeloma cell line derived from human plasma cell myeloma.
Experiment performed on cell lines less than 1 month from resuscitation.


title: WT1_me3


title: KO1_me3


title: F1_3NC_T1

description: The group information is prefixed with F1_3NC_T1 in the column of processed data file


title: ATAC_imMEF643CT_HAT1_WT


title: miRNA-seq_exosomes from isochronic culture of Cord Blood 10

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

description: isochronic culture: umbilical cord blood 10

data_processing:
Raw reads were trimmed and mapped to Hg38 miRNAome
A match score of 1, mismath cost 2, indel linear gap cost 3/gap
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files, includes raw count values for each sample

source_name: mobilized peripheral blood

growth_protocol: The cells were cultured up to one month in RPMI 1640 supplemented with 10% FCS, glutamine and 0.5 µM β-mercaptoethanol. 50% percent of media were replaced every 4 days.

extract_protocol:
Total RNA was isolated from exosomes or cells using the miRCURY RNA Isolation Kit; small and large RNAa were fractionated with the RNeasy MinElute Cleanup Kit, both according to manufacturer’s recommended specifications (Qiagen)
Libraries were prepared using NEBNext Multiplex Small RNA Sample Prep Set for Illumina – Set 1 (NEB), according to the following protocol: (1) ligation of the 3´ SR Adaptor, (2) hybridization of the reverse transcription primer, (3) ligation of the 5´ SR Adaptor, (4) reverse transcription for first strand cDNA synthesis and (5) PCR enrichment

treatment_protocol: Mobilized peripheral blood (MPB) from old donors were cultured with MPB from yound donors or cord blood in a non-contact (transwell) system with 0.4 μm membrane (BD Falcon, ThermoFisher)

tag: cellular component

value: exosomes

value: mobilized peripheral blood

tag: culture type

value: isochronic culture:umbilical cord blood 10

tag: tissue source

value: umbilical cord blood

tag: phenotype

value: young


title: F0_8276OV_T2

description: The group information is prefixed with  F0_8276OV_T2 in the column of processed data file

extract_protocol:
F0 mouse testis were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: F0 mouse testes


title: WT2_me2

source_name: HAT1 WT_imMEFs_H3K9me2

value: HAT1 WT

value: immortalized mouse embryonic fibroblasts (imMEFs)


title: F0_8276OV_T3

description: The group information is prefixed with  F0_8276OV_T3 in the column of processed data file

value: IRC mouse


title: WT1_me2


title: miRNA-seq_exosomes from isochronic culture of Young 2

description: isochronic culture: young donor 2

value: isochronic culture:young donor 2

value: young MPB


title: F0_8276KD_T2

description: The group information is prefixed with  F0_8276KD_T2 in the column of processed data file


title: KO2_me2

source_name: HAT1 KO_imMEFs_H3K9me2

value: HAT1 KO


title: F0_8276KD_T1

description: The group information is prefixed with  F0_8276KD_T1 in the column of processed data file


title: F0_5NC_T3

description: The group information is prefixed with  F0_5NC_T3 in the column of processed data file


title: KO1_me2


title: F0_5NC_T2

description: The group information is prefixed with  F0_5NC_T2 in the column of processed data file


title: F0_5NC_T1

description: The group information is prefixed with  F0_5NC_T1 in the column of processed data file


title: F0_3NC_T2

description: The group information is prefixed with  F0_3NC_T2 in the column of processed data file


title: F0_3NC_T3

description: The group information is prefixed with F0_3NC_T3 in the column of processed data file


title: e6-bcf-32-mut-li-14809

city: Zürich

first: Peter

last: Leary

address: Winterthurerstrasse 190

department: Functional Genomics Center Zürich

country: Switzerland

institute: ETH Zürich

data_processing:
bcl2fastq
MultiQC
fastp
STAR
featureCounts
Genome_build: Grcm38

source_name: Liver Tissue

extract_protocol:
Mice tissue sections were frozen until RNA extraction was performed. RNA was extracted using Trizol reagent (Thermo Fisher) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

tag: age

value: 15 months

tag: Sex


title: F0_3NC_T1

description: The group information is prefixed with F0_3NC_T1 in the column of processed data file


