title: 121420 HDC Sample 2

city: Baltimore

first: Joshua

middle: M

last: Popp

state: Maryland

address: 3100 Wyman Park Drive South Wing, Room S249

department: Biomedical Engineering

institute: Johns Hopkins University

description: 10X Genomics 3 scRNA-seq v3.1

data_processing:
CellRanger v5.0.1 was used to analyze single-cell expression and feature barcodes.
Vireo v0.5.6 was used for demultiplexing
scVI (v0.20.0) and UMAP embeddings were used for visualization, with scanpy v1.9.1
MCA embedding and Cell-ID (v1.6.0) were used for cell type annotation
scDRS (v1.0.2)  was used for trajectory isolation, and PCA for pseudotime inference
Leiden clustering was used for pseudocell assignment
FastTopics v0.6-142 was used for topic modeling based on aggregated pseudocell expression
Assembly: hg38
Supplementary files format and content: matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz
Supplementary files format and content: hdc_filtered_counts.h5ad is an anndata object containing raw gene expression for filtered cells, demultiplexed donor assignments for each cell, scVI and UMAP embeddings (used for visualization), an MCA embedding (used for cell type annotation), cell type labels, pseudotime labels for each of three trajectories, and pseudocell assignments (used for topic modeling)
Supplementary files format and content: pseudocell_topic_loadings.tsv is a tab-separated text file containing each pseudocell's topic loadings

source_name: Heterogeneous differentiating cultures

growth_protocol: We maintained feeder-free iPSC cultures on Matrigel Growth Factor Reduced Matrix with StemFlex Medium

extract_protocol:
HDCs were dissociated for collection 21 days after formation
10X Genomics 3’ scRNA-seq v3.1 kit

treatment_protocol: HDCs were formed using a modified version of the STEMCELL Agrewell400 protocol which was previously described in Rhodes et al. 2022.

value: Heterogeneous differentiating cultures


title: 121420 HDC Sample 3

status: Public on Jul 15 2024

type: SRA

country: USA

description: 10X Genomics 3 scRNA-seq v3.1

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type


title: RNAseq-DOX-OHT-N2

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

description: RNA-seq

library_source: transcriptomic

data_processing:
Basecalls were performed using bcl2fastq v1.1.0 (Illumina) and the quality of the generated FASTQ files was analysed with FastQC.
For mRNA sequencing, reads were aligned to the human genome (hg19/GRCh37) using STAR aligner v2.7.9a with default parameters and gene quantification (--quantMode GeneCounts). The output table with teh gene counts was futher analyzed in R v4.1.1 and processed with DESeq2 package according to the manual. Genes with at least 15 counts in at least 3 samples were kept in the counttable. All samples were then normalized by size factors.
Following read-normalization, the fold average for 3 independent biological replicates (N1, N2, N3) was calculated on treatment to control. Where applicable, the calculated fold-changes were averaged in 100 genes per bin for a total of 140 bins of 14085 genes.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file that includes the raw-counts for all 12 individual samples in a singel table. This count-table was used to carry out all further data-processing steps as outlined above.

molecule: total RNA

source_name: SH-EP NMYC-ER

growth_protocol: Human neuroblastoma derived SH-EP cells expressing an exogenous and 4-OHT inducible NMYC allele (SH-EP-NMYC-ER), were grown in RPMI-1640 medium supplemented with with 10% horse serum and 1% penicillin/ streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
For RNA sequencing, cells were harvested and total RNA was extracted with RNeasy MiniKit (Qiagen) according to manufacturer's instructions. On-column Dnase I digestion was performed followed by mRNA isolation with the NEBNext Poly(A) mRNA Magnetic Isolation Kit (NEB).
Library preparation was done with the NEBNext Ultra II Directional RNA Library Prep for Illumina (NEB) following the manufacturer's manual. Libraries were size-selected using SPRIselect beads (Backman-Coulter) after amplification with 9 PCR cycles using the NEBNext Multiplex Oligos for Illumina Kit (NEB). Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Sequencing was performed in paired-end mode on a NextSeq2000 platform (Illumina).

treatment_protocol: The indcution of NMYC in the SH-EP-NMYC-ER cells was achieved by adding 4-OHT (200 nM) for 4 hours. The expression of an shRNA targeting TF3C5 in the SHEP-NMYCER cells was induced with 1 µg/ml doxycycline for 48 hours.

value: SH-EP NMYC-ER

value: Neuroblastoma

tag: dox-treatment (shrna-tf3c5)

value: induced (shRNA expression)

tag: 4-oht treatment_(nmyc_expresion)

value: induced (NMYC expression)

tag: treatment with_inhibitor

value: not applicable

tag: biological replicate


title: RNA-Seq CD8_Memory_O_1

city: Brisbane

first: Christian

last: Nefzger

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Biology

country: Australia

institute: The University of Queensland

data_processing:
Demultiplexed single end reads per sample here presented were mapped to the mouse GRCm38.p6/mm10 genome primary assembly using Spliced Transcripts Alignment to a Reference (STAR) software version 2.5.2b (Dobin et al. Bioinformatics 2013; https://doi.org/10.1093/bioinformatics/bts635). STAR was run with mode alignReads with parameters “--outFileterMatchMinOverLred 0.3 --outFilerScoreMinOverLread 0.3 --twopassMode Basic –sjdbGTFfile –quanMode GeneCounts”. Reads with duplicated UMIs were removed using the software Je version 2.0.RC option markdupes (Girardot et al. BMC Bioinformatics, 2016; https://doi.org/10.1186/s12859-016-1284-2). Transcript quantification was performed using featureCounts version 2.0.1 with parameters “–Q10 -M" (exonic regions of GENCODE’s vM24 annotation version) (Liao et al. NAR 2019; https://doi.org/10.1093/nar/gkz114).
Assembly: mm10
Supplementary files format and content: (.txt) counts

organism: Mus musculus

source_name: Spleen

growth_protocol: The tissues of 5 healthy animals were pooled per-replicate for cell isolation, with 3-5 replicates (totalling 15-25 animals) collected per cell type/condition. Multi-omic bulk profiling (OMNI-ATAC-seq assay and RNA-seq) was performed on purified populations collected via fluorescence activated cell sorting (FACS).

extract_protocol:
RNA-seq
Poly-A based RNA sequencing libraries were generated as described by us (Sun et al.  Nat Comms 2021;  https://doi.org/10.1038/s41467-021-22863-0.). In brief, a 3-prime biased approach was used to generate sequencing libraries. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template-switching oligonucleotide. The Illumina P5 (5′-AAT GAT ACG GCG ACC ACC GA-3′) and P7 (5′-CAA GCA GAA GAC GGC ATA CGA GAT-3′) sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilises a custom primer (5′-GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C-3′) to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) uses the standard R2 primer to sequence the cDNA in the sense direction for transcript identification.
For RNA sequencing, a 3-prime biased approach was used to generate sequencing libraries as described previously (Sun et al.  Nat Comms 2021;  https://doi.org/10.1038/s41467-021-22863-0.). Barcoded 19bp R1 and 111bp R2 paired-end reads per sequencing lane were assigned to individual samples using the sabre software (version 80faf94) with options “-u –m2 –l 10’ (https://github.com/najoshi/sabre) (Tsyganov et al. JOSS 2018; https://doi.org/10.21105/joss.00583).

value: Spleen

value: CD8 Memory

tag: genotype

value: C57/Bl6 background

tag: treatment

value: 22-24 months


title: 120920 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: 120920 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: 121420 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq CD4_Naive_Y_4

value: CD4 Naive

value: 2 months


title: RNA-Seq CD4_Naive_Y_3


title: RNAseq-EtOH-OHT-N2

description: RNA-seq

value: uninduced (no shRNA expression)


title: M07e_JAK3Q988P_PIM447_biol rep 3

city: Madrid

first: Maria

last: Villa-Morales

email: maria.villa@uam.es, mvilla@cbm.csic.es

state: Madrid

address: Nicolas Cabrera 1

department: Biology

country: Spain

institute: UNIVERSIDAD AUTONOMA DE MADRID

data_processing:
Paired-end sequencing (2x100bp) of the previously enriched, indexed and multiplexed libraries were performed on the high-throughput NovaSeq 6000 platform (Illumina Inc.), with a minimum of 100M PE reads (50+50) per sample, with a read quality of 85%>Q30. For bioinformatics analysis, GRCh38/hg38 (Ensembl version 103) genome was used as a reference. Briefly, quality check and sequence trimming were performed using FASTQC and fastp5 respectively. Then, the trimmed RNA-seq reads were aligned against the reference genome and the transcripts were assembled using HISAT2 tool6. Corresponding genes were obtained and their expression abundance was determined using StringTie suite (https://ccb.jhu.edu/software/stringtie/). On gene counting matrices, reads were subjected to unsupervised filtering in order to discard those genes with very few or no reads throughout all the samples of the study (https://bioconductor.org/packages/release/bioc/html/genefilter.html). Genes with a total abundance below 15 reads were excluded from further analysis.
Assembly: GRCh38/hg38,  Ensembl version 103
Supplementary files format and content: csv file with raw counts of sequencing reads for each sample

source_name: peripheral blood

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quantification and quality were checked by Nanodrop (Thermo Fisher Scientific Inc.), Qubit (Thermo Fisher Scientific Inc) and TapeStation (Agilent Technologies).
Using the TruSeq Stranded Total RNA Library Prep (Illumina, Inc.) and included rRNA depletion, fragmentation, cDNA synthesis and adaptor ligation. The generated libraries were normalized and combined in equimolecular concentrations for optimal generation of DNA clusters.

value: peripheral blood

value: M07e cell line

value: acute megakaryoblastic leukemia

value: expressing JAK3 Q988P

value: treated with 1 µM PIM447 (Selleckchem #LGH44) for 24h


title: RNAseq-EtOH-EtOH-N2

description: RNA-seq

value: SH-EP NMYC-ER

value: uninduced (no NMYC expression)


title: 111920 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1

value: Heterogeneous differentiating cultures


title: 120920 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: RNAseq-DOX-OHT-N1

description: RNA-seq

value: Neuroblastoma

value: induced (shRNA expression)

value: induced (NMYC expression)


title: RNA-Seq CD4_Naive_Y_2

value: Spleen


title: RNAseq-DOX-EtOH-N1

description: RNA-seq

value: not applicable


title: 111620 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1


title: 111620 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1


title: RNAseq-EtOH-EtOH-N3

description: RNA-seq


title: RNA-Seq CD4_Naive_Y_1

value: C57/Bl6 background


title: 111920 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: RNAseq-DOX-EtOH-N2

description: RNA-seq


title: 111620 HDC Sample 7

description: 10X Genomics 3 scRNA-seq v3.1


title: 111620 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: 111620 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: 120920 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: 111620 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: 111920 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: 111620 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: 111220 HDC Sample 7

description: 10X Genomics 3 scRNA-seq v3.1


title: 111220 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq CD4_Memory_Y_5

value: CD4  Memory


title: RNAseq-EtOH-EtOH-N1

description: RNA-seq


title: RNA-Seq CD4_Naive_O_2

value: CD4 Naive

value: 22-24 months


title: RNA-Seq CD4_Naive_O_3


title: RNAseq-EtOH-OHT-N1

description: RNA-seq

value: uninduced (no shRNA expression)


title: RNA-Seq CD4_Memory_Y_4

value: 2 months


title: RNA-Seq CD4_Memory_Y_3


title: 111220 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPRx-RNAPII-unp-Merged-Input-N2

description: ChIP-Rx-seq

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v1.1.0 (Illumina) and the quality of the generated FASTQ files was analysed with FastQC.
For Cut&Run sequencing, ChIP-seq and ChIP-Rx sequencing, reads were aligned to the human genome (hg19/GRCh37) using Bowtie2 v2.3.5.1 with default parameters. Normalization by aligned read number was performed on the input and on all correspondent IP samples. Where applicable, the number of spike-in normalized reads per sample was calculated by dividing the number of reads mapping exclusively to hg19 by the number of reads mapping exclusively to mm10 and multiplying this number with the smallest number of reads mapping to mm10 of all samples.
Following read-normalization, files were converted to bedGraph with bedtools genomecov v2.26 and visualized in a genome browser using the package plotgardener v1.012 in R v4.1.1. MACS2 v2.1.2 was used for peak calling for MYCN, TF3C5 and RAD21. H3K4me1, H3K4me3 and H3K27ac peaks were called with SICER v1.1.
Assembly: hg19
Supplementary files format and content: For CUT&RUN-seq, ChIP-seq and ChIP-Rx sequencing, the provided processed files are bedGraph files for data display in a genome browser.

