title: USP42_KO_RPF_rep3

city: Austin

first: Can

last: Cenik

state: TX

address: Moffett Molecular Biology Building 2.122 2500 Speedway

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
Ribosome profiling and RNA-seq data were processed using RiboFlow. For ribosome profiling data, we extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step.
For ribosome profiling data, we clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”.
After UMI extraction and adapter trimming, ribosome profiling reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. RiboPy
For RNA-seq data, we processed reads using cutadapt and the parameters "-u 1 --quality-cutoff=28". Reads were aligned to the transcriptome with the Bowtie2 parameters "-L 15 --no-unal". Reads were deduplicated based on alignment start and read length.
For differential expression analysis, we used edgeR to measure RBP KO effects on 1) RNA abundance and 2) gene TE. To do this, we respectively modeled 1) RNA-seq counts of a specific RBP KO line to that of the other two RBP KO lines; and 2) Ribo-seq counts, contrasted with RNA-seq counts, for a specific RBP KO line compared to the other two RBP KO lines. All counts were enumerated from mapped reads to the coding regions. We included filtering of counts using edgeR::filterByExpr with default parameters, the TMM method for calculation of size factors, and quasi-likelihood negative binomial models for fitting. Genes were considered differential at FDR < 0.05.
Assembly: A curated transcriptome of primary transcripts was used for alignment. Reference files for use with RiboFlow are located at https://github.com/ribosomeprofiling/references_for_riboflow
Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

growth_protocol: For lentiviral production, HEK293T cells were grown in OPTI-MEM media supplemented with 5% FBS and 100mM Sodium Pyruvate. Subsequently, HEK293T cells were grown in DMEM with 10% FBS and 1% pencillin-streptomycin.

extract_protocol:
Three million cells for the PARK7, USP42, and VIM knockout cell lines, along with a AAVS1 (safe harbor control) knockout line, were plated in three 10 cm2 dishes. 27 h later cells at ~60% confluency were treated with 100 µg/mL cycloheximide (CHX) for 10 min at 37 ˚C, then collected in ice cold PBS with 100 µg/mL CHX. Cells were spun at 100 x g for 7 min at 4 ˚C, then flash frozen in liquid nitrogen and stored at -80 ˚C. Cell pellets were lysed with 400 µL lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton-X, 100 µg/mL CHX, 1x protease inhibitor EDTA free) for 10 min on ice. Lysates were clarified by centrifugation at 1,300 rpm for 10 min at 4 ˚C. 40 µL lysate was saved for total RNA extraction, and the rest of the lysate was digested with 7 µL RNaseI for 1 h at 4 ˚C. Digestion was stopped by adding ribonucleoside vanadyl complex to a final concentration of 20 mM. Digested lysates were then loaded onto 10 mL sucrose cushion (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1 M sucrose) and centrifuged at 38,000 rpm for 2.5 h at 4 ˚C using a SW41-Ti rotor. The pellet and the total RNA aliquot were both solubilized with 1 mL Trizol, and RNA was purified with the Zymo Direct-zol RNA Miniprep Kit, including DNaseI digestion.
RNA-seq: Quality of total RNA was confirmed with Bioanalyzer RNA Pico. All RIN scores were >= 9.8. Libraries were prepared from 1 µg total RNA using the NEBNext Ultra II RNA Library Prep Kit for Illumina according to manufacturer’s protocol and using 8 cycles for PCR. Ribosome profiling: Ribosome protected fragments (RPFs) were size-selected on a 15% TBE urea gel by electrophoresing at 150 V for 1.5 h. RPFs between 28-32 nt were sliced, using 28 nt and 35 nt markers as a guide. Slices were frozen at -20 ˚C for 1 h, crushed with pestles, and the RPFs were eluted in gel extraction buffer (300 mM sodium acetate pH 5.5, 5 mM MgCl2) by rotating overnight at room temperature. Eluates were passed through Costar Spin-X filter tubes at 12,000 x g for 1 min 30 s. Then 1 µL 1 M MgCl2, 2.5 µL GlycoBlue, and 1 mL ethanol were added and the RPFs precipitated for two days at -20 ˚C. Pellets were dried and resuspended in 16 µL water. Libraries were generated from 8 µL RPF eluate using the Diagenode D-Plex Small RNA Kit with minor modifications: in the 3’ dephosphorylation step 0.5 µL T4 PNK was supplemented and incubated for 25 min. The RTPM reverse transcription primer was used and 8 cycles were performed for PCR. Libraries were quantified by Bioanalyzer High Sensitivity DNA Kit, pooled equimolar according to the quantity of the peak for libraries with full-length inserts (~204 nt), and cleaned up with 1.8X AMPure XP beads. Adapter dimers and empty libraries were removed by size-selection on a 12% TBE PAGE gel, followed by extraction with the crush and soak method, and final libraries were resuspended in 20 µL water.


title: Skin_Treg_depleted_D4_rep2

status: Public on Aug 01 2024

type: SRA

city: Clayton

first: Mikaël

last: Martino

state: Victoria

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

description:
42_SKd4_FDG3_S42
Processed_data_BMS_Macro_Treg_depleted.csv

library_source: transcriptomic

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.

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: Skin

tag: time

value: day 4 post-injury

tag: cell type

value: monocytes/macrophages

tag: treatment

value: Treg-depleted (FDG+DT)


title: cardiomyocyte,TAC2w+CDK-i, replicate1-45, 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
TAC2w_CDK_i_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

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.

value: cardiomyocyte

value: heart

tag: strain

tag: age

value: 6-8 weeks old


title: VIM_KO_RPF_rep3

country: USA

organism: Homo sapiens

tag: cell line

tag: genotype


title: PET67Q_T2P

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

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: Second

tag: study group

value: Preeclampsia


title: PCP81G_T2P

value: Extracellular Vesicles from plasma of pregnant women


title: cardiomyocyte,TAC2w+CDK-i, replicate1-44, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Muscle_Control_D7_rep3

description:
28_MUd7_WT1_4_S28
Processed_data_BMS_Macro_Treg_depleted.csv

source_name: Muscle

value: Muscle

value: day 7 post-injury

value: Control (WT+DT)


title: PARK7_KO_RPF_rep3


title: cardiomyocyte,TAC2w+CDK-i, replicate1-43, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PNC75Z.2nd


title: cardiomyocyte,TAC2w+CDK-i, replicate1-42, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: AAVS1_KO_RPF_rep3


title: cardiomyocyte,TAC2w+CDK-i, replicate1-41, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: USP42_KO_RPF_rep2


title: Muscle_Control_D7_rep2

description:
27_MUd7_WT2_6_S27
Processed_data_BMS_Macro_Treg_depleted.csv


title: Muscle_Treg_depleted_D7_rep3

description:
25_MUd7_FDG4_5_S25
Processed_data_BMS_Macro_Treg_depleted.csv


title: VIM_KO_RPF_rep2


title: PARK7_KO_RPF_rep2


title: cardiomyocyte,TAC2w+CDK-i, replicate1-40, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Muscle_Treg_depleted_D7_rep1

description:
23_MUd7_FDG1_2_S23
Processed_data_BMS_Macro_Treg_depleted.csv


title: cardiomyocyte,TAC2w+CDK-i, replicate1-39, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Muscle_Treg_depleted_D7_rep2

description:
24_MUd7_FDG3_6_S24
Processed_data_BMS_Macro_Treg_depleted.csv


title: PWZ84A.2nd


title: AAVS1_KO_RPF_rep2


title: Skin_Treg_depleted_D4_rep1

description:
41_SKd4_FDG2_S41
Processed_data_BMS_Macro_Treg_depleted.csv


title: cardiomyocyte,TAC2w+CDK-i, replicate1-38, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PPF87I.2nd

value: Normal pregnancy


title: PAA85E_T2C


title: Muscle_Control_D4_rep3

description:
34_MUd4_WT4_S34
Processed_data_BMS_Macro_Treg_depleted.csv


title: cardiomyocyte,TAC2w+CDK-i, replicate1-37, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PET80M_2nd


title: PGC81D.2nd


title: Muscle_Control_D7_rep1

description:
26_MUd7_WT3_5_S26
Processed_data_BMS_Macro_Treg_depleted.csv


title: Muscle_Control_D4_rep2

description:
33_MUd4_WT3_S33
Processed_data_BMS_Macro_Treg_depleted.csv


title: VIM_KO_RPF_rep1


title: cardiomyocyte,TAC2w+CDK-i, replicate1-36, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PAP91E.2nd


title: PARK7_KO_RPF_rep1


title: Muscle_Control_D4_rep1

description:
32_MUd4_WT2_S32
Processed_data_BMS_Macro_Treg_depleted.csv


title: PMD88R.2nd


title: cardiomyocyte,TAC2w+CDK-i, replicate1-35, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Muscle_Treg_depleted_D4_rep3

description:
31_MUd4_FDG4_S31
Processed_data_BMS_Macro_Treg_depleted.csv


title: AAVS1_KO_RPF_rep1


title: USP42_KO_RNA_rep3

data_processing:
Ribosome profiling and RNA-seq data were processed using RiboFlow. For ribosome profiling data, we extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step.
For ribosome profiling data, we clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”.
After UMI extraction and adapter trimming, ribosome profiling reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. RiboPy
For RNA-seq data, we processed reads using cutadapt and the parameters "-u 1 --quality-cutoff=28". Reads were aligned to the transcriptome with the Bowtie2 parameters "-L 15 --no-unal". Reads were deduplicated based on alignment start and read length.
For differential expression analysis, we used edgeR to measure RBP KO effects on 1) RNA abundance and 2) gene TE. To do this, we respectively modeled 1) RNA-seq counts of a specific RBP KO line to that of the other two RBP KO lines; and 2) Ribo-seq counts, contrasted with RNA-seq counts, for a specific RBP KO line compared to the other two RBP KO lines. All counts were enumerated from mapped reads to the coding regions. We included filtering of counts using edgeR::filterByExpr with default parameters, the TMM method for calculation of size factors, and quasi-likelihood negative binomial models for fitting. Genes were considered differential at FDR < 0.05.
Assembly: A curated transcriptome of primary transcripts was used for alignment. Reference files for use with RiboFlow are located at https://github.com/ribosomeprofiling/references_for_riboflow
Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.


