title: U2OS, sgRNA targeting HLTF transfected, HLTF-ChIP, repeat 2

city: Stanford

first: Karlene

middle: Anne

last: Cimprich

state: CA

address: 318 Campus Drive

institute: Stanford University

description:
bigWig files showing the spike-in normalized ChIP signal. In U2OS_HLTF_ChIP_sgHLTF_rep2.bw, signal from a single HLTF targeting sgRNA transfected repeat is shown. In U2OS_HLTF_ChIP_sgHLTF.bw, signal from U2OS_HLTF_ChIP_sgHLTF_rep1.bw and U2OS_HLTF_ChIP_sgHLTF_rep2.bw was averaged.
U2OS_HLTF_ChIP_sgHLTF.bw

data_processing:
FASTA files of human (hg38) and mouse (mm39) reference genome were used in bowtie2-build to generate an indexed “hybrid” reference genome.
Raw FASTQ reads from HLTF ChIP-seq and input were aligned to the hybrid reference genome using bowtie2 (2.2.5) –local mode using paired inputs with default parameters.
Picard (2.27.5) MarkDuplicates was used to deduplicate.
Samtools (1.16.1) was used to filter the reads: reads aligned to the chromosomes were kept; unmapped, pairs with only one mate aligned, duplicates and reads aligned to the ENCODE blacklist regions were excluded. Reads are parsed into human versus mouse aligned reads. The total number of mouse aligned reads for each sample were taken to calculate the spike-in normalization factors.
Deeptools (3.5.1) bamCoverage was used to generate bigWig files with the signals scaled using the spike-in normalization factor.
MACS2 (2.2.7.1) was used to identify HLTF ChIP-seq peaks with default settings using FDR=0.05 as cutoff. The peaks were further filtered based on the average ChIP-seq signal intensity within the peak regions following ENCODE guidelines: at least a 2-fold signal enrichment in the control versus HLTF knockdown ChIP-seq sample was used as cutoff.
Assembly: GRCh38.p14 and GRCm39
Supplementary files format and content: bigWig: Spike-in normalized ChIP-seq or input signal.
Supplementary files format and content: narrowPeak: HLTF ChIP-seq peaks

source_name: Bone

growth_protocol: DMEM, supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin/streptomycin. Cells were cultured in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
For each ChIP-seq experiment, ~60 million cells per immunoprecipitation condition were fixed with 1% formaldehyde for 5 min at room temperature and then quenched. Cells were harvested in ice-cold PBS containing protease and phosphatase inhibitors. Murine ESCs expressing MPP8-GFP were added at a 1:10 ratio during cell lysis as spike-in control. After cell lysis, chromatin was fragmented using the Covaris Focused Ultrasonicator E220 and then immunoprecipitated (IP). For each IP reaction, Dynabeads Protein A and Protein G were pre-incubated overnight with 15 μg antibody against GFP (Abcam, ab290). Chromatin was then added to the beads, and IP was performed for at least 6 h at 4 °C with rotation. Beads were washed and chromatin was eluted. Input samples and eluted samples were de-crosslinked. DNA was isolated by phenol-chloroform extraction and ethanol precipitation and then used for library preparation.
Library was prepared using the NEBnext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and NEBNext Multiplex Oligos for Illumina (NEB, E7600) following the manufacturer's instructions. Cycle number was determined by qPCR. Quality and Quantity of the library was assessed on the QUBIT using the Quant-iT™ dsDNA HS Assay Kit, the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA Assay and NEBNext Library Quant Kit for Illumina (NEB, E7630).

treatment_protocol: U2OS cells were transfected using Lipofectamine RNAiMAX according to the manufacturer’s directions with either a non-targeting sgRNA as a negative control, or sgRNA against HLTF. 96 h post-transfection, cells were processed for ChIP-seq.

value: Bone

value: Human Bone Osteosarcoma Epithelial Cells

tag: chip antibody

value: GFP (Abcam, ab290)

value: WT

value: Transfected with a sgRNA targeting HLTF


title: invitro_pgwat_svf_female_O8

status: Public on Aug 13 2024

type: SRA

city: Huddinge

first: Martin

middle: Verner

last: Uhrbom

address: Hälsovägen 7C

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic

data_processing:
bcl2fastq - demultiplexing
Raw fastq-files were collected, sequencing adapters were then trimmed from the remaining libraries using NGmerge (v0.3) and read quality for all libraries was assessed using FastQC (v0.11.9), Qualimap (v2.2.2d) and samtools stats (v1.15). Quality control (QC) metrics for Qualimap and samtools were based on a STAR (v2.7.10a) alignment against the mouse genome (GRCm39, Gencode vM32). UMI information was evaluated with UMI tools. Next, QC metrics were summarized using MultiQC (v1.12). A mouse transcriptome index consisting of cDNA and ncRNA entries from Gencode (vM32) was generated and reads were mapped to the index and quantified using Salmon (v1.9.0). The bioinformatics workflow was organized using Nextflow workflow management system (v22.04.5) and Bioconda software management tool.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file as expression matrix including non-normalized counts of all samples.

molecule: total RNA

organism: Mus musculus

source_name: pgwat

growth_protocol: Crude SVF cells were isolated from pgWAT and iWAT using collagenase/Dispase solution. Cells were then cultivated in PM1 medium (Zenbio) in the present of 1 nM of basic FGF in a 96 well plate for four days.

extract_protocol:
Qiagen’s RNeasy plus micro kit (Cat. No. 74 034).
RNA libraries were prepared using standard SmartSeq3 protocol.

treatment_protocol: 1 nM of basic FGF.

tag: tissue

value: pgwat

tag: cell type

value: Stromal vascular fraction

tag: Sex

value: female

tag: genotype

tag: treatment

value: PM1+bFGF for 4days


title: U2OS, input

country: USA

description:
bigWig file showing the spike-in normalized input signal, averaged from two input samples of non-targeting sgRNA transfected repeats.
HLTF_ChIP_peaks.narrowPeak

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

value: Transfected with a non-targeting sgRNA


title: invitro_iwat_svf_male_P7

source_name: iwat

value: iwat

value: male


title: Methylation - Patient 5

type: genomic

city: Rochester

first: Alexandre

last: Gaspar-Maia

state: MN

address: 200 First street SW

institute: Mayo Clinic

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”.

label: cy3, cy5

source_name: Peripheral blood mononuclear cells

label_protocol: standard protocol

extract_protocol: Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines.

tag: disease state 1

value: Clonal hematopoiesis


title: U2OS, sgRNA targeting HLTF transfected, HLTF-ChIP, repeat 1

description:
bigWig file showing the spike-in normalized ChIP signal. In U2OS_HLTF_ChIP_sgHLTF_rep1.bw, signal from a single HLTF targetting sgRNA transfected repeat is shown.
U2OS_HLTF_ChIP_sgHLTF.bw


title: invitro_iwat_svf_male_N7


title: U2OS, non-targeting sgRNA transfected, HLTF-ChIP, repeat 2

description:
bigWig files showing the spike-in normalized ChIP signal. In U2OS_HLTF_ChIP_sgCON_rep2.bw, signal from a single non-targeting sgRNA transfected repeat is shown. In U2OS_HLTF_ChIP_sgCON.bw, signal from U2OS_HLTF_ChIP_sgCON_rep1.bw and U2OS_HLTF_ChIP_sgCON_rep2.bw is averaged. To call HLTF peaks, both sgCON repeats were used as the IP data file to compare to the input sample as control in MACS2. HLTF peaks were further filtered as described and recorded in HLTF_ChIP_peaks.narrowPeak.
U2OS_HLTF_ChIP_sgCON.bw
HLTF_ChIP_peaks.narrowPeak


title: Methylation - Patient 38

tag: disease state 2


title: U2OS, non-targeting sgRNA transfected, HLTF-ChIP, repeat 1

description:
bigWig file showing the spike-in normalized ChIP signal. In U2OS_HLTF_ChIP_sgCON_rep1.bw, signal from a single non-targeting sgRNA transfected repeat is shown.
U2OS_HLTF_ChIP_sgCON.bw
HLTF_ChIP_peaks.narrowPeak


title: invitro_iwat_svf_male_O7


title: invitro_pgwat_svf_female_L8


title: invitro_pgwat_svf_female_K8


title: HUVECs,  30 min of 15 dyn/cm2 fluid shear stress replicate 3

city: Milwaukee

first: Brandon

middle: J

last: Tefft

state: WI

address: 8701 W Watertown Plank Rd

department: Biomedical Engineering

institute: Medical College of Wisconsin & Marquette University

data_processing:
Trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software
The transcript abundances for each sample was estimated with StringTie
The FPKM value for gene and transcript level were filtered using the R package Ballgown
The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown
Assembly: GRCH37
Supplementary files format and content: Expression_Gene.xlsx, All_Differentially_Expressed_Genes.xlsx

source_name: Adherent HUVECs seeded on fibronectin-coated tissue culture plate exposed to 30 min of 15 dyn/cm2 fluid shear stress

growth_protocol: Primary HUVECs were maintained in vascular basal cell medium supplemented with bovine braine extract (BBE) growth kit, 10% fetal bovine serum and 1x antibiotic-antimycotic

extract_protocol:
RNA from the adherent cells was extracted using the Rneasy Plus Kit (Qiagen). A total of 5 μg RNA was sent to ArrayStar for RNA-sequencing
RNA-seq library preparation using KAPA Stranded RNA-Seq Library and Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library

treatment_protocol: Fluid shear stress was applied using a rectangular parallel plate flow chamber (GlycoTech)

value: Primary human umbilical vein endothelial cells (HUVECs)

value: 30 min fluid shear stress


title: hBMSC-pcDNA3.1

city: Shenzhen

first: Peikai

last: Chen

address: 1 Haiyuan Rd

country: China

institute: The University of Hong Kong - Shenzhen Hospital

data_processing:
The fastq data files were aligned to human reference genome hg38, using hisat (v. 2-2.0.4) with default parameters.
The resulting bam files were processed with cufflinks (v2.2.1) for quantification of FKPM, with gene models provided by GENCODE  (v. 25).
The resulting bam files were also processed with HTSeq count (version 0.11.0) for quantification of gene counts, with gene models provided by GENCODE  (v. 25).
Assembly: GRCh38
Supplementary files format and content: tab delimited files gzipped

source_name: Bone marrow MSCs

extract_protocol:
The transfected bone marrow MSCs (pcDNA3.1 and pcDNA3.1-WNT1) were lysed with Trizol (Thermo Fisher) for RNA extraction. RNA concentration was measured by Qubit and RNA integrity was assessed using the Agilent 2100. A total amount of 2 µg RNA per sample was used for sequencing.
Libraries were generated using VAHTS mRNA-seq Library Prep Kit and sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads in Berry Genomics Co. (Beijing).

treatment_protocol: Bone marrow MSCs were transfected with pcDNA3.1-WNT1 or empty vectors. After selection, cells were treated with osteoblastic and adipogenic differentiation media for 14~28 days followed by staining with Alizarin red (Sigma) or Oil red (Beyotime Biotechnology).