molecule: genomic DNA

extract_protocol:
For Cut&Run sequencing, cells were harvested with Accutase, washed and then coupled to ConA-coated magentic beads (Polysciences Europe). Cells were then permeabilized and incubated with the primary antibody (EXOSC5 #NBP2-14952; 1:100 diluted; Novus Biologicals) in antibody binding buffer over night at 4°C. Cells were then washed in the presence of digitonin and 700 ng/ml MNase was added per sample for 1 hour at 4°C.
For Cut&Run sequencing samples, the MNase treated cells were washed with low-salt rinse buffer. Incubation buffer, containing CaCl2 and digitonin, was added for 30 min at 4°C. The Mnase activity was stoped in the presence of 20 µg/ml Rnase A. DNA fragments were released at 37°C for 30 min and the decrosslinking was done for 1 hour at 50°C by adding 0.01% SDS and 10 mg/ml Proteinase K. DNA was extracted wit phenol-chloroform and resuspended in TE buffer.
For ChIP-seq and ChIP-Rx sequencing, cells were fixed for 5 min at RT with 1% formaldehyde and harvested in cold PBS contianing protease and phosphatase inhibitors. For ChIP-Rx samples, murine NHO2A or NIH3T3 cells were added at a 1:10 cell ratio during cell lysis to serve as an exogenous control (spike-in). Cell lysis was done for 20 min in PIPES buffer containing 85 mM KCl and 0.5% NP-40, followed by collection of nuclei by centrifugation.
For ChIP-seq and ChIP-Rx sequencing, the crosslinked chromatin was extracted from the nuclei in TRIS buffer with 150 mMCaCl, 1 mM EDTA and 1% NP-40, 1% sodium deoxycholate and 0.1% SDS. The chromatin was fragmented using the Covaris Focused Ultrasonicator M220 for 50 min. Dynabeads Protein A and Protein G were pre-incubated overnight with 10-15 µg antibody in the presence of 5 mg/ml BSA.
For ChIP-seq and ChIP-Rx sequencing, chromatin was added to the pre-incubated beads for at least 6h at 4°C with rotation. Beads were then washed with different TRIS buffers containing distinct salt-concentrations, EDTA and detergents, followed by wahsing with only TE-buffer. Chromatin was eluted with 100mM NaHCO3 and 1% SDS for 15 min. Protein and RNA were digested with proteinase K and RNase A. DNA was isolated by phenol-chloroform extraction followed by an ethanol precipitation. DNA was quantified using the Quant-IT PicoGreen dsDNA assay.
The DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. Pre-PCR samples were purified and/or size-selected using AMPureXP beads. The libraries were PCR-amplified with the NEBNext Multiplex Oligos for Illumina Kit and again purified using Agencourt AMPure XP beads (Beckman Coulter). Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Sequencing was performed in single-read or paired-end mode on a NextSeq500 or NextSeq2000 platform (Illumina).
ChIP, ChIP-Rx and CUT&RUN followed by sequencing.

treatment_protocol:
The indcution of NMYC in the SH-EP NMYC-ER cells was achieved by adding 4-OHT (200 nM) for 4 hours. The expression of an shRNA targeting TF3C5 in the SHEP-NMYCER cells was induced with 1 µg/ml doxycycline for 48 hours. Where indicated, SH-EP NMYC-ER cells were treated with DRB (100 µM) for 2 hours.
For ChIP-Rx samples, an exogenous control (spike-in) was used. For that purpose, murine NHO2A or NIH3T3 cells were added at a 1:10 cell ratio to the samples during the cell lysis step.

tag: cell cycle_synchronization

value: unsynchronized

value: merge of samples

tag: spike-in

value: murine cells

tag: chip antibody


title: RNA-Seq CD4_Naive_O_1


title: 110920 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1


title: 110920 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: 111220 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq CD4_Memory_O_5


title: 111220 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: spLHiChIP-MYCN-DOX-OHT-N1

description: spLHiChIP-seq

data_processing:
Basecalls were performed using bcl2fastq v1.1.0 (Illumina) and the quality of the generated FASTQ files was analysed with FastQC.
For pLHi-C, pLHiChIP and spLHiChIP sequencing reads, the program HiC-Pro v2.11.4 was used to trim linker sequences, align to hg19, filter by DpnII restriction fragments and carry out qualtiy controls. HiC-Pro was also used to generate valid pairs outputs (bedpe files). For pLHi-C, the program HiC-Pro was further used to build contact maps and to transform those into HIC format (hic files).
For spLHiChIP, a spike-in (mouse; mm10) normalization was done. The number of spike-in normalized reads per sample was calculated by dividing the number of reads mapping exclusively to hg19 by the number of reads mapping exclusively to mm10 and multiplying this number with the smallest number of reads mapping to mm10 of all samples. For spLHiChIP and pLHiChIP valid pairs, DNA loops were called using the program hichipper v0.7.7.
Assembly: hg19 (GRCh37) and mm10
Supplementary files format and content: For pLHi-C, the provided processed files are hic files for display and further analysis of contact maps. For pLHiChIP and spLHiChIP sequencing experiments, the provided processed files are bedpe files used to describe pairs of genomic regions.

extract_protocol:
For phosphorylated linker Hi-C (pLHi-C), phosphorylated linker HiChIP (pLHiChIP) and spike-in phosphorylated linker HiChIP (spLHiChIP), cells were cross-linked with 1% formaldehyde for 5 min and stopped by adding 125 mM glycine for 10 min at room temperature. Nuclei were isolated and a one-step in situ digestion and dephosphorylation took place by using DpnII and rSAP enzymes. During the nuclei isolation step, only for the spLHiChIP samples, murine NHO2A cells were added as exogenous control (spike-in) at a 1:20 cell ratio. Next, biotinylated oligos with 5’ end phosphate were used with T4 ligase for the ligation step.
Chromatin fragmentation was performed using the Covaris Focused Ultrasonicator M220 for 30 min per ml lysate. Samples were de-crosslinked overnight and Protein and RNA were digested with proteinase K and RNase A. DNA was isolated using ChIP DNA Clean & Concentrator (Zymo Research). Biotin pull-down was performed with MyOne Streptavidin C1 beads (Thermo Fisher Scientific) according to manufacturer’s instructions.
Only for pLHiChIP and spLHiChIP samples, the chromatin fragmentation was followed by an immunoprecipitation of the target protein. To this end, Dynabeads Protein A and Protein G were pre-incubated overnight with 10-15 µg antibody in the presence of 5 mg/ml BSA. Next, chromatin was added to the pre-incubated beads for at least 6h at 4°C with rotation. Beads were then washed with different TRIS buffers containing distinct salt-concentrations, EDTA and detergents, followed by wahsing with only TE-buffer.
The immunoprecipitated chromatin of the pLHiChIP and spLHiChIP samples was eluted with 100mM NaHCO3 and 1% SDS for 15 min. Eluted samples were de-crosslinked overnight. DNA was isolated using ChIP DNA Clean & Concentrator (Zymo Research). Biotin pull-down was performed with MyOne Streptavidin C1 beads (Thermo Fisher Scientific) according to manufacturer’s instructions.
Library preparation was the same for all samples and was done on beads using the NEBNext ChIP-Sequencing Library Prep Master Mix Set for Illumina (NEB) according to manufacturer's instrcutions. The only deviation from the instructions was an additional washing step between each module using a Tris-buffer with 0.5 mM EDTA, 1 M NaCl and 0.05% Tween followed by a washing step with only TE buffer. Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Sequencing was performed in single-read or paired-end mode on a NextSeq500 or NextSeq2000 platform (Illumina).
pLHi-C sequencing (Illumina NextSeq500) and (s)pLHiChIP sequencing (Illumina NextSeq500 or NextSeq2000)

treatment_protocol:
The indcution of NMYC in the SH-EP-NMYC-ER cells was achieved by adding 4-OHT (200 nM) for 4 hours. The expression of an shRNA targeting TF3C5 in the SHEP-NMYCER cells was induced with 1 µg/ml doxycycline for 48 hours. Where indicated, SH-EP-NMYC-ER cells were treated with MLN8237 (1 µM) or DRB (100 µM) for 2 hours.
For spike-in phosphorylated linker HiChIP (spLHiChIP) samples, an exogenous control (spike-in) was used. For that purpose, murine NHO2A cells were added at a 1:20 cell ratio to the samples during the nuclei isolation step.

value: SH-EP NMYC-ER

value: MYCN (B8.4.B) (sc-53993; Santa Cruz)


title: 111220 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1

value: Heterogeneous differentiating cultures


title: spLHiChIP-MYCN-EtOH-OHT-N2

description: spLHiChIP-seq

value: Neuroblastoma


title: 111220 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPRx-RNAPII-unp-DOX-OHT-N2

description: ChIP-Rx-seq

value: induced (shRNA expression)

value: Pol2 (8WG16) (sc-56767; Santa Cruz)


title: RNA-Seq CD4_Memory_O_4

value: Spleen


title: RNA-Seq CD4_Memory_O_3


title: 110920 HDC Sample 8

description: 10X Genomics 3 scRNA-seq v3.1


title: 110520 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1


title: 110920 HDC Sample 7

description: 10X Genomics 3 scRNA-seq v3.1


title: 110920 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq CD4_Memory_O_2


title: 110520 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq CD4_Memory_Y_2


title: spLHiChIP-MYCN-EtOH-OHT-N1

description: spLHiChIP-seq

value: induced (NMYC expression)

value: not applicable


title: spLHiChIP-MYCN-DOX-OHT-N2

description: spLHiChIP-seq


title: RNA-Seq CD4_Memory_Y_1

value: CD4  Memory

value: C57/Bl6 background


title: ChIPRx-RNAPII-unp-Merged-Input-N1

description: ChIP-Rx-seq


title: RNA-Seq CD4_Memory_O_1

value: 22-24 months


title: ChIPRx-RNAPII-unp-EtOH-OHT-N2

description: ChIP-Rx-seq

value: uninduced (no shRNA expression)


title: 110920 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: 110220 HDC Sample 7

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPRx-RNAPII-unp-EtOH-OHT-N1

description: ChIP-Rx-seq


title: 110520 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: 110920 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: 110220 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPRx-RNAPII-unp-EtOH-EtOH-N2

description: ChIP-Rx-seq

value: uninduced (no NMYC expression)


title: RNA-Seq Brain_endothelial_Y_3

source_name: Brain

value: Brain

value: Brain endothelial

value: 2 months


title: 110520 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPRx-RNAPII-unp-DOX-EtOH-N2

description: ChIP-Rx-seq

value: SH-EP NMYC-ER

value: unsynchronized

value: murine cells


title: 110220 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1

value: Heterogeneous differentiating cultures


title: 110220 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq Brain_endothelial_Y_1


title: 110520 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: 110520 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: 110520 HDC Sample 7