title: cardiomyocyte,TAC2w+CDK-i, replicate1-34, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Muscle_Treg_depleted_D4_rep2

description:
30_MUd4_FDG3_S30
Processed_data_BMS_Macro_Treg_depleted.csv


title: cardiomyocyte,TAC2w+CDK-i, replicate1-33, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PSG79Z_T1P


title: PCP81G_T1P

value: First


title: USP42_KO_RPF_rep1


title: Muscle_Treg_depleted_D4_rep1

description:
29_MUd4_FDG1_S29
Processed_data_BMS_Macro_Treg_depleted.csv


title: cardiomyocyte,TAC2w+CDK-i, replicate1-32, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PARK7_KO_RNA_rep3


title: Bone_Control_D10_rep3

description:
3_BNd10_WT6_5_S3
Processed_data_BMS_Macro_Treg_depleted.csv

source_name: Bone

value: Bone

value: day 10 post-injury


title: PRE92W


title: Bone_Control_D10_rep2

description:
4_BNd10_WT3_9_S4
Processed_data_BMS_Macro_Treg_depleted.csv


title: Whole blood, AD patient, 1

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: Whole blood

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: Whole blood

tag: Sex

value: male


title: cardiomyocyte,TAC2w+CDK-i, replicate1-30, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate1-31, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PPD82O


title: Bone_Control_D10_rep1

description:
1_BNd10_WT2_4_S1
Processed_data_BMS_Macro_Treg_depleted.csv

value: monocytes/macrophages


title: cardiomyocyte,TAC2w+CDK-i, replicate1-29, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Bone_Treg_depleted_D10_rep3

description:
10_BNd10_FDG1_6_S10
Processed_data_BMS_Macro_Treg_depleted.csv

value: Treg-depleted (FDG+DT)


title: VIM_KO_RNA_rep2


title: PEW85X.2nd


title: PARK7_KO_RNA_rep2


title: PGR79F


title: VIM_KO_RNA_rep3


title: cardiomyocyte,TAC2w+CDK-i, replicate1-27, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: cardiomyocyte


title: PMG84U


title: AAVS1_KO_RNA_rep2


title: cardiomyocyte,TAC2w+CDK-i, replicate1-26, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: heart


title: PTP86Y


title: Bone_Treg_depleted_D10_rep1

description:
6_BNd10_FDG3_5_S6
Processed_data_BMS_Macro_Treg_depleted.csv


title: PLH87K


title: USP42_KO_RNA_rep1


title: Bone_Control_D7_rep5

description:
22_BNd7_WT6_S22
Processed_data_BMS_Macro_Treg_depleted.csv


title: cardiomyocyte,TAC2w+CDK-i, replicate1-25, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: 6-8 weeks old


title: AAVS1_KO_RNA_rep3


title: PHV89T


title: USP42_KO_RNA_rep2


title: PKO84D


title: cardiomyocyte,TAC2w+CDK-i, replicate1-24, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate1-23, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Bone_Control_D7_rep3

description:
19_BNd7_WT3_S19
Processed_data_BMS_Macro_Treg_depleted.csv


title: PARK7_KO_RNA_rep1


title: PET67Q


title: AAVS1_KO_RNA_rep1


title: Bone_Control_D7_rep4

description:
21_BNd7_WT5_S21
Processed_data_BMS_Macro_Treg_depleted.csv


title: PGC81D


title: cardiomyocyte,TAC2w+CDK-i, replicate1-28, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Bone_Treg_depleted_D10_rep2

description:
8_BNd10_FDG2_7_S8
Processed_data_BMS_Macro_Treg_depleted.csv


title: VIM_KO_RNA_rep1


title: Bone_Control_D7_rep1

description:
17_BNd7_WT1_S17
Processed_data_BMS_Macro_Treg_depleted.csv


title: PNC75Z


title: cardiomyocyte,TAC2w+CDK-i, replicate1-21, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: Bone_Control_D7_rep2

description:
18_BNd7_WT2_S18
Processed_data_BMS_Macro_Treg_depleted.csv


title: cardiomyocyte,TAC2w+CDK-i, replicate1-22, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: SM5PscRXP2

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, BCR, and HTO barcode counts) was performed using the 10x genomics Cell Ranger v6.0.0 multi pipeline and aligning to the cellranger-vdj-GRCh38-alts-ensembl-5.0.0 human reference genome.
Further processing was done with Seurat v4.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: 10x Genomics mRNA and HTO output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: 10x Genomics BCR outpur files: filtered_contig_annotations.csv, consensus.fasta

molecule: protein

source_name: PBMC

extract_protocol:
CD19+ and CD138+ cells were sorted independently and combined in equal numbers
10x 5’ scRNA-seq libraries were generated using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics 1000263) according to the instructions provided.

treatment_protocol: B cells in organoid cultures were stimulated with Influenza H1N1 (Ag), R848, Influenza + R848, or Influenza + R848 plus BCL6 and EZH2 inhibitors at day 16 and 24.

value: PBMC

tag: time point

value: Day 12

tag: library type

value: HTO

tag: antibodies/tags

value: Anti-CD45 + Anti-MHC class I:R848 - TotalSeq-C0301 ; Ag - TotalSeq-C0302 ; R848+Ag  - TotalSeq-C0303 ;

tag: sorting markers

value: mixture of CD19+ and CD138+ cells


title: SM5PscRXP1

value: Day 4


title: SM5PscRXP4

value: Day 24

value: Anti-CD45 + Anti-MHC class I:R848 - TotalSeq-C0301 ; Ag - TotalSeq-C0302 ; R848+Ag  - TotalSeq-C0303 ; R848+Ag+Bcl6/EZH2 Inhibitor  - TotalSeq-C0304 ;


title: Bone_Treg_depleted_D7_rep5

description:
16_BNd7_FDG6_S16
Processed_data_BMS_Macro_Treg_depleted.csv

value: Bone

value: day 7 post-injury


title: PEW85X

value: Extracellular Vesicles from plasma of pregnant women

value: First

value: Normal pregnancy


title: Bone_Treg_depleted_D7_rep4

description:
15_BNd7_FDG5_S15
Processed_data_BMS_Macro_Treg_depleted.csv

value: monocytes/macrophages

value: Treg-depleted (FDG+DT)


title: cardiomyocyte,TAC2w+CDK-i, replicate1-20, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: cardiomyocyte

value: heart


title: cardiomyocyte,TAC2w+CDK-i, replicate1-18, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: 6-8 weeks old


title: Bone_Treg_depleted_D7_rep3

description:
14_BNd7_FDG4__S14
Processed_data_BMS_Macro_Treg_depleted.csv


title: SM5PscRXP3

value: PBMC

value: Day 16


title: PWZ84A

value: Preeclampsia


title: cardiomyocyte,TAC2w+CDK-i, replicate1-19, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: SM5PscRBCR4

description:
BCR library:  read1 file contains cell barcode and UMI; read2 file contains transcript
B cell receptor sequences and annotation
filtered_contig_annotations.csv
consensus.fasta

molecule: other

value: B cell receptor (BCR)

value: mixture of CD19+ and CD138+ cells


title: PMD88R


title: Bone_Treg_depleted_D7_rep2

description:
13_BNd7_FDG3_S13
Processed_data_BMS_Macro_Treg_depleted.csv


title: PVP84J


title: Bone_Treg_depleted_D7_rep1

description:
11_BNd7_FDG1_S11
Processed_data_BMS_Macro_Treg_depleted.csv


title: SM5PscRBCR3


title: cardiomyocyte,TAC2w+CDK-i, replicate1-17, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PKC83M


title: cardiomyocyte,TAC2w+CDK-i, replicate1-16, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: SCAR_mESC_H4K20me0_ClaspindYY_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

library_source: genomic

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

molecule: genomic DNA

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: E14 mouse embryonic stem cells

value: #Claspin_C10, Claspin mutant showing a 57 aa frameshift/deletion (aa 1041 - 1098)

value: mES cells for labelled with 10uM EdU for 10 minutes


title: cardiomyocyte,TAC2w+CDK-i, replicate1-15, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: SM5PscRBCR1

value: Day 4


title: SM5PscRBCR2

value: Day 12


title: SCAR_mESC_H4K20me0_ClaspindYY_rep1

description: EdU-labelled genomic DNA


title: PAA85E

value: Extracellular Vesicles from plasma of pregnant women

value: First


title: PAV82H

value: Normal pregnancy


title: cardiomyocyte,TAC2w+CDK-i, replicate1-14, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: SM5PscRgXP4

