title: OPBG_GBM001_input

city: Sutton

first: Chris

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research

data_processing:
Raw sequence reads were aligned to hg19 using bwa
ChIP peaks were detected using MACS2. Merged peaks were used to generate bigWig covergae files in R
Assembly: hg19
Supplementary files format and content: bigWig coverage files are provided for each sample

source_name: Brain

growth_protocol: Patient-derived cultures OPBG-GBM-001 (H3.3 G34R), HSJD-GBM-002 (H3.3 G34R) and CHOP-GBM-001 (7316-158; H3.3 G34R) were grown in stem cell media consisting of Dulbecco’s Modified Eagles Medium: Nutrient Mixture F12 (DMEM/F12), Neurobasal-A Medium, 10 mM HEPES Buffer Solution, 1 mM sodium pyruvate solution, 1% (v/v) non-essential amino acids solution (100x) and 1% (v/v) Glutamax-I supplement (100x). The media was supplemented with 2% (v/v) B-27 supplement minus vitamin A (50x), 20 ng/ml Human-EGF, 20 ng/ml Human-FGF-basic-154, 20 ng/ml Human-PDGF-AA, 20 ng/ml Human-PDGF-BB (all Shenandoah Biotech, Warwick, PA, USA) and 2 μg/ml Heparin Solution (Stem Cell Technologies, Cambridge, UK). Cells were cultured on Cultrex® 3D Culture Matrix Laminin (Bio-Techne Ltd) except for CHOP-GBM-001 cells, which were cultured on Geltrex (Invitrogen).  KNS42 cells (H3.3 G34V) were obtained from the Japanese Collection of Research Bioresources Cell Bank (#IFO50356) and grown in DMEM/F12 with 10% (v/v) FBS. HEK293FT (RRID:CVCL_6911) cells were purchased from Invitrogen and grown in DMEM containing 10% (v/v) FBS. BT690 (H3.3G34R) were grown in NSA Working Media (Stem Cell Technologies, #5751), supplemented with 20 ng/ml Human-EGF and 20 ng/ml Human-FGF, and 2 µg/ml Heparin Solution.  Cells were incubated at 37℃ in a humidified atmosphere at 5% CO2.

extract_protocol:
ChIP sequencing was performed by Activ Motif using standard protocols using antibodies directed against H3.3 histones, H3.3_G34 mutant histones, H3K27ac, H3K27me3, H3K36me3, H3K9me3, MYCN and RNA Pol II.
ChIP sequencing was performed using Activ Motifs High Throughput ChIP-ITKit according to manufacturers instructions

value: Brain

tag: antibody

value: ChIP Input


title: OPBG_GBM001_MYCN

status: Public on Aug 01 2024

type: SRA

last: Jones

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: genotype

value: MYCN ChIP Antibody


title: ExhaustedCART_RNA-seq Biorep1

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

country: USA

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
Fastq files were first evaluated for quality using FASTQC. Then, Cutadapt was used to remove Illumina adapters before FASTQC was run again to evaluate quality after adapter removal. Next, the paired end reads for each condition were aligned with STAR using the genome reference consortium human build 38 patch release 13 (GRCh38.p13) downloaded from NCBI. HTSeq was used to generate expression counts for each gene.
Assembly: genome reference consortium human build 38 patch release 13 (GRCh38.p13) downloaded from NCBI
Supplementary files format and content: tab-delimited text files contain the gene expression counts for each sample

molecule: total RNA

source_name: T-cell

extract_protocol:
RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA).
SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio USA INC., California, USA)

treatment_protocol: CART19-28ζ cells from three biological replicates were collected before (baseline) or after chronic stimulation (exhausted) in our in vitro model for CART cell exhaustion. In this model, CART cells were chronically stimulated with JeKo-1 cells.

value: T-cell

tag: treatment

value: Exhausted


title: cardiomyocyte,KLH_only, replicate1-51, scRNAseq

city: Bunkyo-ku

first: Manami

last: Katoh

state: Tokyo

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

description:
smartseq2
KLH_4w_1.xlsx

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: heart

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol.
Sample 731-736,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Other samples, single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.

tag: cell type

value: cardiomyocyte

value: heart

tag: strain

tag: age

value: 6-8 weeks old


title: OPBG_GBM001_H3K36me3

value: H3K36me3 ChIP Antibody


title: OPBG_GBM001_Pol2

value: RNA Pol II ChIP Antibody


title: OPBG_GBM001_H3K27ac

value: H3K27ac ChIP Antibody


title: shPRRG1-2_3

city: Shanghai

first: zheng

last: wu

address: 800 Dongchuan Road

country: China

institute: School of Medicine, Shanghai Jiao Tong University

data_processing:
1_quality_control, The raw sequencing data is stored in fastq format files for each sample in this project, which involves paired-end sequencing. Therefore, each sample consists of two fastq files. For each individual fastq file, the sequencing results are assessed for quality using FastQC software.
2_clean_statistic, Using the fastp software to filter sequences, the main objectives are to exclude the following sequences: 1. Remove sequencing adapter sequences contained in the reads. 2. Trim bases with a quality score (Q) lower than 20 from the 3’ end of the reads. 3. Discard reads shorter than 25 bases in length. 4. Remove ribosomal RNA reads from the target sequencing species.
3_mapping_statistic, The software used for sequence alignment is Hisat2. Its alignment algorithm is called the spliced mapping algorithm, which can split reads that cannot be fully matched and then map them. This is suitable for aligning eukaryotic genomes that contain introns.
4_gene_expression_and_differential_expression_genes, Based on the physical location information of genes aligned to the reference genome, the number of reads covering each gene (including newly predicted genes) from start to end is counted. The Stringtie software is used to count the fragments within each gene region after alignment, and then the TMM (trimmed mean of M values) algorithm is used for normalization. Therefore, to comprehensively measure gene expression, the concept of FPKM is used to represent the expression levels of different genes. The resulting FPKM values can be regarded as the expression levels of each gene. Based on this, the software edgeR is used to calculate differentially expressed genes between two groups according to the experimental grouping information.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested by RNeasy Mini Kit (Qiagen). 1.2μg of total RNA was used for the construction of slicing libraries.
RNA libraries for RNA-seq were prepared using TIANSeq Fast RNA Library Prep Kit following manufacture's protocols.


title: shPRRG1-3_1


title: cardiomyocyte,KLH_only, replicate1-50, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: OPBG_GBM001_H3K27me3

value: H3K27me3 ChIP Antibody


title: OPBG_GBM001_H3.3_G34R

value: H3.3_G34R ChIP Antibody


title: OPBG_GBM001_H3.3

value: H3.3 ChIP Antibody


title: shPRRG1-2_2


title: cardiomyocyte,KLH_only, replicate1-49, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: KNS42_input


title: cardiomyocyte,KLH_only, replicate1-56, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: KNS42_Pol2


title: cardiomyocyte,KLH_only, replicate1-48, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-55, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: shPRRG1-2_1


title: KNS42_MYCN


title: shNC_3

value: Control

value: shNC


title: KNS42_H3K9me3

value: H3K9me3 ChIP Antibody


title: OPBG_GBM001_H3K9me3

value: Brain


title: cardiomyocyte,KLH_only, replicate1-47, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: KNS42_H3K27me3


title: KNS42_H3K36me3


title: cardiomyocyte,KLH_only, replicate1-46, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: KNS42_H3.3_G34V

value: H3.3_G34V ChIP Antibody


title: cardiomyocyte,KLH_only, replicate1-45, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: HSJD_GBM002_input

value: ChIP Input


title: KNS42_H3.3


title: KNS42_H3K27ac


title: shNC_2


title: HSJD_GBM002_MYCN

value: MYCN ChIP Antibody


title: shNC_1


title: HSJD_GBM002_H3K9me3


title: HSJD_GBM002_H3K36me3


title: YP11_(HIV-1_cmp9)

city: Cheongju

first: YoungHyun

last: Shin

address: Osongsaengmyeong 2-ro

country: South Korea

institute: Korea National Institute of Health

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic-0.39
Trimmed sequence reads were mapped to GRCh38 using STAR-2.7.4a
Unmapped sequence reads to GRCh38 were extracted using SAMTOOLS
Unmapped sequence reads were mapped to HIV-1pNL4-3 using STAR-2.7.4a
Read count were performed using HTSeq-count
Assembly: GRCh38 and HIV-1pNL4-3
Supplementary files format and content: tab-delimted text file includes raw counts for each sample

source_name: TZM-bl

growth_protocol: TZM-bl cells were cultured in DMEM supplemented with 1% penicillin–streptomycin and 10% (v/v) heat-inactivated fetal bovine serum(FBS) at humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
The total RNA was extracted using the Maxwell® RSC simplyRNA Cells Kit (Promega) according to the manufacturer’s instructions. RNA integrity was evaluated as RNA integrity number > 6 using the Agilent 2100 Bio-analyzer (Agilent Technologies, Santa Clara, CA, USA).
The cDNA libraries were constructed using TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: The TZM-bl cells infected with HIV-1 NL4-3 at an MOI of 1 were treated with the compounds (1.5 μM) for 2 d.

value: TZM-bl

value: epithelial cell

value: WT

value: HIVNL4-3, comp 9

tag: time


title: cardiomyocyte,KLH_only, replicate1-44, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: cardiomyocyte,KLH_only, replicate1-42, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: HSJD_GBM002_Pol2

value: RNA Pol II ChIP Antibody


title: DMSO_minus(no HIV-1_DMSO)

value: DMSO


title: cardiomyocyte,KLH_only, replicate1-43, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: HSJD_GBM002_H3K27me3

value: H3K27me3 ChIP Antibody


title: HSJD_GBM002_H3K27ac

value: H3K27ac ChIP Antibody


title: cardiomyocyte,KLH_only, replicate1-41, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: HSJD_GBM002_H3.3_G34R

value: H3.3_G34R ChIP Antibody


title: KRT_104(HIV-1_cmp21)

value: HIVNL4-3, comp 21


title: HSJD_GBM002_H3.3

value: Brain

value: H3.3 ChIP Antibody


title: KRT_107(HIV-1_cmp20)

value: HIVNL4-3, comp 20


title: CXJ046_input

value: ChIP Input


title: CXJ046_Pol2


title: CXJ046_MYCN

value: MYCN ChIP Antibody


title: DMSOplus_(HIV-1_DMSO)

value: TZM-bl

value: epithelial cell

value: HIVNL4-3, DMSO


title: cardiomyocyte,KLH_only, replicate1-40, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: cardiomyocyte


title: YP12_(HIV-1_cmp13)

value: WT

value: HIVNL4-3, comp 13


title: cardiomyocyte,KLH_only, replicate1-39, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: heart

value: 6-8 weeks old


title: cardiomyocyte,KLH_only, replicate1-38, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: CXJ046_H3K27me3

value: H3K27me3 ChIP Antibody


title: CXJ046_H3K9me3

value: H3K9me3 ChIP Antibody


title: CXJ046_H3K27ac

value: H3K27ac ChIP Antibody


title: CXJ046_H3K36me3

value: H3K36me3 ChIP Antibody


title: SK-N-MC cells, Input control, biol rep 3

city: Hong Kong

first: Ho Yin Edwin

last: Chan

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
PE150 mode
Sample9

data_processing:
Raw sequencing files were checked using FastQC v0.11.8. Adapter and quality trimming were performed using Cutadapt v3.7. FastQC was performed again on the trimmed data to confirm removal of adapter sequence. The reads were then aligned to human genome GRCh38.p14 using Bowtie2 v2.4.1.
The YY1-binding DNA sites (peaks) were identified using MACS3 v3.0.1, annotated using ChIPseeker v1.38.0, and visualized using Trackplot v1.5.10.
Uniquely aligned reads were retrieved using Sambamba v1.0.1 with Input sample as a background, those overlapping with regions in the Encyclopedia of DNA Elements (ENCODE) blacklist were removed using BEDTools v2.29.2.
Assembly: Human genome GRCh38.p14
Supplementary files format and content: Excel file includes read counts in YY1-binding sites (peaks) from each sample

source_name: SK-N-MC

growth_protocol: The human neuroblastoma SK-N-MC cells (HTB-10TM, American Type Culture Collection) were cultured in DMEM (11995065, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (F7524, Sigma-Aldrich) and 1% penicillin–streptomycin (15140122, Thermo Fisher Scientific).