value: Bone marrow MSCs

value: transfected with empty vectors, duplicate 2


title: invitro_iwat_svf_female_P9


title: invitro_pgwat_svf_male_J9


title: HUVECs,  10 min of 15 dyn/cm2 fluid shear stress replicate 3

source_name: Adherent HUVECs seeded on fibronectin-coated tissue culture plate exposed to 10 min of 15 dyn/cm2 fluid shear stress

value: 10 min fluid shear stress


title: HUVECs,  30 min of 15 dyn/cm2 fluid shear stress replicate 2


title: HUVECs,  10 min of 15 dyn/cm2 fluid shear stress replicate 2


title: invitro_iwat_svf_female_J8


title: invitro_pgwat_svf_male_I7


title: HUVECs,  10 min of 15 dyn/cm2 fluid shear stress replicate 1


title: MCF7,IAA,rep2

city: Wuhan

first: Ziang

last: Lu

address: Wuhan University, No.299, Bayi Road, Wuchang District

institute: Wuhan University

data_processing:
After trimming adapters, CUT&TAG raw reads were aligned to hg38 human genome using bowtie2 and duplicate reads were removed from unique mapping reads using Picard MarkDuplicates.
The clean reads were used to call peaks using MACS2. After removing peaks in blacklist, the high repeatability peaks between biological replicates were get using IDR.
After trimming adapters, AMUC-seq raw reads were alinged to human rRNA using bowtie2 to remove rRNA sequences.
Unmapped reads were mapped to hg38 human genome with STAR. Duplicate reads were removed from unique reads using Picard MarkDuplicates .
Mutation sites were collected and annotated with REDItools, and SNP sites were removed.
Assembly: Mutation rate calculation and s4U labeled reads extraction were performed with custom script. Raw counts of s4U labeled mRNA and all mRNA were obtained using htseq. TPM expression matrix and fold change were calculated with custom script.
Supplementary files format and content: hg38
Supplementary files format and content: bigwig, aligned reads or labeled reads in AMUC-seq
Supplementary files format and content: bed, IDR peak result
Library strategy: CUT&TAG

growth_protocol: All cells were cultured with Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco) in the presence of 5% CO2 at 37°C incubators.

extract_protocol:
Genomic DNA was extracted by EasyPure Genomic DNA Kit (TransGen Biotech). Total RNA was extracted by Invitrogen TRIzol (Thermofisher) . PolyA RNA was extracted by NEBNext® High Input Poly(A) mRNA Isolation Module.
CUT&TAG libraries were constructed with CUT&TAG kit (Vazyme, #TD903). AMUC-seq libraries were constructed with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: 500μM s4U and 500μM IAA will be treated in corresponding samples.

tag: antibody

value: BG4 sigma MABE9917

value: IAA treated


title: Ctl1B_Day19_repl2

city: Uppsala

first: Xingqi

address: Husargata

department: Immunology, Genetics and Pathology

institute: uppsala university

data_processing:
adaptors were trimmed.
All reads were aligned to hg38 using bowtie2 with the following parameters  "--end-to-end --very-sensitive -I 10 -X 700"
The aligned BAM files were sorted and filtered with alignment quality of  >Q2 using samtools v.1.9
The bigwig file were generated from BAM file using deeptools with the parameters "bamCoverage –normalizeUsing CPM"
MACS2
Assembly: hg38
Supplementary files format and content: bigwig

source_name: induced pluripotent stem cells (iPSCs)

extract_protocol:
ATAC-Seq libraries were prepared following. In brief, two technical replicates per sample containing 50,000 nuclei each were collected at 500 x g for 5 min at 4°C. Nuclei were resuspended in lysis buffer (10 mM Tris-Cl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Igepal CA-630) and centrifuged at 500 x g for 10 min. The supernatant was removed and each nuclei pellet was resuspended in tagmentation buffer (25 μL 2 × TD buffer) with 2.5 μl Tn5 transposome and incubated at 37°C for 30 min. An equal volume of 2 x reverse crosslinking buffer (50 mM Tris-Cl, 1mM EDTA, 1% SDS, 0.2M NaCl, 5 ng/ml Proteinase K) was added to each sample and incubated at 65°C with agitation at 1200 rpm for overnight. DNA was isolated using a MinElute PCR Purification Kit (Qiagen). Sequencing libraries were prepared following described standard protocol. All libraries were sequenced on an Illumina Nova-seq platform at Novogene Europe.
dsDNA was tagmented with Tn5, then PCR is performed using primers with barcode.

treatment_protocol: Cell cultures were sampled at days 0 (D0), D19, D35 and D65, respectively, by harvesting cells with TryplE and collecting by centrifugation (300 x g, 3 min). Harvested cells were counted and assessed for viability using trypan blue staining and an automated EVE cell counter (NanoEntek).Samples with a viability of>90% were selected for ATAC-Seq library preparation (see below).Additionally, neuronal cell cultures at D65 were treated with valproic acid (VPA; 0,5 mM) for 6 days and subsequently harvested for analysis. Harvested cells were resuspended in 1 ml of 1 x PBS and fixed by adding an equal amount of 2% formaldehyde for 10 min at room temperature. The reaction was quenched by adding 100 ul 2,5 M glycine solution. Fixed cells were collected by centrifugation and washed twice with 1 x PBS. Cells where then resuspended in 1 x PBS, counted using an EVE automatic cell counter (NanoEntek) with Trypan Blue, and subsequently 50’000 cells/sample were processed for library preparation for ATAC sequencing.

value: induced pluripotent stem cells (iPSCs)

tag: group

tag: time point


title: invitro_iwat_svf_male_H9


title: HUVECs,  5 min of 15 dyn/cm2 fluid shear stress replicate 3

source_name: Adherent HUVECs seeded on fibronectin-coated tissue culture plate exposed to 5 min of 15 dyn/cm2 fluid shear stress

value: 5 min fluid shear stress


title: invitro_iwat_svf_female_H8


title: HUVECs,  5 min of 15 dyn/cm2 fluid shear stress replicate 2


title: invitro_iwat_svf_female_H7


title: HUVECs,  5 min of 15 dyn/cm2 fluid shear stress replicate 1


title: invitro_pgwat_svf_female_G10

value: pgwat


title: HUVECs,  0 min of fluid shear stress replicate 3

source_name: Adherent HUVECs seeded on fibronectin-coated tissue culture plate exposed to 0 min of fluid shear stress

value: 0 min fluid shear stress


title: invitro_iwat_svf_male_G9

value: Stromal vascular fraction


title: invitro_iwat_svf_female_G7

value: female

value: PM1+bFGF for 4days


title: HUVECs,  0 min of fluid shear stress replicate 1


title: HUVECs,  0 min of fluid shear stress replicate 2


title: invitro_iwat_svf_female_F7

value: iwat


title: Human primary lung fibroblasts IMR90 - Senescent Mutant HIRA (pQCXIP-HA-HIRA (520-1017)) 9_DHIRA_Sen3

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description: RNA extraction

data_processing:
Real Time Analysis 3.4.4 software used for basecalling.
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks, then transferred to TPM
Assembly: hg38
Supplementary files format and content: TPM matrix contains TPM values for each sample and each gene
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene

source_name: Human primary lung fibroblasts IMR90

growth_protocol: To culture the cells and induce senescence, primary human IMR90 fibroblasts were grown in DMEM supplemented with 10% FBS, 100 U/mL penicillin, 100 μg/mL streptomycin, and 2 mM glutamine at 37°C in a humidified atmosphere with 5% CO2 and 3.5% oxygen. To induce senescence, cells were treated with etoposide, a DNA damaging agent, at a concentration of 25 or 50 μM for 24 hours. Following this treatment, the etoposide-containing media was replaced with complete media.  After eight days, the cells were harvested for senescence assays

extract_protocol:
The TRIzol method was used to extract total RNA according to the manufacturer's instructions (Invitrogen™ TRIzol™ Reagent, Catalog number: 15596026).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Senescence was induced by 50 µM Etoposide, a DNA damaging agent.

value: lung

tag: growing state

value: Senescence

value: Mutant HIRA


title: Human primary lung fibroblasts IMR90 - Senescent Mutant HIRA (pQCXIP-HA-HIRA (520-1017)) 8_DHIRA_Sen2

description: RNA extraction


title: HUVECs,  30 min of 15 dyn/cm2 fluid shear stress replicate 1

value: Primary human umbilical vein endothelial cells (HUVECs)

value: 30 min fluid shear stress


title: invitro_iwat_svf_female_I8


title: invitro_iwat_svf_male_D7

value: male


title: Human primary lung fibroblasts IMR90 - Senescent Mutant HIRA (pQCXIP-HA-HIRA (520-1017)) 7_DHIRA_Sen1

description: RNA extraction


title: invitro_iwat_svf_female_E7


title: invitro_pgwat_svf_male_C9


title: Human primary lung fibroblasts IMR90 - Senescent Empty vector control (pQCXIP) 6_EV_Sen3

description: RNA extraction

value: Empty Vector


title: Human primary lung fibroblasts IMR90 - Senescent Empty vector control (pQCXIP) 5_EV_Sen2

description: RNA extraction


title: invitro_pgwat_svf_female_B10


title: Human primary lung fibroblasts IMR90 - Proliferating Empty vector control (pQCXIP) 3_EV_Prolif3

description: RNA extraction

value: Proliferating


title: Human primary lung fibroblasts IMR90 - Proliferating Empty vector control (pQCXIP) 2_EV_Prolif2

description: RNA extraction


title: invitro_iwat_svf_male_B9


title: invitro_pgwat_svf_male_B8


title: Human primary lung fibroblasts IMR90 - Senescent Empty vector control (pQCXIP) 4_EV_Sen1

description: RNA extraction


title: Human primary lung fibroblasts IMR90 - Proliferating Empty vector control (pQCXIP) 1_EV_Prolif1

description: RNA extraction


title: invitro_pgwat_svf_female_A10


title: invitro_iwat_svf_male_A7


title: invitro_iwat_svf_female_F10


title: invitro_iwat_svf_male_B7


title: Tapestri - Protein - UPN_44

library_source: other

data_processing:
FASTQ files generated by sequencers were processed using the Tapestri Pipeline V2 which handles adapter trimming, sequence alignment (BWA), barcode correction, cell finding and variant calling (using GATK 4.1.7 haplotype caller). Generated loom and H5 files were then processed with Tapestri Insights v2.2 (Mission Bio) and/or the Python-based Mosaic package (GitHub). Tapestri Insights analysis used default filter criteria (for example, genotype quality ≥30 and reads per cell per target ≥10) or whitelisting of known variants and annotation-based information (including ClinVar and DANN). Only cells with complete genotype information for all variants (previously detected in bulk sample) were included for downstream processing.
Assembly: hg38
Library strategy: Tapestri (Mission Bio) - single cell DNA + protein

molecule: protein

extract_protocol: Single-cell DNAseq + proteogenomics was performed using the Mission Bio Tapestri platform according to the manufacturer’s specifications.

value: Peripheral blood mononuclear cells

tag: disease state_1

value: Clonal Hematopoiesis

tag: disease state_2


title: FACS_iwat_female_ovariex_ASC1_P4

data_processing:
bcl2fastq - demultiplexing
Raw fastq-files were collected, sequencing adapters were then trimmed from the remaining libraries using NGmerge (v0.3) and read quality for all libraries was assessed using FastQC (v0.11.9), Qualimap (v2.2.2d) and samtools stats (v1.15). Quality control (QC) metrics for Qualimap and samtools were based on a STAR (v2.7.10a) alignment against the mouse genome (GRCm39, Gencode vM32). UMI information was evaluated with UMI tools. Next, QC metrics were summarized using MultiQC (v1.12). A mouse transcriptome index consisting of cDNA and ncRNA entries from Gencode (vM32) was generated and reads were mapped to the index and quantified using Salmon (v1.9.0). The bioinformatics workflow was organized using Nextflow workflow management system (v22.04.5) and Bioconda software management tool.
Assembly: GRCm39
Supplementary files format and content: Space-delimited text file as expression matrix including non-normalized counts of all samples.

growth_protocol: FACS sorted adipose stem cells (CD45-/CD31-/CD34+/DPP4+/-) from iWAT depot from castrated/ovaryectomized/control mice.

treatment_protocol: Castration or ovariectomy.