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPRx-TF3C5-Merged-Input

description: ChIP-Rx-seq

value: Neuroblastoma

value: merge of samples


title: 102920 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq Brain_endothelial_Y_4


title: 110220 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1


title: 102920 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq Brain_endothelial_O_4


title: ChIPRx-RNAPII-unp-DOX-EtOH-N1

description: ChIP-Rx-seq

value: induced (shRNA expression)

value: Pol2 (8WG16) (sc-56767; Santa Cruz)


title: RNA-Seq Brain_endothelial_O_2


title: RNA-Seq Brain_endothelial_O_1


title: 102920 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPRx-RNAPII-unp-DOX-OHT-N1

description: ChIP-Rx-seq

value: induced (NMYC expression)

value: not applicable


title: RNA-Seq Brain_endothelial_O_3

value: C57/Bl6 background


title: 110220 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: 102920 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPRx-TF3C5-EtOH-DRB

description: ChIP-Rx-seq

value: DRB (Benzimidazole; RNAPII CTD kinase inhibitor)

value: TFIIIC5 (A301-242A; Bethyl Laboratories)


title: 110220 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq Beta-cells_Y_5

source_name: Pancreas

value: Pancreas

value: Beta cells


title: ChIPRx-TF3C5-OHT-DMSO

description: ChIP-Rx-seq

value: DMSO


title: 102620 HDC Sample 7

description: 10X Genomics 3 scRNA-seq v3.1


title: 102620 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPRx-RNAPII-unp-EtOH-EtOH-N1

description: ChIP-Rx-seq

value: uninduced (no shRNA expression)

value: uninduced (no NMYC expression)


title: 102620 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1


title: 102620 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1


title: 102620 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPseq-RNAPII-S-Merged-Input

description: ChIP-seq

value: SH-EP NMYC-ER

value: S-phase synchronized


title: 111920 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1

value: Heterogeneous differentiating cultures


title: 102220 HDC Sample 8

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPseq-RNAPII-A10-S-OHT

description: ChIP-seq

value: Neuroblastoma

value: RNAPII (A-10) (sc-17798; Santa Cruz)


title: 102920 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq Beta-cells_Y_1

value: 2 months


title: 102620 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPRx-TF3C5-OHT-DRB

description: ChIP-Rx-seq

value: unsynchronized

value: murine cells


title: RNA-Seq Beta-cells_Y_3


title: RNA-Seq Beta-cells_O_4

value: 22-24 months


title: 102620 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: CnR-EXOSC5-DOX-OHT

description: CUT&RUN-seq

value: induced (shRNA expression)

value: induced (NMYC expression)

value: not applicable

value: EXOSC5 (Novus Biological #NBP2-14952)


title: 102220 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: 102920 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq Beta-cells_O_3

value: Pancreas

value: Beta cells

value: C57/Bl6 background


title: 102220 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: CnR-EXOSC5-Merged-IgG

description: CUT&RUN-seq

value: merge of samples

value: IgG (control)


title: 102220 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1


title: ChIPRx-TF3C5-EtOH-DMSO

description: ChIP-Rx-seq

value: SH-EP NMYC-ER

value: uninduced (no NMYC expression)

value: DMSO

value: TFIIIC5 (A301-242A; Bethyl Laboratories)


title: 102220 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1

value: Heterogeneous differentiating cultures


title: 101920 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1


title: 102220 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq Beta-cells_Y_4

value: 2 months


title: 101920 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq Beta-cells_O_2


title: CnR-EXOSC5-DOX-EtOH

description: CUT&RUN-seq

value: Neuroblastoma

value: unsynchronized


title: RNA-Seq Beta-cells_O_1

value: 22-24 months


title: RNA-Seq B-cells_Y_4

source_name: Bone Marrow

value: Bone Marrow

value: B-cells


title: 101920 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: CnR-EXOSC5-EtOH-OHT

description: CUT&RUN-seq

value: uninduced (no shRNA expression)

value: induced (NMYC expression)

value: not applicable

value: EXOSC5 (Novus Biological #NBP2-14952)


title: RNAseq_Apar_Isolate9257

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Enzymatic Methyl-seq: All reads were filtered and trimmed with fastp using default parameters. Then the trimmed reads mapped to the reference genome (including a lambda phage and pUC19 sequences as negative and positive controls) using BS-Seeker2 backed with bowtie2. Sambamba (markdup) was used to remove PCR duplicates and CGmapTools was used to obtain the methyl calls, resulting in the CGmap files in this repository. More information on this file format here: https://github.com/BSSeeker/BSseeker2.
RNA-seq: All reads were filtered and trimmed with fastp. To obtain TPMs, we used Kallisto (0.46) against the reference mRNA annotation using default parameters. To obtain a counts file we first used HISAT2 allowing multimapping reads, and then used the TElocal pipeline to obtain counts from the bam files. De novo transcriptome assemblies were obtained using Trinity-v2.8.5 using stranded information and the jaccard_clip option.
Assembly: For all the Amoebidium appalachense experiments, the data was mapped to the reference genome that can be found in ENA number ERZ21989579. Sphaerforma assembly is found here: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_008580545.1/. Creolimax fragrantissima assembly is found here: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002024145.1/. Chromosphaera perkinsii genome can be found here: https://figshare.com/articles/dataset/Genome_-_Chromosphaera_perkinsii/5426494.
Supplementary files format and content: CGmap files are the direct output from CGmapTools / BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain:  (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C /
Supplementary files format and content: Counts / TPM matrixes contain the reads count obtained from the TEcount pipeline (https://github.com/bodegalab/tecount) or the TPMs obtained from Kallisto. Trinity fasta files are the de novo transcriptome assembly for each RNA-seq library.

organism: Amoebidium parasiticum

growth_protocol: Amoebidium isolates were grown on Brain Heart Infusion (10% BHI, ThermoFisher CM1135) liquid media at 25°C in 25 mL culture flasks. Sphaeroforma arctica, Creolimax fragrantissima, and Chromosphaera perkinsii were grown in liquid Marine Broth (Difco™ Marine Broth 2216) at 17°C.

extract_protocol:
Nitrogen liquid grinding followed by NEB Monarch Genomic DNA Purification Kit was used to extract the DNA of all samples. RNA was extracted using the Monarch Total RNA Miniprep Kit.
We used 200 ng of RNA from the samples to build mRNA-seq libraries, first enriching for poly-A transcripts with the NEB Magnetic mRNA Isolation Kit S1550S, and then building the libraries with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L) according to manufacturer's instructions.

treatment_protocol: Amoebidium appalachense DNA and RNA were extracted from cultures grown for 3 days in 10ml 10% BHI with 1% DMSO, and 1% DMSO with 100µM of 5-Azacytidine/Zebularine/Decitabine, in triplicate. Sphaeroforma arctica DNA was extracted from cultures grown for 3 days in 10ml Marine Broth with 1% DMSO and 1% DMSO with 100 µM 5-Azacytidine in duplicate.

tag: strain

value: Axenic culture

tag: growth conditions

value: Brain Heart Infusion (10% BHI, ThermoFisher CM1135) liquid media at 25C

tag: library type

value: mRNA-seq

tag: time

value: 3 days culture


title: 102220 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1


title: 101920 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: 101920 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq B-cells_Y_2

value: C57/Bl6 background


title: RNAseq_Apar_Isolate9182


title: 102220 HDC Sample 7

description: 10X Genomics 3 scRNA-seq v3.1


title: 101520 HDC Sample 7

description: 10X Genomics 3 scRNA-seq v3.1


title: 101520 HDC Sample 8

description: 10X Genomics 3 scRNA-seq v3.1


title: EMseq_Cfra_control

data_processing:
Enzymatic Methyl-seq: All reads were filtered and trimmed with fastp using default parameters. Then the trimmed reads mapped to the reference genome (including a lambda phage and pUC19 sequences as negative and positive controls) using BS-Seeker2 backed with bowtie2. Sambamba (markdup) was used to remove PCR duplicates and CGmapTools was used to obtain the methyl calls, resulting in the CGmap files in this repository. More information on this file format here: https://github.com/BSSeeker/BSseeker2.
RNA-seq: All reads were filtered and trimmed with fastp. To obtain TPMs, we used Kallisto (0.46) against the reference mRNA annotation using default parameters. To obtain a counts file we first used HISAT2 allowing multimapping reads, and then used the TElocal pipeline to obtain counts from the bam files. De novo transcriptome assemblies were obtained using Trinity-v2.8.5 using stranded information and the jaccard_clip option.
Assembly: For all the Amoebidium appalachense experiments, the data was mapped to the reference genome that can be found in ENA number ERZ21989579. Sphaerforma assembly is found here: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_008580545.1/. Creolimax fragrantissima assembly is found here: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002024145.1/. Chromosphaera perkinsii genome can be found here: https://figshare.com/articles/dataset/Genome_-_Chromosphaera_perkinsii/5426494.
Supplementary files format and content: CGmap files are the direct output from CGmapTools / BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain:  (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C /
Supplementary files format and content: Counts / TPM matrixes contain the reads count obtained from the TEcount pipeline (https://github.com/bodegalab/tecount) or the TPMs obtained from Kallisto. Trinity fasta files are the de novo transcriptome assembly for each RNA-seq library.
Library strategy: Enzymatic Methyl-seq

organism: Creolimax fragrantissima

extract_protocol:
Nitrogen liquid grinding followed by NEB Monarch Genomic DNA Purification Kit was used to extract the DNA of all samples. RNA was extracted using the Monarch Total RNA Miniprep Kit.
Enzymatic Methyl-seq samples were performed as per manufacturer's instructions (https://www.neb.com/en-gb/products/e7120-nebnext-enzymatic-methyl-seq-kit) starting from 100 ng of DNA, after sonicating DNA to 300 bp fragments with a Covaris M220.

value: Liquid Marine Broth (Difco™ Marine Broth 2216) at 17C

value: Enzymatic Methyl-seq


title: RNA-Seq B-cells_Y_3

value: 2 months


title: 101920 HDC Sample 7

description: 10X Genomics 3 scRNA-seq v3.1

value: Heterogeneous differentiating cultures


title: RNA-Seq B-cells_Y_5


title: 101520 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1


title: 101520 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1


title: EMseq_Cper_control

organism: Ichthyosporea sp. XGB-2017a

source_name: Ruiz-Trillo Laboratory

value: Ruiz-Trillo Laboratory


title: CnR-EXOSC5-EtOH-EtOH

description: CUT&RUN-seq

value: SH-EP NMYC-ER

value: Neuroblastoma

value: unsynchronized

value: uninduced (no NMYC expression)


title: RNA-Seq B-cells_Y_1

value: Bone Marrow

value: B-cells


title: 101920 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: 101520 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: 101520 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: RNAseq_Sarc_DMSO_rep2

description: In the counts table, column named DMSO2

organism: Sphaeroforma arctica

value: 1% DMSO


title: RNA-Seq B-cells_O_4

value: 22-24 months


title: Wt, INPUT, IP2, Rep1

city: Pittsburgh

first: Karen

last: Arndt

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Fastq files were demultiplexed and aligned to a hybrid K. lactis - S. cerevisiae genome using bowtie2
The resultant sam files were converted to bam and duplicates removed with Picard
Samtools counts of spike-in and sample and bam reads generated counts for Spike-in normalization factors using the inverse counts per-million method
Bam files were normalized and converted to bigwig using deeptools
Assembly: S. cerevisiae: Ensembl R64-3-1/K.lactis: ASM251v1 Hybrid Genome
Supplementary files format and content: spike-in normalized bigwig for IPs or unnormalized bigwigs for inputs

organism:
Saccharomyces cerevisiae
Kluyveromyces lactis

source_name: MATa his4-912δ lys2-128δ leu2Δ1 trp1Δ63 RPB3-3XSer2P::KANMX

growth_protocol: S. cerevisiae and S. pombe were grown in YPD standard rich growth medium supplemented with 400 μM tryptophan at 30°C.

extract_protocol:
Chromatin was fragmented using a Bioruptor® (Diagenode B01060010) with 25 cycles of 30 sec on and 30 sec off at 4°C.
Libraries were built using the NEBNext® Ultra™ II DNA Library Prep Kit (Illumina #E7645S/L) with 1.5 ng of immunoprecipitated or input DNA

treatment_protocol: Yeast cultures were grown to OD600 = 1-1.2 at 30°C. At the time of harvest, cells were fixed with 1% v/v formaldehyde for 20 min at room temperature after 30 min of treatment with 1:1000 v/v vehicle (DMSO) or auxin (final concentration of 500 μM in DMSO) if necessary. Fixation was quenched for 5 min with a 37.5 mL of 3M glycine and 20 mM Tris solution, the culture pelleted at 4,000 rpm at 4°C, and pellets were washed twice in TBS before snap freezing in liquid nitrogen.