extract_protocol:
The genomic DNA was isolated from cells using the Pierce Magnetic ChIP Kit (26157, Thermo Fisher Scientific). Four micrograms of anti-YY1 (22156-1-AP, Proteintech) antibody were used for the IP.
Library preparation was performed by Novogene (Beijing, China).

treatment_protocol: Plasmid DNA transfection was performed using Lipofectamine 2000 (11668019, Thermo Fisher Scientific).

value: SK-N-MC

value: Human neuroblastoma cells

value: Input control


title: CXJ046_H3.3

value: Brain

value: H3.3 ChIP Antibody


title: CXJ046_H3.3_G34R

value: H3.3_G34R ChIP Antibody


title: cardiomyocyte,KLH_only, replicate1-37, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: CHOP_GBM001_MYCN

value: MYCN ChIP Antibody


title: SK-N-MC cells, Htt1-550Q89, biol rep 3

description:
PE150 mode
Sample6

value: Htt1-550Q89 overexpression


title: CHOP_GBM001_input

value: ChIP Input


title: cardiomyocyte,KLH_only, replicate1-36, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: cardiomyocyte


title: SK-N-MC cells, Input control, biol rep 1

description:
PE150 mode
Sample7

value: WT


title: CHOP_GBM001_Pol2

value: RNA Pol II ChIP Antibody


title: cardiomyocyte,KLH_only, replicate1-34, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: heart

value: 6-8 weeks old


title: cardiomyocyte,KLH_only, replicate1-35, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: CHOP_GBM001_H3K9me3

value: H3K9me3 ChIP Antibody


title: SK-N-MC cells, Htt1-550Q23, biol rep 3

description:
PE150 mode
Sample5

value: Htt1-550Q23 overexpression


title: SK-N-MC cells, Input control, biol rep 2

description:
PE150 mode
Sample8


title: SK-N-MC cells, Htt1-550Q89, biol rep 2

description:
PE150 mode
Sample4


title: CHOP_GBM001_H3K36me3

value: H3K36me3 ChIP Antibody


title: CHOP_GBM001_H3.3


title: OPBG_GBM_001_RIBO_rep3

data_processing:
Data was aligned to GRCh37 using STAR (v2.7.11a)
Transcript abundances were counted using htseq-count (v2.0.3)
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted with Trizol according to the maufacturers instructions
RNASeq libraries were prepared using the Illumina NEBNext® Ultra™ II RNA Library Prep Kit according to the maufacturers instructions

treatment_protocol: Patient-derived cultures were treated with CDK6 inhibitors (Abemaciclib or Ribociclib) and a CDK6 degrader at IC50 concentrations in each cell line for 24h. RNA was also collected after transient transfection with two different shRNAs targeting CDK6 and scrambled controls

value: Ribociclib


title: OPBG_GBM_001_RIBO_rep1


title: OPBG_GBM_001_RIBO_rep2


title: cardiomyocyte,KLH_only, replicate1-30, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: CHOP_GBM001_H3K27me3

value: H3K27me3 ChIP Antibody


title: cardiomyocyte,KLH_only, replicate1-33, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-32, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: OPBG_GBM_001_DMSO_RIBO_rep2

value: DMSO


title: SK-N-MC cells, Htt1-550Q23, biol rep 2

description:
PE150 mode
Sample3

value: SK-N-MC

value: Human neuroblastoma cells


title: CHOP_GBM001_H3K27ac

value: Brain

value: H3K27ac ChIP Antibody


title: cardiomyocyte,KLH_only, replicate1-28, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: SK-N-MC cells, mutant PAPD5 D256A & D258A, biol rep 3

description: SE50 mode

library_source: other

data_processing:
Raw sequencing files were checked using FastQC v0.11.8. Adapter and quality trimming were performed using Cutadapt v3.7. FastQC was performed again on the trimmed data to confirm the removal of adapter sequence.
The reads (canonical counts) were aligned to mature human miRNAs retrieved from miRbase release 22.1 using Bowtie v1.3.1. The reads were also mapped to a custom reference with an “A” added to each miRNA using Bowtie (adenylated counts). SAMtools v1.13 was used to retrieve the canonical and adenylated counts.
miRNAs with adenylated counts more than 100 across samples were further processed to calculate their adenylation levels.
Assembly: miRbase release 22.1
Supplementary files format and content: Excel file include processed read counts for both canonical and adenylated miRNAs

molecule: other

source_name: Cell line

extract_protocol:
The small RNA species were isolated from SK-N-MC cells using the mirVana™ miRNA Isolation Kit (AM1560, Thermo Fisher Scientific).
Library preparation was performed by Novogene (Beijing, China).

value: Cell line

value: Mutant PAPD5 D256A & D258A overexpression


title: SK-N-MC cells, wildtype PAPD5, biol rep 3

description: SE50 mode

value: Wildtype PAPD5 overexpression


title: CHOP_GBM001_H3.3_G34R

value: H3.3_G34R ChIP Antibody


title: OPBG_GBM_001_DMSO_ABE_rep1


title: SK-N-MC cells, Htt1-550Q23, biol rep 1

description:
PE150 mode
Sample1

value: WT


title: SK-N-MC cells, Htt1-550Q89, biol rep 1

description:
PE150 mode
Sample2

value: Htt1-550Q89 overexpression


title: HSJD_GBM_002_RIBO_rep3


title: HSJD_GBM_002_RIBO_rep2


title: cardiomyocyte,KLH_only, replicate1-31, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: cardiomyocyte,KLH_only, replicate1-25, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-29, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-24, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: OPBG_GBM_001_DMSO_RIBO_rep3


title: SK-N-MC cells, Untransfected, biol rep 3

description: SE50 mode


title: HSJD_GBM_002_DMSO_RIBO_rep3


title: OPBG_GBM_001_DMSO_ABE_rep3


title: SK-N-MC cells, mutant PAPD5 D256A & D258A, biol rep 1

description: SE50 mode


title: cardiomyocyte,KLH_only, replicate1-23, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-27, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: OPBG_GBM_001_ABE_rep3

value: Abemaciclib


title: cardiomyocyte,KLH_only, replicate1-22, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: OPBG_GBM_001_ABE_rep1


title: SK-N-MC cells, mutant PAPD5 D256A & D258A, biol rep 2

description: SE50 mode


title: OPBG_GBM_001_ABE_rep2


title: SK-N-MC cells, wildtype PAPD5, biol rep 2

description: SE50 mode


title: OPBG_GBM_001_DMSO_ABE_rep2


title: OPBG_GBM_001_DMSO_RIBO_rep1


title: SK-N-MC cells, Untransfected, biol rep 2

description: SE50 mode


title: HSJD_GBM_002_RIBO_rep1

value: Ribociclib


title: HSJD_GBM_002_DMSO_ABE_rep1


title: HSJD_GBM_002_ABE_rep3


title: SK-N-MC cells, wildtype PAPD5, biol rep 1

description: SE50 mode


title: HSJD_GBM_002_ABE_rep2


title: HSJD_GBM_002_ABE_rep1


title: HSJD_GBM_002_DMSO_RIBO_rep2


title: MCF-7, Auphen, replicate 4

city: South Bend

first: Verodia

last: Charlestin

state: IN

address: 1234 N. Notre Dame Ave

department: Chemistry and Biochemistry

institute: University of Notre Dame

data_processing:
Reads were mapped to human (genome GRCh38, transcriptome GRCh38.109) or mouse genomes (genome GRCm39, transcriptome GRCm39.109) using HISAT2, and then the number of reads uniquely mapped to each gene tallied using HTSeq.
When identifying differentially expressed (DE) genes, vehicle and Auphen treated samples were paired.
Next, we did differential expression (DE) analysis using edgeR using the likelihood ratio test (LRT). Low-expression genes whose average number of reads per sample < 2.0 were filtered out except for Aqp7/AQP7.
First condition = Vehicle; Second conditon = Auphen. A positive/negative log2FC means that the gene is up-regulated/down-regulated in the second condition compared to the first condition.), and log2CPM (log2 of the overall average expression, measured by log2 of counts per million. This number indicates whether the gene is a high-expression or low-expression gene, on average, over the two groups.).
Assembly: GRCh38, transcriptome GRCh38.109 and GRCm39, transcriptome GRCm39.109.
Supplementary files format and content: CSV file. The columns for each file are: GeneSymbol (the gene symbol), FDR (the false discovery rate or the adjusted p-value; set to 0.1 as a cutoff), pval (the unadjusted/original p-value), log2FC (log2 fold change.
Supplementary files format and content: A positive/negative log2FC means that the gene is up-regulated/down-regulated in the second condition compared to the first condition.), and log2CPM (log2 of the overall average expression, measured by log2 of counts per million. This number indicates whether the gene is a high-expression or low-expression gene, on average, over the two groups.).

source_name: Breast; Mammary gland

growth_protocol: All cells were maintained at 37°C in humidified incubators with 5% CO2 at atmospheric oxygen levels. MCF-7 and PyMT cells were cultured in DMEM High Glucose media with 10% FBS.

extract_protocol:
RNA extraction was carried out with RNeasy Plus Mini Kit (Qiagen).Total RNA was evaluated with Agilent Tapestation 4150 system and RNA ScreenTape (Agilent Technologies). All samples had an RNA Integrity Number (RIN) of 9 or higher. Samples were quantitated with the Qubit RNA HS Assay Kit.
Total RNA input was normalized to 500 ng. mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) and converted into an Illumina library using NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads (New England BioLabs). Indexed libraries were quality assessed using Qubit dsDNA HS Assay Kit (Invitrogen) and Tapestation 4150 DNA HS 1000 Kit (Agilent Technologies). The individual libraries were normalized, and equal molar amounts were multiplexed. Molar concentration of the multiplex pool was determined with KAPA Library Quantification Kits for Illumina.