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

molecule: polyA RNA

value: Day 24

value: mRNA


title: cardiomyocyte,TAC2w+CDK-i, replicate1-13, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: cardiomyocyte

value: heart


title: SCAR_mESC_H3K27me3_ClaspindYY_rep2

description: EdU-labelled genomic DNA


title: PVA83K


title: SM5PscRgXP3

value: PBMC


title: PTA81A


title: SCAR_mESC_H3K27me3_ClaspindYY_rep1

description: EdU-labelled genomic DNA


title: cardiomyocyte,TAC2w+CDK-i, replicate1-12, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

value: 6-8 weeks old


title: SCAR_mESC_ClickedInput_ClaspindYY_rep2

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


title: PEH80C


title: SM5PscRgXP1


title: SM5PscRgXP2


title: cardiomyocyte,TAC2w+CDK-i, replicate1-11, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: PTG80I


title: SCAR_mESC_ClickedInput_ClaspindYY_rep1


title: SCAR_mESC_H4K20me0_WT_rep2

description: EdU-labelled genomic DNA

value: #410, wildtype cells


title: PPF87I


title: cardiomyocyte,TAC2w+CDK-i, replicate1-9, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: SMR058

data_processing:
Raw sequencing reads were mapped to the hg38 version of the human genome using STAR and the GENCODE v27 reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: hg38
Supplementary files format and content: tab delimited text file of RPKM normalized read counts for each gene

extract_protocol:
1,000 cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

tag: tissue origin

tag: subject id

tag: stimulation

value: Ag


title: SMR060


title: SCAR_mESC_H4K20me0_WT_rep1

description: EdU-labelled genomic DNA


title: PAP91E

tag: tissue


title: SCAR_mESC_H3K27me3_WT_rep2

description: EdU-labelled genomic DNA

tag: cell type


title: SMR054


title: cardiomyocyte,TAC2w+CDK-i, replicate1-7, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

tag: treatment


title: NP13

value: Non pregnant Control


title: SMR052


title: SCAR_mESC_H3K27me3_WT_rep1

description: EdU-labelled genomic DNA

value: E14 mouse embryonic stem cells


title: NP12


title: SMR048


title: cardiomyocyte,TAC2w+CDK-i, replicate1-5, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

tag: strain


title: SCAR_mESC_ClickedInput_WT_rep2


title: cardiomyocyte,TAC2w+CDK-i, replicate1-6, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx

tag: age


title: SMR046


title: cardiomyocyte,TAC2w+CDK-i, replicate1-4, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate1-10, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: SMR042


title: PET80M


title: cardiomyocyte,TAC2w+CDK-i, replicate1-3, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: 6_sc-Lung, Luc-15h_2022-08-17

city: HENNINGSDORF

first: Jörg

last: Kaufmann

state: Brandenburg

address: NEUNDORFSTR 20B

country: Germany

institute: Pantherna Therapeutics GMBH

description: 10x Genomics

data_processing:
For the analysis of the sequencing data a new reference was constructed based on the GRCm39 genome and the GENCODE M29 annotation which included the mRNA-76 transgene contigs along with their annotation
The data was then filtered according to the standard recommendations of 10x CellRanger (v7.0.0)
The data was then packaged for use by the `cellranger mkref` command using default parameters.
All sequencing runs were demultiplexed with `cellranger mkfastq` using default parameters.
The demultiplexed samples were processed with `cellranger count` using the non-default parameter `--expect-cells=5000`.
Assembly: GENCODE M39
Supplementary files format and content: CLOUPE files
Supplementary files format and content: Tab seperated value files and matrix files

source_name: Lung

extract_protocol:
Mice were sacrificed after 2 or 15 hours, livers were enzymatically dissociated for a single cell suspension. Single cell suspensions were loaded onto the chip G (10X Genomics) and processed according to the Chromium NEXT GEM Single Cell 3' workflow using the Chromium Controller device (10x Genomics). For each sample, 11000 single cells were loaded, with an average cell viability of 88%.
The resulting libraries were sequenced using a NextSeq2000 device (Illumina).

treatment_protocol: Mice received intavenous injection through the tail vein containing mRNA_cLNP (1.5 mg/kg).

value: Lung

value: Male

value: 8 to 10 weeks

tag: treatment time


title: SCAR_mESC_ClickedInput_WT_rep1

tag: cell line

tag: genotype

value: mES cells for labelled with 10uM EdU for 10 minutes


title: NP10

value: Extracellular Vesicles from plasma of pregnant women

tag: trimesters

tag: study group


title: NP5


title: SMR040

tag: time point


title: cardiomyocyte,TAC2w+CDK-i, replicate1-2, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: cardiomyocyte,TAC2w+CDK-i, replicate1-8, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: SMR039


title: 2_sc-Lung, PAT001_2022-06-29

description: 10x Genomics

tag: Sex

value: 2 h


title: NP4


title: HEK293T_K36M_KRAB_DOX_HA-tag_Cut&Run_BR2

city: STANFORD

first: Joydeb

last: Sinha

address: 443 VIA ORTEGA

institute: Stanford University

description: HEK293T_K36M_KRAB_DOX_HA-tag_CUT&RUN_BR2

data_processing:
library strategy: CUT&RUN
Make genome file with synthetic reporter integration
For CUT&RUN: Align reads to genome with Bowtie 2 version 2.3.4.1 with command 'bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x {reference genome} -p 16 -1 {first mate of pair} -2 {second mate of pair} -S {output SAM file name}'
For CUT&RUN: Convert SAM files to BAM files and subsequently sort and index BAM files with Samtools version 1.7
For CUT&RUN: Quantify and mark duplicates with Picard version 11.0.7 with command 'java -jar {picard tool} MarkDuplicates -I {input sorted BAM file} -O {output deduplicated BAM file} -M {output metrics file} --REMOVE_DUPLICATES true'
For CUT&RUN: Normalize by reads per million with bamCoverage version 3.3.1 with command 'bamCoverage --bam {input deduplicated BAM file} -o {output bedgraph file}  --outFileFormat bedgraph --extendReads --centerReads -p 12 --binSize 10 --normalizeUsing CPM' for files unless stated otherwise. For H3K9me3 Scaling factors for normalization were calculated as the inverse of the percentage of uniquely aligned reads in each sample that mapped to the E. coli K12 MG1655 reference genome, as defined in the EpiCypher manual, and normalization used the following bamCoverage command: bamCoverage --bam {input deduplicated BAM file} -o {output bedgraph file} -- outFileFormat bedgraph --extendReads --centerReads --binSize 10 --scaleFactor {E. coli spike-in DNA scale factor}. For H3K36me3 Scaling factors for normalization were calculated using barcoded spike-in nucleosomes (EpiCypher 19-1002)  as the inverse of the percentage of reads in each sample containing DNA barcodes for the expected histone modification, and normalization used the following bamCoverage command: bamCoverage --bam {input deduplicated BAM file} -o {output bedgraph file} -- outFileFormat bedgraph --extendReads --centerReads --binSize 10 --scaleFactor {K-MetStat scale factor}.
For Emseq: BWAmeth was used for methylation-specific alignment to the reporter
For Emseq: samtools was used to convert raw alignment files to indexed .bam.
For Emseq: Bulk CpG methylation levels were calculated per site using MethylDackel (https://github.com/dpryan79/MethylDackel)
Assembly: hg19
Supplementary files format and content: bedgraph files

growth_protocol: DMEM-GlutaMAX media (10566024, Gibco) supplemented with 1x Penicillin-Streptomycin-Glutamine (10378016, Gibco) and 10 % FBS (FB-15, Omega Scientific)

extract_protocol:
For CUT&RUN: Cells were permeabilized by 0.025% digitonin followed by incubation with antibody and Mnase excision using CUTANA ChIC/CUT&RUN Kit (14-1048, EpiCypher)
For EMseq: Genomic DNA was extracted from roughly 500,000 HEK293T cells using the Monarch Genomic DNA Purification Kit (NEB T3010L) and fragmented by digestion with XbaI and AccI to excise and release the genomic DNA region corresponding to the AAVS1 reporter. The DNA was then size selected using 1x volume SPRI bead clean up (Beckman Coulter B23317). 200ng of cleaned DNA was used as an input for conversion using a Enzymatic Methyl-seq Kit (NEB E7120S) according to the manufacturer’s recommended protocol.
For CUT&RUN: Library was prepared using  CUTANA™ CUT&RUN Library Prep Kit with Primer Set 1 (14-1001, EpiCypher) or Primer Set 2 (14-1002, EpiCypher)  Library fragment sizes were checked with Agilent 2100 Bioanalyzer.
For EMseq: Briefly, APOBEC converted DNA was PCR amplified using 22x cycles with Q5U master mix (NEB M0597S) with primer pairs cTF378+cTF381 for the promoter and oSA021+oSA023 for the gene body. Amplified DNA was then size enriched using 0.9X volume SPRI beads and subject to another round of PCR using 10x cycles with NEBNext Ultra II (NEB M0544S) using primers pairs cTF383+cTF399 for the promoter and oSA021+oSA023 for the gene body to add Illumina Read1 and Read2 overhangs. DNA was cleaned up using 0.9X volume SPRI beads. The above PCR and clean up steps were repeated for a third PCR reaction with indexing primers to append Illumina indices for sequencing.

value: Human embryonic kidney


title: SMR036


title: NP3


title: HEK293T_K36M_KRAB_DOX_HA-tag_Cut&Run_BR1

description: HEK293T_K36M_KRAB_DOX_HA-tag_CUT&RUN_BR1


title: cardiomyocyte,TAC2w, replicate2-73, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: FU-MMT-1 cells, siANXA2-3

city: Zhengzhou

first: Xuexiang

last: Cha

state: Henan

address: Kexue Avenue 100

department: Basic Medical Science

country: China

institute: Zhengzhou University

data_processing:
PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7sequencer (MGI Tech Co., Ltd. China)  with PE150 model.
Raw sequencing data was first filtered by Trimmomatic (version 0.36) low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the reference genome of homo sapiens from GRCh38 using STRA software (version 2.5.3a)
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Assembly: GRCh38
Supplementary files format and content: files include RPKM values for each Sample

growth_protocol: The human USC cell line FU-MMT-1(Fenghbio, Wuhan, China)were cultured in RPMI-1640 medium with 10% FBS and 100 U/ml of streptomycin and penicillin in a humidified incubator atmosphere containing 5% CO2at 37°C.

extract_protocol:
Total RNAs were extracted from uterine carcinosarcoma cell line FU-MMT-1 cells using TRIzol Reagent (Invitrogen） Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit（Life Technologies，Q10210）
RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: FU-MMT-1 cells transfected with siRNA against ANXA2 or  control non-silencing siRNA 48 hours.

value: Uterine carcinosarcoma cell

value: ANXA2 knockdown

value: 48 hours


title: NP11


title: SMR034


title: HEK293T_PARENT_KRAB_DOX_HA-tag_Cut&Run_BR2

description: HEK293T_PARENT_KRAB_DOX_HA-tag_CUT&RUN_BR2


title: cardiomyocyte,TAC2w, replicate2-72, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

value: cardiomyocyte

value: heart


title: FU-MMT-1 cells, siANXA2-2


title: SMR033

value: PBMC


title: FU-MMT-1 cells, siANXA2-1


title: HEK293T_K36M_KRAB_ND_HA-tag_Cut&Run_BR2


title: cardiomyocyte,TAC2w, replicate2-71, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

value: 6-8 weeks old


title: FU-MMT-1 cells, siControl-3

value: WT


title: cardiomyocyte,TAC2w+CDK-i, replicate1-1, scRNAseq

description:
smartseq2
TAC2w_CDK_i_1.xlsx


title: SMR028

value: Ag


title: SMR027


title: SMR030


title: cardiomyocyte,TAC2w, replicate2-70, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: cardiomyocyte,TAC2w, replicate2-69, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: FU-MMT-1 cells, siControl-1


title: HEK293T_K36M_KRAB_ND_HA-tag_Cut&Run_BR1


title: cardiomyocyte,TAC2w, replicate2-67, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: cardiomyocyte,TAC2w, replicate2-68, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_PARENT_KRAB_ND_HA-tag_Cut&Run_BR2

description: HEK293T_PARENT_KRAB_ND_HA-tag_CUT&RUN_BR2


title: HEK293T_PARENT_KRAB_ND_HA-tag_Cut&Run_BR1

description: HEK293T_PARENT_KRAB_ND_HA-tag_CUT&RUN_BR1


title: HEK293T_K36M_KRAB_DOX_D6_H3K4me3_Cut&Run_BR2

description: HEK293T_K36M_KRAB_DOX_D6_H3K4me3_CUT&RUN_BR2


title: SMR024

value: Tonsil


title: N4 (Ribo-seq)

city: shenyang

first: lv

last: chengzhou

state: liaoing

address: nanjingbeijie 155

department: thyroid surgery

institute: the first hospital of china medical university

data_processing:
Raw reads containing over 50% of low quality bases or over 10% of N bases were removed. Adapter sequences were trimmed. Reads with length between 10-50bp were retained for subsequent analysis.
Short reads alignment tool Bowtie2 [1]was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads will be removed. The remaining reads were further used in downstream analysis.
The rRNA removed reads of each sample were mapped to reference genome by Bowtie2 allowing no mismatches. RFs were assigned to different genomic features (5’UTR, CDS, 3’UTR and others) based on the position of the 5’ end of the alignment.
To monitor sequencing reliability, RFs density at different codon positions was calculated. Generally speaking, RFs have the highest density at the first base of codon.
Reads number in the open reading frame of coding genes was calculated by software RiboTaper[2], and the gene expression level was normalized by using FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method.
Assembly: GRCh38.release 94
Supplementary files format and content: tab-delimited text file includes FPKM and count values for each Sample

source_name: Thyroid

extract_protocol:
Thyroid cancer and adjacent normal tissue were collected, physiological saline cleaning, liquid nitrogen quick freezing.
After obtaining ribosome footprints above, Ribo-seq libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (catalog no.E7300S, E7300L). Briefly, adapters were added to both ends of RFs, followed by reverse transcription and PCR amplification. The 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).

tag: sample pair

value: pair 4

value: Normal tissue adjacent to tumor

tag: tumor stage

value: T2N1aM0, I

value: female


title: cardiomyocyte,TAC2w, replicate2-66, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: N3 (Ribo-seq)

value: pair 3

value: T3bN1aM0, I

value: male


title: SMR022

tag: tissue origin


title: cardiomyocyte,TAC2w, replicate2-65, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_K36M_KRAB_DOX_D6_H3K4me3_Cut&Run_BR1

description: HEK293T_K36M_KRAB_DOX_D6_H3K4me3_CUT&RUN_BR1

value: Human embryonic kidney


title: HEK293T_PARENT_KRAB_DOX_HA-tag_Cut&Run_BR1

description: HEK293T_PARENT_KRAB_DOX_HA-tag_CUT&RUN_BR1


title: N2 (Ribo-seq)

value: pair 2


title: SMR021

tag: subject id


title: FU-MMT-1 cells, siControl-2

value: Uterine carcinosarcoma cell

value: 48 hours


title: HEK293T_PARENT_KRAB_DOX_D6_H3K4me3_Cut&Run_BR2

description: HEK293T_PARENT_KRAB_DOX_D6_H3K4me3_CUT&RUN_BR2


title: cardiomyocyte,TAC2w, replicate2-64, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

value: cardiomyocyte

value: heart


title: SMR018

tag: stimulation


title: cardiomyocyte,TAC2w, replicate2-63, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

tag: tissue

value: 6-8 weeks old


title: T4 (Ribo-seq)

value: Thyroid tumor tissue


title: HEK293T_K36M_KRAB_ND_H3K4me3_Cut&Run_BR2

description: HEK293T_K36M_KRAB_ND_H3K4me3_CUT&RUN_BR2

tag: cell type


title: HEK293T_PARENT_KRAB_DOX_D6_H3K4me3_Cut&Run_BR1

description: HEK293T_PARENT_KRAB_DOX_D6_H3K4me3_CUT&RUN_BR1


title: cardiomyocyte,TAC2w, replicate2-62, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

tag: treatment


title: SMR017


title: N1 (Ribo-seq)

value: pair 1

value: T4aN1bM0, I


title: SMR023

value: Tonsil


title: SMR016

value: Ag


title: T3 (Ribo-seq)


title: T2 (Ribo-seq)


title: cardiomyocyte,TAC2w, replicate2-61, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

tag: strain


title: HEK293T_PARENT_KRAB_ND_H3K4me3_Cut&Run_BR2

description: HEK293T_PARENT_KRAB_ND_H3K4me3_CUT&RUN_BR2


title: cardiomyocyte,TAC2w, replicate2-60, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

tag: age


title: T1 (Ribo-seq)


title: HEK293T_PARENT_KRAB_ND_H3K4me3_Cut&Run_BR1

description: HEK293T_PARENT_KRAB_ND_H3K4me3_CUT&RUN_BR1


title: SMR012


title: cardiomyocyte,TAC2w, replicate2-59, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: SMR011


title: HEK293T_K36M_KRAB_DOX_D6_H3K27me3_Cut&Run_BR2

description: HEK293T_K36M_KRAB_DOX_D6_H3K27me3_CUT&RUN_BR2


title: HEK293T_K36M_KRAB_DOX_D6_H3K27me3_Cut&Run_BR1

description: HEK293T_K36M_KRAB_DOX_D6_H3K27me3_CUT&RUN_BR1


title: cardiomyocyte,TAC2w, replicate2-58, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: cardiomyocyte,TAC2w, replicate2-57, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_PARENT_KRAB_DOX_D6_H3K27me3_Cut&Run_BR2

description: HEK293T_PARENT_KRAB_DOX_D6_H3K27me3_CUT&RUN_BR2


title: HEK293T_K36M_KRAB_ND_H3K4me3_Cut&Run_BR1

description: HEK293T_K36M_KRAB_ND_H3K4me3_CUT&RUN_BR1


title: SMR006


title: SMR015


title: HEK293T_PARENT_KRAB_DOX_D6_H3K27me3_Cut&Run_BR1

description: HEK293T_PARENT_KRAB_DOX_D6_H3K27me3_CUT&RUN_BR1


title: cardiomyocyte,TAC2w, replicate2-55, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: SMR009


title: SMR005


title: cardiomyocyte,TAC2w, replicate2-54, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: SMR004


title: HEK293T_K36M_KRAB_ND_H3K27me3_Cut&Run_BR2

description: HEK293T_K36M_KRAB_ND_H3K27me3_CUT&RUN_BR2


title: SMR003

value: PBMC


title: SerumExosome_POF_rep4

type: RNA

city: Shanghai

first: Xiangyu

last: Kong

address: 168 Changhai Road

department: Gastroenterology

institute: Changhai Hospital

description: Exosomal miRNA levels in serum from AP later developed POF

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Serum exosome

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Blood was collected in a serum clot activator tube and then processed by centrifugation. Centrifugation was performed at 400 g for 15 min, and 1-ml aliquots of serum were stored in Eppendorf tubes at −80 °C for later use. Serum aliquots from individuals selected for this study were retrieved from storage, quick thawed, and centrifuged again at 16,000g at 4 °C for 30 min to remove large microparticles. To isolate exosomes, 1 mL of supernatant was processed with ExoQuick™ (System Biosciences, EXOQ20A-1) according to the manufacturer’s protocol. The acquired exosome pellet was resuspended in 200 μl phosphate buffered saline (PBS).

value: Serum

tag: gender

value: female

tag: condition

value: with POF


title: SerumExosome_POF_rep5


title: SerumExosome_POF_rep3

value: male


title: cardiomyocyte,TAC2w, replicate2-53, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_K36M_KRAB_ND_H3K27me3_Cut&Run_BR1

description: HEK293T_K36M_KRAB_ND_H3K27me3_CUT&RUN_BR1

tag: cell line

value: Human embryonic kidney


title: HEK293T_PARENT_KRAB_ND_H3K27me3_Cut&Run_BR2

description: HEK293T_PARENT_KRAB_ND_H3K27me3_CUT&RUN_BR2


title: SMR010


title: SerumExosome_POF_rep1


title: SerumExosome_POF_rep2


title: SerumExosome_NoPOF_rep5

description: Exosomal miRNA levels in serum from AP without POF

value: without POF


title: HEK293T_PARENT_KRAB_ND_H3K27me3_Cut&Run_BR1

description: HEK293T_PARENT_KRAB_ND_H3K27me3_CUT&RUN_BR1


title: SerumExosome_NoPOF_rep4


title: cardiomyocyte,TAC2w, replicate2-51, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: SMR002


title: cardiomyocyte,TAC2w, replicate2-56, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: SMR001


title: SerumExosome_NoPOF_rep3


title: HEK293T_K36M_KRAB_H3K36me3_Cut&Run


title: cardiomyocyte,TAC2w, replicate2-50, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_PARENT_KRAB_H3K36me3_Cut&Run


title: cardiomyocyte,TAC2w, replicate2-49, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_K36M_KRAB_DOX_D20MEM_H3K9me3_Cut&Run_BR2

description: HEK293T_K36M_KRAB_DOX_D20MEM_H3K9me3_CUT&RUN_BR2


title: iWAT, PH20_TG4, 5-day Dox200 pellet

city: Houston

first: Yi

last: Zhu

institute: BAYLOR COLLEGE OF MEDICINE

data_processing:
FastQC v0.11.9 was employed to check the raw sequencing quality and test for adapter contamination. The raw reads were mapped to the mouse genome using STAR v2.7.9a. The genome index was generated from raw FASTA, and annotation files were downloaded from the GENCODE portal for the mouse genome build GRCm38, release 23. Alignments were stored in BAM format. MultiQC v1.12 provided a summary of raw read quality and alignment quality. Gene expression values for each sample were calculated by the number of reads aligned per gene using STAR’s quantMode GeneCounts. Raw counts were normalized, and genes with an average read count of below 50 across all samples were excluded from the differential analysis. Differential gene expression analysis was performed using DESeq2, applying a p-value threshold of 0.05 to identify significant differentially expressed genes. Overlapping genes from different contrasts were analyzed to determine the directionality of differential expression.
Assembly: GRCm38
Supplementary files format and content: tab-delimited excel file includes raw counts for each Sample
Supplementary files format and content: tab-delimited excel file includes RPKM values for each Sample

source_name: inguinal white adipose tissue

growth_protocol: All experiments were conducted using littermate-controlled male mice, starting at 8-10 weeks of age. Mice were housed in cages with a 12-h dark-light cycle and free access to water and food.

extract_protocol:
Total RNA was extracted using TRIzol reagent, 1μg of total RNA was used for the construction of sequencing libraries.
cDNA libraries were prepared using an Illumina TruSeq RNA sample prep kit. The average size of the library cDNAs was 150 bp (excluding adapters). The integrity and quality of cDNA libraries were assessed using an Agilent 2100 Bioanalyzer and an ABI StepOne Plus real-time PCR system.

treatment_protocol: The mice were fed with 5-day normal chow containing 200mg/kg Doxycycline before harvesting iWAT (inguinal white aidpose tissue)

value: inguinal white adipose tissue

tag: genotype

value: PH20 overexpression

value: 5-day Dox200 pellet


title: Epidermis,Patient 1,Before,51

city: Cambridge

first: Eloi

last: Schmauch

state: Massachusetts

address: 32 Vassar St

department: Computer Science and Artificial Intelligence Laboratory

institute: Massachusetts Institute of Technology

description: Count matrix column name: P1_015_EPI_BEFORE

data_processing:
Raw sequencing FASTQ files are compiled with a configuration file that defines processing parameters. Adapter sequences are then computationally removed from these files, and overlapping paired-end reads are merged. The resulting reads are aligned to RTS-ID barcodes in the reference assay, with raw counts assigned to biological target names. Next, PCR duplicates are eliminated using Unique Molecular Identifiers, producing deduplicated reads. Finally, the processed data is saved as DCC files, which were then uploaded to the GeoMx DSP system for further analysis or for processing with GeomxTools in R.
dcc-metadata = false; save-interim-files = false; quality-trim-score = 20; 2color-trimming = True; adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; adapter-trim-match-length = 10; adapter-trim-max-mismatch = 3; barcode-max-mismatch = 1; stitching-max-mismatch = 2; dedup-hd = 1; threads = 4
The raw count matrix (for each ROI) was obtained with Nanostring GeoMX DSP according to the instruction manual.
Assembly: GRCh38
Supplementary files format and content: Raw counts matrix - countains counts for each gene (rows), for each ROI (columns)
Supplementary files format and content: dcc files (inputs for GeoMX DSP software)
Library strategy: Spatial Transcriptomics

source_name: skin

extract_protocol:
The RNA extraction was performed according to the protocol. The GeoMx Digital Spatial Profiler (DSP) uses nucleic acid probes coupled to photocleavable oligonucleotide tags which hybridize to targets in slide-mounted tissue sections. Via UV exposure the oligonucleotide tags are released from discrete regions of interest (ROIs) in the tissue. The UV-cleaved oligos are transferred to a collection plate for Library Pre with Seq Code primers. Later they are quantitated by Illumina Next Generation Sequencing. Results are mapped back to tissue location, yielding a spatially resolve digital profile.
Library preparation was performed according to Nanostring GeoMX NGS Manual. A specific thermocycler program is set for the PCR process, including various temperature and time settings for steps like UDG incubation, denaturation, annealing, extension, and final holding.
Preparation involves selecting the correct primer plates based on the lab worksheet, thawing them, and mixing them with the GeoMx NGS Master Mix and sample aspirates according to defined volumes. This is followed by aliquoting the master mix, transferring primers, and sample aspirates into a new PCR plate. Post-PCR, products are pooled and undergo AMPure cleanup—a bead-based method for purifying the PCR products.
The purified library's quality is assessed through capillary electrophoresis, ensuring the correct amplicon size and absence of undesirable products. Quantification of the library concentration is done using Qubit or qPCR. Finally, the library is stored at -20°C until sequencing, with recommendations provided for pooling multiple sample pools for a sequencing run and adjusting loading concentrations based on the Illumina platform used.

value: skin

tag: roi selected

value: Epidermis

tag: patient

value: Patient 1

value: Before

tag: technical sample_id


title: CD68+ cells,Patient 1,Before,50

description: Count matrix column name: P1_014_CD68_BEFORE

value: CD68+ cells


title: cardiomyocyte,TAC2w, replicate2-48, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: cardiomyocyte,TAC2w, replicate2-47, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: CD3+ cells,Patient 1,Before,49

description: Count matrix column name: P1_014_CD3_BEFORE

value: CD3+ cells


title: iWAT, PH20_TG3, 5-day Dox200 pellet


title: iWAT, PH20_TG2, 5-day Dox200 pellet


title: iWAT, PH20_TG1, 5-day Dox200 pellet


title: HEK293T_PARENT_KRAB_DOX_D20MEM_H3K9me3_Cut&Run_BR2

description: HEK293T_PARENT_KRAB_DOX_D20MEM_H3K9me3_CUT&RUN_BR2


title: cardiomyocyte,TAC2w, replicate2-52, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_K36M_KRAB_DOX_D6_H3K9me3_Cut&Run_BR2

description: HEK293T_K36M_KRAB_DOX_D6_H3K9me3_CUT&RUN_BR2


title: cardiomyocyte,TAC2w, replicate2-46, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: CD68+ cells,Patient 1,Before,47

description: Count matrix column name: P1_012_CD68_BEFORE


title: SerumExosome_NoPOF_rep1

value: Serum


title: Epidermis,Patient 1,During (8 weeks),48

description: Count matrix column name: P1_013_EPI_8WKS

value: During (8 weeks)


title: HEK293T_K36M_KRAB_DOX_D2_H3K9me3_Cut&Run_BR2

description: HEK293T_K36M_KRAB_DOX_D2_H3K9me3_CUT&RUN_BR2


title: HEK293T_PARENT_KRAB_DOX_D6_H3K9me3_Cut&Run_BR2

description: HEK293T_PARENT_KRAB_DOX_D6_H3K9me3_CUT&RUN_BR2


title: iWAT,PH20_WT4, 5-day Dox200 pellet

value: WT


title: CD3+ cells,Patient 1,Before,46

description: Count matrix column name: P1_012_CD3_BEFORE


title: cardiomyocyte,TAC2w, replicate2-44, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: SerumExosome_NoPOF_rep2

value: male


title: iWAT, PH20_WT3, 5-day Dox200 pellet


title: cardiomyocyte,TAC2w, replicate2-45, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_PARENT_KRAB_DOX_D2_H3K9me3_Cut&Run_BR2

description: HEK293T_PARENT_KRAB_DOX_D2_H3K9me3_CUT&RUN_BR2

value: Human embryonic kidney


title: cardiomyocyte,TAC2w, replicate2-43, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: iWAT, PH20_WT2, 5-day Dox200 pellet

value: inguinal white adipose tissue


title: CD3+ cells,Patient 1,During (8 weeks),44

description: Count matrix column name: P1_011_CD3_8WKS


title: HEK293T_K36M_KRAB_ND_H3K9me3_Cut&Run_BR2

description: HEK293T_K36M_KRAB_ND_H3K9me3_CUT&RUN_BR2


title: cardiomyocyte,TAC2w, replicate2-42, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: iWAT, PH20_WT1, 5-day Dox200 pellet


title: CD68+ cells,Patient 1,During (8 weeks),43

description: Count matrix column name: P1_010_CD68_8WKS


title: HEK293T_PARENT_KRAB_ND_H3K9me3_Cut&Run_BR2

description: HEK293T_PARENT_KRAB_ND_H3K9me3_CUT&RUN_BR2


title: iWAT, Has2_TG4, 5-day Dox200 pellet

value: Has2 overexpression


title: HEK293T_K36M_KRAB_DOX_D20MEM_H3K9me3_Cut&Run_BR1

description: HEK293T_K36M_KRAB_DOX_D20MEM_H3K9me3_CUT&RUN_BR1


title: cardiomyocyte,TAC2w, replicate2-41, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_PARENT_KRAB_DOX_D20MEM_H3K9me3_Cut&Run_BR1

description: HEK293T_PARENT_KRAB_DOX_D20MEM_H3K9me3_CUT&RUN_BR1


title: cardiomyocyte,TAC2w, replicate2-39, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: CD68+ cells,Patient 1,During (8 weeks),41

description: Count matrix column name: P1_009_CD68_8WKS


title: iWAT, Has2_TG2, 5-day Dox200 pellet

value: 5-day Dox200 pellet


title: HEK293T_K36M_KRAB_DOX_D6_H3K9me3_Cut&Run_BR1

description: HEK293T_K36M_KRAB_DOX_D6_H3K9me3_CUT&RUN_BR1


title: CD3+ cells,Patient 1,During (8 weeks),42

description: Count matrix column name: P1_010_CD3_8WKS

value: skin


title: iWAT, Has2_TG1, 5-day Dox200 pellet


title: CD68+ cells,Patient 1,During (8 weeks),39

description: Count matrix column name: P1_008_CD68_8WKS


title: iWAT, Has2_WT4, 5-day Dox200 pellet


title: HEK293T_PARENT_KRAB_DOX_D6_H3K9me3_Cut&Run_BR1

description: HEK293T_PARENT_KRAB_DOX_D6_H3K9me3_CUT&RUN_BR1


title: cardiomyocyte,TAC2w, replicate2-37, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: CD3+ cells,Patient 1,During (8 weeks),38

description: Count matrix column name: P1_008_CD3_8WKS


title: HEK293T_K36M_KRAB_DOX_D2_H3K9me3_Cut&Run_BR1

description: HEK293T_K36M_KRAB_DOX_D2_H3K9me3_CUT&RUN_BR1


title: cardiomyocyte,TAC2w, replicate2-38, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: cardiomyocyte,TAC2w, replicate2-36, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: CD3+ cells,Patient 1,During (8 weeks),40

description: Count matrix column name: P1_009_CD3_8WKS


title: iWAT, Has2_WT3, 5-day Dox200 pellet


title: HEK293T_PARENT_KRAB_DOX_D2_H3K9me3_Cut&Run_BR1

description: HEK293T_PARENT_KRAB_DOX_D2_H3K9me3_CUT&RUN_BR1


title: cardiomyocyte,TAC2w, replicate2-35, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: iWAT, Has2_WT2, 5-day Dox200 pellet


title: CD68+ cells,Patient 1,During (8 weeks),36

description: Count matrix column name: P1_006_CD68_8WKS


title: cardiomyocyte,TAC2w, replicate2-40, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_K36M_KRAB_ND_H3K9me3_Cut&Run_BR1

description: HEK293T_K36M_KRAB_ND_H3K9me3_CUT&RUN_BR1


title: iWAT, Has2_TG3, 5-day Dox200 pellet


title: CD3+ cells,Patient 1,During (8 weeks),35

description: Count matrix column name: P1_006_CD3_8WKS


title: iWAT, Has2_WT1, 5-day Dox200 pellet


title: CD68+ cells,Patient 1,During (8 weeks),45

description: Count matrix column name: P1_011_CD68_8WKS


title: cardiomyocyte,TAC2w, replicate2-33, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: Epidermis,Patient 1,During (8 weeks),34

description: Count matrix column name: P1_005_EPI_8WKS

value: Epidermis


title: 7059

city: Charleston

first: Benjamin

last: Pryce

address: 173 Ashley Ave

institute: Medical University of South Carolina

data_processing:
Sequencing results were initally analyzed using Partek® Flow® software suite
Analysis was done with DESeq2
Assembly: mm10

source_name: skeletal muscle

extract_protocol:
Mononuclear cells were isolated from skeletal muscle, and RNA was extracted using Trizol reagent
Construction of the library using the SureSelect Strand Specific RNA library prep kit

value: skeletal muscle

value: IKKbfl/fl

tag: Sex

value: LLC tumor bearing mice

value: tamoxifen treatment on day 10-14 after tumor cell injection to activate Cre


title: HEK293T_PARENT_DMSO_HA-tag_Cut&Run


title: CD68+ cells,Patient 1,Before,33

description: Count matrix column name: P1_004_CD68_BEFORE

value: CD68+ cells

value: Patient 1

value: Before


title: cardiomyocyte,TAC2w, replicate2-31, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: CD3+ cells,Patient 1,Before,32

description: Count matrix column name: P1_004_CD3_BEFORE

value: CD3+ cells


title: HEK293T_K36M_DMSO_HA-tag_Cut&Run

value: Human embryonic kidney


title: cardiomyocyte,TAC2w, replicate2-30, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_PARENT_DMSO_H3.3_Cut&Run


title: cardiomyocyte,TAC2w, replicate2-29, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: Epidermis,Patient 1,Before,31

description: Count matrix column name: P1_003_EPI_BEFORE


title: 6948

value: Pax7 Cre ErT x IKKbfl/fl

value: male


title: HEK293T_K36M_DMSO_H3.3_Cut&Run


title: 6952


title: cardiomyocyte,TAC2w, replicate2-34, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293T_PARENT_KRAB_ND_H3K9me3_Cut&Run_BR1

description: HEK293T_PARENT_KRAB_ND_H3K9me3_CUT&RUN_BR1


title: CD68+ cells,Patient 1,Before,30

description: Count matrix column name: P1_002_CD68_BEFORE


title: cardiomyocyte,TAC2w, replicate2-28, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: 6951


title: HEK293T_K36M_AUXIN_HA-tag_Cut&Run


title: HEK293T_K36M_AUXIN_H3.3_Cut&Run


title: Adult CoE RNA-seq replicate 3

city: RTP

first: Wendy

last: Jefferson

state: NC

address: 105 T. W. Alexander Drive

institute: NIEHS

data_processing:
The raw RNA-Seq reads were initially processed by filtering with average quality scores greater than 20.
The reads passing the initial processing were aligned to the mouse reference genome (mm10; Genome Reference Consortium Mouse Build 38 from December 2011) using TopHat version 2.0.4
Assembly: mm10
Supplementary files format and content: RNAseq-FPKM.txt

source_name: Adult control estrus, uterus

growth_protocol: Adult mouse uterine tissues were colleclted from control diestrus, control estrus.

extract_protocol:
RNA was extracted using Qiagen RNeasy kit with DNase on column treatment
RNA-seq libraries were generated using Illumina Tru-Seq RNA kit.

treatment_protocol: Mice were unexposed control CD-1 mice

value: mouse uterus

value: 2 months

tag: Stage

value: estrus


title: 6944

value: skeletal muscle


title: Epidermis,Patient 1,Before,28

description: Count matrix column name: P1_001_EPI_BEFORE

value: skin

value: Epidermis


title: cardiomyocyte,TAC2w, replicate2-32, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: Adult CoE RNA-seq replicate 2


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, No TFs, hiPSC_naivereset

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

institute: Harvard University

data_processing:
NextFlow methylseq pipeline (https://nf-co.re/methylseq/), version 2.5.0 with default settings
Assembly: hg38 plus lambda phage and pUC19 spike-in controls
Supplementary files format and content: Methylation coverage (bismark output)

extract_protocol:
Genomic DNA was extracted from hiPSCs, hPGCLCs, and sorted DDX4+ iOLCs using the Qiagen DNeasy Micro kit. Libraries were prepared from 200 ng DNA using the NEB Enzymatic Methyl-Seq kit (NEB #E7120) following the manufacturer’s instructions. Briefly, control DNA (methylated pUC19 and unmethylated λ phage) was spiked into each sample. Next, samples were sheared to ~300 bp using a Covaris S2 sonicator. Enzymatic methyl conversion was performed, and libraries were amplified using unique dual index primers. 2 x 150 bp paired end sequencing was performed on an Illumina NovaSeq.
Methyl-seq (NEB enzymatic kit)

value: DDX4-tdTomato / REC8-mGreenLantern

value: No TFs


title: cardiomyocyte,TAC2w, replicate2-26, scRNAseq

description:
smartseq2
TAC2w_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


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, No TFs, hiPSC_naivereset

value: DDX4-tdTomato / SYCP3-mGreenLantern


title: cardiomyocyte,TAC2w, replicate2-25, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: CD3+ cells,Patient 2,Before,26

description: Count matrix column name: P2_018_CD3_8WKS

value: Patient 2

value: Before


title: Adult CoE RNA-seq replicate 1


title: Immune,Patient 2,During (8 weeks),25

description: Count matrix column name: P2_017_EPI_BEFORE

value: Immune

value: During (8 weeks)


title: cardiomyocyte,TAC2w, replicate2-24, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: CD68+ cells,Patient 2,Before,27

description: Count matrix column name: P2_018_CD68_8WKS

value: CD68+ cells


title: ATCC-BXS0115 DDX4-tdTomato/DAZL-mGreenLantern, No TFs, hiPSC_naivereset

value: DDX4-tdTomato / DAZL-mGreenLantern


title: Immune,Patient 2,Before,24

description: Count matrix column name: P2_016_IMMU_8WKS


title: CD3+ cells,Patient 1,Before,29

description: Count matrix column name: P1_002_CD3_BEFORE

value: CD3+ cells

value: Patient 1


title: cardiomyocyte,TAC2w, replicate2-23, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: Adult CoD RNA-seq replicate 2

source_name: Adult control diestrus, uterus

value: mouse uterus

value: 2 months

value: diestrus


title: cardiomyocyte,TAC2w, replicate2-27, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1+ANHX+ZGLP1, DDX4+ iOLCs, naive reset

value: DDX4+ induced oogonia-like cells, naive reset


title: Immune,Patient 2,Before,22

description: Count matrix column name: P2_014_IMMU_8WKS

value: skin


title: Adult CoD RNA-seq replicate 1


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1+ANHX+ZGLP1, DDX4+ iOLCs

value: DDX4+ induced oogonia-like cells

value: DDX4-tdTomato / REC8-mGreenLantern


title: cardiomyocyte,TAC2w, replicate2-21, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: cardiomyocyte,TAC2w, replicate2-20, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: 6949

value: skeletal muscle

value: Pax7 Cre ErT x IKKbfl/fl

value: male

value: LLC tumor bearing mice

value: tamoxifen treatment on day 10-14 after tumor cell injection to activate Cre