tag: time (min)


title: Wt, INPUT, IP2, Rep2


title: RNAseq_Sarc_DMSO_rep1

description: In the counts table, column named DMSO1


title: RNA-Seq B-cells_O_3

tag: tissue


title: Wt, antiSer2P, IP2, Rep2

tag: cell line


title: RNAseq_Sarc_Aza_rep2

description: In the counts table, column named Aza2

value: 1% DMSO and 100uM 5-Azacytidine


title: RNA-Seq B-cells_O_2

tag: cell type


title: Wt, antiSer2P, IP2, Rep1


title: 101520 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: 101520 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq B-cells_O_1

source_name: Visceral Fat

value: Visceral Fat

value: Adipocytes


title: 101220 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1


title: ctr9D, INPUT, IP2, Rep1

source_name: MATα his4-912δ lys2-128δ leu2Δ1 trp1Δ63 RPB3-3XSer2P::KANMX ctr9∆::KANMX


title: ctr9D, INPUT, IP2, Rep2


title: RNAseq_Sarc_Aza_rep1

description: In the counts table, column named Aza1

value: mRNA-seq

value: 3 days culture


title: treat3: myocardial ischemia-reperfusion injury

city: zhengzhou

first: jing

last: xu

address: Jianshe East Road

country: China

institute: The First Affiliated College of Zhengzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: myocardial ischemia-reperfusion injury

extract_protocol:
Take the intervertebral disc of mice, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: myocardial ischemia-reperfusion injury

value: Retina


title: RNA-Seq Adipocytes_Y_2

value: C57/Bl6 background

value: 2 months


title: RNA-Seq Adipocytes_Y_3


title: 101220 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1

value: Heterogeneous differentiating cultures


title: RNA-Seq Adipocytes_Y_1


title: ctr9D, antiSer2P, IP2, Rep2


title: EMseq_Sarc_control

value: Axenic culture

value: Liquid Marine Broth (Difco™ Marine Broth 2216) at 17C

value: Enzymatic Methyl-seq


title: treat1: myocardial ischemia-reperfusion injury


title: ctr9D, antiSer2P, IP2, Rep1


title: 101220 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: Ctr9, Veh, INPUT, IP2, Rep2

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ1 ura3-52 RPB3-3XSer2P::KANMX CTR9-V5-IAA7(AID)::KANMX


title: RNA-Seq Adipocytes_O_5


title: control3: Wild type

source_name: Wild type

value: Wild type


title: RNA-Seq Adipocytes_O_4


title: 101220 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: RNA-Seq Adipocytes_O_3


title: Ctr9, Veh, antiSer2P, IP2, Rep2


title: control1: Wild type


title: RNA-Seq Adipocytes_O_2


title: Ctr9, Veh, antiSer2P, IP2, Rep1


title: RNA-Seq Adipocytes_O_1


title: Ctr9, Aux, INPUT, IP2, Rep2

value: 1:1000 v/v 0.5 M Auxin in DMSO


title: 100820 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: Ctr9, Aux, INPUT, IP2, Rep1


title: 101220 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: 100820 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: 999_HCP MOUSE 1 lane7950_ATCACGTT_999_HCP

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

institute: Peter MacCallum Cancer Centre

description: 999_HCP MOUSE 1

data_processing:
Standard Illumina base-calling pipelines using bcl2fastq v2.20 were used to make fastqs.
The first 8 bp of Read 2 fastqs were removed and written into the readID of both reads as an in-line barcode, or UMI (Unique Molecular Identifier) using TrimGalore v0.6.6 with --implicon --paired flags.
Demuliplexed fastqs were then re-processed using TrimGalore v0.6.6 in paired-end mode (--paired) using default parameters.
Alignments were carried out with Bismark v0.14.4 using the GRCm38.v5 reference genome. CpG methylation calls were extracted from the mapping output using the Bismark methylation extractor. Deduplication was then carried out with deduplicate_bismark, using the --bacode option to take UMIs into account (see above)).
For allele specific analyses the data was aligned to a hybri/N-masked genome of Black6/CAST (the genome was prepared with the SNPsplit package v0.3.4). Following the same alignment and deduplication in Bismark as above, reads were split allele-specifically with SNPsplit v0.3.4, followed by use of the Bismarck methylation extractor.
Assembly: GRCm38.v5
Supplementary files format and content: The excel spreadsheet "IMPLICON_processed_data.xlsx" contains locus and allele specific methylation information. Rows indicate the CpG location within the IMPLICON locus and columns indicate the individual sample. Values indicate methylation percentage (0-100%) of the CpG or can represent the the deduplicated read counts at each locus in each sample.

source_name: Hippocampus

growth_protocol: Reciprocal crosses between BL6 and CAST strains of mice - BL6/CAST (BL6 female and CAST male) and CAST/BL6 (CAST female and BL6 male) were established to generate F1 animals. Mice were maintained under normal conditions:five per cage in a temperature- and humidity-controlled room (24°C, 45-65%) with a 14/12hr light/dark cycle.

extract_protocol:
Genomic DNA was isolated using the Nucleo Spin TriPrep kit (Macherey-Nagel GmbH & Co.KG, Germany) according to manufacturer’s instructions. 1μg of genomic DNA was bisulfite converted using the EZ DNA methylation Gold kit (Zymo Research) according to manufacturer’s instructions with either magnetic bead or column clean-up and eluted/resuspended in 66μl elution buffer to obtain a final concentration of ^~15ng/μl bisulfite converted DNA.
The IMPLICON protocol consists of 2 PCR reactions. In the first reaction each sample is amplified with each primer pair in individual reactions: 30ng (2μl of 66μl eluted bisulfite treated DNA) of bisulfite treated DNA is amplified with 1.2μl of 10μM primer pool (final 1.5μM) containing both forward and reverse primers in 4μl of 2x KAPA HiFi Uracil+ ReadyMix in a final volume of 8μl. DNA was amplified using the following conditions: initial denaturation at 95°C for 5min, 30 cycles of 98°C denaturation for 20 seconds, variable annealing temperature for 15 seconds and extension at 72°C for 60 seconds; followed by a final extension at 72°C for 10 minutes. All PCR reactions for each individual sample were pooled together and samples cleaned-up using 1.5x AMPure XP beads and eluted in 20μl H2O. In the second PCR reaction, barcoded Illumina adapters are attached to the pooled PCR samples ensuring that each sample pool receives a unique reverse barcoded adapter. The 20μl PCR pool was amplified using 1μl of 10μM Illlumina PE1.0 primer (same for all samples) and 1μl of 10μM Illumina iTAG primer (distinct for each sample) and 25μl 2x KAPA HiFi Uracil+ ReadyMix in a 50μl volume reaction using the following conditions: initial denaturation at 98°C for 45 seconds, 5 cycles of 98°C denaturation for 15 seconds, 65°C annealing for 30 seconds and extension at 72°C for 30 seconds; followed by a final extension at 72°C for 5 minutes. Reactions were cleaned-up with 1x AMPure XP beads and eluted in 20μl. Libraries were verified by running 1:30 dilutions on Agilent bioanalyzer. Libraries weere sequenced on an Illumina MiSeq using a 2x250 kit.
IMPLICON-seq

treatment_protocol: Juvenile and old F1 animals were sacrificed respectively in the range of 8-9 weeks and 102-104 weeks. Culled mice had their organs and brain areas dissected according to the atlas of stereotaxic coordinates of mouse brain (Paxinos and Franklin, 1997) and homogenised.

value: Hippocampus

tag: age category

value: old

tag: Sex

value: female

tag: mother strain

tag: father strain

value: Cast

tag: strain cross

value: BL6 x Cast

tag: age weeks

tag: library format

value: PE 250bp


title: Ctr9, Aux, antiSer2P, IP2, Rep2

tag: treatment


title: Skin-fibroblasts_Y_2

data_processing:
ATAC-seq data processing and alignment were completed using the Harvard pipeline (https://informatics.fas.harvard.edu/atac-seq-guidelines.html). The GRCm38.p6/mm10 genome primary assembly build used for alignment was obtained from the ensemble database (http://asia/ensembl.org/Musc_musculus/Info/Index; ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa)
All fastq files were trimmed to remove the Illumina Nextera Transposase adapter sequence using Cutadapt v.2.4 with “-m 20” parameter (Martin, 2011). After trimming, FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to check overall sequence quality and evaluate proper adapter trimming. Bowtie2 (Langmead and Salzberg, 2012) was used to align reads to the GRCm38.p6/mm10 mouse reference genome using “-p 8, –very-sensitive” options. Picard tools (http://broadinstitute.githyb.io/picard/) were used to mark and remove duplicates using the MarkDuplicates tool with default options. All subsequent analyses were performed on deduplicated reads. Samtools (Li et al., 2009) was used to sort and obtain uniquely mapped reads using “-b -q 10” options. Samtools were also used to remove reads from the mitochondrial chromosome.
Finally, for visualization purposes, BAM files were converted to an index binary format bigWig using bedtools (Quinlan, 2014).
Peak calling was produced in accordance with Corces et al. 2018 to ensure reproducible high-quality fixed-with peaks with a minimal bias due to change in read depth (ranged from 12,870,021 to 121,543,847 ) and data quality (FROT ranged from 5.1 to 39.7).
First, peak calling per sample was performed using the MACS2 callpeak command with the following parameters “-g mm –shift -100 –extsize 200 –nomodel –call-summits –nolambda –keep-dup all -p 0.01” (Zhang et al., 2008; Feng et al., 2012). Next, peak summits were extended by 250 bp on both sides to a final width of 501 bp. Peaks were filtered for mm10 blacklisted regions (Amemiya et al., 2019)(https://www.encodeproject.org/annotations/ENCSR636HFF/).    To avoid overlapping peaks within sample because of the 250bp peak summit extension, we performed an iterative removal approach as in Corces et al. 2018. During this process non overlapping peaks are kept as well as the most significant peaks within an overlap, whereas direct overlapping peaks are disregarded. The process is performed in an iterative manner to avoid the removal of indirect peak overlap. This yielded resulted a set of fixed-width peaks per sample.   Next, we normalized MACS2 “[−log10 (p-value)]” peak significance scores converting them to a score per million values (scpm). In brief, each individual peak score was divided by the sum of all the peak scores in the given sample divided by 1 million. This scpm value corrects the original peak calling scores for sample sequencing depth and quality, as higher quality samples yield a higher number of peaks and higher significance scores using MACS2. Thus, scores per million allow the direct comparison of peaks across biological replicates.   Next, we sought to generate a cell-type specific peak set containing all reproducible peaks within a cell-type and aging stage. For that, we generated a cumulative peak set by combining all previous fixed-width peaks from a given cell-type and ageing stage and performed the previous iterative approach as performed per sample. Only peaks with a scpm >=1 in at least two samples (min. overlap 50%) were further considered, at the exception of Adipocytes and Neurons, where scpm >=3 was selected to increase signal-to-noise ratio due to some of their samples presented lower quality (I.e. FROT <=10). Next, we wanted to identify reproducible peaks within a cell-type and across ageing status. Therefore, we re-normalized the score per million per cell-type and ageing status and performed a cumulative peak which was again trimmed for overlap following the iterative approach mentioned above. This resulted in a set of reproducible, fixed-width per cell type () which we refer as cell-type specific.   Lastly, we wanted to obtain a universal peak set across cell-types and ageing status to perform a pan-somatic ageing analysis. For that, we re-normalized the scpms per cell-type specific peak sets. Then, the 23 peak sets ere combined and again, we performed the iterative approach to remove overlapping peak sets across conditions. This resulted in a universal peak set of 460K, each of 501 bp in width.
Assembly: mm10
Supplementary files format and content: bigWig (.bw), narrowPeak, summits.bed, bed format with score per million score (scpm.bed), bed format and gtf format as well as the counts within the unviersal peak set.

source_name: Skin fibroblast

extract_protocol:
The tissues of 5 healthy animals were pooled per-replicate for cell isolation, with 3-5 replicates (totalling 15-25 animals) collected per cell type/condition. Multi-omic bulk profiling (OMNI-ATAC-seq assay and RNA-seq) was performed on purified populations collected via fluorescence activated cell sorting (FACS).
 OMNI-ATACseq libraries were generated from FACS purified cells according to the standard protocol (Corces et al., 2017). Afterward, libraries were purified using a QIAGEN MinElute PCR purification kit (QIAGEN, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880) according to the manufacturer’s recommendations. Library fragments ranging from 150 to 700 bp were enriched and the final elution volume was 21 ul.

value: Skin fibroblast

tag: genotype


title: treat2: myocardial ischemia-reperfusion injury

tag: strain

value: myocardial ischemia-reperfusion injury


title: 999_PFC MOUSE 1 lane7651_TTAGGCAT_999_PFC

description: 999_PFC MOUSE 1

source_name: Prefrontal cortex

value: Prefrontal cortex


title: 100520 HDC Sample 6

description: 10X Genomics 3 scRNA-seq v3.1

source_name: Heterogeneous differentiating cultures


title: Ctr9, Veh, INPUT, IP2, Rep1


title: Wt, INPUT, IP1, Rep2

source_name: MATa his4-912δ lys2-128δ leu2Δ1 trp1Δ63 RPB3-3XFLAG::KANMX


title: 999_LUNG MOUSE 1 lane7950_TTAGGCAT_999_Lung

description: 999_LUNG MOUSE 1

source_name: Lung

value: Lung


title: Skin-fibroblasts_Y_1

value: C57/Bl6 background

value: 2 months


title: control2: Wild type

value: Retina


title: Ctr9, Aux, antiSer2P, IP2, Rep1


title: 100820 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1

value: Heterogeneous differentiating cultures


title: 100520 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: 101220 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: 100820 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: Skin-fibroblasts_O_3

value: 22-24 months


title: 999_CB MOUSE 1 lane7651_CGATGTTT_999_C

description: 999_CB MOUSE 1

source_name: Cerebellum

value: Cerebellum


title: Skin-fibroblasts_Y_3


title: 100520 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: 999_LUNG MOUSE 1 lane7651_GCCAATGT_999_LUNG

description: 999_LUNG MOUSE 1


title: 999_HCP MOUSE 1 lane7651_ATCACGTT_999_HC

description: 999_HCP MOUSE 1


title: Wt, antiFLAG, IP1, Rep2


title: Skin-fibroblasts_O_2


title: 100520 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: 999_HY MOUSE 1 lane7651_TGACCACT_999_HY

description: 999_HY MOUSE 1

source_name: Hypothalamus

value: Hypothalamus


title: Wt, INPUT, IP1, Rep1


title: Wt, antiFLAG, IP1, Rep1


title: 999_CB MOUSE 1 lane7950_CGATGTTT_999_Cerb

description: 999_CB MOUSE 1


title: 999_NA MOUSE 1 lane7651_ACAGTGGT_999_NA

description: 999_NA MOUSE 1

source_name: Nucleus accumbens

value: Nucleus accumbens


title: Kidney-tubular_Y_4

source_name: Kidney tubular

value: Kidney tubular


title: ctr9D, INPUT, IP1, Rep2

source_name: MATα his4-912δ lys2-128δ leu2Δ1 trp1Δ63 RPB3-3XFLAG::KANMX ctr9∆::KANMX


title: 1679_LUNG MOUSE 8 lane7950_TTGACTCT_1679_Lung

description: 1679_LUNG MOUSE 8

value: young

value: female


title: 100520 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: 100120 HDC Sample 4

description: 10X Genomics 3 scRNA-seq v3.1


title: ctr9D, antiFLAG, IP1, Rep2


title: 100120 HDC Sample 2

description: 10X Genomics 3 scRNA-seq v3.1


title: Skin-fibroblasts_O_1


title: ctr9D, antiFLAG, IP1, Rep1


title: Kidney-tubular_Y_2


title: Thymic-fibroblasts_Y_4

source_name: Thymic fibroblasts

value: Thymic fibroblasts


title: 100120 HDC Sample 1

description: 10X Genomics 3 scRNA-seq v3.1


title: L4,scRNAseq, CRISPR

city: San Francisco

first: Scot

last: Federman

state: CA

address: 499 Illinois St

department: Biochemistry

institute: UCSF

description:
L4_barcodes.tsv.gz
L4_features.tsv.gz
L4_matrix.mtx.gz

library_source: other

data_processing:
Read alignment and cell assignment was performed using Cellranger count v7.0.0, the GRCh38-2020-A human reference transcriptome from 10x, and the protospacer sequences (Included as a supplementary file). Cell doublets were identified using Souporcell using the number of clusters argument -k 4. Doublets were discarded.
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz: gene expression and guide RNA expression count data in Matrix Market Exchange format
Supplementary files format and content: barcodes.tsv.gz: list of cell specific barcodes
Supplementary files format and content: features.tsv.gz: list of gene and guide RNA IDs

molecule: other

source_name: tubule epithelial cells

growth_protocol: HRCEs (Lonza, CC-2554) from 4 donors grown in renal epithelial growth media (Lonza, CC-3190) were transduced with lentivirus encoding dCas9-mCherry-ZIM3. Three days later cells were transduced with lentivirus encoding the sgRNA library and blue fluorescent protein (BFP). Nine days after guide transduction mCherry, BFP double-positive cells from each donor were sorted.

extract_protocol:
Equal numbers of double-positive cells from each donor were pooled and prepared for single cell RNA-sequencing, with 4 GEM groups each loaded with 20,000 cells, using the Chromium Next GEM Single Cell 3’ Kit 3.1 (10x Genomics, 1000268) according to the 10x Genomics protocol for Feature Barcode technology for CRISPR Screening.
Libraries were prepared with the Chromium Next GEM Single Cell 3’ Kit 3.1 (10x Genomics, 1000268) according to the 10x Genomics protocol for Feature Barcode technology for CRISPR Screening. The resulting guide and expression libraries were sequenced on a Novaseq 6000 (Illumina).

value: tubule epithelial cells


title: Ctr9, Veh, antiFLAG, IP1, Rep2

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ1 ura3-52 RPB3-3XFLAG::KANMX CTR9-V5-IAA7(AID)::KANMX


title: 1679_HY MOUSE 8 lane7651_TCAGATTC_1679_HY

description: 1679_HY MOUSE 8

value: Cast

value: BL6 x Cast

value: PE 250bp


title: Thymic-fibroblasts_O_4


title: L1,scRNAseq, CRISPR

description:
L1_barcodes.tsv.gz
L1_features.tsv.gz
L1_matrix.mtx.gz


title: 100520 HDC Sample 5

description: 10X Genomics 3 scRNA-seq v3.1


title: Thymic-fibroblasts_O_3


title: Ctr9, Aux, INPUT, IP1, Rep2

value: 1:1000 v/v 0.5 M Auxin in DMSO


title: L4,scRNAseq, GEX


title: Kidney-tubular_Y_3

value: C57/Bl6 background


title: 1679_HCP MOUSE 8 lane7651_TCATTGAG_1679_HCP

description: 1679_HCP MOUSE 8

value: Hippocampus


title: Thymic-fibroblasts_O_2


title: ctr9D, INPUT, IP1, Rep1


title: 1679_CB MOUSE 8 lane7950_TGCATAGT_1679_Cerb

description: 1679_CB MOUSE 8


title: 100120 HDC Sample 3

description: 10X Genomics 3 scRNA-seq v3.1


title: L3,scRNAseq, GEX


title: 1679_PFC  MOUSE 8 lane7651_TATGCCAG_1679_PFC

description: 1679_PFC  MOUSE 8

value: Prefrontal cortex


title: Thymic-fibroblasts_O_1


title: Ctr9, Aux, antiFLAG, IP1, Rep2


title: Kidney-tubular_O_2


title: Thymic-epithelial_Y_4

source_name: Thymic epithelial

value: Thymic epithelial

value: 2 months


title: Thymic-epithelial_Y_3


title: 1679_HCP MOUSE 8 lane7950_TGATACGT_1679_HCP

description: 1679_HCP MOUSE 8


title: 1679_LUNG MOUSE 8 lane7651_TTCAGCTC_1679_LUNG

description: 1679_LUNG MOUSE 8

value: Lung


title: Thymic-fibroblasts_Y_2


title: Ctr9, Veh, INPUT, IP1, Rep2


title: Ctr9, Veh, INPUT, IP1, Rep1


title: Thymic-fibroblasts_Y_3


title: L3,scRNAseq, CRISPR

description:
L3_barcodes.tsv.gz
L3_features.tsv.gz
L3_matrix.mtx.gz


title: Thymic-epithelial_Y_2


title: L2,scRNAseq, CRISPR

description:
L2_barcodes.tsv.gz
L2_features.tsv.gz
L2_matrix.mtx.gz


title: Ctr9, Veh, antiFLAG, IP1, Rep1


title: Thymic-fibroblasts_Y_1


title: 1678_CB  MOUSE 7 lane7651_TCTCACGG_1678_C

description: 1678_CB  MOUSE 7

value: Cerebellum


title: 1679_CB MOUSE 8 lane7651_TGGCTCAG_1679_C

description: 1679_CB MOUSE 8


title: 1679_NA MOUSE 8 lane7651_TACTAGTC_1679_NA

description: 1679_NA MOUSE 8

value: Nucleus accumbens


title: Ctr9, Aux, INPUT, IP1, Rep1


title: 1678_HCP  MOUSE 7 lane7950_TCTGCTGT_1678_HCP

description: 1678_HCP  MOUSE 7


title: L2,scRNAseq, GEX


title: Ctr9, Aux, antiFLAG, IP1, Rep1


title: 1678_CB  MOUSE 7 lane7950_TTGGAGGT_1678_Cerb

description: 1678_CB  MOUSE 7


title: HeLa cells,T343A-N-1

city: Wuhan

first: Wei

last: Wang

state: Hubei

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology Tongji Medical College

data_processing:
The RNA-seq raw reads were quality-controlled and trimmed using Fastp (v0.20.1) with default parameters. The resulting clean reads were aligned to the human reference genome (GRCh38) using STAR (v2.2.1), and BAM files were generated for each sample. The BAM files were sorted and indexed using Samtools (v1.14). The number of reads (counts) per gene was determined using featureCounts (v2.0.1).
Assembly: GRCh38.105
Supplementary files format and content: tab-delimited text files include raw counts

source_name: HeLa

extract_protocol:
RNAs were extracted using Trizol.
mRNA isolation from total RNA was executed utilizing poly-T oligo-attached magnetic beads. Subsequently, mRNA underwent fragmentation in a buffer containing divalent cations at an elevated temperature. The initial strand of cDNA was synthesized using random hexamers, succeeded by the synthesis of the second cDNA strand. The resultant double-stranded cDNA underwent repair and had an 'A' added to its 3' end. Purification and fragment selection were achieved through Hieff NGS® DNA Selection Beads. Following PCR amplification and enrichment of the products, the target region library underwent denaturation, cycling, and digestion, yielding single-stranded circular DNA. Rolling circle amplification was then employed to amplify the single-stranded circular DNA. The RNA library was sequenced using the MGI T7 platform (BGI Inc., Shenzhen, China), yielding 2 × 150 bp paired-end read datasets.

value: HeLa

value: cervical cancer cell line

value: Untreated


title: 1678_LUNG  MOUSE 7 lane7950_TCGAGCGT_1678_Lung

description: 1678_LUNG  MOUSE 7

value: young

value: female


title: 1678_NA  MOUSE 7 lane7651_TCCAGTCG_1678_NA

description: 1678_NA  MOUSE 7

value: Cast


title: HeLa cells, T343A-C-3


title: IMR90 prolif 3

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

data_processing:
Adapters and low quality bases were trimmed from raw reads using trim_galore (v0.6.7) for paired end reads and default parameters.
Reads were aligned to the human reference genome GRCh38 using STAR (v2.7.10a) with default parameters
SAM files were converted to BAM and sorted using sambamba (v2.098.1)
The count matrix was generated with the function featureCounts of the R package Rsubread (v2.8.2) and annotation from ENSEMBL GRCh38.101
Assembly: GRCh38
Supplementary files format and content: Excel file with raw counts