treatment_protocol: 100,000 cells/well were seeded in 6-well plates . After overnight incubation, the cells were treated with Auphen or Vehicle (DMSO)  for 72 h at determined IC50 concentrations (~4 uM and ~8 uM for MCF-7 and PyMT, respectively).

value: Breast; Mammary gland

value: epithelial cell

value: Auphen

value: adenocarcinoma


title: HSJD_GBM_002_DMSO_RIBO_rep1

value: Brain

value: DMSO


title: HSJD_DMSO_CDKGdeg_rep2


title: MCF-7, Auphen, replicate 3


title: cardiomyocyte,KLH_only, replicate1-19, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: HSJD_DMSO_CDKGdeg_rep3


title: cardiomyocyte,KLH_only, replicate1-20, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-26, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: HSJD_GBM_002_DMSO_ABE_rep2


title: SK-N-MC cells, Untransfected, biol rep 1

description: SE50 mode

value: Cell line

value: SK-N-MC

value: Human neuroblastoma cells


title: cardiomyocyte,KLH_only, replicate1-21, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: MCF-7, Auphen, replicate 1


title: HSJD_GBM_002_DMSO_ABE_rep3


title: cardiomyocyte,KLH_only, replicate1-18, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-17, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: MCF-7, Vehicle, replicate 4

value: Vehicle


title: BT690_shRNA_scramble_rep3

value: shRNA-scramble


title: cardiomyocyte,KLH_only, replicate1-16, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: BT690_shRNA_scramble_rep1


title: HSJD_DMSO_CDKGdeg_rep1


title: BT690_shRNA2_CDK6_rep3


title: HSJD_CDK6deg_rep2

value: CDK6 degrader


title: BT690_shRNA2_CDK6_rep2


title: MCF-7, Vehicle, replicate 3

value: WT


title: BT690_shRNA_scramble_rep2


title: BT690_shRNA2_CDK6_rep1


title: MCF-7, Auphen, replicate 2


title: cardiomyocyte,KLH_only, replicate1-13, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: cardiomyocyte

value: heart


title: BT690_shRNA1_CDK6_rep1


title: cardiomyocyte,KLH_only, replicate1-15, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: 6-8 weeks old


title: cardiomyocyte,KLH_only, replicate1-14, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: MCF-7, Vehicle, replicate 2


title: ATAC-seq Buffy coat, AD patient, 10

city: Fort Collins

first: Alyssa

middle: N

last: Cavalier

state: CO

address: 1582 Campus Delivery, Moby Reception

department: Health and Exercise Science

institute: Colorado State University

data_processing:
RNA-seq: Adapters trimmed & file QC by Fastp.
RNA-seq: Reads aligned using STAR and counted with TEtranscripts.
RNA-seq: Differential expression performed with DESeq2.
WGBS: Reads aligned using Abismal program.
WGBS: Bisulfite conversion rates and site- and regional methylation calculated using MethPipe program.
ATAC-seq: Reads trimmed and filtered using Fastp.
ATAC-seq: Reads aligned with Bowtie2.
ATAC-seq: MACS2 used for ATAC peak identification to call differentially accessible peaks.
Assembly: hg38
Supplementary files format and content: .xlsx formatted as a counts matrix with rows labeled by gene name and columns labeled by sample ID
Supplementary files format and content: .txt with differentially methylated regions (dmrs)
Supplementary files format and content: .xls with MACS2 peaks

source_name: Isolated WBC

extract_protocol:
RNA for RNA-seq extracted using Qiagen PaxGene-specific blood RNA isolation kits; genomic DNA for WGBS extracted using the Zymo DNA Miniprep Plus kit; DNA for ATAC-seq extracted using Active Motif ATAC-seq library kit
RNA libraries generated using Tecan Globin/Ribo depletion kits according to manufacturer's instructions;
DNA bisulfite-converted libraries were prepared using the Swift Accel-NGS Methyl-Seq DNA library kit;
ATAC-seq libraries were prepared using the Active Motif ATAC-seq library kit.
Illumina NovaSEQ 6000 (151-bp, paired-end reads) at 60 Gb/sample for WGBS, 40 M paired-end reads per sample for RNA-seq, and 50 M paired-end reads for ATAC-seq .

value: Isolated WBC

tag: Sex

value: female


title: HSJD_CDK6deg_rep1


title: MCF-7, Vehicle, replicate 1

value: Breast; Mammary gland

value: epithelial cell


title: BT690_RIBO_rep2

value: Ribociclib


title: BT690_RIBO_rep1

value: Brain


title: HSJD_CDK6deg_rep3


title: BT690_DMSO_RIBO_rep3

value: DMSO


title: cardiomyocyte,KLH_only, replicate1-10, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: BT690_DMSO_RIBO_rep2


title: ATAC-seq Buffy coat, AD patient, 9

value: male


title: BT690_RIBO_rep3


title: BT690_shRNA1_CDK6_rep3


title: cardiomyocyte,KLH_only, replicate1-12, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: BT690_shRNA1_CDK6_rep2


title: ATAC-seq Buffy coat, AD patient, 8


title: BT690_DMSO_RIBO_rep1


title: cardiomyocyte,KLH_only, replicate1-11, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: BT690_DMSO_CDK6deg_rep2


title: ATAC-seq Buffy coat, AD patient, 5


title: BT690_DMSO_CDK6deg_rep1


title: J774_circSTOP_uptake_rep2

city: Stanford

first: Laura

last: Amaya

state: CA

address: 269 Campus Drive

institute: Stanford University

data_processing:
Transcript abundances were calculated by pseudocounts using Salmon (version 1.4.0). Normalization and differential gene expression analyses were performed by the DESeq2 package (v1.32.0) in R (version 4.1.1).
Guide composition and comparisons across bound and unbound fractions were analyzed using casTLE
Assembly: mm10
Supplementary files format and content: tab-delimited file with raw counts per sample, salmon’s estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM).
Supplementary files format and content: tab-delimited file with raw counts per sample

extract_protocol:
After 24 hours of incubation, total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.
The integrity of the total RNA was analyzed using an Agilent 2100 Bio-analyzer and RIN numbers were above 9. RNA libraries were prepared with the Illumina Ribo-Zero Plus rRNA Depletion Kit.

value: Macrophage

value: uptake-circSTOP


title: BT690_DMSO_CDK6deg_rep3


title: cardiomyocyte,KLH_only, replicate1-7, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: cardiomyocyte,KLH_only, replicate1-9, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: ATAC-seq Buffy coat, AD patient, 6


title: ATAC-seq Buffy coat, AD patient, 4


title: cardiomyocyte,KLH_only, replicate1-8, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: J774_circSTOP_uptake_rep1


title: ATAC-seq Buffy coat, AD patient, 3


title: cardiomyocyte,KLH_only, replicate1-6, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: BT690_DMSO_ABE_rep3


title: J774_circRNA_uptake_rep2

value: uptake-circRNA


title: ATAC-seq Buffy coat, AD patient, 7


title: BT690_DMSO_ABE_rep1


title: ATAC-seq Buffy coat, AD patient, 2


title: MutuDC_circRNA_transfection_rep1

source_name: MutuDC

value: MutuDC

value: Dendritic cells

value: transfection-circRNA


title: J774_circRNA_uptake_rep1

value: WT


title: cardiomyocyte,KLH_only, replicate1-4, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: cardiomyocyte

value: heart


title: BT690_DMSO_ABE_rep2


title: cardiomyocyte,KLH_only, replicate1-3, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx

value: 6-8 weeks old


title: MutuDC_circRNA_transfection_rep2


title: cardiomyocyte,KLH_only, replicate1-2, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: ATAC-seq Buffy coat, AD patient, 1

value: Isolated WBC


title: cardiomyocyte,KLH_only, replicate1-1, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: MutuDC_circRNA_uptake_rep2


title: ATAC-seq Buffy coat, MCI patient, 10

value: female


title: BT690_CDK6deg_rep2

value: CDK6 degrader


title: BT690_CDK6deg_rep3


title: ATAC-seq Buffy coat, MCI patient, 9


title: MutuDC_circRNA_uptake_rep1


title: ATAC-seq Buffy coat, MCI patient, 8


title: BT690_ABE_rep3

value: Abemaciclib


title: BT690_ABE_rep2

value: Brain


title: RAW264_circRNA_transfection_rep2


title: BT690_ABE_rep1


title: MutuDC_untreated_r1

value: untreated


title: MutuDC_untreated_r2


title: cardiomyocyte,TAC2w+CDK-i, replicate2-84, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate2-83, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate2-82, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: ATAC-seq Buffy coat, MCI patient, 5


title: RAW264_circRNA_transfection_rep1


title: cardiomyocyte,KLH_only, replicate1-5, scRNAseq

description:
smartseq2
KLH_4w_1.xlsx


title: xSCAR_H4K20me0_Mrc1_RKRN_KAF_rep2

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

description: EdU-labelled genomic DNA

data_processing:
Library strategy: SCAR-seq
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.5.0) )
duplicate reads were removed with rmDup from samtools (version 2.0.1)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 500bp bins (mESC: 1kB) and smoothed in a uniform blur considering the neighboring 5 bins (mESC: 30 )on each side. For each 500bp window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero.
Assembly: S.pombe h90 contig and mm10
Supplementary files format and content: SCAR-seq Partition scores in bigwig format

organism: Schizosaccharomyces pombe

growth_protocol: S. pombe cell cultures were grown exponentially in YES media at 30°C, shifted to 20°C for 5h, shifted to 30°C for 30min with addition of 500uM EdU (ChIP-seq). For more details see Methods section in Charlton et al. (2023). ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA or TrypLE.