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1+ANHX+ZGLP1, DDX4+ iOLCs

value: DDX4-tdTomato / SYCP3-mGreenLantern


title: Immune,Patient 2,During (8 weeks),23

description: Count matrix column name: P2_015_IMMU_BEFORE

value: Immune

value: Patient 2

value: During (8 weeks)


title: cardiomyocyte,TAC2w, replicate2-19, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: Adult CoD RNA-seq replicate 4

value: mouse uterus

value: 2 months

value: diestrus


title: ATCC-BXS0115 DDX4-tdTomato/DAZL-mGreenLantern, LHX8+ZNF281+SOHLH1+ANHX+ZGLP1, DDX4+ iOLCs, naive reset

value: DDX4+ induced oogonia-like cells, naive reset

value: DDX4-tdTomato / DAZL-mGreenLantern


title: ATCC-BXS0115 DDX4-tdTomato/DAZL-mGreenLantern, LHX8+ZNF281+SOHLH1+ANHX+ZGLP1, DDX4+ iOLCs

value: DDX4+ induced oogonia-like cells


title: CD3+ cells,Patient 2,Before,20

description: Count matrix column name: P2_013_CD3_8WKS

value: skin

value: CD3+ cells

value: Before


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1, DDX4+ iOLCs

value: DDX4-tdTomato / REC8-mGreenLantern


title: cardiomyocyte,TAC2w, replicate2-18, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: Adult CoD RNA-seq replicate 3


title: cardiomyocyte,TAC2w, replicate2-22, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1+ANHX+ZGLP1, DDX4+ iOLCs, naive reset


title: cardiomyocyte,TAC2w, replicate2-17, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: Epidermis,Patient 1,During (8 weeks),37

description: Count matrix column name: P1_007_EPI_8WKS

value: Epidermis

value: Patient 1


title: CD68+ cells,Patient 2,Before,21

description: Count matrix column name: P2_013_CD68_8WKS

value: CD68+ cells

value: Patient 2


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1, DDX4+ iOLCs

value: DDX4-tdTomato / SYCP3-mGreenLantern


title: CD68+ cells,Patient 2,Before,18

description: Count matrix column name: P2_011_CD68_8WKS


title: SUP_LGA_placental_3

city: Shenyang

first: Dan

last: Wang

state: Liaoning Province, China

address: No.16, Puhe Avenue, Shenbei New District

department: Department of Obstetrics and Gynecology

institute: Shengjing Hospital of China Medical University

description:
Raw data file:
LGA_3.txt
LGA placental tissue-3

hyb_protocol: The “IP” and “Sup” RNAs were treated with RNase R, and then labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit. The cRNAs were combined together and hybridized onto Arraystar Human circRNA Epitranscriptomic Microarray (8x15K, Arraystar).

scan_protocol: After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing:
Data was extracted using Agilent Feature Extraction software. The probe signals passing P or M QC flags in at least 3 samples were retained for further analysis.
IP (Cy5-labelled) and Sup (Cy3-labelled) intensities were normalized by the RNA spike-in calibration controls. m6A methylation levels were calculated for the percentage of modified RNA of a transcript.  IP (Cy5-labelled) intensities were normalized as relative intensities by the RNA spike-in calibration controls. The normalized IP intensities represent the m6A quantity of the transcript comparable across samples.

source_name: placental tissue

label_protocol: And the total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”.

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000.

value: female

value: placental

value: large for gestational age

tag: rip antibody

value: none, RNAs were recovered from the supernatant


title: SUP_LGA_placental_5

description:
Raw data file:
LGA_5.txt
LGA placental tissue-5


title: ATCC-BXS0115 DDX4-tdTomato/DAZL-mGreenLantern, LHX8+ZNF281+SOHLH1, DDX4+ iOLCs


title: cardiomyocyte,TAC2w, replicate2-16, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

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.

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: CD3+ cells,Patient 2,Before,17

description: Count matrix column name: P2_011_CD3_8WKS


title: PGP1 wildtype, No TFs, hiPSC_primed

value: wildtype

value: No TFs


title: Epidermis,Patient 2,Before,16

description: Count matrix column name: P2_010_EPI_8WKS

value: skin


title: cardiomyocyte,TAC2w, replicate2-14, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: SUP_LGA_placental_1

description:
Raw data file:
LGA_1.txt
LGA placental tissue-1


title: CD68+ cells,Patient 2,Before,15

description: Count matrix column name: P2_009_CD68_8WKS

value: Before


title: ATCC-BXS0116 DDX4-tdTomato/NANOS3-mVenus, No TFs, hiPSC_primed

value: DDX4-tdTomato / NANOS3-mVenus


title: cardiomyocyte,TAC2w, replicate2-13, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: CD3+ cells,Patient 2,Before,14

description: Count matrix column name: P2_009_CD3_8WKS

value: CD3+ cells


title: cardiomyocyte,TAC2w, replicate2-12, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: IP_LGA_placental_3

value: RNA immunoprecipitated with anti-N6-methyadenosine (m6A) antibody


title: IP_LGA_placental_5


title: ATCC-BXS0115 wildtype, No TFs, hPGCLC

value: hPGCLC


title: Epidermis,Patient 2,Before,13

description: Count matrix column name: P2_008_EPI_8WKS

value: Epidermis

value: Patient 2


title: ATCC-BXS0116 DDX4-tdTomato/NANOS3-mVenus, LHX8+ZNF281+SOHLH1, DDX4+ iOLCs (no DNMT1i), replicate2

value: DDX4+ induced oogonia-like cells (no DNMT1i)


title: SUP_LGA_placental_2

description:
Raw data file:
LGA_2.txt
LGA placental tissue-2

value: female

value: placental


title: cardiomyocyte,TAC2w, replicate2-15, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: cardiomyocyte,TAC2w, replicate2-11, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: IP_LGA_placental_2

value: large for gestational age


title: IP_LGA_placental_1


title: CD68+ cells,Patient 2,During (8 weeks),12

description: Count matrix column name: P2_007_CD68_BEFORE

value: CD68+ cells

value: During (8 weeks)


title: CD3+ cells,Patient 2,During (8 weeks),11

description: Count matrix column name: P2_007_CD3_BEFORE


title: ATCC-BXS0116 DDX4-tdTomato/NANOS3-mVenus, LHX8+ZNF281+SOHLH1, DDX4+ iOLCs (no DNMT1i)


title: cardiomyocyte,TAC2w, replicate2-10, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: cardiomyocyte,TAC2w, replicate2-9, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: Epidermis,Patient 2,During (8 weeks),10

description: Count matrix column name: P2_006_EPI_BEFORE

value: skin


title: cardiomyocyte,TAC2w, replicate2-8, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: SUP_NGA_placental_4

description:
Raw data file:
NGA_4.txt
NGA placental tissue-4

value: normal for gestational age

value: none, RNAs were recovered from the supernatant


title: HEK293, Input

city: Austin

first: Svetlana

last: Panina

address: 101 East 21st St.

institute: The University of Texas at Austin

data_processing:
After initial assessment of read quality, pSer2 and  RPRD1B (HA-tag) ChIP-Seq data was mapped onto human reference genome, hg38, with Bowtie2 v. 2.5.0 aligner for paired-end reads using default parameters. pThr4 single-end ChIP-Seq reads were mapped onto human reference genome, hg19, using BWA v.0.7.17.
Coverage tracks in .bigwig format were generated from filtered .bam files (mapq > 20).
TSS/TES profiling was done using plotProfile on matrices generated with 50-bp bins using the computeMatrix function from the deeptools v.2.2.3
After alignment, MACS2 v.2.2.7.1 in Galaxy (parameters: --broad; --broad-cutoff of q < 0.1 for pThr4 and HA-RPRD1B; pSer2 -default) was used to call peaks for IP-samples against Input.
Assembly: hg19 (pThr4), hg38 (pSer2, HA-RPRD1B)
Supplementary files format and content: bigWig, broadPeak

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Briefly, for HA-tagged RPRD1B, HEK293 cells were double crosslinked with 2mM DSG for 15 min followed by secondary fixation with 1% formaldehyde for 10 min at room temperature. Single crosslinking was used for RPB1 ChIP using 1% formaldehyde for 10 min. Crosslinking was quenched with 0.125 M glycine for 5 min. Cells were successively lysed in lysis buffer LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× PI), LB2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× PI) and LB3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1× PI). Chromatin was sonicated to an average size of ~200–500 bp using UCD-200 Biorupter (30s on and 30 s off for 30 min). A total of 5 μg of HA antibody (cat: C29F4), pThr4 antibody (Active Motif, cat: 61361), or pSer2 antibody (Sigma, SKU: MABE953) was pre-mixed in a 50μl volume of Dynabeads protein A or protein G (Invitrogen) and was added to each sonicated chromatin sample and incubated overnight at 4°C. The chromatin-bound beads were washed two times with low salt buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 150mM NaCl), once with high salt wash buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 500mM NaCl), once with LiCl wash buffer (250mM LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, 1mM EDTA, 10mM Tris-Cl pH 8.0) and twice in TE buffer. The chromatin was reverse crosslinked overnight at 65°C with shaking at 750rpm. After DNA extraction using phenol-chloroform, the DNA was resuspended in 10mM Tris-HCl pH 8.0.
The extracted DNA was used to construct the ChIP-seq library using the NEBNext Ultra II DNA Library Prep Kit followed by sequencing with an Illumina HiSeq 3000 or NovaSeq X Plus system.

treatment_protocol: To prepare samples for pThr4 ChIP, we treated HEK293 cell lysate with Ssu72/symplekin complex at 4°C for 30 minutes before binding to the 6D7 antibody. To generate T4A and T4WT CTD samples for pSer2 immunoprecipitation, transient transfection of 12 μg of either plasmid was performed using PEI. Following transfection, 2.5 μg of alpha amanitin was added to cells for 48 hours. Finally, to prepare HA-RPRD1B samples, HEK293 were transfected with HA-RPRD1B using PEI (1:7 plasmid to reagent ratio) to overexpress the protein of interest.

