title: TS105_05_Fujioka-MED1

city: Manchester

first: Tim

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

country: United Kingdom

institute: Cancer Research UK

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) using BWA-MEM version 0.7.15 (Li and Durbin 2009). Reads were filtered using Samtools (version 0.1.9) (Li et al., 2009) to keep only reads that mapped to standard chromosomes and Bedtools version 2.25.0 (Quinian and Hall, 2010) to remove reads mapped to blacklisted regions defined by ENCODE (http://mitra.stanford.edu/kundaje). Peaks were called with Model-based Analysis of ChIP-Seq version 2 (MACS2) using the following parameters -f BAMPE, --keep-dup 5 to keep only paired-end reads with up to 5 duplicates (Zhang et al. 2008). Annotation of peaks was performed with Homer version 4.10 (Heinz et al. 2010).
Assembly: GRCh38

source_name: Fujioka Cells

growth_protocol: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).

extract_protocol:
10^8 cells were used for each precipitation using the method described by Lee et al. (2006). Briefly, cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature before the reaction was quenched with 0.125M glycine. Cell pellets were washed twice with PBS and nuclear lysates sonicated for 6 cycles using a Bioruptor® Pico (Diagenode, Liege, Belgium). 10μg of antibody bound to 100μl of magnetic beads (Dynabeads Protein G, Invitrogen, Carlsbad, CA) was added to each sample and immunoprecipitation performed overnight on a rotator at 4°C and 20rpm. After five washes with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl), chromatin IP-bound fractions were extracted by incubating for 15 min at 65°C with elution buffer (50mM TrisHCl pH8, 10mM EDTA, 1% SDS). Crosslinking was then reversed by incubation at 65°C for 6 hours. RNaseA (1mg/ml) and proteinase K (20mg/ml) were added to eliminate RNA and protein from the samples. DNA was extracted using phenol:chloroform:isoamyl alcohol and precipitated by adding 2 volumes of ice-cold 100% ethanol, glycogen (20μg/μl), 200mM NaCl and freezing at -80°C for at least 1hr. Pellets were washed with 70% ethanol and eluted in 50μl 10mM TrisHCl pH8.0.
Libraries were prepared for sequencing using a Microplex Library Preparation Kit (Diagenode). 200-800bp fragments were selected using AMPure beads (Beckman Coulter, Brea, CA) and quantified by qPCR with a KAPA Library Quantification Kit (Kapa Biosystems, Basel, Switzerland). Sequencing was performed using a NextSeq desktop sequencing system (Illumina) with 75bp, paired-end high output generating 65-80M reads per sample.

value: primary AML

tag: chip antibody

value: anti-MED1 (A300-793A, Bethyl, Cambridge, UK; 1μg per ChIP)


title: atac_A9B9 female and male

status: Public on Jan 21 2025

type: SRA

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

description: Control Male

library_source: genomic

data_processing:
FASTQ files were produced with 10x cellranger-atac mkfastq.
Alignments were generated with refdata-cellranger-arc-GRCh38-2020-A-2.0.0 and cellranger-atac count with default paramters. 10x fragment files were converted to peak count matrices using ArchR [release_1.0.1]. The open chromatin peaks were first identified in ArchR using MACS2 (cutOff=0.1) in each of the four pseudobulk replicates generated from each broad cell-type (n=7) and cluster (n=38). Open chromatin peaks identified in atleast two pseudobulk replicates were retained for each cell-type and cluster. We separately merged peaks across cell-types and across clusters using ArchR iterative overlap peak merging and removal (IPR) to generate reproducible, non-overlapping, fixed-with (501bp) chromatin cis-regulatory elements (cCREs). Per cell Tn5 insertion counts were computed using cCREs identified at broad cell-type and cluster levels. For cluster level peak count matrix, only cCREs present in atleast 0.5% of cells were retained.
Assembly: GRCh38

molecule: genomic DNA

organism: Homo sapiens

source_name: Brain BA9

extract_protocol:
Frozen brain tissue sections were dounced for 5mins in the lysis buffer. The lysis suspension was homogeneously mixed by pipetting up and down 10-15 times following which only 80% of the lysis solution was mixed with 5ml of wash buffer to make diluted nuclei suspensions. The samples were mixed and passed through a 30-um cell strainer to remove cellular debris and washed twice in 10ml wash buffer. Next, Optiprep cushion was created followed by gradient centrifugation for 30mins at 10,000g and resuspended in 1ml wash buffer. Nuclei were counted with Hoescht 33342 (1:2000) three times (average was used) with Cell countess (Olumpys). Nuclei were then spun down at 500g for 5mins and diluted in 1xNB (10x Genomics)_x005F_x000D_ to obtain a final concentration of 3080 nuclei/ul.
Equal volume of nuclei suspensions from a male and female subject (either from case or control) were pooled together to obtain a final concentration of 3080 nuclei/ul. The combined nuclei were loaded in one of the lanes of 10x microfluidic chip. Each microfluidic chip was loaded with at least four multiplexed libraries representing both cases and controls. Single-cell capture and library preparations were done using 10x Genomics Chromium Single Cell v1.1 reagents following the protocol outlined by the user guide [https://www.10xgenomics.com/support/single-cell-atac/documentation/steps/library-prep/chromium-single-cell-atac-reagent-kits-user-guide-v-1-1-chemistry]. Cell Ranger atac v2.0 was used for alignment against the GRCh38 reference available on the 10x Genomics website (refdata-cellranger-arc-GRCh38-2020-A-2.0.0).
10x snATAC-seq

tag: tissue

value: Brain BA9

tag: treatment

value: Control


title: Spleen, sgRNA1, replicate4 [amplicon]

city: Beijing

first: zhanzhao

last: liu

address: No. 38, Xueyuan Road

country: China

institute: peking university

data_processing:
The sequencing reads were analyzed by CRISPResso2
Experimentalparameter: FASTQ files for analysis(.fastq or .fastq.gz), Reference amplicon sequence, sgRNA used, quantification window size, quantification window center, Experiment name
code: CRISPResso \ --fastq_r1 base_editor.fastq.gz \ -a amplicon sequence \ -g sgRNA sequence \ -w 20 \ -wc -10 \ --base_editor_output \ --write_cleaned_report \ --place_report_in_output_folder
Assembly: mm10
Supplementary files format and content: Nucleotide_percentage_table
Library strategy: Amplicon-seq

organism: Mus musculus

source_name: Spleen

extract_protocol:
Genomic DNA was extracted from tissues using TIANamp Genomic DNA Kit (DP304, Tiangen, China)
The sgRNA-targeted loci were amplified using Taq PCR MasterMix (KT211, Tiangen, China) and purified by TIANgel Purification Kit (DP219, TIANGEN).

value: Spleen

tag: genotype

value: WT

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA1


title: TS112_7_RNA_500 [re-analyzed]

middle: C

library_source: transcriptomic

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) and gene annotated with their corresponding GTF file (GENCODE GRCh38 release 25) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts (Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21). DEseq2 was used to perform differential gene expression analysis and calculate FPKM (fragments per kilobase of transcript per million mapped reads) values for each gene (Love et al., 2014).
Assembly: GRCh38
Supplementary files format and content: bigwig

molecule: total RNA

source_name: Primary AML

growth_protocol: Cryopreserved leukemic blast cells from bone marrow or blood of patients at presentation were thawed and co-cultured on MS5 stromal cells, as described (van Gosliga et al., 2007) in α-MEM medium (Life Technologies, Carlsbad, CA) supplemented with 12.5% heat-inactivated FBS (Life Technologies), 12.5% heat-inactivated horse serum (Life Technologies), 2 mM L-glutamine (Sigma-Aldrich, St. Louis, MO), 10U/ml penicillin and 10μg/ml streptomycin (Sigma-Aldrich), 57.2 μM β-mercaptoethanol (Sigma- Aldrich), 1 μM hydrocortisone (Sigma-Aldrich), 500nM StemRegenin1 and 500nM UM729 (Stem cell Technologies, Vancouver, BC) to prevent differentiation of acute myeloid leukemia (AML) cells in culture (Pabst et al., 2014) and IL-3, IL-6, SCF, Flt3-L, G-CSF, and TPO (all at 20 ng/ml; PeproTech, London, UK).

extract_protocol:
Total RNA was extracted from 5x105  AML patient leukemic blasts using QIAshredder spin columns and a RNeasy Plus Micro kit (QIAGEN). Extracted RNA was DNAse treated using the TURBO DNA-free Kit (Ambion, Austin, TX) according to the manufacturer’s instructions. Before sequencing, RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies). RNA-seq libraries were prepared using either the Truseq Stranded Total RNA kit (Illumina, San Diego, CA) or Lexogen Quantseq 3’ (Lexogen, Vienna, Austria) according to the manufacturer’s instructions. The Truseq kit includes a ribo-depletion step to eliminate ribosomal RNAs and it captures coding RNA plus multiple forms of non-coding RNA while the Quantseq is designed for 3’ end sequencing of polyA RNA.
Libraries were quantified by quantitative PCR using a Kapa Library Quantification Kit for Illumina sequencing platforms (Roche). Libraries were then barcoded, pooled and sequenced using either a Novaseq6000 or a NextSeq500 desktop sequencing system (Illumina). A single run (400 million reads) of 75 bp paired-end sequencing produced a mean of 49.4-54.72 million reads per sample in the case of Truseq libraries or 100bp single-end with a mean of 17 million reads per sample in the case of Quantseq 3’ libraries.

tag: cell type

value: Primary AML

tag: culture condition

value: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).


title: TS112_8_RNA_575 [re-analyzed]


title: Spleen, sgRNA1, replicate3 [amplicon]


title: G9a-iKO-Veh1

city: Houston

first: Hui-Lin

last: Pan

state: TX

address: 1515 Holcombe Blvd

department: Anesthesiology and Perioperative Medicine

country: USA

institute: University of Texas MD Anderson Cancer Center

data_processing:
Reads were mapped to mouse genome GRCm39 (mm39) using Hisat2 v2.2.1
The mapped files were converted and sorted into bam files using samtools v1.19.2
Then reads abundant of each gene were calculated using FeatureCounts v2.0.6
Estimation of fold change and differentially expressed genes (DEGs) were analyzed using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FeatureCounts values for each Sample.

source_name: Dorsal root ganglion

extract_protocol:
Dorsal root ganglia (DRG) were removed, flash frozen on liquid nitrogen, and total RNA was extracted using RNeasy Plus Universal Mini Kit (Qiagen, #73404)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and G9aiKO mice were treated with vehicle or CFA in the left paw, 14 days later tissues collected.

value: Dorsal root ganglion

value: G9a conditional knockout

value: Vehicle


title: atac_A26B26 female and male

description: Case Male

value: Case


title: N1

city: PITTSBURGH

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

description: UDI-P 111

data_processing:
Stranded reads were checked for quality using FastQC (v0.11.5) and they were trimmed for quality and adapters using Cutadapt (v1.12).
Each sample was mapped to the Homo Sapien Ensembl reference genome GRCh38  or Mus Musculus Ensembl reference genome GRCm39, the appropriate reference was used based on organism, using the fast alignment tool HISAT2 v2.1.0 with default settings
Genes in GRCh38  or GRCm39 were quantified used HTSeq v0.9.0 using default settings.  The appropriate reference was used based on organism
edgeR, an R Bioconductor package, with R version 4.2.1, was used for differential gene analysis comparing various sample groups
Assembly: GRCh38 and GRCm39
Supplementary files format and content: HT-Seq Raw Counts in tab-delimited text file

source_name: Non-lesion Skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared usingRoche Kapa RNA Hyper prep with Riboerase (HMR) for Illumina platforms, version KR1351 – v4.21 (Cat. #: 8098140702)

treatment_protocol: Tamoxifen ip injections induced GPX4 knockdown in select keratin-14 expressing epidermal keratinocytes.

value: Non-lesion Skin

tag: disease

value: Psoriasis

tag: patient

value: patient 1


title: TS112_5_RNA_287 [re-analyzed]


title: atac_A1B1 female and male

description: Case Male


title: Spleen, sgRNA1, replicate1 [amplicon]


title: WT-CFA2

value: Wild type

value: CFA


title: atac_A4B4 female and male

description: Control Male


title: Liver, sgRNA1, replicate4 [amplicon]

source_name: Liver

value: Liver


title: WT-CFA1


title: TS112_4_RNA_221 [re-analyzed]


title: WT-Veh2


title: TL13_HEK_500_60m_LRP_IP_repB

city: Boston

first: Mary

middle: T

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
Mitoribosome-associated RNA
TL13_LRP_IP_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_60m_LRP_IP_B

data_processing:
Fastq files shared by the sequencing facility were concatenated to combine data across the sequencer lanes. The adapter sequences were trimmed from both of the paired-end reads using Cutadapt v2.5 (Martin. EMBnet, 2011). Three more nucleotides were trimmed from the 5’ end of the fragment to remove template switch bases, and five more  from the 3’ end to remove mismatches associated with random hexamer priming that result from the SMARTer Stranded library preparation.
Read alignment was done using STAR 2.7.3 to cell line specific genomic reference sequences with different parameters for experiments with high and low 4sU treatment. For 500 uM 4sU experiments, parameters were --outFilterMismatchNmax 90 --outFilterMismatchNoverLmax 0.3 --outFilterMatchNminOverLread 0.2 --outFilterScoreMinOverLread 0.2. For 50 uM 4sU experiment, parameters were --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNminOverLread 0.66 --outFilterScoreMinOverLread 0.66 --outFilterMultimapScoreRange 0.
Allignment files (.bam) were used as input to the software GRAND-SLAM which uses a statistical approach to determine T to C conversion rates. We further modified these rates according to the details in the publication associated with this repository and retrieved the fraction of new RNA at each time point from the GRAND-SLAM output.
Assembly: hg38, updated with variants for each cell line based on sequencing data collected here (see associated publication for details).
Supplementary files format and content: Processed data files for TimeLapse-Seq experiments are tab separated files that contain the GRAND-SLAM outputs including fraction new RNA, read counts, confidence intervals, etc as described in the GRAND-SLAM documentation. Names of file indicates the experiment ('TLX_*'), gene set (MT: mitochondrial, Nuc: nuclear, MTdsrRNA: mitochondrial but the rRNA has been downsampled), parameters used for alignment (these vary based on the amount of 4sU used and whether mitochondrial or nuclear transcripts are being interrogated). lenient_modeAll indicates GrandSlam parameters, and 'Pc***' indicates the method used to determine the T to C conversion rate, if any. These fractions new do not contain any correction for cell doubling time.
Supplementary files format and content: Processed data files for RNA-seq and ribosome profiling (as well as the TL5 experiment) are tab separated files that contain feature counts as descibed in the file name (RPKM, tpm) for each gene in each sample. For K562 experiments, *all_tpm* indicates transcripts per million of ALL mapped transcripts; *mito_tpm* indicates transcripts per million of mito-encoded mapped transcripts.
Library strategy: TimeLapse-seq

extract_protocol:
After labeling, cells were quickly washed in ice cold PBS before being scraped in mt-polysome lysis buffer. Mitoribosomes were isolated after sucrose gradient fractionation and immunoprecipitated with an MRPL12 antibody. Extracted RNA was treated by TimeLapse-chemistry (0.1M sodium acetate pH 5.2, 4mM EDTA, 5.2% 2,2,2-trifluoroethylamine, and 10mM sodium periodate at 45°C for 1 hour).
SMARTer RNA unique dual index kits (Takara)

tag: cell line

value: LRPPRC KO

tag: growth condition

value: DMEM supplemented with 20 μg/mL of uridine, 3 mM sodium formate, 10% FBS, 1 mM GlutaMAX (Thermo Fisher Scientific) and 1 mM sodium pyruvate

value: 500 uM 4sU for 60 min


title: TS112_3_RNA_200 [re-analyzed]


title: TL13_HEK_500_60m_LRP_IP_repA

description:
Mitoribosome-associated RNA
TL13_LRP_IP_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_60m_LRP_IP_A


title: TS112_2_RNA_189 [re-analyzed]


title: Liver, sgRNA1, replicate3 [amplicon]

value: WT


title: G9a-iKO-Veh2


title: WT-Veh1


title: ST-3

first: Zhiyuan

last: An

address: No.8 gongti south Road

department: Medical Research Center

institute: Beijing Chaoyang Hospital

data_processing:
The data that has undergone quality control will be processed through Cutadapt software to remove connector data or short segments in Read and generate Trimmed Data.
Compare Trimmed Data to the reference genome using Hisat2 software to determine if the alignment results can be used for subsequent analysis.
Use StringTie software to calculate transcription abundance by comparing the results to known transcriptomes.
Calculate the expression level using Ballgown software, expressed in units of FPKM. The expression threshold for genes or transcripts is FPKM ≥ 0.5. Genes or transcripts with an average FPKM exceeding 0.5 in each group are considered to be expressed in the group and subjected to statistical analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited files include FPKM values for each sample

growth_protocol: Mouse macrophage cell line RAW264.7 (ATCC®TIB-71) were obtained from American Type Culture Collection (ATCC).RAW264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA immunoprecipitation (RIP) was performed using the EZ-Magna RIP Kit (Millipore, Burlington, MA, United States) in accordance with the manufacturer’s protocol. In brief, lysis buffer was used to dissolve RAW264.7 cells to prepare a lysate. A monoclonal antibody against NLRP3 was then added to the lysate and then co-precipitated with protein A/G magnetic beads overnight. The next day, protein was removed with protease K and total RNA was extracted using a mixture of phenol, chloroform, and isoamyl alcohol at 125:24:1 and pH 4.3.
The library construction was completed according to the instructions of the reagent kit. Include, mRNA in total RNA enrichment using NEB Next ® Poly (A) mRNA Magnetic Isolation Module reagent or RiboZero Magnetic Gold Kit was used to remove rRNA. Afterwards, the library was constructed using KAPA Stranded RNA Seq Library Prep Kit (Illumina). Briefly, the RNA products obtained from mRNA enrichment (or rRNA removal) treatment are reverse transcribed to generate first stranded cDNA, which is then added to dUTP to synthesize double stranded cDNA. Each polymerase acts to repair the end of the double stranded cDNA and adds A, followed by ligases connecting to Illumina specific ligands, and finally PCR amplification and purification to obtain the final RNA sequencing library.

treatment_protocol: Salmonella typhimurium infection in RAW264.7 cells for 4 hours.

tag: rip antibody

value: NLRP3 (AdipoGen, AG-20B-0014)

value: Mouse monocyte macrophage leukemia cells

value: Infection with Salmonella typhimurium


title: TL13_HEK_500_30m_LRP_IP_repB

description:
Mitoribosome-associated RNA
TL13_LRP_IP_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_30m_LRP_IP_B

value: 500 uM 4sU for 30 min


title: Liver, sgRNA1, replicate2 [amplicon]

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA1


title: TS112_1_RNA_77  [re-analyzed]

value: Primary AML

value: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).


title: Spleen, sgRNA1, replicate2 [amplicon]

value: Spleen


title: TL13_HEK_500_30m_LRP_IP_repA

description:
Mitoribosome-associated RNA
TL13_LRP_IP_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_30m_LRP_IP_A


title: TS108_4_MeDIP_500 [re-analyzed]

data_processing:
MEDIPS (Lienhard et al., 2014) software was used to calculate counts, RPKM (reads per kilobase of transcript per million mapped reads) and RMS (raw methylation score) values and to perform differential methylated region analysis.
Assembly: GRCh38
Supplementary files format and content: bigwig

extract_protocol:
Genomic DNA for human methylated DNA immunoprecipitation (MeDIP) was isolated from AML patient blasts using the QIAamp DNA blood Mini Kit (QIAGEN). gDNA samples were diluted in GenDNA TE buffer (Diagenode) to reach a concentration of 100ng/μl and 100μl were sheared in 0.65ml Bioruptor Microtubes (Diagenode). gDNA samples were sonicated for 13 min at high, 30 sec ON, 30 sec OFF settings to 200–300 bp using the Diagenode’s Bioruptor platform and the size distribution was confirmed through gel electrophoresis. Barcoded adaptors for Illumina sequencing were added to 1μg of fragmented genomic DNA per experiment, using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer’s instructions. This protocol was stopped after end repairing, adaptor ligation and clean-up (and before any amplification steps), and the adaptor ligated fragmented DNA was then used for hydroxy-methylated DNA pulldown. This was performed using the MagMeDIP kit (Diagenode) following the manufacturer’s instructions. Briefly, magnetic beads were washed twice with ice cold bead wash buffer and incubated overnight with the denaturated adaptor-ligated DNA and the 5-methylcytosine monoclonal antibody 33D3 (C15200081, Diagenode). The day after, DNA IP samples were washed three times in ice-cold MagWash Buffer-1 and once in ice-cold MagWash Buffer-2 and DNA was isolated using the IPure kit v2 (C03010014, Diagenode) following the manufacturer’s instructions. Purified methylated genomic DNA was then further processed with NEBNext Ultra II DNA Library Prep Kit for Illumina at the step of PCR enrichment of adaptor-ligated DNA, per the manufacturer’s instructions, continuing with the entire protocol to prepare libraries for Illumina sequencing. Before PCR amplification, DNA concentration was calculated using the Qubit dsDNA HS Assay kit (Life Technologies) to determine the number of cycles required for PCR enrichment.
Libraries were then barcoded, pooled and sequenced using a NextSeq500 desktop sequencing system (Illumina) with 75- bp, paired-end high output generating 73–90 million reads per sample. Reads were aligned to the human genome (hg38) using BWA-MEM version 0.7.15 (Li and Durbin, 2009).

tag: medip antibody


title: ST-1


title: Heart, sgRNA1, replicate4 [amplicon]

source_name: Heart

value: Heart


title: Liver, sgRNA1, replicate1 [amplicon]


title: TS112_6_RNA_35 [re-analyzed]


title: ST-2


title: TS108_6_INPUT_500 [re-analyzed]

value: none; input


title: TL13_HEK_500_0m_LRP_IP_repB

description:
Mitoribosome-associated RNA
TL13_LRP_IP_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_0m_LRP_IP_B

value: 0 uM 4sU


title: UN-3

treatment_protocol: Uninfected

value: Uninfected normal cells


title: Heart, sgRNA1, replicate3 [amplicon]


title: Heart, sgRNA1, replicate2 [amplicon]


title: TS108_3_MeDIP_352 [re-analyzed]

value: 5-methylcytosine monoclonal antibody 33D3 (C15200081, Diagenode)


title: TL13_HEK_500_60m_LRP_tot_repB

description:
rRNA-depleted total RNA
TL13_LRP_tot_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_60m_LRP_tot_B

extract_protocol:
Labeled cells were washed in ice cold PBS  before being directly scraped in Trizol LS. RNA extraction was performed using Trizol LS and treated by TimeLapse-chemistry (0.1M sodium acetate pH 5.2, 4mM EDTA, 5.2% 2,2,2-trifluoroethylamine, and 10mM sodium periodate at 45°C for 1 hour).
SMARTer RNA unique dual index kits (Takara)

value: LRPPRC KO


title: Heart, sgRNA1, replicate1 [amplicon]


title: UN-1


title: TL13_HEK_500_60m_LRP_tot_repA

description:
rRNA-depleted total RNA
TL13_LRP_tot_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_60m_LRP_tot_A

value: DMEM supplemented with 20 μg/mL of uridine, 3 mM sodium formate, 10% FBS, 1 mM GlutaMAX (Thermo Fisher Scientific) and 1 mM sodium pyruvate


title: TS108_2_MeDIP_200 [re-analyzed]


title: N2a, sgRNA10, replicate2 [amplicon]

value: mouse neural crest-derived cell line

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA10


title: E12.5_PGC_Fem_IgG

city: Montpellier

first: Maud

last: Borensztein

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS, Univ of Montpellier

description: IgG control

data_processing:
FastQC (v0.11.9) and MultiQC (v1.13) were used to control CUT&RUN data quality. UMIs were used to confirm the homogeneous yield of library amplification and sequencing for each sample. Paired-end reads with at least one undefined UMI were discarded using Cutadapt v4.1 and seqkit v2.3 . The reads were then trimmed using Trim Galore(v0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/7 ; options “--length 20 –illumina – 2colour 20”). Trimmed reads were mapped with Bowtie2 (v2.4.2) (options “--end-to-end –very-sensitive–reorder”) to the mm10 reference genome, modified as followed: autosomal, sexual and mitochondrial chromosomes are kept, and 20 668 274 SNPs positions (0.76% of genome size) related to Mus musculus Castaneus strain are N-masked using SNPsplit (v0.6) (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-1505- SNPs_Indels/strain_specific_vcfs/CAST_EiJ.mgp.v5.snps.dbSNP142.vcf). SAMtools (v1.11)  was used to sort and convert the data formats. PCR duplicates were removed using GATK MarkDuplicates, and reads were unmapped with or without primary alignment discarded (SAMtools options “-F 0x04 -F 0x100 -F 542 0x800”). The coverage for each developmental stage was calculated from the bam file using the deepTools bamCoverage tool (v3.5.1, normalization by scale factor, bin=10 nt). Peak calling of H3K27me3 histone marks was performed for E11.5 and E12.5 female samples using immunoglobulin G (IgG) as input for each stage (E11.5 IgG from male PGC, E12.5 IgG from female PGC) with MACS2 (v2.2.7.1, options “-f BAMPE –broad –broad-cutoff 0.1”). Allele-specific reads (i.e. reads from B6: Xa and Cast: Xi) were sorted using SNPsplit. The d-score parameter (reads Cast / reads B6 + reads Cast]) was calculated using featureCounts from the Rsubread R package(v2.12.3). H3K27me3 enrichment heatmaps show the log2 fold change in the coverage difference between the H3K27me3 mark and the IgG control for each developmental stage, normalized by the sequencing depth using deepTools bamCompare (bin= 10 nt). computeMatrix and plotHeatmap.
Assembly: mm10
Supplementary files format and content: BigWig, broad peak, except for IgG
Supplementary files format and content: CSV files including FeatureCount library
Library strategy: Cut&Run-seq

source_name: Primordial Germ Cells

extract_protocol:
genomic DNA
DNA was isolated with antibody and PA-Mnase incubation. Library preparation was performed according to manufacturer’s instructions (NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina) using the following modified library amplification program: 98 °C for 30 s (98 °C for 10 s, 65 °C for 15 s) × 15 cycles, 65 °C for 5 min), hold at 4 °C. Average library size and quality control were performed using a Fragment Analyzer (High Sensitivity NGS kit) and qPCR (Roche Light Cycler 480).

value: Primordial Germ Cells

tag: embryonic stage

tag: strain

value: B6 x Cast

value: Xist KO/+:Oct4-eGFP+/-

tag: Sex

value: Female

tag: antibody

value: IgG


title: TS108_1_MeDIP_189 [re-analyzed]

value: Primary AML


title: TL13_HEK_500_30m_LRP_tot_repA

description:
rRNA-depleted total RNA
TL13_LRP_tot_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_30m_LRP_tot_A

value: 500 uM 4sU for 30 min


title: E11.5_PGC_Male_IgG

description: IgG control

value: Xist KO/Y:Oct4-eGFP+/-

value: Male


title: TL13_HEK_500_30m_LRP_tot_repB

description:
rRNA-depleted total RNA
TL13_LRP_tot_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_30m_LRP_tot_B


title: N2a, sgRNA10, replicate1 [amplicon]

value: WT


title: N2a, sgRNA9, replicate2 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA9


title: E12.5_PGC_Fem_H3K27me3


title: E11.5_PGC_Fem_H3K27me3


title: TL13_HEK_500_0m_LRP_tot_repB

description:
rRNA-depleted total RNA
TL13_LRP_tot_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_0m_LRP_tot_B

value: 0 uM 4sU


title: N2a, sgRNA8, replicate2 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA8


title: Tg_AngII_AA_PVAT_3

city: Ann Arbor

first: Haocheng

last: Lu

state: Michigan

address: 2800 plymouth road

department: Internal Medicine

institute: University of Michigan

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files. The reads were trimmed using Cutadapt v2.3
The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3. Alignment options followed ENCODE standards for RNA-seq.
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7.
Genome_build: GRCm38 (ENSEMBL)
Supplementary_files_format_and_content: Matrix table with transcripts per kilobase million (tpm) for every gene and every sample

molecule: polyA RNA

source_name: Perivascular adipose tissue

extract_protocol:
For WT mice, RNA samples were prepared by using the RNeasy® mini kit (Cat# 74106, Qiagen) according to the manufacturer’s instruction. Each RNA sample was extracted from pooled PVAT from 2-3 mice. For mitoNEET-Tg mice, RNA samples (each sample represents single mouse) were isolated by using the RNeasy® micro kit (Cat# 74004, Qiagen).
The RNA library was prepared with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) with poly A selection. This pool was subjected to 151 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). An average of 40 million paired-reads per samples were generated.

treatment_protocol: Wild type (WT) C57BL/6J mice were from the Jackson Laboratory (stock number 000664), the mitoNEET transgenic mice (mitoNEET-Tg) in a C57BL/6J background were constructed to express human mitoNEET driven by the mouse Ucp1 promoter, as previously described [24]. The mice were housed in ventilated cage at 22°C with 12 h/12 h light/dark cycle and were maintained on a standard chow diet and tap water ad libitum. For Ang II infusion experiment, 8- to 12-week-old mice were subcutaneously implanted with osmotic mini-pumps (Alzet, Model #2004) carrying Ang II (1000 ng/kg/min, BACHEM) or saline (as control) for 7 days. Then the mice were sacrificed and the aortic PVAT were dissected.

value: AngII

value: MitoNEET-Tg

tag: aorta location

value: Abdominal aorta


title: N2a, sgRNA9, replicate1 [amplicon]

value: mouse neural crest-derived cell line


title: TL13_HEK_500_0m_LRP_IP_repA

description:
Mitoribosome-associated RNA
TL13_LRP_IP_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_0m_LRP_IP_A

value: LRPPRC KO

value: DMEM supplemented with 20 μg/mL of uridine, 3 mM sodium formate, 10% FBS, 1 mM GlutaMAX (Thermo Fisher Scientific) and 1 mM sodium pyruvate


title: TS108_5_INPUT_200 [re-analyzed]

value: none; input


title: TS116_07_500_H3K27Ac [re-analyzed]

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) using BWA-MEM version 0.7.15 (Li and Durbin 2009). Reads were filtered using Samtools (version 0.1.9) (Li et al., 2009) to keep only reads that mapped to standard chromosomes and Bedtools version 2.25.0 (Quinian and Hall, 2010) to remove reads mapped to blacklisted regions defined by ENCODE (http://mitra.stanford.edu/kundaje). Peaks were called with Model-based Analysis of ChIP-Seq version 2 (MACS2) using the following parameters -f BAMPE, --keep-dup 5 to keep only paired-end reads with up to 5 duplicates (Zhang et al. 2008). Annotation of peaks was performed with Homer version 4.10 (Heinz et al. 2010).
Assembly: GRCh38
Supplementary files format and content: bigwig

extract_protocol:
ChIP for histone marks or SOX4 transcription factor were performed as previously described in (Lee et al., 2006) using either 1x107 or 5x107 AML patient cells respectively that were thawed and immediately cross-linked. Cells were cross-linked at room temperature using 1% formaldehyde. For SOX4 ChIP-seq a previous step of Gold cross-linking (Diagenode) was included, as per manufacturer’s instructions. After 10 minutes the reaction was quenched by incubation for 10 minutes with 0.125M glycine. Cell pellets were washed twice with cold PBS and 1x107 or 5x107 cells were used per ChIP. Briefly, nuclear lysates were sonicated using a Bioruptor Plus (Diagenode) for 6-10 min at high, 30s ON, 30s OFF settings. Immunoprecipitation was performed overnight at 20rpm and 4°C, with 10μl magnetic beads (Dynabeads (Protein G), Invitrogen, Carlsbad, CA) per 1μg antibody per 1x107 cells. Antibodies used were: acetyl-H3K27 (ab4729, Abcam, Cambridge, UK; 1μg per ChIP), anti-trimethyl H3K27 (9733S, Cell Signalling; 1μg per ChIP), anti-monomethyl-H3K4 (ab8895, Abcam; 1μg per ChIP) anti-trimethyl H3K9 (ab8898, Abcam; 1μg per ChIP) or SOX4 (CS-129-100, Diagenode; 15μl per ChIP). After washing five times with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl), chromatin IP-bound fractions were extracted at 65°C for 30min with elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) vortexing frequently. Cross-linking was then reversed by incubation at 65°C for 16 hours. RNAse A (1mg/ml) and proteinase K (20mg/ml) were used to eliminate any RNA or protein from the samples. Finally DNA was extracted using phenol:chloroform:isoamyl alcohol extraction and precipitated with ethanol (adding two volumes of ice-cold 100% ethanol, glycogen (20μg/μl) and 200mM NaCl) for at least 1 hour at -80°C. Pellets were washed with 70% ethanol and eluted in 30μl 10mM Tris-HCl pH 8.0.
Libraries were prepared for sequencing using a Microplex Library Preparation Kit (Diagenode) or NEBNext UltraII (New England Biolabs) and 1ng ChIP to the manufacturer’s instructions. Fragments of 200–800 bp were selected using AMPure beads (Beckman Coulter, Pasadena, CA) and quantified by quantitative PCR with a KAPA Library Quantification Kit (Kapa Biosystems, Woburn, MA). Sequencing was performed using either a Novaseq6000 or a NextSeq500 desktop sequencer system (Illumina) with 75-bp, paired-end high output generating 18–58 million reads per sample for the histone marks ChIP-seq or 96 million reads for the SOX4 ChIP-seq experiments.

tag: chip antibody


title: TL13_HEK_500_0m_LRP_tot_repA

description:
rRNA-depleted total RNA
TL13_LRP_tot_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_0m_LRP_tot_A


title: UN-2

value: NLRP3 (AdipoGen, AG-20B-0014)

value: Mouse monocyte macrophage leukemia cells

value: Uninfected normal cells


title: Tg_AngII_AA_PVAT_2


title: TS116_05_287_H3K27Ac [re-analyzed]

value: Primary AML

value: acetyl-H3K27 (ab4729, Abcam, Cambridge, UK; 1μg per ChIP)


title: TL13_HEK_500_60m_WT_IP_repA

description:
Mitoribosome-associated RNA
TL13_WT_IP_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_60m_WT_IP_A

value: 500 uM 4sU for 60 min


title: N2a, sgRNA7, replicate2 [amplicon]

value: WT

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA7


title: N2a, sgRNA8, replicate1 [amplicon]


title: TS116_04_221_H3K27Ac [re-analyzed]


title: TS116_09_INPUT [re-analyzed]


title: N2a, sgRNA7, replicate1 [amplicon]


title: Tg_AngII_AA_PVAT_1


title: TS116_06_352_H3K27Ac [re-analyzed]


title: Tg_AngII_DTA_PVAT_3

value: Descending thoracic aort


title: TL13_HEK_500_0m_WT_IP_repB

description:
Mitoribosome-associated RNA
TL13_WT_IP_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_0m_WT_IP_B

value: 0 uM 4sU


title: TS116_03_200_H3K27Ac [re-analyzed]


title: TS116_08_575_H3K27Ac [re-analyzed]


title: TL13_HEK_500_30m_WT_IP_repA

description:
Mitoribosome-associated RNA
TL13_WT_IP_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_30m_WT_IP_A

value: 500 uM 4sU for 30 min


title: N2a, sgRNA6, replicate2 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA6


title: N2a, sgRNA6, replicate1 [amplicon]


title: Tg_AngII_DTA_PVAT_1

value: AngII

value: MitoNEET-Tg


title: TL13_HEK_500_60m_WT_IP_repB

description:
Mitoribosome-associated RNA
TL13_WT_IP_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_60m_WT_IP_B


title: TS116_02_189_H3K27Ac [re-analyzed]


title: N2a, sgRNA5, replicate2 [amplicon]

value: mouse neural crest-derived cell line

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA5


title: TL13_HEK_500_0m_WT_IP_repA

description:
Mitoribosome-associated RNA
TL13_WT_IP_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_0m_WT_IP_A

value: DMEM supplemented with 20 μg/mL of uridine, 3 mM sodium formate, 10% FBS, 1 mM GlutaMAX (Thermo Fisher Scientific) and 1 mM sodium pyruvate


title: Tg_AngII_DTA_PVAT_2


title: TL13_HEK_500_60m_WT_tot_repB

description:
rRNA-depleted total RNA
TL13_WT_tot_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_60m_WT_tot_B


title: TS116_01_77_H3K27Ac [re-analyzed]


title: CytoRP_K562 2

description:
Mitoribosome-protected fragments
K562KOs_featureCounts_allSizesAsite_CDS_multi_noDups_all_tpm_noPseudo_ncRNA.txt
K562_CytoRP_2

data_processing:
Fastq files shared by the sequencing facility were concatenated to combine data across the sequencer lanes. The adapter sequences were trimmed from both of the paired-end reads using Cutadapt v2.5 (Martin. EMBnet, 2011). Three more nucleotides were trimmed from the 5’ end of the fragment to remove template switch bases, and five more  from the 3’ end to remove mismatches associated with random hexamer priming that result from the SMARTer Stranded library preparation.
Read alignment was done using STAR 2.7.3 to cell line specific genomic reference sequences with different parameters for experiments with high and low 4sU treatment. For 500 uM 4sU experiments, parameters were --outFilterMismatchNmax 90 --outFilterMismatchNoverLmax 0.3 --outFilterMatchNminOverLread 0.2 --outFilterScoreMinOverLread 0.2. For 50 uM 4sU experiment, parameters were --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNminOverLread 0.66 --outFilterScoreMinOverLread 0.66 --outFilterMultimapScoreRange 0.
Allignment files (.bam) were used as input to the software GRAND-SLAM which uses a statistical approach to determine T to C conversion rates. We further modified these rates according to the details in the publication associated with this repository and retrieved the fraction of new RNA at each time point from the GRAND-SLAM output.
Assembly: hg38, updated with variants for each cell line based on sequencing data collected here (see associated publication for details).
Supplementary files format and content: Processed data files for TimeLapse-Seq experiments are tab separated files that contain the GRAND-SLAM outputs including fraction new RNA, read counts, confidence intervals, etc as described in the GRAND-SLAM documentation. Names of file indicates the experiment ('TLX_*'), gene set (MT: mitochondrial, Nuc: nuclear, MTdsrRNA: mitochondrial but the rRNA has been downsampled), parameters used for alignment (these vary based on the amount of 4sU used and whether mitochondrial or nuclear transcripts are being interrogated). lenient_modeAll indicates GrandSlam parameters, and 'Pc***' indicates the method used to determine the T to C conversion rate, if any. These fractions new do not contain any correction for cell doubling time.
Supplementary files format and content: Processed data files for RNA-seq and ribosome profiling (as well as the TL5 experiment) are tab separated files that contain feature counts as descibed in the file name (RPKM, tpm) for each gene in each sample. For K562 experiments, *all_tpm* indicates transcripts per million of ALL mapped transcripts; *mito_tpm* indicates transcripts per million of mito-encoded mapped transcripts.
Library strategy: Ribosome profiling

extract_protocol:
Upon removing media, cells were rinsed with ice-cold PBS and resuspended in mitoribosome lysis buffer (0.25% lauryl maltoside,50 mM NH4Cl, 20 mM MgCl2, 0.5 mM DTT, 10 mM Tris, pH 7.5, and 1× EDTA-free protease inhibitor cocktail. Mouse lysate was spiked in to a final volume of 5% and lysates were RNAse digested for 30 min at room temperature to generate mitoribosome footprints using 8 units/µL of RNase If (NEB). The digestion was then inhibited by the addition of 80 units SUPERaseIn (Thermo Fisher Scientific) followed by centrifugation at 10,000 RPM for 5 min. The mitochondrial monosome fraction was collected after sucrose density gradient fractionation and RNA fragments 28 - 40 nt were gel purified.
Custom library prep using 3' linker /5rApp/NNNNNNNNNNCTGTAGGCACCATCAAT/3ddC/, reverse transcription with primer /5Phos/NNNNGATCGTCGGACTGTAGAACTCTGAACCTGTC/iSp18/CACTCA/iSp18/CAAGCAGAAGACGGCATACGAGATATTGATGGTGCCTACAG, and circularization before PCR with Illumina primers  513 /5rApp/NNNNNNCTGTAGGCACCATCAAT/3ddC/) and 5' linker

value: DMEM containing glucose and pyruvate  supplemented with 10% FBS


title: Tg_AngII_ATA_PVAT_3

value: Ascending thoracic aorta


title: N2a, sgRNA5, replicate1 [amplicon]


title: Tg_AngII_ATA_PVAT_2


title: CytoRP_K562 1

description:
Mitoribosome-protected fragments
K562KOs_featureCounts_allSizesAsite_CDS_multi_noDups_all_tpm_noPseudo_ncRNA.txt
K562_CytoRP_1


title: TL13_HEK_500_30m_WT_IP_repB

description:
Mitoribosome-associated RNA
TL13_WT_IP_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_30m_WT_IP_B


title: N2a, sgRNA4, replicate2 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA4


title: Tg_AngII_ATA_PVAT_1


title: MitoRP_K562 2

description:
Mitoribosome-protected fragments
K562KOs_RPF_featureCounts_allSizesAsite_CDSmerge_multi_noDups_mito_tpm_noPseudo_ncRNA.txt
K562_MitoRP_2


title: TL13_HEK_500_30m_WT_tot_repB

description:
rRNA-depleted total RNA
TL13_WT_tot_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_30m_WT_tot_B


title: N2a, sgRNA4, replicate1 [amplicon]


title: MitoRP_K562 1

description:
Mitoribosome-protected fragments
K562KOs_RPF_featureCounts_allSizesAsite_CDSmerge_multi_noDups_mito_tpm_noPseudo_ncRNA.txt
K562_MitoRP_1


title: Tg_Saline_AA_PVAT_2

value: Saline

value: Abdominal aorta


title: TL13_HEK_500_30m_WT_tot_repA

description:
rRNA-depleted total RNA
TL13_WT_tot_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_30m_WT_tot_A


title: N2a, sgRNA3, replicate1 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA3


title: RNAseq_K562 2

description:
Mitoribosome-protected fragments
K562KOs_RNAseq_featureCounts_CDSmerge_multi_noDups_mito_tpm_noPseudo_ncRNA.txt
K562KOs_RNAseq_featureCounts_CDSmerge_multi_noDups_mito_tpm_noPseudo_ncRNA.txt
K562_RNAseq_2

data_processing:
Fastq files shared by the sequencing facility were concatenated to combine data across the sequencer lanes. The adapter sequences were trimmed from both of the paired-end reads using Cutadapt v2.5 (Martin. EMBnet, 2011). Three more nucleotides were trimmed from the 5’ end of the fragment to remove template switch bases, and five more  from the 3’ end to remove mismatches associated with random hexamer priming that result from the SMARTer Stranded library preparation.
Read alignment was done using STAR 2.7.3 to cell line specific genomic reference sequences with different parameters for experiments with high and low 4sU treatment. For 500 uM 4sU experiments, parameters were --outFilterMismatchNmax 90 --outFilterMismatchNoverLmax 0.3 --outFilterMatchNminOverLread 0.2 --outFilterScoreMinOverLread 0.2. For 50 uM 4sU experiment, parameters were --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNminOverLread 0.66 --outFilterScoreMinOverLread 0.66 --outFilterMultimapScoreRange 0.
Allignment files (.bam) were used as input to the software GRAND-SLAM which uses a statistical approach to determine T to C conversion rates. We further modified these rates according to the details in the publication associated with this repository and retrieved the fraction of new RNA at each time point from the GRAND-SLAM output.
Assembly: hg38, updated with variants for each cell line based on sequencing data collected here (see associated publication for details).
Supplementary files format and content: Processed data files for TimeLapse-Seq experiments are tab separated files that contain the GRAND-SLAM outputs including fraction new RNA, read counts, confidence intervals, etc as described in the GRAND-SLAM documentation. Names of file indicates the experiment ('TLX_*'), gene set (MT: mitochondrial, Nuc: nuclear, MTdsrRNA: mitochondrial but the rRNA has been downsampled), parameters used for alignment (these vary based on the amount of 4sU used and whether mitochondrial or nuclear transcripts are being interrogated). lenient_modeAll indicates GrandSlam parameters, and 'Pc***' indicates the method used to determine the T to C conversion rate, if any. These fractions new do not contain any correction for cell doubling time.
Supplementary files format and content: Processed data files for RNA-seq and ribosome profiling (as well as the TL5 experiment) are tab separated files that contain feature counts as descibed in the file name (RPKM, tpm) for each gene in each sample. For K562 experiments, *all_tpm* indicates transcripts per million of ALL mapped transcripts; *mito_tpm* indicates transcripts per million of mito-encoded mapped transcripts.

value: WT


title: N2a, sgRNA3, replicate2 [amplicon]


title: TL13_HEK_500_0m_WT_tot_repB

description:
rRNA-depleted total RNA
TL13_WT_tot_B_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_0m_WT_tot_B


title: Tg_Saline_AA_PVAT_1


title: TL11_Hela_500_60m_IP

description:
Mitoribosome-associated RNA
TL11_IP_MTdsrRNA_t5MMinformed4_modeAll_PcBin1_2_3_4.tsv
TL11_60m_IP

source_name: HeLa

value: HeLa

value: 500 uM 4sU for 60 min


title: N2a, sgRNA2, replicate1 [amplicon]

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA2


title: N2a, sgRNA2, replicate2 [amplicon]


title: Tg_Saline_DTA_PVAT_3

value: Descending thoracic aort


title: Tg_Saline_DTA_PVAT_2


title: TL11_Hela_500_30m_IP

description:
Mitoribosome-associated RNA
TL11_IP_MTdsrRNA_t5MMinformed4_modeAll_PcBin1_2_3_4.tsv
TL11_30m_IP

value: 500 uM 4sU for 30 min


title: RNAseq_K562 1

description:
Mitoribosome-protected fragments
K562KOs_RNAseq_featureCounts_CDSmerge_multi_noDups_mito_tpm_noPseudo_ncRNA.txt
K562KOs_RNAseq_featureCounts_CDSmerge_multi_noDups_mito_tpm_noPseudo_ncRNA.txt
K562_RNAseq_1


title: TL13_HEK_500_60m_WT_tot_repA

description:
rRNA-depleted total RNA
TL13_WT_tot_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_60m_WT_tot_A


title: Hela_tot

description:
rRNA-depleted total RNA
SS1_MTMMinformed6_featureCounts_CDSmulti_tpm_noPseudo_ncRNA.txt
Total_1

extract_protocol:
Labeled cells were washed in ice cold PBS  before being directly scraped in Trizol LS. RNA extraction was performed using Trizol LS.
Illumina TruSeq kit


title: TL5_Hela_poly

description:
Mito polysome-associated RNA
TL5_poly_t5MTMMinformed6_featureCounts_multi_RPKM_noPseudo_ncRNA.txt
TL5_0m_poly

extract_protocol:
After labeling, cells were quickly washed in ice cold PBS before being scraped in mt-polysome lysis buffer. Mitoribosomes from monosome and polysome fractions were isolated after sucrose gradient fractionation. Extracted RNA was treated by TimeLapse-chemistry (0.1M sodium acetate pH 5.2, 4mM EDTA, 5.2% 2,2,2-trifluoroethylamine, and 10mM sodium periodate at 45°C for 1 hour).
SMARTer Stranded Total RNA HI Mammalian kit (Takara)

value: 0 uM 4sU


title: Tg_Saline_DTA_PVAT_1

value: MitoNEET-Tg


title: Tg_Saline_ATA_PVAT_3


title: N2a, sgRNA1, replicate2 [amplicon]

value: mouse neural crest-derived cell line

value: pAAV-EFS-TadA8e-Sauri-U6-Camk2d sgRNA1


title: Tg_Saline_AA_PVAT_3


title: TL5_Hela_tot

description:
rRNA-depleted total RNA
TL5_tot_t5MTMMinformed6_featureCounts_multi_RPKM_noPseudo_ncRNA.txt
TL5_0m_tot


title: N2a, sgRNA1, replicate1 [amplicon]


title: TL11_Hela_500_0m_IP

description:
Mitoribosome-associated RNA
TL11_IP_MTdsrRNA_t5MMinformed4_modeAll_PcBin1_2_3_4.tsv
TL11_0m_IP


title: Tg_Saline_ATA_PVAT_2


title: Heart, control, replicate3

data_processing:
Assess the quality of raw sequencing data using tools like FastQC to identify issues such as adapter contamination or low-quality reads.
Trim adapters, low-quality bases, and filter out short reads using Cutadapt.
Map trimmed reads to a reference genome using STAR.
Quantify gene expression levels by counting reads mapped to each gene using featureCounts.
Assembly: mm10
Supplementary files format and content: Reads_count_matrix

extract_protocol:
RNA was extracted from tissues using TransZol Up Plus RNA Kit (Q41206, Transgen, China)
1. Fragment the mRNA into smaller pieces using divalent cations or enzymes such as RNase III. 2. Reverse transcribe RNA fragments into first-strand cDNA using random primers or oligo(dT) primers. 3. Synthesize the second cDNA strand by adding dNTPs, DNA polymerase, and RNase H. 4. Perform end repair to generate blunt ends, followed by A-tailing by adding an adenine nucleotide to the 3' end. 5. Ligating sequencing adapters to cDNA fragments for subsequent PCR amplification. 6. PCR amplify the cDNA fragments with attached adapters to increase the amount of material for sequencing.

tag: tissue

value: Heart


title: TL11_Hela_500_60m_tot

description:
rRNA-depleted total RNA
TL11_tot_MTdsrRNA_t5MMinformed4_modeAll_PcBin1_2_3_4.tsv
TL11_60m_tot

value: DMEM containing glucose and pyruvate  supplemented with 10% FBS

tag: treatment


title: TL11_Hela_500_15m_IP

description:
Mitoribosome-associated RNA
TL11_IP_MTdsrRNA_t5MMinformed4_modeAll_PcBin1_2_3_4.tsv
TL11_15m_IP

tag: genotype

value: 500 uM 4sU for 15 min


title: TL13_HEK_500_0m_WT_tot_repA

description:
rRNA-depleted total RNA
TL13_WT_tot_A_MTdsrRNA_t5MTMMinformed6_modeAll_PcBrute1.tsv
TL13_0m_WT_tot_A

value: DMEM supplemented with 20 μg/mL of uridine, 3 mM sodium formate, 10% FBS, 1 mM GlutaMAX (Thermo Fisher Scientific) and 1 mM sodium pyruvate


title: Heart, control, replicate2


title: Heart, control, replicate1


title: TL11_Hela_500_30m_tot

description:
rRNA-depleted total RNA
TL11_tot_MTdsrRNA_t5MMinformed4_modeAll_PcBin1_2_3_4.tsv
TL11_30m_tot


title: Hela_mito

description:
rRNA-depleted total RNA
SS1_MTMMinformed6_featureCounts_CDSmulti_tpm_noPseudo_ncRNA.txt
Mito_1

value: Mitochondrial enrichment


title: TL11_Hela_50o_15m_tot

description:
rRNA-depleted total RNA
TL11_tot_MTdsrRNA_t5MMinformed4_modeAll_PcBin1_2_3_4.tsv
TL11_15m_tot


title: Heart, sgRNA7, replicate3

value: AAV-MYL2-TadA8e-Sauri-U6-Camk2d sgRNA7


title: TL1_Hela_500_60m

description:
rRNA-depleted total RNA
TL1_MT_t5MMinformed4_modeAll.tsv
TL1_Nuc_t5MMinformed4_lenient_modeAll.tsv
TL1_60m

extract_protocol:
Labeled cells were washed in ice cold PBS  before being directly scraped in Trizol LS. RNA extraction was performed using Trizol LS and treated by TimeLapse-chemistry (0.1M sodium acetate pH 5.2, 4mM EDTA, 5.2% 2,2,2-trifluoroethylamine, and 10mM sodium periodate at 45°C for 1 hour).
SMARTer Stranded Total RNA HI Mammalian kit (Takara)


title: AngII_AA_PVAT_2

value: AngII

value: wild type

value: Abdominal aorta


title: TL1_Hela_500_30m

description:
rRNA-depleted total RNA
TL1_MT_t5MMinformed4_modeAll.tsv
TL1_Nuc_t5MMinformed4_lenient_modeAll.tsv
TL1_30m

value: HeLa

value: WT


title: TL11_Hela_500_0m_tot

description:
rRNA-depleted total RNA
TL11_tot_MTdsrRNA_t5MMinformed4_modeAll_PcBin1_2_3_4.tsv
TL11_0m_tot


title: Heart, sgRNA7, replicate2


title: AngII_AA_PVAT_1


title: TL1_Hela_500_15m

description:
rRNA-depleted total RNA
TL1_MT_t5MMinformed4_modeAll.tsv
TL1_Nuc_t5MMinformed4_lenient_modeAll.tsv
TL1_15m


title: TL9_Hela_50_60m_IP_repB

description:
Mitoribosome-associated RNA
TL9_IP_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL9_60m_IP

value: 50 uM 4sU for 60 min


title: Heart, sgRNA7, replicate1


title: TL1_Hela_500_0m

description:
rRNA-depleted total RNA
TL1_MT_t5MMinformed4_modeAll.tsv
TL1_Nuc_t5MMinformed4_lenient_modeAll.tsv
TL1_0m


title: TL8_Hela_50_60m_IP_repA

description:
Mitoribosome-associated RNA
TL8_IP_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL8_60m_IP


title: Cortex,BKOQ331K5

city: Ithaca

first: Cha

last: Yang

state: NY

address: 100 Fairview Sq

institute: Cornell University

description: Library name: CX22

data_processing:
Reads were trimmed to remove low-quality and adaptor sequences with TrimGalore (a wrapper for cutadapt and fastQC), requiring a minimum trimmed length of 50 nt.
Assembly: mouse GRCm38/mm10
Supplementary files format and content: excel files including raw counts for each sample

source_name: Brain

extract_protocol:
Total RNA was extracted from the liver or brain cortex of 10-month-old mice using Trizol (Thermo Scientific).
RNAseq libraries were generated by the Cornell TREx Facility using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) using 700 ng input total RNA per sample.

value: Brain


title: AngII_DTA_PVAT_3

value: Descending thoracic aort


title: TL1_Hela_500_240m

description:
rRNA-depleted total RNA
TL1_MT_t5MMinformed4_modeAll.tsv
TL1_Nuc_t5MMinformed4_lenient_modeAll.tsv
TL1_240m

value: 500 uM 4sU for 240 min


title: TL9_Hela_50_30m_IP_repB

description:
Mitoribosome-associated RNA
TL9_IP_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL9_30m_IP

value: 50 uM 4sU for 30 min


title: Cortex,BKOQ331K4

description: Library name: CX21


title: Tg_Saline_ATA_PVAT_1

value: Saline

value: MitoNEET-Tg

value: Ascending thoracic aorta


title: AngII_DTA_PVAT_4


title: AngII_AA_PVAT_4


title: TL3_Hela_50_240m_rep1

description:
rRNA-depleted total RNA
TL3_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL3_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL3_240m

value: DMEM containing glucose and pyruvate  supplemented with 10% FBS

value: 50 uM 4sU for 240 min


title: AngII_DTA_PVAT_2


title: AngII_DTA_PVAT_1


title: TL1_Hela_500_120m

description:
rRNA-depleted total RNA
TL1_MT_t5MMinformed4_modeAll.tsv
TL1_Nuc_t5MMinformed4_lenient_modeAll.tsv
TL1_120m

value: 500 uM 4sU for 120 min


title: TL8_Hela_50_30m_IP_repA

description:
Mitoribosome-associated RNA
TL8_IP_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL8_30m_IP


title: Cortex,BKOQ331K2

description: Library name: CX19


title: TL9_Hela_50_15m_IP_repB

description:
Mitoribosome-associated RNA
TL9_IP_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL9_15m_IP

value: 50 uM 4sU for 15 min


title: Cortex,BKOQ331K3

description: Library name: CX20


title: AngII_ATA_PVAT_4

value: AngII


title: AngII_ATA_PVAT_3

value: wild type


title: TL8_Hela_50_15m_IP_repA

description:
Mitoribosome-associated RNA
TL8_IP_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL8_15m_IP


title: TL3_Hela_50_120m_rep1

description:
rRNA-depleted total RNA
TL3_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL3_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL3_120m

value: 50 uM 4sU for 120 min


title: Cortex,BKOQ331K1

description: Library name: CX18


title: TL4_Hela_50_90m_rep2

description:
rRNA-depleted total RNA
TL4_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL4_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL4_90m

value: HeLa

value: 50 uM 4sU for 90 min


title: TL9_Hela_50_0m_IP_repB

description:
Mitoribosome-associated RNA
TL9_IP_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL9_0m_IP

value: WT

value: 0 uM 4sU


title: TL3_Hela_50_90m_rep1

description:
rRNA-depleted total RNA
TL3_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL3_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL3_90m


title: AngII_ATA_PVAT_2


title: Cortex,BKO5

description: Library name: CX16

value: Brain


title: TL4_Hela_50_240m_rep2

description:
rRNA-depleted total RNA
TL4_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL4_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL4_240m


title: TL8_Hela_50_0m_IP_repA

description:
Mitoribosome-associated RNA
TL8_IP_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL8_0m_IP


title: AngII_ATA_PVAT_1


title: Cortex,BKO4

description: Library name: CX15


title: TL4_Hela_50_60m_rep2

description:
rRNA-depleted total RNA
TL4_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL4_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL4_60m

value: 50 uM 4sU for 60 min


title: TL9_Hela_50_60m_tot_repB

description:
rRNA-depleted total RNA
TL9_tot_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL9_60m_tot


title: Saline_AA_PVAT_4

value: Abdominal aorta


title: Cortex,BKO3

description: Library name: CX14


title: TL3_Hela_50_60m_rep1

description:
rRNA-depleted total RNA
TL3_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL3_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL3_60m


title: TL8_Hela_50_60m_tot_repA

description:
rRNA-depleted total RNA
TL8_tot_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL8_60m_tot


title: Cortex,BKO2

description: Library name: CX13


title: Saline_AA_PVAT_3

value: Saline


title: Cortex,BKO1

description: Library name: CX12


title: TL9_Hela_50_30m_tot_repB

description:
rRNA-depleted total RNA
TL9_tot_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL9_30m_tot

value: 50 uM 4sU for 30 min


title: Saline_AA_PVAT_2


title: TL3_Hela_50_45m_rep1

description:
rRNA-depleted total RNA
TL3_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL3_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL3_45m

value: 50 uM 4sU for 45 min


title: Cortex,Q331K6

description: Library name: CX11


title: Saline_DTA_PVAT_4

value: Descending thoracic aort


title: TL8_Hela_50_30m_tot_repA

description:
rRNA-depleted total RNA
TL8_tot_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL8_30m_tot

value: DMEM containing glucose and pyruvate  supplemented with 10% FBS


title: TL4_Hela_50_30m_rep2

description:
rRNA-depleted total RNA
TL4_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL4_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL4_30m


title: Cortex,Q331K5

description: Library name: CX10


title: Saline_DTA_PVAT_3


title: TL9_Hela_50_15m_tot_repB

description:
rRNA-depleted total RNA
TL9_tot_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL9_15m_tot


title: TL3_Hela_50_30m_rep1

description:
rRNA-depleted total RNA
TL3_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL3_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL3_30m


title: Cortex,Q331K4

description: Library name: CX9


title: TL8_Hela_50_15m_tot_repA

description:
rRNA-depleted total RNA
TL8_tot_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL8_15m_tot


title: Saline_DTA_PVAT_2


title: TL9_Hela_50_0m_tot_repB

description:
rRNA-depleted total RNA
TL9_tot_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL9_0m_tot


title: TL8_Hela_50_0m_tot_repA

description:
rRNA-depleted total RNA
TL8_tot_MTdsrRNA_t5MTMMinformed6_modeAll_PcBruteBinCombo.tsv
TL8_0m_tot


title: Saline_DTA_PVAT_1


title: Cortex,Q331K3

description: Library name: CX8


title: Saline_ATA_PVAT_4

value: Ascending thoracic aorta


title: Cortex,Q331K2

description: Library name: CX7


title: Saline_ATA_PVAT_3


title: TL4_Hela_50_45m_rep2

description:
rRNA-depleted total RNA
TL4_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL4_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL4_45m


title: TL3_Hela_50_7m_rep1

description:
rRNA-depleted total RNA
TL3_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL3_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL3_7m

value: 50 uM 4sU for 7 min


title: TL12_HEK_500_120m_LRP_repB

description:
rRNA-depleted total RNA
TL12_LRP_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL12_LRP_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL12_120m_LRP

value: LRPPRC KO

value: DMEM supplemented with 20 μg/mL of uridine, 3 mM sodium formate, 10% FBS, 1 mM GlutaMAX (Thermo Fisher Scientific) and 1 mM sodium pyruvate

value: 500 uM 4sU for 120 min


title: Cortex,Q331K1

description: Library name: CX6


title: Saline_ATA_PVAT_2

value: wild type


title: TL10_HEK_500_120m_LRP_repA

description:
rRNA-depleted total RNA
TL10_LRP_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL10_LRP_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL10_120m_LRP


title: Cortex,WT5

description: Library name: CX5


title: TL4_Hela_50_120m_rep2

description:
rRNA-depleted total RNA
TL4_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL4_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL4_120m

value: HeLa

value: 50 uM 4sU for 120 min


title: TL4_Hela_50_0m_rep2

description:
rRNA-depleted total RNA
TL4_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL4_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL4_0m

value: WT

value: 0 uM 4sU


title: Cortex,WT4

description: Library name: CX4

value: Brain


title: Saline_ATA_PVAT_1


title: TL12_HEK_500_60m_LRP_repB

description:
rRNA-depleted total RNA
TL12_LRP_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL12_LRP_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL12_60m_LRP

value: 500 uM 4sU for 60 min


title: TL10_HEK_500_60m_LRP_repA

description:
rRNA-depleted total RNA
TL10_LRP_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL10_LRP_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL10_60m_LRP


title: TL3_Hela_50_0m_rep1

description:
rRNA-depleted total RNA
TL3_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL3_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL3_0m


title: Cortex,WT3

description: Library name: CX3


title: TS160_07_IRX3_NTC-1

description: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) and gene annotated with their corresponding GTF file (GENCODE GRCh38 release 25) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts (Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21). DEseq2 was used to perform differential gene expression analysis and calculate FPKM (fragments per kilobase of transcript per million mapped reads) values for each gene (Love et al., 2014).
Assembly: GRCh38

growth_protocol: Fujioka cells were cultured in R10 media: Roswell Park Memorial Institute (RPMI) 1640 1x (Sigma Aldrich) supplemented with the addition of 2mM L-Glutamine (Life Technologies, Warrington, UK), 10% foetal bovine serum (FBS) (Sigma Aldrich) and 1% penicillin/streptomycin antibiotics (Sigma Aldrich). Cells were cultured according to DMSZ recommendations. Primary samples came from peripheral blood and bone marrow samples and were processed by the MCRC Biobank’s scientific officer. Mononuclear cells (MNCs) were separated by density gradient centrifugation, aliquoted into cryovials, labeled with a unique barcode and cryopreserved.  Cells were then thawed in a 37°C water bathand  transferred to a 15 mL sterile falcon tube. The cells were centrifuged at 200xg for 10 minutes and after discarding the supernatant, the pellet was washed twice in PBS and resuspended in the primary AML medium. Primary AML were cultured in Minimum Essential Medium with alpha modification (α-MEM) supplemented with 12.5% heat-inactivated FBS, 12.5% heat-inactivated horse serum, 2mM L-glutamine (Sigma Aldrich), 57.2μM β-mercaptoethanol (Sigma Aldrich), 1μM hydrocortisone (Sigma Aldrich) and 20ng/mL IL-3, G-CSF and TPO (PeproTech, Rocky Hill, NJ).

extract_protocol:
Total RNA was extracted from 2x106 Fujioka cells using the RNeasy Plus Mini kit (QIAGEN). Samples were homogenized using QIAshredder spin columns while genomic DNA was removed by using gDNA eliminator columns. Before sequencing, RNA quality was evaluated using a 2100 Bioanalyzer (Agilent Technologies). RNA-seq libraries were prepared using the Sureselect –polyA (Agilent Technologies) according to the manufacturer’s instructions.
Libraries were quantified by quantitative PCR using a Kapa Library Quantification Kit for Illumina sequencing platforms (Roche). Libraries were then barcoded, pooled and sequenced using Novaseq6000 (Illumina). A single run (400 million reads) of 100 bp paired-end sequencing produced a mean of 56.6-68.2 million reads per sample.

value: Fujioka Cells


title: TL4_Hela_50_15m_rep2

description:
rRNA-depleted total RNA
TL4_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL4_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL4_15m

value: 50 uM 4sU for 15 min


title: N2a hnRNPDL-KO rep3

city: Hefei

first: Qingyang

last: Zhang

state: Anhui

address: No.443, HuangShan Road Shushan District

department: Division of Life Sciences and Medicine

institute: University of Science and Technology of China for School of Life Sciences

description: hnRNP DL-/- N2a cells

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0
Reads Count for each gene in each sample was counted by HTSeq v0.6.0
Alternative splicing analyzationwas conducted with rMATS v4.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files include genes with differential alternative splicingpatterns

source_name: N2a cells

growth_protocol: Standard protocol for N2a cells culture for RNA-seq

extract_protocol:
Total RNA was extracted by Trizol.Total amount of 2 μg RNA per sample was used as input material for the RNA   sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA   Library  Prep  Kit  for  Illumina following the manufacturer’s   recommendations  and  index  codes  were  added  to  attribute  sequences  to  each  sample
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hnRNP DL-/-


title: TL12_HEK_500_30m_LRP_repB

description:
rRNA-depleted total RNA
TL12_LRP_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL12_LRP_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL12_30m_LRP

value: 500 uM 4sU for 30 min


title: Cortex,WT2

description: Library name: CX2


title: N2a hnRNPDL-KO rep2

description: hnRNP DL-/- N2a cells


title: TS160_06_FTO_NTC-1


title: TL10_HEK_500_30m_LRP_repA

description:
rRNA-depleted total RNA
TL10_LRP_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL10_LRP_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL10_30m_LRP


title: N2a hnRNPDL-KO rep1

description: hnRNP DL-/- N2a cells


title: Cortex,WT1

description: Library name: CX1


title: LATS1/2 KO replicate 2

first: Lina

last: Kroehling

address: 91 E Concord St

institute: Boston Unviersity

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger Version 3.1.0 was used for data processing with mm10 version 2.1.0
Assembly: mm10
Supplementary files format and content: barcods,matrix,features tsv per sample

source_name: Mammary gland

extract_protocol:
The third, fourth, and fifth pairs of mammary glands from each mouse were excised and lymph nodes removed from the fourth pair. Following this, each sample was chopped using a McIlwain tissue chopper. Samples were then dissociated using a solution of 2 mg/mL collagenase A, 0.5 units/mL dispase, 0.01 mg/mL DNAse, and 1x penicillin-streptomycin in DMEM with rotating at 37°C for 1 hour. ACK Lysing Buffer was then used to lyse red blood cells, TrypLE Express with 0.01 mg/mL DNAse was used to dissociate samples to single cells, and samples were strained using a 40 μM cell strainer. Samples were then incubated in 1 μM Calcein Blue, AM for 15 minutes, washed with PBS, and strained into tubes for flow cytometry. Live cells were sorted into a solution of 0.04% BSA in PBS to proceed with processing for single-cell sequencing.
Library construction was performed using 10x Genomics protocols (3'v3), including fragmentation, A-tailing, adaptor ligation, and PCR. The quality of the resulting libraries was checked using the Bioanalyzer High Sensitivity DNA Assay (Agilent Technologies).

treatment_protocol: Mice were administered 2 mg of Tamoxifen diluted in corn oil intraperitoneally on 5 consecutive days. Samples were collected seven days after the last Tamoxifen dose.

value: Mammary gland

tag: cell type

value: Live cells


title: TL12_HEK_500_0m_LRP_repB

description:
rRNA-depleted total RNA
TL12_LRP_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL12_LRP_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL12_0m_LRP


title: Liver,BKOQ331K4

description: Library name: Liver16

value: Liver


title: TL3_Hela_50_15m_rep1

description:
rRNA-depleted total RNA
TL3_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL3_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL3_15m

value: DMEM containing glucose and pyruvate  supplemented with 10% FBS


title: N2a WT rep3

description: wild type N2a cells


title: TL4_Hela_50_7m_rep2

description:
rRNA-depleted total RNA
TL4_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL4_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL4_7m

value: 50 uM 4sU for 7 min


title: TL10_HEK_500_0m_LRP_repA

description:
rRNA-depleted total RNA
TL10_LRP_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL10_LRP_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL10_0m_LRP

value: LRPPRC KO

value: DMEM supplemented with 20 μg/mL of uridine, 3 mM sodium formate, 10% FBS, 1 mM GlutaMAX (Thermo Fisher Scientific) and 1 mM sodium pyruvate


title: Liver,BKOQ331K3

description: Library name: Liver15


title: TL12_HEK_500_120m_WT_repB

description:
rRNA-depleted total RNA
TL12_WT_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL12_WT_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL12_120m_WT

value: 500 uM 4sU for 120 min


title: WT replicate 2

description: 10x Genomics


title: N2a WT rep2

description: wild type N2a cells

value: wild type


title: Liver,BKOQ331K2

description: Library name: Liver14


title: TL10_HEK_500_120m_WT_repA

description:
rRNA-depleted total RNA
TL10_WT_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL10_WT_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL10_120m_WT

value: WT


title: Liver,BKOQ331K1

description: Library name: Liver13


title: WT replicate 1

description: 10x Genomics


title: TL12_HEK_500_60m_WT_repB

description:
rRNA-depleted total RNA
TL12_WT_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL12_WT_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL12_60m_WT


title: Pseudomonas putida KT2440, solid media, 24 hours, rep1

city: Madrid

first: Ángeles

last: Hueso-Gil

state: Madrid

address: c/ Darwin 3

department: Systems Biology

country: Spain

institute: Centro Nacional de Biotecnología (CNB, CSIC)

description: Library name: KT2440_solid_media_24h_replicate1

data_processing:
Quality control of FASTQ files was performed using FastQC software.
Alignments were done with Bowtie 2.
HT-seq set in union mode was used to count reads per gene.
DESeq2 was used to normalize counts and set differential expression.
Fiesta was the programme that helped to build tables with the parameters of interest per gene.
Assembly: Pseudomonas putida KT2440, NCBI Reference Sequence: NC_002947.4; assembly: GCA_000007565.2 ASM756v2
Supplementary files format and content: csv files that includes comparison between liquid and solid media at 6 hours of incubation (file: SOL6hvsLIQ6h_Annotated_modif.csv).
Supplementary files format and content: csv files that includes comparison between liquid and solid media at 12 hours of incubation (file: SOL12hvsLIQ12h_Annotated_modif.csv).
Supplementary files format and content: csv files that includes comparison between liquid and solid media at 24 hours of incubation (file: SOL24hvsLIQ24h_Annotated_modif.csv).

organism: Pseudomonas putida KT2440

source_name: Bacterial culture

growth_protocol: M9 minimal media supplemented with 0.2% (v/w) citrate was used for all the experiments. When solid media was used, 1.5% (v/w) agar was added to the media.

extract_protocol:
RNA was extracted using RNeasy Kit (Qiagen, Venlo, Netherlands), and samples were purified from DNA using DNA‐free kit (Ambion) (Invitrogen, Carlsbad, CA, USA).
Libraries were prepared from RNA samples by the same Helmholtz Centre for Infection Research (HZI) in Braunschweig (Germany) that obtained RNASeq data.

treatment_protocol: No treatment

value: Bacterial culture


title: Pseudomonas putida KT2440, solid media, 24 hours, rep2

description: Library name: KT2440_solid_media_24h_replicate2


title: TL10_HEK_500_60m_WT_repA

description:
rRNA-depleted total RNA
TL10_WT_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL10_WT_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL10_60m_WT


title: Liver,BKO3

description: Library name: Liver11


title: Pseudomonas putida KT2440, liquid media, 24 hours, rep2

description: Library name: KT2440_liquid_media_24h_replicate2


title: WTC

description: UDI-P 132

source_name: Skin Epidermis

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared usingRoche Kapa RNA Hyper prep with Riboerase (HMR) for Illumina platforms, version KR1351 – v4.21 (Cat. #: 8098140702)

value: Skin Epidermis

value: Tamoxifen inducible


title: WTD

description: UDI-P 133


title: TL12_HEK_500_30m_WT_repB

description:
rRNA-depleted total RNA
TL12_WT_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL12_WT_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL12_30m_WT


title: Liver,BKO2

description: Library name: Liver10


title: WTA

description: UDI-P 131


title: LATS1/2 KO replicate 1

description: 10x Genomics


title: K03

description: UDI-P 130


title: Liver,BKO1

description: Library name: Liver9


title: TL10_HEK_500_30m_WT_repA

description:
rRNA-depleted total RNA
TL10_WT_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL10_WT_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL10_30m_WT


title: Pseudomonas putida KT2440, solid media, 12 hours, rep2

description: Library name: KT2440_solid_media_12h_replicate2


title: Pseudomonas putida KT2440, solid media, 12 hours, rep1

description: Library name: KT2440_solid_media_12h_replicate1


title: Liver,Q331K4

description: Library name: Liver8


title: K02

description: UDI-P 129


title: TL12_HEK_500_0m_WT_repB

description:
rRNA-depleted total RNA
TL12_WT_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL12_WT_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL12_0m_WT

value: 0 uM 4sU


title: N2a WT rep1

description: wild type N2a cells


title: TL10_HEK_500_0m_WT_repA

description:
rRNA-depleted total RNA
TL10_WT_MT_t5MTMMinformed6_modeAll_PcMTnorRNA.tsv
TL10_WT_Nuc_t5MMinformed5_lenient_modeAll.tsv
TL10_0m_WT


title: Pseudomonas putida KT2440, liquid media, 12 hours, rep2

description: Library name: KT2440_liquid_media_12h_replicate2


title: K01

description: UDI-P 128


title: Liver,Q331K3

description: Library name: Liver7


title: Liver,BKO4

description: Library name: Liver12


title: WT9 WS

description: H1 UDI-P 08

source_name: Skin

value: Skin


title: TS160_03_IRX3_KD-2

description: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).

source_name: Fujioka Cells

value: Fujioka Cells


title: WT8 WS

description: E1 UDI-P 05


title: Pseudomonas putida KT2440, liquid media, 12 hours, rep1

description: Library name: KT2440_liquid_media_12h_replicate1


title: TS160_05_IRX3_KD-1


title: Pseudomonas putida KT2440, solid media, 6 hours, rep2

description: Library name: KT2440_solid_media_6h_replicate2


title: WT7 WS

description: D1UDI-P 04


title: Liver,WT4

description: Library name: Liver4


title: Pseudomonas putida KT2440, liquid media, 24 hours, rep1

description: Library name: KT2440_liquid_media_24h_replicate1


title: TS160_01_IRX3_NTC-2


title: Pseudomonas putida KT2440, solid media, 6 hours, rep1

description: Library name: KT2440_solid_media_6h_replicate1


title: TS160_02_FTO_KD-2


title: K06 WS

description: G1 UDI-P 07


title: Liver,WT3

description: Library name: Liver3


title: TS160_08_FTO_KD-1


title: Liver,WT2

description: Library name: Liver2


title: K05 WS

description: B1 UDI-P 02


title: K03 WS

description: A1 UDI-P 01


title: TS160_04_FTO_NTC-2


title: 14plex_Patient U184

status: Public on Jan 20 2025

type: protein

city: Palo Alto

first: Lorinda

last: Chung

address: 1000 Welch Road

institute: Stanford University

description:
U184
59 year old Low risk Female

hyb_protocol: Samples were diluted 1:100 in assay buffer and run in duplicate. Diluted samples were incubated with magnetic beads for 1 hour. Beads were washed twice and incubated with detection antibody for 30 mins, followed by two washes and incubation with with Streptavidin-PE for 30 mins. Beads were washed twice, resuspended in reading buffer.

scan_protocol: A Luminex FlexMAP 3D instrument was used to measure fluorescence (in MFI) from each  barcoded bead.

data_processing:
Sample replicate MFI values were averaged for each antigen. The average barebead MFI was then subtracted from the average MFI of each sample and antigen. Samples were normalized by background correction and removed if correlation between technical replicates was <0.8.
Processed data file includes: each numerical value represents the mean fluorescent intensity (MFI) of each sample and bead after data processing.

molecule: protein

source_name: serum from patients at low risk of PAH

label_protocol: Immune Monitoring 14-plex

extract_protocol: Blood samples from patients  were collected in red top tubes from the Pulmonary Hypertension Assessment and Recognition of Outcomes in Scleroderma (PHAROS) study, a US-based, multi-center registry of SSc patients  .   The blood was then processed into serum which was then run on our arrays.

value: serum

tag: age in year

value: Female

tag: group

value: Low risk

tag: race

value: Caucasian

tag: ssc subtype

value: Limited

value: anticentromer


title: Liver,WT1

description: Library name: Liver1

value: Liver


title: 14plex_Patient U182

description:
U182
44 year old Low risk Female

value: Asian/Pacific Islander


title: Liver,Q331K2

description: Library name: Liver6


title: 14plex_Patient U181

description:
U181
57 year old Low risk Female


title: 14plex_Patient U180

description:
U180
62 year old Low risk Female

value: Hispanic


title: 14plex_Patient U183

description:
U183
50 year old Low risk Female

value: Diffuse


title: 14plex_Patient U179

description:
U179
52 year old Low risk Female

value: Scl 70


title: Liver,Q331K1

description: Library name: Liver5


title: 14plex_Patient U176

description:
U176
36 year old Low risk Female

value: negative


title: 14plex_Patient U178

description:
U178
53 year old Low risk Female


title: 14plex_Patient U173

description:
U173
59 year old PAH Female

source_name: serum from patient with PAH

value: PAH

value: Black

value: isolated nucleolar pattern


title: 14plex_Patient U172

description:
U172
59 year old PAH Female


title: 14plex_Patient U175

description:
U175
39 year old Low risk Male

value: Male

value: Other Ethnic Origin


title: 14plex_Patient U171

description:
U171
61 year old High risk Female

source_name: serum from patients at high risk of PAH

value: serum

value: High risk


title: 14plex_Patient U170

description:
U170
52 year old High risk Female

value: Female

value: Mixed or other


title: 14plex_Patient U169

description:
U169
55 year old PAH Female

value: Caucasian

value: Limited


title: 14plex_Patient U168

description:
U168
64 year old High risk Male


title: Pseudomonas putida KT2440, liquid media, 6 hours, rep2

description: Library name: KT2440_liquid_media_6h_replicate2

value: Bacterial culture


title: 14plex_Patient U167


title: Pseudomonas putida KT2440, liquid media, 6 hours, rep1

description: Library name: KT2440_liquid_media_6h_replicate1


title: 14plex_Patient U166

description:
U166
69 year old High risk Male


title: 14plex_Patient U165

description:
U165
45 year old PAH Female


title: 14plex_Patient U164

description:
U164
73 year old High risk Female

value: polymerase III


title: 14plex_Patient U162

description:
U162
68 year old PAH Female

value: anticentromer


title: 14plex_Patient U161

description:
U161
63 year old PAH Female

value: Diffuse


title: 14plex_Patient U160

description:
U160
71 year old PAH Female


title: 14plex_Patient U163

description:
U163
72 year old High risk Female


title: 14plex_Patient U159

description:
U159
67 year old PAH Female


title: 14plex_Patient U158

description:
U158
69 year old PAH Female


title: 14plex_Patient U156

description:
U156
49 year old High risk Female

value: Scl 70


title: 14plex_Patient U154

description:
U154
53 year old PAH Male


title: 14plex_Patient U157

description:
U157
54 year old High risk Female


title: 14plex_Patient U177

description:
U177
71 year old Low risk Female

value: Low risk

value: Asian/Pacific Islander


title: 14plex_Patient U155

description:
U155
52 year old High risk Female


title: 14plex_Patient U174

description:
U174
61 year old PAH Female

value: PAH

value: Black


title: 14plex_Patient U152

description:
U152
65 year old PAH Female

value: isolated nucleolar pattern


title: 14plex_Patient U150

description:
U150
62 year old PAH Female


title: 14plex_Patient U153

description:
U153
67 year old PAH Male

value: Male


title: 14plex_Patient U149

description:
U149
53 year old PAH Male

value: serum


title: 14plex_Patient U151

description:
U151
66 year old PAH Female


title: 14plex_Patient U147

description:
U147
58 year old High risk Female

value: High risk

value: negative


title: 14plex_Patient U148

description:
U148
68 year old PAH Female

value: Female


title: 14plex_Patient U144

description:
U144
36 year old PAH Female


title: 14plex_Patient U145

description:
U145
42 year old PAH Female


title: 14plex_Patient U142

description:
U142
56 year old High risk Male

value: Caucasian


title: 14plex_Patient U141

description:
U141
55 year old High risk Male

value: Limited


title: 14plex_Patient U139

description:
U139
54 year old High risk Female


title: 14plex_Patient U138

description:
U138
66 year old High risk Female


title: 14plex_Patient U140

description:
U140
60 year old High risk Female


title: 14plex_Patient U137

description:
U137
59 year old High risk Female


title: 14plex_Patient U136

description:
U136
57 year old High risk Female


title: 14plex_Patient U134

description:
U134
38 year old PAH Female


title: 14plex_Patient U135

description:
U135
52 year old High risk Female


title: 14plex_Patient U133

description:
U133
63 year old High risk Female

value: Mixed or other


title: 14plex_Patient U132

description:
U132
81 year old High risk Female


title: 14plex_Patient U131

description:
U131
75 year old High risk Female


title: 14plex_Patient U130

description:
U130
41 year old High risk Female


title: 14plex_Patient U127

description:
U127
58 year old High risk Female

value: polymerase III


title: 14plex_Patient U128

description:
U128
56 year old High risk Female

value: anticentromer


title: 14plex_Patient U126

description:
U126
71 year old PAH Female


title: 14plex_Patient U129

description:
U129
74 year old PAH Female

value: Unclassified


title: 14plex_Patient U122

description:
U122
46 year old PAH Female


title: 14plex_Patient U124

description:
U124
49 year old PAH Female

value: Diffuse

value: Scl 70


title: 14plex_Patient U125

description:
U125
61 year old High risk Female


title: 14plex_Patient U146

description:
U146
43 year old PAH Female

value: Asian/Pacific Islander


title: 14plex_Patient U119

description:
U119
69 year old High risk Female


title: 14plex_Patient U121

description:
U121
73 year old High risk Female


title: 14plex_Patient U123

description:
U123
65 year old High risk Female


title: 14plex_Patient U143

description:
U143
75 year old PAH Female

value: PAH


title: 14plex_Patient U116

description:
U116
57 year old PAH Female


title: 14plex_Patient U117

description:
U117
64 year old PAH Male


title: 14plex_Patient U120

description:
U120
51 year old PAH Male


title: 14plex_Patient U114

description:
U114
49 year old PAH Female


title: 14plex_Patient U113

description:
U113
73 year old PAH Male


title: 14plex_Patient U112

description:
U112
56 year old High risk Female


title: 14plex_Patient U109

description:
U109
70 year old High risk Female


title: 14plex_Patient U110

description:
U110
76 year old High risk Female


title: 14plex_Patient U107

description:
U107
74 year old High risk Female


title: 14plex_Patient U106

description:
U106
78 year old PAH Female


title: 14plex_Patient U108

description:
U108
80 year old High risk Female


title: 14plex_Patient U105

description:
U105
61 year old PAH Male


title: 14plex_Patient U104

description:
U104
73 year old PAH Female


title: 14plex_Patient U103

description:
U103
37 year old High risk Female

value: Other Ethnic Origin


title: 14plex_Patient U099

description:
U099
62 year old High risk Female

value: Hispanic

value: isolated nucleolar pattern


title: 14plex_Patient U098

description:
U098
59 year old High risk Female

value: serum


title: 14plex_Patient U100

description:
U100
69 year old High risk Female

value: High risk


title: 14plex_Patient U102

description:
U102
54 year old High risk Female

value: negative


title: 14plex_Patient U097

description:
U097
62 year old High risk Female

value: Female

value: Native American (i.e. American Indian)


title: 14plex_Patient U096

description:
U096
57 year old High risk Female

value: Limited


title: 14plex_Patient U092

description:
U092
33 year old High risk Female

value: Caucasian


title: 14plex_Patient U115

description:
U115
67 year old High risk Female


title: 14plex_Patient U093

description:
U093
38 year old High risk Female


title: 14plex_Patient U118

description:
U118
68 year old High risk Female


title: 14plex_Patient U094

description:
U094
63 year old PAH Female


title: 14plex_Patient U090

description:
U090
40 year old PAH Male

value: Male

value: Mixed or other


title: 14plex_Patient U091

description:
U091
44 year old PAH Male

value: anticentromer


title: 14plex_Patient U088

description:
U088
42 year old High risk Female


title: 14plex_Patient U087

description:
U087
62 year old High risk Female


title: 14plex_Patient U111

description:
U111
58 year old PAH Female

value: Diffuse


title: 14plex_Patient U089

description:
U089
45 year old High risk Female

value: Scl 70


title: 14plex_Patient U085

description:
U085
58 year old High risk Female


title: 14plex_Patient U083

description:
U083
53 year old High risk Female


title: 14plex_Patient U084

description:
U084
54 year old High risk Female


title: 14plex_Patient U082

description:
U082
47 year old High risk Female


title: 14plex_Patient U081

description:
U081
66 year old High risk Female


title: 14plex_Patient U079

description:
U079
74 year old High risk Female


title: 14plex_Patient U080

description:
U080
77 year old High risk Female


title: 14plex_Patient U078

description:
U078
71 year old High risk Female


title: 14plex_Patient U101

description:
U101
50 year old High risk Female

value: Unclassified


title: 14plex_Patient U077

description:
U077
70 year old High risk Female


title: 14plex_Patient U076

description:
U076
62 year old PAH Female

value: PAH


title: 14plex_Patient U073

description:
U073
41 year old High risk Male


title: 14plex_Patient U095

description:
U095
68 year old PAH Female


title: 14plex_Patient U074

description:
U074
48 year old High risk Male


title: 14plex_Patient U071

description:
U071
60 year old PAH Female


title: 14plex_Patient U075

description:
U075
53 year old PAH Female


title: 14plex_Patient U069

description:
U069
64 year old PAH Male


title: 14plex_Patient U070

description:
U070
59 year old PAH Female


title: 14plex_Patient U068

description:
U068
65 year old PAH Female


title: 14plex_Patient U064

description:
U064
58 year old PAH Male


title: 14plex_Patient U063

description:
U063
39 year old PAH Female

value: Black


title: 14plex_Patient U066

description:
U066
55 year old High risk Male


title: 14plex_Patient U061

description:
U061
40 year old PAH Male


title: 14plex_Patient U065

description:
U065
51 year old PAH Female


title: 14plex_Patient U067

description:
U067
60 year old High risk Male


title: 14plex_Patient U086

description:
U086
58 year old High risk Female


title: 14plex_Patient U060

description:
U060
37 year old PAH Female


title: 14plex_Patient U058

description:
U058
35 year old PAH Female


title: 14plex_Patient U059

description:
U059
63 year old PAH Female


title: 14plex_Patient U057

description:
U057
54 year old PAH Female


title: 14plex_Patient U056

description:
U056
65 year old High risk Female


title: 14plex_Patient U053


title: 14plex_Patient U052

description:
U052
56 year old PAH Male


title: 14plex_Patient U054

description:
U054
72 year old High risk Female


title: 14plex_Patient U055

description:
U055
73 year old PAH Female


title: 14plex_Patient U050

description:
U050
79 year old PAH Female


title: 14plex_Patient U049

description:
U049
81 year old PAH Male


title: 14plex_Patient U051

description:
U051
71 year old High risk Male


title: 14plex_Patient U072

description:
U072
62 year old PAH Female


title: 14plex_Patient U046

description:
U046
55 year old PAH Male


title: 14plex_Patient U044

description:
U044
67 year old PAH Female

value: polymerase III


title: 14plex_Patient U043

description:
U043
67 year old PAH Female


title: 14plex_Patient U062

description:
U062
58 year old PAH Female


title: 14plex_Patient U042

description:
U042
57 year old PAH Male

value: isolated nucleolar pattern


title: 14plex_Patient U045

description:
U045
50 year old PAH Male

value: serum


title: 14plex_Patient U040

description:
U040
62 year old PAH Female


title: 14plex_Patient U041

description:
U041
55 year old PAH Male


title: 14plex_Patient U037

description:
U037
61 year old PAH Female


title: 14plex_Patient U039

description:
U039
59 year old PAH Male


title: 14plex_Patient U035

description:
U035
54 year old High risk Female

value: High risk


title: 14plex_Patient U038

description:
U038
52 year old PAH Female


title: 14plex_Patient U032

description:
U032
61 year old PAH Female


title: 14plex_Patient U033

description:
U033
77 year old High risk Female


title: 14plex_Patient U034

description:
U034
52 year old High risk Female


title: 14plex_Patient U031

description:
U031
54 year old PAH Female


title: 14plex_Patient U030

description:
U030
64 year old PAH Male


title: 14plex_Patient U029

description:
U029
57 year old PAH Female


title: 14plex_Patient U028

description:
U028
50 year old PAH Female


title: 14plex_Patient U024

description:
U024
66 year old High risk Female


title: 14plex_Patient U023

description:
U023
46 year old PAH Female


title: 14plex_Patient U047

description:
U047
50 year old High risk Female


title: 14plex_Patient U048

description:
U048
74 year old PAH Female


title: 14plex_Patient U020

description:
U020
71 year old Healthy Female

source_name: serum from healthy control

value: Healthy


title: 14plex_Patient U021

description:
U021
68 year old Healthy Female

value: Female


title: 14plex_Patient U019

description:
U019
69 year old Healthy Female


title: 14plex_Patient U016

description:
U016
53 year old Healthy Female


title: 14plex_Patient U018

description:
U018
77 year old Healthy Female


title: 14plex_Patient U017

description:
U017
55 year old Healthy Female


title: 14plex_Patient U014

description:
U014
53 year old Healthy Female


title: 14plex_Patient U012

description:
U012
68 year old Healthy Female


title: 14plex_Patient U013

description:
U013
58 year old Healthy Female


title: 14plex_Patient U011

description:
U011
66 year old Healthy Female


title: 14plex_Patient U010

description:
U010
68 year old Healthy Male


title: 14plex_Patient U009

description:
U009
53 year old Healthy Male


title: 14plex_Patient U008

description:
U008
47 year old Healthy Male


title: 14plex_Patient U007

description:
U007
59 year old Healthy Female


title: 14plex_Patient U005

description:
U005
52 year old Healthy Female


title: 14plex_Patient U006

description:
U006
52 year old Healthy Male


title: 14plex_Patient U004

description:
U004
48 year old Healthy Female


title: 14plex_Patient U003

description:
U003
52 year old Healthy Male


title: 14plex_Patient U026

description:
U026
29 year old PAH Female


title: 14plex_Patient U025

description:
U025
49 year old PAH Female

value: Hispanic


title: 14plex_Patient U027

description:
U027
62 year old PAH Female

value: Limited

value: negative


title: 14plex_Patient U022

description:
U022
69 year old Healthy Female


title: 65plex_Patient U183

description:
U183
50 year old Low risk Female

data_processing: Sample replicate MFI values were averaged for each antigen. The average barebead MFI was then subtracted from the average MFI of each sample and antigen. Samples were normalized by background correction and removed if correlation between technical replicates was <0.8.

label_protocol: Immune Monitoring 65-plex

value: Low risk

value: Caucasian


title: 65plex_Patient U184

description:
U184
59 year old Low risk Female

value: anticentromer


title: 14plex_Patient U015

description:
U015
55 year old Healthy Female


title: 65plex_Patient U179

description:
U179
52 year old Low risk Female

value: Diffuse


title: 65plex_Patient U181

description:
U181
57 year old Low risk Female


title: 65plex_Patient U175

description:
U175
39 year old Low risk Male

value: Male

value: Other Ethnic Origin


title: 65plex_Patient U176

description:
U176
36 year old Low risk Female

value: Asian/Pacific Islander


title: 65plex_Patient U177

description:
U177
71 year old Low risk Female

value: Scl 70


title: 65plex_Patient U172

description:
U172
59 year old PAH Female

value: PAH

value: Black


title: 65plex_Patient U173

description:
U173
59 year old PAH Female

value: serum

value: isolated nucleolar pattern


title: 65plex_Patient U171

description:
U171
61 year old High risk Female

value: High risk


title: 65plex_Patient U180

description:
U180
62 year old Low risk Female

value: Female


title: 65plex_Patient U174

description:
U174
61 year old PAH Female


title: 65plex_Patient U170

description:
U170
52 year old High risk Female

value: Mixed or other


title: 65plex_Patient U178

description:
U178
53 year old Low risk Female

value: Hispanic

value: Limited


title: 65plex_Patient U169

description:
U169
55 year old PAH Female


title: 65plex_Patient U167


title: 65plex_Patient U166

description:
U166
69 year old High risk Male


title: 65plex_Patient U168

description:
U168
64 year old High risk Male


title: 65plex_Patient U164

description:
U164
73 year old High risk Female

value: polymerase III


title: 65plex_Patient U165

description:
U165
45 year old PAH Female


title: 65plex_Patient U163

description:
U163
72 year old High risk Female

value: Caucasian


title: 65plex_Patient U162

description:
U162
68 year old PAH Female

value: anticentromer


title: 65plex_Patient U182

description:
U182
44 year old Low risk Female

value: Low risk


title: 65plex_Patient U159

description:
U159
67 year old PAH Female

value: Diffuse


title: 65plex_Patient U158

description:
U158
69 year old PAH Female


title: 65plex_Patient U161

description:
U161
63 year old PAH Female


title: 65plex_Patient U155

description:
U155
52 year old High risk Female


title: 65plex_Patient U160

description:
U160
71 year old PAH Female


title: 14plex_Patient U036

description:
U036
63 year old High risk Female


title: 65plex_Patient U157

description:
U157
54 year old High risk Female


title: 65plex_Patient U156

description:
U156
49 year old High risk Female


title: 65plex_Patient U154

description:
U154
53 year old PAH Male

value: Male


title: 65plex_Patient U153

description:
U153
67 year old PAH Male


title: 65plex_Patient U152

description:
U152
65 year old PAH Female


title: 65plex_Patient U151

description:
U151
66 year old PAH Female


title: 65plex_Patient U150

description:
U150
62 year old PAH Female


title: 65plex_Patient U143

description:
U143
75 year old PAH Female


title: 65plex_Patient U138

description:
U138
66 year old High risk Female


title: 65plex_Patient U140

description:
U140
60 year old High risk Female

value: negative


title: 65plex_Patient U142

description:
U142
56 year old High risk Male


title: 65plex_Patient U148

description:
U148
68 year old PAH Female


title: 65plex_Patient U147

description:
U147
58 year old High risk Female

value: Asian/Pacific Islander


title: 65plex_Patient U146

description:
U146
43 year old PAH Female

value: PAH


title: 65plex_Patient U133

description:
U133
63 year old High risk Female


title: 65plex_Patient U145

description:
U145
42 year old PAH Female

value: Black


title: 65plex_Patient U141

description:
U141
55 year old High risk Male

value: serum


title: 65plex_Patient U131

description:
U131
75 year old High risk Female


title: 65plex_Patient U130

description:
U130
41 year old High risk Female


title: 65plex_Patient U132

description:
U132
81 year old High risk Female

value: Scl 70


title: 65plex_Patient U134

description:
U134
38 year old PAH Female

value: isolated nucleolar pattern


title: 65plex_Patient U137

description:
U137
59 year old High risk Female

value: Female

value: High risk


title: 65plex_Patient U139

description:
U139
54 year old High risk Female


title: 65plex_Patient U136

description:
U136
57 year old High risk Female


title: 65plex_Patient U135

description:
U135
52 year old High risk Female


title: 65plex_Patient U149

description:
U149
53 year old PAH Male


title: 65plex_Patient U128

description:
U128
56 year old High risk Female


title: 65plex_Patient U144

description:
U144
36 year old PAH Female


title: 65plex_Patient U126

description:
U126
71 year old PAH Female


title: 65plex_Patient U122

description:
U122
46 year old PAH Female

value: Unclassified


title: 65plex_Patient U124

description:
U124
49 year old PAH Female


title: 65plex_Patient U123

description:
U123
65 year old High risk Female


title: 65plex_Patient U129

description:
U129
74 year old PAH Female


title: 65plex_Patient U125

description:
U125
61 year old High risk Female

value: Limited


title: 65plex_Patient U127

description:
U127
58 year old High risk Female

value: polymerase III