extract_protocol:
See Charlton et al, 2023 for details. Cells were fixed for 15min in 1% formaldehyde, lysed using bead-beating, sonicated, and incubated with anti-H3K36me3 antibody (ab9050) or anti-H4K20me0 antibody (ab227804). Bound chromatin was washed, extracted, and decrosslinked overnight. Then, decrosslinked DNA was incubated with Protease K and RNase A before clean up with Ampure XP beads. For mESC SCAR-seq, chromatin was digested with MNase. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced.
For details, see Charlton et al, 2023. Briefly, xSCAR-seq library preparation involved library preparation followed by Click-IT with Biotin-TEG-Azide. Biotinylated EdU-labelled DNA was purified using Streptaviding T1 Dynabeads including 3 washes with 100mM NaoH. Stranded, EdU-Biotin-labelled DNA was PCR-amplified using KAPA Hyper Prep HiFi Polymerase for 12 cycles. For native SCAR-seq in mESCs,

treatment_protocol: See growth protocol

value: S. pombe cell culture

value: h90 (XmnI)::ura4+ mat2-P kint2::YFP mat3-M(RV)::mCherry mrc1-R784A-K785A-R786A-N787A-K833A-F835A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18

value: Temperature-induced M-arrest at 20C, shift to 30C for 30min, add EdU (500uM)


title: xSCAR_H4K20me0_Mrc1_RKRN_KAF_rep1

description: EdU-labelled genomic DNA


title: cardiomyocyte,TAC2w+CDK-i, replicate2-81, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: ATAC-seq Buffy coat, MCI patient, 3


title: ATAC-seq Buffy coat, MCI patient, 7

value: male


title: RAW264_circRNA_uptake_rep2

value: Macrophage

value: uptake-circRNA


title: RAW264_circRNA_uptake_rep1


title: xSCAR_H4K20me0_Mrc1_RKRN_rep1

description: EdU-labelled genomic DNA

value: h90 (XmnI)::ura4+ mat2-P kint2::YFP mat3-M(RV)::mCherry mrc1-R784A-K785A-R786A-N787A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: ATAC-seq Buffy coat, MCI patient, 4


title: cardiomyocyte,TAC2w+CDK-i, replicate2-79, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate2-78, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: ATAC-seq Buffy coat, MCI patient, 2


title: ATAC-seq Buffy coat, MCI patient, 6


title: BT690_CDK6deg_rep1


title: RAW264_untreated_r2

value: WT


title: ATAC-seq Buffy coat, MCI patient, 1


title: xSCAR_H4K20me0_Mrc1_RKRN_rep2

description: EdU-labelled genomic DNA


title: xSCAR_H4K20me0_Mrc1_KAF_rep2

description: EdU-labelled genomic DNA

value: h+ ura4-D18 mrc1-K833A-F835A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-77, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: cardiomyocyte

value: heart


title: ATAC-seq Buffy coat, older adult, 14

value: Isolated WBC


title: RAW264_untreated_r1


title: xSCAR_H4K20me0_Mrc1_KAF_rep1

description: EdU-labelled genomic DNA


title: GW_M_IONP_rep2_u


title: xSCAR_H4K20me0_Mrc1_MFL_rep3

description: EdU-labelled genomic DNA

value: h+ mrc1-M755A-F758A-L774A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-80, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: 6-8 weeks old


title: cardiomyocyte,TAC2w+CDK-i, replicate2-75, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: ATAC-seq Buffy coat, older adult, 12


title: xSCAR_H4K20me0_Mrc1_MFL_rep2

description: EdU-labelled genomic DNA


title: cardiomyocyte,TAC2w+CDK-i, replicate2-74, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: GW_M_mRNA_rep2_u


title: cardiomyocyte,TAC2w+CDK-i, replicate2-73, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: ATAC-seq Buffy coat, older adult, 10

value: female


title: xSCAR_H4K20me0_MCM2_2A_rep3

description: EdU-labelled genomic DNA

value: h90 (XmnI)::ura4+ mat2-P kint2::YFP mat3-M(RV)::mCherry mcm2-Y80A-Y89A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: xSCAR_H4K20me0_Mrc1_MFL_rep1

description: EdU-labelled genomic DNA


title: ATAC-seq Buffy coat, older adult, 9


title: GW_M_CircRNA_rep2_u


title: xSCAR_H4K20me0_WT_rep3

description: EdU-labelled genomic DNA

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: cardiomyocyte,TAC2w+CDK-i, replicate2-76, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate2-71, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: ATAC-seq Buffy coat, older adult, 13


title: ATAC-seq Buffy coat, older adult, 8


title: cardiomyocyte,TAC2w+CDK-i, replicate2-70, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: ATAC-seq Buffy coat, older adult, 7


title: GW_M_CircRNA_rep1_u


title: GW_M_IONP_rep2_b


title: xSCAR_K36me3_Mrc1_RKRN_KAF_rep2

description: EdU-labelled genomic DNA

value: S. pombe cell culture


title: xSCAR_K36me3_Mrc1_RKRN_KAF_rep1

description: EdU-labelled genomic DNA

value: h90 (XmnI)::ura4+ mat2-P kint2::YFP mat3-M(RV)::mCherry mrc1-R784A-K785A-R786A-N787A-K833A-F835A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: ATAC-seq Buffy coat, older adult, 6


title: xSCAR_K36me3_Mrc1_RKRN_rep2

description: EdU-labelled genomic DNA

value: Temperature-induced M-arrest at 20C, shift to 30C for 30min, add EdU (500uM)


title: cardiomyocyte,TAC2w+CDK-i, replicate2-69, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: GW_M_IONP_rep1_u


title: ATAC-seq Buffy coat, older adult, 11

value: male


title: cardiomyocyte,TAC2w+CDK-i, replicate2-68, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: ATAC-seq Buffy coat, older adult, 5


title: GW_M_mRNA_rep1_u

value: Macrophage


title: GW_M_mRNA_rep2_b


title: cardiomyocyte,TAC2w+CDK-i, replicate2-72, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: xSCAR_K36me3_Mrc1_RKRN_rep1

description: EdU-labelled genomic DNA


title: cardiomyocyte,TAC2w+CDK-i, replicate2-66, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate2-67, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: GW_M_mRNA_rep1_b


title: ATAC-seq Buffy coat, older adult, 4


title: GW_M_CircRNA_rep2_b


title: xSCAR_K36me3_Mrc1_KAF_rep2

description: EdU-labelled genomic DNA


title: GW_M_CircRNA_rep1_b


title: cardiomyocyte,TAC2w+CDK-i, replicate2-64, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: ATAC-seq Buffy coat, older adult, 2


title: xSCAR_K36me3_Mrc1_MFL_rep3

description: EdU-labelled genomic DNA


title: brain, tMCAO, rep3

city: shanghai

first: wan

last: hanxi

state: 上海

address: shanghai

institute: tongji university

description:
ONT_BMK210615-AK695-01O0006
M-3

data_processing:
The reverse transcriptase was used to enrich full-length cDNAs and added defined PCR adapters to both ends of the first-strand of cDNA and following cDNA PCR for 14 circles with LongAmp Tag DNA polymerase (New England Biolabs, Ipswich, MA, USA) (8 min for elongation time).
Agencourt XP beads (Beckman Coulter, Brea, USA) were used for DNA purification. The final cDNA libraries were subjected to FLO- MIN109 flow cells and analyzed on a PromethION platform at Biomarker Technology Company (Beijing, China).
The PCR products were then subjected to ONT adaptor ligation using T4 DNA ligase (New England Biolabs, Ipswich, MA, USA).
Agencourt XP beads (Beckman Coulter, Brea, USA) were used for DNA purification.
The final cDNA libraries were subjected to FLO-MIN109 flow cells and analyzed on a PromethION platform at Biomarker TechnologyCompany (Beijing, China).
Raw reads were first filtered with minimum average read quality score=7 and minimum read length=500bp.
Ribosomal RNA were discarded after mapping to rRNA database.
Next, full-length, non-chemiric (FLNC) transcripts were determined by searching for primer at both ends of reads.
Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2, and consensus isoforms were obtained after polishing within each cluster by pinfish.
Assembly: Consensus sequences were mapped to reference genome using minimap2
Supplementary files format and content: Tab-delimited text file includes raw counts and CPM of each sample

source_name: brain

extract_protocol:
Total RNA was extracted from the tissue using TRIzol reagent (Takara, Kyoto, Japan) according to the manufacturer’s instructions. RNA purity was tested using the Nano Photometer spectrophotometer (IMPLEN, Westlake Village, USA).
cDNA libraries were constructed from 1 μg of total RNA by using a cDNA-PCR Sequencing Kit (SQK-PCS109) according to the protocol.

treatment_protocol: Perform Sham and tMCAO modeling on WT mice.

value: brain

value: microglia

value: tMCAO


title: ATAC-seq Buffy coat, older adult, 1


title: ATAC-seq Buffy coat, older adult, 3


title: GW_M_IONP_rep1_b


title: xSCAR_K36me3_Mrc1_KAF_rep1

description: EdU-labelled genomic DNA

value: h+ ura4-D18 mrc1-K833A-F835A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-65, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: cardiomyocyte


title: cardiomyocyte,TAC2w+CDK-i, replicate2-63, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: heart


title: brain, tMCAO, rep2

description:
ONT_BMK210615-AK695-01O0005
M-2

value: WT


title: xSCAR_K36me3_Mrc1_MFL_rep1

description: EdU-labelled genomic DNA

value: h+ mrc1-M755A-F758A-L774A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1


title: xSCAR_K36me3_Mrc1_MFL_rep2

description: EdU-labelled genomic DNA


title: xSCAR_K36me3_MCM2_2A_rep3

description: EdU-labelled genomic DNA


title: cardiomyocyte,TAC2w+CDK-i, replicate2-62, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: 6-8 weeks old


title: brain, sham, rep3

description:
ONT_BMK210615-AK695-01O0003
S-3

value: sham


title: ATAC-seq Buffy coat, middle-aged/older adult, 9

value: Isolated WBC


title: ATAC-seq Buffy coat, middle-aged/older adult, 11


title: ATAC-seq Buffy coat, middle-aged/older adult, 10


title: cardiomyocyte,TAC2w+CDK-i, replicate2-60, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: ATAC-seq Buffy coat, middle-aged/older adult, 8


title: brain, sham, rep2

description:
ONT_BMK210615-AK695-01O0002
S-2


title: xSCAR_K36me3_WT_rep3

description: EdU-labelled genomic DNA

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: xSCAR_ClickedInput_Mrc1_RKRN_KAF_rep2

description:
EdU-labelled genomic DNA
no processed data file (Input)

value: S. pombe cell culture


title: ATAC-seq Buffy coat, middle-aged/older adult, 7

value: female


title: cardiomyocyte,TAC2w+CDK-i, replicate2-59, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: brain, sham, rep1

description:
ONT_BMK210615-AK695-01O0001
S-1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-58, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: mouse intestine MODEK cells, 12Gy, 1d, rep3 [IR1d12G3]

city: Beijing

first: Changhui

last: Ge

email: chge502@163.com, chge88@sina.com

address: 27 Taiping Rd., Haidian Dist.

department: Department of Experimental Hematology and Biochemistry

institute: Beijing institute of Radiation Medicine

description: MODEK cells were irradated with 12Gy gamma-ray, and collected at 24h, rep3

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. 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). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Supplementary files format and content: tab-delimited text files include FPKM values

source_name: MODEK cells

growth_protocol: Mouse intestinal epithelial cells MODE-K was cultured in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum, 100 U/ml penicillin and 100 µg/ml streptomycin at 37°C in T25 cell culture flasks.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell was irradiated with 0, 4 and 12 Gy at 25°C with a dose rate of 87 cGy/min using a 60Co gamma-ray source. Each radiation dose included three parallel experimental groups, and cell pellets were collected at 0 h, 24 h and 48 h.

