title: BALB/cByJcl D5 after ADR glomeruli RNA-seq replicate 3

city: Towada

first: Masaki

last: Watanabe

department: School of Veterinary Medicine

institute: Kitasato University

description:
Library name: ByJcl_D5ADR_3
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
ADR_gene_counts.tsv

data_processing:
Raw sequencing reads were quality-checked using FastQC.
Adapters and low-quality bases were trimmed using Trimmomatic.
Trimmed reads were aligned to the mouse reference genome (Mus musculus, GRCm39) using STAR aligner.
Aligned reads were summarized at the gene level using featureCounts based on the corresponding gene annotation.
Assembly: Mus musculus reference genome GRCm39.
Supplementary files format and content: Gene-level raw count matrix (tab-delimited text file; rows = gene symbols, columns = sample IDs).

source_name: Glomerulus

growth_protocol: Male BALB/cAjcl and BALB/cByJcl mice (8 weeks old) were obtained from CLEA Japan (Tokyo, Japan). Animals were maintained under specific pathogen–free conditions in a temperature-controlled facility (22 ± 2°C) on a 12-h light/dark cycle with ad libitum access to standard laboratory chow and water. Mice were acclimated prior to experimentation.

extract_protocol:
Glomeruli were isolated from baseline and D5 kidneys using a Dynabeads-based perfusion method (Takemoto et al., 2002). Briefly, mice were perfused via the left ventricle with phosphate-buffered saline containing Dynabeads™ M-450 (4.5 µm diameter; Thermo Fisher Scientific), allowing bead entrapment within glomerular capillaries. Kidneys were excised, minced, and digested in collagenase at 37°C. The suspension was passed through a 100-µm cell strainer, and bead-containing glomeruli were collected using a magnetic separator and washed repeatedly with PBS. Purity was confirmed by light microscopy. Total RNA was extracted from isolated glomeruli using the NucleoSpin RNA kit (Takara Bio, Shiga, Japan) according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent Bioanalyzer, and only samples with RNA integrity number (RIN) ≥ 7.0 were used for sequencing.
RNA-seq libraries were prepared using poly(A) selection for strand-specific RNA sequencing. Library preparation and sequencing were performed by GENEWIZ, Inc. (Tokyo, Japan). Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 2 × 150 bp paired-end reads, yielding approximately 6 Gb of data per sample.

treatment_protocol: Adriamycin (doxorubicin hydrochloride; Fujifilm Wako Pure Chemical Corp., Osaka, Japan) was administered as a single intravenous injection at 10 mg/kg via retro-orbital route under isoflurane anesthesia. Control animals received sterile saline. Mice were monitored daily. Kidneys were harvested on Day 5 (D5) after ADR administration for glomerulus-enriched transcriptomic analysis. Baseline (untreated) mice were also analyzed for comparison.

value: Glomerulus

value: Glomerulus-enriched

value: BALB/cByJcl

value: ADR 10 mg/kg; Day 5

tag: batch


title: BALB/cByJcl D5 after ADR glomeruli RNA-seq replicate 2

status: Public on Mar 02 2026

type: SRA

country: Japan

description:
Library name: ByJcl_D5ADR_2
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
ADR_gene_counts.tsv

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: CUMC_S29

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 2.1.7) was used to convert BCL to fastq format, coupled with adaptor trimming
Salmon v1.3.0 was used to quantify transcript abundance after generating a full decoy-aware transcriptome index.
tximport v1.18.0 was used to import transcript level count estimates from Salmon and summarize them at the gene level using the "lengthScaledTPM" option for the countsFromAbundance argument.
Genome_build: GENCODE Release 34 (GRCh38.p5)
Supplementary_files_format_and_content: tab-delimited text file containing estimated counts per gene for each sample

organism: Homo sapiens

source_name: PDAC

extract_protocol:
Qiagen RNAeasy Plus Micro Kit
NuGEN Ovation RNA-Seq System V2

tag: compartment

value: Stroma

tag: group

value: Primary


title: CUMC_S3


title: CUMC_S28


title: HSJ019, K27M, DM, R1

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Raw sequences were trimmed using fastp with default settings
Expression quantification was performed using salmon v1.4.0 with default settings against GENCODE annotations (v36/vM25)
Assembly: mm10 or hg38
Supplementary files format and content: quant.sf are TSV files generated by salmon containing transcript abundances

extract_protocol:
Total RNA was extracted from cell pellets and mouse tumors using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts

tag: cell line

value: Glioma cell line

value: DMSO


title: CUMC_EI4

value: Epithelium

value: IPMN


title: CUMC_EI3


title: HSJ019, K27M, 4976, DM, R1


title: BALB/cByJcl D5 after ADR glomeruli RNA-seq replicate 1

description:
Library name: ByJcl_D5ADR_1
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
ADR_gene_counts.tsv


title: HSJ019, K27M, 4976, DM, R2


title: CUMC_S26


title: CUMC_S27


title: CUMC_EI2


title: BALB/cByJcl baseline glomeruli RNA-seq replicate 3

description:
Library name: ByJcl_BL_3
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
BL_gene_counts.tsv

value: untreated baseline


title: CUMC_EI1


title: DIPGXIII, KO, DM, R2

source_name: DIPGXIII

value: DIPGXIII


title: CUMC_S25


title: BALB/cByJcl baseline glomeruli RNA-seq replicate 2

description:
Library name: ByJcl_BL_2
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
BL_gene_counts.tsv


title: DIPGXIII, KO, DM, R1


title: BALB/cByJcl baseline glomeruli RNA-seq replicate 1

description:
Library name: ByJcl_BL_1
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
BL_gene_counts.tsv


title: CUMC_S24


title: CUMC_S125


title: CUMC_S22


title: CUMC_S23


title: CUMC_S124


title: CUMC_S21


title: BALB/cAjcl D5 after ADR glomeruli RNA-seq replicate 3

description:
Library name: Ajcl_D5ADR_3
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
ADR_gene_counts.tsv

value: BALB/cAjcl


title: BALB/cAjcl D5 after ADR glomeruli RNA-seq replicate 2

description:
Library name: Ajcl_D5ADR_2
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
ADR_gene_counts.tsv


title: BALB/cAjcl D5 after ADR glomeruli RNA-seq replicate 1

description:
Library name: Ajcl_D5ADR_1
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
ADR_gene_counts.tsv


title: CUMC_S123


title: DIPGXIII, K27M, DM, R2


title: DIPGXIII, K27M, 4976, DM, R1


title: DIPGXIII, K27M, 4976, DM, R2


title: CUMC_S122


title: DIPGXIII, K27M, DM, R1


title: BALB/cAjcl baseline glomeruli RNA-seq replicate 3

description:
Library name: Ajcl_BL_3
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
BL_gene_counts.tsv


title: BT245, KO, DM, R2


title: CUMC_S121


title: CUMC_S20


title: BALB/cAjcl baseline glomeruli RNA-seq replicate 2

description:
Library name: Ajcl_BL_2
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
BL_gene_counts.tsv


title: CUMC_S2


title: CUMC_S120


title: BT245, KO, DM, R1


title: CUMC_S119


title: CUMC_S19


title: BT245, K27M, DM, R2


title: CUMC_S118


title: BT245, K27M, DM, R1


title: CUMC_S17


title: BALB/cAjcl baseline glomeruli RNA-seq replicate 1

description:
Library name: Ajcl_BL_1
Poly(A)-selected, strand-specific RNA-seq; PE150; isolated glomeruli
BL_gene_counts.tsv


title: FT AML, Control, 2, IP

city: Philadelphia

first: Sara

middle: E

last: Meyer

state: PA

department: Cancer Biology

country: USA

institute: Thomas Jefferson University

description:
Library name: FT2_DMSO_IP
vehicle control treated Tet2/Flt3-mutant leukemia, mouse 2, H3K27ac IP

library_source: genomic

data_processing:
Paired-end FASTQ files were aligned to the mouse reference genome (GRCm38, Ensembl) using Chromap with the preset “chip” option
SAM to BAM conversion, sorting and indexing was performed with samtools. Reads overlapping blacklist regions from iGenomes were removed with bedtools intersect. For signal visualization, normalized coverage tracks (bigWig) were generated from filtered BAM files using bedtools genomecov and scaled to 1 million mapped reads per sample. Tracks were sorted and converted to bigWig format using UCSC tools bedSort and bedGraphToBigWig. Peak calling was performed using MACS2 with matched input controls, using default parameters and a q-value threshold of 0.01. Peak annotation was conducted using HOMER. Peaks across conditions were merged using mergePeaks. Quantification of ChIP-seq signal over merged peaks was conducted using featureCounts (Rsubread). Differentially enriched peaks were determined using DESeq2. Peaks were classified as promoter-proximal or enhancer-associated based on distance to the nearest TSS (±1000 bp). All plots were generated using ggplot2 and ggpubrin R.
Assembly: mouse genome GRCm38
Supplementary files format and content: Bigwig

molecule: genomic DNA

source_name: leukemic splenocytes

growth_protocol: Dnmt3afl/fl,Flt3ITD/ITD,Mx1Cre (D/F AML) and Tet2fl/fl,Flt3ITD/ITD,Mx1Cre (T/F AML)  leukemic splenocytes were isolated from moribund mice (n=2 mice/genotype) and c-Kit enriched using CD117 microbeads (Miltenyi BioTech). Equal numbers of cells were plated in standard growth medium RPMI 1640 (Thermo Fisher Scientific) containing 20% FBS (HyClone) supplemented with mouse recombinant SCF (60ng/ml), IL6 (20ng/ml), and IL3 (20ng/ml) (Miltenyi Biotech).

extract_protocol:
At the end of the treatment protocol cells were crosslinked using 1% formaldehyde for 10 minutes and quenced with the addition of 0.125M glycine. Nuclear preparation was preforming using the truCHIP Chromatin Shearing Kit (Covaris) and chromatin was sonicated using a S220 ultrasonicator (Covaris) for 5 minutes. Immunoprecipitation for H3K27ac (Abcam 4729).
ChIP-seq libraries were preparied using Illumina libary preparation kit.

treatment_protocol: Cells were treated with either 4 µM or 2 µM CCS1477 for D/F or T/F AML, respectively, or equivalent volume of vehicle control. Cells were incubated with CCS1477 or vehicle for 1 hour at 37°C with 5% CO2.