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and antibiotics.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Mini Kit (Cat #74106) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using the kits Illumina® Stranded mRNA Prep, Ligation (20040534) and IDT® for Illumina® RNA UD Indexes Set A, Ligation (20040553), following manufacturer´s instructions and 10 cycles of amplification.

treatment_protocol: Senescent was induced with doxorubicin (200nM, 48h) and then medium free of drug was used with every change. For genetic interventions, siRNA transfection was performed and one day after senescence was induced for up to 7 days. For drug treatments, senescence was induced by doxorubicin for 7 days and then treated with Bi (10μM),  MFI8 (20μM) or vehicle (DMSO) for 48h. Untreated cells transfected with siSCR or treated with vehicle (DMSO) were used as control. Media was changed every third day.

value: cNEG

tag: senescence

value: prolif


title: Thymic-epithelial_O_3

value: 22-24 months


title: IMR90 Doxo siMFN1+2 3

value: Doxo


title: L1,scRNAseq, GEX

value: tubule epithelial cells


title: HeLa cells, T343A-N-3


title: IMR90 Doxo siMFN 2 3


title: 1678_LUNG  MOUSE 7 lane7651_TGTATGCG_1678_LUNG

description: 1678_LUNG  MOUSE 7

value: BL6 x Cast

value: PE 250bp


title: Heat4-encoding plasmid

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisallee 30

department: Klinik und Poliklinik für Kardiologie

institute: Universitätsklinikum Leipzig

description: 10x Genomics

data_processing:
Cellranger-6.1.1 count pipeline was used to align sequencing reads in FASTQ files to a reference transcriptome including lncRNA from LNCipedia.
Assembly: Reference transcriptome consisting of: human hg38 and lncipedia 5.2
Supplementary files format and content: Tab-separated values files and matrix files

source_name: human primary monocytes (> 90% puritiy)

growth_protocol: Monocytes were isolated out of PBMCs by their size and density using a JE-5.0 counter-flow centrifugal elutriation system (Beckman Coulter, Brea, CA, USA) at 1,080 g centrifugal force. Size analysis and cell counts of the sorted cells were determined on a Beckman Coulter Z2 particle counter and size analyzer. Fractions containing more than 90% monocytes were used for further experiments.

extract_protocol:
Monocytes were harvested by centrifugation and cell concentration was set to 700-1200 cells/µl as described in 10x Genomics protocol #CG00039.
10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (User Guide, #CG000204) was used for GEM Generation & Barcoding, Post GEM-RT Cleanup & cDNA Amplification as well as 3' Gene Expression Library Construction.

treatment_protocol: Monocytes were seeded in cell culture plates in RPMI-1640 medium (Merck, #R8758) supplemented with 10% fetal bovine serum (FBS; Gibco, #10500064) and Opti-MEM-PEI-plasmid mixture (3.5 ml Opti-MEM (ThermoFisher, #31985070), 7.5 µl PEI (Polysciences, #23966-1) and plasmid) was added. Monocytes were transfected with control (pcDNA) or Heat4-encoding plasmids for 24 h.

value: human primary monocytes (> 90% puritiy)

value: transfection with Heat4-encoding plasmid


title: HeLa cells, T343A-N-2


title: control plasmid (pcDNA)

description: 10x Genomics

value: transfection with control plasmid (pcDNA)


title: 1678_HY MOUSE 7 lane7651_TAAGTTCG_1678_HY

description: 1678_HY MOUSE 7

value: Hypothalamus


title: Thymic-epithelial_Y_1

value: Thymic epithelial

value: C57/Bl6 background

value: 2 months


title: 1678_PFC  MOUSE 7 lane7651_TCAGGAGG_1678_PFC

description: 1678_PFC  MOUSE 7

value: Prefrontal cortex

value: young


title: Thymic-epithelial_O_2


title: HeLa cells, T343A-C-2

value: HeLa

value: cervical cancer cell line

value: Untreated


title: Thymic-epithelial_O_1

value: 22-24 months


title: HeLa cells, T343A-C-1


title: IMR90 Doxo siMFN1 3

value: Doxo


title: 1678_HCP MOUSE 7 lane7651_TACTTCGG_1678_HCP

description: 1678_HCP MOUSE 7

source_name: Hippocampus

value: Hippocampus

value: female

value: Cast


title: Satellite-stem-cells_Y_2

source_name: Satellite stem cells

value: Satellite stem cells


title: HeLa cells, HS-KD-3

value: CLK2 knockdown

value: Heat shock


title: Satellite-stem-cells_Y_3


title: HeLa cells,HS-KD-1


title: 1622_LUNG MOUSE 6 lane7950_TTCTGTGT_1622_Lung

description: 1622_LUNG MOUSE 6

value: Lung

value: Cast x BL6

value: PE 250bp


title: 1622_CB MOUSE 6 lane7950_TGTACCTT_1622_Cerb

description: 1622_CB MOUSE 6

value: Cerebellum


title: IMR90 Doxo BI 3

value: BI


title: HeLa cells, HS-KD-2


title: Satellite-stem-cells_Y_1

value: C57/Bl6 background

value: 2 months


title: 1622_HCP MOUSE 6 lane7950_TCCGTCTT_1622_HCP

description: 1622_HCP MOUSE 6

value: young


title: IMR90 Doxo MFI8 3


title: 1622_NA MOUSE 6 lane7651_TTGGTATG_1622_NA

description: 1622_NA MOUSE 6

value: Nucleus accumbens


title: Satellite-stem-cells_O_4

value: 22-24 months


title: IMR90 Doxo DMSO 3

value: DMSO

value: Doxo


title: HeLa cells, HS-WT-3

value: HeLa

value: cervical cancer cell line

value: CLK2 (WT)


title: HeLa cells, HS-WT-2


title: IMR90 prolif  DMSO  3

value: prolif


title: 1622_LUNG MOUSE 6 lane7651_TGAACTGG_1622_LUNG

description: 1622_LUNG MOUSE 6

value: female

value: Cast


title: IMR90 Doxo cNeg 3

value: cNEG


title: Fat-progenitors_Y_1

source_name: Fat progenitors

value: Fat progenitors


title: 1622_PFC MOUSE 6 lane7651_TCGAAGTG_1622_PFC

description: 1622_PFC MOUSE 6

source_name: Prefrontal cortex

value: Prefrontal cortex

value: Cast x BL6

value: PE 250bp


title: HeLa cells, HS-Control-2

value: Control

value: Heat shock


title: HeLa cells, HS-Control-3


title: Fat-progenitors_O_4

value: C57/Bl6 background


title: Fat-progenitors_O_2

value: 22-24 months


title: IMR90 Doxo DMSO 2

value: DMSO


title: IMR90 Doxo MFI8 2

value: Doxo


title: 1622_HCP MOUSE 6 lane7651_TAGTCTTG_1622_HCP

description: 1622_HCP MOUSE 6

value: Hippocampus

value: young


title: 1622_HY MOUSE 6 lane7651_TAACGCTG_1622_HY

description: 1622_HY MOUSE 6

value: Hypothalamus


title: IMR90 Doxo BI 1

value: BI


title: IMR90 prolif DMSO  2

value: prolif


title: 1619_HCP MOUSE 5 lane7950_TGGTTGTT_1619_HCP

description: 1619_HCP MOUSE 5

value: female

value: Cast


title: Fat-progenitors_Y_2

value: Fat progenitors

value: 2 months


title: Neurons_Y_2

source_name: Neurons

value: Neurons


title: Neurons_Y_3


title: Fat-progenitors_O_1


title: HeLa cells, Control-2

value: HeLa

value: cervical cancer cell line

value: Untreated


title: HeLa cells,HS-Control-1

value: Control

value: Heat shock


title: IMR90 Doxo MFI8 1


title: IMR90 Doxo BI 2


title: Neurons_Y_1

value: C57/Bl6 background


title: 1619_LUNG MOUSE 5 lane7950_TAAGCGTT_1619_Lung

description: 1619_LUNG MOUSE 5

source_name: Lung

value: Lung

value: Cast x BL6

value: PE 250bp


title: 1619_CB MOUSE 5 lane7950_TCTCGGTT_1619_Cerb

description: 1619_CB MOUSE 5

source_name: Cerebellum

value: Cerebellum

value: young


title: 1622_CB MOUSE 6 lane7651_TTCCATTG_1622_C

description: 1622_CB MOUSE 6


title: HeLa cells,HS-WT-1

value: CLK2 (WT)


title: HeLa cells, Control-1


title: IMR90 Doxo DMSO 1

value: DMSO

value: Doxo


title: Neurons_O_3

value: 22-24 months


title: iMA9_Dox_TFIIE_rep2

city: Shang Hai

first: Zimei

last: Yang

address: Dongchuan road 800

institute: Shang Hai Jiaotong University

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. Reads were aligned using bowtie2 v2.3.4.1.
For CUT&Tag, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Assembly: hg38, mm10
Supplementary files format and content: BigWig files contains normalized read count (CPM, in 50-bp bins)
Library strategy: CUT&Tag

source_name: iMA9 (also known as 37-5) originally described in Zuber, J. et al, Cell Rep 26, 1303-1317 e1307 (2019).

growth_protocol: Mouse cell iMA9 was cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.

extract_protocol:
DNA was extracted by Phenol-Chloroform-Isoamylol and amplified by PCR
Cells were bound to Concanavalin A-coated beads without fixation and chromatin opening. After primary and secondary antibodies binding, pA-Tn5 transposome binding, and tagmentation.  DNA was extracted and amplified by PCR. The product was purified by AMpure XP beads. After size seletion of purified production, library will be analyzed by Illumina NovaSeq 6000.

value: acute myeloid leukemia

tag: cut&tag antibody

value: TFIIEβ (GeneTex, GTX105029)


title: IMR90 prolif DMSO  1

value: prolif


title: SKMel  prolif  3

value: cNEG


title: iMA9_Ctrl_TFIIE_rep2

value: iMA9 (also known as 37-5) originally described in Zuber, J. et al, Cell Rep 26, 1303-1317 e1307 (2019).


title: 1619_LUNG MOUSE 5 lane7651_TGTGGTTG_1619_LUNG

description: 1619_LUNG MOUSE 5

value: female

value: Cast


title: Neurons_O_2

value: Neurons

value: C57/Bl6 background

tag: time


title: HeLa cells, Control-3

value: HeLa

value: cervical cancer cell line

value: Control

value: Untreated


title: Neurons_O_1


title: iMA9_Dox_TFIIE_rep1


title: 1619_HCP MOUSE 5 lane7651_TGCGATCT_1619_HC

description: 1619_HCP MOUSE 5

value: Hippocampus

value: young

value: Cast x BL6

value: PE 250bp


title: iMA9_Ctrl_TFIIE_rep1

value: acute myeloid leukemia


title: 1619_NA MOUSE 5 lane7651_TCCTCAAT_1619_NA

description: 1619_NA MOUSE 5

source_name: Nucleus accumbens

value: Nucleus accumbens


title: SKMel Doxo siMFN1+2 3

value: Doxo


title: 1619_PFC MOUSE 5 lane7651_TAGTGACT_1619_PFC

description: 1619_PFC MOUSE 5

value: Prefrontal cortex


title: Muscle-fibroblasts_Y_4

source_name: Muscle fibroblasts

value: Muscle fibroblasts

value: 2 months


title: Muscle-fibroblasts_Y_3


title: SKMel Doxo siMAVS 3

value: siMAVS


title: SKMel Doxo siMFN 2 3


title: iMA9_Ctrl_TBP_rep2

value: iMA9 (also known as 37-5) originally described in Zuber, J. et al, Cell Rep 26, 1303-1317 e1307 (2019).

value: TBP (Santa, SC-56795)


title: iMA9_Dox_TBP_rep2


title: SKMel Doxo siMFN1 3


title: 1619_HY MOUSE 5 lane7651_TACAGGAT_1619_HY

description: 1619_HY MOUSE 5

source_name: Hypothalamus

value: Hypothalamus

value: female

value: Cast


title: 1086_HCP MOUSE 4 lane7950_TAGCTTGT_1086_HCP

description: 1086_HCP MOUSE 4

value: old


title: iMA9_Dox_TBP_rep1


title: Muscle-fibroblasts_O_4

value: C57/Bl6 background

value: 22-24 months


title: 1619_CB MOUSE 5 lane7651_TTCCTGCT_1619_C

description: 1619_CB MOUSE 5

value: Cerebellum

value: young

value: Cast x BL6


title: iMA9_Ctrl_TBP_rep1

value: acute myeloid leukemia


title: Muscle-fibroblasts_O_2


title: SKMel prolif 2

value: cNEG

value: prolif


title: iMA9_Dox_PolII_rep2

value: Pol ll (Santa, SC-47701)


title: 1086_CB MOUSE 4 lane7950_GGCTACAG_1086_Cerb

description: 1086_CB MOUSE 4

value: PE 250bp


title: SKMel Doxo siMAVS 2

value: siMAVS

value: Doxo


title: 1086_LUNG MOUSE 4 lane7950_CTTGTACT_1086_Lung

description: 1086_LUNG MOUSE 4

value: Lung


title: iMA9_Ctrl_PolII_rep2

value: iMA9 (also known as 37-5) originally described in Zuber, J. et al, Cell Rep 26, 1303-1317 e1307 (2019).


title: Lymph-fibroblasts_O_1

source_name: Lymph endothelial

value: Lymph endothelial


title: 1086_CB MOUSE 4 lane7651_TTGGAGGT_1086_C

description: 1086_CB MOUSE 4

value: female

value: Cast


title: Muscle-fibroblasts_Y_2

value: Muscle fibroblasts

value: C57/Bl6 background

value: 2 months


title: iMA9_Ctrl_PolII_rep1


title: iMA9_Dox_PolII_rep1


title: 1086_LUNG MOUSE 4 lane7651_TTGACTCT_1086_LUNG

description: 1086_LUNG MOUSE 4

value: old


title: Lymph-endothelial_Y_3


title: SKMel Doxo siMFN1+2 2


title: 1086_NA MOUSE 4 lane7651_TGCATAGT_1086_NA

description: 1086_NA MOUSE 4

value: Nucleus accumbens

value: Cast x BL6


title: SKMel Doxo cNeg 3

value: cNEG


title: SKMel Doxo siMFN1 2


title: iMA9_Dox_MLL1_rep2

value: acute myeloid leukemia

value: MLL1 (456, thanks to E. Canaani lab)


title: SKMel Doxo siMFN2 2


title: Lymph-endothelial_Y_2


title: 1086_HY MOUSE 4 lane7651_TGATACGT_1086_HY

description: 1086_HY MOUSE 4

value: Hypothalamus

value: PE 250bp


title: Lymph-endothelial_Y_1


title: SKMel Doxo cNeg 2

value: Doxo


title: Lymph-endothelial_O_3

value: 22-24 months


title: 1086_HCP MOUSE 4 lane7651_TCTGCTGT_1086_HCP

description: 1086_HCP MOUSE 4

value: Hippocampus


title: iMA9_Ctrl_MLL1_rep2

value: iMA9 (also known as 37-5) originally described in Zuber, J. et al, Cell Rep 26, 1303-1317 e1307 (2019).


title: Lymph-fibroblasts_O_2

value: Lymph endothelial


title: SKMel  prolif  1

value: prolif


title: iMA9_Dox_MLL1_rep1


title: Lymph-endothelial_O_2


title: 1086_PFC MOUSE 4 lane7651_TCGAGCGT_1086_PFC

description: 1086_PFC MOUSE 4

value: Prefrontal cortex

value: female

value: Cast


title: Lymph-endothelial_O_1

value: C57/Bl6 background


title: SKMel Doxo siMAVS 1

value: siMAVS


title: iMA9_Ctrl_MLL1_rep1


title: SKMel Doxo siMFN1+2 1


title: 1084_LUNG MOUSE 3 lane7950_GATCAGCG_1084_Lung

description: 1084_LUNG MOUSE 3

value: Lung

value: old

value: Cast x BL6


title: iMA9_Dox_MLL-AF9_rep2

value: acute myeloid leukemia

value: Anti-FLAG M2 (Sigma-Aldrich, F1804)


title: Liver-progenitors_Y_3

source_name: Liver progenitors

value: Liver progenitors

value: 2 months


title: iMA9_Ctrl_MLL-AF9_rep2


title: SKMel Doxo siMFN1 1

value: Doxo


title: SKMel Doxo cNeg 1

value: cNEG


title: SKMel Doxo siMFN 2


title: 1084_LUNG MOUSE 3 lane7651_TTCTGTGT_1084_LUNG

description: 1084_LUNG MOUSE 3

value: PE 250bp


title: Liver-progenitors_Y_2


title: Liver-progenitors_Y_1


title: Liver-progenitors_O_3

value: 22-24 months


title: IMR90 Doxo siMAVS 3


title: 1084_HCP MOUSE 3 lane7950_CAGATCTG_1084_HCP

description: 1084_HCP MOUSE 3

value: Hippocampus


title: 1084_HCP MOUSE 3 lane7651_TGGTTGTT_1084_HC

description: 1084_HCP MOUSE 3


title: Liver-progenitors_O_2


title: IMR90 prolif  2

value: prolif


title: Microglia_Control_Sympt_biol rep 5

city: Paris

first: Severine

last: Boillee

address: 47 Blvd de l'Hopital

country: France

institute: ICM - Paris Brain Institute, INSERM, CNRS, Sorbonne University

data_processing:
Poor quality sequences were trimmed or removed with Trimmomatic (Bolger et al., 2014 PMID:24695404) software to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used to align reads on mm10 reference genome and quantification with gencode v25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Differential analysis were conducted with DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expecting counts, TPM of genes

source_name: Lumbar Spinal Cord

extract_protocol:
RNA was extracted using the RNeasy plus micro kit (Qiagen). RNA quality was determined with TapeStation 2200, Agilent
Whole total eluted RNA of microglia (between 400-700 pg)   was used to perform cDNA synthesis using the Smart-Seq v4 Ultra Low Input RNA kit for sequencing (TaKaRa) with linear pre-amplification. Library preparation was made with 150 pg of amplified cDNA for every sample using the Nextera XT DNA Library Preparation Kit (Illumina).
Samples were sequenced on a NovaSeqXplus sequencing system (Illumina) with an average coverage of 2X50 millions of reads per sample (150bp, paired-end) after demultiplexing.

value: Lumbar Spinal Cord

value: primary microglial cell

tag: disease stage

value: Symptomatic

value: Female

value: Control


title: Microglia_Control_Sympt_biol rep 4

tag: tissue


title: 1084_CB MOUSE 3 lane7651_TCTCGGTT_1084_C

description: 1084_CB MOUSE 3

value: Cerebellum

value: old

value: female

value: Cast


title: Liver-progenitors_O_1

value: Liver progenitors

value: C57/Bl6 background


title: Keratinocytes_Y_4

source_name: Kerationcytes

value: Kerationcytes

value: 2 months


title: iMA9_Dox_MLL-AF9_rep1

tag: cell line

value: iMA9 (also known as 37-5) originally described in Zuber, J. et al, Cell Rep 26, 1303-1317 e1307 (2019).

value: acute myeloid leukemia

value: Anti-FLAG M2 (Sigma-Aldrich, F1804)


title: IMR90 Doxo siMAVS 2

value: siMAVS

value: Doxo


title: 1084_HY MOUSE 3 lane7651_TCCGTCTT_1084_HY

description: 1084_HY MOUSE 3

value: Hypothalamus

value: Cast x BL6

value: PE 250bp


title: Microglia_Control_Sympt_biol rep 2

value: Lumbar Spinal Cord

tag: cell type

value: primary microglial cell

value: Symptomatic

value: Female

value: Control


title: 1084_CB MOUSE 3 lane7950_ACTTGATG_1084_Cerb

description: 1084_CB MOUSE 3

value: Cerebellum

tag: age category

value: old

value: female

value: Cast


title: 1084_PFC MOUSE 3 lane7651_TAAGCGTT_1084_PFC

description: 1084_PFC MOUSE 3

value: Prefrontal cortex

tag: Sex


title: Keratinocytes_Y_3

value: Kerationcytes

value: C57/Bl6 background

value: 2 months


title: IMR90 Doxo siMFN 2 2

value: Doxo


title: 1084_NA MOUSE 3 lane7651_TGTACCTT_1084_NA

description: 1084_NA MOUSE 3

value: Nucleus accumbens

tag: mother strain


title: iMA9_Ctrl_MLL-AF9_rep1

value: iMA9 (also known as 37-5) originally described in Zuber, J. et al, Cell Rep 26, 1303-1317 e1307 (2019).

value: acute myeloid leukemia

value: Anti-FLAG M2 (Sigma-Aldrich, F1804)


title: Microglia_Control_Sympt_biol rep 1

value: Lumbar Spinal Cord

value: primary microglial cell


title: 1000_HCP MOUSE 2 lane7950_TGACCACT_1000_HCP

description: 1000_HCP MOUSE 2

value: Hippocampus

tag: father strain

value: BL6 x Cast

value: PE 250bp


title: IMR90 Doxo siMFN1 2


title: Keratinocytes_Y_2


title: Keratinocytes_Y_1


title: 1000_LUNG MOUSE 2 lane7950_GCCAATGT_1000_Lung

description: 1000_LUNG MOUSE 2

value: Lung

value: old

tag: strain cross


title: Microglia_US_Sympt_biol rep 5

value: Symptomatic

value: Female

value: Ultra sound treated (US)


title: Keratinocytes_O_4

value: Kerationcytes

value: C57/Bl6 background

value: 22-24 months


title: Microglia_Control_Sympt_biol rep 3

value: Control


title: IMR90 prolif 1

value: cNEG

value: prolif


title: Microglia_US_Sympt_biol rep 3


title: Keratinocytes_O_3


title: Microglia_US_Sympt_biol rep 4


title: IMR90 Doxo siMAVS 1

value: siMAVS

value: Doxo


title: Keratinocytes_O_2


title: 1000_HY MOUSE 2 lane7651_TAGCTTGT_1000_HY

description: 1000_HY MOUSE 2

value: Hypothalamus

value: female

value: Cast

tag: age weeks


title: IMR90 Doxo siMFN1+2 2


title: IMR90 Doxo siMFN1+2 1


title: 1000_NA MOUSE 2 lane7651_GGCTACAG_1000_NA

description: 1000_NA MOUSE 2

value: Nucleus accumbens

value: BL6 x Cast

tag: library format

value: PE 250bp


title: Keratinocytes_O_1


title: 1000_PFC MOUSE 2 lane7651_GATCAGCG_1000_PFC

description: 1000_PFC MOUSE 2

value: Prefrontal cortex

value: old


title: Microglia_US_Sympt_biol rep 1

value: Lumbar Spinal Cord

value: primary microglial cell

value: Symptomatic

value: Female

tag: treatment

value: Ultra sound treated (US)


title: IMR90 Doxo siMFN 2 1


title: HSC_Y_3

source_name: Hematopoietic stem cells

value: Hematopoietic stem cells

tag: genotype

value: C57/Bl6 background

value: 2 months


title: KO, snRNAseq

city: Los Angeles

first: Tamer

last: Sallam

address: 650 Charles E. Young Dr. South

institute: UCLA

data_processing:
Sequencing data de-multiplexing was performed using CellRanger mkfastq software v7.2.0 (10X Genomics).
Sequenced reads in FASTQ format were aligned and analyzed via the CellRanger count pipeline v7.2.0 (10X Genomics) using the refdata-gex-mm10-2020-A mouse (10X Genomics) reference database under default settings.
The R package Seurat was used to cluster the cells in the merged matrix.
Assembly: mm10
Supplementary files format and content: h5

molecule: nuclear RNA

source_name: liver

extract_protocol:
Frozen livers from 4 mice of liver-specific LBP KO group or 4 mice of WT group were cut and pooled according to the group. Samples were minced and transferred to the Dounce homogenizer. We added 4 ml of lysis buffer consisting of 10 mM Tris-HCl, 10 mM NaCl, 1 mM MgCl2, 0.1% IGEPAL and 0.3 U/μL RNase inhibitor to pooled liver samples, then homogenized the tissue carefully. WRB buffer (PBS, 2% BSA, and 0.2 U/μL RNase inhibitor) was added and centrifuged to remove the lipid layer. After filter again with 40 μm Flowmi cell strainer, nuclei were pelleted by centrifuging at 500 g for 5 min at 4 °C and resuspended in WRB buffer.
Single-nucleus RNA sequencing was prepared using 10X Genomics' Chromium Next GEM Single Cell 3' Kit v3.1 following manufacturer's protocol.