value: MODEK cells

value: small intestine epithelium

value: Wild Type

value: 12Gy radiation, harvest at 24h


title: ATAC-seq Buffy coat, middle-aged/older adult, 6


title: xSCAR_ClickedInput_Mrc1_RKRN_rep2

value: h90 (XmnI)::ura4+ mat2-P kint2::YFP mat3-M(RV)::mCherry mrc1-R784A-K785A-R786A-N787A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18

value: Temperature-induced M-arrest at 20C, shift to 30C for 30min, add EdU (500uM)


title: xSCAR_ClickedInput_Mrc1_RKRN_KAF_rep1

value: h90 (XmnI)::ura4+ mat2-P kint2::YFP mat3-M(RV)::mCherry mrc1-R784A-K785A-R786A-N787A-K833A-F835A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: brain, tMCAO, rep1

description:
ONT_BMK210615-AK695-01O0004
M-1

value: brain

value: microglia

value: tMCAO


title: cardiomyocyte,TAC2w+CDK-i, replicate2-57, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: cardiomyocyte

value: heart


title: mouse intestine MODEK cells, 12Gy, 1d, rep2 [IR1d12G2]

description: MODEK cells were irradated with 12Gy gamma-ray, and collected at 24h, rep2


title: cardiomyocyte,TAC2w+CDK-i, replicate2-56, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: 6-8 weeks old


title: ATAC-seq Buffy coat, middle-aged/older adult, 5

value: Isolated WBC

value: male


title: cardiomyocyte,TAC2w+CDK-i, replicate2-61, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: xSCAR_ClickedInput_Mrc1_KAF_rep2

value: S. pombe cell culture

value: h+ ura4-D18 mrc1-K833A-F835A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1


title: mouse intestine MODEK cells, 12Gy, 2d, rep3 [IR2d12G3]

description: MODEK cells were irradated with 12Gy gamma-ray, and collected at 48h, rep3

value: MODEK cells

value: 12Gy radiation, harvest at 48h


title: mouse intestine MODEK cells, 12Gy, 1d, rep1 [IR1d12G1]

description: MODEK cells were irradated with 12Gy gamma-ray, and collected at 24h, rep1

value: small intestine epithelium

value: Wild Type


title: xSCAR_ClickedInput_Mrc1_RKRN_rep1

value: h90 (XmnI)::ura4+ mat2-P kint2::YFP mat3-M(RV)::mCherry mrc1-R784A-K785A-R786A-N787A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: xSCAR_ClickedInput_Mrc1_KAF_rep1

value: Temperature-induced M-arrest at 20C, shift to 30C for 30min, add EdU (500uM)


title: cardiomyocyte,TAC2w+CDK-i, replicate2-54, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: ATAC-seq Buffy coat, middle-aged/older adult, 4

value: female


title: ATAC-seq Buffy coat, middle-aged/older adult, 2


title: mouse intestine MODEK cells, 12Gy, 2d, rep2 [IR2d12G2]

description: MODEK cells were irradated with 12Gy gamma-ray, and collected at 48h, rep2


title: xSCAR_ClickedInput_Mrc1_MFL_rep3

value: h+ mrc1-M755A-F758A-L774A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-53, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: mouse intestine MODEK cells, 12Gy, 2d, rep1 [IR2d12G1]

description: MODEK cells were irradated with 12Gy gamma-ray, and collected at 48h, rep1


title: ATAC-seq Buffy coat, middle-aged/older adult, 1


title: xSCAR_ClickedInput_Mrc1_MFL_rep2


title: cardiomyocyte,TAC2w+CDK-i, replicate2-52, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, AD patient, 10


title: xSCAR_ClickedInput_Mrc1_MFL_rep1


title: xSCAR_ClickedInput_MCM2_2A_rep3

value: h90 (XmnI)::ura4+ mat2-P kint2::YFP mat3-M(RV)::mCherry mcm2-Y80A-Y89A nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: cardiomyocyte,TAC2w+CDK-i, replicate2-50, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate2-51, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, AD patient, 9


title: cardiomyocyte,TAC2w+CDK-i, replicate2-55, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: mouse intestine MODEK cells, 4Gy, 2d, rep1 [IR2d4G1]

description: MODEK cells were irradated with 4Gy gamma-ray, and collected at 48h, rep1

value: 4Gy radiation, harvest at 48h


title: xSCAR_ClickedInput_WT_rep3

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: mouse intestine MODEK cells, 4Gy, 2d, rep2 [IR2d4G2]

description: MODEK cells were irradated with 4Gy gamma-ray, and collected at 48h, rep2


title: mouse intestine MODEK cells, control,rep3 [IRcon3]

description: MODEK cells, control group, rep3

value: no treatment


title: WGBS Buffy coat, AD patient, 7


title: mouse intestine MODEK cells, control,rep2 [IRcon2]

description: MODEK cells, control group, rep2


title: cardiomyocyte,TAC2w+CDK-i, replicate2-49, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: H3K9me2_ChIP_mrc1dHBS_CenKdelta_rep3

data_processing:
reads were mapped to the genome with bowtie2 (v2.5.0)
duplicate reads were removed with rmDup from samtools (version 2.0.1)
For ChIP-seq, Bam files were converted to bigwig and input normalized using deeptools bamCompare (--normalizeUsing CPM --centerReads --maxFragmentLength 1000 --scaleFactorsMethod None --pseudocount 1). Replicates were merged using wiggletools and converted to bigwig using UCSC BedGraphToBigWig. For BrdU-seq, bedgraphs were generated using MACS2 (version 2.2.7.1) and converted to bigwig using USCS BedGraphToBigWig. Minus/Plus ura datasets and Cend datasets were input normalized in a linear manner using deeptools (see above) with the additional comment --operation ratio
Assembly: S.pombe h90
Supplementary files format and content: bigwig files, genome.fa file for reference genome, gff3 for genome annotations.

source_name: S. pombe cell culture

growth_protocol: S. pombe cell cultures were grown exponentially in YES media at 30°C, shifted to 20°C for 5h, shifted to 30°C for 60min with addition of 200ug/mL BrdU and 25mM HU(BrdU-seq) or 30 min with addition of 500uM EdU (ChIP-seq). For more details see Methods section in Charlton et al. (2023). For minus/plus ura and CenK datasets, cells were grown in either EMM medium with/without uracil or YES (CenK) medium at 30°C.

extract_protocol:
See Charlton et al, 2023 for details. For BrdU-seq, gDNA was extracted, sonicated, and incubated with anti-BrdU antibody (2B1, MBL, Cat# MI-11-3). Bound BrdU-labelled DNA was washed and purified. For ChIP-seq, cells were fixed for 15min in 1% formaldehyde, lysed using bead-beating, sonicated, and incubated with anti-H3K9me2 antibody (MABI0307). Bound H3K9me2 chromatin was washed, extracted, and decrosslinked overnight. Then, decrosslinked DNA was incubated with Protease K and RNase A before clean up with Ampure XP beads.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit (BrdU-Seq) or the KAPA Roche Library Prep Kit (H3K9me2-ChIP).

value: S. pombe cell culture

value: h{delta}K mat3-M(RV)::ura4+ leu1-32 ura4-D18 ade6-210

value: Growth at 30°C until OD 1.2 in YES medium


title: WGBS Buffy coat, AD patient, 6

value: Isolated WBC


title: ATAC-seq Buffy coat, middle-aged/older adult, 3


title: cardiomyocyte,TAC2w+CDK-i, replicate2-47, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate2-48, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: mouse intestine MODEK cells, control,rep1 [IRcon1]

description: MODEK cells, control group, rep1

value: MODEK cells

value: small intestine epithelium


title: WGBS Buffy coat, AD patient, 8

value: male


title: H3K9me2_ChIP_mrc1dHBS_CenKdelta_rep2


title: WGBS Buffy coat, AD patient, 5


title: cardiomyocyte,TAC2w+CDK-i, replicate2-46, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: H3K9me2_ChIP_mrc1dHBS_CenKdelta_rep1


title: mouse intestine MODEK cells, 4Gy, 2d, rep3 [IR2d4G3]

description: MODEK cells were irradated with 4Gy gamma-ray, and collected at 48h, rep3

value: Wild Type


title: H3K9me2_ChIP_mrc1dHBS_CenK_rep2


title: WGBS Buffy coat, AD patient, 4


title: slr1-1-R3

city: Nanjing

first: xiaohan

last: zhang

address: Weigang

institute: Nanjing Agricultural University

description: slr1-1-R3 mRNA-seq

data_processing:
Low-quality reads had been eliminated.
All reads were mapped onto the O.sativa genome (MSU version 7.0) by Tophat.

organism: Oryza sativa Japonica Group

growth_protocol: RIce plants grown in paddy field in Nanjing, China.

extract_protocol:
Total RNA was extrated using TRIzol method.
1.Total RNA used DNaseI to digest DNA, and enriched mRNA using magnetic beads with Oligo(dT).  2.Adding reagent in Thermomixer to interrupt mRNA into short fragments.  3.The fragmented mRNA was used as template to synthesize the first strand of cDNA, and then synthesized the second strand.  4.Purified, repaired, added "A" and adapters in the DNA, then selected 200-300bp fragments and performed PCR amplification.   5.The libraries were checked with Agilent 2100 Bioanalyzer and ABI Real-Time PCR System, the qualified libraries were sequenced using sequencing platform.