value: ovariex


title: Tapestri - Protein - UPN_45


title: FACS_iwat_female_ovariex_ASC2_P3


title: Tapestri - Protein - UPN_43


title: Tapestri - Protein - UPN_42


title: FACS_iwat_male_castration_ASC1_P2

value: castration


title: Tapestri - Protein - UPN_41


title: FACS_iwat_male_castration_ASC2_P1


title: FACS_iwat_female_ovariex_ASC2_O3


title: Tapestri - Protein - UPN_39


title: invitro_iwat_svf_male_C7


title: FACS_iwat_male_castration_ASC1_O2


title: FACS_iwat_male_castration_ASC2_O1


title: Tapestri - Protein - UPN_38


title: Tapestri - Protein - UPN_48


title: FACS_iwat_female_ovariex_ASC1_N4


title: FACS_iwat_female_ovariex_ASC2_N3


title: Tapestri - Protein - UPN_36


title: Tapestri - Protein - UPN_33


title: Tapestri - Protein - UPN_32


title: Tapestri - Protein - UPN_47


title: FACS_iwat_male_castration_ASC1_N2


title: Tapestri - Protein - UPN_26


title: FACS_iwat_male_castration_ASC1_M2


title: Tapestri - Protein - UPN_30


title: Tapestri - Protein - UPN_22


title: FACS_iwat_female_ovariex_ASC2_M3


title: FACS_iwat_male_castration_ASC2_M1


title: FACS_iwat_female_ovariex_ASC1_L4


title: Tapestri - Protein - UPN_17


title: Tapestri - Protein - UPN_21


title: Tapestri - Protein - UPN_8


title: Tapestri - Protein - UPN_7


title: FACS_iwat_male_castration_ASC1_L2


title: FACS_iwat_female_ovariex_ASC2_K3


title: Tapestri - Protein - UPN_6


title: FACS_iwat_male_castration_ASC1_K2


title: Tapestri - Protein - UPN_5


title: Tapestri - Protein - UPN_31


title: FACS_iwat_male_castration_ASC2_K1


title: FACS_iwat_male_castration_ASC2_N1


title: Tapestri - Protein - UPN_1


title: Tapestri - DNA - UPN_48


title: Tapestri - DNA - UPN_47


title: FACS_iwat_male_castration_ASC1_J2


title: FACS_iwat_female_ovariex_ASC2_J3


title: FACS_iwat_male_castration_ASC2_J1


title: Tapestri - DNA - UPN_45


title: Tapestri - DNA - UPN_44


title: Tapestri - DNA - UPN_43


title: FACS_iwat_male_castration_ASC1_I2


title: Tapestri - DNA - UPN_42


title: FACS_iwat_female_ovariex_ASC2_L3


title: FACS_iwat_male_castration_ASC2_I1


title: FACS_iwat_female_ovariex_ASC2_I3


title: FACS_iwat_female_control_ASC2_H3

value: control


title: FACS_iwat_female_control_ASC1_H4


title: FACS_iwat_male_castration_ASC2_L1


title: Tapestri - DNA - UPN_39


title: Tapestri - DNA - UPN_41


title: FACS_iwat_male_control_ASC1_H2


title: Tapestri - Protein - UPN_4


title: FACS_iwat_male_control_ASC2_H1


title: Tapestri - DNA - UPN_36


title: FACS_iwat_female_control_ASC1_G4


title: Tapestri - DNA - UPN_33


title: Tapestri - DNA - UPN_38


title: FACS_iwat_female_control_ASC2_G3


title: Tapestri - DNA - UPN_32


title: hBMSC-WNT1-A

value: Bone marrow MSCs

value: transfected with pcDNA3.1-WNT1, duplicate 1


title: FACS_iwat_male_control_ASC2_G1


title: FACS_iwat_male_control_ASC1_G2


title: Tapestri - DNA - UPN_30


title: FACS_iwat_female_control_ASC1_F4

value: female


title: Tapestri - DNA - UPN_26


title: FACS_iwat_female_control_ASC1_E4

value: iwat


title: FACS_iwat_female_control_ASC2_E3


title: Tapestri - DNA - UPN_17


title: Tapestri - DNA - UPN_7


title: Tapestri - DNA - UPN_5


title: Tapestri - DNA - UPN_21


title: FACS_iwat_male_control_ASC2_E1


title: FACS_iwat_female_control_ASC2_D3


title: FACS_iwat_female_control_ASC1_D4


title: FACS_iwat_female_control_ASC2_F3


title: Tapestri - DNA - UPN_6


title: Tapestri - DNA - UPN_31


title: FACS_iwat_male_control_ASC2_F1


title: DNA-seq - Patient 227

data_processing:
library strategy: Target Capture Chip Assay for Bulk Sequencing
Bioinformatics analysis included quality assessment and alignment to the hg19 build reference genome using Novoalign, followed by GATK based single nucleotide and small insertion / deletion variant calling, structural variation discovery, and annotation. Somatic single nucleotide variations (SNVs) were genotyped using SomaticSniper, whereas insertions and deletions were called by GATK Somatic Indel Detector. Each variant in coding regions was functionally annotated by SnpEff, SAVANT, ClinVar, dbNSFP, OMIM, and the Human Gene Annotation Database to predict biological effects. Each variant was also annotated with allele frequency from the Exoma Aggregation Consortium. The total list of all variants was internally compared for internal duplicates indicative of false positives, and variants of concern are additionally hand annotated for identification using Alamut Software. Interpretation for relevant alterations included absence in international normal variant allele databases (GnomAD, ExAC), deleterious effect on protein function by multiple phenotype prediction models, somatic and functional annotation in literature, consequence of variant (nonsense, truncating, etc.) and location proximal to important domains.
Assembly: hg19
Supplementary files format and content: Supplementary file containing the variant calls for mutations associated with Clonal Hematopoiesis.

extract_protocol:
Sample DNA was extracted from peripheral blood mononuclear cells isolated by gradient centrifugation and re-suspended in a concentration of 500 ng in 50µl of low TE buffer.
Paired-end indexed libraries were prepared using the Sureselect XT Low Input Library prep protocol on the Agilent Bravo liquid handler following the manufacturer’s protocol (NewEngland Biolabs, Ipswitch, MA, and Agilent Technologies, Ankeny, IA). Briefly, 200ng of target DNA was fragmented using the Covaris LE220 plus sonicator. The settings of duty factor 30%, peak incident power (PIP) 450, cycles per burst 200, time 180 seconds generated double-stranded DNA fragments with blunt or sticky ends with a fragment size mode of between 150-200bp. The ends were repaired using the Sureselect End-Repair-A-Tailing enzyme mix. Adapter ligated DNA fragments were size selected to enrich for 200 bp inserts (~320 bp total library size) using AMPURE XP bead purification. The size selected adapter-modified fragments were enriched, and specific indexes were added by 12 cycles of PCR using universal index primers. The concentration and size distribution of the libraries was determined on an Agilent Bioanalyzer DNA 1000 chip. The Custom Capture hybrid-target enrichment probes were designed using Agilent SureSelect design software (Agilent Technologies, Santa Clara, CA). The targeted gene panel was comprised of 62,962 single probes with size 1.805Mbp, and covered the coding regions, UTRs, and overlapping intron/exon regions for 205 genes described and / or enriched for CH mutations (see Appendix: Target Gene Panel). The custom capture was carried out using the Agilent Bravo liquid handler following Agilent’s SureSelect XT Low. Purified capture products were then amplified using the SureSelect Post-Capture primer mix for 14 cycles. Libraries were validated and quantified on the Agilent Bioanalyzer. Samples were sequenced by 150 paired end reads, 21 samples to a Flow Cell, on an Illumina NovaSeq 6000 SP with an expected depth of ≥1,000X coverage (Illumina, SanDiego, CA).


title: Tapestri - DNA - UPN_22


title: FACS_iwat_male_control_ASC1_D2


title: FACS_iwat_male_control_ASC2_D1


title: FACS_iwat_male_control_ASC1_C2


title: DNA-seq - Patient 226


title: DNA-seq - Patient 224


title: FACS_iwat_male_control_ASC2_C1


title: Tapestri - DNA - UPN_8


title: FACS_iwat_female_control_ASC1_C4


title: FACS_iwat_female_control_ASC2_C3


title: FACS_iwat_male_control_ASC1_F2


title: DNA-seq - Patient 223


title: DNA-seq - Patient 222


title: DNA-seq - Patient 225


title: FACS_iwat_female_control_ASC1_B4


title: DNA-seq - Patient 221


title: FACS_iwat_male_control_ASC2_B1


title: DNA-seq - Patient 220


title: FACS_iwat_female_control_ASC1_A4


title: DNA-seq - Patient 217


title: DNA-seq - Patient 218


title: FACS_iwat_female_control_ASC2_A3


title: DNA-seq - Patient 215


title: DNA-seq - Patient 214


title: FACS_iwat_male_control_ASC2_A1


title: DNA-seq - Patient 213


title: 96h-2_FRAS210090030-1r

city: Beijing

first: Duo

last: Su

address: Street Dongdajie

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
After sequencing, low-quality reads of raw data were filtered out to obtain clean data.
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%.
Clean reads were mapped to the reference genome (mouse) using Hisat2 v2.0.5.
Gene expression levels were estimated by calculating the fragments per kilobase of exon per million fragments mapped (FPKM) of each gene [19]
Assembly: mm9
Supplementary files format and content: tab-delimited text file inlude FPKM for each sample

source_name: lung

extract_protocol:
Total RNA was extracted from the lung tissue using the PureLink™ RNA mini kit (Thermo Fisher Scientific, Waltham, MA, USA)
Library construction and sequencing were conducted by the Novogene Company (Beijing, China).  Libraries for transcriptome sequencing were constructed with NEBNext® Ultra™ RNA Library Prep Kit (NEB, Ipswich, MA, USA) and qualified libraries were pooled into flowcell and then sequenced on the Illumina sequencing platform (NovaSeq 6000, Illumina, San Diego, CA, USA).

treatment_protocol: Mice were sacrificed at 0, 12, 24, 48, and 96 hpi and lungs were submerged in RNAlater™ stabilization solution (Invitrogen)

value: lung

value: Lung tissue cells

value: WT

value: infected with PAO1


title: 48h-3_FRAS210090028-1r


title: 96h-1_FRAS210090029-1r


title: DNA-seq - Patient 212


title: Tapestri - DNA - UPN_4


title: 48h-2_FRAS210090027-1r


title: 96h-3_FRAS210090031-1r


title: DNA-seq - Patient 209


title: DNA-seq - Patient 211


title: DNA-seq - Patient 210


title: DNA-seq - Patient 208


title: FACS_iwat_male_control_ASC1_B2


title: 24h-3_FRAS210090025-1r


title: 48h-1_FRAS210090026-1r


title: DNA-seq - Patient 219


title: DNA-seq - Patient 207


title: DNA-seq - Patient 206


title: DNA-seq - Patient 216


title: 12h-3_FRAS210090022-1r


title: DNA-seq - Patient 205


title: FACS_iwat_female_control_ASC2_B3


title: DNA-seq - Patient 204


title: 12h-2_FRAS210090021-1r


title: DNA-seq - Patient 203


title: 0h-3_FRAS210090019-1r

value: untreated


title: 12h-1_FRAS210090020-1r


title: Tapestri - DNA - UPN_1


title: 0h-2_FRAS210090018-1r


title: DNA-seq - Patient 201


title: 0h-1_FRAS210090017-1b


title: DNA-seq - Patient 200


title: DNA-seq - Patient 199


title: DNA-seq - Patient 198


title: DNA-seq - Patient 202


title: Ii-cKO_mice_CD4_T_cells, mRNA-derived cDNA

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description:
GA73246
poly A RNA