treatment_protocol: FPC diet

value: liver

tag: strain

value: male

value: whole liver population

value: LBP-KO

value: FPC diet


title: 1000_LUNG MOUSE 2 lane7651_CTTGTACT_1000_LUNG

description: 1000_LUNG MOUSE 2

value: Lung

value: female

value: Cast

value: BL6 x Cast


title: 1000_HCP MOUSE 2 lane7651_CAGATCTG_1000_HC

description: 1000_HCP MOUSE 2

source_name: Hippocampus

value: Hippocampus

value: old

value: PE 250bp


title: IMR90 Doxo cNeg 2

value: cNEG

tag: senescence

value: Doxo


title: IMR90 Doxo siMFN1 1


title: 1000_CB MOUSE 2 lane7950_ACAGTGGT_1000_Cerb

description: 1000_CB MOUSE 2

value: Cerebellum


title: HSC_Y_2

value: Hematopoietic stem cells

value: C57/Bl6 background


title: MLL1 KD RNA-seq rep3

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
Fragment count were obtained using featureCounts v1.6.1.
hg38
Tab-delimited text files include fragment count values of genes for each sample.

source_name: HEL cell line

growth_protocol: Human cells HEL were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.

value: HEL cell line

value: Human erythroblast

value: MLL1 knockdown


title: PARG29b_r2

city: Grand Forks

first: Yaroslava

last: Karpova

state: ND

address: 501 Columbia Road

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Illumina FQ sequencing files were imported into CLC Genomics Workbench version 12.0.
The reads were trimmed to remove adapters then the trimmed reads were mapped to the Mouse genome using CLC’s default parameters (mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, auto-detect paired distanc-es, maximum number of hits per read = 10).
Assembly: GRCm38 - mm10
Supplementary files format and content: PARP1ko_testis_gene_counts.xlsx
Supplementary files format and content: Expression value, TPM, RPKM, reads number

source_name: testis

extract_protocol:
RNA was extracted using the RNeasy kit according to the manufacturer’s protocol (Qiagen).
RNA library and 150 bp paired-end sequencing were conducted by Novogene Corporation.
NEB’s Ultra II RNA library kit

value: testis


title: 1000_CB MOUSE 2 lane7651_ACTTGATG_1000_C

description: 1000_CB MOUSE 2


title: Microglia_US_Sympt_biol rep 2

value: Lumbar Spinal Cord

value: primary microglial cell

value: Symptomatic

value: Female

value: Ultra sound treated (US)


title: AF9 KD RNA-seq rep2

value: AF9 knockdown


title: MLL1 KD RNA-seq rep2


title: IMR90 Doxo cNeg 1


title: HSC_O_3

value: 22-24 months


title: AF9 KD RNA-seq rep1


title: MLL1 KD RNA-seq rep1


title: HSC_O_4


title: PARG29b_r1


title: wild_type_r1

value: WT


title: HSC_O_2


title: Ctrl RNA-seq rep2 (AF9 KD)


title: HSC_O_1


title: Ctrl RNA-seq rep3


title: Nrf2Act-Hep + AAV8-FBP1 C8

city: Chongqing

first: Yahui

last: Zhu

address: ACampus, Chongqing University,Shapingba District, Chongqing, China

institute: Chongqing University

description: Nrf2Act-Hep + AAV8-FBP1

data_processing:
The clustering of index-coded samples was performed on an Illumina Novaseq sequencer 6000 according to the manufacturer’s instructions.
After cluster generation, the libraries were sequenced on the same machine and paired-end reads were generated.
Assembly: RNA-seq reads were aligned to the mouse genome (GRCm38/mm10) using STAR. Biological and technical replicates were used in all experiments.
Supplementary files format and content: Transcript quantification was performed with HOMER (v.4.11). Principal component analysis (PCA) was done using fragments per kilobase million (FPKM) on all genes from all the samples
Supplementary files format and content: Expression value for each transcript was calculated using the analyzeRepeat Pl tool of HOMER.

source_name: Liver

growth_protocol: Mice were maintained in filter-topped cages on autoclaved food and water with a 12 h light /dark cycle. Experiments were performed according to UCSD Institutional Animal Care and Use Committee (protocol S00218) and NIH guidelines and regulations.

extract_protocol:
Total RNA was isolated as above together with RNase-Free DNase kit (Qiagen, #79254) to obtain pure RNA. RNA degradation and contamination were monitored on 1% agarose gels and RNA purity was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed with the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For library preparation, a total of 1 μg RNA per sample was used as input for RNA sample preparations. Sequencing libraries were generated with NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s protocols and index codes were added to attribute sequences to each sample.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and fragmented using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5×). First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was performed with DNA polymerase Ⅰ and RNase H. Remaining overhangs were converted into blunt ends by exonuclease/polymerase activities. After 3’ end adenylation of DNA fragments, NEBNext adaptors with hairpin loop structures were ligated to prepare for hybridization. Library fragments were then purified with AMPpure XP system (Beckman Coulter, Beverly, USA) and 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNAs at 37℃ for 15 min followed by 5 min at 95℃. PCR was then performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: For HCC induction by hydrodynamic injection, Fbp1ΔHep or  Nfe2l2Act-Hep mice were intravenously(i.v.) injected with NRASG12V (12.5 μg/ml) and Sleeping Beauty transposase (SB13) (2.5 μg/ml) plasmids diluted in Ringer’s solution at 0.1 ml/g body weight in 5-7 seconds.

value: Liver

value: No

value: hepatocyte


title: HSC_Y_1

value: Hematopoietic stem cells

value: 2 months


title: Ctrl RNA-seq rep1 (AF9 KD)

value: HEL cell line


title: WT, snRNAseq

value: liver

value: male

value: whole liver population

value: FPC diet


title: Kidney-endothelial_Y_5

source_name: Kidney endothelial

value: Kidney endothelial

value: C57/Bl6 background


title: Nrf2Act-Hep + AAV8-FBP1 C7

description: Nrf2Act-Hep + AAV8-FBP1


title: Nrf2Act-Hep + AAV8-FBP1 C6

description: Nrf2Act-Hep + AAV8-FBP1


title: Ctrl RNA-seq rep1

value: Human erythroblast


title: Ctrl RNA-seq rep2


title: Kidney-endothelial_Y_4


title: HK2_Arid5a_3_Med

first: Greg

last: Delgoffe

address: 5051 Centre Avenue, 4051

department: Microbiology and Immunology

data_processing:
The raw sequence reads were mapped to GrCH38/hg38 using default parameters in STAR (v2.7.9) and quantified using RSEM (v1.3.1)
Read count extraction and normalization were performed using DESeq2 (v1.36.0) in R(v4.2.0)
Assembly: hg38
Supplementary files format and content: comma-separated values file include FPKM and count values for each Sample

source_name: human kidney epithelial

growth_protocol: HK2 were plated in 150mm tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator overnight.

extract_protocol:
Cells were trypsinized and extracts were isolated with lysis buffer with RNase Inhibitor (40 U/μl; Thermo Scientific). Buffers included protease inhibitor cocktail (Sigma-Aldrich). Lysates were immunoprecipitated with Abs against FLAG or mouse IgG1. Beads were washed with NT2 buffer and digested with DNase I (Roche Applied Science) and protease K (Sigma-Aldrich). Total RNA was extracted with acid phenol or TRIzol.
RIP-seq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA kit

treatment_protocol: Cells were transfected with 10ug FLAG-hArid5a encoding plasmid by using FuGeneHD transfection reagent (Promega Cat#E2311). Cells were stimulated with IL-17 (200 ng/mL) or medium control for 3 hours .

value: human kidney epithelial

value: human kidney epithelial cell line

tag: rip antibody

value: FLAG; Cat# F3165; Sigma-Aldrich Lot SLCG2330

value: medium control


title: wild_type_r2

value: testis

value: WT


title: Kidney-endothelial_Y_2

tag: time


title: HEL_AF9shRNA2_AF9KD_MLL1_rep1

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. Reads were aligned using bowtie2 v2.3.4.1.
For CUT&Tag, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
hg38
BigWig files contains normalized read count (CPM, in 50-bp bins)

source_name: HEL

growth_protocol: Human cells HEL and THP1 were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.

value: HEL

tag: cut and_tag_antibody

value: MLL1 (468, thanks to E. Canaani lab)


title: HK2_Arid5a_2_Med

tag: tissue


title: Nrf2Act-Hep + AAV8-CTRL C5

description: Nrf2Act-Hep + AAV8-CTRL

value: Liver

tag: cell line

value: No

value: hepatocyte


title: HEL_AF9shRNA2_Ctrl_MLL1_rep1

tag: cell type


title: Nrf2Act-Hep + AAV8-CTRL C3

description: Nrf2Act-Hep + AAV8-CTRL


title: HEL_AF9shRNA2_AF9KD_AF9_rep1


title: Kidney-endothelial_O_4

value: 22-24 months


title: HK2_IgG_3_Med

value: Mouse IgG1; Cat# 5415S; CST Lot 10


title: HK2_Arid5a_1_Med


title: Nrf2Act-Hep + AAV8-CTRL C4

description: Nrf2Act-Hep + AAV8-CTRL


title: HEL_AF9shRNA2_Ctrl_AF9_rep1


title: Fbp1△Hep + HD B16

description: Fbp1△Hep + HD


title: Kidney-endothelial_O_1


title: Fbp1△Hep + HD B15

description: Fbp1△Hep + HD


title: HEL_MLL1shRNA2_MLL1KD_AF9_rep1


title: HK2_Arid5a_3_IL17


title: HEL_MLL1shRNA2_Ctrl_AF9_rep1


title: HK2_IgG_1_Med


title: Fbp1△Hep + HD B14

description: Fbp1△Hep + HD


title: HK2_Arid5a_2_IL17


title: HEL_MLL1shRNA2_MLL1KD_MLL1_rep1


title: CD8-Virtual-Mem_Y_4

source_name: CD8 Virtual Memory

value: CD8 Virtual Memory

value: 2 months


title: Fbp1F/F + HD B12

description: Fbp1F/F + HD


title: Kidney-endothelial_O_2

value: Kidney endothelial

value: C57/Bl6 background


title: HEL_MLL1shRNA2_Ctrl_MLL1_rep1

value: Human erythroblast


title: HK2_IgG_2_Med

value: human kidney epithelial

value: human kidney epithelial cell line


title: HK2_IgG_3_IL17


title: HEL_AF9shRNA1_AF9KD_TBP_rep2

value: TBP (Santa, SC-56795)


title: Fbp1F/F + HD B10

description: Fbp1F/F + HD


title: Kidney-endothelial_Y_1


title: Fbp1F/F + HD B11

description: Fbp1F/F + HD


title: CD8-Virtual-Mem_O_4


title: CD8-Virtual-Mem_Y_1


title: HEL_AF9shRNA1_AF9KD_TBP_rep1


title: HK2_IgG_2_IL17


title: HEL_AF9shRNA1_Ctrl_TBP_rep2


title: Fbp1△Hep  B8

value: Ctrl


title: CD8-Virtual-Mem_O_3