treatment_protocol: no treament

value: leaves of 3-month-old plants


title: slr1-1-R2

description: slr1-1-R2 mRNA-seq


title: WGBS Buffy coat, AD patient, 3

value: female


title: cardiomyocyte,TAC2w+CDK-i, replicate2-44, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, AD patient, 2


title: slr1-1-R1

description: slr1-1-R1 mRNA-seq


title: H3K9me2_ChIP_mrc1dHBS_CenK_rep1


title: H3K9me2_ChIP_WT_CenKdelta_rep2


title: cardiomyocyte,TAC2w+CDK-i, replicate2-43, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: H3K9me2_ChIP_WT_CenKdelta_rep1


title: OsNPR1-OE/slr1-1-R3

description: G316Xslr1-1-R3 mRNA-seq


title: cardiomyocyte,TAC2w+CDK-i, replicate2-42, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, AD patient, 1


title: H3K9me2_ChIP_WT_CenK_rep3

value: h90 mat3-M(RV)::ura4+ leu1-32 ura4-DS/E ade6-210


title: OsNPR1-OE/slr1-1-R1

description: G316Xslr1-1-R1 mRNA-seq


title: OsNPR1-OE/slr1-1-R2

description: G316Xslr1-1-R2 mRNA-seq


title: WGBS Buffy coat, MCI patient, 10


title: cardiomyocyte,TAC2w+CDK-i, replicate2-40, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate2-41, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, MCI patient, 9


title: H3K9me2_ChIP_WT_CenK_rep2


title: OsNPR1-OE-R3

description: G316-R3 mRNA-seq


title: H3K9me2_ChIP_WT_CenK_rep1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-45, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate2-38, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: H3K9me2_Input_mrc1dHBS_CenKdelta_rep3

description: no processed file (Input)


title: WGBS Buffy coat, MCI patient, 8


title: OsNPR1-OE-R1

description: G316-R1 mRNA-seq


title: WGBS Buffy coat, MCI patient, 7


title: cardiomyocyte,TAC2w+CDK-i, replicate2-39, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: OsNPR1-OE-R2

description: G316-R2 mRNA-seq


title: WGBS Buffy coat, MCI patient, 6


title: cardiomyocyte,TAC2w+CDK-i, replicate2-37, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, MCI patient, 5


title: WT-R3

description: WT-R3 mRNA-seq

source_name: WT


title: cardiomyocyte,TAC2w+CDK-i, replicate2-36, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: H3K9me2_Input_mrc1dHBS_CenKdelta_rep1

description: no processed file (Input)


title: WGBS Buffy coat, MCI patient, 4


title: cardiomyocyte,TAC2w+CDK-i, replicate2-35, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: H3K9me2_Input_mrc1dHBS_CenK_rep2

description: no processed file (Input)


title: WT-R1

description: WT-R1 mRNA-seq


title: H3K9me2_Input_mrc1dHBS_CenK_rep1

description: no processed file (Input)


title: cardiomyocyte,TAC2w+CDK-i, replicate2-34, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: H3K9me2_Input_WT_CenKdelta_rep2

description: no processed file (Input)


title: WGBS Buffy coat, MCI patient, 1


title: root, Spermidine 0.1mM + NaCl 100mM, T3

city: Zhanjiang

first: Mingming

last: Chen

address: Haida Street No.1

institute: Guangdong Ocean University

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
Alignment with bowtie2
Read quantitation using RSEM
Genome_build: Assembled transcriptome using Trinity
Supplementary_files_format_and_content: csv file contains nine types of information: 1. ID;2-13. FPKM for each sample;3. KEGG; 4. NR; 5. SwissProt; 6. TrEMBL; 7.KOG; 8. GO; 9. Pfam

organism: Oryza sativa

source_name: root

extract_protocol: RNA extraction, poly-A pulling, reverse transcription, 3'end adenylation, linker ligation, and PCR amplification

treatment_protocol: Spermidine, NaCl or Spermidine+NaCl for 72hrs

value: Spermidine 0.1mM + NaCl 100mM

tag: genetic background

value: WT

value: root


title: cardiomyocyte,TAC2w+CDK-i, replicate2-32, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: cardiomyocyte


title: WGBS Buffy coat, older adult, 14


title: root, Spermidine 0.1mM + NaCl 100mM, T2


title: H3K9me2_Input_WT_CenK_rep3

description: no processed file (Input)


title: WGBS Buffy coat, MCI patient, 2


title: cardiomyocyte,TAC2w+CDK-i, replicate2-31, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: heart


title: H3K9me2_Input_WT_CenKdelta_rep1

description: no processed file (Input)


title: root, NaCl 100mM, C3

value: NaCl 100mM


title: WGBS Buffy coat, older adult, 13


title: H3K9me2_Input_mrc1dHBS_CenKdelta_rep2

description: no processed file (Input)

value: S. pombe cell culture


title: cardiomyocyte,TAC2w+CDK-i, replicate2-30, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: 6-8 weeks old


title: root, Spermidine 0.1mM + NaCl 100mM, T1


title: WT-R2

description: WT-R2 mRNA-seq


title: root, NaCl 100mM, C2


title: WGBS Buffy coat, older adult, 12


title: root, NaCl 100mM, C1


title: H3K9me2_Input_WT_CenK_rep1

description: no processed file (Input)

value: Growth at 30°C until OD 1.2 in YES medium


title: WGBS Buffy coat, MCI patient, 3

value: Isolated WBC


title: cardiomyocyte,TAC2w+CDK-i, replicate2-29, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, older adult, 11


title: H3K9me2_ChIP_plusUra_rep3

value: Growth at 30°C until OD 1.2 in EMM complete medium


title: WGBS Buffy coat, older adult, 10


title: cardiomyocyte,TAC2w+CDK-i, replicate2-33, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: H3K9me2_ChIP_plusUra_rep2


title: cardiomyocyte,TAC2w+CDK-i, replicate2-28, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: root, Spermidine 0.1mM, B2

value: Spermidine 0.1mM


title: cardiomyocyte,TAC2w+CDK-i, replicate2-27, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: H3K9me2_ChIP_plusUra_rep1


title: WGBS Buffy coat, older adult, 9


title: H3K9me2_Input_WT_CenK_rep2

description: no processed file (Input)


title: WGBS Buffy coat, older adult, 8


title: H3K9me2_ChIP_minusUra_rep3

value: Growth at 30°C until OD 1.2 in EMM complete medium lacking uracil


title: H3K9me2_ChIP_minusUra_rep2


title: root, untreated, A3

value: untreated


title: cardiomyocyte,TAC2w+CDK-i, replicate2-24, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, older adult, 7

value: male


title: WGBS Buffy coat, older adult, 6


title: H3K9me2_ChIP_minusUra_rep1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-23, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: root, Spermidine 0.1mM, B3


title: root, untreated, A1


title: WGBS Buffy coat, older adult, 5

value: female


title: cardiomyocyte,TAC2w+CDK-i, replicate2-22, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: IMR90-iPSC-NFIA-SOX9_3

city: New York

first: Andrew

middle: A

last: Sproul

state: NY

address: 650 West 168th Street

institute: Columbia Univeristy

data_processing:
Illumina bcl2fastq 2.17 software
Possible adapter sequences and mucleotides rewmoed by using Trimmomatic v.0.36
Trimmed reads were mapped to Homo sapiens reference genome with STAR aligner v.2.5.2b
Hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited files contain raw counts for each sample

extract_protocol:
RNAs were harvested using QIAGEN mini RNA easy kit. 2 ul RNA was used for construction of RNA sequence
RNA libraries built woth NEBNext Ultra II RNA Library Prep Kit.


title: H3K9me2_Input_plusUra_rep2

description: no processed file (Input)


title: IMR90-iPSC-NFIA-SOX9_2


title: root, Spermidine 0.1mM, B1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-26, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, older adult, 4


title: H3K9me2_Input_plusUra_rep1

description: no processed file (Input)


title: WGBS Buffy coat, older adult, 2


title: cardiomyocyte,TAC2w+CDK-i, replicate2-21, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: H3K9me2_Input_minusUra_rep3

description: no processed file (Input)


title: IMR90-iPSC-NFIA-SOX9_1


title: root, untreated, A2


title: WGBS Buffy coat, older adult, 3


title: WGBS Buffy coat, older adult, 1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-25, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, middle-aged/older adult, 11


title: FA10-NPC-NFIA_3


title: cardiomyocyte,TAC2w+CDK-i, replicate2-18, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: H3K9me2_Input_plusUra_rep3

description: no processed file (Input)


title: FA10-NPC-NFIA_2


title: FA10-NPC-NFIA_1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-17, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, middle-aged/older adult, 10


title: xSCAR_ClickedInput_mcm2_2a_r3

description: Sample 25

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.5.0) )
duplicate reads were removed with rmDup from samtools (version 2.0.1)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 500bp bins and smoothed in a uniform blur considering the neighboring 5 bins on each side. For each 500bp window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero.
Assembly: S.pombe h90 contig
Supplementary files format and content: SCAR-seq Partition scores in bigwig format.
Supplementary files format and content: GSE62108_origin_20plus_chromosome_liftover.bed reflects a dataset that should facilitate the interpretation of samples 1-25.  The bed file was generated as follows: GSE62108_origin-effici.bedgraph.gz was remapped to the S.pombe h90 genome and filtered for origins with efficiency scores >20.
Library strategy: SCAR-seq

growth_protocol: S. pombe cell cultures were grown exponentially in YES media at 30°C, shifted to 20°C for 5h, shifted to 30°C for 30min with addition of 500uM EdU (ChIP-seq). For more details see Methods section in Charlton et al. (2023).

extract_protocol:
See Charlton et al, 2023 for details. Cells were fixed for 15min in 1% formaldehyde, lysed using bead-beating, sonicated, and incubated with anti-H3K36me3 antibody (ab9050) or anti-H4K20me0 antibody (ab227804). Bound chromatin was washed, extracted, and decrosslinked overnight. Then, decrosslinked DNA was incubated with Protease K and RNase A before clean up with Ampure XP beads.
For details, see Charlton et al, 2023. Briefly, xSCAR-seq library preparation involved library preparation followed by Click-IT with Biotin-TEG-Azide. Biotinylated EdU-labelled DNA was purified using Streptaviding T1 Dynabeads including 3 washes with 100mM NaoH. Stranded, EdU-Biotin-labelled DNA was PCR-amplified using KAPA Hyper Prep HiFi Polymerase for 12 cycles.

value: yeast cell

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mcm2-2A ura4-D18

value: Temperature-induced M-arrest at 20C, shift to 30C for 30min, add EdU (500uM)


title: H3K9me2_Input_minusUra_rep1

description: no processed file (Input)


title: FA10-NPC-No-NFIA_3


title: cardiomyocyte,TAC2w+CDK-i, replicate2-19, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol.
Sample 731-736,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Other samples, single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.


title: WGBS Buffy coat, middle-aged/older adult, 9


title: cardiomyocyte,TAC2w+CDK-i, replicate2-16, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: xSCAR_ClickedH4K20me0_mrc1dHBS_mcm2_2a_r2

description: Sample 24

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mrc1{delta}(782-879) mcm2-2A ura4-D18


title: cardiomyocyte,TAC2w+CDK-i, replicate2-15, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: cardiomyocyte


title: WGBS Buffy coat, middle-aged/older adult, 8


title: cardiomyocyte,TAC2w+CDK-i, replicate2-20, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: heart


title: FA10-NPC-No-NFIA_2


title: FA10-NPC-No-NFIA_1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-14, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: H3K9me2_Input_minusUra_rep2

description: no processed file (Input)


title: xSCAR_ClickedH4K20me0_mcm2_2a_r2

description: Sample 23


title: cardiomyocyte,TAC2w+CDK-i, replicate2-13, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: xSCAR_ClickedH4K20me0_mrc1dHBS_r2

description: Sample 22

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mrc1{delta}(782-879) ura4-D18


title: cardiomyocyte,TAC2w+CDK-i, replicate2-12, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: WGBS Buffy coat, middle-aged/older adult, 6


title: shCLIC1 rep3

first: De-Jun

last: Liu

state: Shanghai

address: Pujian Road 160

department: Department of Biliary-Pancreatic Surgery

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include TPM values for each sample.