value: leukemic splenocytes

value: acute myeloid leukemia


title: CUMC_S117


title: BT245, K27M, 4976, DM, R2


title: CUMC_S116


title: CUMC_S16


title: CUMC_S14


title: CUMC_S115


title: CUMC_S15


title: FT AML, Control, 1, IP

description:
Library name: FT1_DMSO_IP
vehicle control treated Tet2/Flt3-mutant leukemia, mouse 1, H3K27ac IP


title: CUMC_S13


title: FD AML, Control, 2, IP

description:
Library name: FD2_DMSO_IP
vehicle control treated Dnmt3a/Flt3-mutant leukemia, mouse 2, H3K27ac IP


title: BT245, K27M, 4976, DM, R1


title: CUMC_S113


title: FT AML, CCS1477, 2, IP

description:
Library name: FT2_CCS_IP
CCS1477 treated Tet2/Flt3-mutant leukemia, mouse 2, H3K27ac IP


title: FT AML, CCS1477, 1, IP

description:
Library name: FT1_CCS_IP
CCS1477 treated Tet2/Flt3-mutant leukemia, mouse 1, H3K27ac IP


title: hiPSC, NSD1het, H3K9me3

data_processing:
Raw sequences were first trimmed using fastp v0.22.0 with default settings before alignment using bwa-mem2 v2.2.1 to a combined reference of hg38+dm6 or mm10+dm6 with default settings
After identification of duplicates using picard v2.26.2’s “MarkDuplicates” module with default settings, alignments with MAPQ>3 mapping to each species was extracted into separate BAM files using samtools v1.14’s “view” module
Depth-normalized coverage tracks were generated using deepTools v3.5.1’s bamCoverage module with parameters “--normalizeUsing CPM --centerReads -e 200”
Regions with focal ChIP-seq enrichment with respect to input controls were identified using MACS v2.2.7.1 with settings “—broad --broad-cutoff 0.1”
Assembly: hg38, mm10, and dm6
Supplementary files format and content: BW files correspond to count-per-million normalized coverage tracks
Supplementary files format and content: broadPeak files correspond to enriched regions identified by MACS

extract_protocol:
Cells (cell lines or dissociated tumor cells) were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 18-30 cycles, 30s on 30s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing (see below).  ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Dynabeads Protein A beads (Invitrogen) Dynabaeds M-280 Sheep anti-Mouse IgG beads (Invitrogen) were washed and then incubated with antibodies (anti-H3K27me3 (1:40, CST 9733), anti-H3K4me3 (1:40, CST 9751), anti-H2AK119ub (1:40, CST 8240), anti-H3K27ac (1:100, Diagenode C15410196), anti-H3K36me2 (1:50, CST 2901)). One-two million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers.   ChIP reactions for SUZ12, RING1B, CBX2 and CTCF were performed as follows: antibodies (anti-SUZ12 (1:150, CST 3737), anti-RING1B (1:200, Active Motif 39663), anti-CBX2 (Bethyl A302-524 1:200), anti-CTCF (1:400, Diagenode C15410210)) were conjugated by incubating with 40ul protein A or G beads at 4°C for 6 hours, then chromatin from 5-10 million cells was added in RIPA buffer, incubated at 4°C o/n, washed using buffers from Ideal ChIP-seq Kit (1 wash with each buffer, corresponding to RIPA, RIPA+500mM NaCl, LiCl, TE), eluted from beads by incubating with Elution buffer for 30 minutes at room temperature.   Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked, and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents. Briefly, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

tag: chip antibody

value: H3K9me3 (Abcam ab8898)

value: Induced pluripotent stem cell


title: hiPSC, NSD1het, H3K36me3

value: H3K36me3 (Active Motif 61021)


title: hiPSC, NSD1het, Input


title: CUMC_S18


title: FD AML, CCS1477, 2, IP

description:
Library name: FD2_CCS_IP
CCS1477 treated Dnmt3a/Flt3-mutant leukemia, mouse 2, H3K27ac IP


title: CUMC_S114


title: FD AML, CCS1477, 1, IP

description:
Library name: FD1_CCS_IP
CCS1477 treated Dnmt3a/Flt3-mutant leukemia, mouse 1, H3K27ac IP


title: CUMC_S12


title: hiPSC, NSD1het, H3K36me2


title: CUMC_S112


title: FD AML, Control, 1, IP

description:
Library name: FD1_DMSO_IP
vehicle control treated Dnmt3a/Flt3-mutant leukemia, mouse 1, H3K27ac IP


title: hiPSC, NSD1het, H3K27me3


title: CUMC_S101


title: FT AML, CCS1477, 2, Input

description:
Library name: FT2_CCS_IN
CCS1477 treated Tet2/Flt3-mutant leukemia, mouse 2, input


title: CUMC_S110


title: HSJ019, KO, inputForCBX2RING1B


title: CUMC_S100


title: FT AML, Control, 2, Input

description:
Library name: FT2_DMSO_IN
vehicle control treated Tet2/Flt3-mutant leukemia, mouse 2, input


title: CUMC_S109


title: CUMC_S1


title: CUMC_S111


title: CUMC_S107


title: HSJ019, K27M, inputForCBX2RING1B


title: CUMC_E197


title: FT AML, CCS1477, 1, Input

description:
Library name: FT1_CCS_IN
CCS1477 treated Tet2/Flt3-mutant leukemia, mouse 1, input


title: CUMC_S108


title: FD AML, CCS1477, 2, Input

description:
Library name: FD2_CCS_IN
CCS1477 treated Dnmt3a/Flt3-mutant leukemia, mouse 2, input


title: CUMC_S106


title: HSJ019, KO, CBX2

value: CBX2 (Bethyl A302-524)


title: HSJ019, KO, RING1B

value: RING1B (Active Motif 39663)


title: HSJ019, K27M, RING1B


title: CUMC_S11


title: CUMC_E195


title: CUMC_E194


title: HSJ019, K27M, CTCF

value: CTCF (Diagenode C15410210)


title: CUMC_S104

value: Stroma


title: FD AML, CCS1477, 1, Input

description:
Library name: FD1_CCS_IN
CCS1477 treated Dnmt3a/Flt3-mutant leukemia, mouse 1, input


title: FT AML, Control, 1, Input

description:
Library name: FT1_DMSO_IN
vehicle control treated Tet2/Flt3-mutant leukemia, mouse 1, input


title: HSJ019, K27M, CBX2


title: CUMC_E196

value: Primary


title: FD AML, Control, 1, Input

description:
Library name: FD1_DMSO_IN
vehicle control treated Dnmt3a/Flt3-mutant leukemia, mouse 1, input


title: FD AML, Control, 2, Input

description:
Library name: FD2_DMSO_IN
vehicle control treated Dnmt3a/Flt3-mutant leukemia, mouse 2, input


title: G477, WT, inputForCBX2RING1B

value: Glioma cell line

value: H3 WT


title: CUMC_S105


title: CUMC_E192

value: Epithelium


title: G477, WT, RING1B


title: CUMC_S102


title: CUMC_E191


title: FT AML, CCS1477, 2

description:
Library name: FT-9539-p300i_S10_001
CCS1477 treated Tet2/Flt3-mutant leukemia, mouse 9539

data_processing:
FASTQ sequence files were aligned to the mouse genome version 10 using Kallisto with de novo junction discovery in AltAnalyze.
The fastq files were aligned to mouse genome Mm10 Kallisto and gene level FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were obtained using AltAnalyze 2.1.3 (Emig et al., 2010; Salomonis et al., 2009; Salomonis et al., 2010). To identify differentially expressed genes using default parameters moderated t-test with Benjamini-Hochberg multiple testing correction, raw p-value cut-off of 0.05, and an expression cut-off of 2-fold.
For all RNAseq experiments pathways and ontology enrichment analyses were performed with ToppGene (Chen et al., 2009) and GO-Elite (Zambon et al., 2012). All heatmaps from AltAnalyze were created using the HOPACH package via a connection to R (Salomonis et al., 2005).
Assembly: mouse genome mm10
Supplementary files format and content: tab-delimited text file

growth_protocol: Dnmt3afl/fl,Flt3ITD/ITD,Mx1Cre (D/F AML) and Tet2fl/fl,Flt3ITD/ITD,Mx1Cre (T/F AML)  leukemic splenocytes were isolated from moribund mice (n=3 mice/genotype) and c-Kit enriched using CD117 microbeads (Miltenyi BioTech). Equal numbers of 0.5x106 leukemia cells were plated in standard growth medium RPMI 1640 (Thermo Fisher Scientific) containing 20% FBS (HyClone) supplemented with mouse recombinant SCF (60ng/ml), IL6 (20ng/ml), and IL3 (20ng/ml) (Miltenyi Biotech).

extract_protocol:
At the end of the treatment protocol cells were lysed with Trizol. RNA was extracted according to Meyer et al., 2009. RNA quality and quantity were measured by Agilant 2200 Tape Station. Then samples with a RIN>8.0 were processed by ribosome depletion, stranded True-seq, paired-end 150 base pair (bp), 30 million reads.
RNA Seq libraries were generated with Illumina TruSeq Stranded mRNA HT kits.

treatment_protocol: Cells were treated with either 4 µM or 2 µM CCS1477 for D/F or T/F AML, respectively, or equivalent volume of vehicle control. Cells were incubated with CCS1477 or vehicle for 6 hours at 37°C with 5% CO2. Then cells were washed and snap fozen in TriZol.


title: FT AML, CCS1477, 3

description:
Library name: FT-9394-p300i_S12_001
CCS1477 treated Tet2/Flt3-mutant leukemia, mouse 9394


title: FT AML,Control, 3

description:
Library name: FT-9394-DMSO_S11_001
vehicle control treated Tet2/Flt3-mutant leukemia, mouse 9394

value: DMSO


title: G477, K27M, inputForCBX2RING1B


title: CUMC_E190


title: CUMC_E193


title: CUMC_E189


title: G477, K27M, RING1B


title: FT AML, Control, 2

description:
Library name: FT-9539-DMSO_S9_001
vehicle control treated Tet2/Flt3-mutant leukemia, mouse 9539


title: G477, K27M, CBX2


title: Line31_Transfer20_H3K9me3_ChIPseq

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

description: Library name: Line31_Transfer20_H3K9me3_ChIPseq

data_processing:
Raw ChIP-seq data files, as fastq files, were mapped to version 14 of the Neurospora crassa genome (nc14; for 50bp bigwig files) or to version 12 of the Neurospora crassa genome (nc12; for 500 bp bedgraph files)  with bowtie2 version 2.4.2, and output sam files were converted to sorted bam files using samtools (version 1.14), which were used by Deeptools (version 3.5.0) to produce bigwig files with resolutuions at either 50 basepair bins, or bedgraph files at 500 basepair or 5000 basepair bins for display on the Integrative Genomics Viewer (IGV). All bigwig and bedgraph files were normalized by Reads per Kilobase Per Million Reads (RPKM).
Assembly: Assembly: nc14_genome-seq-name.fasta (version 14; Rodriguez et al., [Pubmed ID: 35244156]) for all bigwig files, or nc12 (neurospora_crassa_or74a_12_supercontigs_mtDNA_mata.fasta; version 12 of the Neurospora crassa genome, provided here as a supplemental file) for all bedgraph files.
Supplementary files format and content: the bigwig files are generated by Deeptools; briefly, these files divide the genome into bins and the number (count) of sequencing reads per bin is reported for each bin. The bigwig file format is a single column with the RPKM-enrichment per bin displayed, and the seven headers indicate the chromosome and bin size. The bedgraph file format is a four column format with the first column being the chromosome name, the second column being the bin start position, the third column being the bin end position, and the fourth column being the RPKM-normalized enrichment per bin.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: Cultures of the individual isolates from a Mutation Accumulation (MA) experiment were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. For the MA experiment, Briefly, two ancestors of the FGSC 2489 (74-OR23-1VA) wild type background that were otherwise isogenic but differed in mating type were used to start the experiment. Each ancestor was divided into 20 lines, 40 lines in total. Lines were transferred by plating asexual spores, picking a single colony from a plate, moving the colony to a test tube for producing asexual spores, then plating the spores and isolating a single colony again. This process was repeated for 40 transfers. H3K9me3 ChIP-seq was performed on transfers five, eight, ten, twenty, and forty from lines 5, 11, 25, and 31; four ChIP-seq replicates (two techinical replicates for each of the two biological replicates) were performed for the mat A ancestor while two biological replicates were performed for the mat a ancestor.

extract_protocol:
Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and was disrupted by sonication, which simultaneously sheared chromatin, using a Bioruptor Pico (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 1uL) and samples were nutated overnight at 4oC. The next day, equilibrated protein A/G magnetic agarose beads (Pierce/Thermo Scientific; cat # PI78609) was added to bind the antibody, incubated for 2 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC. Samples (IP and input) were decrosslinked at 65oC overnight. The next day, samples were RNaseA treated for two hours at 50oC, then proteinase K treated for 2 hours at 50oC, the DNA was extracted with phenol:chloroform:IAA (25:24:1), and DNA was precipitated with ethanol, sodium acetate, and glycogen, and allowed to precipitate overnight at -80oC. The next day, samples were precipitated by centrifugation, washed, dried in a Speedvac and resuspended in 30uL TE. ChIP DNA was quantified with a Qubit 3.0 using the HS method.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries. Each library was prepared using the NEB Next Ultra II Library Preparation Kit (New England Biolabs, #E7645L) with the adapters from the NEBNext® Multiplex Oligos for Illumina®(Index Primers Set 1 [E7335L] or 2 [E7500L]) according to the manufacturer’s instructions, except that final libraries were PCR-amplified using only eight cycles for amplification. Libraries were sequenced on a NovaSeq 6000 at the University of Oregon Genomics and Cell Characterization Core Facility (UO GC3F).

treatment_protocol: Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 15 min in 0.5% formaldehyde at room temperature, with shaking at 100 rpm, and then quenched with 0.125M glycine for histone modification ChIP.

value: mycelia

value: asexual fungal hyphae

value: wildtype [FGSC 2489 (74-OR23-1VA) background]; mat a

value: overnight growth (16hrs) in 1xVogels+1.5% sucrose

tag: chip-seq antibody

value: Active Motif anti-H3K9me3 (cat# 39161)


title: Line31_Transfer10_H3K9me3_ChIPseq

description: Library name: Line31_Transfer10_H3K9me3_ChIPseq


title: CUMC_S103


title: CUMC_E187


title: FT AML, CCS1477, 1

description:
Library name: FT-9538-p300i_S8_001
CCS1477 treated Tet2/Flt3-mutant leukemia, mouse 9538

value: leukemic splenocytes

value: acute myeloid leukemia


title: FT AML, Control, 1

description:
Library name: FT-9538-DMSO_S7_001
vehicle control treated Tet2/Flt3-mutant leukemia, mouse 9538


title: Line31_Transfer40_H3K9me3_ChIPseq

description: Library name: Line31_Transfer40_H3K9me3_ChIPseq


title: DIPGXIII, KO, inputForRING1B

value: DIPGXIII


title: Line31_Transfer5_H3K9me3_ChIPseq

description: Library name: Line31_Transfer5_H3K9me3_ChIPseq


title: CUMC_E186


title: FD AML, CCS1477, 3

description:
Library name: FD-9276-p300i_S2_001
CCS1477 treated Dnmt3a/Flt3-mutant leukemia, mouse 9276


title: Line25_Transfer40_H3K9me3_ChIPseq

description: Library name: Line25_Transfer40_H3K9me3_ChIPseq


title: DIPGXIII, KO, inputForK4me3


title: CUMC_E185


title: Line31_Transfer8_H3K9me3_ChIPseq

description: Library name: Line31_Transfer8_H3K9me3_ChIPseq


title: CUMC_E184


title: FD AML, Control, 3

description:
Library name: FD-9276-DMSO_S1_001
vehicle control treated Dnmt3a/Flt3-mutant leukemia, mouse 9276


title: FD AML, CCS1477, 2

description:
Library name: FD-9383-p300i_S4_001
CCS1477 treated Dnmt3a/Flt3-mutant leukemia, mouse 9383


title: Line25_Transfer10_H3K9me3_ChIPseq

description: Library name: Line25_Transfer10_H3K9me3_ChIPseq


title: Line25_Transfer20_H3K9me3_ChIPseq

description: Library name: Line25_Transfer20_H3K9me3_ChIPseq


title: CUMC_E182


title: CUMC_E183


title: CUMC_E188


title: DIPGXIII, KO, H3K4me3


title: FD AML, CCS1477, 1

description:
Library name: FD-9388-p300i_S6_001
CCS1477 treated Dnmt3a/Flt3-mutant leukemia, mouse 9388


title: Line25_Transfer8_H3K9me3_ChIPseq

description: Library name: Line25_Transfer8_H3K9me3_ChIPseq


title: Line25_Transfer5_H3K9me3_ChIPseq

description: Library name: Line25_Transfer5_H3K9me3_ChIPseq


title: FD AML, Control, 2

description:
Library name: FD-9383-DMSO_S3_001
vehicle control treated Dnmt3a/Flt3-mutant leukemia, mouse 9383


title: CUMC_E180


title: CUMC_E181


title: Line5_Transfer40_H3K9me3_ChIPseq

description: Library name: Line5_Transfer40_H3K9me3_ChIPseq

value: wildtype [FGSC 2489 (74-OR23-1VA) background]; mat A


title: FD AML, Control, 1

description:
Library name: FD-9388-DMSO_S5_001
vehicle control treated Dnmt3a/Flt3-mutant leukemia, mouse 9388


title: Line5_Transfer20_H3K9me3_ChIPseq

description: Library name: Line5_Transfer20_H3K9me3_ChIPseq


title: DIPGXIII, K27M, inputForK4me3


title: scRNAseq, Py8119 tumor, WT (CA) rep2

city: Perth

first: Michael

middle: William

last: Murrey

state: WA

address: 35 Stirling Hwy, Crawley

department: Biomedical Sciences

country: Australia

institute: University of Western Australia

description:
WT_ca2
10x genomics

library_source: transcriptomic single cell

data_processing:
All single cell libraries were sequenced on the Illumina NovaSeq 6000. The BCL sequencing files were demultiplexed and converted into FASTQ using the bcl2fastq utility of Illumina BaseSpace Sequence Hub
FASTQ files were processed using Cell Ranger 7.0.0 using the Cell Ranger-compatible transcriptome refdata-gex-mm10-2020-A reference. Both intronic and exonic reads were counted.
Assembly: mm10-2020-A
Supplementary files format and content: Cellranger filtered Tab-seperated values file and matrix files

source_name: Py8119 Orthotopic Mammary tumor

extract_protocol:
Py8119 tumors were minced with scalpel blades and dissociated in 0.1 mg/ml DNAse 1 and 1.5 mg/ml collagenase type 4 for 1 hour at 37°C with an additional 0.1 mg/ml of DNAse 1 added for 30 minutes. Dissociated tumors were then passed through a 100µM cell strainer followed by red cell lysis. Aliquots of 1x106 cells were stored at -80°C in 50% FCS, 10% DMSO in F12K media. Frozen aliquots were thawed for use in single cell experiments.
For the Vehicle and RK20449 treated tumors, the 10x Chromium 3′ v2 workflow was used according to the manufacturer’s directions with approximately 9000 cells captured per sample. All other tumors were processed using the 10x Chromium 3′ v3 workflow and approximately 6000 cells captured per sample.

value: Py8119 Orthotopic Mammary tumor

value: untreated


title: DIPGXIII, KO, inputForCBX2


title: DIPGXIII, KO, H2AK119ub


title: DIPGXIII, KO, RING1B

value: RING1B (Active Motif 39663)


title: CUMC_E179

value: Primary


title: DIPGXIII, K27M, inputForCBX2H2Aub

value: Glioma cell line


title: DIPGXIII, K27M, H3K4me3


title: scRNAseq, Py8119 tumor, WT (CA) rep1

description:
WT_ca1
10x genomics


title: DIPGXIII, K27M, H2AK119ub


title: Line5_Transfer10_H3K9me3_ChIPseq

description: Library name: Line5_Transfer10_H3K9me3_ChIPseq


title: DIPGXIII, KO, CBX2

value: CBX2 (Bethyl A302-524)


title: DIPGXIII, K27M, CTCF

value: CTCF (Diagenode C15410210)


title: Line5_Transfer8_H3K9me3_ChIPseq

description: Library name: Line5_Transfer8_H3K9me3_ChIPseq


title: CUMC_E177

value: Epithelium


title: scRNAseq, Py8119 tumor, CA, rep2

description:
HckCa2
10x genomics

value: C57black6 HckCA


title: CUMC_E176


title: scRNAseq, Py8119 tumor, WT (KO), rep3

description:
WT_ko3
10x genomics


title: scRNAseq, Py8119 tumor, CA, rep1

description:
HckCa1
10x genomics


title: CUMC_E174


title: Line5_Transfer5_H3K9me3_ChIPseq

description: Library name: Line5_Transfer5_H3K9me3_ChIPseq

value: mycelia

value: asexual fungal hyphae


title: BT245, KO, inputForK4me3


title: Line11_Transfer40_H3K9me3_ChIPseq

description: Library name: Line11_Transfer40_H3K9me3_ChIPseq

value: overnight growth (16hrs) in 1xVogels+1.5% sucrose


title: DIPGXIII, K27M, CBX2


title: Line11_Transfer20_H3K9me3_ChIPseq

description: Library name: Line11_Transfer20_H3K9me3_ChIPseq

value: Active Motif anti-H3K9me3 (cat# 39161)


title: scRNAseq, Py8119 tumor, WT (KO), rep1

description:
WT_ko1
10x genomics


title: Line11_Transfer10_H3K9me3_ChIPseq

description: Library name: Line11_Transfer10_H3K9me3_ChIPseq


title: BT245, KO, inputForCBX2RING1B


title: BT245, KO, inputForH2Aub


title: Line11_Transfer5_H3K9me3_ChIPseq

description: Library name: Line11_Transfer5_H3K9me3_ChIPseq


title: Line11_Transfer8_H3K9me3_ChIPseq

description: Library name: Line11_Transfer8_H3K9me3_ChIPseq


title: BT245, KO, RING1B


title: scRNAseq, Py8119 tumor, KO, rep3

description:
HckKo3
10x genomics

value: C57black6, HckKO


title: CUMC_E178


title: scRNAseq, Py8119 tumor, KO, rep2

description:
HckKo2
10x genomics


title: CUMC_E175


title: scRNAseq, Py8119 tumor, KO, rep1

description:
HckKo1
10x genomics


title: Neonatal cardiomyocytes, Ad-SPTBN1-3

city: Xi’an

first: Rongjin

last: Yang

address: 169 Changle West Road

department: Department of Cardiology

country: China

institute: Air Force Medical University

description: Sample 18

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence_low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38_mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: neonatal cardiomyocytes

growth_protocol: Mouse neonatal cardiomyocytes were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol® Reagent (Invitrogen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

value: neonatal cardiomyocytes

value: {beta}II spectrin overexpression

value: normal culture

tag: time

value: Day 2


title: Neonatal cardiomyocytes, Ad-SPTBN1-2

description: Sample 17


title: CUMC_E173


title: mat-a_ancestor_rep2_H3K9me3_ChIPseq

description: Library name: mat-a_ancestor_rep2_H3K9me3_ChIPseq

value: wildtype [FGSC 2489 (74-OR23-1VA) background]; mat a


title: scRNAseq, Py8119 tumor, WT (KO), rep2

description:
WT_ko2
10x genomics

value: Py8119 Orthotopic Mammary tumor

value: untreated


title: BT245, KO, H3K4me3

value: Glioma cell line


title: Neonatal cardiomyocytes, Ad-SPTBN1-1

description: Sample 16


title: Neonatal cardiomyocytes, Ad-scramble-3

description: Sample 15

value: Ad-scramble


title: BT245, KO, CBX2

value: CBX2 (Bethyl A302-524)


title: BT245, K27M, inputForK4me3


title: BT245, KO, H2AK119ub


title: matA_ancestor_rep3_H3K9me3_ChIPseq

description: Library name: matA_ancestor_rep3_H3K9me3_ChIPseq

value: wildtype [FGSC 2489 (74-OR23-1VA) background]; mat A


title: Neonatal cardiomyocytes, Ad-scramble-2

description: Sample 14


title: mat-a_ancestor_rep1_H3K9me3_ChIPseq

description: Library name: mat-a_ancestor_rep1_H3K9me3_ChIPseq


title: scRNAseq, Py8119 tumor, Day 14,  rep1

description:
Day14_1
10x genomics


title: matA_ancestor_rep4_H3K9me3_ChIPseq

description: Library name: matA_ancestor_rep4_H3K9me3_ChIPseq


title: scRNAseq, Py8119 tumor, Day 10, rep2

description:
Day10_2
10x genomics


title: BT245, K27M, inputForCBX2H2Aub


title: Neonatal cardiomyocytes, Ad-scramble-1

description: Sample 13


title: BT245, K27M, H3K4me3


title: scRNAseq, Py8119 tumor, Day 10, rep1

description:
Day10_1
10x genomics


title: BT245, K27M, H2AK119ub


title: scRNAseq, Py8119 tumor, Rk20449  treated, rep3

description:
Rk3
10x genomics


title: PCP Patient_035

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

description:
Library name: PCP035
Survivor

data_processing:
Trimmomatic (v0.38) for quality and adapter trimming
STAR aligner (v2.7.11b) to human genome (Ensembl GRCh38 build 88)
RSEM (v.1.3.0) for gene counting
DEseq2 (v1.42.1 for differential expression analysis
Assembly: Ensembl GRCh38 build 88
Supplementary files format and content: tab delimited text file includes raw count for each sample

source_name: BAL fluid

extract_protocol:
Zymo Direct-zol mini-Prep kit
NEBNext Ultra II Directional RNA Library Prep kit and mammalian rRNA was depleted with NEBNext rRNA Depletion kit

value: BAL fluid


title: Dictionary of random substrate library (replicate 2)

city: Hong Kong

first: Joe

last: Lam

address: 21 Sassoon road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description: Library name: biol rep 2 dict-oKW2182

library_source: other

data_processing:
Adaptor sequences and the random nucleotides were trimmed using cutadapt. The insert sequences were then collapsed and exported with fastx_collapser and seqkit. The uncleaved input sample was used as a dictionary to map the cleaved sequences with pandas. Cleaved sequences of 15 to 25 nucleotides were used to find the original uncleaved sequences from the dictionary. Cleavage efficiencies were calculated by dividing the number of cleaved reads by that of reads found in the dictionary.
Assembly: Uncleaved substrate were used as a reference to determine the cleavage sites
Supplementary files format and content: Excel files containing read count of each cleavage products from each sample

molecule: other

organism: synthetic construct

source_name: In vitro cleavage reaction

extract_protocol:
Cleavage products were collected and purified with acid-phenol:choloform and ethanol precipitation
Random 35-nucleotide-containing RNA substrates were incubated with and without Cas13 proteins. Input and cleaved RNAs were collected with acid-phenol:chloroform extraction and ethanol precipitation. 3´ adaptor ligation was then performed. The RNA was subsequently subjected to reverse transcription. A total of 3 rounds of PCR were performed to amplify the libraries.

treatment_protocol: Random substrates were cleaved by active Cas13 complex in vitro

value: In vitro cleavage reaction

value: biological replicate 2


title: PCP Patient_037

description:
Library name: PCP037
Survivor


title: matA_ancestor_rep1_H3K9me3_ChIPseq

description: Library name: matA_ancestor_rep1_H3K9me3_ChIPseq

value: mycelia

value: asexual fungal hyphae

value: overnight growth (16hrs) in 1xVogels+1.5% sucrose


title: scRNAseq, Py8119 tumor, Rk20449  treated, rep2

description:
Rk2
10x genomics


title: PCP Patient_036

description:
Library name: PCP036
Survivor


title: scRNAseq, Py8119 tumor, Rk20449  treated, rep1

description:
Rk1
10x genomics


title: In vitro Cas13 cleavage of random substrate library (CasRx; targeting crRNA; replicate 2)

description: Library name: biol rep 2 Rx-16


title: PCP Patient_034

description:
Library name: PCP034
Survivor


title: In vitro Cas13 cleavage of random substrate library (CasRx; no protein; replicate 2)

description: Library name: biol rep 2 Rx-noPro


title: scRNAseq, Py8119 tumor, Vehicle treated, rep3

description:
Veh3
10x genomics

value: Captisol


title: matA_ancestor_rep2_H3K9me3_ChIPseq

description: Library name: matA_ancestor_rep2_H3K9me3_ChIPseq

value: Active Motif anti-H3K9me3 (cat# 39161)


title: scRNAseq, Py8119 tumor, Day 14,  rep2

description:
Day14_2
10x genomics


title: scRNAseq, Py8119 tumor, Vehicle treated, rep1

description:
Veh1
10x genomics


title: scRNAseq, Py8119 tumor, Vehicle treated, rep2

description:
Veh2
10x genomics


title: PCP Patient_033

description:
Library name: PCP033
Non-Survivor


title: In vitro Cas13 cleavage of random substrate library (Cas13bt3;  targeting crRNA; replicate 2)

description: Library name: biol rep 2 bt3-16


title: In vitro Cas13 cleavage of random substrate library Cas13bt3; no protein; replicate 2)

description: Library name: biol rep 2 bt3-noPro


title: BT245, K27M, CTCF

value: CTCF (Diagenode C15410210)


title: hiPSC, WT, RING1B

value: RING1B (Active Motif 39663)

value: Induced pluripotent stem cell

value: WT NSD1


title: PCP Patient_032

description:
Library name: PCP032
Survivor


title: KO3

city: Seoul

first: Si-Won

last: Park

address: Anam-ro

country: South Korea

institute: Korea University

data_processing:
The raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Mus musculus (mm10) using HISAT v2.1.0.
HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes). These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2.
Transcript assembly and abundance estimation using StringTie(2, 3). After alignment, StringTie v1.3.4d was used to assemble aligned reads into transcripts and to estimate their abundance.
It provides the relative abundance estimates as FPKM values (Fragments Per Kilobase of exon per Million fragments mapped) of transcript and gene expressed in each sample.
Genes with one more than zeroed FPKM values in the samples were excluded. To facilitate log2 transformation, 1 was added to each FPKM value of filtered genes
Assembly: GCF_000001635.20 (mm10)
Supplementary files format and content: Excel spreadsheet format which includes contents; 1) Gene_symbol, 2) NCBI Protein accession ID, 3) Product, 4) Fold change, 5) Volume, 6) GOmap stat, 7) GOmap genes, 8) KEGG stat, 9) KEGG genes

source_name: LDB1fl/fl Vav1-cre(+) (cKO) fetal liver erythroblast stage 1

extract_protocol:
Total RNA was isolated from sorted E14.5 fetal liver erythroblast stage 1 using miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
In order to construct cDNA libraries with the TruSeq Stranded mRNA Sample Prep kit (Illumina, USA), 1 mg of total RNA was used. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100 nt paired-end sequencing by Illumina NovaSeq (Illumina, USA).

value: LDB1fl/fl Vav1-cre(+)

value: liver

value: proerythroblast

tag: age

value: embryonic day 14.5


title: In vitro Cas13 cleavage of random substrate library (PspCas13b;  targeting crRNA; replicate 2)

description: Library name: biol rep 2 Psp-16


title: In vitro Cas13 cleavage of random substrate library (PspCas13b; no protein; replicate 2)

description: Library name: biol rep 2 Psp-noPro


title: hiPSC, WT, Input


title: PCP Patient_029

description:
Library name: PCP029
Survivor


title: KO2


title: hiPSC, WT, H3K9me3

value: H3K9me3 (Abcam ab8898)


title: KO1


title: In vitro Cas13 cleavage of random substrate library (LwaCas13a; targeting crRNA; replicate 2)

description: Library name: biol rep 2 Lwa-16


title: hiPSC, WT, SUZ12


title: BT245, K27M, CBX2

value: CBX2 (Bethyl A302-524)

value: Glioma cell line


title: hiPSC, WT, H3K4me3


title: PCP Patient_028

description:
Library name: PCP028
Survivor

value: BAL fluid


title: In vitro Cas13 cleavage of random substrate library (LwaCas13a; no protein; replicate 2)

description: Library name: biol rep 2 Lwa-noPro

value: In vitro cleavage reaction

value: biological replicate 2


title: WT3

source_name: LDB1fl/fl Vav1-cre(-) (WT) fetal liver erythroblast stage 1

value: LDB1fl/fl Vav1-cre(-)


title: PCP Patient_031

description:
Library name: PCP031
Survivor


title: hiPSC, WT, H3K36me2


title: hiPSC, WT, H3K36me3

value: H3K36me3 (Active Motif 61021)


title: In vitro Cas13 cleavage of random substrate library (LbuCas13a; targeting crRNA; replicate 2)

description: Library name: biol rep 2 Lbu-16


title: PCP Patient_026

description:
Library name: PCP026
Survivor


title: WT2


title: PCP Patient_027

description:
Library name: PCP027
Survivor


title: Dictionary of random substrate library (replicate 1)

description: Library name: biol rep 1 dict-oKW2182

value: biological replicate 1


title: hiPSC, WT, H3K27me3


title: PCP Patient_020

description:
Library name: PCP020
Survivor


title: PCP Patient_018

description:
Library name: PCP018
Non-Survivor


title: mESC, WT, R2

value: Embryonic stem cell


title: In vitro Cas13 cleavage of random substrate library (CasRx; no protein; replicate 1)

description: Library name: biol rep 1 Rx-noPro


title: hiPSC, WT, H2AK119ub


title: mESC, NSD1KO, R2


title: mESC, WT, R1


title: PCP Patient_019

description:
Library name: PCP019
Survivor


title: hiPSC, WT, H3K27ac

value: H3K27ac (Diagenode C15410196)


title: In vitro Cas13 cleavage of random substrate library (CasRx; targeting crRNA; replicate 1)

description: Library name: biol rep 1 Rx-16


title: In vitro Cas13 cleavage of random substrate library (LbuCas13a; no protein; replicate 2)

description: Library name: biol rep 2 Lbu-noPro


title: mESC, NSD1KO, R1


title: PCP Patient_017

description:
Library name: PCP017
Non-Survivor


title: hiPSC, WT, CTCF

value: CTCF (Diagenode C15410210)

value: Induced pluripotent stem cell


title: PCP Patient_021

description:
Library name: PCP021
Survivor


title: mESC, WT, inputForRING1B, R2

value: WT NSD1


title: PCP Patient_016

description:
Library name: PCP016
Survivor


title: WT1

value: liver


title: hiPSC, WT, CBX2


title: In vitro Cas13 cleavage of random substrate library (Cas13bt3;  targeting crRNA; replicate 1)

description: Library name: biol rep 1 bt3-16


title: PCP Patient_015

description:
Library name: PCP015
Survivor


title: In vitro Cas13 cleavage of random substrate library Cas13bt3; no protein; replicate 1)

description: Library name: biol rep 1 bt3-noPro


title: mESC, WT, inputForRING1B, R1


title: hiPSC, NSD1het, SUZ12


title: hiPSC, NSD1het, RING1B

value: RING1B (Active Motif 39663)


title: PCP Patient_014

description:
Library name: PCP014
Survivor


title: mESC, WT, inputForCBX2, R2


title: In vitro Cas13 cleavage of random substrate library (PspCas13b; no protein; replicate 1)

description: Library name: biol rep 1 Psp-noPro


title: hiPSC, NSD1het, H3K4me3


title: mESC, WT, inputForCBX2, R1


title: PCP Patient_012

description:
Library name: PCP012
Non-Survivor


title: In vitro Cas13 cleavage of random substrate library (LwaCas13a; targeting crRNA; replicate 1)

description: Library name: biol rep 1 Lwa-16


title: hiPSC, NSD1het, H2AK119ub


title: PCP Patient_013

description:
Library name: PCP013
Survivor


title: mESC, WT, RING1B, R2


title: PCP Patient_011

description:
Library name: PCP011
Survivor


title: In vitro Cas13 cleavage of random substrate library (LwaCas13a; no protein; replicate 1)

description: Library name: biol rep 1 Lwa-noPro


title: mESC, WT, RING1B, R1


title: hiPSC, NSD1het, CTCF


title: In vitro Cas13 cleavage of random substrate library (PspCas13b;  targeting crRNA; replicate 1)

description: Library name: biol rep 1 Psp-16


title: In vitro Cas13 cleavage of random substrate library (LbuCas13a; targeting crRNA; replicate 1)

description: Library name: biol rep 1 Lbu-16


title: In vitro Cas13 cleavage of random substrate library (LbuCas13a; no protein; replicate 1)

description: Library name: biol rep 1 Lbu-noPro


title: PCP Patient_009

description:
Library name: PCP009
Survivor


title: SMNV3

city: hangzhou

first: Zhao

last: lan

state: Zhejiang Province

address: Dinglan Street

institute: Hangzhou Traditional Chinese Medicine Hospital

description: Library name: sample6

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: mRatBN7.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Rat mesenchymal stem cells

growth_protocol: Rat mesenchymal stem cells were cultured in a high-glucose DMEM medium containing 10% serum at 37°C and 5% CO2 in an incubator.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

treatment_protocol: Rat mesenchymal stem cells were incubated with 200 nM doxorubicin for 24 hours, followed by replacement with fresh complete medium for an additional 6 days to induce senescence. During this subsequent period, cells were treated with either 100 µg/ml SMNV or a vehicle control.

value: Rat mesenchymal stem cells

value: WT

value: SMNV intervenes in doxorubicin-induced senescence of rMSCs


title: hiPSC, NSD1het, CBX2

value: CBX2 (Bethyl A302-524)


title: mESC, WT, CBX2, R2


title: PCP Patient_008

description:
Library name: PCP008
Survivor

value: BAL fluid


title: hNPC, H3K4me3

value: Neural progenitor cell


title: mESC, WT, CBX2, R1


title: Xenograft Bone Marrow TARGET-seq Genotyping

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

institute: University Health Network

description: Library name: Xenograft_BM_TARGETseq_Genotyping

data_processing:
RNA sequencing data were pre-processed with a custom pipeline (https://github.com/asgerjakobsen/TARGET-seq-plus-RNA) to trim and demultiplex reads into single-cell barcodes using cutadapt (v3.4) and then map them to the hg38 reference genome and ERCC92 transcripts with STARsolo (v2.7.10a) using the GENCODE v38 reference gene annotation.
Genotyping amplicon data were demultiplexed and processed to generate tables of allelic counts, which were used to call cell genotypes as described in Jakobsen et al. 2024.
FACS indexing, genotyping and transcriptome data were integrated for downstream analysis in Seurat.
The following QC filters were applied to the starting dataset of 10,640 cells: minimum 5000 RNA reads per cell, minimum 1000 genes per cell, maximum % mitochondrial reads = 15%, and maximum % ERCC reads = 65%, leaving 8,998 cells remaining. The filtered data were integrated with the 13,247 primary BM cells from the original TARGET-seq+ dataset (Jakobsen et al. 2024).
Assembly: hg38
Supplementary files format and content: RDS file containing Seurat object with quality controlled TARGET-seq+ data from 13 primary bone marrow samples (Jakobsen et al. 2024) integrated with data from 5 xenografted bone marrow samples and 1 control primary sample (this study).
Supplementary files format and content: Table of tab-separated values for TARGET-seq+ genotyping data from 5 xenografted bone marrow samples and 1 control sample. For each mutation and each single cell, data are provided for the genomic DNA amplicon and the heterozygous germline SNP.

source_name: Bone Marrow

extract_protocol:
FACS sorting into 384-well plates containing lysis buffer, as per the TARGET-seq+ protocol (Jakobsen et al. 2024).
TARGET-seq+ protocol (Jakobsen et al. 2024) for 3' RNA sequencing and targeted genotyping from single cells.

value: Bone Marrow


title: hNPC, CBX2


title: mESC, NSD1KO, inputForRING1B, R1


title: SMNV2

description: Library name: sample5


title: mESC, NSD1KO, inputForRING1B, R2


title: PFA4, normoxia

data_processing:
Raw sequences were processed using Juicer v1.6 with default parameters against hg38 or mm10
Juicer .hic files were converted to cooler .mcool files using hic2cool v0.8.3
Bias vectors were re-computed using the balance module of cooler v0.8.11 with default settings
CNV-aware bias vectors were determined using OneD with default parameters
Boundary scores were calcualted using RobusTAD with default parameters
Compartment scores were computed using cooltools with GC content as the sign-orienting signal
Assembly: hg38
Supplementary files format and content: MCOOL files contain multi-resolution contact maps in the Cooler format
Supplementary files format and content: CSV files contain the first eigenvector of 100-kb balanced matrices (i.e., compartment score)
Supplementary files format and content: TSV files contain RobusTAD boundary scores computed using 50-kb balanced matrices

extract_protocol:
Cells were crosslinked using formaldehyde, after which proximity-ligated DNA was digested using a 4-base cutter restriction enzyme (DpnII) with intact permeabilized nuclei. Following fill in and biotinylation of the resulting 5' overhangs and ligation of the blunt ends, DNA was sheared and then pulled down using streptavidin beads
Libraries were prepared following manufacturer guidelines using the NEB kit, and the amplified libraries were ultimately sequenced in paired-end mode

value: Ependymoma cell line

value: Normoxia


title: BT245, UNC4976, RING1B

value: Glioma cell line


title: SMNV1

description: Library name: sample4


title: BT245, DMSO, RING1B

value: DMSO


title: PFA4, hypoxia

value: Hypoxia


title: mESC, NSD1KO, inputForCBX2, R1

value: Embryonic stem cell


title: BT245, UNC4976, CBX2


title: G477, K27M


title: Dox3

description: Library name: sample3

value: Doxorubicin-induced senescence


title: mESC, NSD1KO, inputForCBX2, R2


title: Dox2

description: Library name: sample2


title: BT245, DMSO, CBX2


title: Dox1

description: Library name: sample1


title: hNPC, wt

value: WT NSD1


title: 12week homo

city: Nishinomiya

first: Takuma

last: Yamamoto

address: 1-1 Mukogawa-Cho

institute: Hyogo Medical University

data_processing:
The sequencing reads were trimmed using Cutadapt v1.1 and Trimmomatic v0.32 with the following options:  --match-read-wildcards -O 1 (Cutadapt) / -phred33 LEADING:0 TRAILING:0 SLIDINGWINDOW:20:20 MINLEN:50 (Trimmomatic).
Trimmed  reads were aligned to the GRCm38 genome assembly using TopHat v2.0.14 and bowtie v1.1.1 with the following options: --microexon-search --bowtie1.
Aligned reads were used as input for PSI.sh v2.0 to determine alternative splicing expression levels (PSI).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include PSI values for each Sample

source_name: Skeltal muscle

extract_protocol:
Total RNAs from mouse skeltal muscle at the age of 1, 12 and 36 weeks were extracted by using RNeasy Plus Universal Mini Kit (Qiagen). Nine representative libraries were generated for the nine groups (Wild-type, Heterozygote and Homozygote of 1 week, 12 weeks and 36 weeks) by RNA-seq with SMART-seq v4 Ultra Low Input RNA kit for sequencing (Takara Bio Inc.) and Nextera XT DNA Library Prep Kit (Illumina, Tokyo, Japan) and sequenced on a NovaSeq 6000 instrument (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Skeltal muscle

value: homozygote


title: HSJ019, K27M


title: mESC, NSD1KO, RING1B, R2

value: RING1B (Active Motif 39663)


title: mESC, NSD1KO, RING1B, R1


title: HSJ019, KO


title: DIPGXIII, KO

value: DIPGXIII


title: BT245, KO


title: mESC, NSD1KO, CBX2, R2


title: hiPSC, WT

value: Induced pluripotent stem cell


title: S9_CB102_InVitro_1

status: Public on Mar 01 2026

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

description: Library name: s9

data_processing:
Raw fastq files were processed with the nfcore/rnaseq pipeline v3.19.0
Assembly: custom-built genome based on the GRCh38 assembly and v114 of the Ensembl annotations plus the forward and reverse fusion transcripts
Supplementary files format and content: TAB-separated text file with raw counts per gene and sample

source_name: Human cord blood-derived cells

growth_protocol: In vitro t(9;11) cells derived from human cord blood were maintained in StemMACS™ HSC Expansion Media (Miltenyi) supplemented with 10% FCS, 1% Penicillin/Streptomycin, human cytokines (IL-3, IL-6, SCF, FLT3L, SCF, G-CSF, 50 ng/ml each), SR-1 and UM-729 (0.75 µM each). To analyze cells from the same human cord blood donors in vivo, t(9;11) cells were transplanted in the tail vein of NSG mice. At signs of sickness or after one year the mice were sacrificed and the t(9;11) cells were isolated from the bone marrow by fluorescence-activated cell sorting (humanCD45+, murineCD45-).

extract_protocol:
A modified SmartSeq 2 protocol was applied with total RNA input amounts ranging between 50 and 100 ng. RNA was primed by adding 1 µM Oligo‐dT Primer (final conc.; 5´AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN; V = A/C/G, N = any base), 1 mM dNTPs (final conc.) followed by a denaturation step at 72 °C for 3 min and immediately cooling on ice. Reverse transcription was performed in a 10 µL volume reaction by using 0.5 µL Superscript II RT (200 U/µL, Thermo Fisher Scientific, 18064022), 0.4 µL RNAse inhibitor (40 U/µL, Promega, N2515), 5 mM DTT, 1 M Betaine, 6 mM MgCl2 and 1 µm TSO (B‐AAGCAGTGGTATCAACGCAGAGTACAT997, B = 5’ biotin, 7 = LNA g, 9 = RNA‐G) under the following incubation conditions: 42 °C for 90 min, 10 × cycling of 50 °C for 2 min and 42 °C for 2 min, finalized by 70 °C for 15 min. The  pre-amplification of the cDNA was carried out by utilizing the KAPA HiFi HotStar Ready Mix (Roche, KK2601) and 0.1 µM of the IS PCR primers (5´AAGCAGTGGTATCAACGCAGAGT) in a 25 µL volume reaction under the following PCR conditions: 98 °C for 3 min, 12× cycling of 98 °C for 20 s, 67 °C for 15 s, 72 °C for 6 min and a final elongation at 72 °C for 5 min. The cDNA was purified with 0.8× Agencourt AMPure XP Beads (Beckman Coulter, A63881), quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32851) and the cDNA integrity was examined via the analysis of the fragment size distribution by using the Agilent 2100 Bioanalyzer (High Sensitivity DNA Analysis Kit, Agilent, 5067‐4626).
The final libraries were prepared by applying a tagmentation‐based approach using the Nextera DNA Library Preparation Kit (Illumina, FC‐131‐1024). Of each cDNA, 2 ng were tagmented for 10 min at 55 °C by the use of 0.25 µL of the Tagment DNA Enzyme 1 in a 20 µL reaction. Tagmented cDNAs were purified with MinElute PCR Purification Kit (Qiagen, 28004) following the manufacturer's instructions. The amplification of the libraries was performed in a 30 µL reaction using the NEBNext High‐Fidelity 2X PCR Master Mix (New England Biolabs, M0541S) and 0.33 µM indexed adapters (5′AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC and 5″CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG; Illumina). 8 PCR cycles were done of the following PCR program: 75 °C 5 min, 98 °C 10 s, cycling of 98 °C 30 s, 63 °C 30 s and 7 2 °C 1 min, finalized by a long elongation at 72 °C for 7 min. The libraries were purified by utilizing 0.9 × Agencourt AMPure XP Beads, the DNA concentrations and fragment distributions were measured as before. The libraries were sequenced on the Aviti sequencing platform (Element Biosciences).

treatment_protocol: No treatment

value: Human cord blood-derived cells

value: Isolated from cord blood donor CB102 (Donor 2)

value: Differentiated human hematopoietic stem and progenitor cells

value: In vitro culture


title: mESC, NSD1KO, CBX2, R1

value: CBX2 (Bethyl A302-524)


title: 12week wild

value: wild type


title: hiPSC, NSD1het


title: 12week hetero

value: heterozygote


title: S10_CB102_InVitro_2

description: Library name: s10


title: S5_CB102_48

description: Library name: s5

source_name: Human cord blood-derived cells isolated from the bone marrow of NSG mice

value: Xenograft experiment, NSG mouse


title: T-ALL3, day 7, technical replicate 1

city: Chicago

first: Caner

last: Saygin

state: IL

address: 900 E 57th Street, KCBD 7123B

institute: The University of Chicago

description: Library name: TALL3_day7_R1

data_processing:
Raw reads wre quality and adapter trimmed using TrimGalore. Trimmed reads were aligned to the human reference genome (hg38) using STAR aligner. Gene-level count matrices were generated from BAM files using HTseq.
Assembly: hg38
Supplementary files format and content: txt files, raw expression matrices

source_name: peripheral blood

growth_protocol: For in vitro assays, cells were thawed and cultured in RPMI-1640 medium supplemented with 10% FBS, 2 mM L-glutamine, and an insulin–transferrin–selenium supplement at 37°C and 5% CO2 in the gas phase.

extract_protocol:
Total RNA was extracted on days 4 and 7 using TRIzol reagent (Thermo Fisher Scientific), following the manufacturer’s instructions. Untreated baseline samples (day 0) were also collected, and all conditions were processed in technical replicates.
TruSeq

treatment_protocol: Cells were treated with 2.5 mM ziftomenib.

value: peripheral blood

value: primary cells

value: leukemic blasts

value: KMT2A/KNL1 rearrangement

value: ziftomenib


title: S7_CB96_InVitro_1

description: Library name: s7

value: Cells from cord blood donor CB96 (Donor 1)


title: S8_CB96_InVitro_2

description: Library name: s8


title: S4_CB102_46

description: Library name: s4

value: Human cord blood-derived cells isolated from the bone marrow of NSG mice


title: S6_CB102_49

description: Library name: s6


title: S3_CB96_20

description: Library name: s3


title: S1_CB96_18

description: Library name: s1


title: Karpas-45, shMEF2CKD2, technical replicate 3

description: Library name: Karpas_MEF2CKD2_R3

data_processing:
Raw reads were quality and adapter trimmed using TrimGalore. Trimmed reads were aligned to the human reference genome (hg38) using STAR aligner. Gene-level count matrices were generated from BAM files using HTseq.
Assembly: hg38
Supplementary files format and content: txt files, raw expression matrices

source_name: bone marrow

growth_protocol: Karpas-45 cells were thawed and cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin-glutamine at 37°C and 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific), following the manufacturer’s instructions. All conditions were processed in technical triplicates.
TruSeq

treatment_protocol: No treatments.

value: bone marrow

value: MEF2C KD

value: untreated


title: Karpas-45, shMEF2CKD2, technical replicate 1

description: Library name: Karpas_MEF2CKD2_R1


title: Karpas-45, scramble control, technical replicate 3

description: Library name: Karpas_scr_R3

value: WT


title: T-ALL3, day 0, technical replicate 2

description: Library name: TALL3_day0_R2


title: T-ALL3, day 4, technical replicate 1

description: Library name: TALL3_day4_R1


title: T-ALL3, day 7, technical replicate 2

description: Library name: TALL3_day7_R2


title: Karpas-45, MEF2COE, technical replicate 3

description: Library name: Karpas_MEF2COE_R3

value: MEF2C OE


title: Karpas-45, scramble control, technical replicate 1

description: Library name: Karpas_scr_R1


title: hfPSCs_H9_DNA methylation

city: Beijing

first: Qizhi

last: Wang

address: Chaoyang District

institute: Chinese Academy of Sciences

description: Library name: hfPSCs_H9_DNA methylation

data_processing:
After trimming low quality sequencing reads and adapters, the clean reads were mapped to hg19 by Bismark (v0.23.1) following the default parameters. Unconverted reads, multiple mapped reads and duplicate reads introduced by PCR were also removed
Assembly: hg19
Supplementary files format and content: null

source_name: hfPSCs

extract_protocol:
Genomic DNA was extracted using the phenol-chloroform method. First, cells were lysed with a buffer containing SDS and proteinase K. Then, proteins were removed by phenol-chloroform extraction. Finally, genomic DNA was precipitated with ethanol.
Starting with 500ug of genomic DNA for library construction, bisulfite conversion was performed following the protocol of the EZ DNA Methylation-Gold™ Kit (D5006) for DNA methylation analysis to prepare the WGBS library. This workflow primarily includes the following steps: 1) DNA Fragmentation; 2) End Repair; 3) A-Tailing (Adding 'A' to DNA ends); 4) Ligating Methylated Adapters; 5) Size selection via 2% agarose gel electrophoresis and target fragment recovery; 6) C-T conversion (Bisulfite treatment) and purification; 7) PCR amplification to generate the WGBS library

value: hfPSCs

value: hPSCs


title: hfPSCs_MGT3_DNA methylation

description: Library name: hfPSCs_MGT3_DNA methylation


title: Karpas-45, MEF2COE, technical replicate 2

description: Library name: Karpas_MEF2COE_R2


title: Karpas-45, MEF2COE, technical replicate 1

description: Library name: Karpas_MEF2COE_R1


title: T-ALL3, day 0, technical replicate 1

description: Library name: TALL3_day0_R1


title: Karpas-45, control, technical replicate 2

description: Library name: Karpas_control_R2


title: Karpas-45, control, technical replicate 3

description: Library name: Karpas_control_R3


title: S2_CB96_19

description: Library name: s2

value: Differentiated human hematopoietic stem and progenitor cells


title: Karpas-45, shMEF2CKD2, technical replicate 2

description: Library name: Karpas_MEF2CKD2_R2


title: Karpas-45, control, technical replicate 1

description: Library name: Karpas_control_R1


title: Karpas-45, scramble control, technical replicate 2

description: Library name: Karpas_scr_R2


title: T-ALL3, day 4, technical replicate 2

description: Library name: TALL3_day4_R2


title: hESCs_sus_2

description:
Library name: hESCs_sus_2
human_stem_cell_count.txt

data_processing:
Low-quality RNA sequencing reads and adapters were removed by cutadapt v1.11 and then the clean reads were aligned to human cDNA database (hg19) using HISAT2(v2.2.1). The gene counts was calculated with gene annotation from UCSC database using FeatureCounts (v2.0.1)
Assembly: hg19 for human cells and mm9 for mouse cells
Supplementary files format and content: txt format; count

source_name: hESCs

extract_protocol:
Bulk-RNA seq: Total RNA was isolated cells using TRIzol® Reagent (MRC, Cat# RN 190). Genomic DNA (gDNA) contamination was eliminated from the total RNA by the digestion of RQ1 DNase (Promega, Cat# M610A) for 1 h at 37 °C. RNA integrity was verified by Bioanalyzer 2100 (Agilent Technologies) with RNA Integrity Number (RIN) > 8.0.
Total RNA samples were tested and then enriched for eukaryotic mRNA by Oligo(dT) magnetic beads; Add Fragmentation Buffer for mRNA fragmentation; One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; PCR enrichment was performed to obtain cDNA libraries.RNA-seq libraries were sequenced on Illumina NovaSeq X paktform.

value: hESCs


title: hESCs_H9

description:
Library name: hESCs_H9
human_stem_cell_count.txt


title: hESCs_MGT3

description:
Library name: hESCs_MGT3
human_stem_cell_count.txt


title: Plated SRR2 Cells, KOLF2, shTKT, Week9

city: Stanford

first: Aparna

last: Bhaduri

state: CA

address: 269 Campus Drive

institute: Stanford University

description: Library name: KOLF2_shTKT_SRR2_Week9

data_processing:
Cellranger v8
Assembly: GRCh38
Supplementary files format and content: Counts Matrix

molecule: nuclear RNA

source_name: Cortical Organoid

extract_protocol:
single-cell or single-nuclei purification
10X GEM-X

value: Cortical Organoid

value: Neural

value: shTKT


title: hALSCs_2

description:
Library name: hALSCs_2
human_stem_cell_count.txt

source_name: hALSCs

value: hALSCs


title: hESCs_sus_1

description:
Library name: hESCs_sus_1
human_stem_cell_count.txt


title: hifPSCs

description:
Library name: hifPSCs
human_stem_cell_count.txt


title: hfPSCs_MGT3

description:
Library name: hfPSCs_MGT3
human_stem_cell_count.txt


title: Plated SRR2 Cells, UCLA6, shSCR, Week9

description: Library name: UCLA6_shScr_SRR2_Week9

value: shScr


title: Plated SRR2 Cells, UCLA1, shTKT, Week9

description: Library name: UCLA1_shTKT_SRR2_Week9


title: Cortical Organoid, KOLF2, Vehicle Control, Week12

description: Library name: KOLF2_DMSO_Week12

value: DMSO


title: hfPSCs_H9

description:
Library name: hfPSCs_H9
human_stem_cell_count.txt


title: Plated SRR2 Cells, UCLA1, shG6PD, Week9

description: Library name: UCLA1_shG6PD_SRR2_Week9


title: Cortical Organoid, UCLA6, Vehicle Control, Week12

description: Library name: UCLA6_DMSO_Week12


title: Plated SRR2 Cells, UCLA6, shG6PD, Week9

description: Library name: UCLA6_shG6PD_SRR2_Week9


title: hALSCs_1

description:
Library name: hALSCs_1
human_stem_cell_count.txt


title: Cortical Organoid, UCLA1, Vehicle Control, Week12

description: Library name: UCLA1_DMSO_Week12


title: Cortical Organoid, UCLA1, ORX TKT Inhibition, Week12

description: Library name: UCLA1_ORX_Week12

value: ORX


title: Cortical Organoid, UCLA6, 6AN G6PD Inhibition, Week12

description: Library name: UCLA6_6AN_Week12


title: Plated SRR2 Cells, UCLA6, shTKT, Week9

description: Library name: UCLA6_shTKT_SRR2_Week9


title: Cortical Organoid, UCLA6, Low Glucose, Week12

description: Library name: UCLA6_2.5mMglucose_Week12


title: Cortical Organoid, KOLF2, 6AN G6PD Inhibition, Week12

description: Library name: KOLF2_6AN_Week12


title: Cortical Organoid, KOLF2, Low Glucose, Week12

description: Library name: KOLF2_2.5mMglucose_Week12


title: Plated SRR2 Cells, KOLF2, shSCR, Week9

description: Library name: KOLF2_shScr_SRR2_Week9


title: Cortical Organoid, UCLA6, ORX TKT Inhibition, Week12

description: Library name: UCLA6_ORX_Week12


title: Cortical Organoid, UCLA1, 6AN G6PD Inhibition, Week12

description: Library name: UCLA1_6AN_Week12


title: Plated SRR2 Cells, KOLF2, shG6PD, Week9

description: Library name: KOLF2_shG6PD_SRR2_Week9


title: Plated SRR2 Cells, UCLA1, shSCR, Week9

description: Library name: UCLA1_shScr_SRR2_Week9


title: Cortical Organoid, UCLA1, Half Glucose, Week12

description: Library name: UCLA1_8.75mMglucose_Week12


title: Cortical Organoid, UCLA6, Half Glucose, Week12

description: Library name: UCLA6_8.75mMglucose_Week12


title: Cortical Organoid, KOLF2, Baseline Glucose, Week12

description: Library name: KOLF2_17.5mMglucose_Week12


title: Cortical Organoid, UCLA1, Low Glucose, Week12

description: Library name: UCLA1_2.5mMglucose_Week12


title: Cortical Organoid, UCLA1, Baseline Glucose, Week12

description: Library name: UCLA1_17.5mMglucose_Week12


title: Cortical Organoid, KOLF2, Half Glucose, Week12

description: Library name: KOLF2_8.75mMglucose_Week12


title: asf1∆ 3' READS  Rep B

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

description:
Library name: 4
3' READS

data_processing:
Prep fastq files for mapping (discard reads with ambiguous base calls, remove of library adapters, count/remove of initial Ts in each read) python
Map to Sac cer 3 genome, using first 17 nt after adapter and initial T removal; no mismatches allowed, keeping only uniquely mapped reads, Bowtie
Discard reads for which the number of initial Ts could be explained by A residues in the genome adjacent to the mapped position, python
Tally remaining read starts by strand and genomic position, scaling each replicate to 25M total reads (or combined reps scaled to 50M), python
Assembly: Sac cer 3
Supplementary files format and content: Tab-delimited text files giving relative 3' isoform end frequencies by coordinate in the 400nt downstream of each CDS
Supplementary files format and content: Tab-delimited text files of merged A and B replicates giving relative isoform frequencies by genomic coordinate  in the 400nt downstream of each CDS

organism: Saccharomyces cerevisiae

source_name: log phase yeast cells

growth_protocol: Growth to mid-log phase in YPD medium at 30°C

extract_protocol:
Hot acid phenol method to isolate total RNA, followed by purfcation using Qiagen RNEasy with Dnase treatment
3' READS (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17)

treatment_protocol: The anchor-away strains were treated for 1hr with 1µM rapamycin before harvesting cells; cells from deletion strains were harvested without treatment

tag: strain

value: asf1 deletion in JGY2000 parental strain

value: growth to mid-log phase in YPD

value: log phase yeast cells


title: sample 1 of a FALD liver and a normal donor liver

type: RNA

city: Suita

first: Seiya

last: Kato

state: Osaka

address: 2-2, Yamadaoka

department: Gastroenterology and Hepatology

institute: Osaka University

hyb_protocol: Hybridization was performed using the above panel, according to the manufacturer’s protocol, CosMX SMI Manual Slide Preparation for RNA Assays (MAN-10184-04, Nanostring). Anti-B2M/CD298, anti-PanCK, anti-CD45, and anti-CK8/18 antibodies and DAPI were used as morphological markers.

scan_protocol: Cell segmentation was performed by combining image preprocessing and CellPose neural network models.

data_processing: The data were analyzed by the CosMx SMI instrument, followed by quality control, normalization, principal component analysis and clustering using the count matrix and subpopulation assignments of the reference scRNA-seq dataset on the AtoMx platform.

source_name: liver

label_protocol: The CosMx Human Universal Cell Characterization RNA Panel (1000-plex) + 9 custom genes, including CCN2, was used for the CosMx assay.

growth_protocol: FFPE samples of 3 FALD livers and 1 donor liver were used.

extract_protocol: CosMx technology (Nanostring, Seattle, WA, USA), a high-plex spatial molecular imager (SMI), was used to analyze these samples. The samples were stained with H&E and Sirius red for field of view (FOV) determination. Each FOV was 0.5 × 0.5 mm in size.

treatment_protocol: FFPE samples were sectioned (5 μm), mounted on VWR Superfrost Plus microscope slides (#48311-703; VWR International, Wayne, PA).

value: liver


title: AR1Flex

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

description:
Library name: AR1Flex
10X genomics

data_processing:
Sequenced data were processed into expression matrices with the Cell Ranger Single Cell Software (v 6.1.2) of 10X Genomics against the GRCh38 human reference genome with default parameters.
Assembly: GRCh38
Supplementary files format and content: 10X Cellranger format

source_name: aortic valve

extract_protocol:
Samples were washed, chopped into small pieces, and digested in an enzymatic digestion buffer containing 3 mg/ml collagenase type II (#LS004176, Worthington Biochemical Corp, NJ, USA), 0.15 mg/ml collagenase type XI (#H3506, Sigma Aldrich, MO, USA), 0.25 mg/ml soybean trypsin inhibitor (#LS003571, Worthington Biochemical Corp), 0.1875 mg/ml elastase lyophilized (#LS002292, Worthington Biochemical Corp), 0.24 mg/ml hyaluronidase type I (#H3506, Sigma Aldrich), and 2.38 mg/ml 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES, #H4034, Sigma Aldrich) in PBS with Ca2+ and Mg2+, at 37°C for 90 minutes with shaking. The digested samples were filtered through 40 μm cell strainers (#352340, BD Biosciences, NJ, USA), washed, and centrifuged at 3000 × g for 10 minutes.
ScRNA-seq (3’) libraries were prepared using the Single Cell 3’Reagent Kits v3 for scRNA-seq (10x Genomics, CA, USA). Sequencing libraries were generated following the User Guide (CG000388).

value: aortic valve

value: total fixed cells


title: AS2.1Flex

description:
Library name: AS2.1Flex
10X genomics


title: AS11Flex

description:
Library name: AS11Flex
10X genomics


title: Cortical Organoid, UCLA6, Baseline Glucose, Week12

description: Library name: UCLA6_17.5mMglucose_Week12


title: worms-F49-ERCC

city: Hefei

first: Ruikun

last: Wu

state: Anhui

address: No.443 Huangshan Road

institute: University of Science and Technology of China

description:
Library name: sample5
worms-mRNA-ERCC-L-C46-F49.txt

data_processing:
For data processing, raw reads were first processed with fastp to obtain clean reads. Clean Reads were then aligned to the reference genome (Human: hg19; C. elegans: ce10)Bowtie2. For linear RNA, read counts were generated using BEDTools. For poly(A)-selected RNA-seq with ERCC spike-in, clean reads were aligned to a combined reference consisting of the human/C. elegans genome and ERCC spike-in sequences. Read counts for endogenous genes and ERCC transcripts were obtained using standard counting procedures. ERCC read counts were modeled using a negative binomial distribution to estimate sample-specific scaling factors, which were subsequently applied to normalize endogenous gene expression levels for assessment of global mRNA abundance.
Assembly: hg19(human), ce11(C. elegans)
Supplementary files format and content: tab-delimited text files include count values for each Sample

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol:
Total RNA from cells or C. elegans strains was extracted by TRIzol Reagent or TRIzol LS Reagent according to the manufacturer’s procedures.
The concentration of isolated RNAs was verified by Nanodrop, and RNA quality was checked with gel electrophoresis. For poly(A)-selected RNA-seq, external RNA Control Consortium (ERCC) spike-in RNA controls (Invitrogen, 4456740) were diluted and added according to the manufacturer’s instructions. Specifically, 1 μL of 1:100 diluted ERCC spike-in RNA mix was added to 5 μg total RNAs prior to enrichment using oligo(dT) magnetic beads and library preparation.

value: whole worm


title: HSP6_ribominus_RNAicco-1

description: Library name: sample9

data_processing:
For data processing, raw reads were first processed with fastp to obtain clean reads.
Clean Reads were then aligned to the reference genome (Human: hg19; Mouse: mm10; C. elegans: ce10) with BWA-MEM or Bowtie2. For circRNA prediction, backsplicing junctions (BSJs) were identified using both CIRI2 and Find_circ, and BSJ reads identified by CIRI2 were used to quantify circRNAs. For linear RNA, read counts were generated using BEDTools.
Assembly: hg19(human), mm10(mouse), ce11(C. elegans)

extract_protocol:
Total RNA from cells or C. elegans strains was extracted by TRIzol Reagent or TRIzol LS Reagent according to the manufacturer?s procedures.
The concentration of isolated RNAs was verified by Nanodrop, and RNA quality was checked with gel electrophoresis. For ribosomal RNA-depleted (Ribo-) RNA-seq, rRNA in total RNA was depleted with the Illumina Ribo-Zero Gold kit (Illumia) and subjected to library preparation with the TruSeq Ribo Profile Library Prep Kit (Illumina) according to the manufacturer?s instructions. For Ribo-/RNase R+ RNA-seq, total RNA was rRNA-depleted, RNase R-treated and subjected to library preparation according to the manufacturer?s instructions.

value: strain

value: WT


title: AS5Flex

description:
Library name: AS5Flex
10X genomics


title: AS2.2Flex

description:
Library name: AS2.2Flex
10X genomics


title: sample 2 of a FALD liver

description: FALD 2

data_processing:
The data were analyzed by the CosMx SMI instrument, followed by quality control, normalization, principal component analysis and clustering using the count matrix and subpopulation assignments of the reference scRNA-seq dataset on the AtoMx platform.
comma-separated values files containing cell barcodes, gene expression counts and cell position

label: SMI imaging barcodes

growth_protocol: FFPE samples of 2 FALD livers and 1 donor liver was used.

tag: disease state

value: FALD


title: AS1Flex

description:
Library name: AS1Flex
10X genomics


title: sample 1 of a FALD liver

description: FALD 1


title: worms-L4440-ERCC

description:
Library name: sample3
worms-mRNA-ERCC-L-C46-F49.txt


title: sample 1 of a normal donor liver

description: normal 1

value: normal


title: HSP4_ribominus_DMSO

description: Library name: sample6


title: sample 2 of 2 FALD livers


title: HSP16.2_ribomimus_20_L4440

description: Library name: sample1


title: worms-C46-ERCC

description:
Library name: sample4
worms-mRNA-ERCC-L-C46-F49.txt


title: AR2Flex

description:
Library name: AR2Flex
10X genomics


title: HSP4_ribominus_Tuni

description: Library name: sample7


title: HSP16.2_ribomimus_HS_RNAiF49

description: Library name: sample5


title: HSP16.2_ribomimus_HS_L4440+CQ

description: Library name: sample2


title: Cortical Organoid, KOLF2, ORX TKT Inhibition, Week12

description: Library name: KOLF2_ORX_Week12

value: Cortical Organoid

value: Neural


title: nop2 sibling zebrafish (48 dpf) brain tissues for ribo-seq

city: Zhan Jiang

first: Xiaoyu

last: Li

state: Guangdong

address: 57 People's Avenue

institute: Affiliated Hospital of Guangdong Medical University

description:
Library name: sample1
sibling-vs-mutant.all.annot.txt

data_processing:
For ribo-seq: Low quality reads were filtered by fastp. Raw reads containing over 50% of low quality bases or over 10% of N bases were removed. Adapter sequences were trimmed. Reads with length between 20-40bp were retained for subsequent analysis. Short reads alignment tool Bowtie2 was used for mapping reads to ribosome RNA (rRNA) database, GenBank, Rfam database. The reads mapped to rRNAs, transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), and miRNA were removed. Processed RNA-seq reads were aligned to the genome using whole genome alignment by STAR with 2- pass setting enabled. The reads mapped to classical noncoding RNAs (including long noncoding RNAs, microRNA precursors) were abandoned. Then remaining RFs were assigned to different genomic features (5’UTR, CDS, 3’UTR and intron) based on the position of the 5’ end of the alignment. For BS-seq: Low quality bases and Adapter sequences were trimmed by using Trimmomatic V0.38. The parameter settings used was “ HEADCROP:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20”. The cleaned reads were mapped back to Petunia hybrida genome reference (v1.6.2). using BS-RNA V1.0. The parameter settinds used was default parameter recomanded by BS-RNA document , detailed data processing steps were listed as below:The first step is the pre-treatment of reference genome sequences, sequencing data, and gene annotation file: (1) the reference genome sequence is converted twice in parallel as follows: (A) cytosines are replaced by thymines and (B) guanines are replaced by adenines. This genome sequence conversion only need to be performed the first time one uses the reference genome sequence, which means it could be reused for all the following analysis which use the same reference genome sequence. (2) cytosines in reads of the T-rich sequencing read file are replaced by thymines, while guanines in reads of the A-rich sequencing read file are replaced by adenines. And (3) the gene annotation file in GTF format is revised to fit the converted reference genome sequences. Each annotation line is converted twice simultaneously: "C-T" and "G-A" are appended to the chromosome label in the gene annotation file, respectively. Next, the HISAT2 program is invoked by BS-RNA to build alternative splicing according to the modified annotation gene file and align pre-processed reads to the converted reference genome sequence. BS-RNA filters out two types of reads that are mapped to the reference genome sequence as follows: (1) reads mapped to multiple positions and (2) reads mapped to the wrong strands (T-rich reads mapped to reverse-complement of reference sequence converted C to T or to reference sequence converted G to A, A-rich reads mapped to reference sequence converted C to T or to reverse complements of reference sequence converted G to A). The original mapping file (SAM format), filtered mapping file (SAM format), and mapping report file will be provided by BS-RNA when the mapping step is finished.  Further, BS-RNA splits the filtered mapping file into two files: a Watson-strand SAM format file (mapped to reference converted C to T) and a Crick-strand SAM format file (mapped to reference converted G to A). SAMtools is embedded into BS-RNA to convert the Watson-strand and Crick-strand SAM format files to BAM format and then sort these two BAM files according to the chromosome coordination. Single-base coverage information is extracted using the mpileup command of SAMtools from the sorted BAM files. For each cytosine position in the genome, the read base (SAMtools mpileup output information) is deemed to support methylated cytosine sequencing if it matches a dot or a comma, otherwise it is deemed to support an unmethylated cytosine sequencing. We excluded the reference skips (which menas "<" or ">" is not counted). BS-RNA provides the annotation result for each covered cytosine in a BED (.bed.txt) file with information related to the methylation character: location of the covered cytosine in the reference, sequence context type (CG/CHG/CHH, H = A, T, or C), reference sequencing depth (total number of reads mapped to the cytosine site), cytosine sequencing depth (total number of reads that supported a methylated cytosine at this site), and methylation level (the ratio of cytosine sequencing depth to sequencing depth at the cytosine site) on the Watson strand and Crick strands for each chromosome to the users. Differentially methylated cytosine (DMCs) were detected using MethylKit [3] among CpG sites with at least 10x coverage. The parameter settings used was “--mincov 5 --m_cutoff 0.05 --q_cutoff 0.05”. Then detected DMCs were filtered according to the standard: (1) corrected q-value must be less than 0.05; (2) methylation level difference must be greater than 0.05.
Assembly: GRCz11
Supplementary files format and content: bed and xlsx format which contains m5c peaks of bs-seq and gene expression value of ribo-seq
Library strategy: Ribo-Seq

organism: Danio rerio

source_name: brain

extract_protocol:
For ribo-seq: Tissues were immediately frozen in liquid nitrogen and ground to power in liquid nitrogen with a mortar and pestle, then dissolved in 400μL of lysis buffer. The resuspended extracts in lysis buffer were transferred to new microtubes, pipetted several times and incubated on ice for 10 min. Then cells were triturated ten times through a 26-G needle. The lysate was centrifuged at 20000g for 10min at 4℃, and the supernatant was collected. To prepare RFs , 10μL of RNase I (NEB, Ipswich, MA, USA) and 6μL of DNase I (NEB, Ipswich, MA, USA) were added to 400μL of lysate，which was then incubated for 45 min at room temperature with gentle mixing on a Nutator mixer. Nuclease digestion was stopped by adding 10μL of SUPERase·In RNase inhibitor (Ambion, Austin, TX, USA). Size exclusion columns (illustra MicroSpin S-400 HR Columns; GE Healthcare; catalog no. 27- 5140-01) were equilibrated with 3 mL of polysome buffer by gravity flow and centrifuged at 600g for 4 min at room temperature. 100μL of digested RFs were added to the column and centrifuged at 600g for 2 min. Next, 10μL 10% (wt/vol) SDS was added to the elution, and RFs with a size greater than 17nt was isolated according to the RNA Clean and Concentrator-25 kit (Zymo Research;R1017). rRNA was removed using the method reported previously[2]. Briefly, short (50–80 bases) antisense DNA probes complementary to rRNA sequences was added to solution containing RFs, then RNase H (NEB, Ipswich, MA, USA) and DNase I (NEB, Ipswich, MA, USA) was added to digest rRNA and residual DNA probes. Finally, RFs were further purified using magnet beads (Vazyme, Nanjing, Jiangsu, China) For BS-seq: Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific) and the concentration and integrity of total RNA were measured by Qubit RNA BR Assay and 2% agarose gel electrophoresis, respectively.
For ribo-seq: After obtaining ribosome footprints above, Ribo-seq libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (catalog no.E7300S, E7300L). Briefly, adapters were added to both ends of RFs, followed by reverse transcription and PCR amplification. The 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina NovaSeq X plus Gene Denovo Biotechnology Co. (Guangzhou, China). For BS-seq: After quality testing, the RNA-Bis libraries were constructed by E-GENE Co. Ltd. as follows. Briefly, the extracted total RNA was firstly subjected to DNase I (NEB) treatment at 37℃ for 30min to remove residual DNA. After purification, mRNA was isolated using Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. The isolated mRNA was quantified by Qubit RNA HS Assay and then 1/500 amount of artificial spike-in RNA about 700nt length from pUC19 plasmid was mixed in as control. RNA bisulfite conversion of the isolated RNA samples with spike-in control was conducted using EZ RNA Methylation Kit (Zymo Research) with two cycles of 70 ℃ for 5min followed by 54℃ for 45min incubation and then purified using the provided Zymo-Spin IC Column according to the manufacturer’s instructions. After purification, an UMI adapter was ligated to the 3’ end of the converted RNA using T4 RNA ligase (NEB). Seven bases of UMI were designed for PCR based duplication evaluation. Ligated RNA was reverse transcribed using SuperScript II (Invitrogen) and the cDNA was subjected to a 3′ ligation with a second adaptor using T4 ligase. The strand-specific libraries were finally amplified for about 10 cycles in a PCR reaction. After analyzed by Agilent Bioanalyzer (Agilent Technologies，USA) and quantified by real time PCR, RNA-Bis libraries were sequenced using Illumina sequencer platform (Illumina，USA).

value: brain

value: primary cells

value: whole brain cells

value: nop2 sibling


title: nop2 mutant zebrafish (48 dpf) brain tissues for ribo-seq

description:
Library name: sample2
sibling-vs-mutant.all.annot.txt

value: nop2 mutant


title: HSP16.2_ribomimus_HS_L4440

description: Library name: sample3


title: OE-NtispH-3

city: GuiYang

first: Zeyang

last: Song

state: GuiZhou

address: West Campus: Jiaxiu South Road, Huaxi District.

institute: Guizhou University

description: Library name: sample 6

data_processing:
Raw reads were quality-controlled and filtered using fastp  to remove low-quality data, including adapter sequences, low-quality bases, and short reads, resulting in high-quality clean reads.
Ribosomal RNA (rRNA) was removed by aligning the clean reads to the rRNA reference sequences using Bowtie2
The remaining reads were aligned to the reference genome using HISAT2  to generate alignment files
Transcripts were reconstructed using StringTie, and gene expression levels were quantified as FPKM using RSEM for each sample.
Assembly: Ntab-TN90
Supplementary files format and content: tab-delimited text file includes FPKM counts for each Sample

organism: Nicotiana tabacum

source_name: mature leaf

extract_protocol:
mrna extraction by Trizol
1) By utilizing the structural characteristic that most eukaryotic mRNAs carry a polyA tal, mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads; 2) The purified mRNAs were cleaved into small fragments with fragmentation buffer at a suitable temperature;3) First-strand cDNAs were produced by reverse transcription using a random hexamer primer;4) Second-strand cDNAs are synthesized (strand-specific lilbrary: dUTPs were used instead of dTTPs in thesecond-strand synthesis to incorporate dUTPs in the second-strand cDNAs, while the high-fidelity DNApolymerase used in this method could not amplify uracil-containing DNA templates, thus realizing thestrand-specificity), while simultaneously performing end repair and dA-Tailing;5) Sequencing adapter ligation was performed, followed by DNA magnetic bead purification and fragment selectionafter ligation was completed to yield a library with 250-350 bp insert fragments;6) The ligated products were amplified by PCR and purified again using DNA magnetic beads, where the productswere solubilized with nuclear-free water:7) After the initial library was constructed, a Qubit fluorescence quantifier was used for concentration detectionfollowed by a Qsep400 high-throughput biofragment analyzer for fragment size detection

value: mature leaf


title: OE-NtispH-1

description: Library name: sample 4


title: OE-NtispH-2

description: Library name: sample 5


title: HSP16.2_ribomimus_HS_RNAiC46

description: Library name: sample4


title: WT-2

description: Library name: sample 2


title: HSP6_ribominus_L4440

description: Library name: sample8


title: WT-1

description: Library name: sample 1


title: sample 4 of liver constituent cells from a FALD liver

description:
Library name: FALD 4
10x Genomics

data_processing:
The resulting raw data were processed with Cell Ranger 7.1.0 (10x Genomics). Briefly, trimmed FASTQ files were generated using the CellRanger mkfastq command. Primary data analysis for alignment, filtering, and unique molecular identifier counting were performed to determine the gene transcript counts per cell using CellRanger software. GRCh38 (hg19) was used for genome assembly/annotation references.
Assembly: GRCh38
Supplementary files format and content: HDF files containing cell barcodes and Gene Expression Counts

extract_protocol:
Frozen surgical liver tissue was cut into pieces approximately 1 mm3, fixed with formalin using a Chromium Next GEM Single-Cell Fixed RNA Sample Preparation Kit (10x Genomics, Pleasanton, CA), and then dispersed into single cells using gentleMACS (Miltenyi Biotec) according to the manufacturer’s instructions.
For the construction of the scRNA-seq library, a Chromium Fixed RNA Kit, Human Transcriptome, 1BC (10x Genomics) was used according to the manufacturer’s instructions. Libraries were sequenced on a DNBSEQ-G400RS (MGI Tech) at a read length of 28 × 90.

value: liver constituent cells


title: WT-3

description: Library name: sample 3


title: sample 3 of liver constituent cells from a normal liver

description:
Library name: normal 3
10x Genomics

value: liver


title: ad-CTSV 4

city: changsha

first: Chan

state: Hunan

address: No 87 Xiangya road, Changsha, Hunan, China.

institute: Xiangya Hospital, Central South University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by
(1) Removing reads containing sequencing adapter
(2) Removing reads whose low-quality base ratio (base   quality less than or equal to 5) is more than 20%
(3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored   in FASTQ format.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Umbilical Vein

growth_protocol: Primary human vein endothelial cells (HUVECs) were obtained from sciencecell research laboratory and cultured with endothelial cell medium (ECM) containing 5% fetal bovine serum (FBS) and 1% endothelial cell growth supplement (ECGS) at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according   to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2   mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The   mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a   new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for   15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper   aqueous phase where RNA remained was transferred into a new tube with equal volume of   supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After   deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix   was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the   pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated   water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using   a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented   into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was   generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA   synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end   repair. The cDNA fragments obtained from previous step were amplified by PCR, and products   were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on   the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products   from previous step were heated denatured and circularized by the splint oligo sequence to get the   final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The   final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300   copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases   reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Recombinant CatV adenovirus (ad-CatV, Shanghai Genechem Co., Ltd, China) or negative control adenovirus (ad-NC, Shanghai Genechem Co., Ltd, China) was added to 60% confluent cultured HUVECs and removed after 8 hours. Subsequently, HUVECs were cultured in complete growth medium for 40 hours and simulated with 400μM H2O2 for another 24 hours before RNA extraction.

value: Umbilical Vein

value: HUVEC

value: endothelial cell

value: ad-CTSV


title: H2O2+ad-CTSV 1

value: WT


title: H2O2 3


title: sample 3 of liver constituent cells from a FALD liver

description:
Library name: FALD 3
10x Genomics


title: ad-CTSV 1


title: H2O2+ad-CTSV 3


title: ad-CTSV 3


title: H2O2 4


title: sample 2 of liver constituent cells from a normal liver

description:
Library name: normal 2
10x Genomics


title: H2O2+ad-CTSV 2


title: sample 1 of liver constituent cells from a FALD liver

description:
Library name: FALD 1
10x Genomics