title: e6-bcf-29-mut-li-14809

value: female


title: miRNA-seq_exosomes from heterochronic culture of Aged 3 & Cord Blood 10

description: heterochronic culture: aged donor 3 + umbilical cord blood 10

source_name: mobilized peripheral blood;umbilical cord blood

value: heterochronic culture:aged donor 3 + umbilical cord blood 10

value: aged MPB

value: restored


title: miRNA-seq_exosomes from isochronic culture of Aged 3

description: isochronic culture: aged donor 3

value: exosomes

value: mobilized peripheral blood

value: isochronic culture:aged donor 3

value: aged


title: 8276OV_2

description: The group information is prefixed with  C18_8276OV_2 in the column of processed data file

extract_protocol:
C18-4  cells were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: C18-4 cells


title: F0_8276OV_T1

description: The group information is prefixed with  F0_8276OV_T1 in the column of processed data file

value: F0 mouse testes


title: miRNA-seq_exosomes from heterochronic culture of Aged 3 & Young 2

description: heterochronic culture: aged donor 3 + young donor 2

value: heterochronic culture:aged donor 3 + young donor 2


title: e6-bcf-28-wtcr-li-14809

value: WT


title: F0_8276KD_T3

description: The group information is prefixed with  F0_8276KD_T3 in the column of processed data file

value: IRC mouse


title: e6-bcf-24-wtcr-li-14809


title: 8276KD_3

description: The group information is prefixed with  C18_8276KD_3 in the column of processed data file


title: 8276OV_1

description: The group information is prefixed with  C18_8276OV_1 in the column of processed data file


title: 8276KD_2

description: The group information is prefixed with  C18_8276KD_2 in the column of processed data file


title: miRNA-seq_exosomes from isochronic culture of Aged 2

description: isochronic culture: aged donor 2

value: isochronic culture:aged donor 2


title: 8276KD_1

description: The group information is prefixed with  C18_8276KD_1 in the column of processed data file


title: 5NC_3

description: The group information is prefixed with  C18_5NC_3 in the column of processed data file


title: miRNA-seq_exosomes from isochronic culture of Young 1

description: isochronic culture: young donor 1

value: isochronic culture:young donor 1

value: young MPB

value: young


title: 5NC_2

description: The group information is prefixed with  C18_5NC_2 in the column of processed data file


title: miRNA-seq_exosomes from isochronic culture of Cord Blood 9

description: isochronic culture: umbilical cord blood 9

source_name: umbilical cord blood

value: umbilical cord blood

value: isochronic culture:umbilical cord blood 9


title: e6-bcf-33-wtcr-li-14809

value: Liver

value: 15 months

value: female


title: miRNA-seq_exosomes from heterochronic culture of Aged 2 & Young 1

description: heterochronic culture: aged donor 2 + young donor 1

value: exosomes

value: mobilized peripheral blood

value: heterochronic culture:aged donor 2 + young donor 1

value: aged MPB

value: restored


title: e6-bcf-22-mut-li-14809


title: e6-bcf-21-wtcr-li-14809


title: 3NC_3

description: The group information is prefixed with C18_3NC_3 in the column of processed data file

value: C18-4 cells


title: 8276OV_3

description: The group information is prefixed with  C18_8276OV_3 in the column of processed data file


title: 3NC_2

description: The group information is prefixed with  C18_3NC_2 in the column of processed data file


title: 3NC_1

description: The group information is prefixed with C18_3NC_1 in the column of processed data file


title: miRNA-seq_isochronic culture of Cord Blood 10

description: isochronic culture: umbilical cord blood 10

value: cellular

value: isochronic culture:umbilical cord blood 10


title: e6-bcf-18-mut-li-14809


title: miRNA-seq_isochronic culture of Cord Blood 9


title: miRNA-seq_isochronic culture of Young 1

description: isochronic culture: young donor 1


title: F1_5251OV_T2

description: The group information is prefixed with  F1_5251OV_T2 in the column of processed data file

value: IRC mouse

value: Testis

tag: genotype/variation

value: lncRNA5251 overexpression


title: F1_5251OV_T3

description: The group information is prefixed with  F1_5251OV_T3 in the column of processed data file


title: F1_5251OV_T1

description: The group information is prefixed with  F1_5251OV_T1 in the column of processed data file


title: F1_5251KD_T2

description: The group information is prefixed with  F1_5251KD_T2 in the column of processed data file

value: lncRNA5251 knockdown


title: miRNA-seq_exosomes from heterochronic culture of Aged 2 & Cord Blood  10

description: heterochronic culture: aged donor 2 + umbilical cord blood 9

source_name: mobilized peripheral blood; umbilical cord blood

value: heterochronic culture:aged donor 2 + umbilical cord blood 9


title: e6-bcf-15-mut-li-14809


title: miRNA-seq_isochronic culture of Aged 3

description: isochronic culture: aged donor 3

value: isochronic culture:aged donor 3

value: aged


title: e6-bcf-23-mut-li-14809

value: Liver

value: 15 months


title: F1_5251KD_T1

description: The group information is prefixed with  F1_5251KD_T1 in the column of processed data file


title: e6-bcf-13-wtcr-li-14809

value: WT

value: female


title: F1_5NC_T2

description: The group information is prefixed with  F1_5NC_T2 in the column of processed data file


title: e6-bcf-11-mut-li-14809


title: 5NC_1

description: The group information is prefixed with  C18_5NC_1 in the column of processed data file


title: miRNA-seq_heterochronic culture of Aged 3 & Cord Blood 10

description: heterochronic culture: aged donor 3 + umbilical cord blood 10

value: mobilized peripheral blood

value: heterochronic culture:aged donor 3 + umbilical cord blood 10


title: F1_5NC_T1

description: The group information is prefixed with  F1_5NC_T1 in the column of processed data file


title: miRNA-seq_heterochronic culture of Aged 3 & Young 2

description: heterochronic culture: aged donor 3 + young donor 2

value: heterochronic culture:aged donor 3 + young donor 2

value: aged MPB

value: restored


title: e6-bcf-07-mut-li-14809


title: F1_3NC_T3

description: The group information is prefixed with F1_3NC_T3 in the column of processed data file


title: F1_3NC_T2

description: The group information is prefixed with  F1_3NC_T2 in the column of processed data file


title: miRNA-seq_isochronic culture of Young 2

description: isochronic culture: young donor 2

value: cellular

value: isochronic culture:young donor 2

value: young MPB

value: young


title: miRNA-seq_isochronic culture of Aged 2

description: isochronic culture: aged donor 2

value: isochronic culture:aged donor 2


title: e6-bcf-06-wtcr-li-14809


title: miRNA-seq_heterochronic culture of Aged 2 & Cord Blood  10

value: heterochronic culture:aged donor 2 + umbilical cord blood 9


title: e6-bcf-05-mut-li-14809


title: F0_5251OV_T2

description: The group information is prefixed with  F0_5251OV_T2 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression

value: IRC mouse

value: Testis

value: lncRNA5251 overexpression


title: F0_5251OV_T3

description: The group information is prefixed with  F0_5251OV_T3 in the column of processed data file


title: F0_5251KD_T2

description: The group information is prefixed with  F0_5251KD_T2 in the column of processed data file

value: lncRNA5251 knockdown


title: F0_5251OV_T1

description: The group information is prefixed with  F0_5251OV_T1 in the column of processed data file


title: F0_5251KD_T3

description: The group information is prefixed with  F0_5251KD_T3 in the column of processed data file


title: F0_5251KD_T1

description: The group information is prefixed with  F0_5251KD_T1 in the column of processed data file


title: e6-bcf-14-wtcr-li-14809

value: Liver

value: WT

value: 15 months


title: e6-bcf-04-wtcr-li-14809

value: female


title: isochronic culture of Young 3

description: isochronic culture of Young 3

data_processing:
STAR 2.6.1 aligned to HG38
Quantified to Ensembl human genome 92
Normalized via Log2 Counts per million with offset of 1
Lognormal shrinkage was used to remove batch effect between runs
Counts with a maximum of less than 2 were filtered out for a normal distribution
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files, includes RPKM values for each sample

extract_protocol:
Total RNA extraction was performed according to manufacturer’s protocols with the RNeasy Mini Kit (Qiagen). Poly A RNA was purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA).
Libraries were prepared using the NEB Ultra II Library Preparation Kit and NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set 1) (New England BioLabs) following the manufacturer’s protocol.

treatment_protocol: Mobilized peripheral blood (MPB) from old and yound donors were cultured in non-contact (transwell system) with 0.4 μm membrane (BD Falcon, ThermoFisher). The inner wells contained 10e7 young MPB and the same number of old MPBs in the outer wells.

tag: culture method

value: isochronic culture of Young 3

value: mobilized peripheral blood


title: e6-bcf-03-mut-li-14809


title: F1_5NC_T3

description: The group information is prefixed with  F1_5NC_T3 in the column of processed data file


title: F0_5NC_T3

description: The group information is prefixed with  F0_5NC_T3 in the column of processed data file