source_name: pancreatic cancer

growth_protocol: All cells were cultured in the recommended medium according to American Type Culture Collection protocols supplemented with 10% fetal bovine serum (FBS) and 1% streptomycin/penicillin (P/S) in a humidified incubator under 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using RNAiso Plus reagent (Takara Bio, #9109) following the manufacturer’s protocol. Then, RNA quality was determined by a 5300 Bioanalyzer (Agilent) and quantified using an ND-2000 (NanoDrop Technologies). Only high-quality RNA samples (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1 μg) were used to construct the sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The lentiviral vector hU6-MCS-Ubiquitin-EGFP-IRES-puromycin was used for CLIC1 knockdown assays. For lentiviral transfection, cells were plated 24 h in advance and a lentiviral suspension was added to the medium in the presence of 25× HitransG P (GeneChem, Shanghai, China). After 48 h of transfection, 5 μg/mL puromycin was added to the medium to screen for stable cell lines for 2 weeks.

value: pancreatic cancer

value: Human pancreatic cancer cell


title: xSCAR_ClickedH4K20me0_WT_r2

description: Sample 21

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: WGBS Buffy coat, middle-aged/older adult, 7

value: Isolated WBC


title: WGBS Buffy coat, middle-aged/older adult, 5


title: shCLIC1 rep2


title: shCLIC1 rep1


title: cardiomyocyte,TAC2w+CDK-i, replicate2-11, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: 6-8 weeks old


title: cardiomyocyte,TAC2w+CDK-i, replicate2-10, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: shNC rep3

value: control


title: WGBS Buffy coat, middle-aged/older adult, 4


title: xSCAR_ClickedH4K20me0_mcm2_2a_r3

description: Sample 19


title: WGBS Buffy coat, middle-aged/older adult, 3


title: xSCAR_ClickedH4K20me0_mrc1dHBS_r1

description: Sample 18


title: cardiomyocyte,TAC2w+CDK-i, replicate2-9, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: shNC rep2


title: WGBS Buffy coat, middle-aged/older adult, 2


title: cardiomyocyte,TAC2w+CDK-i, replicate2-8, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: xSCAR_ClickedH4K20me0_WT_r1

description: Sample 17


title: shNC rep1


title: xSCAR_ClickedH3K36me3_mrc1dHBS_mcm2_2a_r2

description: Sample 16


title: WGBS Buffy coat, middle-aged/older adult, 1


title: Whole blood, AD patient, 10

source_name: Whole blood

value: Whole blood


title: NHEK PC

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

data_processing:
Samples were sequenced with the HiSeq2500 instrument using paired-end sequencing chemistry. Number of lanes used in sequencing was 4. with 100bp read length.
The reads obtained from the instrument were base called using the instrument manufacturer’s base calling software and aligned against to human GRCh38 (hg38) genome assembly using STAR aligner, version 2.6.1
Assembly: GRCh38 (hg38)
Supplementary files format and content: Data normalisation  analysis was performed using DESeq2, v. 1.20.0. The normalized counts are represented as RPKM values.

source_name: normal skin

extract_protocol:
Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water (miRNAeasy Mini Kit, Qiagen GmbH, Hilden, Germany).
Total RNA libraries were prepared for sequencing using standard Illumina protocols

value: normal skin

value: normal keratinocytes

value: NHEK PC


title: xSCAR_ClickedH3K36me3_mcm2_2a_r2

description: Sample 15

value: yeast cell


title: cardiomyocyte,TAC2w+CDK-i, replicate2-7, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate2-6, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate2-5, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: NHEK 70

value: NHEK 70


title: NHEK 64

value: NHEK 64


title: xSCAR_ClickedH4K20me0_mrc1dHBS_mcm2_2a_r1

description: Sample 20

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mrc1{delta}(782-879) mcm2-2A ura4-D18

value: Temperature-induced M-arrest at 20C, shift to 30C for 30min, add EdU (500uM)


title: xSCAR_ClickedH3K36me3_mrc1dHBS_r2

description: Sample 14


title: cardiomyocyte,TAC2w+CDK-i, replicate2-4, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: cardiomyocyte

value: heart


title: NHEK 59

value: NHEK 59


title: Whole blood, AD patient, 9

value: male


title: xSCAR_ClickedH3K36me3_mrc1dHBS_mcm2_2a_r1

description: Sample 12


title: Whole blood, AD patient, 7

value: female


title: Whole blood, AD patient, 8


title: UT-SCC115

source_name: Cutaneous squamous cell carcinoma

value: Cutaneous squamous cell carcinoma

value: Cutaneous SCC


title: Whole blood, AD patient, 6


title: cardiomyocyte,TAC2w+CDK-i, replicate2-3, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx

value: 6-8 weeks old


title: cardiomyocyte,TAC2w+CDK-i, replicate2-2, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: Whole blood, AD patient, 5

value: Whole blood


title: UT-SCC59A


title: cardiomyocyte,TAC2w+CDK-i, replicate2-1, scRNAseq

description:
smartseq2
TAC2w_CDK_i_2.xlsx


title: xSCAR_ClickedH3K36me3_mcm2_2a_r1

description: Sample 11

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mcm2-2A ura4-D18


title: xSCAR_ClickedH3K36me32_WT_r1

description: Sample 9

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: Whole blood, AD patient, 4


title: cardiomyocyte,TAC2w+CDK-i, replicate1-84, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Whole blood, AD patient, 3


title: UT-SCC118


title: xSCAR_ClickedInput_mrc1dHBS_mcm2_2a_r2

description: Sample 8


title: UT-SCC111


title: cardiomyocyte,TAC2w+CDK-i, replicate1-83, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Whole blood, AD patient, 2


title: xSCAR_ClickedInput_mcm2_2a_r2

description: Sample 7


title: xSCAR_ClickedH3K36me3_WT_r2

description: Sample 13


title: xSCAR_ClickedInput_mrc1dHBS_r2

description: Sample 6

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mrc1{delta}(782-879) ura4-D18


title: UT-SCC105


title: cardiomyocyte,TAC2w+CDK-i, replicate1-81, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: UT-SCC91


title: xSCAR_ClickedInput_WT_r2

description: Sample 5

value: yeast cell


title: UT-SCC12A


title: cardiomyocyte,TAC2w+CDK-i, replicate1-79, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate1-80, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Whole blood, MCI patient, 9


title: Whole blood, MCI patient, 8


title: xSCAR_ClickedInput_mcm2_2a_r1

description: Sample 3


title: xSCAR_ClickedH3K36me3_mrc1dHBS_r1

description: Sample 10


title: Whole blood, MCI patient, 10


title: cardiomyocyte,TAC2w+CDK-i, replicate1-78, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: UT-SCC7


title: PNC75Z.4th

city: los angeles

first: Shubhamoy

last: Ghosh

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

data_processing:
Raw sequencing files were demultiplexed using in-house python script.
miRDeep2 package was used to align sequencing reads to known human miRNAs and quantification.
The raw sequencing files were processed using the script mapper.pl, which removed adapter sequences, discarded short reads, and aligned them to the GrCm38 genome using Bowtie.
The quantification of genome-aligned reads against known human miRNAs from miRBase version 21 was performed using the script quantifier.pl with specific options. Raw read counts were normalized for sequencing depth and RNA composition
Differential expression analysis was conducted using DESeq2. We applied a log2-fold-change threshold and false discovery rate (FDR) criteria to determine differentially expressed miRNAs.

source_name: Extracellular Vesicles from plasma of pregnant women

growth_protocol: Pregnant women were recruited in the first trimester of pregnancy for a prospective cohort study “PARENTs”, approved by the UCLA Institutional Review Board (IRB:15–001388) (clinicaltrials.gov: #NCT02786420). Peripheral blood samples were collected from pregnant women at first, second, third trimester and delivery.

extract_protocol:
Extracellular vesicles (EVs) were isolated from peripheral blood of pregnant women using a polymer-based precipitation method (EXOQ5TM-1, System Biosciences, Mountain View CA, USA) and total RNA was extracted from isolated extracellular vesicles (EVs) using the miRNeasy Mini Kit (Qiagen, Valencia, CA)
miRNA libraries were prepared using Total RNA extracted from EVs by utilizing  NEB Next Multiplex small RNA Library prep kit (NEB E7300S; New England Biolabs, Inc, Ipswich, MA, USA).

treatment_protocol: The clinical grouping of preeclampsia versus normal pregnancies was achieved based on established criteria.  The criteria include an sysolic blood pressure of 140 mm Hg or more or diastolic blood pressure of 90 mm Hg or more on two occassions at least 4 hours apart after 20 weeks of gestation and proteinuria (either 300 mg or more per 24 hour urine collection  or a protein/creatinine ratio of 0.3 or more on a dipstick reading).

tag: trimesters

value: Delivery

tag: study group

value: Preeclampsia


title: xSCAR_ClickedInput_mrc1dHBS_r1

description: Sample 2


title: PSG79Z_T4P

value: Extracellular Vesicles from plasma of pregnant women


title: Whole blood, MCI patient, 5


title: PKO84D_T4P


title: cardiomyocyte,TAC2w+CDK-i, replicate1-75, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

source_name: heart


title: Whole blood, MCI patient, 6


title: cardiomyocyte,TAC2w+CDK-i, replicate1-76, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: H3K9me2_ChIP_mrc1dHBS_mcm2_2a_r2

data_processing:
reads were mapped to the genome with bowtie2 (v2.5.0)
duplicate reads were removed with rmDup from samtools (version 2.0.1)
For ChIP-seq, Bam files were converted to bigwig and input normalized using deeptools bamCompare (--normalizeUsing CPM --centerReads --maxFragmentLength 1000 --scaleFactorsMethod None --pseudocount 1). Replicates were merged using wiggletools and converted to bigwig using UCSC BedGraphToBigWig. For BrdU-seq, bedgraphs were generated using MACS2 (version 2.2.7.1) and converted to bigwig using USCS BedGraphToBigWig.
bigWig files normalized to Input and counts per million. Text files containing the genome assembly of h90 fission yeast and gff3 file for gene annotations.
Assembly: S.pombe h90
Supplementary files format and content: bigwig files, genome.fa file for reference genome, gff3 for genome annotations.

growth_protocol: S. pombe cell cultures were grown exponentially in YES media at 30°C, shifted to 20°C for 5h, shifted to 30°C for 60min with addition of 200ug/mL BrdU and 25mM HU(BrdU-seq) or 30 min with addition of 500uM EdU (ChIP-seq). For more details see Methods section in Charlton et al. (2023).