value: Human embryonic kidney

tag: chip antibody


title: CD68+ cells,Patient 2,During (8 weeks),9

description: Count matrix column name: P2_005_CD68_BEFORE


title: SUP_NGA_placental_1

description:
Raw data file:
NGA_1.txt
NGA placental tissue-1


title: HEK293, HA-RPRD1B, rep2

value: HA (Cell Signaling, #C29F4)


title: cardiomyocyte,TAC2w, replicate2-7, scRNAseq

city: Bunkyo-ku

first: Manami

last: Katoh

institute: The University of Tokyo

description:
smartseq2
TAC2w_2.xlsx


title: SUP_NGA_placental_2

description:
Raw data file:
NGA_2.txt
NGA placental tissue-2


title: CD3+ cells,Patient 2,During (8 weeks),8

description: Count matrix column name: P2_005_CD3_BEFORE

value: CD3+ cells


title: IP_NGA_placental_2

value: RNA immunoprecipitated with anti-N6-methyadenosine (m6A) antibody


title: cardiomyocyte,TAC2w, replicate2-6, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293, HA-RPRD1B, rep1


title: CD68+ cells,Patient 2,During (8 weeks),7

description: Count matrix column name: P2_004_CD68_BEFORE

value: Patient 2


title: cardiomyocyte,TAC2w, replicate2-5, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: HEK293, pSer2, T4A, rep2

value: pSer2 (Sigma, #MABE953)


title: ATAC-seq_my7:GFP- CMs_replicate1

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Processing steps were implemented within the Snakemake framework.
UMIs were extracted from paired-end reads using UMI-tools and mapped to the danRer11 genome assembly using Bowtie2;
-X 2000 --no-discordant --no-mixed). Mapped reads were sorted, indexed, and converted to .bam format with samtools then filtered for MAPQ 30 and deduplicated using UMI-tools.
Input-subtracted .bigwig for visualization (--operation subtract --binSize 50 --scaleFactorsMethod None --normalizeUsing CPM --smoothLength 250 --extendReads) tracks were generated using deepTools

organism: Danio rerio

source_name: non-cardiomyocyte nuclei

extract_protocol:
scRNA-seq: FACS sorted for GFP+ cells from wt and hand2 mutant embryos; ATAC-seq and CHIP-seq: Sorted GFP positive and GFP negative nuclei were washed and lysed in 1 ml of water and spun at 12 000 g for 20 minutes.
scRNA-seq: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).  ATAC-seq:The DNA was then purified using the Qiagen Minelute column.  Both samples were amplified for 14 cycles as described in Buenostro 2013 ( PMID: 24097267).    CHIP-seq: The library was prepared using NEXTflex qRNA-Seq Kit v2 (BioScientific #5130-12).

value: non-cardiomyocyte nuclei

value: non-cardiomyocytes

value: WT


title: IP_NGA_placental_1

value: female

value: placental


title: A4 wildtype, No TFs, hPGCLC

value: hPGCLC

value: wildtype

value: No TFs


title: CD3+ cells,Patient 2,During (8 weeks),6

description: Count matrix column name: P2_004_CD3_BEFORE

value: skin

value: During (8 weeks)


title: cardiomyocyte,TAC2w, replicate2-4, scRNAseq

address: 7-3-1 Hongo

description:
smartseq2
TAC2w_2.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: HEK293, pSer2, T4A, rep1

value: Human embryonic kidney


title: input_ChIP-seq_myl7:GFP- CMs


title: Epidermis,Patient 2,During (8 weeks),5

description: Count matrix column name: P2_003_EPI_BEFORE

value: Epidermis


title: Epidermis,Patient 2,Before,19

description: Count matrix column name: P2_012_EPI_8WKS

value: Patient 2

value: Before


title: cardiomyocyte,TAC2w, replicate2-3, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: H3K27ac_ChIP-seq_myl7:GFP- CMs

value: non-cardiomyocyte nuclei


title: HEK293, pSer2, T4WT, rep1

value: pSer2 (Sigma, #MABE953)


title: CD68+ cells,Patient 2,During (8 weeks),4

description: Count matrix column name: P2_002_CD68_BEFORE

value: CD68+ cells


title: input_ChIP-seq_myl7:GFP+ CMs

source_name: cardiomyocyte nuclei

value: cardiomyocyte nuclei

value: cardiomyocytes

value: WT


title: ATAC-seq_my7:GFP+ CMs_replicate1


title: cardiomyocyte,TAC2w, replicate2-2, scRNAseq

description:
smartseq2
TAC2w_2.xlsx

source_name: heart


title: HEK293, pSer2, untrasfected, rep2


title: cardiomyocyte,TAC2w, replicate2-1, scRNAseq

description:
smartseq2
TAC2w_2.xlsx


title: H3K27ac_ChIP-seq_myl7:GFP+ CMs


title: HEK293, pSer2, untransfected, rep1


title: cardiomyocyte,TAC2w, replicate1-77, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: Epidermis,Patient 2,During (8 weeks),2

description: Count matrix column name: P2_001_EPI_BEFORE


title: PIF4S344A-28_biol rep 2

city: New Delhi

first: Alok

middle: Krishna

state: Delhi

address: Aruna Aasaf Ali Marg

department: National Institute of Plant Genome Research

country: India

data_processing:
Raw sequencing reads were mapped to theArabidopsis thaliana genome (TAIR10) by Bowtie2 version 2.4.2 with default parameters (Langmead and Salzberg, 2012).
Reads were normalized as reads per kilobase per million mapped reads (RPKM) in 10 bp windows using the bamCoverage tool in deepTools and visualized in Integrative Genomics Viewer (IGV). The fragment size distribution was obtained from the bamPEFragmentSize tool in deepTools (Ramirez etal., 2014).
To obtain the enrichment signal around the transcription start site (TSS), we employed computeMatrix tool in deepTools. Using the ChIPpeakAnno  package, we determined the intersection of peaks in two replicates as the final set of enriched peaks for each sample.
DiffBind was used to perform differential enrichment analysis of H2A.Z. Differentially enriched peaks with FDR ≤ 0.05 were filtered.
The differentially bound sites predicted by Diffbind were converted to gene using seq2gene. These genes were then input for KEGG and GO enrichment analysis.
Supplementary_files_format_and_content: bdg files were generated using  using Macs2 with SPMR normalization.
Assembly: TAIR10
Supplementary files format and content: bdg

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Seeds were surface-sterilized by treatment with 70% alcohol for 5 min and then washed with HgCl2, and then washed with water for 8 times. After sterilization, seeds were sown onto 1/ 2MS nutrient medium and were incubated at 4°C overnight and then in darkness for more than 3 days, followed by short-day condition (8h light and 16h dark at 22℃ and 28℃) for 10 days.

extract_protocol:
ChIP was performed as previously described (Yang et al., 2020).
The paired-end sequencing libraries were prepared from the DNA samples using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. Briefly, approximately 10ng of DNA was processed for end-repair followed by adaptor ligation as per the kit protocol. The ligated products were subjected to purification using NEBNext Sample purification beads. The purified products were PCR amplified with the index primer followed by AMPureXP bead purification. The PCR enriched libraries were analyzed on 4200 Tape Station system (Agilent Technologies) using D1000 Screen tape as per manufacturer instructions. After obtaining the Qubit concentration for the libraries and the mean peak sizes from Agilent Tape Station profile, the PE illumina libraries were loaded onto Novaseq6000 for cluster generation and sequencing.

treatment_protocol: Seedlings given ambient and elevated temperature treatments of 22 and 28℃.

value: Seedling

value: 10 days old seedlings

tag: antibody

value: temperature treatment


title: technical_control,1

description: Count matrix column name: Not included

tag: tissue


title: cardiomyocyte,TAC2w, replicate1-76, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

tag: cell type


title: bacteria in mineral water, day 7, replicate 3

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE - Université Paris-Saclay

data_processing:
Sequencing data was demultiplexed with bcl2fastq2 (v2.18.12, Illumina), adapters were trimmed with Cutadapt (v3.2), and only reads longer than 10bp were kept.
Alignment to the reference sequence of the L. monocytogenes EGDe (Genbank RefSeq NC_003210.1) was done using the Bowtie2 alignment tool version 2.4.4.
Stranded read counts per gene annotated in NC_003210.1 were obtained with featureCounts program included subread v2.0.1 (options “-p -Q 30 -s 2")
Relative library sizes were estimated on genes with a count of at least 5 in at least 3 out of the 6 samples using the robust estimation method implemented in DESeq2 v1.38.3.
Fragment counts normalised per kilobase of feature length per million mapped fragments (FPKM) were computed with DESeq2 based on relative library sizes.
Assembly: Genbank RefSeq NC_003210.1
Supplementary files format and content: tab-delimited text file
Supplementary files format and content: First five columns : location of the feature on NC_003210.1, source (Genbank or Listeriomics), locus tag,
Supplementary files format and content: Next six columns : raw counts for each sample
Supplementary files format and content: Last six columns : normalized expression levels (FPKM) for each sample

organism: Listeria monocytogenes EGD-e

source_name: planktonic cells (10^8 cells/mL)

growth_protocol:
Bacteria were grown overnight to stationary phase at 37°C in brain and heart infusion (BHI) broth (with agitation).
Cells were pelleted by centrifugation (3,000×g, 3min) and washed with sterile-filtered (0.22µm) mineral water for three times before resuspension in mineral water at a concentration of 10^8 CFU/ml.
Cells suspensions in mineral water were incubated statically at room temperature in an upright-standing, sterile tissue-culture flask (25cm2, vented cap).
Samples were collected immediately after preparation (“day0”) and after 7 days.

extract_protocol:
Total RNAs were recovered from bead-beaten bacterial cells using a phenol/chloroform extraction method.
The quality of RNA extracts was assessed in an Agilent Bioanalyzer 2100, using the RNA 6000 pico kit (Agilent Technologies).
Total RNAs (450ng) were treated with DNase (Baseline-ZERO DNase, Epicentre).
Library construction -including ribosomal RNA depletion- and sequencing was performed by I2BC sequencing facility (Gif-sur-Yvette).
Ribosomal RNA was removed using the Illumina Ribo-Zero Magnetic Kit (Bacteria), according to the manufacturer recommendations.
Directional RNA sequencing libraries were constructed using the TruSeq Stranded Total RNA Library Prep kit (Illumina), and library quality was assessed on an Agilent Bioanalyzer 2100, using the Agilent High Sensitivity DNA Kit (Agilent Technologies).
Libraries were pooled and sequenced in 2×75-bp paired-end runs on a NextSeq500 instrument, using a NextSeq500 High Output 150 cycles kit (Illumina).

treatment_protocol: Bacteria (10^9 cells) were harvested (5000×g, 3min) from mineral water suspensions and immediately flash-frozen in liquid nitrogen and stored at −80°C until further processing.

value: planktonic cells (10^8 cells/mL)

tag: treatment

value: suspension in mineral water, after seven day