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-7.1.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0 and refdata-gex-mm10-2020-A
Supplementary files format and content: features.tsv.gz : tab-delimited text file including the information of features (gene and HTO)
Supplementary files format and content: airr_rearrangement.tsv : tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv : comma-delimited text file including the TCR clonotype information
Supplementary files format and content: matrix_Ii-cKO_mice_CD4_T_cells.csv : comma-delimited text files including UMI counts for each feature (gene or HTO) and cell (barcode) conbination

source_name: Spleen

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. Hashtag oligonucleotides or cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

value: Spleen

value: T cell

value: invariant chain knockout

tag: library type

value: mRNA


title: 24h-2_FRAS210090024-1r


title: DNA-seq - Patient 196

value: Peripheral blood mononuclear cells


title: PVR_3_RNA

city: Tianjin

first: Yumei

address: No22.Qixiangtai Rd.,Heping Dist

institute: Tianjin Medical University

data_processing:
DESeq2  was used to generated DEGs (differential expressed genes) between WT and PVR.
Assembly: mm10
Supplementary files format and content: FPKM

molecule: polyA RNA

source_name: Eye

extract_protocol:
Total RNAs were extracted from primary RPE cells using TRIzol (15596018; Invitrogen).
Construction of RNA-seq library was completed by Novogene company (Beijing,China).

value: Eye

value: primary retinal pigment epithelium cells

value: PVR


title: Ii-cKO_mice_CD4_T_cells, TCR-derived cDNA

description:
GA73247
TCR V(D)J segments

value: TCR V(D)J


title: DNA-seq - Patient 195


title: Normal_3_RNA

value: normal


title: DNA-seq - Patient 197


title: 24h-1_FRAS210090023-1r


title: PVR_ATAC_3

data_processing:
The reads were aligned to the mouse reference genome (mm9) by bowtie2.
The deepTools was used to produce the BigWig files.
Annotation of peaks was performed using HOMER.
Assembly: mm9
Supplementary files format and content: Bigwig files were generated by deepTools.

extract_protocol:
A total of 200,00 RPE cells were lysed in cold lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.4, 3 mM MgCl2, 0.1% (v/v) IGPAL CA-630,) for 20 min on ice. The nuclei were resuspend with reaction buffer (10 μl l TruePrep Tagment Buffer L, 3 μl TruePrep Tagment Enzyme, and 35 μl ddH2O from Vazyme, TD501) at 37°C for 30 min.
The cells were subjected to transposition with Tn5 transposase (TD501, Vazyme) for 20 min at 37°C. DNA was purified with QIAquick PCR Purification Kit (28106, QIAGEN) for final library construction.


title: Normal_ATAC_3

value: Normal


title: DNA-seq - Patient 193


title: DNA-seq - Patient 194


title: PVR_ATAC_2


title: DNA-seq - Patient 192

value: Clonal Hematopoiesis


title: Normal_ATAC_2


title: DNA-seq - Patient 191


title: DNA-seq - Patient 190


title: Normal_Input_3

extract_protocol:
Isolated primary retinal pigment epithelium cells were lysed in lysis buffer (0.5% Tween-20, 0.1% SDS, 0.5% NP-40, and Protease Inhibitor Cocktail) for 10 min on ice. Then MNase buffer (2 mM CaCl2, 100 mM Tris-HCl pH 8.0) containing 0.02 U MNase was added and incubated at 37°C for 5 min. The reaction was terminated by adding stop buffer (55 mM EDTA, 110 mM Tris-HCl pH 8.0) and incubated with 2x RIPA buffer (280 mM NaCl, 0.1% SDS, 1% Triton X-100, 5 mM EGTA, 0.2% sodium deoxycholate, and Protease Inhibitor Cocktail) for 10 min on ice. Then the sample was centrifuged at 14500 rpm for 15 min, the supernatant was collected and added with RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 140 mM NaCl, 0.1% SDS, 1% Triton X-100, and 0.1% sodium deoxycholate). Immunoprecipitation was performed using 1 μg antibody.
The library preparation according to the VAHTS Universal DNA Library Prep Kit for Illumina V3 Kit (ND607, Vazyme)


title: PVR_Input_3


title: Ii-cKO_mice_CD4_T_cells, HTO-derived cDNA

description:
GA73248
Hashtag oligonucleotide (HTO)
matrix_Ii-cKO_mice_CD4_T_cells.csv
features.tsv.gz

value: HTO


title: DNA-seq - Patient 188


title: DNA-seq - Patient 187


title: DNA-seq - Patient 189


title: Normal_Input_2


title: DNA-seq - Patient 186


title: Normal_Input_1


title: PVR_Input_2


title: PVR_K9me3_3

value: anti-H3K9me3 (ab8898, Abcam)


title: DNA-seq - Patient 185


title: DNA-seq - Patient 183


title: DNA-seq - Patient 182


title: PVR_K4me3_3

value: anti-H3K4me3 (05-745R, Millipore)


title: DNA-seq - Patient 184


title: DNA-seq - Patient 181


title: PVR_K36me3_3

value: anti-H3K36me3 (ab9050, Abcam)


title: PVR_K27me3_3

value: anti-H3K27me3 (ab192985, Abcam)


title: PVR_K27ac_3

value: anti-H3K27ac (ab4729, Abcam)


title: DNA-seq - Patient 179


title: DNA-seq - Patient 180


title: PVR_K4me1_3

value: anti-H3K4me1 (ab8895, Abcam)


title: DNA-seq - Patient 177


title: PVR_K9me3_2


title: DNA-seq - Patient 176


title: PVR_K4me3_2


title: PVR_K4me1_2


title: DNA-seq - Patient 175


title: PVR_Input_1


title: PVR_K36me3_2


title: DNA-seq - Patient 174


title: PVR_K27me3_2


title: PVR_K27ac_2


title: Normal_K9me3_3


title: DNA-seq - Patient 171


title: DNA-seq - Patient 172


title: Normal_K36me3_3


title: DNA-seq - Patient 170


title: DNA-seq - Patient 178


title: Normal_K4me3_3


title: Normal_K27me3_3


title: Normal_K4me1_3


title: DNA-seq - Patient 168


title: FACS_iwat_male_control_ASC1_E2

value: iwat

value: male

value: control


title: DNA-seq - Patient 169

value: Peripheral blood mononuclear cells


title: DNA-seq - Patient 166


title: Normal_K27ac_3

value: Eye

value: primary retinal pigment epithelium cells


title: DNA-seq - Patient 167


title: Normal_K36me3_2


title: Normal_K9me3_2


title: DNA-seq - Patient 164


title: DNA-seq - Patient 165


title: Normal_K4me3_2


title: DNA-seq - Patient 163


title: Normal_K4me1_2


title: Normal_K27me3_2


title: Normal_K27ac_2


title: DNA-seq - Patient 173


title: DNA-seq - Patient 162


title: DNA-seq - Patient 160


title: DNA-seq - Patient 161


title: DNA-seq - Patient 159


title: DNA-seq - Patient 158


title: DNA-seq - Patient 157


title: DNA-seq - Patient 156


title: DNA-seq - Patient 154


title: DNA-seq - Patient 153


title: DNA-seq - Patient 152


title: DNA-seq - Patient 151


title: DNA-seq - Patient 155


title: DNA-seq - Patient 148


title: DNA-seq - Patient 150


title: DNA-seq - Patient 144


title: DNA-seq - Patient 146


title: DNA-seq - Patient 147


title: DNA-seq - Patient 142


title: Patient7_APA_KCNJ5_MUT

city: Munich

first: Tracy

middle: Ann

last: Williams

address: Ziemssenstraße

country: Germany

institute: LMU Munich

description: Fresh Frozen spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to hg38 genome to gene expresison count using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Library strategy: Spatial transcriptomics

source_name: APA

extract_protocol:
Fresh frozen tissue were OCT embeded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufactrue's construction

value: APA


title: DNA-seq - Patient 143


title: DNA-seq - Patient 145


title: DNA-seq - Patient 141


title: DNA-seq - Patient 140


title: Patient6_APA_KCNJ5_WT


title: Patient6_Adjacent

source_name: Adjacent

value: Adjacent


title: DNA-seq - Patient 138


title: DNA-seq - Patient 139


title: DNA-seq - Patient 149


title: Patient5_APA_KCNJ5_MUT


title: Patient4_Adjacent


title: Patient4_APA_KCNJ5_WT


title: Patient3_Adjacent


title: Patient2_Adjacent


title: Patient7_Adjacent


title: Patient2_APA_KCNJ5_WT


title: DNA-seq - Patient 137


title: DNA-seq - Patient 136


title: Patient1_Adjacent


title: Patient1_APA_KCNJ5_MUT


title: CCE-Rx, OTX2, ChIP

city: Oxford

first: Samuel

last: Clokie

state: Oxfordshire

address: Harcourt Hill Campus

department: Dept of Biological & Medical Science

country: United Kingdom

institute: Oxford Brookes University

data_processing:
FASTQ trimmed using Trimmomatic (v0.36) with settings 2:30:10, trailing:3, crop 51 and a sliding window of 4, average quality of Q15
Aligned to mm10 using hisat2 in very sensitive mode
sample data concerted to a tag directory using homer, with defualt settings.
Peaks called using homer (2022 version), using -region setting with  a size of 180 bases and a -minDist of 400 between peaks and a -fdr .00001.
Peaks were called using IgG as input, to improve peak calling specificity (homer)
Assembly: BigWig files were generated using homer
Supplementary files format and content: mm10
Supplementary files format and content: bigwig, bed files

source_name: CCE-Rx

growth_protocol: LIF-free medium

extract_protocol:
Formaldehyde for 10 minutes chromatin prepared, and ChIP performed according to the Upstate (Millipore) protocol, using 10μg of anti-OTX2 antibody (abcam, ab21990-100), anti-SOX2 (Santa Cruz Biotechnology, sc-17320), or mouse IgG (Millipore, PP54) as a control.
ChIP-seq libraries were prepared and sequenced using the standard Illumina protocol.

value: CCE-Rx

value: transformed ganglion cells


title: CCE-Rx, IgG, ChIP

data_processing:
FASTQ trimmed using Trimmomatic (v0.36) with settings 2:30:10, trailing:3, crop 51 and a sliding window of 4, average quality of Q15
Aligned to mm10 using hisat2 in very sensitive mode
sample data concerted to a tag directory using homer, with defualt settings.
Peaks called using homer (2022 version), using -region setting with  a size of 180 bases and a -minDist of 400 between peaks and a -fdr .00001.
Peaks were called using IgG as input, to improve peak calling specificity (homer)
Assembly: BigWig files were generated using homer
Supplementary files format and content: mm10
Supplementary files format and content: bigwig file

value: IgG


title: Human primary lung fibroblasts IMR90-15_shPML-Sen3

description: RNA extraction

data_processing:
Real Time Analysis 3.4.4 software used for basecalling.
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Assembly: hg19
Supplementary files format and content: FPKM matrix contains FPKM values for each sample and each gene
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene

treatment_protocol: Senescence was induced by 50 µM Etoposide, a DNA damaging agent. Infected with lentivirus containing non targeting sequences and short hairpin sequences to knock-down HIRA and PML.

value: Senescence

value: shPML


title: DNA-seq - Patient 134


title: Human primary lung fibroblasts IMR90-13_shPML-Sen1

description: RNA extraction


title: DNA-seq - Patient 133

value: Clonal Hematopoiesis


title: Human primary lung fibroblasts IMR90-12_sh2HIRA-sen3

description: RNA extraction


title: Patient5_Adjacent


title: Human primary lung fibroblasts IMR90-11_sh2HIRA-sen2

description: RNA extraction


title: DNA-seq - Patient 132


title: Patient3_APA_KCNJ5_MUT


title: Human primary lung fibroblasts IMR90-07_sh1HIRA-sen1

description: RNA extraction


title: DNA-seq - Patient 129


title: DNA-seq - Patient 131


title: Human primary lung fibroblasts IMR90-08_sh1HIRA-sen2

description: RNA extraction


title: Human primary lung fibroblasts IMR90-06_TRC-Sen3

description: RNA extraction

value: TRC


title: Human primary lung fibroblasts IMR90-09_sh1HIRA-sen3

description: RNA extraction


title: CCE-Rx, SOX2, ChIP


title: Human primary lung fibroblasts IMR90-10_sh2HIRA-sen1

description: RNA extraction


title: Human primary lung fibroblasts IMR90-02_TRC-Pro2

description: RNA extraction

value: Proliferating


title: Human primary lung fibroblasts IMR90-03_TRC-Pro3

description: RNA extraction


title: Human primary lung fibroblasts IMR90-05_TRC-Sen2

description: RNA extraction


title: DNA-seq - Patient 128


title: Human primary lung fibroblasts IMR90-01_TRC-Pro1

description: RNA extraction


title: Human primary lung fibroblasts IMR90-04_TRC-Sen1

description: RNA extraction


title: DNA-seq - Patient 127


title: DNA-seq - Patient 135


title: Postnatal (P24) whole ventricle, rep2

city: Showa-ku, Nagoya

first: Shingo

last: Narita

state: Aichi

address: 65 Tsurumai-cho

department: Cardiology

institute: Nagoya University Graduate School of Medicine

data_processing:
151-bp pair-end sequencing was performed with a HiSeq 2500 system.
Quality of raw sequence data was assessed using fastq.gzC (Version: fastq.gzC 0.10.0).
fastq.gz files were trimmed for adapters and Phred score (>20) using TrimGalore! (0.6.4).
Trimmed sequenced reads were aligned to the mouse genome assembly (GRCm39 GENCODE vM30) using STAR (2.7.3a).
Aligned reads were used to quantify mRNA with HTSeq-count (0.11.2). Differential gene expression analysis across samples was performed using DESeq2 package (1.32.0) on protein-coding genes. The calculated Fragments Per Kilobase Million (FPKM) was plotted using GraphPad Prism 7 version 7.0 (GraphPad Software, USA).
Assembly: GRCm39 GENCODE vM30
Supplementary files format and content: Excel file includes row counts for each Sample
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Whole ventricle

extract_protocol:
Total RNA was extracted using the QIAzol Lysis Reagent (79306, QIAGEN) and miRNeasy Micro Kit (217084, QIAGEN) followed by digestion of DNA using the TURBO DNA-free™ Kit (AM1907, Invitrogen). Isolated RNA quality was assessed using an Agilent 2200 TapeStation system (Agilent).
1 µg of RNA with a RIN e score of 7 or higher was used for preparation of sequencing libraries with Poly(A) Magnetic Isolation Module (E7490S, New England Bio Labs) and NEBNext Ultra RNA Prep Kit for Illumina (E7530S, New England Bio Labs).

tag: developmental stage

value: Whole ventricle

tag: strain


title: Postnatal (P24) whole ventricle, rep1

tag: tissue


title: DNA-seq - Patient 126

tag: cell type


title: Human primary lung fibroblasts IMR90-14_shPML-Sen2

description: RNA extraction


title: DNA-seq - Patient 125


title: Postnatal (P12) whole ventricle, rep1


title: Postnatal (P12) whole ventricle, rep2


title: hfd_75ko3

city: Dallas

first: Zhao

last: Zhang

state: Texas

address: 5323 Harry Hines Blvd.

department: Center for the Genetics of Host Defense

institute: The University of Texas Southwestern Medical Center

data_processing:
BioHPC Astrocyte RNASeq Analysis Workflow
1) Trim the ends of sequences with remaining adapter or quality scores < 25. Remove any sequence less than 35bp after trimming, then generate a file for capturing information about how many sequences were trimmed.
2) Trimmed Fastq files are aligned to the selected reference genome using STAR (Dobin et al. 2012).
3) Marks Duplicates using SAMBAMBA.
4) Features (genes, transcripts and exons) are counted using featureCounts (Liao et al 2014) and StringTie (Pertea et al. 2015) using the Gencode feature table(Harrow et al. 2012).
5) Basic pairwise differential expression analysis is performed using DESeq2.
6) Abundances of transcripts are calculated using ballgown (Frazee et al. 2014).
Assembly: Mouse GRCm39
Supplementary files format and content: tab-delimited text file includes differential expression data analyzed by DeSeq2

source_name: Hypothalamus

extract_protocol:
Total RNA was extracted from tissues by TRIzol and PureLink RNA Mini Kit (Invitrogen) following a standard protocol.
The cDNA synthesis and library preparation were carried out by the SMART-Seq mRNA LP kit (Takara, 634768).

value: Hypothalamus

value: HFD


title: Postnatal (P6) whole ventricle, rep1


title: DNA-seq - Patient 124


title: hfd_75ko2


title: DNA-seq - Patient 130


title: Postnatal (P3) whole ventricle, rep2


title: Postnatal (P3) whole ventricle, rep1


title: DNA-seq - Patient 123


title: DNA-seq - Patient 122


title: Opa1-/- + OPA1 4

city: Bronx

first: Felix

last: Liang

state: New York

address: 1300 Morris Park Ave, Forchheimer G01

institute: Albert Einstein College of Medicine

data_processing:
Sequencing reads were trimmed to remove adapter sequences or sequences with poor quality using Illumina’s bcl2fastq 2.17 software.
Trimmed reads were mapped to the GRCh38/mm10 reference genome on ENSEMBL using the STAR aligner v.2.5.2b.
Transcript counts were calculated by using feature Counts from the Subread package v1.5.2.
Assembly: mm10
Supplementary files format and content: csv files include TPM values for each sample

source_name: immortalized MEFs

growth_protocol: MEFs were cultured in DMEM supplemented with 10% (w/v) FBS and 100 units/mL penicillin/100 ug/mL streptomycin under 5% CO2 at 37 C.

extract_protocol:
RNA was extracted from MEFs using the RNeasy Plus Kit (Qiagen).
RNA libraries for sequencing were prepared using the NEBNext Ultra II RNA Library Prep Kit following manufacturer's instructions.

value: immortalized MEFs

value: embryonic fibroblasts

value: Opa1-/- + OPA1


title: hfd_75ko1


title: DNA-seq - Patient 121

source_name: Peripheral blood mononuclear cells

value: Peripheral blood mononuclear cells


title: REST_NP_R1

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Assembly: CTCF_tile5_REST.fasta
Reads were trimmed to remove adapters using Trimmomatic version 0.32.
Reads were mapped using the Bioconductor package QuasR with default settings for bisulfite-converted templates.
Methylation of Cs in the GpC contexts was quantified using qMeth, excluding GCG and GCCG contexts and Cs with coverage <10. Such GpCs were defined as GCH.
Methylation of Cs in the CpG contexts was quantified using qMeth, excluding GCG and GCCG contexts and Cs with coverage <10. Such CpGs were defined as CGH.
Assembly: Fasta files containing sequences of constructs used.
Supplementary files format and content: Average methylation data are tab separated tables with three columns: position of the Cs in the GCH context, average methylation values, inserted constructs.
Supplementary files format and content: Average methylation data are tab separated tables with three columns: position of the Cs in the CGH context, average methylation values, inserted constructs.

extract_protocol:
DNA was extracted with Phenol/Chlroform, bisulfite converted and then PCR was performed. PCR was purified with SPRI beads and submitted to library preparation.
Libraries were prepared using the NEBNext ChIP-Seq Library Prep Master Mix Set following manufacturer instructions.

value: embryonic stem cells


title: REST_NP_R2


title: Opa1-/- + OPA1 3


title: hfd_wt2


title: Opa1-/- + OPA1 2


title: hfd_wt1


title: REST_ES_R3


title: REST_ES_R2


title: DNA-seq - Patient 119


title: chow_75ko3

value: Chow diet


title: Opa1-/- + OPA1 1


title: Postnatal (P6) whole ventricle, rep2


title: REST_ES_R1


title: Opa1-/- 4


title: Opa1-/- 3


title: BANP_dTAG_R2

data_processing:
Assembly: CTCF_tile5_BANP.fasta
Reads were trimmed to remove adapters using Trimmomatic version 0.32.
Reads were mapped using the Bioconductor package QuasR with default settings for bisulfite-converted templates.
Methylation of Cs in the GpC contexts was quantified using qMeth, excluding GCG and GCCG contexts and Cs with coverage <10. Such GpCs were defined as GCH.
Methylation of Cs in the CpG contexts was quantified using qMeth, excluding GCG and GCCG contexts and Cs with coverage <10. Such CpGs were defined as CGH.
Assembly: Fasta files containing sequences of constructs used.
Supplementary files format and content: Average methylation data are tab separated tables with three columns: position of the Cs in the GCH context, average methylation values, inserted constructs.
Supplementary files format and content: Average methylation data are tab separated tables with three columns: position of the Cs in the CGH context, average methylation values, inserted constructs.


title: chow_75ko1


title: REST_NP_R3


title: Opa1-/- 2


title: hfd_wt3


title: DNA-seq - Patient 120


title: Opa1-/- 1


title: DNA-seq - Patient 116


title: chow_wt3


title: DNA-seq - Patient 115


title: chow_wt2


title: BANP_DMSO_R2


title: chow_wt1


title: BANP_DMSO_R1


title: PRVCMs treated with ATRA 1, rep 3

data_processing:
150-bp pair-end sequencing was performed with a HiSeq X system.
Quality of raw sequence data was assessed using fastq.gzC (Version: fastq.gzC 0.10.0).
fastq.gz files were trimmed for adapters and Phred score (>20) using TrimGalore! (0.6.4).
Trimmed sequenced reads were aligned to the Rattus norvegicus genome assembly (mRatBN7.2 Ensembl release 108) using STAR (2.7.3a).
Aligned reads were used to quantify mRNA with HTSeq-count (0.11.2). Differential gene expression analysis across samples was performed using DESeq2 package (1.32.0) on protein-coding genes. The calculated Fragments Per Kilobase Million (FPKM) was plotted using GraphPad Prism 7 version 7.0 (GraphPad Software, USA).
Assembly: mRatBN7.2 Ensembl release 108
Supplementary files format and content: Excel file includes row counts for each Sample
Supplementary files format and content: Excel file includes FPKM values for each Sample

organism: Rattus norvegicus

source_name: PRVCMs were enzymatically isolated from E18.5 Wistar rat ventricles. After isolation, PRVCMs were treated with 10 µM ATRA for 48 h.

growth_protocol: Minced perinatal rat ventricle tissue was suspended in 15 mg Trypsin (27250-018, Gibco) / 25 ml Hank's Balanced Salt Solution (HBSS) in 4 °C for 18 h, replaced with 10 mg of Collagenase 2 (LS004176, Worthington Biochemical Corp) / 10 ml HBSS solution under continuous agitation, 150 rpm, at 38 °C for 4.5 min five times. Cells were pelleted by centrifugation at 200 g for 5 min and resuspended in culture medium. Cells underwent two pre-platings of 1 h each to minimize fibroblast contamination. Isolated cardiomyocytes were seeded to 70% confluence on laminin-coated (final concentration 38.25 μg/ml, L2020, Sigma) 60 mm culture dishes. Cardiomyocytes were maintained in Dulbecco’s Modified Eagle Medium (12320-032, Gibco) containing 1.5 mM Vitamin B12 (V2876, Sigma), 7% fetal bovine serum and 1% penicillin / streptomycin and incubated for 24 h (37°C, 5% CO2).

extract_protocol:
Total RNA was extracted using the QIAzol Lysis Reagent (79306, QIAGEN) and miRNeasy Micro Kit (217084, QIAGEN) followed by digestion of DNA using the TURBO DNA-free™ Kit (AM1907, Invitrogen).
Extracted RNA quality was assessed, and 100 ng of RNA were used for library preparation with NEBNext Poly(A) Isolation Module (E7490, New England Bio Labs) and NEBNext Ultra II RNA Prep Kit for Illumina (E7770, New England Bio Labs)

treatment_protocol: After incubation, cardiomyocytes were exposed ATRA (R2625, Sigma) or DMSO as vehicle for 48 h.

value: PRVCMs

value: Cardiomyocytes

value: Wistar

tag: agent

value: ATRA


title: DNA-seq - Patient 114


title: chow_75ko2

tag: genotype


title: PRVCMs treated with ATRA 1, rep 2


title: PRVCMs treated with ATRA 1, rep 1


title: DNA-seq - Patient 117


title: DNA-seq - Patient 118


title: DNA-seq - Patient 112


title: NRF1_pool_R2

data_processing:
Assembly: NRF1_pool.fasta
Reads were trimmed to remove adapters using Trimmomatic version 0.32.
Reads were mapped using the Bioconductor package QuasR with default settings for bisulfite-converted templates.
Methylation of Cs in the GpC contexts was quantified using qMeth, excluding GCG and GCCG contexts and Cs with coverage <10. Such GpCs were defined as GCH.
Methylation of Cs in the CpG contexts was quantified using qMeth, excluding GCG and GCCG contexts and Cs with coverage <10. Such CpGs were defined as CGH.
Assembly: Fasta files containing sequences of constructs used.
Supplementary files format and content: Average methylation data are tab separated tables with three columns: position of the Cs in the GCH context, average methylation values, inserted constructs.
Supplementary files format and content: Average methylation data are tab separated tables with three columns: position of the Cs in the CGH context, average methylation values, inserted constructs.


title: WTCLPBrain3

city: Shanghai

first: Shenjia

last: Gao

address: 130 Dong 'an Road, Xuhui District, Shanghai

institute: Fudan university

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4).
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted using Trizol reagent .Total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.).
Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: Brain

value: hippocampus

value: WT

tag: treatment

value: cecal ligation and puncture (CLP) surgery


title: NRF1_pool_R3

tag: cell line


title: DNA-seq - Patient 111

data_processing:
library strategy: Target Capture Chip Assay for Bulk Sequencing
Bioinformatics analysis included quality assessment and alignment to the hg19 build reference genome using Novoalign, followed by GATK based single nucleotide and small insertion / deletion variant calling, structural variation discovery, and annotation. Somatic single nucleotide variations (SNVs) were genotyped using SomaticSniper, whereas insertions and deletions were called by GATK Somatic Indel Detector. Each variant in coding regions was functionally annotated by SnpEff, SAVANT, ClinVar, dbNSFP, OMIM, and the Human Gene Annotation Database to predict biological effects. Each variant was also annotated with allele frequency from the Exoma Aggregation Consortium. The total list of all variants was internally compared for internal duplicates indicative of false positives, and variants of concern are additionally hand annotated for identification using Alamut Software. Interpretation for relevant alterations included absence in international normal variant allele databases (GnomAD, ExAC), deleterious effect on protein function by multiple phenotype prediction models, somatic and functional annotation in literature, consequence of variant (nonsense, truncating, etc.) and location proximal to important domains.
Assembly: hg19
Supplementary files format and content: Supplementary file containing the variant calls for mutations associated with Clonal Hematopoiesis.


title: WTCLPBrain2


title: PRVCMs treated with DMSO (Control), rep 3

source_name: PRVCMs were enzymatically isolated from E18.5 Wistar rat ventricles. After isolation, PRVCMs were treated with DMSO for 48 h.

value: DMSO


title: WTCLPBrain1


title: DNA-seq - Patient 110


title: tiles_pool14_R3

data_processing:
Reads were trimmed to remove adapters using Trimmomatic version 0.32.
Reads were mapped using the Bioconductor package QuasR with default settings for bisulfite-converted templates.
Methylation of Cs in the GpC contexts was quantified using qMeth, excluding GCG and GCCG contexts and Cs with coverage <10. Such GpCs were defined as GCH.
Supplementary files format and content: Average methylation data are tab separated tables with three columns: position of the Cs in the GCH context, average methylation values, inserted constructs.
Supplementary files format and content: Single molecule data are tar.gz archives containing tab separated tables for each inserted construct. Each table is a matrix where each column is the position of the Cs in the GCH context, and each row is the binary methylation data for a single read.


title: BANP_dTAG_R1


title: NRF1_pool_R1


title: WTCONBrain3

value: control


title: PRVCMs treated with DMSO (Control), rep 1


title: DNA-seq - Patient 113


title: PRVCMs treated with DMSO (Control), rep 2


title: tiles_pool14_R2


title: scRNA-seq - Patient 46

data_processing:
Sequenced reads were processed using 10x Genomics Cell Ranger v6.0.1. The reads were aligned to the pre-built human reference transcriptome GRCh38 - v2020-A (July 7, 2020) provided by 10X Genomics. Doublet prediction on scRNA-seq data was done using Scrublet v0.2.1 with default parameters. Downstream processing was done using Seurat v4.0.4. Count matrices from all samples were combined and batch-corrected using Seurat v4 integration method. Cell type identification was done with SingleR v1.10.0 using immune data from celldex v1.6.0 as reference.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Frozen PBMCs were thawed in a 37°C water bath for 3-5 min until no ice was visible. Cells were washed twice with 1 mL PBS + 0.04% BSA and pelleted (300×g for 5 min at 4°C). Dead cells were removed according to the Demonstrated Protocol: Removal of Dead Cells from Single Cell Suspensions for Single Cell RNA Sequencing (10X Genomics). Using the MACS Dead Cell Removal Kit (Miltenyi Biotec), the pellet was resuspended in 100 mL Dead Cell Removal MicroBeads and incubated for 15 minutes at room temperature. After incubation, the cell suspension was diluted with 1X Binding Buffer and applied to a MS column. The dead cells were retained on the column and the live cells passed through the column and were collected. After dead cell removal, the samples were washed twice with 1 mL PBS + 0.04% BSA and the cell concentration was determined using a Cellometer K2 cell counter (Nexcelom Biosciences). The cells were then aliquoted for scRNA-seq.
The cells were first counted and measured for viability using either the Vi-Cell XR Cell Viability Analyzer (Beckman-Coulter, Brea, CA) or a basic hemocytometer and light microscope. The barcoded Gel Beads were thawed from -80°C and the cDNA master mix was prepared according to the manufacturer’s instruction for Chromium Next GEM Single Cell 3’ Library and Gel Bead Kit (10x Genomics, Pleasanton, CA). Based on the desired number of cells to be captured for each sample, a volume of live cells was mixed with the cDNA master mix. A per sample concentration of 400,000 cells per milliliter or better is required for the standard targeted cell recovery of approximately 4000 cells. The stock concentration requirements would not change for higher cell recovery numbers. The cell suspension and master mix, thawed Gel Beads and partitioning oil were added to a Chromium Single Cell G chip. The filled chip was loaded into the Chromium Controller, where each sample was processed and the individual cells within the sample were captured into uniquely labeled GEMs (Gel Beads-In-Emulsion). The GEMs were collected from the chip and taken to the bench for reverse transcription, GEM dissolution, and cDNA clean-up. The resulting cDNA contained a pool of uniquely barcoded molecules. A portion of the cleaned and measured pooled cDNA continued to library construction, where standard Illumina sequencing primers and a 10x Genomics unique i7 Sample index were added to each cDNA pool. All cDNA pools and resulting libraries were measured using Qubit High Sensitivity assays (Thermo Fisher Scientific, Waltham, MA) and Agilent Bioanalyzer High Sensitivity chips (Agilent, Santa Clara, CA).

value: Clonal Hematopoiesis


title: tiles_pool14_R1


title: DNA-seq - Patient 109


title: DNA-seq - Patient 107


title: WTCONBrain1


title: scRNA-seq - Patient 45


title: WTCONBrain2


title: PVR_2_RNA

data_processing:
DESeq2  was used to generated DEGs (differential expressed genes) between WT and PVR.
Assembly: mm10
Supplementary files format and content: FPKM

value: Eye

value: primary retinal pigment epithelium cells

value: PVR


title: Normal_2_RNA

value: normal


title: DNA-seq - Patient 106

value: Peripheral blood mononuclear cells


title: scRNA-seq - Patient 43


title: scRNA-seq - Patient 42


title: tiles_pool13_R3

value: embryonic stem cells


title: tiles_pool13_R1


title: DNA-seq - Patient 105


title: tiles_pool13_R2


title: DNA-seq - Patient 104


title: scRNA-seq - Patient 41


title: PVR_1_RNA


title: Normal_1_RNA


title: tiles_pool12_R3


title: DNA-seq - Patient 103


title: scRNA-seq - Patient 40


title: scRNA-seq - Patient 38


title: PVR_ATAC

data_processing:
The reads were aligned to the mouse reference genome (mm9) by bowtie2.
The deepTools was used to produce the BigWig files.
Annotation of peaks was performed using HOMER.
Assembly: mm9
Supplementary files format and content: Bigwig files were generated by deepTools.


title: DNA-seq - Patient 102


title: DNA-seq - Patient 108


title: tiles_pool12_R2


title: tiles_pool12_R1


title: tiles_pool11_R3


title: DNA-seq - Patient 100


title: scRNA-seq - Patient 36


title: PVR_K36me3

tag: chip antibody

value: anti-H3K36me3(ab9050, Abcam)


title: scRNA-seq - Patient 35


title: tiles_pool11_R1


title: scRNA-seq - Patient 37


title: DNA-seq - Patient 99


title: PVR_K4me3

value: anti-H3K4me3(05-745R, Millipore)


title: DNA-seq - Patient 98


title: PVR_K4me1

value: anti-H3K4me1(ab8895, Abcam)


title: tiles_pool10_R3


title: DNA-seq - Patient 97


title: scRNA-seq - Patient 30


title: scRNA-seq - Patient 34


title: tiles_pool10_R2


title: PVR_K27me3

value: anti-H3K27me3(ab192985, Abcam)


title: scRNA-seq - Patient 29


title: DNA-seq - Patient 96


title: PVR_K27ac

value: anti-H3K27ac(ab4729, Abcam)


title: tiles_pool10_R1


title: Normal_ATAC

value: Normal


title: DNA-seq - Patient 95


title: PVR_K9me3

value: anti-H3K9me3(ab8898, Abcam)


title: Normal_K9me3


title: DNA-seq - Patient 101


title: tiles_pool11_R2


title: scRNA-seq - Patient 28


title: DNA-seq - Patient 94


title: tiles_pool9_R3


title: scRNA-seq - Patient 27


title: tiles_pool9_R2


title: scRNA-seq - Patient 25


title: Normal_K36me3


title: DNA-seq - Patient 92


title: DNA-seq - Patient 93


title: tiles_pool9_R1


title: Normal_K4me1


title: scRNA-seq - Patient 23


title: scRNA-seq - Patient 24


title: Normal_K27me3


title: Normal_K4me3


title: DNA-seq - Patient 90


title: Normal_K27ac


title: tiles_pool8_R1


title: DNA-seq - Patient 89


title: scRNA-seq - Patient 21


title: tiles_pool7_R3


title: scRNA-seq - Patient 20


title: Tet2 knockout, Malat1 knockout bone marrow mononuclear rep2

city: Tampa

first: Ben-Crentsil

last: Nana Adjoa

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

data_processing:
The quality of the raw reads was assessed using the FastQC program v0.12.1 (Andrews, Krueger et al. 2010) and visualized using MultiQC v1.7 (Ewels, Magnusson et al. 2016). The low-quality bases (Phred score less than 30) and adapters were removed by trimming using the Trimmomatic v0.39 in pair-end mode (ILLUMINACLIP:TruSeq3-PE-2.fa:2:40:15:8:true, HEADCROP:10, LEADING:5, TRAILING:5 SLIDINGWINDOW:4:5, MINLEN:25) (Bolger, Lohse et al. 2014). High-quality reads were mapped against the primary coding sequences ofmouse (Frankish, Diekhans et al. 2019)
Assembly: The coding sequences (gencode.vM31.transcripts.fa) were obtained from the Gencode database (https://www.gencodegenes.org/mouse/release_M21.html#) and aligned using Salmon v1.4.0 (Patro, Duggal et al. 2015).
Supplementary files format and content: .txt

source_name: bone marrow

extract_protocol:
Femurs and Tibias were harvested from 8-week-old male mice and bone marrow was extracted by centrifugation. Red blood cells were lysed with ACK buffer for five minutes after which cells were washed with PBS. Lineage negative cells were then selected with LS columns using a direct lineage cell depletion kit following the manufacturer’s instructions. Zombie NIR was used as viability stain. Cells were then incubated with mouse FcR blocking reagent for ten minutes, stained with anti Sca1 and CD117 (ckit) antibodies and sorted by FACS. Sorted LSK cells were washed with PBS and total RNA was extracted with Qiagen RNeasy micro kit following the manufacturer’s instructions.
RNA samples were processed with theTakaraSMARTer Stranded Total RNA-Seq Kit v2 Picoand sequenced in one NovaSeq-6000 SP-200 sequencing run (101x101).

value: bone marrow

value: bone marrow mononuclear


title: scRNA-seq - Patient 19

city: Rochester

first: Alexandre

address: 200 First street SW

institute: Mayo Clinic


title: scRNA-seq - Patient 16


title: DNA-seq - Patient 88


title: tiles_pool7_R1


title: DNA-seq - Patient 87


title: scRNA-seq - Patient 18


title: DNA-seq - Patient 86


title: Tet2 knockout, Malat1 knockout bone marrow mononuclear rep3


title: tiles_pool7_R2


title: tiles_pool8_R3


title: Tet2 knockout, Malat1 knockout bone marrow mononuclear rep1


title: DNA-seq - Patient 91


title: scRNA-seq - Patient 15


title: Tet2 knockout bone marrow mononuclear, untreated rep3


title: DNA-seq - Patient 85


title: DNA-seq - Patient 84


title: tiles_pool6_R1


title: tiles_pool8_R2


title: scRNA-seq - Patient 14


title: tiles_pool6_R2


title: WT Bone marrow mononuclear, untreated, rep6

value: wild type


title: scRNA-seq - Patient 12

value: Clonal Hematopoiesis


title: scRNA-seq - Patient 13


title: tiles_pool5_R2


title: WT Bone marrow mononuclear, untreated, rep5


title: tiles_pool5_R3


title: DNA-seq - Patient 83


title: Tet2 knockout bone marrow mononuclear, untreated rep1


title: DNA-seq - Patient 81


title: scRNA-seq - Patient 9


title: tiles_pool5_R1


title: DNA-seq - Patient 79


title: tiles_pool6_R3


title: WT Bone marrow mononuclear, untreated, rep3


title: scRNA-seq - Patient 7


title: DNA-seq - Patient 80


title: tiles_pool4_R3


title: WT Bone marrow mononuclear, untreated, rep4


title: scRNA-seq - Patient 8


title: WT Bone marrow mononuclear, untreated, rep2


title: DNA-seq - Patient 78


title: Tet2 knockout bone marrow mononuclear, untreated rep2


title: scRNA-seq - Patient 6


title: tiles_pool4_R2


title: WT Bone marrow mononuclear, untreated, rep1


title: tiles_pool4_R1


title: DNA-seq - Patient 77


title: scRNA-seq - Patient 5


title: DNA-seq - Patient 82


title: tiles_pool3_R3


title: IP_159_snf2hko_R4

data_processing:
ChIP-seq reads were mapped using the qAlign function from the QuasR Bioconductor package version 1.32.082, which internally uses bowtie, was used with default parameters, except for paired=”fr” which was used for NovaSeq paired-end reads. Only reads with a unique match to the genome were reported as alignments.
bigWig files were generated by first generating wig files using the qExportWig function from the QuasR Bioconductor package version 1.32.082 with default parameters and then converting them to bigWig using the function wigToBigWig from the package rtracklayer version 1.60.0 with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
ChIP DNA was extracted with SPRI beads and submitted to library preparation.
Libraries were prepared using the NEBNext UltraII Library Prep Master Mix Set following manufacturer instructions.

tag: fraction

value: IP


title: scRNA-seq - Patient 4


title: DNA-seq - Patient 76

extract_protocol:
Sample DNA was extracted from peripheral blood mononuclear cells isolated by gradient centrifugation and re-suspended in a concentration of 500 ng in 50µl of low TE buffer.
Paired-end indexed libraries were prepared using the Sureselect XT Low Input Library prep protocol on the Agilent Bravo liquid handler following the manufacturer’s protocol (NewEngland Biolabs, Ipswitch, MA, and Agilent Technologies, Ankeny, IA). Briefly, 200ng of target DNA was fragmented using the Covaris LE220 plus sonicator. The settings of duty factor 30%, peak incident power (PIP) 450, cycles per burst 200, time 180 seconds generated double-stranded DNA fragments with blunt or sticky ends with a fragment size mode of between 150-200bp. The ends were repaired using the Sureselect End-Repair-A-Tailing enzyme mix. Adapter ligated DNA fragments were size selected to enrich for 200 bp inserts (~320 bp total library size) using AMPURE XP bead purification. The size selected adapter-modified fragments were enriched, and specific indexes were added by 12 cycles of PCR using universal index primers. The concentration and size distribution of the libraries was determined on an Agilent Bioanalyzer DNA 1000 chip. The Custom Capture hybrid-target enrichment probes were designed using Agilent SureSelect design software (Agilent Technologies, Santa Clara, CA). The targeted gene panel was comprised of 62,962 single probes with size 1.805Mbp, and covered the coding regions, UTRs, and overlapping intron/exon regions for 205 genes described and / or enriched for CH mutations (see Appendix: Target Gene Panel). The custom capture was carried out using the Agilent Bravo liquid handler following Agilent’s SureSelect XT Low. Purified capture products were then amplified using the SureSelect Post-Capture primer mix for 14 cycles. Libraries were validated and quantified on the Agilent Bioanalyzer. Samples were sequenced by 150 paired end reads, 21 samples to a Flow Cell, on an Illumina NovaSeq 6000 SP with an expected depth of ≥1,000X coverage (Illumina, SanDiego, CA).


title: tiles_pool3_R2


title: IP_159_snf2hko_R3


title: DNA-seq - Patient 75


title: Multiome - ATAC - Patient 43

data_processing:
Sequenced reads were processed using 10x Genomics Cell Ranger ARC v2.0.0. The reads were aligned to the pre-built human reference genome GRCh38 - v2020-A-2.0.0 (May 3, 2021) provided by 10X Genomics. Downstream processing was done using Seurat v4.0.4 and Signac v1.4.0.70 GEX and ATAC count matrices were integrated (batch-corrected) independently using Seurat. Cell type identification was done by using Azimuth algorithm to map the scMultiome GEX data to the scRNA-seq data (from the same study cohort). The labels were then transferred from the scRNA-seq data to the single-cell Multiome data.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Frozen PBMCs were thawed in a 37°C water bath for 3-5 min until no ice was visible. Cells were washed twice with 1 mL PBS + 0.04% BSA and pelleted (300×g for 5 min at 4°C). Dead cells were removed according to the Demonstrated Protocol: Removal of Dead Cells from Single Cell Suspensions for Single Cell RNA Sequencing (10X Genomics). Using the MACS Dead Cell Removal Kit (Miltenyi Biotec), the pellet was resuspended in 100 mL Dead Cell Removal MicroBeads and incubated for 15 minutes at room temperature. After incubation, the cell suspension was diluted with 1X Binding Buffer and applied to a MS column. The dead cells were retained on the column and the live cells passed through the column and were collected. After dead cell removal, the samples were washed twice with 1 mL PBS + 0.04% BSA and the cell concentration was determined using a Cellometer K2 cell counter (Nexcelom Biosciences).
Nuclei were isolated according to the Demonstrated Protocol: Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression (10x Genomics, CG000365 Rev A). Briefly, cells were added to a 2.0 mL low binding tube and centrifuged (300×g for 5 min at 4°C) using a swinging bucket rotor. The supernatant was removed, and the cell pellet was resuspended in 100 µL of chilled 10x Genomics Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1 % NP-40 Substitute, 0.01% digitonin, 1% BSA, 1 mM DTT, 1 U/mL RNase inhibitor 40 U/mL) by pipette-mixing 10 times. Cells were incubated on ice for 3 min, followed by dilution with 1 mL of chilled Wash Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/mL RNase inhibitor 40 U/mL). Nuclei were then centrifuged (500×g for 3 min at 4°C), and the supernatant was slowly removed. The nuclei were washed one additional time with 1 mL Wash Buffer. Nuclei were resuspended in chilled Nuclei Buffer (1X Nuclei Buffer (10x Genomics), 1 mM DTT, 1 U/mL RNase inhibitor 40 U/mL); the concentration was determined using a Cellometer K2 cell counter (Nexcelom Biosciences) and the samples were adjusted to a concentration appropriate for our targeted nuclei recovery. The single-cell ATAC library construction and gene expression library construction were carried out as described in the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338 Rev A). ATAC and GEX libraries were sequenced separately on an HiSeq 4000 (Illumina) before demultiplexing, alignment to the reference genome, and post-alignment quality control.


title: IP_159_snf2hko_R2


title: scRNA-seq - Patient 1


title: tiles_pool2_R3


title: Multiome - ATAC - Patient 42


title: DNA-seq - Patient 74


title: DNA-seq - Patient 73


title: IP_159_wt_R4

value: wt


title: IP_159_snf2hko_R1


title: DNA-seq - Patient 71


title: DNA-seq - Patient 72


title: Multiome - ATAC - Patient 38


title: Multiome - ATAC - Patient 41


title: tiles_pool2_R2


title: IP_159_wt_R3


title: tiles_pool1_R3


title: IP_159_wt_R2


title: Multiome - ATAC - Patient 36


title: DNA-seq - Patient 70


title: tiles_pool1_R2


title: Multiome - ATAC - Patient 35


title: tiles_pool1_R1


title: IP_159_wt_R1


title: tiles_pool3_R1


title: Input_159_snf2hko_R4

value: Input


title: Multiome - ATAC - Patient 30


title: tiles_pool2_R1


title: DNA-seq - Patient 67


title: DNA-seq - Patient 69


title: nuc_pool5_R3


title: DNA-seq - Patient 68


title: Input_159_snf2hko_R3


title: Multiome - ATAC - Patient 21


title: Multiome - ATAC - Patient 24


title: nuc_pool5_R1


title: Input_159_wt_R4


title: nuc_pool5_R2


title: Input_159_snf2hko_R2


title: DNA-seq - Patient 66


title: DNA-seq - Patient 64


title: nuc_pool4_R3


title: Multiome - ATAC - Patient 18


title: Multiome - ATAC - Patient 15


title: Input_159_snf2hko_R1


title: DNA-seq - Patient 63


title: Multiome - ATAC - Patient 16


title: DNA-seq - Patient 65


title: nuc_pool4_R1


title: nuc_pool4_R2


title: Multiome - ATAC - Patient 12


title: Input_159_wt_R2


title: nuc_pool3_R3


title: DNA-seq - Patient 62


title: Multiome - ATAC - Patient 8


title: Input_159_wt_R1


title: DNA-seq - Patient 61


title: nuc_pool3_R2


title: DNA-seq - Patient 60


title: Multiome - ATAC - Patient 7


title: GFP+Sfrp4-/-  Periosteal cells 2

city: Boston

first: Francesca

last: Gori

state: MA

address: 188 Longwood Avenue

institute: Harvard School of Dental Medicine

data_processing:
Raw data by CASAVA base recognition
Raw-data stored in FASTQ format file, data quality control
GC Content distribution, data filtering to obtain clean reads (remove reads containging adaptors, reads containing N>10%, and reads of low quality)
Alignment and Mapping (Hisat2 2.0.5), quantification (featureCounts 1.00-p3),  Differential analysis (Deseq2 1.20.0), Enrichment analysis (clusterProfiler 3.8.1)
Assembly: mm10
Supplementary files format and content: gene_count_all samples.xlsx

source_name: Periosteum

growth_protocol: Microdissection of mouse long bone periosteum from 4 weeks old GFP+;Sfrp4-/- and GFP+ mice was performed under a dissecting microscope.  Periosteum was scraped and subjected to enzymatic digestion with Collagenase P in PBS for 10 min at 37 °C with agitation. Samples were centrifuged, resuspended in ice-cold FACS buffer, incubated with stem cell surface markers and CD45-CD31-Ter119-(Lin-) Thy1.2-6C3-GFP+CD105- CD200+ cells (PSC) sorted using a FACS Aria II cytometer equipped with 4 lasers (BD Biosciences).

extract_protocol:
RNA was isolated using the microQiagen kit (Qiagen)
Ultra-low input mRNA non-directional libraries  prepered using  SMARTer Kit (Novogene)

value: Periosteum

value: 4 weeks

value: Ctsk-lineage periosteal stem cells


title: GFP+Sfrp4-/-  Periosteal cells 1


title: nuc_pool3_R1

value: embryonic stem cells


title: DNA-seq - Patient 59

value: Peripheral blood mononuclear cells


title: Multiome - ATAC - Patient 5


title: Input_159_wt_R3


title: GFP+ Periosteal cells 2

value: WT


title: Multiome - ATAC - Patient 4


title: nuc_pool2_R2


title: GFP+ Periosteal cells 1


title: non-diabetic (db/m) mice 4

city: Changzhou

first: Chao

last: Tu

state: Jiangsu

address: 185 Juqian Road

department: Department of Internal Medicine

institute: The Third Affiliated Hospital of Soochow University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Mus musculus reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: renal cortex

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

tag: Sex

value: male

tag: disease

value: non-diabetic (db/m)


title: Multiome - ATAC - Patient 1

last: Gaspar-Maia


title: DNA-seq - Patient 58


title: Multiome - GEX - Patient 43

molecule: nuclear RNA


title: DNA-seq - Patient 57


title: nuc_pool2_R1


title: nuc_pool1_R3


title: DNA-seq - Patient 56


title: Multiome - GEX - Patient 42


title: non-diabetic (db/m) mice 3


title: DNA-seq - Patient 55


title: nuc_pool1_R2


title: DNA-seq - Patient 54


title: nuc_pool2_R3


title: DNA-seq - Patient 53


title: non-diabetic (db/m) mice 2


title: nuc_pool1_R1


title: Multiome - GEX - Patient 41


title: non-diabetic (db/m) mice 1


title: Multiome - GEX - Patient 38


title: DNA-seq - Patient 52


title: Type 2 diabetic (db/db) mice 4

value: Type 2 diabetic (db/db)


title: DNA-seq - Patient 51


title: Multiome - GEX - Patient 35


title: Type 2 diabetic (db/db) mice 2


title: DNA-seq - Patient 50


title: non_nuc_pool2_R3


title: Multiome - GEX - Patient 24


title: Multiome - GEX - Patient 30


title: DNA-seq - Patient 49


title: non_nuc_pool2_R2


title: Type 2 diabetic (db/db) mice 3


title: cKO2, TCR-derived cDNA

description:
GA29193
TCR V(D)J segments

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene-cell (barcode) combination and B cell and T cell receptor repertoire profiling.
Assembly: refdata-gex-mm10-2020-A and refdata-cellranger-vdj-GRCm38-alts-ensembl-4.0.0
Supplementary files format and content: genematrix.csv: Comma-delimited text files including raw counts for all cells detected.
Supplementary files format and content: airr_rearrangement.tsv: Tab-delimited text files including detected clonotypes for each cell (barcode).
Supplementary files format and content: clonotypes.csv: Comma-delimited text files including the BCR or TCR clonotype information.

extract_protocol:
Single cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell 5' Reagent Kits v2 User Guide.

value: Spleen

value: Lymphocytes

value: invariant chainfl/fl Cre-ERT2+/-

value: Tamoxifen

tag: age

value: 16 weeks

value: female


title: Multiome - GEX - Patient 21


title: non_nuc_pool3_R3


title: Multiome - GEX - Patient 18


title: non_nuc_pool2_R1


title: non_nuc_pool3_R2


title: DNA-seq - Patient 47

value: Clonal Hematopoiesis


title: cKO1, TCR-derived cDNA

description:
GA29192
TCR V(D)J segments


title: Multiome - GEX - Patient 36


title: WT2, TCR-derived cDNA

description:
GA29191
TCR V(D)J segments

value: invariant chainfl/fl Cre-ERT2-/-


title: DNA-seq - Patient 46


title: non_nuc_pool1_R2


title: DNA-seq - Patient 45


title: cKO2, BCR-derived cDNA

description:
GA29190
BCR V(D)J segments


title: Multiome - GEX - Patient 15


title: non_nuc_pool3_R1


title: Type 2 diabetic (db/db) mice 1


title: cKO1, BCR-derived cDNA

description:
GA29189
BCR V(D)J segments


title: Multiome - GEX - Patient 16


title: Multiome - GEX - Patient 12


title: unphased_pool18_R2


title: non_nuc_pool1_R1


title: WT2, BCR-derived cDNA

description:
GA29188
BCR V(D)J segments


title: Multiome - GEX - Patient 8


title: DNA-seq - Patient 43


title: unphased_pool18_R1


title: DNA-seq - Patient 42


title: Multiome - GEX - Patient 7


title: cKO2, mRNA-derived cDNA

description:
GA29187
polyA RNA


title: non_nuc_pool1_R3


title: unphased_pool17_R2


title: Multiome - GEX - Patient 5


title: unphased_pool17_R1


title: cKO1, mRNA-derived cDNA

description:
GA29186
polyA RNA


title: WT2, mRNA-derived cDNA

description:
GA29185
polyA RNA


title: DNA-seq - Patient 40


title: DNA-seq - Patient 41


title: Multiome - GEX - Patient 4


title: unphased_pool16_R2


title: DNA-seq - Patient 39


title: DNA-seq - Patient 44


title: OSKM iPSC,Tsc1 KO+shTfe3-2,Day10,rep2

city: Guangzhou

first: shuhui

last: xu

address: 190 Kaiyuan Avenue, Huangpu District

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

data_processing:
the libraries were sequenced on an MGISEQ-2000 sequencer in paired-end 100 mode.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: OSKM D10

extract_protocol:
RNA from reprogramming day 5 and 10 were extracted from all experimental groups using a standard protocol. A total of 1 µg RNA per sample was utilized for library preparation at China National GeneBank (CNGB).
The sequencing libraries were generated using the MGIEasy RNA Library Prep Set (MGI, 1000006384) following the manufacturer's protocol

value: OSKM D10

value: Tsc1 KO


title: unphased_pool16_R1


title: unphased_pool15_R2


title: WT1, TCR-derived cDNA

description:
GA24853
TCR V(D)J segments


title: OSKM iPSC,Tsc1 KO+shTfe3-2,Day10,rep1


title: Multiome - GEX - Patient 1


title: OSKM iPSC,Tsc1 KO+shTfe3-1,Day10,rep2


title: DNA-seq - Patient 36


title: OSKM iPSC,Tsc1 KO+shTfe3-1,Day10,rep1


title: unphased_pool14_R2


title: DNA-seq - Patient 37


title: DNA-seq - Patient 35


title: cKO6, BCR-derived cDNA

description:
GA24852
BCR V(D)J segments


title: cKO6, TCR-derived cDNA

description:
GA24855
TCR V(D)J segments


title: unphased_pool14_R1


title: unphased_pool13_R2


title: OSKM iPSC,Tsc1 KO,Day10,rep2


title: DNA-seq - Patient 33


title: unphased_pool13_R1


title: OSKM iPSC,Tsc1 KO,Day10,rep1


title: DNA-seq - Patient 38


title: DAS male rep3

city: Paris

first: Boris

last: BARDOT

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: total ribo-depleted RNA

data_processing:
Reads were mapped on mouse genome version GRCm38 with tophat version 2.1.1, with the following parameters : -g 1 -N 3 --read-edit-dist 3 -r 155 --mate-std-dev 80 –no-coverage-search --library-type fr-firststrand.
Only unique mapped reads were kept for further analysis.
Read counting was performed using featureCounts version 1.6.0 on the annotation gencode.vM18, with the following parameters : -F "GTF" -p -s 2 -O.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing raw read counts for each gene

source_name: Splenocytes

extract_protocol:
Spleens were removed from 4-6 weeks-old  Em-Myc transgenic mice, flash frozen on liquid nitrogen, and RNA was extracted using Nucleopsin RNA II (Macherey-Nagel). The quality of RNA was checked with Bioanalyzer Agilent and RNAs with a RIN > 6 retained for further analysis.
RNA was depleted from ribosomal RNA, then converted into cDNA using a TruSeq Stranded Total Library preparation kit (Illumina).

value: C57BL/6 (> 10 Back-cross)

value: spleen

value: 4-6 weeks-old

value: p53DAS/DAS Em-Myc


title: DAS male rep4

description: total ribo-depleted RNA


title: OSKM iPSC,wildtype,Day10,rep2

value: Tsc1 WT


title: OSKM iPSC,wildtype,Day10,rep1


title: WT1, BCR-derived cDNA

description:
GA24850
BCR V(D)J segments

source_name: Spleen


title: unphased_pool15_R1

value: embryonic stem cells


title: DAS male rep2

description: total ribo-depleted RNA


title: DNA-seq - Patient 32

value: Peripheral blood mononuclear cells


title: unphased_pool12_R1


title: cKO6, mRNA-derived cDNA

description:
GA24849
polyA RNA

value: Spleen


title: DAS male rep1

description: total ribo-depleted RNA


title: OSKM iPSC,Tsc1 KO+shTfe3-2,Day5,rep2

source_name: OSKM D5

value: OSKM D5


title: DNA-seq - Patient 30


title: DNA-seq - Patient 29


title: unphased_pool11_R2


title: WT male rep3

description: total ribo-depleted RNA

value: p53+/+ Em-Myc


title: DNA-seq - Patient 34


title: DNA-seq - Patient 31


title: WT1, mRNA-derived cDNA

description:
GA24847
polyA RNA

value: Lymphocytes

value: Tamoxifen


title: unphased_pool11_R1


title: OSKM iPSC,Tsc1 KO+shTfe3-2,Day5,rep1


title: WT male rep2

description: total ribo-depleted RNA


title: DNA-seq - Patient 28


title: OSKM iPSC,Tsc1 KO+shTfe3-1,Day5,rep2


title: OSKM iPSC,Tsc1 KO+shTfe3-1,Day5,rep1


title: WT male rep1

description: total ribo-depleted RNA


title: DNA-seq - Patient 27


title: unphased_pool10_R2


title: unphased_pool12_R2


title: unphased_pool10_R1