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mrc1{delta}(782-879) mcm2-2A ura4-D18

value: Temperature-induced M-arrest at 20C, shift to 30C for 30min, add EdU (500uM)

value: anti-H3K9me2 antibody (MABI0307)


title: Whole blood, MCI patient, 4


title: PHV89T_T4P


title: cardiomyocyte,TAC2w+CDK-i, replicate1-74, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: cardiomyocyte

value: heart


title: H3K9me2_ChIP_mcm2_2a_r2

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mcm2-2A  ura4-D18


title: Whole blood, MCI patient, 2

value: male


title: cardiomyocyte,TAC2w+CDK-i, replicate1-73, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: H3K9me2_ChIP_mrc1dHBS_r2

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mrc1{delta}(782-879)  ura4-D18


title: H3K9me2_ChIP_WT_r2


title: cardiomyocyte,TAC2w+CDK-i, replicate1-72, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: 6-8 weeks old


title: PLJ84G_T4P


title: Whole blood, MCI patient, 3

value: Whole blood

value: female


title: cardiomyocyte,TAC2w+CDK-i, replicate1-77, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Whole blood, MCI patient, 1


title: Whole blood, MCI patient, 7


title: H3K9me2_ChIP_mrc1dHBS_mcm2_2a_r1


title: cardiomyocyte,TAC2w+CDK-i, replicate1-71, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: xSCAR_ClickedInput_WT_r1

description: Sample 1

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: cardiomyocyte,TAC2w+CDK-i, replicate1-82, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PAP91E_T4C

value: Normal pregnancy


title: H3K9me2_ChIP_mcm2_2a_r1

value: yeast cell


title: Whole blood, older adult, 13


title: PAA85E_T4C

value: Delivery


title: cardiomyocyte,TAC2w+CDK-i, replicate1-70, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Whole blood, older adult, 12


title: PSG79Z_T3P

value: Third

value: Preeclampsia


title: H3K9me2_ChIP_WT_r1


title: PRE92W_T3P

value: Extracellular Vesicles from plasma of pregnant women


title: PVA83K_T4C


title: H3K9me2_ChIP_mrc1dHBS_r1

value: Temperature-induced M-arrest at 20C, shift to 30C for 30min, add EdU (500uM)


title: cardiomyocyte,TAC2w+CDK-i, replicate1-68, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Whole blood, older adult, 11


title: H3K9me2_Input_mrc1dHBS_mcm2_2a_r2

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mrc1{delta}(782-879) mcm2-2A ura4-D18


title: H3K9me2_Input_mcm2_2a_r2


title: PLJ84G_T3P


title: cardiomyocyte,TAC2w+CDK-i, replicate1-69, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: cardiomyocyte


title: cardiomyocyte,TAC2w+CDK-i, replicate1-67, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: heart


title: H3K9me2_Input_mrc1dHBS_r2


title: Whole blood, older adult, 14


title: cardiomyocyte,TAC2w+CDK-i, replicate1-66, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Whole blood, older adult, 10


title: Whole blood, older adult, 8


title: Whole blood, older adult, 9


title: PKO84D_T3P


title: cardiomyocyte,TAC2w+CDK-i, replicate1-65, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: H3K9me2_Input_WT_r2


title: cardiomyocyte,TAC2w+CDK-i, replicate1-64, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Whole blood, older adult, 7


title: cardiomyocyte,TAC2w+CDK-i, replicate1-63, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: H3K9me2_Input_mrc1dHBS_mcm2_2a_r1


title: PNC75Z.3rd


title: Whole blood, older adult, 6


title: H3K9me2_Input_mcm2_2a_r1

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 mcm2-2A  ura4-D18


title: Whole blood, older adult, 5


title: cardiomyocyte,TAC2w+CDK-i, replicate1-62, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PGR79F_T3P


title: PGC81D.3rd


title: H3K9me2_Input_mrc1dHBS_r1


title: cardiomyocyte,TAC2w+CDK-i, replicate1-61, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PWZ84A.3rd


title: Whole blood, older adult, 3

value: male


title: cardiomyocyte,TAC2w+CDK-i, replicate1-60, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate1-59, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Skin_Control_D7_rep4

city: Clayton

first: Mikaël

last: Martino

state: Victoria

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

description:
49_SKd7_WT4_S49
Processed_data_BMS_Macro_Treg_depleted.csv

data_processing:
Fastq files were processed using the nfCore/RNAseq (v3.3) pipeline using the umi function (Patel, H., Ewels, P. & Peltzer, 2013, A. nf-core/rnaseq: nf-core/rnaseq v3.2 - Copper Flamingo, Zenodo)
Reads were aligned to the Mus musculus GRCm38 reference using STAR aligner (Dobin, A., et al., 2013, Bioinformatics)
Reads were quantified using featureCounts (Liao, Y., et al., 2014, Bioinformatics) producing the raw genes count matrix and various quality control metrics.
Raw counts were then analysed with Degust web tool (Powell, D.R., et al., 2019, Zenodo) which performs normalisation using trimmed mean of M values (TMM) (Robinson, M.D. and Oshlack, A., 2010, Genome Biol) and differential gene expression analysis using limma/voom (Law, C.W., et al., 2014, Genome Biol)
Assembly: GRCm39
Supplementary files format and content: csv file where rows represent genes and each column represents different information, including gene name, gene ID and raw gene counts corresponding to the individual samples.

source_name: Skin

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, #74034) according to the manufacturer’s instructions
RNA samples (20 ng) with RIN value ≥ 7 were used for library preparation. First strand synthesis was performed using a dT primer which also adds the Illumina P7 (5ʹ CAA GCA GAA GAC GGC ATA CGA GAT 3ʹ), 8 bp i7 index for each sample and a 10 bp unique molecular identifier (UMI). The modified reverse transcriptase reaction also adds a template switching sequence at the 5’ end of the RNA during the generation of indexed cDNA. These first stand indexed cDNA were pooled and amplified using primers to P7 and the template switch sequence. The Illumina P5 was added by tagmentation by Nextera transposase during amplification. The standard Illumina R1 primer was used (main cDNA read), followed by standard i7 primer for index/UMI. The R2 primer was present but not used as it will read into poly-A tail.

value: Skin

value: day 7 post-injury

value: monocytes/macrophages

value: Control (WT+DT)


title: H3K9me2_Input_WT_r1

value: h90 (XmnI)::ura4+ mat2-P (Kint2)::YFP mat3-M (EcoRV)::mCherrry nda3-KM311 AUR1:aur1r-Adh1-TK-Adh1-scENT1 ura4-D18


title: Whole blood, older adult, 2

value: Whole blood

value: female


title: Skin_Control_D7_rep3

description:
48_SKd7_WT3_S48
Processed_data_BMS_Macro_Treg_depleted.csv


title: PMD88R.3rd


title: PCP81G_T3P


title: cardiomyocyte,TAC2w+CDK-i, replicate1-58, scRNAseq

first: Manami

last: Katoh

institute: The University of Tokyo

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: 6-8 weeks old


title: PPF87I.3rd

value: Third

value: Normal pregnancy


title: xSCAR_ClickedInput_mrc1dHBS_mcm2_2a_r1

description: Sample 4

value: yeast cell


title: Skin_Control_D7_rep2

description:
47_SKd7_WT2_S47
Processed_data_BMS_Macro_Treg_depleted.csv


title: cardiomyocyte,TAC2w+CDK-i, replicate1-57, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Whole blood, older adult, 4


title: Whole blood, middle-aged/older adult, 11


title: PEW85X.3rd

value: Extracellular Vesicles from plasma of pregnant women


title: Whole blood, middle-aged/older adult, 10


title: PET80M_3rd


title: Skin_Treg_depleted_D7_rep4

description:
58_SKd7_FDG7_S58
Processed_data_BMS_Macro_Treg_depleted.csv

value: Treg-depleted (FDG+DT)


title: cardiomyocyte,TAC2w+CDK-i, replicate1-55, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: cardiomyocyte


title: PPD82O_T3P

value: Preeclampsia


title: Skin_Treg_depleted_D7_rep3

description:
57_SKd7_FDG6_S57
Processed_data_BMS_Macro_Treg_depleted.csv


title: Whole blood, middle-aged/older adult, 9


title: cardiomyocyte,TAC2w+CDK-i, replicate1-54, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: heart


title: PAP91E_T3C


title: Whole blood, middle-aged/older adult, 8

value: male


title: Skin_Control_D7_rep1

description:
46_SKd7_WT1_S46
Processed_data_BMS_Macro_Treg_depleted.csv

value: Skin


title: cardiomyocyte,TAC2w+CDK-i, replicate1-53, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PVA83K_T3C


title: Whole blood, middle-aged/older adult, 7


title: Skin_Treg_depleted_D7_rep2

description:
56_SKd7_FDG5_S56
Processed_data_BMS_Macro_Treg_depleted.csv

value: day 7 post-injury


title: PAA85E_T3C


title: Whole blood, older adult, 1


title: Skin_Treg_depleted_D7_rep1

description:
55_SKd7_FDG4_S55
Processed_data_BMS_Macro_Treg_depleted.csv

value: monocytes/macrophages


title: Whole blood, middle-aged/older adult, 6


title: cardiomyocyte,TAC2w+CDK-i, replicate1-52, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate1-56, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Skin_Control_D4_rep4

description:
38_SKd4_WT4_S38
Processed_data_BMS_Macro_Treg_depleted.csv

value: day 4 post-injury

value: Control (WT+DT)


title: PSC84U_T2P

value: Second


title: Whole blood, middle-aged/older adult, 5

value: Whole blood


title: cardiomyocyte,TAC2w+CDK-i, replicate1-51, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: 6-8 weeks old


title: Skin_Control_D4_rep3

description:
37_SKd4_WT3_S37
Processed_data_BMS_Macro_Treg_depleted.csv


title: cardiomyocyte,TAC2w+CDK-i, replicate1-50, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PRE92W_T2P


title: PPD82O_T2P


title: PGC81D.4th

value: Delivery


title: cardiomyocyte,TAC2w+CDK-i, replicate1-49, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Skin_Control_D4_rep2

description:
36_SKd4_WT2_S36
Processed_data_BMS_Macro_Treg_depleted.csv


title: cardiomyocyte,TAC2w+CDK-i, replicate1-48, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PKO84D_T2P


title: Whole blood, middle-aged/older adult, 3

value: female


title: Whole blood, middle-aged/older adult, 4


title: Skin_Control_D4_rep1

description:
35_SKd4_WT1_S35
Processed_data_BMS_Macro_Treg_depleted.csv


title: Whole blood, middle-aged/older adult, 1


title: Whole blood, middle-aged/older adult, 2


title: cardiomyocyte,TAC2w+CDK-i, replicate1-47, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Skin_Treg_depleted_D4_rep4

description:
44_SKd4_FDG5_S44
Processed_data_BMS_Macro_Treg_depleted.csv


title: PTP86Y_T4P


title: Skin_Treg_depleted_D4_rep3

description:
43_SKd4_FDG4_S43
Processed_data_BMS_Macro_Treg_depleted.csv


title: PGR79F_T2P


title: PKK81U_T2P


title: PTP86Y_T2P


title: cardiomyocyte,TAC2w+CDK-i, replicate1-46, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx